cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5519737
title: Constitutive depletion of brain serotonin differentially affects rats' social and cognitive abilities

description: <strong>Background</strong> Central serotonin is an essential neuromodulator for mental disorders. It appears a promising transdiagnostic marker of distinct psychiatric disorders and a common modulator of some of their key behavioral symptoms. We aimed to identify the behavioral markers of serotonergic function in rats and compare them to human deficits. <strong>Methods</strong> We applied a comprehensive profiling approach in adult male <em>Tph2<sup>−/−</sup></em> rats constitutively lacking central serotonin. Under classical and ethological testing conditions, we tested each individual’s cognitive, social and non-social abilities and characterized the group organization (i.e. social network, hierarchy). Using unsupervised machine learning, we identified the functions most dependent on central serotonin. <strong>Results</strong> In classical procedures, <em>Tph2<sup>−/−</sup></em> rats presented an unexpected normal cognitive profile. Under the complex and experimenter-free conditions of their home-cage, the same <em>Tph2<sup>−/−</sup></em> rats presented drastic changes in their daily life. Brain serotonin depletion induced compulsive aggression and sexual behavior, hyperactive and hypervigilant stereotyped behavior, reduced self-care and body weight, and exacerbated corticosterone levels. Group-housed <em>Tph2<sup>−/−</sup></em> rats showed strong social disorganization with disrupted social networks and hierarchical structure, which may arise from communication deficits and cognitive blunting. <strong>Conclusions</strong> Serotonin depletion induced a profile reminiscent of the symptomatology of impulse control and anxiety disorders. Serotonin was necessary for behavioral adaptation to dynamic social environments. In classical testing conditions, our animal model challenged the concept of an essential role of serotonin in decision-making, flexibility, and impulsivity, although developmental compensations may have occurred. These contrasting findings highlight the need to generalize the evaluation of animal models’ multidimensional functions within the complexity of the social living environment.
DOI: 10.5281/zenodo.4912528
title: Constitutive depletion of brain serotonin differentially affects rats' social and cognitive abilities

description: <strong>Background</strong> Central serotonin is an essential neuromodulator for mental disorders. It appears a promising transdiagnostic marker of distinct psychiatric disorders and a common modulator of some of their key behavioral symptoms. We aimed to identify the behavioral markers of serotonergic function in rats and compare them to human deficits. <strong>Methods</strong> We applied a comprehensive profiling approach in adult male <em>Tph2<sup>−/−</sup></em> rats constitutively lacking central serotonin. Under classical and ethological testing conditions, we tested each individual’s cognitive, social and non-social abilities and characterized the group organization (i.e. social network, hierarchy). Using unsupervised machine learning, we identified the functions most dependent on central serotonin. <strong>Results</strong> In classical procedures, <em>Tph2<sup>−/−</sup></em> rats presented an unexpected normal cognitive profile. Under the complex and experimenter-free conditions of their home-cage, the same <em>Tph2<sup>−/−</sup></em> rats presented drastic changes in their daily life. Brain serotonin depletion induced compulsive aggression and sexual behavior, hyperactive and hypervigilant stereotyped behavior, reduced self-care and body weight, and exacerbated corticosterone levels. Group-housed <em>Tph2<sup>−/−</sup></em> rats showed strong social disorganization with disrupted social networks and hierarchical structure, which may arise from communication deficits and cognitive blunting. <strong>Conclusions</strong> Serotonin depletion induced a profile reminiscent of the symptomatology of impulse control and anxiety disorders. Serotonin was necessary for behavioral adaptation to dynamic social environments. In classical testing conditions, our animal model challenged the concept of an essential role of serotonin in decision-making, flexibility, and impulsivity, although developmental compensations may have occurred. These contrasting findings highlight the need to generalize the evaluation of animal models’ multidimensional functions within the complexity of the social living environment.
DOI: 10.5281/zenodo.7526514
title: Constitutive depletion of brain serotonin differentially affects rats' social and cognitive abilities

