cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8256473
title: Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of <i>Trypanosoma cruzi</i>: an example of cooperative behavior

description: The <i>Trypanosoma cruzi</i> ribose-5-phosphate isomerase B (TcRpiB) is a crucial piece in the pentose phosphate pathway and thus is a potential drug target for treatment of Chagas’ disease. TcRpiB residues, such as Cys69, Asp45, Glu149 and Pro47, have confirmed their roles in substrate recognition, catalytic reaction and binding site conformation. However, the joint performance of His11 and His102, in the D-ribose-5-phosphate (R5P) in the catalysis is not well understood. In this work, we probed the influence of different protonation states of His11 and His102 on the behavior of the ligand R5P using molecular dynamics simulations, network analysis and thermodynamic integration. Simulations revealed that a protonated His11 combined with a neutral His102 (His11<sup>+</sup>‒His102) was able to stabilize the ligand R5P in the binding site. Moreover, calculated relative free energy differences showed that when protonated His11 was coupled to a neutral His102 an exergonic process takes place. On the other hand, neutral His11 combined with a protonated His102 (His11‒His102<sup>+</sup>), sampled conformations that resembled the catalyzed product D-ribulose-5-phosphate (Ru5P). Network analysis also demonstrated some peculiarities for these systems with some negatively correlated nodes in the binding site for His11‒His102<sup>+</sup>, and exclusive suboptimal paths for His11<sup>+</sup>‒His102. Therefore, the combined approach presented in this paper proposes two suitable protonation states for the TcRpiB catalytic mechanism, where an extra proton in either histidines might favor R5P binding or influence isomerization reaction to Ru5P. Our results may guide further <i>in silico</i> drug discovery studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8256473.v1
title: Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of <i>Trypanosoma cruzi</i>: an example of cooperative behavior

description: The <i>Trypanosoma cruzi</i> ribose-5-phosphate isomerase B (TcRpiB) is a crucial piece in the pentose phosphate pathway and thus is a potential drug target for treatment of Chagas’ disease. TcRpiB residues, such as Cys69, Asp45, Glu149 and Pro47, have confirmed their roles in substrate recognition, catalytic reaction and binding site conformation. However, the joint performance of His11 and His102, in the D-ribose-5-phosphate (R5P) in the catalysis is not well understood. In this work, we probed the influence of different protonation states of His11 and His102 on the behavior of the ligand R5P using molecular dynamics simulations, network analysis and thermodynamic integration. Simulations revealed that a protonated His11 combined with a neutral His102 (His11<sup>+</sup>‒His102) was able to stabilize the ligand R5P in the binding site. Moreover, calculated relative free energy differences showed that when protonated His11 was coupled to a neutral His102 an exergonic process takes place. On the other hand, neutral His11 combined with a protonated His102 (His11‒His102<sup>+</sup>), sampled conformations that resembled the catalyzed product D-ribulose-5-phosphate (Ru5P). Network analysis also demonstrated some peculiarities for these systems with some negatively correlated nodes in the binding site for His11‒His102<sup>+</sup>, and exclusive suboptimal paths for His11<sup>+</sup>‒His102. Therefore, the combined approach presented in this paper proposes two suitable protonation states for the TcRpiB catalytic mechanism, where an extra proton in either histidines might favor R5P binding or influence isomerization reaction to Ru5P. Our results may guide further <i>in silico</i> drug discovery studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8256458
title: Dataset for coding module - factors

description: Small forestry inventory dataset from NEON (Ordway Swisher Biological Station), to be used in a coding exercies
DOI: 10.6084/m9.figshare.8256452
title: Supplementary Material for: The Prevalence of Intradialytic Hypotension in Patients on Conventional Hemodialysis: A Systematic Review with Meta-Analysis

description: <b><i>Background:</i></b> Intradialytic hypotension (IDH) is considered to be a frequent complication of hemodialysis (HD) and is associated with symptom burden, increased incidence of access failure, cardiovascular events, and higher mortality. This systematic literature review aims to analyse studies that investigated the prevalence of IDH. A complicating factor herein is that many different definitions of IDH are used in literature. <b><i>Methods:</i></b> A systematic literature search from databases, Medline, Cinahl, EMBASE, and the Cochrane library to identify studies reporting on the actual prevalence of IDH was conducted. Studies were categorized by the type of definition used for the prevalence of IDH. A meta-analysis of the prevalence of IDH was performed. <b><i>Results:</i></b> In a meta-analysis comprising 4 studies including 1,694 patients and 4 studies including 13,189 patients, the prevalence of HD sessions complicated by IDH was 10.1 and 11.6% for the European Best Practice Guideline (EBPG) definition and the Nadir &lt;90 definition, respectively. The proportion of patients with frequent IDH could not reliably be established because of the wide range in cutoff values that were used to identify patients with frequent IDH. There was a large variety in the prevalence of symptoms and interventions. Major risk factors associated with IDH across studies were diabetes, a higher interdialytic weight gain, female gender, and lower body weight. <b><i>Conclusion:</i></b> Our meta-analysis suggests that the prevalence of IDH is lower than 12% for both the EBPG and the Nadir &lt;90 definition which is much lower than stated in most reviews.
DOI: 10.6084/m9.figshare.8256458.v1
title: Dataset for coding module - factors

