cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22926227
title: Supplementary Material for: Optical genome mapping for a patient with a congenital disorder and chromosomal translocation

description: We performed optical genome mapping (OGM), a newly developed cytogenetic technique, for a patient with a disorder of sex development (DSD) and a 46,XX,t(9;11)(p22;p13) karyotype. The results of OGM were validated using other methods. OGM detected a 9;11 reciprocal translocation and successfully mapped its breakpoints to small regions of 0.9–12.3 kb. OGM identified 46 additional small structural variants, only three of which were detected by array-based comparative genomic hybridization. OGM suggested the presence of complex rearrangements on chromosome 10; however, these variants appeared to be artifacts. The 9;11 translocation was unlikely to be associated with DSD, while the pathogenicity of the other structural variants remained unknown. These results indicate that OGM is a powerful tool for detecting and characterizing chromosomal structural variations, although the current methods of OGM data analyses need to be improved.
DOI: 10.6084/m9.figshare.23261561
title: Supplementary Material for: Complete Response to Enfortumab Vedotin in a Hemodialysis Patient with Metastatic Urothelial Carcinoma: A Case Report

description: Enfortumab vedotin (EV) is an antibody-drug conjugate and a promising agent for metastatic urothelial carcinoma (mUC). However, evaluations in end-stage renal disease patients undergoing hemodialysis are unreported. Here, we report such a case. A 74-year-old woman with mUC, on hemodialysis for complete urinary tract extirpation, was diagnosed with multiple pulmonary metastases after treatment with gemcitabine-carboplatin followed by pembrolizumab. As third-line therapy, she received a standard dose of EV. She achieved complete response after 2 cycles without grade 3 or higher adverse events, demonstrating the utility of EV in this setting.
DOI: 10.6084/m9.figshare.23541147
title: Supplementary Material for: Varieties of Religious and Spiritual Struggles by Type of Mental Disorder: A Qualitative Approach

description: <b><i>Introduction:</i></b> Little is known about types of religious/spiritual (R/S) struggles with regard to various diagnostic groups in mental health care. The current qualitative study aims to give an impression of R/S struggles as observed in six diagnostic groups in clinical mental health care. <b><i>Methods:</i></b> Inductive thematic content analysis was applied to 34 semi-structured interviews. The interviews were performed among (day) clinical mental health care patients in two institutions. <b><i>Results:</i></b> Among patients with depression, a lack of positive R/S experiences, isolation, and feelings of guilt and shame were present. Those with cluster C and anxiety disorders reported uncertainty toward God and faith and R/S reticence. Psychotic disorders were accompanied by impressive R/S experiences, reticence to share these, and mistrust toward health professionals. Patients with bipolar disorder struggled with the interpretation of their R/S experiences and with both attraction and distance toward R/S. Cluster B patients showed ambivalence and anger toward God and others, and some reported existential tiredness. Patients with autism mentioned doubts and troubles with religious beliefs. In all groups, many patients had questions like “why?” or “where is God?” <b><i>Conclusion:</i></b> R/S struggles to some extent may be the language of the illness. Mental health professionals are recommended to take this into account, taking heed of the content of individual R/S struggles and considering using R/S interventions.
DOI: 10.6084/m9.figshare.23551446
title: Supplementary Material for: Non-surgical site pain in women following breast cancer surgery: a systematic review and meta-analysis

description: Background: Chronic pain after breast cancer surgery affects up to 60% of patients. Evidence supports the fact that pain out-with the surgical site is a significant issue. This systematic review and meta-analysis sought to evaluate the prevalence of non-surgical site pain (NSSP) in women after breast cancer surgery at 6 months post-operatively. Methods: Adult women with a confirmed breast cancer diagnosis who had undergone breast cancer surgery were identified. The outcome pursued was pain out-with the surgical site measured on either NRS/VRS or VAS rating scale. CENTRAL, Embase, PubMed, MEDLINE, CINAHL, PsycInfo, Web of Science (WoS) and Scopus were searched to identify studies that examined NSSP after breast cancer surgery at 6 months. Data was gathered via pre-piloted Excel forms and analysed both quantitively and qualitatively. Meta-analysis was carried out using a random effects model to assess risk difference with 95% confidence interval (CI). Results: A total of sixteen studies were identified for inclusion. Eleven studies failed to provide sufficient data and consequently were analysed qualitatively. Five studies were adequate for quantitative analysis, including a total of 995 patients. Meta-analysis identified a risk difference of 18% (95%CI: 5 to 31%) between patients who had breast cancer surgery and a reference, however this is low quality evidence. Conclusion: This review has highlighted that breast cancer surgery increases the risk of pain out-with the surgical site post-operatively. It was additionally identified that NSSP data is often gathered in research yet rarely presented in results or highlighted as a primary outcome. As quality of evidence was low, research specifying NSSP as a primary outcome is required to provide more certainty.
DOI: 10.6084/m9.figshare.23559966
title: Supplementary Material for: Hepatic fibrosis evaluated in patients with type 2 diabetes with and without chronic kidney disease

