cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6587141.v1
title: A systematic review and combined analysis of therapeutic drug monitoring studies for oral paliperidone

description: <b>Introduction</b>: This article includes a combined analysis of therapeutic drug monitoring (TDM) studies and a review of the marketer’s data on pharmacological mechanisms. <b>Areas covered</b>: An article search led to the inclusion of 21 paliperidone studies in the systematic review plus 2 case reports. Paliperidone clearance was calculated from: 1) steady-state studies using concentration/dose (C/D) ratios, and 2) single-dose studies describing 24-h area under the curve calculations. The marketed extended-release formulation has 28% bioavailability. Calculated mean C/D ratios (ng/ml/mg/d) were: 1) 4.09 in 6 studies of 221 non-Korean and non-geriatric adult patients, 2) 2.59 in 2 studies of 100 Korean adult patients, and 3) 6.89 in 1 study with 15 elderly Japanese patients. The limited drug–drug interaction studies indicated that carbamazepine is a clinically relevant inducer requiring three times the dosage, and that valproate, probably an inhibitor, requires half the dosage. Renal impairment markedly decreased paliperidone elimination, and other antipsychotics should be considered. <b>Expert Commentary</b>: We recommend more use of: 1) paliperidone TDM in clinical practice, 2) TDM when moving from oral to long-acting paliperidone, 3) better designs for paliperidone TDM studies, 4) laboratory studies on paliperidone pharmacokinetic mechanisms, and 5) TDM studies comparing paliperidone and risperidone dosing.
DOI: 10.6084/m9.figshare.6587132
title: Per- and polyfluoroalkyl substances impact human spermatogenesis in a stem-cell-derived model

description: Per- and polyfluoroalkyl substances (PFASs) represent a highly ubiquitous group of synthetic chemicals used in products ranging from water and oil repellents and lubricants to firefighting foam. These substances can enter and accumulate in multiple tissue matrices in up to 100% of people assessed. Though animal models strongly identify these compounds as male reproductive toxicants, with exposed rodents experiencing declines in sperm count, alterations in hormones, and DNA damage in spermatids, among other adverse outcomes, human studies report conflicting conclusions as to the reproductive toxicity of these chemicals. Using an innovative, human stem-cell-based model of spermatogenesis, we assessed the effects of the PFASs perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and a mixture of PFOS, PFOA, and PFNA for their impacts on human spermatogenesis <i>in vitro</i> under conditions relevant to the general and occupationally exposed populations. Here, we show that PFOS, PFOA, PFNA, and a mixture of PFOS, PFOA, and PFNA do not decrease <i>in vitro</i> germ cell viability, consistent with reports from human studies. These compounds do not affect mitochondrial membrane potential or increase reactive oxygen species generation, and they do not decrease cell viability of spermatogonia, primary spermatocytes, secondary spermatocytes, or spermatids <i>in vitro</i> under the conditions examined. However, exposure to PFOS, PFOA, and PFNA reduces expression of markers for spermatogonia and primary spermatocytes. While not having direct effects on germ cell viability, these effects suggest the potential for long-term impacts on male fertility through the exhaustion of the spermatogonial stem cell pool and abnormalities in primary spermatocytes. <b>Abbreviations:</b> CDC: Centers for Disease Control; DMSO: dimethyl sulfoxide; GHR: growth hormone receptor; hESCs: human embryonic stem cells; PFASs: per- and polyfluoroalkyl substances; PFCs: perfluorinated compounds; PFNA: perfluorononanoic acid; PFOS: perfluorooctanesulfonic acid; PFOA: perfluorooctanoic acid; PLZF: promyelocytic leukemia zinc finger; ROS: reactive oxygen species; HILI: RNA-mediated gene silencing 2; SSC: spermatogonial stem cell
DOI: 10.6084/m9.figshare.6587132.v1
title: Per- and polyfluoroalkyl substances impact human spermatogenesis in a stem-cell-derived model