description: Small forestry inventory dataset from NEON (Ordway Swisher Biological Station), to be used in a coding exercies
DOI: 10.6084/m9.figshare.8256452.v1
title: Supplementary Material for: The Prevalence of Intradialytic Hypotension in Patients on Conventional Hemodialysis: A Systematic Review with Meta-Analysis

description: <b><i>Background:</i></b> Intradialytic hypotension (IDH) is considered to be a frequent complication of hemodialysis (HD) and is associated with symptom burden, increased incidence of access failure, cardiovascular events, and higher mortality. This systematic literature review aims to analyse studies that investigated the prevalence of IDH. A complicating factor herein is that many different definitions of IDH are used in literature. <b><i>Methods:</i></b> A systematic literature search from databases, Medline, Cinahl, EMBASE, and the Cochrane library to identify studies reporting on the actual prevalence of IDH was conducted. Studies were categorized by the type of definition used for the prevalence of IDH. A meta-analysis of the prevalence of IDH was performed. <b><i>Results:</i></b> In a meta-analysis comprising 4 studies including 1,694 patients and 4 studies including 13,189 patients, the prevalence of HD sessions complicated by IDH was 10.1 and 11.6% for the European Best Practice Guideline (EBPG) definition and the Nadir &lt;90 definition, respectively. The proportion of patients with frequent IDH could not reliably be established because of the wide range in cutoff values that were used to identify patients with frequent IDH. There was a large variety in the prevalence of symptoms and interventions. Major risk factors associated with IDH across studies were diabetes, a higher interdialytic weight gain, female gender, and lower body weight. <b><i>Conclusion:</i></b> Our meta-analysis suggests that the prevalence of IDH is lower than 12% for both the EBPG and the Nadir &lt;90 definition which is much lower than stated in most reviews.
DOI: 10.6084/m9.figshare.8256188
title: An on-line fault location approach based on robust state estimation for scientific cabled seafloor observatories.xlsx

description: The data is the experimental data of fault location of Y-type cabled seafloor observatorie prototype.
DOI: 10.6084/m9.figshare.8256143
title: List of bird species (Common and Latin name) used in sampling of NISC (description of colour and area on the body where feather was sampled); Details of melanosomes sampling from E. brachyptera fossil and results of their measurements; Trait database used for Ancestral state reconstruction and posterior probabilities of colour state for E. brachyptera; Posterior probabilities of colour state for E. brachyptera; 1000 phylogenetic trees downloaded from birdtree.org in Nexus format; Tukey's post-hoc test results (pairwise comparison); Forward stepwise regression results and plot of the first two variables; Li et al. database with measurements of melanosomes isolated from feathers expressing non-iridescent structural colour included. Added samples are indicated with blue colour in the database.; Results of simulation of correct classification of colour categories with quadratic discriminant analysis; Figure 2D, figure 2E, figure 2F, figure 2G, figure 2H - melanosome extraction details

description: We have uploaded separate file in the Step 3 section where we have listed entire content of our Supplementary material.
DOI: 10.6084/m9.figshare.8256143.v1
title: List of bird species (Common and Latin name) used in sampling of NISC (description of colour and area on the body where feather was sampled); Details of melanosomes sampling from E. brachyptera fossil and results of their measurements; Trait database used for Ancestral state reconstruction and posterior probabilities of colour state for E. brachyptera; Posterior probabilities of colour state for E. brachyptera; 1000 phylogenetic trees downloaded from birdtree.org in Nexus format; Tukey's post-hoc test results (pairwise comparison); Forward stepwise regression results and plot of the first two variables; Li et al. database with measurements of melanosomes isolated from feathers expressing non-iridescent structural colour included. Added samples are indicated with blue colour in the database.; Results of simulation of correct classification of colour categories with quadratic discriminant analysis; Figure 2D, figure 2E, figure 2F, figure 2G, figure 2H - melanosome extraction details

description: We have uploaded separate file in the Step 3 section where we have listed entire content of our Supplementary material.
DOI: 10.6084/m9.figshare.8256131
title: Matrilineal Transitions Coding/Data File from Why does matriliny fail? Frequency and causes of matrilineal transitions estimated from a de novo coding of a cross-cultural sample