description: Background. Non-alcoholic fatty liver disease (NAFLD), and particularly liver fibrosis, has been suggested as a risk factor of chronic kidney disease (CKD). Given that NAFLD affects every fourth person globally, better insight is needed. Our aim was to investigate the association between hepatic fibrosis and CKD in patients with type 2 diabetes and to compare different methods for diagnosing liver fibrosis in this study population. Methods. Cross-sectional study including patients with type 2 diabetes with CKD Stages 3–5 (N=50) or without CKD (N=50). CKD was defined as eGFR &lt;60 mL/min/1.73 m2 with or without proteinuria. Three methods were used to detect significant liver fibrosis defined as either ≥8 kilopascal measured by transient elastography (FibroScan®), fibrosis-4 (FIB-4) score ≥2.67 or NAFLD fibrosis score (NFS) &gt;0.675. Results. Significant liver fibrosis was found in 38% and 28% of the patients with and without CKD, respectively, using at least one of the three methods. Both FIB-4 score and NFS were significantly higher in patients with CKD (P&lt;0.0009 and P&lt;0.0001, respectively), although insignificant after adjustments for age, sex, BMI, and duration of diabetes. In patients without CKD, a significant association between steatosis and fibrosis was observed (P=0.0007). Discussion/ Conclusion. Our data do not support any strong independent association between liver fibrosis and established CKD as assessed by FibroScan, FIB-4 score and NFS, respectively.
DOI: 10.6084/m9.figshare.23581932
title: learn2therm relational database

description: DescriptionA dataset of prokaryotes, proteins, organism pairs, and protein homologous pairs across temperature, up to 102 celsius. The data is presented in the form of a duckdb relational database, and contains 24 million proteins belonging to 9.5k prokaryotes. The proteins have been pairs by homology, producing 70 millions pairs of mesophilic-thermophilic proteins. Please see the README contained within the zipped file for instructions on usage and access of the relational data file. See the code repository, in this Figshare project and the main paper (TODO) for details on how this data was created<br>Contents`learn2therm.ddb` - duckdb file containing the data`environment.yaml` - minimal conda environment necessary to access the data`README.md` - instructions on accessing the data, including some example queries. Also contains the schema of the tables in the relational database.- `csvs/` , Colon-seperated dump files from the data tablesAll material in this project:- Database pipeline source code: 10.6084/m9.figshare.23589390- (here) Database: 10.6084/m9.figshare.23581932- Classifier source code: 10.6084/m9.figshare.23589210- Trained classifier: 10.6084/m9.figshare.23582325<br>ManuscriptTODO
DOI: 10.6084/m9.figshare.23598711
title: Supplementary Material for: Adiponectin Levels in Inflammatory Bowel Disease – A Systematic Review and Meta-analysis

