cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6973880
title: NMR spectra, chiral HPLC chromatograms and full protein LC-MS chromatograms and mass spectra related to carbapenems as water soluble organocatalysts

description: This dataset consists of Proton Nuclear Magnetic Resonance (NMR) spectroscopy, chiral high-performance liquid chromatography (HPLC) and full protein Liquid chromatography–mass spectrometry (LC-MS) data on the water-soluble carbapenem antibiotics meropenem, doripenem, and ertapenem.<br>The related study investigates the potential for sustainable catalysts in chemical transformations, specifically the secondary amine organocatalysts listed above. The study reports the potential of carbapenems functioning in aqueous environments to enable sustainable chemical transformations and allow tandem reactions with biocatalysts, like enzymes. <br>The model reaction in this study is the Michael addition of nitromethane to cinnamaldehyde, analysed by NMR spectroscopy. HPLC data are used in the related study for the determination of enantioselectivity, while LC-MS data are used to confirm protein-carbapenem complexes.<br>Wild-type Mycobacterium tuberculosis β-lactamase (BlaC) was used as the basis for cloning, expression and purification in LC-MS. See the Supporting Information of the related publication for the relevant DNA sequence.<br><br>Raw data from the above steps are provided in five <b>.zip</b> files, containing BlaC-carbapenem complexes for meropenem and doripenem, all NMR and HPLC data.<br><b>LCMS_BlaC_Meropenem.raw.zip</b><b><br></b><b>LCMS_BlaC_Doripenem.raw.zip</b><b><br></b><b>LCMS_BlaC.raw.zip</b><b> </b><b><br></b><b>NMR.zip</b><b><br></b><b>Chiral_HPLC.zip</b><br><br>Data are further structure in subdirectories according to variables such as carbapenem name, relevant buffer and pH, and organic co-solvents content. Data files are accompanied by metadata files containing experimental setups. <br>
DOI: 10.6084/m9.figshare.6973880.v1
title: NMR spectra, chiral HPLC chromatograms and full protein LC-MS chromatograms and mass spectra related to carbapenems as water soluble organocatalysts

description: This dataset consists of Proton Nuclear Magnetic Resonance (NMR) spectroscopy, chiral high-performance liquid chromatography (HPLC) and full protein Liquid chromatography–mass spectrometry (LC-MS) data on the water-soluble carbapenem antibiotics meropenem, doripenem, and ertapenem.<br>The related study investigates the potential for sustainable catalysts in chemical transformations, specifically the secondary amine organocatalysts listed above. The study reports the potential of carbapenems functioning in aqueous environments to enable sustainable chemical transformations and allow tandem reactions with biocatalysts, like enzymes. <br>The model reaction in this study is the Michael addition of nitromethane to cinnamaldehyde, analysed by NMR spectroscopy. HPLC data are used in the related study for the determination of enantioselectivity, while LC-MS data are used to confirm protein-carbapenem complexes.<br>Wild-type Mycobacterium tuberculosis β-lactamase (BlaC) was used as the basis for cloning, expression and purification in LC-MS. See the Supporting Information of the related publication for the relevant DNA sequence.<br><br>Raw data from the above steps are provided in five <b>.zip</b> files, containing BlaC-carbapenem complexes for meropenem and doripenem, all NMR and HPLC data.<br><b>LCMS_BlaC_Meropenem.raw.zip</b><b><br></b><b>LCMS_BlaC_Doripenem.raw.zip</b><b><br></b><b>LCMS_BlaC.raw.zip</b><b> </b><b><br></b><b>NMR.zip</b><b><br></b><b>Chiral_HPLC.zip</b><br><br>Data are further structure in subdirectories according to variables such as carbapenem name, relevant buffer and pH, and organic co-solvents content. Data files are accompanied by metadata files containing experimental setups. <br>
DOI: 10.6084/m9.figshare.6973892.v1
title: Potential value of patient record review to assess and improve patient safety in general practice: A systematic review