description: <strong>Background</strong> Central serotonin is an essential neuromodulator for mental disorders. It appears a promising transdiagnostic marker of distinct psychiatric disorders and a common modulator of some of their key behavioral symptoms. We aimed to identify the behavioral markers of serotonergic function in rats and compare them to human deficits. <strong>Methods</strong> We applied a comprehensive profiling approach in adult male <em>Tph2<sup>−/−</sup></em> rats constitutively lacking central serotonin. Under classical and ethological testing conditions, we tested each individual’s cognitive, social and non-social abilities and characterized the group organization (i.e. social network, hierarchy). Using unsupervised machine learning, we identified the functions most dependent on central serotonin. <strong>Results</strong> In classical procedures, <em>Tph2<sup>−/−</sup></em> rats presented an unexpected normal cognitive profile. Under the complex and experimenter-free conditions of their home-cage, the same <em>Tph2<sup>−/−</sup></em> rats presented drastic changes in their daily life. Brain serotonin depletion induced compulsive aggression and sexual behavior, hyperactive and hypervigilant stereotyped behavior, reduced self-care and body weight, and exacerbated corticosterone levels. Group-housed <em>Tph2<sup>−/−</sup></em> rats showed strong social disorganization with disrupted social networks and hierarchical structure, which may arise from communication deficits and cognitive blunting. <strong>Conclusions</strong> Serotonin depletion induced a profile reminiscent of the symptomatology of impulse control and anxiety disorders. Serotonin was necessary for behavioral adaptation to dynamic social environments. In classical testing conditions, our animal model challenged the concept of an essential role of serotonin in decision-making, flexibility, and impulsivity, although developmental compensations may have occurred. These contrasting findings highlight the need to generalize the evaluation of animal models’ multidimensional functions within the complexity of the social living environment.
DOI: 10.6084/m9.figshare.21555318
title: Proximal Learning for Individualized Treatment Regimes Under Unmeasured Confounding

description: Data-driven individualized decision making has recently received increasing research interest. However, most existing methods rely on the assumption of no unmeasured confounding, which cannot be ensured in practice especially in observational studies. Motivated by the recently proposed proximal causal inference, we develop several proximal learning methods to estimate optimal individualized treatment regimes (ITRs) in the presence of unmeasured confounding. Explicitly, in terms of two types of proxy variables, we are able to establish several identification results for different classes of ITRs respectively, exhibiting the tradeoff between the risk of making untestable assumptions and the potential improvement of the value function in decision making. Based on these identification results, we propose several classification-based approaches to finding a variety of restricted in-class optimal ITRs and establish their theoretical properties. The appealing numerical performance of our proposed methods is demonstrated via extensive simulation experiments and a real data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21555318.v1
title: Proximal Learning for Individualized Treatment Regimes Under Unmeasured Confounding

description: Data-driven individualized decision making has recently received increasing research interest. However, most existing methods rely on the assumption of no unmeasured confounding, which cannot be ensured in practice especially in observational studies. Motivated by the recently proposed proximal causal inference, we develop several proximal learning methods to estimate optimal individualized treatment regimes (ITRs) in the presence of unmeasured confounding. Explicitly, in terms of two types of proxy variables, we are able to establish several identification results for different classes of ITRs respectively, exhibiting the tradeoff between the risk of making untestable assumptions and the potential improvement of the value function in decision making. Based on these identification results, we propose several classification-based approaches to finding a variety of restricted in-class optimal ITRs and establish their theoretical properties. The appealing numerical performance of our proposed methods is demonstrated via extensive simulation experiments and a real data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19686345
title: Data from: Habitat fragmentation reduces survival and drives source-sink dynamics for a large carnivore

