cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23768463
title: Supplementary Material for: Effects of Testosterone Replacement Therapy on Muscle Strength in Older Men with Low to Low-Normal Testosterone Levels: A Systematic Review and Meta‐Analysis

description: Background Previous studies and meta-analyses have explored the relationship among testosterone, muscle strength, and physical function, to the best of our knowledge, no meta-analysis has investigated the effects of Testosterone replacement therapy (TRT) on subgroup of relatively hypogonadal older men. Objective To evaluate the effect of TRT in older men with low testosterone levels. Methods PubMed, Embase, and Web of Science were systematically searched for articles published between January 1990, and April 2020. We included randomized controlled studies that investigated the effect of TRT and included older men (age &gt; 60 years) with relatively low testosterone levels. Studies were extracted following the PRISMA flowchart, and the included randomized controlled trials were evaluated using RoB 2.0. Our main outcome was muscle strength changes after TRT evaluated using a metaregression of confounding factors. Secondary outcomes included changes in physical performance and the risk ratio of adverse events. Random-effects meta-analyses of TRT on muscle strength and physical function were performed. Results Thirteen studies with 2043 patients were included. The mean age of subjects in various studies ranged from 65.9 years to 76 years. Transdermal testosterone dosages ranged from 5-10 g/day, while intramuscular options were 125 mg/week or 200 mg every two weeks. Oral testosterone supplementation was given at 160 mg/day in one study. Pooled meta‐analyses revealed greater muscle strength improvement after TRT compared with placebo (Hedges’ g = 0.21; 95% CI = 0.15–0.28). Intramuscular administration of TRT had greater efficacy (Hedges’ g = 0.74; 95% CI = 0.34–1.14) than transdermal and oral TRT. (p &lt; 0.001). A metaregression revealed that baseline serum total testosterone was associated with muscle strength improvement (β = -0.004, p = 0.002). The risk ratios of adverse events, including elevated prostate-specific antigen, acute coronary syndrome, and prostate cancer, were not significantly different. Conclusion TRT improved muscle strength in older, relatively hypogonadal men. The effect was more pronounced in populations with lower baseline testosterone levels.
DOI: 10.6084/m9.figshare.23813400
title: Source Data.xlsx

description: Source data are provided with this paper.
DOI: 10.6084/m9.figshare.23827854
title: Supplementary Material for: Auditory-Perceptual Assessments of Cough: Characterizing Rater Reliability and the Effects of a Standardized Training Protocol

description: Introduction: Auditory-perceptual assessments of cough are commonly used by speech-language pathologists working with people with swallowing disorders with emerging evidence beginning to demonstrate their validity, however their reliability amongst novice clinicians is unknown. Therefore, the primary aim of this study was to characterize the reliability of auditory-perceptual assessments of cough amongst a group of novice clinicians. As a secondary aim, we assessed the effects of a standardized training protocol on the reliability of auditory-perceptual assessments of cough. Methods: 12 novice clinicians blindly rated ten auditory-perceptual cough descriptors for 120 cough audio clips. Standardized training was then completed by the group of clinicians. The same cough audio clips were then re-randomized and blindly rated. Reliability was analyzed pre- and post-training within each clinician (intra-rater), between each unique pair of raters (dyad-level inter-rater), and for the entire group of raters (group-level inter-rater) using intraclass correlation coefficients and Cohen’s Kappa. Results: Pre-training reliability was greatest for measures of strength, effectiveness, and normality, and lowest when judging the type of expiratory maneuver (cough, throat clear, huff, other). The measures that improved the most with training were ratings of perceived crispness, amount of voicing, and type of expiratory maneuver. Intra-rater reliability coefficients ranged from .580-.903 pre-training and .756-.904 post-training. Dyad-level inter-rater reliability coefficients ranged from .295-.745 pre-training and .450-.804 post-training. Group-level inter-rater reliability coefficients ranged from .454-.919 pre-training and .558-.948 post-training. Discussion/Conclusion: Reliability of auditory-perceptual assessments varied across perceptual cough descriptors, but all appeared within the range of what has been historically reported for auditory-perceptual assessments of voice and visual-perceptual assessments of swallowing and cough airflow. Reliability improved for most cough descriptors following 30-60 minutes of standardized training. Future research is needed to examine the validity of auditory-perceptual assessments of cough by assessing the relationship between perceptual cough descriptors with instrumental measures of cough effectiveness to better understand the role of perceptual assessments in clinical practice.
DOI: 10.6084/m9.figshare.24015516
title: Supplementary Material for: A Chromosome 9p24.1 Amplification in Colorectal Cancer with Metastases to the Kidney and Adrenal Gland: a Case Report

