Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 49 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 6294 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 49 specie 7 host 6 bat 5 Fig 4 virus 4 disease 3 site 3 pathogen 3 human 3 group 3 Australia 2 sample 2 plant 2 infection 2 habitat 2 dna 2 cell 2 Copepoda 1 zoo 1 zone 1 wetland 1 water 1 vector 1 tree 1 transmission 1 temperature 1 taxonomy 1 study 1 strain 1 station 1 stage 1 squirrel 1 skin 1 rodent 1 reptile 1 reactive 1 rat 1 protein 1 plot 1 pas 1 parasitic 1 parasite 1 oxygen 1 number 1 native 1 mouse 1 mixed 1 microalgae 1 life 1 lesion Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 3874 specie 1478 host 899 % 895 bat 826 disease 816 virus 722 group 664 species 660 study 658 plant 571 pathogen 563 number 542 animal 540 parasite 525 site 490 infection 443 habitat 442 analysis 438 population 422 diversity 409 cell 391 community 385 datum 383 sequence 368 life 359 effect 357 area 350 fish 348 transmission 324 alkaloid 316 year 312 stage 312 change 295 example 293 case 291 time 291 human 287 cycle 283 tree 276 level 273 gene 273 bird 268 distribution 256 strain 256 food 254 individual 245 sample 242 use 237 value 233 result Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1122 al 939 et 783 . 264 Fig 256 ROS 233 GenBank 204 R. 169 Williams 163 P. 156 C. 134 Table 129 Australia 124 M. 102 Africa 92 E. 82 Europe 79 × 76 C 74 T. 70 astrovirus 66 nov 66 West 66 RNA 65 South 63 diam 63 A 61 United 61 SARS 60 brown 59 de 58 Group 57 PCR 57 NRA 56 LSU 56 G+C)% 55 Rhinolophus 54 Nile 54 America 53 μm 53 PEFF 52 China 51 States 51 North 51 G. 51 D. 50 USA 50 New 50 L. 49 sp 49 US Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 947 we 816 it 678 they 182 them 121 i 38 us 36 itself 28 themselves 24 he 16 one 9 its 5 she 4 me 3 you 2 s 2 her 2 em 1 u 1 theirs 1 ourselves 1 imagej 1 his 1 clustalx 1 a4b8bb2e6ce939978adf9d2146b7102bd6196159 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 10891 be 2277 have 906 use 525 find 473 include 399 do 384 show 348 occur 344 increase 333 base 318 cause 314 associate 308 see 290 know 264 consider 254 provide 254 identify 239 emerge 234 suggest 226 describe 223 reduce 221 produce 216 make 204 represent 204 infect 201 become 199 indicate 193 relate 190 give 184 support 177 follow 167 detect 162 report 161 live 159 form 156 observe 154 affect 153 lead 149 contain 148 develop 142 feed 141 introduce 137 remain 136 take 135 involve 133 isolate 132 appear 130 compare 126 determine 124 require Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1118 not 796 also 786 other 770 more 606 high 577 such 500 - 498 most 474 only 450 different 445 new 437 many 428 human 416 however 378 large 367 small 323 important 307 well 303 native 290 first 288 low 257 e.g. 254 invasive 251 similar 245 long 241 present 241 often 233 ecological 229 natural 227 same 224 thus 222 several 222 infectious 215 very 215 common 213 viral 212 few 195 parasitic 195 local 195 even 191 non 191 less 188 likely 185 specific 183 great 181 potential 176 genetic 170 as 169 significant 166 molecular Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 185 most 93 high 78 least 58 close 56 Most 52 good 36 large 25 great 14 low 9 Least 8 small 8 near 5 simple 5 short 5 old 4 rich 4 broad 3 long 3 late 3 few 3 fast 3 -1-septate 2 strong 2 hard 2 early 2 dry 2 clear 2 bad 1 young 1 wide 1 stickn 1 rare 1 overharv 1 oldfor 1 molossid 1 light 1 hot 1 fine 1 easy 1 deep 1 dark 1 cord-010149-zupx8qn1 1 cord-009716-oxahu8nz 1 -6.5(-8 1 -36(-39.5 1 -)45 Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 313 most 43 least 15 well 1 smallest 1 latest 1 hard 1 close 1 -)27 Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 4 doi.org 1 zenodo.org 1 www.phylo.org 1 www.nyu.edu 1 www.mammalparasites.org 1 www.iucnredlist.org 1 www.indexfungorum.org 1 www.health.harvard.edu 1 www.gbif.org 1 www.ersaf.lombardia.it 1 www.dnr.wi.gov 1 www.catalogueoflife.org 1 www.biorxiv.org 1 www 1 tree.opentreeoflife.org 1 tree.bio.ed.ac.uk 1 thomsonreuters.com 1 species.h-its.org 1 pypi.org 1 orcid.org 1 github.com 1 figshare 1 ethnobiology.net 1 ec.europa 1 doi 1 datadryad.org 1 commons.wikimedia.org 1 beast.bio.ed.ac.uk 1 2009.botanyconference.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 3 http://doi.org/10 1 http://zenodo.org/ 1 http://www.phylo.org/sub_sections/portal/ 1 http://www.nyu.edu/ 1 http://www.mammalparasites.org/ 1 http://www.iucnredlist.org/technical-documents/spatial-data 1 http://www.indexfungorum.org/names/names.asp 1 http://www.health.harvard.edu/staying-healthy/thedangers-of-the-herb-ephedra 1 http://www.gbif.org/grscicoll 1 http://www.ersaf.lombardia.it/upload/ersaf/gestionedocumentale/WEB_Libro_-suolo_EN_784_11577.pdf 1 http://www.dnr.wi.gov/lakes/ 1 http://www.catalogueoflife.org/ 1 http://www.biorxiv.org/ 1 http://www 1 http://tree.opentreeoflife.org/ 1 http://tree.bio.ed.ac.uk/software/figtree/ 1 http://thomsonreuters.com/products_services/science 1 http://species.h-its.org/ptp/ 1 http://pypi.org/project/pdftotext/ 1 http://orcid.org/ 1 http://github.com/ 1 http://figshare 1 http://ethnobiology.net/code-of-ethics/ 1 http://ec.europa 1 http://doi.org/10.6084/m9 1 http://doi 1 http://datadryad.org/ 1 http://commons.wikimedia.org/ 1 http://beast.bio.ed.ac.uk/tracer 1 http://2009.botanyconference.org/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 tomkotik@rambler.ru 1 pp.pastoret@oie.int 1 petr.hamal@fnol.cz 1 monica.gutierrez@sag.gob.cl 1 maria.asenjo@sag.gob.cl 1 keesing@bard.edu 1 giuseppe.bogliani@unipv.it 1 e_malysheva@binran.ru 1 anna.kiyashko@binran.ru Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 20 sequence had highest 9 species are not 5 bats are natural 5 data are available 5 data were available 5 species is not 4 pathogens are not 4 sequence was available 4 species are likely 4 species are present 4 species were not 4 viruses were first 3 bats are more 3 data were not 3 host is not 3 hosts are more 3 species are most 3 species are often 3 species are sensitive 3 species are usually 3 species become more 3 species do not 3 species were present 3 species were randomly 3 viruses have also 2 % were absent 2 animals represented individual 2 bats is high 2 bats were positive 2 communities have not 2 diseases are zoonotic 2 diseases have rarely 2 diseases is still 2 effect has not 2 groups were not 2 hosts is due 2 infections are probably 2 pathogens are disproportionately 2 pathogens is not 2 plants are usually 2 populations makes management 2 sequence is montagnula 2 sequence was forliomyces 2 species are able 2 species are almost 2 species are also 2 species are carnivorous 2 species are more 2 species are responsible 2 species did not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 data were not available 2 host is not necessary 2 pathogens are not strongly 1 communities have not only 1 communities have not yet 1 data are not available 1 data were not multivariate 1 diseases is not simple 1 groups were not equally 1 groups were not significant 1 habitats were not random 1 infections are not body 1 infections do not obviously 1 pathogens are not highly 1 pathogens are not unusual 1 pathogens is not complete 1 pathogens is not uniform 1 population are not advisable 1 populations have no longer 1 sequences are not available 1 site was not independent 1 species are no longer 1 species are not cosmopolitan 1 species are not hosts 1 species are not normally 1 species are not simple 1 species are not yet 1 species does not necessarily 1 species has not yet 1 species is not constant 1 species is