description: Introduction: Adipose tissue plays an important role in the pathogenesis of inflammatory conditions. The role of adipokines in inflammatory bowel disease (IBD) has been evaluated in the current literature with conflicting results. The aim of this study was to evaluate adiponectin levels in IBD patients, including Crohn's disease (CD) and ulcerative colitis (UC), compared to controls, as well as further subgroup analyses. Hence, assessing the potential role of adiponectin as a surrogate marker. Methods: We performed a systematic electronic search on PubMed, EMBASE, Scopus and Cochrane Library, including observational or interventional studies evaluating serum or plasma adiponectin levels in IBD patients on humans. The primary summary outcome was the mean difference (MD) in serum or plasma adiponectin levels between IBD patients vs. controls. Subgroups analyses were conducted involving adiponectin levels in CD and UC compared to controls, as well as CD compared to UC. Results: A total of 20 studies were included in our qualitative synthesis and 14 studies in our quantitative synthesis, with a total population sample of 2,085 subjects. No significant MD in serum adiponectin levels was observed between IBD patients vs. controls (-1.331 [95% CI -3.135–0.472]), UC patients vs. controls (-0.213 [95% CI -1.898–1.472]), and CD patients vs. controls (-0.851 [95% CI -2.263–0.561]). Nevertheless, a significant MD was found between UC patients vs. CD patients (0.859 [95% CI 0.097–1.622]). Conclusions: Serum adiponectin levels were not able to differentiate between IBD, UC and CD patients compared to controls. However, significantly higher serum adiponectin levels were observed in UC compared to CD patients.
DOI: 10.6084/m9.figshare.23600199
title: Supplementary Material for: Tolvaptan’s association with low risk of acute kidney injury in patients with advanced chronic kidney disease and acute decompensated heart failure

description: Introduction Furosemide, a loop diuretic, is often empirically used to treat acute decompensated heart failure (ADHF) initially. Conversely, decongestion using tolvaptan, an aquaretic, is thought to maintain renal function compared to furosemide. However, it has not been investigated in patients with advanced chronic kidney disease (CKD) at high risk of developing acute kidney injury (AKI). This study aimed to investigate AKI incidence using tolvaptan add-on treatment, compared to increased furosemide treatment for patients with ADHF complicated by advanced CKD. Methods We retrospectively studied patients with advanced CKD (estimated glomerular filtration rate [eGFR] &lt; 45 ml/min/1.73 m2) who developed ADHF under outpatient furosemide treatment. The exposure was set to tolvaptan add-on treatment, and the control was set to increased furosemide treatment. Results Of the 163 patients enrolled, 79 were in the tolvaptan group and 84 in the furosemide group. The mean age was 71.6 years, the percentage of males was 63.8%, the mean eGFR was 15.7 ml/min/1.73m2, and patients with CKD stage G5 were 61.9%. AKI incidence was 17.7% in the tolvaptan group and 42.9% in the furosemide group (odds ratio [95% confidence interval]: 0.34 [0.13 to 0.86], P = 0.023 in multivariate logistic regression analysis). Persistent AKI incidence was 11.8% in the tolvaptan group and 32.9% in the furosemide group (odds ratio [95% confidence interval]: 0.34 [0.10 to 1.06], P = 0.066 in the multinomial logit analysis). Discussion/Conclusion This study suggests that tolvaptan may be better than furosemide in patients with ADHF experiencing complicated advanced CKD.
DOI: 10.6084/m9.figshare.23640789
title: Supplementary Material for: Multicenter Phase II trial of lenvatinib plus hepatic intra-arterial infusion chemotherapy with cisplatin for advanced hepatocellular carcinoma: LEOPARD

description: Introduction: Hepatic arterial infusion chemotherapy (HAIC) with cisplatin and lenvatinib exhibit strong antitumor effects against advanced hepatocellular carcinoma (HCC). Higher antitumor activity is expected for the combination treatment. The aim of this trial was to evaluate the efficacy and safety of lenvatinib in combination with HAIC using cisplatin in patients with advanced HCC. Methods: In this multicenter, open-labeled, single-arm, phase II trial, patients with advanced HCC categorized as Child–Pugh class A with no prior history of systemic therapy were enrolled. Patients received lenvatinib plus HAIC with cisplatin (lenvatinib: 12 mg once daily for patients ≥60 kg, 8 mg once daily for patients &lt;60 kg; HAIC with cisplatin: 65 mg/m2, day 1, every 4 to 6 weeks, maximum of six cycles). The primary endpoint was the objective response rate (ORR) assessed using modified RECIST by the independent review committee. The secondary endpoints were the ORR assessed using RECIST v1.1, progression-free survival, overall survival, and frequency of adverse events associated with the treatment. Results: A total of 36 patients were enrolled between September 2018 and March 2020. In the 34 evaluable patients, the ORR assessed by the independent review committee using modified RECIST and RECISTv1.1 were 64.7% (95% confidence interval (CI): 46.5%–80.3%) and 45.7% (95% CI: 28.8%–63.4%), respectively. The median progression-free survival and overall survival were 6.3 months (95% CI: 5.1–7.9 months) and 17.2 months (95% CI: 10.9–not available, months), respectively. The main grade 3–4 adverse events were increased aspartate aminotransferase (34%), leukopenia (22%), increased alanine aminotransferase (19%), and hypertension (11%). Conclusion: Lenvatinib plus HAIC with cisplatin yielded a favorable ORR and overall survival and was well-tolerated in patients with advanced HCC. Further evaluation of this regimen in a phase III trial is warranted.
DOI: 10.6084/m9.figshare.23659857
title: Supplementary Material for: Delayed diagnosis of T-cell prolymphocytic leukemia: Approach to chronic lymphocytosis