description: <b>Background:</b> There is limited research, and guidance, on how to address safety in general practice proactively. <b>Objectives:</b> This review aimed to synthesize the literature describing the use of patient record review (PRR) to measure and improve patient safety in primary care. The PRR methodologies utilized and the resulting outcomes were examined. <b>Methods:</b> Searches were conducted using Medline, Embase, CINAHL and PsycINFO in February 2017. Reference lists of included studies and existing review papers were also screened. English language, peer-reviewed studies that utilized PRR to identify patient safety incidents (PSIs) occurring in general practice were included. Two researchers independently extracted data from articles and applied the Quality Assessment Tool for Studies with Diverse Designs. <b>Results:</b> A total of 3265 studies were screened, with 15 included. Trigger tools were the most frequent method used for the PRRs (<i>n</i> = 6). The mean number of safety incidents per 100 records was 12.6. Within studies, a mean of 30.6% of incidents were associated with severe harm (range 8.6–50%), and a mean of 55.6% of incidents was considered preventable (range 32.7–93.5%). The most commonly identified types of PSIs related to medication and prescribing, diagnosis, communication and treatment. Three studies reported on improvement actions taken after the PRRs. <b>Conclusion:</b> This review suggests that PRR may be a promising means of proactively identifying patient safety incidents and informing improvements.
DOI: 10.6084/m9.figshare.6973871
title: MALT alignment of fungal ITS agains the ITS RefSeq database

description: MALT alignment files of fungal ITS sequences against the ITS RefSeq database. To view the alignment, open the .rma files in MEGAN.<br>
DOI: 10.6084/m9.figshare.6973868
title: Comprehensive functional annotation of susceptibility SNPs from GWASs identified key genes for osteoporosis

description: We used a variety of databases to annotate osteoporosis-associated SNPs identified in previous genome-wide association studies (GWAS) and genetic association studies to identify key genes for osteoporosis.
DOI: 10.5281/zenodo.4005841
title: SGB.Jun19

description: PhyloPhlAn metagenomic database "SGB.Jun19"
DOI: 10.6084/m9.figshare.6973868.v1
title: Comprehensive functional annotation of susceptibility SNPs from GWASs identified key genes for osteoporosis

description: We used a variety of databases to annotate osteoporosis-associated SNPs identified in previous genome-wide association studies (GWAS) and genetic association studies to identify key genes for osteoporosis.
DOI: 10.5281/zenodo.4005840
title: SGB.Jun19

description: PhyloPhlAn metagenomic database "SGB.Jun19"
DOI: 10.6084/m9.figshare.6973856
title: Supplementary Material for: The Impact of Depressive Disorder Symptoms and Subtypes on 6-Year Incidence of Somatic Diseases

description: Medicine
DOI: 10.6084/m9.figshare.6973841
title: Merged fungal ITS reads

description: Reads clipped and paired-end reads merged with Clip&Merge<br>
DOI: 10.6084/m9.figshare.6973847
title: Lecture capture survey

description: This dataset contains information on UK university lecture capture policies as of April 2018. The dataset was used for the paper "Employee Surveillance: The Road to Surveillance is Paved with Good Intentions", by Lilian Edwards, Laura Martin and Tristan Henderson, accepted for presentation at the Amsterdam Privacy Conference, October 2018.
DOI: 10.6084/m9.figshare.6973847.v1
title: Lecture capture survey

description: This dataset contains information on UK university lecture capture policies as of April 2018. The dataset was used for the paper "Employee Surveillance: The Road to Surveillance is Paved with Good Intentions", by Lilian Edwards, Laura Martin and Tristan Henderson, Amsterdam Privacy Conference, October 2018.
DOI: 10.6084/m9.figshare.6973835
title: Supplementary Material for: Identifying Barriers to Idiopathic Pulmonary Fibrosis Treatment: A Survey of Patient and Physician Views

description: <b><i>Background:</i></b> Antifibrotics are recommended for the treatment of individuals with idiopathic pulmonary fibrosis (IPF), but treatment use remains at ∼60%. <b><i>Objective:</i></b> To investigate the views of individuals with IPF and pulmonologists on the diagnosis and management of IPF to understand treatment patterns. <b><i>Methods:</i></b> Interviews and/or online surveys were completed by patients and pulmonologists from Canada, France, Germany, Italy, Spain, and the UK. Responses from physicians were analyzed by time between diagnosis and treatment initiation in the majority of patients with IPF (group A, &gt; 4 months; group B, ≤4 months). Statistical comparisons between physicians were undertaken using <i>z</i> tests, with <i>p</i> &lt; 0.05 considered statistically significant. <b><i>Results:</i></b> The physicians in group A saw fewer patients, were less comfortable discussing the IPF prognosis with patients, and had less belief in the benefits of antifibrotic treatments than the physicians in group B. These physicians’ attitudes contrasted with those of the patients, who wanted more information about the IPF prognosis and pharmacological treatment options at diagnosis and were more concerned about preventing disease progression than avoiding medication side effects. Differences between countries were found regarding physicians’ comfort in discussing the prognosis at diagnosis and access to care. <b><i>Conclusions:</i></b> Several barriers to antifibrotic treatment, principally reflecting the differing views and values of patients and physicians, were identified in this study, suggesting a need for better patient-physician communication about pharmacological therapy for IPF.
DOI: 10.6084/m9.figshare.6973847.v3
title: Lecture capture survey

