cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6825386
title: Supplementary Material for: Sensitivity of Initial Thoracentesis for Malignant Pleural Effusion Stratified by Tumor Type in Patients with Strong Evidence of Metastatic Disease

description: <b><i>Background:</i></b> Thoracentesis with cytological examination of pleural fluid is the initial test of choice for evaluation of pleural effusions in patients with suspected malignant pleural effusion (MPE). There is limited data on the sensitivity of thoracentesis stratified by tumor type. A better understanding of stratified sensitivities is of clinical interest, and may guide early and appropriate referral for pleural biopsy. <b><i>Objective:</i></b> The primary objective was sensitivity of thoracentesis with pleural fluid cytology stratified by tumor type. <b><i>Methods:</i></b> This is a retrospective cohort study of consecutive patients with a solid tumor malignancy with proven or strong suspicion for metastatic disease with new pleural effusions that underwent an initial thoracentesis. Only patients with metastatic disease were included. <b><i>Results:</i></b> Of the 725 patients examined, 63% had pleural fluid cytology positive for malignancy. Sensitivity of thoracentesis varied from a low of 0.38 (95% CI 0.13–0.68) in head and neck malignancy, 0.38 (95% CI 0.15–0.65) in sarcoma, and 0.53 (95% CI 0.34–0.72) in renal cancer to a high of 93 (95% CI 88–97) in breast cancer, and 100 (95% CI 0.82–100) in pancreatic cancer. Factors associated with an increased risk of MPE included larger amount of fluid drained (<i>p</i> = 0.014) and higher pleural fluid protein (<i>p</i> = 0.002). The only factor associated with decreased risk of MPE if first cytology was negative for malignancy was the presence of contralateral effusion (<i>p</i> = 0.005). <b><i>Conclusions:</i></b> Sensitivity of thoracentesis for solid tumors varies significantly depending on the type of tumor and is lowest in those with sarcomas, head and neck malignancies, and renal cell cancers.
DOI: 10.6084/m9.figshare.6825344
title: Supplementary Material for: PLA1A Participates in the Antiviral Innate Immune Response by Facilitating the Recruitment of TANK-Binding Kinase 1 to Mitochondria

description: As a key molecule in the antiviral innate immune response, the activation of TANK-binding kinase 1 (TBK1) is under tight regulation. In this report, we identified phosphatidylserine-specific phospholipase PLA1A as a host factor that modulates the TBK1 activation. Knockdown of PLA1A expression suppressed the innate immune signaling induced by RNA viruses, while PLA1A overexpression enhanced the signaling. PLA1A functioned at the TBK1 level of the signaling pathway, as PLA1A silencing blocked TBK1, but not interferon regulatory factor 3 (IRF3) induced interferon-β (IFN-β) promoter activity. The phosphorylation and kinase activity of TBK1 was reduced in PLA1A knockdown cells. Mechanistically, PLA1A was required in TBK1-mitochondrial antiviral signaling protein (MAVS) interactions but not the interactions of TBK1 with other adaptor proteins. Furthermore, PLA1A knockdown reduced the recruitment of TBK1 and IRF3 to mitochondria, concomitant with altered mitochondria morphology.
DOI: 10.6084/m9.figshare.6825338
title: ROI depth images

description: Raw data utilized in the study "Investigating the impact of a motion capture system on Microsoft Kinect v2 recordings: a caution for using the technologies together"<br>QK file are presenting the depth recordings in presence of Qulisys motion capture system.K are presenting the depth recordings in absence of Qulisys motion capture system.
DOI: 10.6084/m9.figshare.6825344.v1
title: Supplementary Material for: PLA1A Participates in the Antiviral Innate Immune Response by Facilitating the Recruitment of TANK-Binding Kinase 1 to Mitochondria

description: As a key molecule in the antiviral innate immune response, the activation of TANK-binding kinase 1 (TBK1) is under tight regulation. In this report, we identified phosphatidylserine-specific phospholipase PLA1A as a host factor that modulates the TBK1 activation. Knockdown of PLA1A expression suppressed the innate immune signaling induced by RNA viruses, while PLA1A overexpression enhanced the signaling. PLA1A functioned at the TBK1 level of the signaling pathway, as PLA1A silencing blocked TBK1, but not interferon regulatory factor 3 (IRF3) induced interferon-β (IFN-β) promoter activity. The phosphorylation and kinase activity of TBK1 was reduced in PLA1A knockdown cells. Mechanistically, PLA1A was required in TBK1-mitochondrial antiviral signaling protein (MAVS) interactions but not the interactions of TBK1 with other adaptor proteins. Furthermore, PLA1A knockdown reduced the recruitment of TBK1 and IRF3 to mitochondria, concomitant with altered mitochondria morphology.
DOI: 10.6084/m9.figshare.6825338.v1
title: ROI depth images