not different 1 species is not well 1 species were not amenable 1 species were not independent 1 studied are no more 1 virus was not formally 1 viruses have not yet A rudimentary bibliography -------------------------- id = cord-017537-ztdz4a2s author = Bologna, Mauro title = Biological Agents and Bioterrorism date = 2014-09-18 keywords = human; infection; specie; virus summary = For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. In the light of recent concern and interest about the potential for biological terrorism (biofarware) there are several diseases and bacterial toxins that must be considered in particular, like anthrax [ 1 , 2 ] , smallpox [ 3 , 4 ] , plague [ 5 ] , botulinum toxin [ 6 ] , and tularemia [ 7 ] . doi = 10.1007/978-94-017-9238-7_1 id = cord-278195-1sle0d1j author = Castillo-Huitrón, Nathalia M. title = The Importance of Human Emotions for Wildlife Conservation date = 2020-06-24 keywords = Prokop; animal; emotion; fear; human; specie summary = The very diverse and continuous human-wildlife interactions can be seen from three main perspectives: (1) Utilitarian, in which wild species provide goods for human well-being, such as food, clothing, transport, tools, raw materials, and companionship, among others; (2) Affective, where human beings feel sympathy, admiration, and respect for animals because of religious, mystical, or philosophical reasons (Kellert et al., 1996) , which has greatly contributed to cultural development worldwide (Herzog and Galvin, 1992; Alves, 2012) ; and (3) Conflictive, because of the real or potential damage that wild species may inflict on people and their interests (e.g., attacks on humans, livestock predation, damage on crops, and infrastructure, among others; Lescureux and Linnell, 2010) . Emotions such as fear and anger may be induced by predators that are bigger and heavier than persons, as in the case of large carnivores (e.g., bears, wolves, and big cats) (Røskaft et al., 2003) or by those species unattractive for most people, like worms, small carnivores, bats, and reptiles, which are often perceived as harmful (Knight, 2008; Prokop and Tunnicliffe, 2008; Prokop et al., 2009) . doi = 10.3389/fpsyg.2020.01277 id = cord-255018-dhkz23co author = Chamorro, Melina Fernanda title = Native and exotic plants with edible fleshy fruits utilized in Patagonia and their role as sources of local functional foods date = 2020-05-24 keywords = Berberis; Manzano; PEFF; Patagonia; food; plant; specie summary = In this study we focus on native and exotic plants with edible fleshy fruits (PEFF) that grow in Patagonia; that is, species that may be wild, cultivated or in an intermediate state of domestication, which bear fruit that is distinguished by its flavor, preferably sweet, and its use principally as a food resource. In this study we propose a cross-sectional approach which enables exotic and native species richness, local foods, medicines and their use patterns to be evaluated, and which will also help us understand in greater depth, from an ethnobotanical perspective, that diet and health are linked concepts. The principal functional species according to the CIF values were the native Aristotelia chilensis, Ribes magellanicum, Ephedra ochreata, Berberis microphylla, Fragaria chiloensis, Luma apiculata and Amomyrtus luma, and the exotic Sambucus nigra, Rosa rubiginosa and Prunus cerasus ( Table 2) . doi = 10.1186/s12906-020-02952-1 id = cord-316999-712rit8h author = Chinchio, Eleonora title = Invasive alien species and disease risk: An open challenge in public and animal health date = 2020-10-22 keywords = IAS; pathogen; specie summary = To this aim, we provide here an overview of how animal IAS may affect local disease dynamics both directly and indirectly, i.e., acting as pathogen hosts or disrupting the recipient ecosystem structure, through real-case examples from the ecological literature, and, in the last paragraph, we propose future initiatives aimed at improving our capacity for targeted actions toward the IAS most likely to threaten human and animal health, calling for an increased involvement of people working in the fields of animal and public health in a new invasion epidemiology field. IAS may host pathogens that are absent in the area of release and cause their establishment and subsequent spillover to local species, possibly resulting in an increase of disease risk for humans, domestic animals, and native wildlife. doi = 10.1371/journal.ppat.1008922 id = cord-263282-a7emso89 author = Coghlan, Megan L. title = Egg forensics: An appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs date = 2011-07-07 keywords = 12S; dna; identification; specie summary = Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. In wildlife forensics, DNA species identification is commonly carried out by amplifying and sequencing fragments of the mitochondrial DNA (mtDNA) genes cytochrome oxidase I (COI), cytochrome b (Cytb), or 12S ribosomal RNA (12S) [15, 17, 20, 21] . doi = 10.1016/j.fsigen.2011.06.006 id = cord-276372-q1fzxt3r author = Conde, Dalia A. title = Zoos through the Lens of the IUCN Red List: A Global Metapopulation Approach to Support Conservation Breeding Programs date = 2013-12-11 keywords = ISIS; specie; zoo summary = To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. To understand the complexity of maintaining CBPs of threatened species across the ISIS zoo network, we developed a second algorithm to find the optimal radial distance from any given zoo at which the probability of finding a metapopulation size of at least 50, 100 or 250 recruited living individuals was highest relative to that radial distance. As expected, the optimal distance radii and the number of zoos required to maximize the probability of reaching a given population increase with the metapopulation size threshold (.50, .100 and .250 individuals) ( Figure 3) . Therefore, for the zoo community, one of the main challenges of managing their threatened species in CBPs is the complexity of moving individuals across borders and the coordination of conservation efforts among zoos and other institutions at a global level. doi = 10.1371/journal.pone.0080311 id = cord-343461-vj6o1b18 author = Crous, P.W. title = Fungal Planet description sheets: 1042–1111 date = 2020-06-29 keywords = Australia; CBS; Crous; Fungal; GenBank; LSU; MEA; PDA; brown; diam; identity; specie summary = Conidia aseptate, hyaline, smooth, guttulate, subcylindrical to fusoid to irregular, straight to somewhat curved, apex subobtuse, base truncate, (9 -) Notes -Coleophoma includes species that are plant pathogenic or saprobic, occurring on a wide range of plant hosts (Crous et al. Based on a megablast search of NCBIs GenBank nucleotide database, the closest hits using the ITS sequence had highest similarity to Helgardia anguioides ( Notes -Pseudopezicula accommodates two species of apothecial ascomycetes that cause angular leaf scorch on Vitis vinifera. Based on a megablast search of NCBIs GenBank nucleotide database, the closest hits using the ITS sequence had highest similarity to Satchmopsis brasiliensis ( Notes -The phylogeny and morphology of Torrendiella and Hymenotorrendiella was discussed in detail by Johnston et al. Culture characteristics -(after 2 wk at 20 °C in the dark): On potato dextrose agar (PDA), colonies reach 44-47 mm diam, round shape, flat, dark olive green, dusty, aerial mycelium absent, profuse sporulation, margin white and glabrous, exudates (blackish droplets) produced mainly on the outermost colony surface; reverse olive green to olive black. doi = 10.3767/persoonia.2020.44.11 