cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23652840
title: Supplementary Material for: Nephropathy in a Child with Severe Recessive Dystrophic Epidermolysis Bullosa Treated with Cyclophosphamide: A Case Report

description: Long-term inflammation and recurrent skin infections in recessive dystrophic epidermolysis bullosa (RDEB) are associated with the presence of immunoglobulin A (IgA)-containing immune complexes in the glomerulus. Only eight pediatric RDEB cases with IgA nephropathy (IgAN) have been documented in English-language literature. Most RDEB patients with IgAN progress to kidney failure within five years of diagnosis, indicating that these patients may require more intensive early treatment compared to those with primary IgAN. However, diagnosing IgAN in RDEB cases with severe cutaneous manifestations can be challenging. Herein, we report a rare case of nephropathy in an 11-year-old boy with severe RDEB and a frameshift mutation on the COL7A1 gene, which may manifest as kidney disorders. He presented with persistent hematuria and progressing proteinuria. A presumptive IgAN diagnosis was based on clinical features and increased IgA serum levels, as kidney biopsy was refused by his parents. Nephrotic-range proteinuria persisted despite initial steroid and lisinopril treatment. Monthly intravenous cyclophosphamide (IV CPA; 500 mg/m2) led to proteinuria remission and preservation of kidney function for two years post-treatment. We conclude that COL7A1 mutations may result in extracutaneous manifestations, including kidney disorders. The association between IgA-containing immune complex deposits in the glomerulus and recurrent skin infections in RDEB may indicate IgAN, particularly when kidney biopsy is infeasible due to severe skin manifestations. In our case, positive results with IV CPA suggest further investigation is needed to explore its potential role in non-rapidly progressing IgAN in children with RDEB.
DOI: 10.6084/m9.figshare.23627754.v1
title: Supplementary Material for: Detection of abdominal lymph node metastasis from pancreatic neuroendocrine tumor by somatostatin receptor scintigraphy: Comparison with somatostatin receptors type 2 immunostaining

description: We report a 58-year-old male with a histopathological-proven grade 2 (G2) pancreatic neuroendocrine neoplasm and multiple abdominal node metastases by use of a laparoscopic pancreatic body and tail resection procedure, plus abdominal lymph node dissection. A primary pancreatic tail neuroendocrine tumor sized 20×25 mm was detected by contrast-enhanced CT, somatostatin receptor scintigraphy (SRS), and fluorodeoxyglucose positron emission tomography (FDG-PET) examinations, and pathologically diagnosed as a pancreatic neuroendocrine tumor (PNET, G2) based on positive immunostaining for somatostatin receptor (SSTR) type 2. Of three metastatic histopathological lymph nodes, two measured 18×21 and 10×12 mm, respectively, with whole strong SSTR immunostaining showing moderate uptake in SRS findings, whereas the other node, sized 8×10 mm, had strong SSTR immunostaining only in a small 6×6-mm sized portion and showed no uptake in SRS findings, likely because of the limited spatial resolution of scintigraphy. On the other hand, only the largest node (18×21 mm) was visualized by FDG-PET. SRS may be useful for metastatic lymph node diagnosis based on SSTR immunostaining, though a disadvantage is the spatial resolution limitation.
DOI: 10.6084/m9.figshare.22308628.v1
title: Supplementary Material for: The consistency between registered acupuncture-moxibustion clinical studies and their published studies and update status of registered information

description: Background: Few studies have analyzed the consistency between registered acupuncture-moxibustion clinical studies and their published research results as well as their update status of registered information. Methods: We searched for acupuncture-moxibustion clinical studies that were registered at the World Health Organization International Clinical Trials Registry Platform between 2013 and 2015 and collected data regarding their characteristics and update status. Published results of these registered studies were identified and compared with registered information. Results: A total of 425 registered acupuncture-moxibustion clinical studies were included; 379 (89.2%) of them were interventional studies, and the remaining 46 (10.8%) were observational studies. Forty-six studies (10.8%) were found to have published results, and 51 published articles were identified. Overall, 73.2% (311) of registered studies did not update the research status in time; 46.6% (198) stopped updating before recruiting; 21.6% (92) stopped updating after recruiting; and 4.9% (21) stopped updating after completion. Regarding the 46 studies with published results, 29 (63.0%) were considered to be affected by reporting bias. These reporting biases predominantly involved the omission of some predefined outcomes or endpoints (16 studies), contradictions regarding descriptions of sample sizes (9 studies), discrepancies in treatment measurements or group distribution (7 studies), and inconsistent treatment durations (4 studies). When compared with other studies, significant and various reporting biases could also be commonly found in fields other than acupuncture-moxibustion. Conclusions: There were many discrepancies between registered information and published reports on acupuncture-moxibustion, which could also be commonly observed in other fields. Moreover, a large proportion of registered studies did not update their research status in time. Efforts should be made to improve the reporting quality and timely updates.
DOI: 10.6084/m9.figshare.23295536
title: Supplementary Material for: Unilateral wing-beating tremor in neuronal intranuclear inclusion disease

description: Neuronal intranuclear inclusion disease (NIID) is a rare neurodegenerative disease with various neurological manifestations, including tremor. Here, we report a case involving a 68-year-old man with an 8-year history of tremor in his right arm. Subsequently, examination revealed that the patient was suffering from a low-frequency, high-amplitude, and posture-induced proximal arm tremor elicited by sustained arm abduction with flexed elbows (wing-beating tremor), which was partially improved by zonisamide treatment. Abnormal expansion of GGC repeats in the NOTCH2NLC gene confirmed the diagnosis of NIID. This case highlights the fact that unilateral wing-beating tremor can be a manifestation of NIID. Zonisamide may be effective for controlling tremors associated with NIID.
DOI: 10.6084/m9.figshare.23295536.v1
title: Supplementary Material for: Unilateral wing-beating tremor in neuronal intranuclear inclusion disease

