cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b82g9b
title: 0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains

description: These are initial and final (75ns) configurations in PDB format
 of  glycosylated ACE2-FC fusion proteins which are
 promising targets for a COVID-19 therapeutic. Some of them are
 in interaction witha fragment of the receptor-binding domain
 (RBD) of the Spike Protein S of the SARS-CoV-2 virus. We used
 two  glycosylation variants for ACE2-FC, variant 1 is fully
 glycosylated with Man8 glycans, variant 2 is fully glycosylated with
 GnGnXF3. The Spike RBD is glycosylated with ANaF^6.
description: Molecular Dynamics Simulations using Gromacs
   Details: Fuse ACE2 with Fc to ACE2-Fc
 using Modeller  Model Zn<sup>2+</sup>
 and coordinating residues with MCPB.py  Attach glycans using
 glycam.org  Merge structures from 2. and 3. using
 github.com/austenb28/MCPB_Glycam_merge  Generate topology files using
 AmberTools  Convert topology files to Gromacs
 format using Acpype  Perform rigid energy minimization
 (EM) of glycans using github.com/austenb28/GlyRot Perform EM (emtol = 1000
 kJ/mol/nm) Solvate and add ions
 Perform 10 ps constant
 volume (NVT) (dt = 0.2 fs, T = 310 K) Perform EM (emtol = 1000
 kJ/mol/nm) Perform 100 ps NVT (dt = 2 fs, T
 = 310 K) Perform 100 ps constant pressure
 (NPT) (dt = 2 fs, T = 310 K, P = 1 atm) Perform 75 ns
 production NPT (dt = 2 fs, T = 310 K, P = 1 atm)
description: Any molecular simulation software which can read pdb files can be
 used for simulations (e.g. gromacs which is open source was used to
 generate the data). For simple viewing any pdb reader, e.g. Jmol can be
 used.
DOI: 10.5061/dryad.w6m905qn0
title: Data from: Spatial structure maintains diversity of pyocin inhibition in household Pseudomonas aeruginosa

description: Nearly all bacteria produce narrow-spectrum antibiotics called
 bacteriocins. Studies have shown that bacteriocins can mediate
 microbial interactions, but the mechanisms underlying patterns of
 inhibition are less well understood. We assembled a spatially structured
 collection of isolates of Pseudomonas aeruginosa from
 bathroom and kitchen sink drains in nine households. Growth inhibition of
 these P. aeruginosa by bacteriocins, known as pyocins in
 this species, was measured using pairwise inhibition
 assays.  Carbon source usage of these isolates was
 measured and genetic distance was estimated using multilocus
 sequencing.  We found that as the distance between sites
 of isolation increased, there was a significantly higher probability of
 inhibition, and that pyocin inhibition and susceptibility vary greatly
 among isolates collected from different houses. We also detected support
 for other mechanisms influencing diversity: inhibition outcomes were
 influenced by the type of drain from which isolates were collected, and
 while we found no indication that carbon source utilization influences
 inhibition, inhibition was favored at an intermediate genetic distance.
 Overall, these results suggest that the combined effects of dispersal
 limitation among sites and competitive exclusion within them maintain
 diversity in pyocin inhibition and susceptibility phenotypes, and that
 additional processes such as local adaptation and effects of phylogenetic
 distance could further contribute to spatial variability.
DOI: 10.5061/dryad.ncjsxksrw
title: Data from Evidence of phenotypic plasticity in the response of unionid mussels to turbidity.