id = cord-022505-17khcmta author = Delaney, Martha A. title = Rodentia date = 2018-10-26 keywords = Fig; Krinke; Rattus; disease; lesion; mouse; rat; rodent; skin; specie; squirrel summary = Common microscopic findings in rodents that may be misinterpreted as lesions include: multinucleated, karyomegalic, and cytomegalic hepatocytes are common in several rodent species and can increase with age ( Fig. 20 .1); hepatocellular intranuclear cytoplasmic invaginations (pseudoinclusions) (Fig. 20 .1); eosinophilic cytoplasmic spherical inclusions in renal tubular epithelial cells and hepatocytes seen predominantly male mice, rats, and hamsters; splenic extramedullary hematopoiesis, which is very common in healthy rodents of all ages (Fig. 20 .2); hemosiderin, lipofuscin, ceroid, and melanin (in dark or black coated animals) are commonly detected in various tissues, such as spleen, liver, kidney, and adrenal glands; cardiac muscle in the tunica of pulmonary veins in the lung is a normal finding in mice; male rodents may have refluxed seminal coagula in the urinary bladder and urethra that is thought to occur peri mortem; and adrenal X-zone vacuolation in female mice. doi = 10.1016/b978-0-12-805306-5.00020-1 id = cord-003838-u8zjzqbr author = Demos, Terrence C. title = Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics date = 2019-08-22 keywords = Africa; Fig; Rhinolophus; specie; tree summary = CONCLUSIONS: Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. The species limits of morphologically conservative or cryptic lineages of bats have been greatly clarified by an integrative approach using multi-locus genetic delimitation methods as a starting point for identifying candidate species and then testing them using additional, corroborative data from behavioral, morphological, distributional, and/or ecological information ( [4] , cf. Maximum likelihood (ML) and Bayesian inference (BI) inferred trees with similar topologies; the ML gene tree is shown for the 351 sequence cyt-b alignment of 74 Rhinolophus species/clades ( Fig. 3 ; see also Additional file 4 for the phylogeny with all 351 terminals labeled). denti/ simulator; and finally 8 of 8 lineages in the fumigatus group, including three possibly new species as well as support for the recent recognition of R. doi = 10.1186/s12862-019-1485-1 id = cord-002561-7j43yic1 author = Donato, Celeste title = The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses date = 2017-05-10 keywords = Avastrovirus; HMO; figure; specie; strain summary = Astroviruses within the Mamastrovirus genus are derived from numerous mammalian species in addition to humans (HAstV), including farmed species such as pigs (PAstV), sheep (OAstV), cattle (BoAstV), domesticated animals including cats (FAstV), and dogs (CaAstV), rodents and small mammals including mink (MiAstV), bats (BAstV), rats (RAstV), mice, rabbit (RabAstV), fox, marmot (HHMastV), porcupine, shrew, vole, and larger species including deer (CcAstV), monkeys, water buffalo (BufAstV), yak, camel (DcAstV), and cheetah (ChAstV) (Figure 1a,b) . Viruses from the Avastrovirus genus have been characterized from numerous farmed avian species including turkeys (TAstV), ducks (DAstV), chicken (CAstV), guineafowl (GFAstV), pigeon (PiAstV), goose, as well as wild aquatic and terrestrial birds including heron, doves, penguins, and many other species (Figure 2a) . Astrovirus strains identified from fecal samples of multiple non-human primate species from wild, captive, and peri-urban environments in Bangladesh and Cambodia reveal multiple interspecies transmission events, with viruses closely related to the VA/HMO lineage of human viruses, and non-human mammalian and avian astroviruses (Figure 1a,b) [28] . doi = 10.3390/v9050102 id = cord-032623-32m3qko4 author = Durkin, Louisa title = When mycologists describe new species, not all relevant information is provided (clearly enough) date = 2020-09-10 keywords = author; description; specie; study; taxonomy summary = To assess whether fungal species descriptions are attuned to both the wants and needs of a target audience beyond taxonomists and the sign of the times, we explored 10 years'' worth of fungal species descriptions of extant mycological taxa in five major mycological journals (plus one botany journal for reference) for a range of factors pertaining to inter-and intra-scientific terms and concepts, science-demographical aspects, and illustrations and visualisations (Tables 1, 2; Suppl. Dark green -proportion of studies mentioning the word "ecology" or its variations; brown -proportion of studies giving a complete account of the taxonomic affiliation of the new species (family, order, and phylum); purple -proportion of studies with a macroscopic colour photo/illustration of the new species; pink -proportion of studies with macroscopic photos, that also indicate the size of the depicted object through a scale bar or a fiducial marker; light green -proportion of studies with an identification key; yellow -proportion of openly available papers for each year as assessed in 2020 B demographical and publication trends showing the average number of coauthors (dark green), departments (brown), countries (purple), continents (pink), and number of data visualizations (light green) over time. doi = 10.3897/mycokeys.72.56691 id = cord-022879-j6cecioe author = Fager, Edward W. title = Determination and Analysis of Recurrent Groups date = 1957-10-01 keywords = group; sample; specie summary = Transformation of the data or the use of rank correlation could overcome this difficulty, but any method which involves a measure of abundance may, in certain cases, not lead to the desired results : two species may always occur together and never separately and yet, unless there is a nearly constant relation between the relative numbers of individuals of the two species, a correlation coefficient will indicate no relationship even though they are a constant part of each other''s biological environment. The following example shows that it is not a satisfactory criterion for grouping if the groups are to be composed of species which form a nearly constant part of each other''s biological environment: Species 1 and 2 show no evidence of association when examined by Cole''s method and yet they nearly always occur together-over 80% of the occurrences of each are in company with the other -and should be considered together in any grouping based on this set of samples. doi = 10.2307/1943124 id = cord-017156-ximzvqbm author = Forsdyke, Donald R. title = Chargaff’s GC rule date = 2010-05-18 keywords = G+C)%; chapter; dna; gene; specie summary = The model predicts that, for preventing recombination (i.e. creating reproductive isolation), a non-complementarity between the sequences of potentially pairing strands, in itself, might be less important than a noncomplementarity associated with sequence differences that change the pattern of stem-loops. By continuous backcrossing to sylvestris the chromosomes deriv ed from sylvestris can be tested because they form tetrads with the sylvestrisThe surv ival of a duplicate copy of a gene depends on a var iety of factors , including (i) natural selection favouring organisms where a function encoded by the gene is either increased or changed (i.e . Each isochore would have arisen as a random fluctuation in the base composition of a genomic region such that a copy of a duplicated gene that had transposed to that region was able to survive without recombination with the original gene for a sufficient number of generations to allow differentiation between