cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7648802
title: Patient reported outcome measures, load-induced blood marker kinetics, and ambulatory knee load in patients with medial compartment knee osteoarthritis

description: The goal of this study was (i) to quantify the mechanoresponse of this array of potential blood markers for joint pathology (COMP, MMP-1, MMP-3, MMP-9, CPII, C2C, C2C/CPII, ADAMTS-4, PRG-4, IL-6 and resistin) to a walking stress test in patients with knee OA and to determine the correlation (ii) among the kinetics of these blood markers, (iii) with accumulated knee load during the walking stress, and (iv) with patient reported osteoarthritis outcome and QoL. The dataset includes 24 patients with knee osteoarthritis scheduled to receive high tibial osteotomy. All participants completed questionnaires, and a walking stress test with six blood samples analyzed using enzyme-linked immunosorbent assays for cartilage oligomeric matrix protein (COMP), matrix metalloproteinases (MMP)-1, -3, and -9, epitope resulting from cleavage of type II collagen by collagenases (C2C), type II procollagen (CPII), interleukin (IL)-6, proteoglycan (PRG)-4, A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS)-4, and resistin, and gait analysis. Joint load was computed from gait analysis data and musculoskeletal modelling in AnyBody Modeling System (AnyBody Technology A/S). Discrete loading parameters were extracted for each step using an inhouse algorithm written in Matlab. The detailed experimental protocol of the umbrella study has been described in Mündermann A, Vach W, Pagenstert G, Egloff C, Nüesch C. Assessing in vivo articular cartilage mechanosensitivity as outcome of high tibial osteotomy in patients with medial compartment osteoarthritis: Experimental protocol. Osteoarthr Cartil Open. 2020 Feb 24;2(2):100043. doi: 10.1016/j.ocarto.2020.100043. PMID: 36474590; PMCID: PMC9718245. The study is registered on clinicaltrials.gov (identifier NCT02622204). The method for computing joint loading has been described in detail in De Pieri E, Nüesch C, Pagenstert G, Viehweger E, Egloff C, Mündermann A. High tibial osteotomy effectively redistributes compressive knee loads during walking. J Orthop Res. 2022 Jun 22. doi: 10.1002/jor.25403. Epub ahead of print. PMID: 35730475.
description: {"references": ["M\u00fcndermann, A., Vach, W., Pagenster, G., Egloff, C. & N\u00fcesch, C. Assessing in vivo articular cartilage mechanosensitivity as outcome of high tibial osteotomy in patients with medial compartment osteoarthritis: Experimental protocol. Osteoarthritis and Cartilage Open 2, 100043, doi:10.1016/j.ocarto.2020.100043 (2020).", "De Pieri E, N\u00fcesch C, Pagenstert G, Viehweger E, Egloff C, M\u00fcndermann A. High tibial osteotomy effectively redistributes compressive knee loads during walking. J Orthop Res. 2022 Jun 22. doi: 10.1002/jor.25403. Epub ahead of print. PMID: 35730475."]}
DOI: 10.5281/zenodo.8191584
title: Molecular dynamics simulation data 1: Structure of the connexin-43 gap junction channel in a putative closed state

description: Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2 The dataset includes: 1. The starting coordinates, topology, MD inputs 2. Production run gromacs trajectories for the Cx43 gap junction channel
description: {"references": ["Qi, Acosta-Gutierrez et al. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2"]}
DOI: 10.5281/zenodo.8192013
title: Molecular dynamics simulation data 2: Structure of the connexin-43 gap junction channel in a putative closed state

description: Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2 The dataset includes: 1. The starting coordinates, topology, MD inputs 2. Production run gromacs trajectories for the Cx43 hemichannel
description: {"references": ["Qi, Acosta-Gutierrez et al. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2"]}
DOI: 10.5281/zenodo.8193133
title: Molecular dynamics simulation data 3: Structure of the connexin-43 gap junction channel in a putative closed state

description: Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2 The dataset includes: Production run gromacs trajectories for the Cx43 gap junction channel (500 mV)
description: {"references": ["Qi, Acosta-Gutierrez et al. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2"]}
DOI: 10.6084/m9.figshare.13365140
title: Supplementary Material for: Language Impairment with a Partial Duplication of <b><i>DOCK8</i></b>