description: Colorectal cancer (CRC) is the third leading cause of mortality worldwide. The Food and Drug Administration recently designated pembrolizumab, an immune checkpoint inhibitor (ICI) against a programmed death-1 (PD-1) receptor, as a breakthrough drug for the treatment of patients with mCRC whose tumors have deficient mismatch repair gene (dMMR) expression (as evidenced by microsatellite instability-high [MSI-H]) and patients with solid tumors with a high tumor mutational burden (TMB-H) with ≥ 10 mutations/megabase. We present a patient with metastatic CRC who had renal and adrenal gland metastases with multiple genomic alterations characteristic of CRC and rare chromosome 9p24.1 amplification, resulting in a co-amplification of the PDL1, PDL2, and JAK2 genes. Although this genomic alteration may predict the response to ICI, the lack of pembrolizumab prevented the patient from receiving targeted treatment and succumbing to the disease.
DOI: 10.6084/m9.figshare.24041952
title: Supplementary Material for: Development and validation of a nomogram for predicting all-cause mortality in patients with hemodialysis having pulmonary hypertension

description: Introduction: Patients with end-stage renal disease receiving hemodialysis (HD) have a high morbidity and mortality rate associated with pulmonary hypertension (PH). A nomogram was developed to predict all-cause mortality in HD patients with PH. In this study, we aimed to validate the usefulness of this nomogram. Methods: A total of 274 HD patients with PH were hospitalized at the Affiliated Hospital of Xuzhou Medical University between January 2014 and June 2019 and followed up for 3 years. Echocardiography detected PH when the peak tricuspid regurgitation velocity (TRV) was more than 2.8 m/s. To evaluate the all-cause mortality for long-term HD patients with PH, Cox regression analysis was performed to determine the factors of mortality that were included in the prediction model. Next, the area under the receiver-operating characteristic curve (AUC-ROC) was used to assess the predictive power of the model. Calibration plots and decision curve analysis (DCA) were used to assess the accuracy of the prediction results and the clinical utility of the model. Results: The all-cause mortality rate was 29.1% throughout the follow-up period. The nomogram comprised six commonly available predictors: age, diabetes mellitus, cardiovascular disease, hemoglobin, left ventricular ejection fraction, and TRV. The 1-year, 2-year, and 3-year AUC-ROC values were 0.842, 0.800, and 0.781, respectively. The calibration curves revealed an excellent agreement with the nomogram, while the DCA demonstrated favorable clinical practicability. Conclusion: The first developed nomogram for predicting all-cause mortality in HD patients with PH could guide clinical decision-making and intervention planning.
DOI: 10.6084/m9.figshare.24087816
title: Supplementary Material for: Antidepressants and Social Functioning in Patients with Major Depressive Disorder – Systematic Review and Meta-analysis of Double-blind, Placebo-controlled RCTs

description: Introduction: Social functioning (SF) is the ability to fullfill one’s social obligations and a key outcome in treatment. Objective: To estimate the effects of antidepressants on SF in patients with MDD. Methods: This meta-analysis and its reporting are based on Cochrane Collaboration’s Handbook of Systematic Reviews and Meta-Analyses and PRISMA guidelines (protocol registration at OSF). We systematically searched CENTRAL, Medline, PubMed Central, and PsycINFO for double-blind RCTs comparing antidepressants with placebo and reporting on SF. We computed standardized mean differences (SMD) with 95%-CIs and prediction intervals. Results: We selected 40 RCTs out of 1188 records screened, including 16.586 patients (age 46.75 years, 64.2% women). In 27 studies investigating patients with major depressive disorder (primary depression), antidepressants resulted in a SMD of 0.25 compared to placebo ([95%-CI: 0.21; 0.30] I2: 39%). In 13 trials with patients suffering from major depressive disorder comorbid with physical conditions or disorders the summary estimate was 0.24 ([0.10; 0.37] I2 : 75%). In comorbid depression, studies with high/uncertain risk of bias had higher SMDs than low risk studies: 0.29 [0.13; 0.44] vs. 0.04 [-0.16; 0.24]; no such effect was evident in primary depression. There was no indication of sizeable reporting bias. SF efficacy correlates with efficacy on depression scores, Spearman’s rho 0.67 (p&lt;0.001), and QoL, 0.63 (p&lt;0.001). Conclusions: The effect of antidepressants on social functioning is small, similar to its effect on depressive symptoms in primary major depressive disorder and doubtful in comorbid depression. Strong correlations with both antidepressive and QoL effects suggest overlap among domains.
DOI: 10.6084/m9.figshare.24155526
title: Supplementary Material for: MicroRNA-9-1 Attenuates Influenza A Virus Replication via Targeting Tankyrase 1