description: Raw data utilized in the study "Investigating the impact of a motion capture system on Microsoft Kinect v2 recordings: a caution for using the technologies together"<br>
DOI: 10.6084/m9.figshare.6825227
title: Supplementary Material for: Long-Term Opioid Agonist Treatment Participation after First Treatment Entry is Similar across 4 European Regions but Lower in Non-Nationals

description: Heroin users in opioid agonist treatment (OAT) show markedly reduced heroin consumption, less crime and a lower mortality rate. However, the extent of long-term OAT participation over subsequent treatment episodes remains unclear. We analysed the annual proportion of patients in treatment (at least 1 day) since the start of first OAT in 4 European regions: Barcelona (BA) 1996–2012: 8,602 patients; Czech ­Republic (CZ) 2000–2014: 4,377 patients; Netherlands (NL) 1994–2014: 33,235 patients, Zurich (ZU) 1992–2015: 11,795. We estimated the long-term decline of treatment need due to mortality or abstinence and also a “nuisance” short-term decline until the equilibrium level of cycling in and out of OAT is reached to obtain the adjusted treatment participation value. The adjusted treatment participation was around 50% (BA: 47.4–51.4%; CZ: 49.8–53.9%; NL: 52.3–54.0%; ZU: 46.4–49.3%), and the annual decline of treatment need was close to 4%. Non-nationals (NL patients with a migrant background) showed substantial lower adjusted treatment participation (rate ratio BA: 0.059–0.343; NL: 0.710–0.751; ZU: 0.681–0.797; CZ: n.a.). Our method may provide a policy-relevant indicator of long-term provision, quality and access to OAT following first treatment.
DOI: 10.6084/m9.figshare.6825227.v1
title: Supplementary Material for: Long-Term Opioid Agonist Treatment Participation after First Treatment Entry is Similar across 4 European Regions but Lower in Non-Nationals

description: Heroin users in opioid agonist treatment (OAT) show markedly reduced heroin consumption, less crime and a lower mortality rate. However, the extent of long-term OAT participation over subsequent treatment episodes remains unclear. We analysed the annual proportion of patients in treatment (at least 1 day) since the start of first OAT in 4 European regions: Barcelona (BA) 1996–2012: 8,602 patients; Czech ­Republic (CZ) 2000–2014: 4,377 patients; Netherlands (NL) 1994–2014: 33,235 patients, Zurich (ZU) 1992–2015: 11,795. We estimated the long-term decline of treatment need due to mortality or abstinence and also a “nuisance” short-term decline until the equilibrium level of cycling in and out of OAT is reached to obtain the adjusted treatment participation value. The adjusted treatment participation was around 50% (BA: 47.4–51.4%; CZ: 49.8–53.9%; NL: 52.3–54.0%; ZU: 46.4–49.3%), and the annual decline of treatment need was close to 4%. Non-nationals (NL patients with a migrant background) showed substantial lower adjusted treatment participation (rate ratio BA: 0.059–0.343; NL: 0.710–0.751; ZU: 0.681–0.797; CZ: n.a.). Our method may provide a policy-relevant indicator of long-term provision, quality and access to OAT following first treatment.
DOI: 10.6084/m9.figshare.6824873
title: Supplementary Material for: Gender Differences in Anxiety and Depression before and after Alcohol Detoxification: Anxiety and Depression as Gender-Related Predictors of Relapse

description: <b><i>Background/Aims:</i></b> The aim of this prospective study was to estimate gender differences in anxiety, depression, and alcohol use severity among patients with alcohol use disorder (AUD) before and after detoxification program and within 12 months after discharge. <b><i>Methods:</i></b> AUD severity, state and trait anxiety, and depression were assessed in 187 patients entering an inpatient alcohol detoxification program. Follow-up assessments were performed at 6 and 12 months after discharge. A between- and within-subjects analyses explored gender differences. The predictive value of anxiety and depression for alcohol relapse was analyzed by logistic and linear regression in both genders. <b><i>Results:</i></b> Females had higher levels of anxiety and depression than males both at admission and after discharge. Trait anxiety and depression significantly increased 6 months after discharge in males and females respectively. Both state and trait anxiety levels at the 6-month follow-up predicted alcohol relapse at the 12-month follow-up in males. Conversely, in females, depression level at the 6-month follow-up was a predictor of relapse at the 12-month follow-up. <b><i>Conclusions:</i></b> In both genders, the psychopathological dimension that showed the most significant worsening at 6-month follow-up (i.e., anxiety in males and depression in females) was found to be a significant predictor of relapse at the 12-month follow-up.
DOI: 10.6084/m9.figshare.6824798
title: Electroencephalography-based endogenous brain-computer interface might be used for the online communication with a completely locked-in patient