description: Duplications of the distal region of the short arm of chromosome 9 are rare, but are associated with learning disabilities and behavioral disturbances. We report in detail the cognitive and language features of a child with a duplication in the 9p24.3 region, arr[hg19] 9p24.3(266,045–459,076)×3. The proband exhibits marked expressive and receptive problems, which affect both structural and functional aspects of language. These problems might result from a severe underlying deficit in working memory. Regarding the molecular causes of the observed symptoms, they might result from the altered expression of selected genes involved in procedural learning, particularly some of components of the SLIT/ROBO/FOXP2 network, strongly related to the development and evolution of language. Dysregulation of specific components of this network can result in turn from an altered interaction between DOCK8, affected by the microduplication, and CDC42, acting as the hub component of the network encompassing language-related genes.
DOI: 10.6084/m9.figshare.21333069
title: Supplementary Material for: Efficacy of individualized homeopathic medicines in treatment of cervical spondylosis: Double-blind, randomized, placebo-controlled trial

description: Introduction: Cervical spondylosis (CS) is a degenerative condition of the cervical spine, with approximately 80-90% of people suffering from disc degeneration by the age of 50 years. This trial attempts at evaluating the efficacy of individualized homeopathic medicines (IHMs) against placebos in the treatment of CS. Methods: A 3-months, double-blind, randomized, placebo-controlled trial was conducted at the Organon of Medicine outpatient department of the National Institute of Homoeopathy, India. Patients were randomized to receive either IHMs (n=70) or identical-looking placebos (n=70) in the mutual context of concomitant conservative and standard physiotherapeutic care. Primary outcome measures were 0-10 Numeric Rating Scales (NRSs) for pain, stiffness, numbness, tingling, weakness, and vertigo, and the secondary outcome was Neck Disability Index (NDI); measured at baseline and every month, until 3 months. The intention-to-treat sample was analyzed to detect group differences and effect sizes. Results: Overall, improvements were clinically significant and higher in the IHMs group than placebo, but group differences were statistically non-significant with small effect sizes (all P&gt;0.05, two-way repeated measure analysis of variance). After 2 months of time points, improvements observed in the IHMs group were significantly higher than placebo on a few occasions (e.g., pain NRS: P&lt;0.001; stiffness NRS: P=0.024; weakness NRS: P=0.003). Sulfur (n=21; 15%) was the most frequently prescribed medication. No harm, unintended effects, or any serious adverse events were reported from either group. Conclusions: An encouraging, but non-significant direction of effect was elicited favoring IHMs against placebos in the treatment of CS. Trial registration: CTRI/2018/10/016156; UTN: U1111-1221-8064
DOI: 10.6084/m9.figshare.21367764
title: Supplementary Material for: Effectiveness of Progressive Resistance Training in Parkinson’s Disease: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The aim of this study was to systematically explore progressive resistance training (PRT) effects in Parkinson’s disease (PD). <b><i>Methods:</i></b> Eligible literature was systematically searched from five electronic databases (PubMed, Web of Science, Ovid, Wanfang, and China National Knowledge Infrastructure) from their inception to February 2022. Included studies were selected based on strict eligibility criteria. RevMan 5.3 software was used for statistical analysis. <b><i>Results:</i></b> A total of 14 studies with 761 PD patients were selected for eligibility in this systematic review and meta-analysis. A total of 383 performed trunk or upper or lower extremity PRT and 378 underwent balance training, modified fitness counts, or did not change their lifestyle. The results demonstrated positive PRT effect on freezing of gait (standardized mean difference [SMD] = −0.55, 95% CI = −0.95 to −0.16, <i>p</i> = 0.006), muscular strength (SMD = 1.9, 95% CI = 0.55–3.24, <i>p</i> = 0.006), and quality of life (SMD = −0.86, 95% CI = −1.66 to −0.06, <i>p</i> = 0.04) in adults with PD compared with other training programmes but not for gait velocity, stride length, timed up and go test, and Berg Balance Scale. <b><i>Conclusions:</i></b> This meta-analysis revealed that PRT had positive effects on freezing of gait, muscle strength, and improved quality of life during rehabilitation in PD patients.
DOI: 10.6084/m9.figshare.21388128
title: Supplementary Material for: Effect of Traditional Chinese Medicine on Psoriasis Vulgaris: A Meta Analysis and Systematic Review