description: The question of when and why societies have transitioned away from matriliny towards other types of kinship systems—and when and why they transition towards matriliny—has a long history in anthropology, one that is heavily engaged with both evolutionary theory and cross-cultural research methods. This article presents tabulations from a new coding of ethnographic documents from the Standard Cross-Cultural Sample, tallying claims of transitions in kinship systems both away from and to matriliny using various levels of stringency. We then use our counts as the outcome variables in a set of Bayesian analyses that simultaneously estimate the probability of a transition occurring given societal covariates alongside the conditional probability of detecting a transition given the volume of ethnographic data available to code. Our goal is to estimate the cross-cultural and comparative frequency of transitions away from and to matriliny, as well as to explore potential causes underlying these patterns. We find that transitions away from matriliny have been significantly more common than ‘reverse transitions' to matriliny. Our evidence suggests that both rates may be, in part, an artefact of the colonial and globalizing period during which the data comprising much of the current ethnographic record was recorded. Analyses of the correlates of transitions away from matriliny are consistent with several of the key causal arguments made by anthropologists over the last century, especially with respect to subsistence transition (to pastoralism, intensive agriculture and market economies), social complexity and colonialism, highlighting the importance of ecological factors in such transitions.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8256128
title: Matrilineal Transitions R Code and Related Documents from Why does matriliny fail? Frequency and causes of matrilineal transitions estimated from a de novo coding of a cross-cultural sample

description: The question of when and why societies have transitioned away from matriliny towards other types of kinship systems—and when and why they transition towards matriliny—has a long history in anthropology, one that is heavily engaged with both evolutionary theory and cross-cultural research methods. This article presents tabulations from a new coding of ethnographic documents from the Standard Cross-Cultural Sample, tallying claims of transitions in kinship systems both away from and to matriliny using various levels of stringency. We then use our counts as the outcome variables in a set of Bayesian analyses that simultaneously estimate the probability of a transition occurring given societal covariates alongside the conditional probability of detecting a transition given the volume of ethnographic data available to code. Our goal is to estimate the cross-cultural and comparative frequency of transitions away from and to matriliny, as well as to explore potential causes underlying these patterns. We find that transitions away from matriliny have been significantly more common than ‘reverse transitions' to matriliny. Our evidence suggests that both rates may be, in part, an artefact of the colonial and globalizing period during which the data comprising much of the current ethnographic record was recorded. Analyses of the correlates of transitions away from matriliny are consistent with several of the key causal arguments made by anthropologists over the last century, especially with respect to subsistence transition (to pastoralism, intensive agriculture and market economies), social complexity and colonialism, highlighting the importance of ecological factors in such transitions.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8256131.v1
title: Matrilineal Transitions Coding/Data File from Why does matriliny fail? Frequency and causes of matrilineal transitions estimated from a de novo coding of a cross-cultural sample

description: The question of when and why societies have transitioned away from matriliny towards other types of kinship systems—and when and why they transition towards matriliny—has a long history in anthropology, one that is heavily engaged with both evolutionary theory and cross-cultural research methods. This article presents tabulations from a new coding of ethnographic documents from the Standard Cross-Cultural Sample, tallying claims of transitions in kinship systems both away from and to matriliny using various levels of stringency. We then use our counts as the outcome variables in a set of Bayesian analyses that simultaneously estimate the probability of a transition occurring given societal covariates alongside the conditional probability of detecting a transition given the volume of ethnographic data available to code. Our goal is to estimate the cross-cultural and comparative frequency of transitions away from and to matriliny, as well as to explore potential causes underlying these patterns. We find that transitions away from matriliny have been significantly more common than ‘reverse transitions' to matriliny. Our evidence suggests that both rates may be, in part, an artefact of the colonial and globalizing period during which the data comprising much of the current ethnographic record was recorded. Analyses of the correlates of transitions away from matriliny are consistent with several of the key causal arguments made by anthropologists over the last century, especially with respect to subsistence transition (to pastoralism, intensive agriculture and market economies), social complexity and colonialism, highlighting the importance of ecological factors in such transitions.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8256128.v1
title: Matrilineal Transitions R Code and Related Documents from Why does matriliny fail? Frequency and causes of matrilineal transitions estimated from a de novo coding of a cross-cultural sample