description: Brain-computer interfaces (BCIs) have demonstrated the potential to provide paralyzed individuals with new means of communication, but an electroencephalography (EEG)-based endogenous BCI has never been successfully used for communication with a patient in a completely locked-in state (CLIS). In this study, we investigated the possibility of using an EEG-based endogenous BCI paradigm for the online binary communication by patients in CLIS.A female patient in CLIS participated in this study. She had not communicated even with her family for more than one year with complete loss of motor function. Offline and online experiments were conducted to validate the feasibility of the proposed BCI system. In the offline experiment, we determined the best combination of mental tasks and the optimal classification strategy leading to the best performance. In the online experiment, we investigated whether our BCI system could be used for real-time communication with the patient. An online classification accuracy of 87.5 % was achieved when Riemannian geometry-based classification was applied to real-time EEG data recorded while the patient was performing one of two mental imagery tasks for 5 s. Our results suggest that an EEG-based endogenous BCI might be potentially used for online communication with a patient in CLIS.
DOI: 10.6084/m9.figshare.6824789
title: Supplementary Material for: The Pattern of Elevated Liver Function Tests in Nonalcoholic Fatty Liver Disease Predicts Fibrosis Stage and Metabolic-Associated Comorbidities

description: <b><i>Background:</i></b> Patients with nonalcoholic fatty liver disease (NAFLD) and with abnormal liver function tests (LFTs) most commonly present with elevated hepatocellular enzymes (H pattern), but a subset of patients is found to have elevated cholestatic enzymes (C pattern) or a mixed (M) pattern. <b><i>Aims and Methods:</i></b> To determine whether the epidemiologic background and comorbidities, as well as the degree of liver fibrosis, differ between NAFLD patients with different patterns of elevated LFTs by retrospectively analyzing data of 106 patients with a biopsy-proven diagnosis of NAFLD. The pattern of elevated LFTs was determined by adopting the “R-Ratio” formula commonly used for drug-induced liver injury. <b><i>Results:</i></b> Advanced fibrosis (F &gt; 2) was found in 15 out of 48 (31.3%) patients with a C pattern of elevated LFTs as compared to 2 out of 44 (4.5%) in M patients and 2 out of 11 (18.2%) in H patients (<i>p</i> = 0.004). Group C patients are older and also had a higher prevalence of diabetes, a higher mean hemoglobin A1c, and a higher prevalence of hypertension, as well as a trend for a higher prevalence of hypertriglyceridemia. <b><i>Conclusions:</i></b> Using a simple formula incorporating routine LFTs can help to categorize NAFLD patients as low or high risk for advanced fibrosis stage and metabolic-associated comorbidities.
DOI: 10.6084/m9.figshare.6824789.v1
title: Supplementary Material for: The Pattern of Elevated Liver Function Tests in Nonalcoholic Fatty Liver Disease Predicts Fibrosis Stage and Metabolic-Associated Comorbidities

description: <b><i>Background:</i></b> Patients with nonalcoholic fatty liver disease (NAFLD) and with abnormal liver function tests (LFTs) most commonly present with elevated hepatocellular enzymes (H pattern), but a subset of patients is found to have elevated cholestatic enzymes (C pattern) or a mixed (M) pattern. <b><i>Aims and Methods:</i></b> To determine whether the epidemiologic background and comorbidities, as well as the degree of liver fibrosis, differ between NAFLD patients with different patterns of elevated LFTs by retrospectively analyzing data of 106 patients with a biopsy-proven diagnosis of NAFLD. The pattern of elevated LFTs was determined by adopting the “R-Ratio” formula commonly used for drug-induced liver injury. <b><i>Results:</i></b> Advanced fibrosis (F &gt; 2) was found in 15 out of 48 (31.3%) patients with a C pattern of elevated LFTs as compared to 2 out of 44 (4.5%) in M patients and 2 out of 11 (18.2%) in H patients (<i>p</i> = 0.004). Group C patients are older and also had a higher prevalence of diabetes, a higher mean hemoglobin A1c, and a higher prevalence of hypertension, as well as a trend for a higher prevalence of hypertriglyceridemia. <b><i>Conclusions:</i></b> Using a simple formula incorporating routine LFTs can help to categorize NAFLD patients as low or high risk for advanced fibrosis stage and metabolic-associated comorbidities.
DOI: 10.26180/5b4d965923ca6
title: IPD Deception Modelling Experimental Data 2017-2018