description: Per- and polyfluoroalkyl substances (PFASs) represent a highly ubiquitous group of synthetic chemicals used in products ranging from water and oil repellents and lubricants to firefighting foam. These substances can enter and accumulate in multiple tissue matrices in up to 100% of people assessed. Though animal models strongly identify these compounds as male reproductive toxicants, with exposed rodents experiencing declines in sperm count, alterations in hormones, and DNA damage in spermatids, among other adverse outcomes, human studies report conflicting conclusions as to the reproductive toxicity of these chemicals. Using an innovative, human stem-cell-based model of spermatogenesis, we assessed the effects of the PFASs perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and a mixture of PFOS, PFOA, and PFNA for their impacts on human spermatogenesis <i>in vitro</i> under conditions relevant to the general and occupationally exposed populations. Here, we show that PFOS, PFOA, PFNA, and a mixture of PFOS, PFOA, and PFNA do not decrease <i>in vitro</i> germ cell viability, consistent with reports from human studies. These compounds do not affect mitochondrial membrane potential or increase reactive oxygen species generation, and they do not decrease cell viability of spermatogonia, primary spermatocytes, secondary spermatocytes, or spermatids <i>in vitro</i> under the conditions examined. However, exposure to PFOS, PFOA, and PFNA reduces expression of markers for spermatogonia and primary spermatocytes. While not having direct effects on germ cell viability, these effects suggest the potential for long-term impacts on male fertility through the exhaustion of the spermatogonial stem cell pool and abnormalities in primary spermatocytes. <b>Abbreviations:</b> CDC: Centers for Disease Control; DMSO: dimethyl sulfoxide; GHR: growth hormone receptor; hESCs: human embryonic stem cells; PFASs: per- and polyfluoroalkyl substances; PFCs: perfluorinated compounds; PFNA: perfluorononanoic acid; PFOS: perfluorooctanesulfonic acid; PFOA: perfluorooctanoic acid; PLZF: promyelocytic leukemia zinc finger; ROS: reactive oxygen species; HILI: RNA-mediated gene silencing 2; SSC: spermatogonial stem cell
DOI: 10.6084/m9.figshare.6587126
title: Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-<i>cas</i> gene cassettes reveals 39 new <i>cas</i> gene families

description: A study was undertaken to identify conserved proteins that are encoded adjacent to <i>cas</i> gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in <i>Synechocystis</i> confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
DOI: 10.6084/m9.figshare.6587126.v1
title: Comprehensive search for accessory proteins encoded with archaeal and bacterial Type III CRISPR-Cas gene cassettes reveals 39 new <i>cas</i> gene families

description: A study was undertaken to identify conserved proteins that are encoded adjacent to <i>cas</i> gene cassettes of Type III CRISPR-Cas (Clusters of Regularly IntersSpaced Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in <i>Synechocystis</i> confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application on metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
DOI: 10.6084/m9.figshare.6587126.v3
title: Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-<i>cas</i> gene cassettes reveals 39 new <i>cas</i> gene families

description: A study was undertaken to identify conserved proteins that are encoded adjacent to <i>cas</i> gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in <i>Synechocystis</i> confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
DOI: 10.6084/m9.figshare.6587126.v2
title: Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-<i>cas</i> gene cassettes reveals 39 new <i>cas</i> gene families

description: A study was undertaken to identify conserved proteins that are encoded adjacent to <i>cas</i> gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in <i>Synechocystis</i> confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
DOI: 10.6084/m9.figshare.6587036
title: Outcomes of Surgery as Part of the Management of Metastatic Non–Small-Cell Lung Cancer: A Surveillance, Epidemiology and End Results Database Analysis

description: The role of local treatment in patients with oligometastatic non–small-cell lung cancer (NSCLC) is a subject of ongoing debate. This study assessed the survival impact of combined surgery to the primary tumor and metastatic disease in the management of metastatic NSCLC. Stage IV NSCLC patients at presentation, diagnosed from 2004 to 2013 were identified from the SEER (Surveillance, Epidemiology, and End Results) database. Propensity-matched analysis was performed considering baseline characteristics (age, gender, race, histology, TN stage, and site of metastases). A total of 144,334 patients were identified. The median age group was 65–70 years, and 1139 patients (0.8% of the patients) have received surgical treatment to both the primary tumor and metastatic disease. Both before and after propensity score matching, cancer-specific and overall survival were better in the surgical therapy group (P &lt; 0.0001 for all). When the analysis was restricted to the subsets of patients with brain only M1 disease or isolated contra lateral nodule, overall survival was improved by combined surgery. However, in multivariate analysis of the overall population (postmatching), combined surgery was not associated with a better overall survival (0.576). Despite the apparently beneficial role of surgery in this study for some patients with metastatic disease, the absence of adequate information about systemic therapy as well as associated comorbidity hinders the generation of definite conclusions. Prospective studies are needed to confirm the role of surgery in the setting of metastatic disease.
DOI: 10.6084/m9.figshare.6587036.v1
title: Outcomes of Surgery as Part of the Management of Metastatic Non–Small-Cell Lung Cancer: A Surveillance, Epidemiology and End Results Database Analysis

