cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14405333.v1
title: Supplementary Material for: Variable Learning Curve of Basic Rigid Bronchoscopy in Trainees

description: <b><i>Background:</i></b> Despite increased use of rigid bronchoscopy (RB) for therapeutic indications and recommendations from professional societies to use performance-based competency, an assessment tool has not been utilized to measure the competency of trainees to perform RB in clinical settings. <b><i>Objectives:</i></b> The aim of the study was to evaluate a previously developed assessment tool – <i>Rigid Bronchoscopy Tool for Assessment of Skills and Competence</i> (RIGID-TASC) – for determining the RB learning curve of interventional pulmonary (IP) trainees in the clinical setting and explore the variability of learning curve of trainees. <b><i>Methods:</i></b> IP fellows at 4 institutions were enrolled. After preclinical simulation training, all RBs performed in patients were scored by faculty using RIGID-TASC until competency threshold was achieved. Competency threshold was defined as unassisted RB intubation and navigation through the central airways on 3 consecutive patients at the first attempt with a minimum score of 89. A regression-based model was devised to construct and compare the learning curves. <b><i>Results:</i></b> Twelve IP fellows performed 178 RBs. Trainees reached the competency threshold between 5 and 24 RBs, with a median of 15 RBs (95% CI, 6–21). There were differences among trainees in learning curve parameters including starting point, slope, and inflection point, as demonstrated by the curve-fitting model. Subtasks that required the highest number of procedures (median = 10) to gain competency included ability to intubate at the first attempt and intubation time of &lt;60 s. <b><i>Conclusions:</i></b> Trainees acquire RB skills at a variable pace, and RIGID-TASC can be used to assess learning curve of IP trainees in clinical settings.
DOI: 10.6084/m9.figshare.12063642
title: <i>In-silico</i> approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel

description: Recent outbreak of Coronavirus disease (COVID-19) pandemic around the world is associated with ‘severe acute respiratory syndrome’ (SARS-CoV2) in humans. SARS-CoV2 is an enveloped virus and E proteins present in them are reported to form ion channels, which is mainly associated with pathogenesis. Thus, there is always a quest to inhibit these ion channels, which in turn may help in controlling diseases caused by SARS-CoV2 in humans. Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ‘SARS-CoV2 E’ protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. However, after binding with Belachinal, Macaflavanone E, and Vibsanol B, the random motion of the human ‘SARS-CoV2 E’ protein gets reduced, this, in turn, inhibits the function of the ‘SARS-CoV2 E’ protein. It is pertinent to note that two amino acids, namely VAL25 and PHE26, play a key role while interacting with these three phytochemicals. As these three phytochemicals, namely, Belachinal, Macaflavanone E & Vibsanol B, have passed the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) property as well as ‘Lipinski’s Rule of 5s’, they may be utilized as drugs in controlling disease caused via SARS-COV2, after further investigation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12063642.v2
title: <i>In-silico</i> approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel

description: Recent outbreak of Coronavirus disease (COVID-19) pandemic around the world is associated with ‘severe acute respiratory syndrome’ (SARS-CoV2) in humans. SARS-CoV2 is an enveloped virus and E proteins present in them are reported to form ion channels, which is mainly associated with pathogenesis. Thus, there is always a quest to inhibit these ion channels, which in turn may help in controlling diseases caused by SARS-CoV2 in humans. Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ‘SARS-CoV2 E’ protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. However, after binding with Belachinal, Macaflavanone E, and Vibsanol B, the random motion of the human ‘SARS-CoV2 E’ protein gets reduced, this, in turn, inhibits the function of the ‘SARS-CoV2 E’ protein. It is pertinent to note that two amino acids, namely VAL25 and PHE26, play a key role while interacting with these three phytochemicals. As these three phytochemicals, namely, Belachinal, Macaflavanone E & Vibsanol B, have passed the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) property as well as ‘Lipinski’s Rule of 5s’, they may be utilized as drugs in controlling disease caused via SARS-COV2, after further investigation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12046404.v2
title: HIV long-term non-progressors share similar features with simian immunodeficiency virus infection of chimpanzees