description: Background: Psoriasis is a chronic, inflammatory autoimmune skin disease that affects 2%–3% of the world’s population. Lesions are mainly found on the limbs, trunk, and scalp, but may also affect other parts of the body, and the cause is not yet known. The chronic and relapsing nature of psoriasis makes it one of the most complex and important diseases in current dermatology research. Methods: The search was conducted using PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Internet, Wanfang Data, VIP journals database, and Chinese biomedical literature database (CBM). The retrieval time limit was from the establishment of the database to January 2021. The quality of the selected literature were evaluated, and ReView Manager 5.3 was used for Meta-analysis after randomized controlled trials were filtered. Results: Finally, 16 randomized controlled trials involving 1967 patients were included. The total effective rate (OR =3.68,95% CI[2.73,4.95], P&lt;0.00001), cure rate (OR =2.01, 95% CI[1.62,2.49]c, P &lt;0.00001), and PASI score (OR =-1.83, 95% CI[-2.39, -1.26], P &lt;0.00001) of the traditional Chinese medicine (TCM) were superior than the Diyin tablet.. Conclusion: In the treatment of psoriasis, traditional Chinese medicine (TCM) shows higher efficacy than the Diyin tablet. However, due to the limitations of the included literature, we still need more double-blind, placebo-controlled trials with large samples and multiple centers to provide high-quality clinical evidence.
DOI: 10.6084/m9.figshare.21436737
title: Supplementary Material for: Low baseline CXCL9 predicts early progressive disease in unresectable HCC with atezolizumab plus bevacizumab treatment

description: Introduction: Atezolizumab plus bevacizumab treatment is highly effective in patients with unresectable hepatocellular carcinoma (HCC). However, progressive disease (PD) occurs in approximately 20% of HCC patients treated with atezolizumab plus bevacizumab, resulting in a poor prognosis. Thus, the prediction and early detection of HCC is crucial. Methods: Patients with unresectable HCC treated with atezolizumab plus bevacizumab and had baseline preserved serum (n = 68) were screened and classified according to their PD, six weeks after treatment initiation (early PD; n = 13). Of these, four patients each with and without early PD were selected for cytokine array and genetic analyses. The identified factors were validated in the validated cohort (n = 60) and evaluated in patients treated with lenvatinib. Results: No significant differences were observed in the genetic alterations in circulating tumor DNA. Cytokine array data revealed that baseline MIG (CXCL9), ENA-78, and RANTES differed substantially between patients with and without early PD. Subsequent analysis in the validation cohort revealed that baseline CXCL9 was significantly lower in patients with early PD than that in patients without early PD, and the best cut-off value of serum CXCL9 to predict early PD was 333 pg/mL (sensitivity: 0.600, specificity: 0.923, AUC = 0.75). In patients with lower serum CXCL9 (&lt; 333 pg/mL), 35.3% (12/34) experienced early PD with atezolizumab plus bevacizumab, while progression-free survival (PFS) was significantly shorter relative to that in patients without (median PFS, 126 days vs 227 days; HR: 2.41, 95% CI: 1.22–4.80, p = 0.0084). While patients with objective response to lenvatinib had significantly lower CXCL9 levels compared with those of patients without. Conclusion: Baseline low serum CXCL9 (&lt; 333 pg/mL) levels may predict early PD in patients with unresectable HCC treated with atezolizumab plus bevacizumab.
DOI: 10.6084/m9.figshare.21673889
title: Supplementary Material for: Neurochemical Correlates of Cue Reactivity in Individuals with Excessive Smartphone Use