description: This dataset contains information on UK university lecture capture policies as of April 2018. The dataset was used for the paper "Employee Surveillance: The Road to Surveillance is Paved with Good Intentions", by Lilian Edwards, Laura Martin and Tristan Henderson, accepted for presentation at the Amsterdam Privacy Conference, October 2018.
DOI: 10.6084/m9.figshare.6973835.v1
title: Supplementary Material for: Identifying Barriers to Idiopathic Pulmonary Fibrosis Treatment: A Survey of Patient and Physician Views

description: <b><i>Background:</i></b> Antifibrotics are recommended for the treatment of individuals with idiopathic pulmonary fibrosis (IPF), but treatment use remains at ∼60%. <b><i>Objective:</i></b> To investigate the views of individuals with IPF and pulmonologists on the diagnosis and management of IPF to understand treatment patterns. <b><i>Methods:</i></b> Interviews and/or online surveys were completed by patients and pulmonologists from Canada, France, Germany, Italy, Spain, and the UK. Responses from physicians were analyzed by time between diagnosis and treatment initiation in the majority of patients with IPF (group A, &gt; 4 months; group B, ≤4 months). Statistical comparisons between physicians were undertaken using <i>z</i> tests, with <i>p</i> &lt; 0.05 considered statistically significant. <b><i>Results:</i></b> The physicians in group A saw fewer patients, were less comfortable discussing the IPF prognosis with patients, and had less belief in the benefits of antifibrotic treatments than the physicians in group B. These physicians’ attitudes contrasted with those of the patients, who wanted more information about the IPF prognosis and pharmacological treatment options at diagnosis and were more concerned about preventing disease progression than avoiding medication side effects. Differences between countries were found regarding physicians’ comfort in discussing the prognosis at diagnosis and access to care. <b><i>Conclusions:</i></b> Several barriers to antifibrotic treatment, principally reflecting the differing views and values of patients and physicians, were identified in this study, suggesting a need for better patient-physician communication about pharmacological therapy for IPF.
DOI: 10.6084/m9.figshare.6973847.v2
title: Lecture capture survey

description: This dataset contains information on UK university lecture capture policies as of April 2018. The dataset was used for the paper "Employee Surveillance: The Road to Surveillance is Paved with Good Intentions", by Lilian Edwards, Laura Martin and Tristan Henderson, accepted for presentation at the Amsterdam Privacy Conference, October 2018.
DOI: 10.6084/m9.figshare.6973805
title: Supplementary Material for: Associated Pulmonary Hypertension Is an Independent Contributor to Exercise Intolerance in Chronic Fibrosing Interstitial Pneumonias