description: We present a case of lymphocytosis assumed and managed initially as a chronic lymphocytic leukemia. Shortly after initial visit the patient’s condition deteriorated rapidly with hepatosplenomegaly, pleural effusion, ascites, and skin lesions. Flow cytometry (FC) showed the presence of clonal cell T-cell population, reported as T-cell lymphoma. Due to rapid clinical deterioration, urgent therapy with CHOEP (cyclophosphamide, doxorubicin, vincristine, etoposide, prednisone) was initiated, but with minimal response. This prompted further diagnostic testing and demonstrated tumor cells positivity for CD3, CD30 and TCL-1 markers. The diagnosis was changed to T-cell prolymphocytic leukemia. The patient responded well to Alemtuzumab (anti-CD52 monoclonal antibody) and reached complete remission. FC is an essential modality in assessing and screening circulating lymphocytes when a lymphoproliferative disorder (LPD) is suspected. There are several LPD that present with different degrees of clonal lymphocytosis. Reactive lymphocytosis should be appropriately investigated. Indolent LPDs can be surveyed by the internist or family physician, while more aggressive LPDs typically require management by hematologists.
DOI: 10.6084/m9.figshare.23666688
title: Supplementary Material for: Comparison of different internal limiting membrane peeling sizes for idiopathic macular holes: a systematic review and meta-analysis

description: Background: Although internal limiting membrane (ILM) peeling facilitates macular hole (MH) closure and reduces late hole reopening, it brings some detrimental consequences to the retinal microstructure and functional outcomes. So far, previous studies have not reached a consensus on the optimal ILM peeling size. Objectives: To evaluate the outcomes of different ILM peeling sizes for idiopathic MHs. Methods: PubMed, EMBASE, Cochrane Library, Web of Science, CNKI and WANFANG were searched until April 10th, 2022. Studies in English or Chinese that comparing effects of two ILM peeling sizes (&gt; 2 disk diameters [DD] vs ≤ 2DD) for idiopathic MHs were included. The overall closure rate, postoperative best-corrected visual acuity (BCVA), type 1 closure, and adverse events were extracted. BCVA was converted to logarithm of the minimum angle of resolution (LogMAR). Results: Seven eligible studies (560 eyes) including 3 randomized clinical trials, 3 prospective trials and one retrospective cohort were included. Pooled results showed a significantly better postoperative BCVA (mean difference = -0.16; 95% confidence interval [CI]: -0.27 to -0.04; LogMAR) and higher type 1 closure rate (risk ratio = 1.24; 95% CI: 1.08 to 1.43) in eyes with ILM peeling &gt; 2DD than those with peeling ≤ 2DD. No significant difference was found in overall closure rate and adverse events between the two groups. Subgroup analysis indicated that in MHs &gt; 400μm, peeling &gt; 2DD helped obtain a better postoperative BCVA (mean difference = -0.17; 95% CI: -0.29 to -0.04; LogMAR) and higher frequency of type 1 closure (risk ratio = 1.25; 95% CI: 1.03 to 1.51). Conclusions: Peeling &gt; 2DD shares similar safety level with peeling ≤ 2DD and has a superiority of facilitating visual recovery. Larger ILM peeling may be more beneficial for large MHs.
DOI: 10.6084/m9.figshare.23761248
title: Supplementary Material for: The Diagnostic and Management Performance of the ChatGPT in Obstetrics and Gynecology