description: Datasets for Paper Entitled <i>"Information-theoretic models of deception: modelling cooperation and diffusion in populations exposed to ``fake news''"</i> by Kopp, Korb and Mills<br>Archived data files have been separated from the data plotting scripts to permit incremental downloads of data due to the large size of the archived data.<br>README text files contain explanatory notes.<br>
DOI: 10.6084/m9.figshare.6824783
title: Supplementary Material for: Clinical Management of Chronic Kidney Disease Patients in Italy: Results from the IRIDE Study

description: <b><i>Background:</i></b> Lack of adequate management of chronic kidney disease (CKD) often results in delayed diagnosis and inadequate treatment. This study assessed the clinical management and outcome of stages 1–5 CKD patients. <b><i>Methods:</i></b> Patients were prospectively followed for 3 years in 25 nephrology centers across Italy. Clinical characteristics were measured at baseline and every 6 months. Outcome measures included CKD staging, presence of comorbidities, treatment, mineral bone disorder (MBD) parameters, and patient outcomes. <b><i>Results:</i></b> Of 884 enrolled patients (59.7% males, aged 66.2 ± 14.6 years), 587 (66.4%) completed the study. The majority of patients were referred by a general practitioner (44.7%) and had stage 3 or 4 CKD (40.9 and 23.8% respectively). Data reveal that 91.3% of patients had at least 1 concomitant disease, most frequently hypertension (80.1%) and dyslipidemia (42.5%); 94.6% of patients were receiving cardiovascular medication and 52.6% were receiving lipid-lowering medication. Approximately 40% of patients had proteinuria and intact parathyroid hormone levels outside the normal range. As expected, stages 4 and 5 CKD patients had a higher prevalence of proteinuria (68 and 74%), MBD (59 and 88%) and anemia (28 and 73%), as well as a higher risk of hospitalization (34.3 and 51.9%) and need for dialysis (69.5 and 70%). The overall probability of survival over 36 months was 90.6%. <b><i>Conclusions:</i></b> This is the first Italian prospective study performed with a large cohort of CKD patients over a 3-year period. Considering the multifactorial burden of diseases associated with CKD patients, the need for greater attention to CKD and related disorders is paramount.
DOI: 10.6084/m9.figshare.6824783.v1
title: Supplementary Material for: Clinical Management of Chronic Kidney Disease Patients in Italy: Results from the IRIDE Study

description: <b><i>Background:</i></b> Lack of adequate management of chronic kidney disease (CKD) often results in delayed diagnosis and inadequate treatment. This study assessed the clinical management and outcome of stages 1–5 CKD patients. <b><i>Methods:</i></b> Patients were prospectively followed for 3 years in 25 nephrology centers across Italy. Clinical characteristics were measured at baseline and every 6 months. Outcome measures included CKD staging, presence of comorbidities, treatment, mineral bone disorder (MBD) parameters, and patient outcomes. <b><i>Results:</i></b> Of 884 enrolled patients (59.7% males, aged 66.2 ± 14.6 years), 587 (66.4%) completed the study. The majority of patients were referred by a general practitioner (44.7%) and had stage 3 or 4 CKD (40.9 and 23.8% respectively). Data reveal that 91.3% of patients had at least 1 concomitant disease, most frequently hypertension (80.1%) and dyslipidemia (42.5%); 94.6% of patients were receiving cardiovascular medication and 52.6% were receiving lipid-lowering medication. Approximately 40% of patients had proteinuria and intact parathyroid hormone levels outside the normal range. As expected, stages 4 and 5 CKD patients had a higher prevalence of proteinuria (68 and 74%), MBD (59 and 88%) and anemia (28 and 73%), as well as a higher risk of hospitalization (34.3 and 51.9%) and need for dialysis (69.5 and 70%). The overall probability of survival over 36 months was 90.6%. <b><i>Conclusions:</i></b> This is the first Italian prospective study performed with a large cohort of CKD patients over a 3-year period. Considering the multifactorial burden of diseases associated with CKD patients, the need for greater attention to CKD and related disorders is paramount.
DOI: 10.6084/m9.figshare.6824192
title: Dataset for: Mapping of Fine Scale Rat Prefrontal Cortex Connections: Evidence for Detailed Ordering of Inputs and Outputs Connecting the Temporal Cortex and Sensory-Motor Regions