description: <b><i>Background:</i></b> Excessive smartphone use (ESU), that is, a pattern of smartphone use that shows specific features of addictive behavior, has increasingly attracted societal and scientific interest in the past years. On the neurobiological level, ESU has recently been related to structural and functional variation in reward and salience processing networks, as shown by, for example, aberrant patterns of neural activity elicited by specific smartphone cues. <b><i>Objectives:</i></b> Expanding on these findings, using cross-modal correlations of magnetic resonance imaging (MRI)-based measures with nuclear imaging-derived estimates, we aimed at identifying neurochemical pathways that are related to ESU. <b><i>Methods:</i></b> Cross-modal correlations between functional MRI data derived from a cue-reactivity task administered in persons with and without ESU and specific PET/SPECT receptor probability maps. <b><i>Results:</i></b> The endogenous mu-opioid receptor (MOR) system was found to be significantly (FDR-corrected) correlated with fMRI data, and z-transformed correlation coefficients showed an association (albeit nonsignificant after FDR-correction) between MOR and the Smartphone Addiction Inventory “withdrawal” dimension. <b><i>Conclusions:</i></b> We could identify the MOR system as a neurochemical pathway associated with ESU. The MOR system is closely linked to the reward system, which has been recognized as a key player in addictive disorders. Together with its potential link to withdrawal, the MOR system hints toward a biologically highly relevant marker, which should be taken into consideration in the ongoing scientific discussion on technology-related addictive behaviors.
DOI: 10.6084/m9.figshare.21863142
title: Supplementary Material for: National Weekly SARS-CoV-2 RT-PCR Screening of All Workers in Long-Term Care Facilities Associated with Decrease in Resident Mortality Rate

description: Introduction Outbreaks of COVID-19 in long-term care facilities (LTCFs) have resulted mainly from disease transmission by asymptomatic health care workers. This study examines whether routine screening tests carried out on health care workers can help in reducing COVID-19 outbreaks, morbidity, and mortality of LTCF residents. Methods The study followed a weekly, nationwide, government-funded screening program of LTCF personnel for SARS-CoV-2, by using reverse transcription polymerase chain reaction as the main testing technology. It included all residents and employees in Israeli LTCFs who were screened weekly during the second wave of COVID-19, during the time period between July 13, 2020, and November 21, 2020. Results During the study period, 1,107 LTCFs were screened on a weekly basis, including 62,159 HCWs and 100,046 residents. The program screened a median of 55,282 (Range 16,249, min 45,910, max 62,159) employees per week, 0.05-1.5% of which were positive for SARS-CoV-2. LTCF mortality in the first wave accounted for 45.3% of all COVID-19 deaths recorded nationally (252 of 556), and in the second wave this ratio was reduced to 30.3% (709 of 2,337) representing a reduction of 33.8% in expected mortality (P&lt;0.001). A significant reduction was detected also in hospitalization rate (13.59% vs. 11.41%, p&lt;0.001) and elder (≥75 years-old) mortality rate (52.89% vs. 41.42%, p&lt;0.001). 214 outbreaks in the second wave were avoided by early identification of SARS-CoV-2 positive HCWs and successful prevention of subsequent infections in the facility. Conclusions and relevance Routine weekly SARS-CoV-2 RT-PCR testing of LTCF employees was associated with reduced national LTCF residents’ hospitalizations and mortality rate.
DOI: 10.6084/m9.figshare.21878604
title: Supplementary Material for: <b><i>CYP1B1</i></b> Genetic Variants (rs10916 and rs2855658) Are Associated with Increased Risk of Ischemic Stroke in Chinese Han Population