description: Data from: Nisi, A. C., Benson, J. F., King, R., and C. C. Wilmers. 2023. Habitat fragmentation reduces survival and drives source-sink dynamics for a large carnivore. Ecological Applications. In press. <br> See metadata for detailed description of each dataset.
DOI: 10.6092/unibo/amsacta/7126
title: HFValid collection: Hip-Fracture validation collection

description: The HFValid dataset is composed of 101 calibrated CT scans of whole femurs, the corresponding segmentations, and selected anatomical landmarks. The CT scans were collected at Rizzoli Orthopaedic Institute (IOR) from 1999 to 2016 for surgical planning of hip arthroplasty at the contralateral femur.
DOI: 10.6084/m9.figshare.21867810
title: PRISMA Checklist

description: Literature Review methodology, risk bias etc are listed in various places in literature review article. Same can be seen in the prisma checklist
DOI: 10.6084/m9.figshare.21867810.v1
title: PRISMA Checklist

description: Literature Review methodology, risk bias etc are listed in various places in literature review article. Same can be seen in the prisma checklist
DOI: 10.5281/zenodo.7515850
title: The world of GPCR dimers - mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements

description: G protein-coupled receptors (GPCRs) are known to dimerize, but the molecular and structural basis of GPCR dimers is not well understood. We developed a computational framework to generate models of the dopamine receptor D2 (D<sub>2</sub>R) homodimer in different activation states of the monomers and identified their most likely interfaces with molecular detail and contacts formed between interfacial residues. Such contacts were followed along a 3 replicates of 500 ns molecular dynamics simulation. The dataset presented here is a summary of all interfacial contacts, such as hydrogen bonds, pi-cation, pi-stacking, salt-bridges and t-stacking interactions, which occur within the interfaces of the different dimer configurations. The information can be viewed as dynamical flareplots, by uploading the .json files to https://gpcrviz.github.io/flareplot/. Contacts were measured using GetContacts (https://getcontacts.github.io/). 6CM4-6CM4 = inactive-inactive 6CM4-6U1N = inactive-arrestin 6U1N-6U1N = arrestin-arrestin 6VMS-6CM4 = active-inactive 6VMS-6U1N = active-arrestin 6VMS-6VMS = active-active
description: D2R-homodimer-flareplots-jsons
DOI: 10.5281/zenodo.7515851
title: The world of GPCR dimers - mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements

description: G protein-coupled receptors (GPCRs) are known to dimerize, but the molecular and structural basis of GPCR dimers is not well understood. We developed a computational framework to generate models of the dopamine receptor D2 (D<sub>2</sub>R) homodimer in different activation states of the monomers and identified their most likely interfaces with molecular detail and contacts formed between interfacial residues. Such contacts were followed along a 3 replicates of 500 ns molecular dynamics simulation. The dataset presented here is a summary of all interfacial contacts, such as hydrogen bonds, pi-cation, pi-stacking, salt-bridges and t-stacking interactions, which occur within the interfaces of the different dimer configurations. The information can be viewed as dynamical flareplots, by uploading the .json files to https://gpcrviz.github.io/flareplot/. Contacts were measured using GetContacts (https://getcontacts.github.io/). 6CM4-6CM4 = inactive-inactive 6CM4-6U1N = inactive-arrestin 6U1N-6U1N = arrestin-arrestin 6VMS-6CM4 = active-inactive 6VMS-6U1N = active-arrestin 6VMS-6VMS = active-active
description: D2R-homodimer-flareplots-jsons
DOI: 10.6084/m9.figshare.17005681.v4
title: ALIGNN models on JARVIS-DFT dataset

description: ALIGNN models on JARVIS-DFT datasethttps://github.com/usnistgov/alignn<br>
DOI: 10.6084/m9.figshare.21867828
title: Data associated with "The timing of heat waves has multiyear effects on milkweed and its insect community".