description: 1. Increases in total suspended solids (TSS) reduce feeding and
 reproductive success of unionid mussels, but mussels in turbid rivers are
 less affected than those in clear rivers, probably due to differences in
 gill and palp morphology. This study was designed to determine whether the
 differences observed between adult mussels in populations from turbid
 versus clear rivers are due to phenotypic plasticity. 2. Parasitic larvae
 (glochidia) of Lampsilis siliquoidea (Fatmucket) obtained from a low
 turbidity river (TSS &lt; 5 mg/L) were transformed on Ambloplites
 rupestris (Rock Bass) in the laboratory to obtain juvenile mussels for
 rearing under clear and turbid conditions in the laboratory (i.e.
 nominally 0 versus 50 mg/L suspended river sediment). Juveniles obtained
 were reared under these contrasting conditions until age 3–4 weeks, when
 they were examined in a feeding experiment under a range of TSS
 concentrations (0, 5, 10, 15, 20, 25 mg/L). 3. The clearance rate (volume
 cleared of particles per unit time) of algae by juveniles from both
 rearing conditions was similar for the no-TSS control and declined with
 increased TSS. The rate of decline was, however, lower in the group reared
 under turbid conditions, which is consistent with reports for adult
 mussels. 4. Our results indicate that differences in the clearance rate
 response to high TSS observed in mussels in clear and turbid rivers are
 probably driven in part by phenotypic plasticity. This finding provides a
 mechanism to explain how freshwater mussels thrive under turbid conditions
 as well as informs conservation efforts involving reintroduction of
 mussels in this highly imperiled taxon.
description: These are the results from an emperical study conducted in the
 laboratory.
description: The data are labeled in the attached Excel file.
DOI: 10.5061/dryad.gtht76hjc
title: A kaleidoscopic view of ovarian genes associated with infertility, subfertility and senescence

description: Ovarian infertility and subfertility presenting with premature ovarian
 insufficiency (POI) and diminished ovarian reserve are major issues facing
 in the developed world due to the trend of delaying child
 birth. Polycystic ovary syndrome (PCOS) is a common endocrine and
 metabolic disorder affecting 6-10% of women in reproductive age. Based on
 advances in whole exome sequencing, evaluation of gene copy variants,
 together with family-based and genome-wide association studies (GWAS), we
 discussed genes responsible for the POI, PCOS, and ovarian
 senescence. We used a gene-centric approach to sort out
 literature deposited in the Ovarian Kaleidoscope database
 (http://okdb.appliedbioinfo.net) by sub-categorizing candidate genes as
 ligand-receptor signaling, meiosis and DNA repair, transcriptional
 factors, RNA metabolism, enzymes, and others. We discussed
 individual gene mutations found in POI patients and verification of gene
 functions in gene-deleted model organisms. Decreases in the
 expression of some of the POI genes could be responsible for early
 menopause, especially those essential for DNA repair and
 meiosis. Although multiple individual candidate gene single
 nucleotide polymorphisms have been analyzed in PCOS patients, only a
 limited number of findings have been verified and dealing with genes with
 known ovarian functions. We propose to set up a panel of
 candidate genes for targeted sequencing in POI patients and investigate
 ovarian expression of a set of candidate genes in PCOS patients, together
 with studies on mitochondria-associated genes in middle-aged subfertile
 patients. Continuing studies on POI and PCOS as well as ovarian
 senescence genes could allow better diagnosis and formulation of treatment
 strategies.
description: Based on literature review.
DOI: 10.5061/dryad.6hdr7sqxx
title: International consensus guidance for management of myasthenia gravis

description: OBJECTIVE: To update the 2016 formal consensus-based guidance for the
 management of myasthenia gravis (MG) based on the latest evidence in the
 literature. METHODS: In October 2013, the Myasthenia Gravis Foundation of
 America appointed a Task Force to develop treatment guidance for MG, and a
 panel of 15 international experts was convened. The RAND/UCLA
 appropriateness method was used to develop consensus recommendations
 pertaining to seven treatment topics. In February 2019, the international
 panel was reconvened with the addition of one member to represent South
 America.  All prior recommendations were reviewed for currency,
 and new consensus recommendations were developed on topics that required
 inclusion or updates based on recent literature.  Up to three
 rounds of anonymous e-mail votes were used to reach consensus, with
 modifications to recommendations between rounds based on panel input. A
 simple majority vote (80% of panel members voting ‘yes’) was used to
 approve minor changes in grammar and syntax to improve clarity. RESULTS:
  The previous recommendations for thymectomy were updated. New
 recommendations were developed for the use of rituximab, eculizumab and
 methotrexate as well as for the following topics: early immunosuppression
 in ocular MG and MG associated with immune checkpoint inhibitor treatment.
 CONCLUSION: This updated formal consensus guidance of international MG
 experts, based on new evidence, provides recommendations to clinicians
 caring for MG patients worldwide.
description: These are the tables of all combined recommendations that
 achieved consensus for each topic in the treatment of myasthenia gravis.
 these tables incorporate both the recommendations from the initial MG
 consensus guidance published in neurology 2016 and the present update. the
 recommendations were developed using the RAND-UCLA appropriateness method
 of formal consensus. 
description: An international expert panel participated in this process. The
 voting scores for all these recommendations (median and range) are
 available.
DOI: 10.5061/dryad.4mw6m907s
title: Data from: Integrating climate and host richness as drivers of global parasite diversity