the copy and its original to occur. doi = 10.1007/978-0-387-33419-6_8 id = cord-010305-z5c7zgp7 author = GARDEN, JENNI G. title = Habitat structure is more important than vegetation composition for local‐level management of native terrestrial reptile and small mammal species living in urban remnants: A case study from Brisbane, Australia date = 2007-08-06 keywords = Brisbane; Group; habitat; reptile; specie summary = title: Habitat structure is more important than vegetation composition for local‐level management of native terrestrial reptile and small mammal species living in urban remnants: A case study from Brisbane, Australia Patterns in the occurrence of native terrestrial reptile and small mammal species in 59 sites located in remnant urban habitat fragments of Brisbane City were assessed against local‐level environmental characteristics of each site. Investigations were based in urban habitat fragments located within the Brisbane City Council (BCC) local government area, where local government is responsible for setting within-patch management priorities and actions.We applied cluster analysis, multidimensional scaling and principal axis correlation to identify significant habitat attributes and examine their importance for reptile and small mammal assemblages. Our results initially appear to imply that both vegetation composition (weed cover and grass trees) and habitat structure (termite mounds, wood volume and soil compaction) are important for native reptile and small mammal species. doi = 10.1111/j.1442-9993.2007.01750.x id = cord-010529-c8saxwfj author = Guzy, Jacquelyn C. title = Urbanization interferes with the use of amphibians as indicators of ecological integrity of wetlands date = 2012-07-17 keywords = Fig; Florida; MPX; specie; wetland summary = Our objectives were to (i) conduct a long-term study of cypress domes in south-west Florida to evaluate the potential utility of anurans in providing a quick and reliable assessment of wetland decline resulting from groundwater withdrawal and (ii) to determine whether urbanization interferes with the ability to use anurans as indicators for excessive groundwater withdrawal. These variables included (1) distance to nearest study wetland (indication of possible spatial dependence), (2) distance to nearest natural wetland, (3-5) per cent forest cover within 500, 1000 and 2000 m, and (6-8) mean proximity index (MPX) of forest cover within 500, 1000 and 2000 m; other measured variables included (9) average hydroperiod and (10) water depth at deepest point and (11-13) time (month, year or month plus year) as calling activity of anurans is strongly seasonal. doi = 10.1111/j.1365-2664.2012.02172.x id = cord-354757-jy47l6zm author = Havel, John E. title = Aquatic invasive species: challenges for the future date = 2015-01-25 keywords = AIS; aquatic; impact; invasion; invasive; native; specie summary = doi = 10.1007/s10750-014-2166-0 id = cord-023706-gs3oo3no author = Kaandorp, Jacques title = Veterinary Challenges of Mixed Species Exhibits date = 2011-06-22 keywords = exhibit; mixed; specie summary = Most often, zoos still show single species exhibits because of lack of space or simply to prevent problems associated with mixing different species. In this chapter, an incomplete listing of diseases and problems is presented to make the reader aware of the broad variety of veterinary challenges of mixed species exhibits. In mixed species exhibits, trauma is the most frequent and serious cause of health problems ( Fig. 4-4) . 6 To prevent trauma, next to appropriate size of the exhibit, pole gates (creeps), where small animals can flee from larger animals, creation of large obstacles in phillipsi) and sable antelope (Hypotrachus niger), or toxicities such as vitamin E toxicity in pelicans or iron storage disease in birds and some primate species, should be avoided when developing feeding protocols for mixed species exhibits. They are responsible for an enormous variety of disease problems, especially in mixed species exhibits. doi = 10.1016/b978-1-4377-1986-4.00004-4 id = cord-269505-7g8lio9l author = Keesing, Felicia title = Impacts of biodiversity on the emergence and transmission of infectious diseases date = 2010-12-01 keywords = disease; host; specie; transmission summary = For hantavirus pulmonary syndrome, a directly transmitted zoonotic disease, correlational and experimental studies have shown that a lower diversity of small mammals increases the prevalence of hantaviruses in their hosts, thereby increasing risk to humans (Box 2). Diversity has a similar effect for plant diseases, with species losses increasing the transmission of two fungal rust pathogens that infect perennial rye grass and other plant species 10 . This is because field studies like those on West Nile virus, hantaviruses and rye grass have typically not controlled for changes in host density that can result from changes in ''species richness'' (the number of species present in a community, which is a measure of taxonomic diversity). In sum, reducing biodiversity can increase disease transmission when the lost species are either not hosts for the pathogen or are suboptimal ones. In several case studies, the species most likely to be lost from ecological communities as diversity declines are those most likely to reduce pathogen transmission. doi = 10.1038/nature09575 id = cord-009716-oxahu8nz author = Lawes, Roger A. title = Comparing agglomerative clustering and three weed classification frameworks to assess the invasiveness of alien species across spatial scales date = 2006-10-27 keywords = cover; site; specie summary = A combination of three published weed classification frameworks and multivariate techniques were employed to classify species based on their frequency and cover at a range of spatial scales. (2000) ; Colautti & MacIsaac (2004) ; Davis & Thompson (2000) Introduction Barrier based on three distinct characteristics: dispersal distance (short/ long), uniqueness (novel/common to the region colonized), and impact on the new environment (small/great) ( Table 1 ). The data requirements necessary to implement the frameworks vary, although each draws heavily on frequency and abundance information to classify the invasive characteristics of a species. We propose evaluating weed invasions as part of a larger, existing plant community where invasive species are classified based on their relative abundance, frequency, and cover at local and landscape scales. Colautti & MacIsaac (2004)''s classification system is largely devised around concepts of frequency and abundance and it was a relatively simple process to classify species based on the survey data, where cover provided a surrogate measure of abundance. doi = 10.1111/j.1472-4642.2006.00291.x id = cord-024166-t3qxscbp author = Losvik, Mary H. title = Plant species diversity in an old, traditionally managed hay meadow compared to abandoned hay meadows in southwest Norway date = 2008-06-28 keywords = Losvik; plot; site; specie summary = The species group indicators of traditional management was preliminary defined in Losvik (1993b) , and later (Losvik 1996b ) was shown to comprise species occurring in less than 60 YO of 548 plots (1-16 m2) of hay meadow vegetation analysed in western Norway by 6 different authors 1972-1991. The aim of the study was to compare the vegetation and ecology of 4 sites which formed a chronosequence, representing a successional series from a species-rich, old, traditionally managed hay-meadow to sites which had been abandoned for about 10, 20 and 30 years, respectively. Themes of special