description: HIV-1 infection in human beings has been an outcome of cross-species transmission event of simian immunodeficiency virus from chimpanzees (SIVcpz). Present study reveals differential features of envelope genes representing different categories of HIV-1 disease progression in human beings, namely, rapid progressors (RP), slow progressors (SP) and long-term non-progressors (LTNP) with respect to SIVcpz, based on their amino acid usage patterns. It was evident that SP, LTNP and SIVcpz envelope genes displayed similar patterns of amino acid usage which strongly contrasted with the features exhibited by the envelope genes representing RP category. Robust analysis revealed that selection constraint of human host on SP and LTNP associated envelope genes and chimpanzee host on SIVcpz envelope genes were more severe compared to selection pressure operational on RP associated envelope genes. Evolutionary forces of selection appeared to be comparatively more relaxed on the RP envelope genes in contrast to SP, LTNP and SIVcpz types. Better binding of RP envelope glycoprotein 120 (gp120) compared to envelope gp120 representing SP, LTNP and SIVcpz with host cellular receptor CD4, as inferred employing molecular docking approaches, promises to confer meaningful insights into the event of speedy progression of HIV in rapid progressors. It was interesting to note that envelope glycoprotein exhibited a tendency of hindering proper interaction of host (human/chimpanzee) CD4 and major histocompatibility complex II (MHC II), with a better efficacy in rapid progressors, thus, facilitating highest degrees of immune suppression. Proper identification of the contrasting features might confer a scope to modulate rapid progression of HIV to a long-term non-progressive controlled case, as observed in LTNP and SIVcpz infection, simultaneously aiding therapeutic research against AIDS targeted at drug and vaccine development. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12046404
title: HIV long-term non-progressors share similar features with simian immunodeficiency virus infection of chimpanzees

description: HIV-1 infection in human beings has been an outcome of cross-species transmission event of simian immunodeficiency virus from chimpanzees (SIVcpz). Present study reveals differential features of envelope genes representing different categories of HIV-1 disease progression in human beings, namely, rapid progressors (RP), slow progressors (SP) and long-term non-progressors (LTNP) with respect to SIVcpz, based on their amino acid usage patterns. It was evident that SP, LTNP and SIVcpz envelope genes displayed similar patterns of amino acid usage which strongly contrasted with the features exhibited by the envelope genes representing RP category. Robust analysis revealed that selection constraint of human host on SP and LTNP associated envelope genes and chimpanzee host on SIVcpz envelope genes were more severe compared to selection pressure operational on RP associated envelope genes. Evolutionary forces of selection appeared to be comparatively more relaxed on the RP envelope genes in contrast to SP, LTNP and SIVcpz types. Better binding of RP envelope glycoprotein 120 (gp120) compared to envelope gp120 representing SP, LTNP and SIVcpz with host cellular receptor CD4, as inferred employing molecular docking approaches, promises to confer meaningful insights into the event of speedy progression of HIV in rapid progressors. It was interesting to note that envelope glycoprotein exhibited a tendency of hindering proper interaction of host (human/chimpanzee) CD4 and major histocompatibility complex II (MHC II), with a better efficacy in rapid progressors, thus, facilitating highest degrees of immune suppression. Proper identification of the contrasting features might confer a scope to modulate rapid progression of HIV to a long-term non-progressive controlled case, as observed in LTNP and SIVcpz infection, simultaneously aiding therapeutic research against AIDS targeted at drug and vaccine development. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12129471.v1
title: Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species

description: Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12129471
title: Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species

description: Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12254492.v1
title: Understanding the thermal response of rice eukaryotic transcription factor <i>eIF4A1</i> towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation

description: Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degradation. It is well known that ATP-binding and subsequent hydrolysis activities are crucial for the functionality of such helicases. Although the stress-responsive upregulation of <i>eIF4A1</i> has been reported in plants during stress, it is difficult to anticipate the functionality of the corresponding protein product. Therefore, to understand the activity of <i>eIF4A1</i> in rice in response to temperature stress, we first conducted an expression analysis of the gene and further investigated the structural stability of the eIF4A1-ATP/Mg<sup>2+</sup> complex through molecular dynamics (MD) simulations at different temperature conditions (277 K, 300 K, and 315 K). Our results demonstrated a three to fourfold increased expression of rice <i>eIF4A1</i> both in root and shoot at 42 °C compared to control. Furthermore, the MD simulation portrayed strong ATP/Mg<sup>2+</sup> binding at a higher temperature in comparison to control and cold temperature. Overall, the increased expression pattern of <i>eIF4A1</i> and strong ATP/Mg<sup>2+</sup> binding at higher temperature indicated the heat stress-tolerant capacity of the gene in rice. The results from our study will help in understanding the activity of gene and guide the researchers for screening of novel stress inducible candidate genes for the engineering of temperature stress tolerant plants. Communicated by Ramaswamy H. Sarma
DOI: 10.15151/esrf-es-416429069
title: High-pressure behaviour of benitoite

description: From a crystallographic point of view, is rather interesting being the prototype structure for the P6 ̅2c space group and it has been the focus of previous high-pressure crystallographic investigations due to the presence of the (Si3O9)6– silicate-ring units (Hejny et al. 2012). Indeed, numerous synthetic germanate compounds are either isostructural to benitoite or represent a topologically equivalent structure of reported lower (in all cases trigonal) symmetry. For these reasons the high-pressure behaviour of benitoite will be studied up to 20 GPa in a DAC using He as P-transmitting medium.
DOI: 10.15151/esrf-es-409219942
title: Magnetic excitations in rare-earth Mn 122 compounds

description: The feasibility of RIXS measurements of the spin wave dispersion at the Mn edge will be tested for Mn 122 compounds.
DOI: 10.5281/zenodo.4671804
title: Dataset for "Boosting spin orbit coupling in graphene/WSe2 heterostructures via hydrostatic pressue".

description: This is the dataset used in the paper "Boosting spin orbit coupling in graphene/WSe2 heterostructures via hydrostatic pressue". See Readme.txt for data format details.
DOI: 10.5281/zenodo.4671803
title: Dataset for "Boosting spin orbit coupling in graphene/WSe2 heterostructures via hydrostatic pressue".

description: This is the dataset used in the paper "Boosting spin orbit coupling in graphene/WSe2 heterostructures via hydrostatic pressue". See Readme.txt for data format details.
DOI: 10.6084/m9.figshare.12852525.v1
title: Empathic emotion regulation in prosocial behaviour and altruism

description: Emotions evoked in response to others’ distress are important for motivating concerned prosocial responses. But how emotion regulation shapes prosocial responding is not yet well understood. We tested the role of empathic emotion regulation in promoting prosocial motivation and costly donations across two studies, first in a community sample and then in a sample of altruistic kidney donors and a matched comparison sample. Participants engaged in hopeful and distancing reappraisals while viewing images of others in distress, then decided whether to help by donating to charity. Whereas hope was expected to evoke approach-based motivation indexed by increased donations, distance was expected to evoke avoidance-based motivation indexed by decreased donations, via varying effects of the two reappraisals on positive and negative affect. Across both studies, both reappraisals decreased negative affect and hopeful reappraisal increased positive affect. In the community sample, hope resulted in higher donations than distancing. Altruists were more prosocial overall, but the associations between affect and donation behaviour in this group mirrored the hopeful reappraisal in the community sample, suggesting that altruists might adopt this strategy by default. These findings clarify the role of empathic emotion regulation in prosocial behaviour and also independent effects of positive and negative affect.
DOI: 10.6084/m9.figshare.12852546.v1
title: Anxiety & inhibition: dissociating the involvement of state and trait anxiety in inhibitory control deficits observed on the anti-saccade task