description: The question of when and why societies have transitioned away from matriliny towards other types of kinship systems—and when and why they transition towards matriliny—has a long history in anthropology, one that is heavily engaged with both evolutionary theory and cross-cultural research methods. This article presents tabulations from a new coding of ethnographic documents from the Standard Cross-Cultural Sample, tallying claims of transitions in kinship systems both away from and to matriliny using various levels of stringency. We then use our counts as the outcome variables in a set of Bayesian analyses that simultaneously estimate the probability of a transition occurring given societal covariates alongside the conditional probability of detecting a transition given the volume of ethnographic data available to code. Our goal is to estimate the cross-cultural and comparative frequency of transitions away from and to matriliny, as well as to explore potential causes underlying these patterns. We find that transitions away from matriliny have been significantly more common than ‘reverse transitions' to matriliny. Our evidence suggests that both rates may be, in part, an artefact of the colonial and globalizing period during which the data comprising much of the current ethnographic record was recorded. Analyses of the correlates of transitions away from matriliny are consistent with several of the key causal arguments made by anthropologists over the last century, especially with respect to subsistence transition (to pastoralism, intensive agriculture and market economies), social complexity and colonialism, highlighting the importance of ecological factors in such transitions.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8256137.v1
title: Non-Cardiovascular Comorbidities as Evaluated by Elixhauser Comorbidity Score in Individuals Undergoing TAVR

description: <b>Background</b>: To explore the relationship between comorbidity burden and mortality, peri-procedural complications, and length of stay in patients treated with TAVR in the National Inpatient Sample (NIS). Patients undergoing transcatheter aortic valve replacement (TAVR) often have multiple comorbidities. Whilst the impact of individual comorbid conditions on clinical outcomes following TAVR has been previously assessed, the impact of more global measures of comorbidity remain unknown in this cohort. <b>Methods</b>: TAVR procedures were identified between 2011 and 2014 and comorbidities were defined by the Elixhauser classification system (ECS) consisting of 30 comorbidity measures. Endpoints included in-hospital mortality, periprocedural complications, and length of stay. Patients were classified based on their ECS in five categories (ECS I&lt;0, ECS II=0, ECS III=1-5, ECS IV=6-13, ECS V ≥ 14). <b>Results</b>: A total of 40,604 TAVR patients were identified. Mean age was 81.2±8.5 years. Patients with ECS category V accounted for more than 40% of the cohort and experienced almost a 2.5-fold increase in in-hospital mortality (OR 2.42, 95% CI: 1.28-4.56), acute kidney injury (OR: 6.23, 95% CI: 4.13-9.41), major bleeding (OR: 2.26, 95% CI: 1.71-2.99), post procedural stroke or TIA (OR: 2.02, 95% CI: 1.08-3.78). It was also associated with a mean 4.14-day increased length of stay (95% CI: 3.67 to 4.65) compared to patients with lower ECS category after adjusting for confounding factors. <b>Conclusions</b>: Our study of over 40,000 TAVRs shows that Elixhauser comorbidity score was independently associated with higher mortality, periprocedural complications, and length of stay. Global comorbidity burden is an important consideration for risk stratification in patients undergoing TAVR.
DOI: 10.6084/m9.figshare.8255996
title: Differential expression analysis of susceptible and tolerant larval population

description: DESeq2 between tolerant and susceptible larval population.
DOI: 10.6084/m9.figshare.8255996.v1
title: Differential expression analysis of susceptible and tolerant larval population

description: DESeq2 between tolerant and susceptible larval population.
DOI: 10.6084/m9.figshare.8255993
title: Annotation of each transcript of the assembled transcriptome

description: Annotation of transcript using BLASTP algorithm.
DOI: 10.6084/m9.figshare.8255948
title: Data and script (Predation risk influences food-web structure by constraining species diet choice)

description: The empirical food-web data (as R lists) and the R script for conducting simulations within the study "Predation risk influences food-web structure by constraining species diet choice". Please read the README for details.
DOI: 10.6084/m9.figshare.8255993.v1
title: Annotation of each transcript of the assembled transcriptome

description: Annotation of transcript using BLASTP algorithm.
DOI: 10.6084/m9.figshare.8255897
title: Dataset from Regional climate affects salmon lice dynamics, stage structure and management

description: Regional variation in climate can generate differences in population dynamics and stage structure. Where regional differences exist, the best approach to pest management may be region-specific. Salmon lice are a stage-structured marine copepod that parasitizes salmonids at aquaculture sites worldwide, and have fecundity, development and mortality rates that depend on temperature and salinity. We show that in Atlantic Canada and Norway, where the oceans are relatively cold, salmon lice abundance decreases during the winter months, but ultimately increases from year to year, while in Ireland and Chile, where the oceans are warmer, the population size grows monotonically without any seasonal declines. In colder regions, during the winter the stage structure is dominated by the adult stage, which is in contrast to warmer regions where all stages are abundant year round. These differences translate into region-specific recommendations for management: regions with slower population growth have lower critical stocking densities, and regions with cold winters have a seasonal dependence in the timing of follow-up chemotherapeutic treatments. Predictions of our salmon lice model agree with empirical data, and our approach provides a method to understand the effects of regional differences in climate on salmon lice dynamics and management.