interest were: how important are the ecological factors years since abandonment and cover of tree canopy in deciding the composition of the vegetation, what differences in species diversity, as measured by species-area curves, are there between the sites, for how long are species which are characteristic for the agricultural landscape able to persist during overgrowing in such sites, and finally, what forest species and additional species are most important in the sites of this series of abandoned haymeadows. doi = 10.1111/j.1756-1051.1999.tb01231.x id = cord-304481-yqc8r3ll author = Luis, Angela D. title = Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date = 2015-08-24 keywords = Fig; bat; specie; virus summary = Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. Rodents are a suitable group for comparison because they also host many important zoonotic viruses and share many of the characteristics hypothesised to make bats suitable as viral reservoirs. Host traits that correlated with the highest degree within the bat network (the most connections or viruses shared), in order of importance, were gregariousness and sympatry; diet was marginally important (Fig. 2b, Table S6 and S7). For rodents, sympatry was the most important host trait; species whose distributions overlapped with a greater number of other rodent species had more viruses and higher degree and betweenness (Fig. 2d-f and Table S11-S19). doi = 10.1111/ele.12491 id = cord-305857-2409me0p author = López-Roig, Marc title = Seroprevalence Dynamics of European Bat Lyssavirus Type 1 in a Multispecies Bat Colony date = 2014-09-04 keywords = EBLV-1; bat; specie summary = In recent years, bats have been implicated in numerous emerging infectious disease events and have been recognized as important reservoir hosts for viruses that can cross the species barrier to infect humans and other domestic and wild mammals [3] . Persistent viral infections occurring among long-lived bats, coupled with their often gregarious roosting behavior, could greatly increase the potential for intra-and inter-species transmission of viruses [7] , especially in summer and winter periods. To study the variation in EBLV-1-antibody prevalence, we conducted two analyses: first, three explanatory variables (sex, species and year) were first screened using a univariate analysis and a chi-square test to check for statistically significant associations with serological status (0: negative; 1: positive). We report the results of the prevalence of specific EBLV-1 neutralizing antibody analysis from the 2004-2012 period in nine bat species roosting in the same refuge. doi = 10.3390/v6093386 id = cord-010307-sxh5mq1q author = MILNE, D. J. title = Structure and environmental relationships of insectivorous bat assemblages in tropical Australian savannas date = 2005-11-23 keywords = Australia; bat; end; site; specie summary = Abstract Patterns in the composition of assemblages of microbat species sampled during the late dry season (the ''build‐up'') in north Australian savannas were assessed against a range of environmental factors as well as four a priori defined habitat types (riparian, escarpments, coastal and woodlands). However, we expect this will have a negligible effect on our results as shot sampling at all other sites, used in conjunction with Anabat detectors, enabled us to collect an extensive reference call library for ''high-flying'' bat species for the entire study area (Milne 2002) . Group 5 also had relatively few sites and low species richness, but was associated with the minima or maxima of several environmental variables including long distances to escarpments, flat terrain at low elevations with no rock, low local roost potential, high annual temperatures and low fire frequency. doi = 10.1111/j.1442-9993.2005.01535.x id = cord-261466-b9r4cyp7 author = Maritz, Julia M. title = What is the importance of zoonotic trichomonads for human health? date = 2014-06-18 keywords = Trichomonas; host; human; specie summary = Four species of trichomonad are considered human parasites: Trichomonas vaginalis (found in the urogenital tract) [6] , Trichomonas tenax (localized to the oral cavity) [7] , and Pentatrichomonas hominis and Dientamoeba fragilis (located in the digestive tract) [8, 9] . In addition, several trichomonad species are of veterinary importance, such as the avian pathogens Trichomonas gallinae, Tetratrichomonas gallinarum, and Histomonas meleagridis [16] [17] [18] [19] , and Tritrichomonas foetus, the causative agent of a venereal disease in cattle [20] . Thus, the presence of an increasing number of distinct trichomonads in a broader range of clinical samples from patients with diverse diseases, such as AIDS, rheumatoid arthritis, prostate cancer, pulmonary infections (empyema and pneumonia in addition to PcP and ARDS), and digestive conditions such as diarrhea and IBS [33] [34] [35] , is becoming increasingly apparent. doi = 10.1016/j.pt.2014.05.005 id = cord-335915-2apj4qy9 author = Melillo, Alessandro title = Applications of Serum Protein Electrophoresis in Exotic Pet Medicine date = 2013-01-22 keywords = albumin; globulin; protein; specie summary = The main difference between the 2 products is the absence in the serum of fribrinogen, the protein involved in the processes of coagulation; the concentration of total solids of the plasma is thus slightly higher than that of serum (about 5%) and the electrophoretic pattern from it will result in a higher incidence of b-globulin fraction where the fibrinogen normally migrates. In rabbits, the normal Serum Protein Electrophoresis (SPE) pattern lacks a clear distinction between b1-globulins and b2-globulins, as present in dogs and cats, but when gammopathies in the b region occur, usually an extension of the electrophoretic band is seen, with consequent demarcation of the 2 peaks. The first studies of serum proteins in birds were performed on domestic chickens, showing many similarities with the layout of mammals (eg, the production of APPs 18, 19 ), but also several differences: the widespread presence of prealbumin, for example, the lowest concentration of g-globulin, and conversely the more marked response to inflammatory stimuli in the b-globulin field. doi = 10.1016/j.cvex.2012.11.002 id = cord-021152-6znmkvy9 author = Montecino-Latorre, Diego title = Reproduction of East-African bats may guide risk mitigation for coronavirus spillover date = 2020-02-07 keywords = SARS; bat; coronavirus; detection; specie summary = METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. Assuming that higher spillover risk is a function of higher viral shedding [67] and that all coronaviruses with zoonotic potential behave ecologically similarly to coronaviruses detected in this study, managers could target the prevention of human-bat direct (consumption) or indirect (bat droppings) contact specifically during the high-risk season: around and just after weaning, the timing of observable juveniles or individuals smaller than adults. Our proposed risk-driven strategy i) is evidence-based, as it builds upon coronavirus shedding patterns observed across several chiropteran species present around the world; ii) does not require the advanced laboratory capacity often lacking in resource-restricted settings where intense bat-human interfaces usually occur; iii) is a good alternative to the ideal but expensive and resourceintensive longitudinal surveys; and iv) it may prevent the exposure to viruses belonging to other taxa whose observed bat shedding dynamics resemble our findings for coronaviruses (e.g. paramyxoviruses [97] ), doi = 10.1186/s42522-019-0008-8 id = cord-289555-1z4vbldd author = Mühldorfer, Kristin title = Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates date = 2011-12-28 keywords = Germany; bat; european; specie summary = Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats. In this study, we provide new data on infectious diseases in European bat species, considering factors likely to affect the susceptibility of bats to infectious agents including effects of seasonality, individual and species-specific heterogeneities, and possible intra-and inter-species transmission dynamics. Comparative bacteriologic and histo-pathologic analysis identified 22 different bacterial species that were clearly associated with pathological lesions and/or systemic infection, found in 17% (n = 73) of bats investigated bacteriologically ( Table 5) . doi = 10.1371/journal.pone.0029773 id = cord-010149-zupx8qn1 author = Ni, Yijun title = Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria date = 2020-04-21 keywords = COI; Copepoda; Cyclopidae; Nigeria; specie summary = title: Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. By analyzing sequence variation in the COI gene, we aimed to explore the species diversity and distribution of copepods among these populations. Based on the haplotype network, seven out of 12 species detected through analysis of the COI gene occurred at more than one locality in Nigeria (Fig. 1b) . Through analysis of COI sequence variation, we explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems, the first such study for West Africa. Our results suggested a high species diversity of Cyclopidae copepods over a small geographic sampling range. doi = 10.1186/s12862-020-01608-5 id = cord-005845-axrv8zfg author = O''Brien, Stephen J. title = Genomic prospecting date = 1995 keywords = FIV; genetic; specie summary = When cheetahs became exposed recently to feline infectious peritonitis virus, a coronavirus with low morbidity and mortality in domestic cats (about 1 per cent affected), 100 per cent of infected cheetahs developed symptoms (diarrhea, jaundice, depression, fever) and 60 per cent died 7 • The cheetah''s homogeneous sensitivity to this agent in the face of genetic monomorphism at the MHC provided a rationale for the critical importance of MHC genetic variation in natural populations. Some fascinating insight about lethal infectious disease and natural genetic defences appeared from a wild mouse population in a squab farm near Lake Casitas, forty miles north of Los Angeles'' 0 • Murray Gardner (University of California at Davis) discovered that the mice were suffering a raging epidemic with a retrovirus that caused fatal hindlimb paralysis. Finally, with the recent development of high resolution comparative gene maps of primate, cat, and other mammalian species, the genetic basis of lentivirus resistance can now be approached''". doi = 10.1038/nm0895-742 id = cord-010620-4ghzpqct author = Odasz, Ann Marie title = Nitrate reductase activity in vegetation below an arctic bird cliff, Svalbard, Norway date = 2009-02-24 keywords = Fig; NRA; specie; zone summary = The aim of this study was to investigate the relationship between the distribution of plant species in bird cliff vegetation and the amount of soil nitrate available in the region of sea-bird guano deposition. In this study I used the maximally induced nitrate reductase activities of species to establish nitrogen indicator figures for arctic plants, thus extending the system of Ellenberg (1991) for central-European plants for different levels of nitrogen, using a scalar system from 1, environments poor in N, through 9, rich in N. Induced NRA values for the dominant species in each zone decreased significantly downslope: Cochlearia groenlandica: 4.35; Oxyria digyna: 6.06; Cerastium arcticum: 4.26; Saxifraga hieracifolia: 1.36; Saxifraga cespitosa: 1.23; and Dryas octopetala representative of the tundra sites: 1.10 (Table 2) . doi = 10.2307/3236203 id = cord-022883-chrxyrls author = Owen, Jennifer title = Trophic variety and abundance of hoverflies (Diptera, Syrphidae) in an English suburban garden date = 2006-06-30 keywords = Malaise; garden; specie summary = The trophic composition of the Malaise trap catch varied to some extent from year to year, as shown in Tab, 3, Although hoverflies with aphid-feeding larvae (group 2) constituted the majority of the sample in every year, their relative frequency was considerably lower in 1973 , 1976 . This is not reflected in the relative frequency of group 2 hovertlics in these years (see Tab. 3), largely because the numbers of resident species of Melanostoma and Platycheirus in the catch were far lower than usual; Melanostoma mellinum, for instance, whieh breeds in the garden and is usually common, was represented by only two individuals in 1977, and M. when Eristalis arbustorum and other species with larvae that feed on decaying organic material became particularly abundant in August such that, by September, the relative frequency of aphid-feeders had fallen io38.87o. doi = 10.1111/j.1600-0587.1981.tb01001.x id = cord-271076-436nxsua author = Paul-Pierre, Pastoret title = Emerging diseases, zoonoses and vaccines to control them date = 2009-10-30 keywords = infection; specie; virus summary = In Northern America, the spectacular spread of West Nile virus infection, another vector transmitted disease, in humans and horses, was rapidly followed by the development of several vaccines, including a DNA-based vaccine for horses. To prevent Nipah virus (Henipavirus) infection in pigs a vaccine has recently been developed but, unfortunately, in countries like Bangladesh, humans are directly infected by the reservoir, a fruit bat species. The changes following globalisation, climatic change [6, 7] , and the opening of previously closed ecosystems, have considerably modified the pattern of endemic (or enzootic) infections/diseases, and contributed to the emergence of new agents that are pathogenic for humans and domestic animals. It is even more true when facing a really emerging disease that moreover is zoonotic such as Nipah virus infection [27] for which no vaccine was available yet, because the causative agent was previously unknown; the only solution is once again to kill and destroy the infected and in-contact animals. doi = 10.1016/j.vaccine.2009.06.021 id = cord-300727-v3spbo5u author = Peterson, A. Townsend title = Biogeography of diseases: a framework for analysis date = 2008-03-05 keywords = Peterson; disease; ecological; specie summary = The ways in which these differences may influence disease transmission geography are complex; I illustrate their effects by means of worked examples regarding West Nile Virus, plague, filoviruses, and yellow fever. Three example disease systems are illustrated: West Nile Virus, the filoviruses (Ebola and Marburg viruses), and plague: Changes are illustrated as the difference between broken (original) and entire (present) outlines of circles; particular geographic occurrences of the disease are labeled to illustrate points discussed in the text appropriate from both abiotic and biotic perspectives and that are accessible to the species in terms of dispersal. In niche modeling, known occurrences of species (or diseases, in some cases) are related to raster geographic information system (GIS) coverages summarizing relevant environmental parameters in an evolutionary computing environment; the result is a picture of the species'' ecological distribution, which can be projected onto geography to identify a potential distribution for