description: An unstable influenza genome leads to the virus resistance to antiviral drugs that target viral proteins. Thus, identification of host factors essential for virus replication may pave the way to develop novel antiviral therapies. In this study, we investigated the roles of the poly(ADP-ribose) polymerase enzyme, tankyrase1 (TNKS1) and the endogenous small noncoding RNA, miR-9-1 in influenza A virus (IAV) infection. Increased expression of TNKS1 was observed in IAV-infected human lung epithelial cells and mouse lungs. TNKS1 knock-down by RNA interference repressed influenza viral replication. A screen using TNKS1 3’-untranslation region (3’-UTR) reporter assays and predicted microRNAs identified that miR-9-1 targeted TNKS1. Overexpression of miR-9-1 reduced influenza viral replication in lung epithelial cells as measured by viral mRNA and protein levels as well as virus production. miR-9-1 induced type I interferon production and enhanced the phosphorylation of STAT1 in cell culture. The ectopic expression of miR-9-1 in the lungs of mice by using an adenoviral viral vector enhanced type I interferon response, inhibited viral replication and reduced susceptibility to IAV infection. Our results indicate that miR-9-1 is an antiinfluenza microRNA that targeting TNKS1 and enhanced cellular antiviral state.
DOI: 10.17026/dans-xrf-82dc
title: Green Campus Universities: Problems and Prospects

description: A new knowledge of creating green campus universities in Malaysia and as a means to create sustainability in higher education setting.Audio record of an interview session.Consent form and info sheet.
DOI: 10.25326/308
title: M161 Rainwater Isotopic Composition

description: Rainwater samples were collected using a Palmex RS1 rain sampler (Gröning et al. 2012), installed in a relatively unshielded location on the aft, starboard railing of the navigation deck at ~17.5 m.a.s.l.. The location was chosen to limit the effects of wind interactions with the ship and to avoid obstruction of the area above the sampler by the main mast. The sampler funnel was cleaned regularly. Immediately after rainfall ended, samples were transferred to 2-mL vials, which were filled to minimize headspace, sealed with parafilm, and stored in a refrigerator at ~4° C during the cruise, at ambient temperatures for shipment, and then again in a refrigerator at ~4° C prior to lab measurement. Samples were processed on a Picarro L-2140-i at the University of New Mexico Center for Stable Isotopes. In total 15 rain samples were collected on the Meteor from 20 January to 19 February, representing 15 separate rain events. Bulk uncertainties are ±0.20 and ±0.51 per mil for δ18O and δD respectively. Dataset contains rain onset and rain end times and locations for each event.
DOI: 10.5281/zenodo.8319390
title: WRF-Chem output- concentrations for the two simulations: Business as Usual and COVID for the two periods, March-April and May

description: The WRF-Chem model was utilized to calculate the changes in O3 chemistry during the COVID lockdown period. We ran two simulations: (1) Business As Usual (BAU) and (2) COVID for the lockdown (30 March to 12 April 2020) and relaxation (18- 25 to 30 May 2020) periods. Here, we provide modelled concentrations for several chemical and physical species for 30 March to 12 April (only weekdays) and 18 to 30 May (only weekdays) for both simulations, BAU and COVID, over the AMB area during the morning (6-8 UTC), afternoon (13-15 UTC) and evening (19-21 UTC) hours. We also provide the WRF-Chem output used to create the air parcel trajectories and the ozone concentrations from the Metropolitan Area of Barcelona to the Pyrenees.
DOI: 10.6084/m9.figshare.22109546
title: Supplementary Material for: Early onset outlet obstruction of a temporary diverting loop ileostomy secondary to urinary retention