description: Objectives: The use of artificial intelligence (AI) in clinical patient management and medical education has been advancing over time. ChatGPT was developed and trained recently, using a large quantity of textual data from the internet. Medical science is expected to be transformed by its use. The present study was conducted to evaluate the diagnostic and management performance of the ChatGPT artificial intelligence model in obstetrics and gynecology. Design: A cross-sectional study Participants/Materials, Setting, Methods: This study was conducted in Iran in March 2023. Medical histories and examination results of 30 cases were determined in six areas of obstetrics and gynecology. The cases were presented to a gynecologist and ChatGPT for diagnosis and management. Answers from gynecologists and ChatGPT were compared, and the diagnostic and management performance of ChatGPT were determined. Results: Ninety percent (27 of 30) of the cases in obstetrics and gynecology were correctly handled by ChatGPT. Its responses were eloquent, informed, and free of a significant number of errors or misinformation. Even when the answers provided by ChatGPT were incorrect, the responses contained a logical explanation about the case as well as information provided in the question stem. Limitations: The data used in this study were taken the electronic book may reflect of bias in the diagnosis of ChatGPT. Conclusions: This is the first evaluation of ChatGPT 's performance in diagnosis and management in the field of obstetrics and gynecology. It appears that ChatGPT has potential applications in the practice of medicine and is (currently) free and simple to use. However, several ethical considerations and limitations such as bias, validity, copyright infringement, and plagiarism need to be addressed in future studies.
DOI: 10.6084/m9.figshare.23776623
title: Supplementary Material for: Genetic polymorphisms of rs9949644 in MAPK4 are associated with clinical response to methotrexate in patients with psoriasis

description: Background The study aimed to investigate the relationship of MAPK4 genetic variants with the efficacy of MTX in psoriasis patients. Methods Patients treated with MTX were classified as responders or nonresponders if the Psoriasis Area and Severity Index (PASI) at week 12 was reduced to greater than 75% or lower than 75%, respectively. The genotypes of 14 MAPK4 single nucleotide polymorphisms (SNPs) in 310 patients were analyzed. The expression levels of MAPK4 protein were detected by western blot. Results Only rs9949644 polymorphisms were associated with the efficacy after adjusting for the confounding factors. Patients with the rs9949644 AG or GG genotype had a better clinical response compared to patients with the AA genotype. Rs9949644 polymorphisms were significantly associated with the PASI improvement rate. Besides, the protein level of MAPK4, positively associated with the psoriasis severity, was higher in patients. There were no significant differences of MAPK4 protein levels among three groups. While after treatment, MAPK4 levels in the AG or GG group showed a significantly down-regulated trend. Conclusions By demonstrating the significant association of MAPK4 with the efficacy of MTX, this study indicates that MAPK4 may be involved in the psoriasis progression and act as a predictor of therapeutic response.
DOI: 10.6084/m9.figshare.23802972
title: Supplementary Material for: Atezolizumab in combination with bevacizumab for the management of patients with hepatocellular cancer in the first-line setting: systematic literature review and meta-analysis

description: Background & aims: The objective of this systematic literature review (SLR) and network meta-analysis (NMA) is to compare randomised controlled trial evidence for atezolizumab-bevacizumab with globally relevant pharmacological comparators for first-line treatment of patients with unresectable hepatocellular carcinoma (HCC). Methods: Randomised controlled trials investigating first-line treatment of HCC in adults with no prior systemic treatment were eligible for inclusion into the SLR and were retrieved from Embase, MEDLINE, and Evidence Based Medicine (EBM) Reviews. Interventions of interest for the NMA included atezolizumab-bevacizumab, sorafenib, lenvatinib, durvalumab (including in combination with tremelimumab), cabozantinib (including in combination with atezolizumab), camrelizumab (including in combination with rivoceranib), pembrolizumab (including in combination with lenvatinib) and tislelizumab. Random effects NMA was conducted for survival endpoints within a Bayesian framework with an informative prior distribution for between study heterogeneity. The hazard ratios for relative treatment effect were estimated with 95% credible intervals (CrIs). Results: The SLR identified 49 studies, of which eight formed a connected evidence network permitting the indirect treatment comparison of atezolizumab-bevacizumab with comparators of interest. The indirect comparisons suggested an improved overall survival (OS) with atezolizumab-bevacizumab versus most comparators. All indirect treatment comparison results for atezolizumab-bevacizumab included the null value within the 95% CrI (n=1) for OS and progression free survival (PFS). Conclusions: The results of the NMA indicate atezolizumab-bevacizumab is associated with superior or comparable OS and PFS together with a manageable safety profile compared with globally relevant comparators in the unresected HCC indication. The findings support that atezolizumab-bevacizumab remains standard of care for the management of first-line unresectable HCC patients.