description: Aim: Climate and host richness are essential drivers of global gradients
 in parasite diversity, and the few existing studies on parasites have
 mostly investigated their effects separately. The advantages of combining
 these factors into a single analytical framework include unravelling the
 relative roles of abiotic and biotic drivers of parasite diversity. We
 compiled a dataset of helminths of amphibians to investigate the direct
 and indirect effects of temperature seasonality, annual precipitation,
 precipitation seasonality and host richness as drivers of parasite
 diversity at the global scale. Our analyses focus not only on the least
 studied group of vertebrates regarding macroecology of parasite diversity,
 but also the host group most sensitive to climatic conditions, especially
 temperature seasonality and water availability. Location: Global Time
 period: 1955-2017. Major taxa studied: Helminth parasites of amphibians.
 Methods: We used piecewise structural equation modelling on a global
 dataset of helminths of amphibians, comprising 613 populations of 319
 anuran species and 94 populations of 43 salamander species from ten
 zoogeographical realms. Results:  We found that precipitation
 seasonality and host richness both affect parasite diversity positively,
 but the latter presented a stronger effect. Additionally, we found that
 both temperature seasonality and total precipitation indirectly affected
 parasite richness through their respective negative and positive effects
 on host richness. Main Conclusions: Future studies on global gradients in
 parasite diversity should include both direct and indirect effects of
 climatic factors as drivers of parasite diversity. Integrating multiple
 predictors into a single statistical framework that measures both direct
 and indirect effects increases our theoretical understanding of the
 relative importance and interactions among different diversity drivers at
 the macroecological scale. The indirect effects of temperature seasonality
 and total precipitation on parasite diversity are an interesting new
 insight brought by our study, with implications for future studies dealing
 with host-parasite coextinctions due to climate change.
description: This is a dataset of helminth parasite richness of amphibians
 composed from a compilation of the published literature. Additionally, we
 included the predictor variables we used for the models presented in the
 manuscript as well as other relevant information. See the README file for
 a detailed explanation of column headings and the list of references used
 for parasite richness data.
DOI: 10.5061/dryad.69p8cz8zx
title: Data from: Male serrate-legged treefrogs adjust competition strategies according to visual or chemical cues from females

description: There is increasing evidence that many anurans use multimodal cues to
 detect, discriminate and/or locate conspecifics and thus modify their
 behaviors. To date, however, most studies have focused on the roles of
 multimodal cues in female choice or male–male interactions. In the present
 study, we conducted an experiment to investigate whether male
 serrate-legged small treefrogs (Kurixalus odontotarsus) used visual or
 chemical cues to detect females and thus altered their competition
 strategies in different calling contexts. Three acoustic stimuli
 (advertisement calls, aggressive calls and compound calls) were broadcast
 in a randomized order after a spontaneous period to focal males in one of
 four treatment groups: combined visual and chemical cues of a female, only
 chemical cues, only visual cues and a control (with no females). We
 recorded the vocal responses of the focal males during each 3 min period.
 Our results demonstrate that males reduce the total number of calls in
 response to the presence of females, regardless of how they perceived the
 females. In response to advertisement calls and compound calls, males that
 perceived females through chemical cues produced relatively fewer
 advertisement calls but more aggressive calls. In addition, they produced
 relatively more aggressive calls during the playback of aggressive calls.
 Taken together, our study suggests that male K. odontotarsus adjust their
 competition strategies according to the visual or chemical cues of
 potential mates and highlights the important role of multisensory cues in
 male frogs' perception of females.
description: Please see README file. adv: advertisement
 calls<br> agg: aggressive calls<br> comp: compound
 calls
DOI: 10.5061/dryad.x3ffbg7gc
title: Effects of mixing legume species on germination