description: A mechanical obstruction is not a physiological entity and when it occurs within the 30-day postoperative period, is called an early postoperative small bowel obstruction. Kinking of small bowel segments at the ileostomy outlet secondary to a distended bladder is an unusual source of early postoperative small bowel obstruction. A 36-year-old female underwent a redo J-Pouch surgery and creation of loop ileostomy after pouch failure related to recurrent small bowel obstruction and perianal fistulae. Her foley catheter was removed on postoperative day three and she passed a trial of void test. On postoperative day six, the abdomen became progressively more distended. CT imaging with IV contrast showed small bowel distension extending to the midline anterior to the urinary bladder where it demonstrated a narrowed lumen. These findings were thought to be the cause of small bowel obstruction at this level before the ileostomy. Immediately after CT, a foley catheter was applied with which two liters of urine was removed and consequently gas and stool were observed in the ostomy soon thereafter. Although rare, urinary retention may cause intestinal obstruction, especially in the presence of a loop ileostomy in close proximity.
DOI: 10.6084/m9.figshare.22353790
title: Supplementary Material for: Candesartan-induced enteropathy that mimics celiac disease in a 90-year-old patient

description: Sprue-like enteropathy (SLE) is a clinical syndrome similar to celiac disease and has been associated with the use of various angiotensin receptor blockers (ARB), a class of medications frequently used in the management of hypertension. Currently, there has only been one documented case report which has observed this occurrence with the use of the ARB Candesartan. A 90-year-old female patient presented with chronic diarrhea and weight loss of unclear etiology. Diagnostic esophagogastroduodenoscopy and ileocolonoscopy were macroscopically unremarkable but histological samples revealed complete villous atrophy, chronic mucosal inflammation and intraepithelial T-lymphocytic infiltration. However, serological studies could not confirm celiac disease as a cause for the patient’s symptoms of malabsorption. After exclusion of other intestinal inflammation etiologies with noted ongoing candesartan use, the diagnosis of SLE was made and candesartan therapy was discontinued. Additionally, we decided to initiate a lactose-free diet. Clinical remission was achieved without any recurrences. Candesartan is a commonly prescribed therapeutic agent in the treatment of hypertension. Our case underlines the importance of considering it as a potential cause for unexplained symptoms of malabsorption.
DOI: 10.6084/m9.figshare.22598449
title: Supplementary Material for: Association of non-melanoma skin cancers, melanoma and merkel cell carcinoma with dermatologic medications, a case control pharmacovigilance study of the FDA Adverse Events Reporting System

description: Background: Medications used in the treatment of dermatologic conditions have been associated with squamous cell carcinoma (SCC), basal cell carcinoma (BCC), melanoma and Merkel cell carcinoma (MCC). Objective: To examine the relationship between systemic dermatologic medications and skin cancer in the FDA Adverse Event Reporting System (FAERS). Methods: Case control analyses were performed in FAERS from 1968-2021 to examine the reporting odds ratios (ROR) for SCC, BCC, melanoma and MCC. Results: The oral immunosuppressants were all associated with increased ROR of SCC, BCC, melanoma and MCC. Azathioprine had the highest ROR for SCC (34.13, 95%CI 29.07-40.08), BCC (21.15, 95%CI 20.63-25.98) and MCC (44.76, 95%CI 31.52-63.55), while quinacrine and guselkumab had the highest ROR for melanoma (13.14, 95%CI 1.84-93.89 vs. 12.73, 95%CI 10.60-15.30 respectively). The TNF-a inhibitors were associated with an increased ROR for all skin cancers investigated. Conclusions: The oral immunosuppressants and many biologic medications were associated with an increased ROR of skin cancers including TNF-alpha inhibitors (etanercept, adalimumab, infliximab), IL-23 or IL 12/23 inhibitors (ustekinumab, risankizumab), and the CD-20 inhibitor rituximab, but not dupilumab or IL-17 inhibitors.
DOI: 10.6084/m9.figshare.22678132
title: A comprehensive dataset of animal-associated sarbecoviruses