description: The role of local treatment in patients with oligometastatic non–small-cell lung cancer (NSCLC) is a subject of ongoing debate. This study assessed the survival impact of combined surgery to the primary tumor and metastatic disease in the management of metastatic NSCLC. Stage IV NSCLC patients at presentation, diagnosed from 2004 to 2013 were identified from the SEER (Surveillance, Epidemiology, and End Results) database. Propensity-matched analysis was performed considering baseline characteristics (age, gender, race, histology, TN stage, and site of metastases). A total of 144,334 patients were identified. The median age group was 65–70 years, and 1139 patients (0.8% of the patients) have received surgical treatment to both the primary tumor and metastatic disease. Both before and after propensity score matching, cancer-specific and overall survival were better in the surgical therapy group (P &lt; 0.0001 for all). When the analysis was restricted to the subsets of patients with brain only M1 disease or isolated contra lateral nodule, overall survival was improved by combined surgery. However, in multivariate analysis of the overall population (postmatching), combined surgery was not associated with a better overall survival (0.576). Despite the apparently beneficial role of surgery in this study for some patients with metastatic disease, the absence of adequate information about systemic therapy as well as associated comorbidity hinders the generation of definite conclusions. Prospective studies are needed to confirm the role of surgery in the setting of metastatic disease.
DOI: 10.6084/m9.figshare.6586958
title: Geometric description of self-interaction potential in symmetric protein complexes

description: The data submitted is described in detail in a manuscript submitted to <i>Scientific Data</i> entitled "Geometric description of self-interaction potential in symmetric protein complexes"
DOI: 10.6084/m9.figshare.6586958.v2
title: Geometric description of self-interaction potential in symmetric protein complexes

description: The data submitted is described in detail in a manuscript submitted to <i>Scientific Data</i> entitled "Geometric description of self-interaction potential in symmetric protein complexes"
DOI: 10.6084/m9.figshare.6586958.v1
title: Geometric description of self-interaction potential in symmetric protein complexes

description: The data submitted is described in detail in a manuscript submitted to <i>Scientific Data</i> entitled "Geometric description of self-interaction potential in symmetric protein complexes"
DOI: 10.21942/uva.6586685.v1
title: 16S rRNA gene amplicon sequence data soda sediments

description: Pre-processed amplicon Pyrotag sequence files (quality & length trimmed, adaptor sequences & primers removed, dereplicated) targeting the V4-V6 region of the 16S rRNA gene obtained from hypersaline soda lake sediments in the Kulunda Steppe (Siberia, Russia).
DOI: 10.6084/m9.figshare.6586643
title: isl-95.SeqDepthNorm.bw

description: CPC ATAC-seq bigwig
DOI: 10.6084/m9.figshare.6586643.v1
title: isl-95.SeqDepthNorm.bw

description: CPC ATAC-seq bigwig
DOI: 10.7284/103289
title: Singlebeam Echosounder data collected during research cruise W0904A using a Knudsen 3260 instrument system onboard the platform RV Wecoma

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6585188
title: Patient reported experiences of using community rehabilitation and/or support services whilst living with a long-term neurological condition: a qualitative systematic review and meta-aggregation

description: <b>Objectives:</b> The objective of this study is to identify patient reported experiences of using community rehabilitation and/or support services whilst living with a long-term neurological condition, and perceptions of their impact on quality of life. <b>Methods</b>: Nine electronic databases were searched for peer-reviewed qualitative studies from 2005 to 2016, which met the inclusion criteria. Critical appraisal, data extraction, and quality assessment of 37 included papers were performed by three reviewers. One hundred and one findings were extracted. Meta-aggregation was used to synthesize findings. <b>Findings:</b> Seven ‘synthesized findings’ [SF] were produced: Interactions with some professionals provide active participation, choice, confidence and autonomy [SF1]; Interactions with some professionals are disempowering and depersonalized [SF2]; Effective communication, specialist knowledge and an individualized approach to information provision is needed [SF3]; Indicators of success vary and may not be clear [SF4]; Informal support from family/friends is valued [SF5]; Opportunities for peer support/social interaction is valued [SF6]; Coordination required to ensure continuity during transition to community [SF7]. <b>Conclusion:</b> Patient reported experiences identified common factors associated with process quality (respect, choice, autonomy, information provision, communication) and activities of patient centered care (personalized care, shared decision-making, self-management support) despite heterogeneity of neurological conditions, service configurations, and geographical location. These factors impact quality of life.Implications for RehabilitationPatient reported experiences provide useful information about courtesy, respect, choice, autonomy, information provision, and communication.Outcomes of self-efficacy and self-management are important for people with stable and progressive long-term neurological conditions.Interactions with individual professionals influence engagement, self-efficacy, and self-management for people with long-term neurological conditions.Training for health and social care professionals should develop the advanced communication skills and behavior required to facilitate self-efficacy and self-management. Patient reported experiences provide useful information about courtesy, respect, choice, autonomy, information provision, and communication. Outcomes of self-efficacy and self-management are important for people with stable and progressive long-term neurological conditions. Interactions with individual professionals influence engagement, self-efficacy, and self-management for people with long-term neurological conditions. Training for health and social care professionals should develop the advanced communication skills and behavior required to facilitate self-efficacy and self-management.