description: While intercropping is known to have positive effects on crop
 productivity, it is unclear whether the effects of mixing species start at
 the very beginning of the plants’ life, i.e. during germination. We tested
 whether germination is affected by mixing cover crop species, using two
 legume species with a contrasting response to water availability and
 temperature, alsike clover (AC) and black medic (BM). We set up four
 experiments in each of which we compared a 1:1 mixture against the two
 monocultures, and combined this with various other experimental factors.
 These additional factors were (i) varied seed densities (50%, 100% and
 150% of a reference density) in two field trials in 2016 and 2017, (ii)
 varied seed densities (high and low) and water availability (6 levels,
 between 25% and 100% of water holding capacity, WHC) in a greenhouse pot
 trial, (iii) varied seed spacing in a climate chamber, and (iv) varied
 temperatures (12°C, 20°C, 28°C) and water availability (4 levels between
 25% and 100% of WHC) in a climate chamber. Across all experiments, the
 absolute mixture effects (AME) on germination ranged between -9% and +11%,
 with a median of +1.3%. Within experiments, significant mixture effects
 were observed, but the direction of these effects was inconsistent. In the
 field, AME on germination was significantly negative at some of the tested
 seed densities. A positive AME was observed in the climate chamber at
 12°C, and the mean AME decreased with increasing temperature. Higher
 density was associated with decreased germination in the field, indicating
 negative interaction through competition or allelopathy, among seedlings.
 Our findings indicate that seed interaction in mixtures may be ongoing as
 early as during germination, but that the direction of the mixture effect
 is affected by complex interactions with abiotic and biotic factors.
DOI: 10.5061/dryad.cvdncjt24
title: Colonization history affects heating rates of invasive cane toads

description: Amphibians in hot climates may be able to avoid high temperatures by
 controlling their rates of heating. In northern Australia, invasive cane
 toads (Rhinella marina) experience hot dry conditions in newly-colonized
 (western) sites but milder conditions in longer-occupied (eastern) sites.
 Under standardized conditions, toads from western sites heated less
 rapidly than did conspecifics from an eastern site. The availability of
 free water slowed heating rates of eastern but not western toads. Thus,
 the colonization of climatically extreme sites has been accompanied by a
 rapid shift in the toads’ ability to remain cool under hot conditions,
 even when free water is not available.
DOI: 10.5061/dryad.08kprr50g
title: Data from: Divergence of seminal fluid gene expression and function among natural snail populations

description: Seminal fluid proteins (SFPs) can trigger drastic changes in mating
 partners, mediating post-mating sexual selection and associated sexual
 conflict. Also, cross-species comparisons have demonstrated that SFPs
 evolve rapidly and hint that post-mating sexual selection drives their
 rapid evolution. In principle, this pattern should be detectable within
 species as rapid among-population divergence in SFP expression and
 function. However, given the multiple other factors that could vary among
 populations, isolating divergence in SFP-mediated effects is not
 straightforward. Here we attempted to address this gap by combining the
 power of a common garden design with functional assays involving
 artificial injection of SFPs in the simultaneously hermaphroditic
 freshwater snail, Lymnaea stagnalis. We detected among-population
 divergence in SFP gene expression, suggesting that seminal fluid
 composition differs among four populations collected in western Europe.
 Furthermore, by artificially injecting seminal fluid extracted from these
 field-derived snails into standardized mating partners, we also detected
 among-population divergence in the strength of post-mating effects induced
 by seminal fluid. Both egg production and subsequent sperm transfer of
 partners differed depending on the population origin of seminal fluid,
 with the response in egg production seemingly closely corresponding to
 among-population divergence in SFP gene expression. Our results thus lend
 strong intraspecific support to the notion that SFP expression and
 function evolve rapidly, and confirm L. stagnalis as an amenable system
 for studying processes driving SFP evolution.
DOI: 10.5061/dryad.cjsxksn3s
title: Antimicrobial capacity is related to body colouration and reproductive success in female spotless starlings