the species (Peterson 2007; Soberón 2007) . doi = 10.1007/s00114-008-0352-5 id = cord-016379-lcog1654 author = Pimentel, David title = Plant,Animal, and Microbe Invasive Species in the United States and World date = 2007 keywords = Pimentel; States; United; specie summary = Calculating the negative economic impacts associated with the invasion of exotic species is difficult.For a few species, there are sufficient data to estimate some impacts on agriculture, forestry, fisheries, public health, and the natural ecosystem in the US and worldwide. Worldwide, an estimated 30,000 species of exotic plants have been intentionally introduced as crops, and have escaped to become established in various natural ecosystems. In the United States, introduced plant species are spreading and invading approximately 700,000 ha of US natural ecosystems per year (Babbitt 1998) . In the Great Lakes, for instance, nearly 50 invasive species are found, and these invaders are causing an estimated $ 5 billion in damages to the fisheries per year (Pimentel 2005) . This investigation reports on various economic damages associated with invasive species in various nations of the world that total more than $ 1.4 trillion per year (Pimentel 2002) . doi = 10.1007/978-3-540-36920-2_18 id = cord-276585-m1dkkbq7 author = Pulliam, Juliet R. C. title = Viral Host Jumps: Moving toward a Predictive Framework date = 2008-02-13 keywords = host; specie; virus summary = Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred. Although he makes no attempt to quantitatively determine the relative frequency of emergence for different types of pathogens, Burke claims that recent pandemics in humans and wildlife have mostly been caused by RNA viruses, citing multiple examples (influenza A, HIV-1, enteroviruses 70 and 71, human T-cell lymphoma virus, three paramyxoviruses, porcine respiratory coronavirus, and a calicivirus that causes hemorrhagic disease in rabbits). doi = 10.1007/s10393-007-0149-6 id = cord-254713-ghcwfcx2 author = Razanajatovo, Norosoa H title = Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date = 2015-03-12 keywords = Madagascar; RNA; bat; specie summary = RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species. doi = 10.1186/s12985-015-0271-y id = cord-290253-hxxizipk author = Roberts, Katherine E. title = Changes in temperature alter the potential outcomes of virus host shifts date = 2018-10-19 keywords = Drosophila; host; specie; temperature summary = Susceptibility to infection is known to vary with temperature, due to within individual physiological changes in factors such as the host immune response, metabolic rate or behavioural adaptations [22] [23] [24] [25] . However, if the host phylogeny also explains much of the variation in thermal tolerance, then phylogenetic patterns in virus susceptibility could be due to differences between species'' natural thermal optima and the chosen assay temperatures. We infected 45 species of Drosophilidae with Drosophila C Virus (DCV; Dicistroviridae) at three different temperatures and measured how viral load changes with temperature. We also examine how proxies for thermal optima and cellular function (thermal tolerances and basal metabolic rate) relate to virus susceptibility across temperatures, as increasing temperatures may have broad effects on both host and parasite [43] [44] [45] . To investigate the effect of temperature on virus host shifts we quantified viral load in 12,827 flies over 396 biological replicates, from 45 species of Drosophilidae at three temperatures ( Fig 1) . doi = 10.1371/journal.ppat.1007185 id = cord-312545-io2jmp7o author = Roche, Benjamin title = Ecosystem dynamics, biological diversity and emerging infectious diseases date = 2011-04-30 keywords = host; specie; vector summary = Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective. Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective. This raises two important questions concerning: (i) the effects on local disease transmission of the accidental introduction or biological invasion by exotic vectors, even when they show a low competence to transmit the infection; and (ii) the role of low to very low In species-rich reservoir communities, generally a decrease in the prevalence of disease pathogens in the vectors is observed. doi = 10.1016/j.crvi.2011.02.008 id = cord-301991-n87le8ix author = Saxena, Abhishek title = Diatoms recovery from wastewater: Overview from an ecological and economic perspective date = 2020-10-16 keywords = cell; culture; diatom; isolation; microalgae; sample; specie; water summary = Because diatoms produce organic matter to a large extent that permits natural inbuilt capacity to withstand toxicity levels in water bodies, extended survival rate, short regeneration time than microalgae, fishes, and other micro invertebrates thus making them one of the best candidate for water quality monitoring, and excellent bioindicators of aquatic biological integrity [12, 13] . Isolation and identification of benthic diatoms are problematic in comparison with planktonic species due to difficulties in sample treatment, sampling, and microscopic observation though benthic diatoms play the main role as bioindicators in the aquatic ecosystem because they attached to the substratum with secreted mucilage from their cell wall [44, 45] . An outline of isolation of pure diatom species getting affected by the surrounding contaminants is challenging since they get heavily occupied with different interfering organisms, which pose a significant threat in obtaining axenic culture, as presented in Fig. 3 . doi = 10.1016/j.jwpe.2020.101705 id = cord-022973-soaz8b74 author = Trivellini, Guido title = Nestedness of habitat specialists within habitat generalists in a butterfly assemblage date = 2016-09-25 keywords = butterfly; group; habitat; specie summary = Butterflies (Lepidoptera) are a well-studied insect group both taxonomically and ecologically (e.g. Gilbert, 1984; Kocher & Williams, 2000; Ghazoul, 2002; Stefanescu et al., 2004 Stefanescu et al., , 2011 , particularly because they interact with plants both as larval herbivores and adult pollinators (Borges et al., 2003; Hardy et al., 2007) and have different habitat requirements even at each life stage (New et al., 1995; Samways & Lu, 2007; Dennis, 2010) . E-mail: giuseppe.bogliani@unipv.it These largely specialised butterfly-habitat associations are influenced by many physical and biological factors (Leps & Spitzer, 1990; Spitzer et al., 1993) , including temperature, humidity, light levels, rainfall patterns, local microclimate conditions, grassland type and host-plant species richness and distribution (Hill et al., 2001; Meyer & Sisk, 2001; Collinge et al., 2003; Men endez et al., 2007) . To do this, we first defined the requirements, i.e., which habitat types positively or negatively correlate with species abundances, and then used a network-based approach (Bl€ uthgen et al., 2006) to analyse the degree of habitat use overlap within groups of species with similar habitat requirements. doi = 10.1111/icad.12193 id = cord-023036-rnt6ivcy author = Turc̄ek, F. J. title = THE BIRD SUCCESSION IN THE CONIFER PLANTATIONS ON MAT‐GRASS LAND IN SLOVAKIA (CSR). date = 2008-04-03 keywords = bird; specie summary = The three groups of areas studied were: (1) bare pastures, with an intermediate number of bird species, few individuals and high biomass of mainly carnivorous and insectivorous birds; (2) conifer plantations 1 to 5 years old, with the smallest number of bird species and the smallest biomass, but an intermediate number of