description: The existence of a relationship between heightened anxiety and impaired inhibitory control is well established. However, it remains unknown whether such reduced inhibitory control is a stable characteristic of elevated trait anxiety, is driven by elevated state anxiety, or is a joint function of both trait and state anxiety. The present study sought to resolve this issue, by having high and low trait anxious participants complete an anti-saccade task, following a manipulation of state anxiety level using a video-based state anxiety induction procedure. We found that impaired inhibitory control was interactively determined by trait and state anxiety. Specifically, in high but not low trait anxious participants, the induction of heightened state anxiety served to impair inhibitory control. In addition to shedding light on how inhibitory control may potentially contribute to dispositional anxiety, these findings suggest that the anxiolytic benefits of inhibitory control training procedures may be greatest when delivered to high trait anxious individuals during periods of elevated state anxiety.
DOI: 10.6084/m9.figshare.12852546
title: Anxiety & inhibition: dissociating the involvement of state and trait anxiety in inhibitory control deficits observed on the anti-saccade task

description: The existence of a relationship between heightened anxiety and impaired inhibitory control is well established. However, it remains unknown whether such reduced inhibitory control is a stable characteristic of elevated trait anxiety, is driven by elevated state anxiety, or is a joint function of both trait and state anxiety. The present study sought to resolve this issue, by having high and low trait anxious participants complete an anti-saccade task, following a manipulation of state anxiety level using a video-based state anxiety induction procedure. We found that impaired inhibitory control was interactively determined by trait and state anxiety. Specifically, in high but not low trait anxious participants, the induction of heightened state anxiety served to impair inhibitory control. In addition to shedding light on how inhibitory control may potentially contribute to dispositional anxiety, these findings suggest that the anxiolytic benefits of inhibitory control training procedures may be greatest when delivered to high trait anxious individuals during periods of elevated state anxiety.
DOI: 10.6084/m9.figshare.12852519.v1
title: Understanding visual attention to face emotions in social anxiety using hidden Markov models

description: Theoretical models propose that attentional biases might account for the maintenance of social anxiety symptoms. However, previous eye-tracking studies have yielded mixed results. One explanation is that existing studies quantify eye-movements using arbitrary, experimenter-defined criteria such as time segments and regions of interests that do not capture the dynamic nature of overt visual attention. The current study adopted the Eye Movement analysis with Hidden Markov Models (EMHMM) approach for eye-movement analysis, a machine-learning, data-driven approach that can cluster people’s eye-movements into different strategy groups. Sixty participants high and low in self-reported social anxiety symptoms viewed angry and neutral faces in a free-viewing task while their eye-movements were recorded. EMHMM analyses revealed novel associations between eye-movement patterns and social anxiety symptoms that were not evident with standard analytical approaches. Participants who adopted the same face-viewing strategy when viewing both angry and neutral faces showed higher social anxiety symptoms than those who transitioned between strategies when viewing angry versus neutral faces. EMHMM can offer novel insights into psychopathology-related attention processes.
DOI: 10.6084/m9.figshare.12852519
title: Understanding visual attention to face emotions in social anxiety using hidden Markov models

description: Theoretical models propose that attentional biases might account for the maintenance of social anxiety symptoms. However, previous eye-tracking studies have yielded mixed results. One explanation is that existing studies quantify eye-movements using arbitrary, experimenter-defined criteria such as time segments and regions of interests that do not capture the dynamic nature of overt visual attention. The current study adopted the Eye Movement analysis with Hidden Markov Models (EMHMM) approach for eye-movement analysis, a machine-learning, data-driven approach that can cluster people’s eye-movements into different strategy groups. Sixty participants high and low in self-reported social anxiety symptoms viewed angry and neutral faces in a free-viewing task while their eye-movements were recorded. EMHMM analyses revealed novel associations between eye-movement patterns and social anxiety symptoms that were not evident with standard analytical approaches. Participants who adopted the same face-viewing strategy when viewing both angry and neutral faces showed higher social anxiety symptoms than those who transitioned between strategies when viewing angry versus neutral faces. EMHMM can offer novel insights into psychopathology-related attention processes.