description: Pathogenic microorganisms select for a plethora of defensive mechanisms on
 their hosts. In males of some species, flashy traits might signal
 antimicrobial capacity and, thus, they might be favoured in scenarios of
 sexual selection. Antimicrobial capacity of individuals may predict
 reproductive success in males, and it could be adapted to changing
 environments. However, evidence for these associations is still scarce in
 females. Here, we evaluated antimicrobial capacity of spotless starling
 (Sturnus unicolor) females during the mating and nestling-provisioning
 phase. We did this by measuring (i) the blood plasma inhibition capacity
 against 12 bacterial strains (antagonistic index), (ii) the constitutive
 innate humoral immunity (lysis and agglutination capacity, a non-specific
 first barrier of protection of hosts against microbial parasites), and
 (iii) the uropygial gland size and volume of secretion produced, relevant
 traits in the protection against, among others, feather-degrading
 bacteria. We also measured colouration of throat and back feathers, and of
 leg and beak integuments. This information was collected during the
 pre-laying and nestling stages to compare values from these two periods.
 We found an increase in the plasma antagonistic index from the pre-laying
 to the nestling period, while a decrease on the plasma capacity of
 agglutination of foreign antigens. Both plasma antagonistic index and
 humoral immune response measured before breeding were positively related
 to future female reproductive success. In addition, the level of
 antimicrobial capacity was related to colouration of leg skin and beak
 integuments and of back feathers. These associations suggest that, similar
 to males, females might show through their physical appearance their
 capacity to fight microbial infections; information that could be
 evaluated by their potential partners and by female competitors.
DOI: 10.5061/dryad.rn8pk0p7c
title: Collateral benefits of targeted supplementary feeding on demography and growth rate of a threatened population

description: 1. Effective evidence-based conservation requires full quantification of
 the impacts of targeted management interventions on focal populations.
 Such impacts may extend beyond target individuals to also affect
 demographic rates of non-target conspecifics (e.g. different age classes).
 However, such collateral (i.e. unplanned) impacts are rarely evaluated,
 despite their potential to substantially alter conservation outcomes.
 Subsequent management decisions may then be poorly informed or erroneous.
 2. We used 15 years of individual-based demographic data in a
 “before-after control-impact” (BACI) analysis to quantify collateral
 demographic impacts of a targeted multi-year supplementary feeding
 programme designed to increase sub-adult survival and hence viability of a
 small, threatened red-billed chough (Pyrrhocorax pyrrhocorax) population.
 Specifically, we assessed whether the intervention also affected adult
 survival and reproductive success, and whether such collateral effects
 were themselves sufficient to stabilise population size and hence achieve
 short-term conservation aims. 3. The probabilities of adult survival and
 successful reproduction increased substantially between the
 “before-feeding” and “during-feeding” periods in those choughs associated
 with supplementary feeding, but not otherwise. Overall breeding success
 (i.e. number of chicks fledged per occupied territory) also tended to
 increase, even though brood sizes did not increase. These relationships,
 which were detectible only through BACI analyses, suggest that
 supplementary feeding targeted at sub-adults had unplanned positive
 impacts on adult demographic rates. 4. Deterministic matrix models
 designed to project population growth demonstrate that these estimated
 collateral effects were sufficient to make a substantial contribution to
 increasing population growth rate and achieving short-term population
 stability. 5. Synthesis and applications. Our results indicate substantial
 positive collateral impacts of a targeted supplementary feeding
 intervention on population viability, despite no a priori expectation that
 the non-target adults were food-limited. This case-study illustrates how
 thorough assessment of collateral impacts of targeted interventions can
 affect assessment of short-term efficacy and reveal new opportunities for
 future interventions, thereby informing subsequent management decisions.
DOI: 10.5061/dryad.x0k6djhgq
title: Genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations

description: Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in
 Tanzania. In addition to its importance for biodiversity conservation,
 Rufiji tilapia is also attractive for farming due to its high growth-rate,
 salinity tolerance, and the production of all-male hybrids when crossed
 with Nile tilapia (Oreochromis niloticus). The aim of the current study
 was to assess the genetic diversity and population structure of both wild
 and farmed Rufiji tilapia populations in order to inform conservation and
 aquaculture practices.
description: Table S1 contains pairwise Fst values and corresponding
 confidence intervals amongst the tested populations
 Figure S1 contains the BIC values for different number of K
 clusters