description: Field data (MW_FullData_Cleaned) and cardenolide data (MW_CardenolidesFull) from the article "The timing of heat waves has multiyear effects on milkweed and its insect community" in the journal Ecology.
DOI: 10.5067/ym8bprv258km
title: Sounder SIPS: Suomi NPP CrIS Level-1B NSR Calibration Subset: Random full spectra, V2
DOI: 10.5067/aqm5c14cmnqi
title: Sounder SIPS: Suomi NPP CrIS Level-1B NSR Calibration Subset: Summary, V2
DOI: 10.5067/kmj8q9za1y3k
title: Sounder SIPS: Aqua AIRS Level-1C Calibration Subset: Random full spectra, V2
DOI: 10.5067/7q4p1lbizyz7
title: Sounder SIPS: Aqua AIRS Level-1B Calibration Subset: Summary, V2
DOI: 10.5517/ccdc.csd.cc2bpkg2
title: CCDC 2165674: Experimental Crystal Structure Determination

description: Related Article: Jinxu Gao, Kiana Amini, Thomas Y. George, Yan Jing, Tatsuhiro Tsukamoto, Dawei Xi, Roy G. Gordon, Michael J. Aziz|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bpkh3
title: CCDC 2165675: Experimental Crystal Structure Determination

description: Related Article: Jinxu Gao, Kiana Amini, Thomas Y. George, Yan Jing, Tatsuhiro Tsukamoto, Dawei Xi, Roy G. Gordon, Michael J. Aziz|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bpkj4
title: CCDC 2165676: Experimental Crystal Structure Determination

description: Related Article: Jinxu Gao, Kiana Amini, Thomas Y. George, Yan Jing, Tatsuhiro Tsukamoto, Dawei Xi, Roy G. Gordon, Michael J. Aziz|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cbjnx
title: CCDC 2184869: Experimental Crystal Structure Determination

description: Related Article: Changjiang Yu, Yingzhu Sun, Xingbao Fang, Jiazhu Li, Qinghua Wu, Weibin Bu, Xing Guo, Hua Wang, Lijuan Jiao, Erhong Hao|2022|Inorg.Chem.|61|16718|doi:10.1021/acs.inorgchem.2c02517
description: Related Article: Changjiang Yu, Yingzhu Sun, Xingbao Fang, Jiazhu Li, Qinghua Wu, Weibin Bu, Xing Guo, Hua Wang, Lijuan Jiao, Erhong Hao|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7527303
title: Seismic Newtonian Noise Reduction - COMSOL Henge Datasets

description: COMSOL configuration files and study results for a variety of seismic noise reducing henges and berms.
DOI: 10.5281/zenodo.7527302
title: Seismic Newtonian Noise Reduction - COMSOL Henge Datasets

description: COMSOL configuration files and study results for a variety of seismic noise reducing henges and berms.
DOI: 10.3886/e183721v1
title: Investigating the Prevalence of Gastrointestinal Symptomology Following Receipt of the COVID-19 Vaccine

description: The coronavirus disease of 2019 (COVID-19) pandemic presented novel and devastating conditions for both the general and high-risk populations. SARS-CoV-2 is known to affect the respiratory tract, however studies have reveals that changes in gastrointestinal (GI) symptomology are also a prevalent side effect. Although the COVID-19 vaccine has been able to alleviate some of the tumultuous circumstances, there is limited research on the lesser-known side effects experienced following receipt of the COVID-19 vaccination.<br>This study investigated the association between the COVID-19 vaccination and, when applicable, the contraction of acute COVID-19 infection, and resulting onset and/or changes in GI symptomology. The focus of the study was on both the general population and on those previously diagnosed with GI disorders, such as Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD), the latter defined as a special needs population.<br>Through a short, anonymous survey, 215 participants were assessed for acute onset of GI issues and/or worsening of pre-existing GI issues following the receipt of one or more COVID-19 vaccine doses and, when it occurred, following contraction of a COVID-19 infection. Participants were requested to report demographic variables as well as descriptive statistics regarding side effects experienced post-COVID-19 vaccination and post-COVID-19 infection, when applicable. All analyses were performed using SAS version 9 and ANOVA was conducted for each survey item to assess for statistically significant differences between the groups, indicated by an omnibus p-value less than 0.05.<br>The resulting database demonstrates the prevalence of side effects following receipt of the COVID-19 vaccination to gain an understanding of how both the general and high-risk populations are being affected by the COVID-19 vaccine and booster doses.
description: Response Rates: Inclusion criteria: having received at least one COVID-19 vaccination<br>Exclusion criteria: not having received at least one COVID-19 vaccination
description: Convenience sampling to collect de-identified survey data from participants who had received at least one COVID-19 vaccination
description: web-based survey;
DOI: 10.58020/wyz7-0r97
title: Adult Living Donor Liver Transplantation Studies