description: Cerebral cortex structure is crucially important for cortical organisation and function. The organisation of prefrontal cortex (PFC) is controversial and here we seek to understand it more clearly through the study of fine scale cortical connections. To determine the ordering of micro-scale input and output connections in the rat PFC we injected small volumes (20-30nl) of anterograde (Fluro-Ruby) and retrograde (Fluoro-Gold) neuroanatomical tracers into PFC. These injections revealed several connected regions of the brain but here we report findings restricted to PFC to temporal cortex and sensory-motor cortex pathways. In agreement with previous studies incorporating larger injection volumes we found that smaller injection volumes revealed a more detailed, fine scale ordering of both prefrontal inputs and output connections to the temporal cortex and sensory-motor cortex regions. These findings are also supported by labelling observed from additional tracer injections made into corresponding regions of temporal cortex. The topography observed reflected the ordering seen at a larger level (i.e with larger injection volumes) but there were some differences in the topography, such as in relation to the direction of ordering. In agreement with earlier work, we found that fine scale input and output connections were not always aligned with respect to one another. These results provide evidence for topographically arranged inputs and outputs in two distinct PFC pathways, along with evidence for different connectional patterns within the same pathways. Based on theories of functional connectivity, these findings provide evidence for prefrontal cortical regions residing within networks that contribute to different cognitive functions.
DOI: 10.6084/m9.figshare.6824117
title: Additional file 1: of GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

description: Includes supplementary Tables S1-S5 containing additional results. (XLSX 294 kb)
DOI: 10.6084/m9.figshare.6824039
title: MOESM1 of Identification of genome-wide binding sites of heat shock factor 1, Hsf1, under basal conditions in the human pathogenic yeast, Candida albicans

description: Additional file 1. Additional tables.
DOI: 10.6084/m9.figshare.6824039.v1
title: MOESM1 of Identification of genome-wide binding sites of heat shock factor 1, Hsf1, under basal conditions in the human pathogenic yeast, Candida albicans

description: Additional file 1. Additional tables.
DOI: 10.6084/m9.figshare.6824030
title: MOESM3 of Imprint cytology: a useful screening test for diagnosis of Helicobacter pylori in resource poor settings

description: Additional file 3: Book 1. Contains detailed results of all subjects enrolled for the study.
DOI: 10.6084/m9.figshare.6824030.v1
title: MOESM3 of Imprint cytology: a useful screening test for diagnosis of Helicobacter pylori in resource poor settings

description: Additional file 3: Book 1. Contains detailed results of all subjects enrolled for the study.
DOI: 10.6084/m9.figshare.6824000
title: Additional file 9: of Profiling of testis-specific long noncoding RNAs in mice

description: Table S9. Testis-specific lncRNAs and mRNAs in three mouse germ cell-related cell lines (F9, GC-1 and GC-2). (XLSX 712 kb)
DOI: 10.6084/m9.figshare.6824000.v1
title: Additional file 9: of Profiling of testis-specific long noncoding RNAs in mice

description: Table S9. Testis-specific lncRNAs and mRNAs in three mouse germ cell-related cell lines (F9, GC-1 and GC-2). (XLSX 712 kb)
DOI: 10.6084/m9.figshare.6823964
title: MOESM2 of ER stress regulates alkaline phosphatase gene expression in vascular smooth muscle cells via an ATF4-dependent mechanism

description: Additional file 2. Proteomics results. List of proteins, that bind the ALP promoter, identified by mass spectrometry. Nuclear extracts were bound and eluted off the biotinylated DNA on beads and analysed by LCâ MS/MS. Raw mass spectrometry data were analysed in Proteome Discoverer (ThermoScientific; v1.3.0.339) utilising the Mascot database. Samples were searched against Uniprot database to identify proteins bound to the ALP promoter and compared with proteins that nonspecifically bound to unconjugated beads.
DOI: 10.6084/m9.figshare.6823964.v1
title: MOESM2 of ER stress regulates alkaline phosphatase gene expression in vascular smooth muscle cells via an ATF4-dependent mechanism

description: Additional file 2. Proteomics results. List of proteins, that bind the ALP promoter, identified by mass spectrometry. Nuclear extracts were bound and eluted off the biotinylated DNA on beads and analysed by LCâ MS/MS. Raw mass spectrometry data were analysed in Proteome Discoverer (ThermoScientific; v1.3.0.339) utilising the Mascot database. Samples were searched against Uniprot database to identify proteins bound to the ALP promoter and compared with proteins that nonspecifically bound to unconjugated beads.