description: <b><i>Background:</i></b> Associated pulmonary hypertension (APH) is frequently observed in fibrosing interstitial pneumonias (FIP), such as idiopathic pulmonary fibrosis (IPF). APH is associated with worse prognosis, but it remains unclear whether it is associated with greater functional impairment. Six-minute walk distance (6MWD) is widely used to assess functional capacity in pulmonary hypertension and FIP. <b><i>Objectives:</i></b> To investigate if APH independently contributes to exercise intolerance in FIP, irrespective of the extent of underlying fibrosis. <b><i>Methods:</i></b> Patients diagnosed with FIP (September 2009 to June 2017) were included in the study if they underwent right heart catheterization, high-resolution chest computed tomography (HRCT), and 6MWD within 3 months. Recruitment was not limited only to patients undergoing lung transplant assessment. APH was defined as mean pulmonary artery pressure (mPAP) ≥25 mm Hg. The extent of fibrosis was quantified on HRCT using a visual fibrosis score by 2 separate observers. <b><i>Results:</i></b> Seventy-two patients (60 with IPF) were identified. Fifty-five patients had APH. mPAP was not significantly different in subgroups stratified according to the extent of fibrosis on HRCT. Pulmonary vascular resistance (PVR) was the strongest predictor of 6MWD on both univariate and stepwise regression analyses, and remained so considering only patients with normal wedge pressure (&lt; 15 mm Hg) (<i>n</i> = 61). HRCT fibrosis score and pulmonary function tests did not significantly correlate with 6MWD. <b><i>Conclusions:</i></b> In patients with FIP, PVR is a significant contributor of 6MWD, independently from the extent of fibrosis on HRCT. These results strengthen both the rationale to use 6MWD as endpoint in FIP and to target APH with specific therapies.
DOI: 10.6084/m9.figshare.6973805.v1
title: Supplementary Material for: Associated Pulmonary Hypertension Is an Independent Contributor to Exercise Intolerance in Chronic Fibrosing Interstitial Pneumonias

description: <b><i>Background:</i></b> Associated pulmonary hypertension (APH) is frequently observed in fibrosing interstitial pneumonias (FIP), such as idiopathic pulmonary fibrosis (IPF). APH is associated with worse prognosis, but it remains unclear whether it is associated with greater functional impairment. Six-minute walk distance (6MWD) is widely used to assess functional capacity in pulmonary hypertension and FIP. <b><i>Objectives:</i></b> To investigate if APH independently contributes to exercise intolerance in FIP, irrespective of the extent of underlying fibrosis. <b><i>Methods:</i></b> Patients diagnosed with FIP (September 2009 to June 2017) were included in the study if they underwent right heart catheterization, high-resolution chest computed tomography (HRCT), and 6MWD within 3 months. Recruitment was not limited only to patients undergoing lung transplant assessment. APH was defined as mean pulmonary artery pressure (mPAP) ≥25 mm Hg. The extent of fibrosis was quantified on HRCT using a visual fibrosis score by 2 separate observers. <b><i>Results:</i></b> Seventy-two patients (60 with IPF) were identified. Fifty-five patients had APH. mPAP was not significantly different in subgroups stratified according to the extent of fibrosis on HRCT. Pulmonary vascular resistance (PVR) was the strongest predictor of 6MWD on both univariate and stepwise regression analyses, and remained so considering only patients with normal wedge pressure (&lt; 15 mm Hg) (<i>n</i> = 61). HRCT fibrosis score and pulmonary function tests did not significantly correlate with 6MWD. <b><i>Conclusions:</i></b> In patients with FIP, PVR is a significant contributor of 6MWD, independently from the extent of fibrosis on HRCT. These results strengthen both the rationale to use 6MWD as endpoint in FIP and to target APH with specific therapies.
DOI: 10.6084/m9.figshare.6973802
title: Willingness to Pay for Hepatitis B Vaccination in Selangor, Malaysia: A Cross-Sectional Household Survey

description: Raw data for manuscript: Willingness to Pay for Hepatitis B Vaccination in Selangor, Malaysia: A Cross-Sectional Household Survey. This manuscript is submitted to Plos ONE. <br>
DOI: 10.6084/m9.figshare.6973793
title: Dataset for: Multisite Phosphorylation Provides a Reliable Mechanism for Making Decisions in Noisy Environments

description: The ability to make decisions at the cellular level is absolutely critical for the survival of organisms. Eukaryotic cells are constantly making binary decisions in response to internal and environmental signals. Among the most notable transducers of information are protein kinases. The regulation of these signaling proteins often relies on the activity of other protein kinases located upstream in the signaling cascade. However, these signaling systems are by their own nature an important source of molecular noise. Herein, we have assessed the role of multisite phosphorylation on detecting signals in the face of molecular noise. To address this issue, we have conceptually envisioned the biochemical transduction machinery as a classifier model that can lead to four possible outputs: true positives and negatives, and false positives and negatives. In this probabilistic framework, we show that multisite phosphorylation represents a mechanism to filter noise during the decision-making process. We present results showing that nonessential phosphorylation sites contribute to increase the rate of true positives while, at the same time, they can lessen the rate of false positives. This simultaneous increase in sensitivity and specificity, makes multisite phosphorylation a valuable and easily implemented mechanism to reliably transduce information in noisy contexts.
DOI: 10.6084/m9.figshare.6973793.v1
title: Dataset for: Multisite Phosphorylation Provides a Reliable Mechanism for Making Decisions in Noisy Environments