description: The Adult-to-Adult Living Donor Liver Transplantation Cohort Study (A2ALL) was a consortium of 9 U.S. liver transplant centers performing adult-to-adult living donor liver transplant (AALDLT) with the primary goal of examining outcomes of AALDLT versus deceased donor liver transplant (DDLT).  AALDLT is a relatively new procedure increasingly used at major transplantation centers. Relatively small numbers of cases are performed at any one center and approaches to the patient and donor are too diverse across centers to provide reliable and generalizable information on donor and recipient outcomes from individual centers. Therefore, the consortium was organized to accrue and follow sufficient numbers of patients being considered for and undergoing AALDLT to provide generalizable results from adequately powered studies.

The Adult to Adult Living Donor Liver Transplantation Cohort Study (A2ALL) consisted of both retrospective and prospective studies of AALDLT. Legacy data from the A2ALL retrospective cohort is housed in the NIDDK Data Repository. The A2ALL retrospective cohort comprised 819 adult patients, each with a potential living donor, evaluated between January 1, 1998 and February 28, 2003. The retrospective study was designed to gain initial insights into outcomes associated with liver transplant procedures, with data drawn from existing medical records and patient materials. It was hypothesized that pursuit of a living liver allograft leads to decreased pre-transplant morbidity and mortality and better long term outcomes for patients starting from the point at which listed patients have a potential donor evaluated (at least a history and physical examination). The study analyzed numerous variables to determine the factors influencing allograft survival in recipients.
 
The A2ALL study showed evidence that AALDLT is a viable option for liver replacement with outcomes that improve with center experience. Donor characteristics associated with survival included younger age and cold ischemia time of the right lobe graft. 

Images from subjects enrolled in A2ALL are not included in the data package, but are now available upon request.
DOI: 10.58020/rn2a-m312
title: Assessing Long Term Outcomes in Living Kidney Donors

description: The Assessing Long Term Outcomes in Living Kidney Donors (ALTOLD) was designed to understand the pathophysiological effects of kidney donation. This is important in assessing donor safety and for improving the understanding of the consequences of reduced kidney function in chronic kidney disease. Most previous studies of living kidney donors have been retrospective and have lacked suitable healthy controls. By including healthy controls, this study permits a better assessment of potential harms to kidney donors, and thereby provides important information for informing future donors and recipients of the risk of donation. ALTOLD was intended to be a prospective controlled study to better understand the effects of a mild reduction in kidney function from kidney donation in otherwise normal individuals.

ALTOLD successfully enrolled 200 pairs of living kidney donors and equally healthy two-kidney controls starting in July 2006, and measured iohexol glomerular filtration rate (GFR) and traditional cardiovascular disease (CVD) risk factors pre- and 6, 12, 24 and 36 months post-donation.  Preliminary short-term results include the fact that GFR slopes increased between 6 and 36 months in donors versus controls, and that serum parathyroid hormone and uric acid levels have increased in donors versus controls. ALTOLD continues to answer important questions regarding the safety and the science of living kidney donation not addressed in previous uncontrolled cross- sectional studies.