description: <b><i>Introduction:</i></b> Ischemic stroke (IS) is an extremely complex disease caused by the combined action of multiple environmental and genetic factors. <i>CYP1B1</i> is a member of the cytochrome P450 protein family, and it is an important human drug-metabolizing enzymes. We aimed to explore the association between <i>CYP1B1</i> genetic variants and IS risk in Chinese Han population. <b><i>Methods:</i></b> We recruited 1,150 participants to conduct a “case-control” study. The assessment of association between candidate <i>CYP1B1</i> genetic variants (rs2855658, rs10916, rs162560, rs2567206) and IS risk was performed by SNPStats online software. In addition, false-positive report probability analysis was used to detect whether the positive findings were just chance or noteworthy observations. Finally, the interaction of candidate SNPs in IS risk was evaluated by multifactor dimensionality reduction. <b><i>Results:</i></b> The results showed that <i>CYP1B1</i>-rs2855658 was a risk factor for IS among ≥60-year-old (dominant: <i>p</i> = 0.034; overdominant: <i>p</i> = 0.026), smoking (heterozygote: <i>p</i> = 0.009; dominant: <i>p</i> = 0.004; overdominant: <i>p</i> = 0.012; log-additive: <i>p</i> = 0.003), and drinking participants (homozygous: <i>p</i> = 0.036; dominant: <i>p</i> = 0.019; recessive: <i>p</i> = 0.012; log-additive: <i>p</i> = 0.006). <i>CYP1B1</i>-rs10916 also was a risk factor for IS patients among ≥60-year-old (heterozygote: <i>p</i> = 0.047; overdominant: <i>p</i> = 0.048), smoking (dominant: <i>p</i> = 0.050; overdominant: <i>p</i> = 0.049), and drinking participants (dominant: <i>p</i> = 0.019; overdominant: <i>p</i> = 0.038; log-additive: <i>p</i> = 0.013). <b><i>Conclusion:</i></b> <i>CYP1B1</i>-rs10916 and <i>CYP1B1</i>-rs2855658 can increase the IS risk in Chinese Han population who are ≥60 years old, smoking, or drinking alcohol.
DOI: 10.6084/m9.figshare.22047821
title: Supplementary Material for: Phytochemical Comparison of Medicinal Cannabis Extracts and Study of Their CYP-Mediated Interactions with Coumarinic Oral Anticoagulants

description: <b><i>Introduction:</i></b> Treatment with cannabis extracts for a variety of diseases has gained popularity. However, differences in herb-drug interaction potential of extracts from different plant sources are poorly understood. In this study, we provide a characterization of cannabis extracts prepared from four cannabis chemotypes and an in vitro assessment of their Cytochrome P450 (CYP)-mediated herb-drug interaction profiles. <b><i>Methods:</i></b> Plant extracts were either commercially obtained or prepared using ethanol as solvent, followed by overnight decarboxylation in a reflux condenser system. The extracts were characterized for their cannabinoid content using NMR and HPLC-PDA-ELSD-ESIMS. CYP inhibition studies with the cannabis extracts and pure cannabinoids (tetrahydrocannabinol [THC] and cannabidiol [CBD]) were performed using pooled, mixed gender human liver microsomes. Tolbutamide and testosterone were used as specific substrates to assess the inhibitory potential of the extracts on CYP2C9 and CYP3A4, and the coumarinic oral anticoagulants warfarin, phenprocoumon, and acenocoumarol were studied as model compounds since in vivo herb-drug interactions have previously been reported for this compound class. <b><i>Results:</i></b> In accordance with the plant chemotypes, two extracts were rich in THC and CBD (at different proportions); one extract contained mostly CBD and the other mostly cannabigerol (CBG). Residual amounts of the corresponding acids were found in all extracts. The extracts with a single major cannabinoid (CBD or CBG) inhibited CYP2C9- and CYP3A4-mediated metabolism stronger than the extracts containing both major cannabinoids (THC and CBD). The inhibition of CYP3A4 and CYP2C9 by the extract containing mostly CBD was comparable to their inhibition by pure CBD. In contrast, the inhibitory potency of extracts containing both THC and CBD did not correspond to the combined inhibitory potency of pure THC and CBD. Although being structural analogs, the three coumarin derivatives displayed major differences in their herb-drug interaction profiles with the cannabis extracts and the pure cannabinoids. <b><i>Conclusion:</i></b> Despite the fact that cannabinoids are the major components in ethanolic, decarboxylated cannabis extracts, it is difficult to foresee their herb-drug interaction profiles. Our in vitro data and the literature-based evidence on in vivo interactions indicate that cannabis extracts should be used cautiously when co-administered with drugs exhibiting a narrow therapeutic window, such as coumarinic anticoagulants, regardless of the cannabis chemotype used for extract preparation.