description: The ability to make decisions at the cellular level is absolutely critical for the survival of organisms. Eukaryotic cells are constantly making binary decisions in response to internal and environmental signals. Among the most notable transducers of information are protein kinases. The regulation of these signaling proteins often relies on the activity of other protein kinases located upstream in the signaling cascade. However, these signaling systems are by their own nature an important source of molecular noise. Herein, we have assessed the role of multisite phosphorylation on detecting signals in the face of molecular noise. To address this issue, we have conceptually envisioned the biochemical transduction machinery as a classifier model that can lead to four possible outputs: true positives and negatives, and false positives and negatives. In this probabilistic framework, we show that multisite phosphorylation represents a mechanism to filter noise during the decision-making process. We present results showing that nonessential phosphorylation sites contribute to increase the rate of true positives while, at the same time, they can lessen the rate of false positives. This simultaneous increase in sensitivity and specificity, makes multisite phosphorylation a valuable and easily implemented mechanism to reliably transduce information in noisy contexts.
DOI: 10.6084/m9.figshare.6973781
title: Mapping of fungal ITS sequences against the Picea abies genome

description: Mapping of merged ITS reads against the genome of the host tree Norway spruce (Picea abies). Mapping was done with BWA-MEM using a seed lenght of 40bp.<br>
DOI: 10.6084/m9.figshare.6973781.v1
title: Mapping of fungal ITS sequences against the Picea abies genome

description: Mapping of merged ITS reads against the genome of the host tree Norway spruce (Picea abies). Mapping was done with BWA-MEM using a seed lenght of 40bp.<br>
DOI: 10.6084/m9.figshare.6973769
title: Lifestyle and demographic factors associated with human semen quality and sperm function

description: In this study, we sought to investigate the effect of lifestyle and demographic factors on classic and functional semen parameters. Three hundred and twenty-eight subjects who underwent semen analysis were recruited. Routine SA, sperm vitality, acrosome reaction (AR) assay and sperm DNA fragmentation index (DFI) were analyzed. Demographic and lifestyle information, including (1) BMI, (2) current smoking and alcohol drinking frequency, (3) sleep habits, (4) daily fluid intake, (5) weekly meat intake, (6) sports frequency, (7) trouser cell phone use, (8) age, and (9) abstinence time, were collected. Generalized additive models were used to analyze the possible non-linear association. The results showed that total sperm count (TSC) was significantly associated with age (<i>P</i> = 0.001), abstinence time (<i>P</i> = 0.001) and daily coffee intake (<i>P</i> = 0.044). Semen volume was significantly associated with age (<i>P</i> &lt; 0.001) and daily coffee intake (<i>P</i> &lt; 0.001). Sperm concentration was significantly associated with abstinence time (<i>P</i> = 0.011) and average sleep duration (<i>P</i> = 0.010). Sperm motility was significantly associated with age (<i>P</i> = 0.002) and daily juice intake (<i>P</i> = 0.001). Total motile sperm count was significantly associated with age (<i>P</i> = 0.003) and abstinence time (<i>P</i> = 0.009). DFI was significantly associated with age (<i>P</i> = 0.002), irregular sleeping habit (<i>P</i> = 0.008) and abstinence time (<i>P</i> = 0.032). The percentage of AR sperm was significantly associated with daily juice intake (<i>P</i> = 0.013). In conclusion, DFI and TSC were the most sensitive semen parameters for demographic and lifestyle features, whereas age had more influence on semen parameters than other demographic and lifestyle features. <b>Abbreviations</b>: BMI: body mass index; SA: semen analysis; AR: acrosome reaction; DFI: DNA fragmentation index; GAM: generalized additive model; TSC: total sperm count; TMC: total motile sperm count; IUI: intrauterine insemination; SCSA: sperm chromatin structure assay; SD: standard deviation; IQR: interquartile range; CBAVD: congenital bilateral absence of vas deferens; NEQAS: national external quality assessment service; HTF: human tubal fluid; HSA: human serum albumin.