description: Zoonotic spillover of sarbecoviruses (SarbeCoVs) from animals to humans under natural conditions has led to two large-scale pandemics, the severe acute respiratory syndrome (SARS) pandemic in 2003 and the ongoing COVID-19 pandemic. Knowledge of the genetic diversity, geographical distribution, and host specificity of sarbecoviruses is therefore of interest in terms of pandemic surveillance and origin tracing of SARS-CoV and SARS-CoV-2. This study presents a comprehensive and up-to-date repository of publicly available animal-associated SarbeCoVs, covering 1,535 viruses identified from 68 animal species distributed in 43 countries worldwide. Relevant meta-information, such as host species, sampling time and location, was manually curated and included in the dataset to facilitate further research on the potential patterns of viral diversity and ecological characteristics. In addition, the dataset also provides well-annotated sequence sets of receptor-binding domains (RBDs) and receptor-binding motifs (RBMs) for the scientific community to highlight the potential determinants of successful cross-species transmission that could be helpful for risk estimation and strategic design of future emerging infectious disease control and prevention.
DOI: 10.6084/m9.figshare.23259359
title: Supplementary Material for: Hybrid Method for Peritoneal Dialysis Catheter Insertion: A New Technique for Improved Outcomes and Reduced Costs

description: Background: Peritoneal Dialysis (PD) is a well-established treatment choice for end-stage kidney disease (ESKD). While there are several methods for PD catheter insertion, they each have limitations. In this study, we present a new hybrid method for PD catheter insertion and compare it to the conventional laparoscopic method. Methods: This retrospective study included 171 patients who were undergoing their first PD catheter insertion, and a total of 20% of the enrolled patients had a past medical history of abdominal surgery. Out of these, 101 patients underwent the laparoscopic method and 70 underwent a new invented hybrid method. The study aimed to compare the surgical outcomes, incidence of early and late complications, hospital stay, and medical expenses between the two groups. Results: There were no notable differences in basic demographic features and comorbid conditions between the two groups. The results of our data revealed that the hybrid group had a significantly shorter break-in period and did not require temporary hemodialysis. Additionally, length of hospital stay and medical costs were significantly lower in the hybrid group. (all p&lt;0.05) The incidence of early complications was lower in the hybrid group, while the incidence of late complications was comparable between the two groups. Conclusion: Our study demonstrates that the hybrid method of PD catheter insertion provides a safe and efficient alternative to the traditional laparoscopic method, enabling urgent-start PD and reducing hospital stays and medical expenses. Our findings support the use of the hybrid method as a new standard of care for ESKD patients undergoing PD catheter insertion.
DOI: 10.6084/m9.figshare.23579445
title: Supplementary Material for: Association of pesticide exposure with cognitive function in farmers

description: Introduction Organophosphate and carbamate are two types of pesticides that can induce cholinesterase suppression in humans. These lead to poisoning symptoms including muscle paralysis and respiratory depression in acute settings. In chronic settings, the mechanism of organophosphate and carbamate poisoning is still openly discussed. Accordingly, this study aimed to identify any correlations between erythrocyte cholinesterase and associations between type of pesticides with cognitive performance of the subjects. Methods This cross-sectional study was conducted in two sampling periods (July 2017 and October 2018) in Ngablak Districts, Magelang Regency, Central Java, Indonesia. The study subjects were farmers with history of pesticide exposure. Cholinesterase levels (ChE) were analyzed from blood samples. Cognitive performance was assessed using the Mini Mental State Examination (MMSE) and Stroop Test. Results In total, 151 subjects aged between 23 – 91 years old were included. The long-term organophosphate exposure group had significantly lower MMSE scores compared with other types of pesticides, but not in carbamate (p=0.017). After comparing “organophosphate only” and “carbamate only” groups, there were significant differences in MMSE scores (p=0.018) but not in blood ChE levels (p=0.286). Detailed assessment in MMSE domains showed significantly lower scores for orientation, attention, and registration domains (p &lt; 0.05) in the organophosphate group. There were no significant associations between types of pesticides and blood ChE levels with the Stroop Test results (p &gt; 0.05). Conclusions Long-term organophosphate exposure could produce lower cognitive function and the insignificant association between blood ChE levels to MMSE could lead to non-cholinergic pathways as its underlying pathology.