individuals; (3) plantations six to twenty years old, with the highest number of both species and individuals of birds, but only intermediate biomass. The bird species found, their density and biomass per hectare in each group of areas are given in Table 1 . In the plantations studied, mainly of Norway spruce and Scots pine mixed with some European larch and a few deciduous trees, we were able to study the development of the bird community from bare pasture up to a forest of about 20 years of age. doi = 10.1111/j.1474-919x.1957.tb03050.x id = cord-016717-2twm4hmc author = Vourc’h, Gwenaël title = How Does Biodiversity Influence the Ecology of Infectious Disease? date = 2011-06-28 keywords = disease; host; pathogen; specie summary = To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. In this chapter, we investigate how biodiversity influences the ecology of infectious diseases at the intraspecific level (genetic variability of pathogens and hosts) and at the level of communities (species composition). The hypothesis underlying the amplification and dilution effect is that for many diseases, the competence of reservoirs, i.e. the ability to become infected and retransmit the pathogen, varies according to the host species (Haydon et al. doi = 10.1007/978-94-007-2114-2_13 id = cord-019068-6j42euvc author = Williams, Ernest H. title = Life Cycle and Life History Strategies of Parasitic Crustacea date = 2019-07-05 keywords = Anilocra; Bunkley; Copepoda; Crustacea; Isopoda; Williams; adult; cycle; female; fish; host; life; parasite; parasitic; specie; stage summary = doi = 10.1007/978-3-030-17385-2_5 id = cord-021013-xvc791wx author = Wink, Michael title = Chapter 1 Allelochemical Properties or the Raison D'être of Alkaloids date = 2008-05-30 keywords = Table; alkaloid; compound; defense; herbivore; number; pas; plant; specie summary = doi = 10.1016/s0099-9598(08)60134-0 id = cord-343139-19t8g7u7 author = Wintle, Brendan A. title = After the Megafires: What Next for Australian Wildlife? date = 2020-07-14 keywords = Australia; fire; specie summary = Unfortunately, there was little strategic priority in fire control operations for the protection of key populations of threatened species, critical habitats, and threatened ecological communities. Clear guidance on how to most effectively organise species and ecosystem conservation activities before, during, and immediately following a major fire event can be helpful (Figure 2 ). and extensive control of other threats that can compound fire impacts; and collection of baseline monitoring and survey data to help identify places critical to protect, prioritise emergency responses, and provide clarity around what has been lost immediately following a fire event. Crucial elements in the preparatory phase ''before the fire'' that were not adequately addressed before the 2019-2020 Australian megafires include analysis and synthesis of species sensitivity to fire, monitoring, surveying, and mapping to delineate critical habitats for protection and emergency postfire action. doi = 10.1016/j.tree.2020.06.009 id = cord-320295-k2i52wgs author = Woolhouse, Mark E.J. title = Host Range and Emerging and Reemerging Pathogens date = 2005-12-17 keywords = pathogen; specie summary = However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population. All the defined host types are potential sources of zoonotic infections, but differences occurred in their importance (ranked by number of pathogen species supported) across viruses, bacteria, fungi, protozoa, and helminths and no 1 type consistently dominates ( Figure 1A) , although ungulates are the most important overall, supporting over 250 species of human pathogen. However, when the fraction of emerging and reemerging species is compared with the breadth of host range (as the number of host types other than humans), a pattern becomes apparent (Figure 2) . Relationship between breadth of host range (as number of nonhuman host types, as listed in Figure 1 ) and the fraction of pathogen species regarded as emerging or reemerging. doi = 10.3201/eid1112.050997 id = cord-005280-a23oy0sz author = Yang, Shenshu title = ROS and diseases: role in metabolism and energy supply date = 2019-12-07 keywords = ROS; cell; oxygen; reactive; specie summary = Although ROS play an important role in pathogen resistance and cellular signalling, they are also broadly recognized as harmful reactive particles to cell as they damage intracellular proteins, lipids and nucleic acids. The homeostasis of ROS plays an important role in reducing oxidative damage and fulfil energy demand. Relatively high levels of ROS may cause oxidative damage or induce apoptosis during immunological defences or pathological conditions. However, ROS themselves could activate extracellular signal-regulated kinase (ERK) by targeting proteins Gαi and Gα0 and protect cardiac cell from oxidative damage [18] . Apart from oxidative damage, ROS also serve as signalling molecules and play an important role in homeostasis, metabolism, growth and differentiation [3] . PGC-1α could protect neural cells from oxidative damage by reducing ROS level via antioxidative enzymes GPx1 and SOD2 [15] . ROS regulate vascular cell proliferation and apoptosis with their fundamental role in metabolism. doi = 10.1007/s11010-019-03667-9 id = cord-010501-kd95xvsg author = Zenetos, Argyro title = Analysis of Benthic Communities in the Cyclades Plateau (Aegean Sea) Using Ecological and Paleoecological Data Sets date = 2008-06-28 keywords = group; specie; station summary = Standard multivariate analysis techniques were applied to both ecological (living benthic fauna) and paleoecological data sets in order to distinguish distribution patterns. The species richness, abundance, and diversity per station is given in Table 2 : the number of species ranged from 21 (station A23) to 100 (station A32), and the number of specimens from 152-m-2 (station A 17) to 432.m-2 (station A26 The dendrograms can be truncated at any level, but the areal presentation derived with MDS based on the total living fauna (Fig. 4 a) indicated that the more justified separation in terms of ecological sense was at the 4 groups level (25% similarity) (two dimensional stress = 0.141). The groups are based on the dendrogram of Fig. 2 Table 5 shows the results of the SPEARMAN rank correlation coefficient between the biotic parameters (number of macrofaunal species, number of specimens, and species diversity) and depth and sediment type. doi = 10.1111/j.1439-0485.1991.tb00247.x id = cord-312555-qytl2vqt author = da Silva, Josivan Soares title = Use of game fauna by Fulni-ô people in Northeastern Brazil: implications for conservation date = 2020-04-17 keywords = Brazil; Fulni; Ouricuri; hunting; specie summary = Also, the use of game meat among the Fulni-ô seems to be actively directed to the preferred species, suggesting that in the case of an urbanized indigenous community, where other sources of income are available, the demand for game meat is lower when compared to other ethnic groups. Thus, this research focused on the hunting of game meat among the Fulni-ô people living in the semi-arid region, being the first study carried out in an ethnic group strongly influenced by urbanization in the Brazilian Northeast. Even when compared to studies of wild animal consumption in the Caatinga region [5, 41] , the number of animals hunted is higher than that reported for the Fulni-ô, which may be indicative of a lower demand for game in relation to other communities in the northeast region [5, 12, 17, 31] . doi = 10.1186/s13002-020-00367-3