description: Neuronal intranuclear inclusion disease (NIID) is a rare neurodegenerative disease with various neurological manifestations, including tremor. Here, we report a case involving a 68-year-old man with an 8-year history of tremor in his right arm. Subsequently, examination revealed that the patient was suffering from a low-frequency, high-amplitude, and posture-induced proximal arm tremor elicited by sustained arm abduction with flexed elbows (wing-beating tremor), which was partially improved by zonisamide treatment. Abnormal expansion of GGC repeats in the NOTCH2NLC gene confirmed the diagnosis of NIID. This case highlights the fact that unilateral wing-beating tremor can be a manifestation of NIID. Zonisamide may be effective for controlling tremors associated with NIID.
DOI: 10.6084/m9.figshare.23522862.v1
title: Supplementary Material for: Immediate Response to Brentuximab Vedotin in a Patient with Localized MF-LCT

description: The large cell transformation of mycosis fungoides (MF-LCT) is a phenomenon observed in the advanced stages of mycosis fungoides (MF), which is the most common primary cutaneous lymphoma. The diagnostic criteria of MF-LCT are a minimum of 25% of large cells or a formation of microscopic nodules of them in the histological examination of skin samples. The clinical outcomes for MF-LCT are poor, as less than 20% of patients survive 5 years after diagnosis, but the expression of the CD30 antigen is generally considered to be associated with a better prognosis. We present a case of a patient with the diagnosis of MF with LCT, with an ulcerated tumor lesion approximately 30 × 20 cm in size on the right lateral abdominal wall. Brentuximab vedotin (BV) treatment was started due to the presence of the CD30 antigen, with a quick and impressive regression of the cutaneous lesion and tumor mass and good treatment tolerance. After follow-up of 20 months, patient remains in complete remission. A schedule of treatment for MF-LCT is directed mainly by the clinical stage of the disease and the comorbidities; the more severe clinical course of the disease requires systemic treatment. If at least 5% of the cells found in the skin lesions biopsy sample express the CD30 antigen, a beneficial effect of BV treatment could be expected. It may seem that the use of BV is one of the optimal therapeutic options in patients with advanced MF-LCT showing expression of CD30.
DOI: 10.6084/m9.figshare.23294741.v1
title: Supplementary Material for: Inflammation on the waiting list is a risk factor for new-onset prediabetes and post-transplant diabetes mellitus: a prospective study.

description: Introduction: Inflammation is a risk factor for diabetes in the general population. The role of inflammation in prediabetes or post-transplant diabetes (PTDM) is not clear. We evaluated the association between inflammatory markers in patients on the waiting list for renal transplantation and the onset of prediabetes and PTDM 12 months after transplantation. Methods: This is a post-hoc analysis of a prospective study, that included non-diabetic patients on the waiting list for kidney transplantation who underwent an oral glucose tolerance test (OGTT) and were followed up to 12 months after transplantation. At this time, those patients without PTDM underwent another OGTT. At pretransplant five cytokines: TNFα, IL6, IL1β, CRP, MCP1 were determined. The association between inflammation and prediabetes/PTDM was evaluated using multiple regression models. Results: 110 patients on the waiting list were enroled: 74 had normal glucose metabolism and 36 had prediabetes or occult diabetes. At 12 months, 53 patients had normal glucose metabolism, 25 prediabetes and 32 PTDM. In multiple regression analysis, pre-transplant inflammation was not a risk factor for prediabetes or PTDM. This was attributed to the high interrelation between obesity, prediabetes and inflammation: about 75% of the cases had these conditions. In a sub-analysis we analysed only patients without prediabetes and occult diabetes on the waiting list and found that TNFα levels and BMI at pre-transplant were independently associated with the onset of prediabetes or PTDM one year after transplantation. Conclusions: Pre-transplant inflammation and BMI are risk factors for prediabetes and PTDM in patients without glucose metabolism alterations.
DOI: 10.6084/m9.figshare.23281208.v1
title: Supplementary Material for: Isoflurane rapidly modifies synaptic and cytoskeletal phosphoproteomes of the supraoptic nucleus of the hypothalamus and the cortex

description: Introduction: Despite the widespread use of general anaesthetics, the mechanisms mediating their effects are still not understood. Although suppressed in most parts of the brain, neuronal activity, as measured by FOS activation, is increased in the hypothalamic supraoptic nucleus (SON) by numerous general anaesthetics, and evidence points to this brain region being involved in the induction of general anaesthesia and natural sleep. Posttranslational modifications of proteins, including changes in phosphorylation, enable fast modulation of protein function which could be underlying the rapid effects of general anaesthesia. In order to identify potential phosphorylation events in the brain mediating general anaesthesia effects, we have explored the phosphoproteome responses in the rat SON, and compared these to cingulate cortex (CC) which displays no FOS activation is response to general anaesthetics. Methods: Adult Sprague-Dawley rats were treated with isoflurane for 15 minutes. Proteins from the CC and SON were extracted and processed for Nano-LC Mass Spectrometry (LC-MS/MS). Phosphoproteomic determinations were performed by LC-MS/MS. Results: We found many changes in the phosphoproteomes of both the CC and SON in response to 15 minutes of isoflurane exposure. Pathway analysis indicated that proteins undergoing phosphorylation adaptations are involved in cytoskeleton remodelling and synaptic signalling events. Importantly, changes in protein phosphorylation appeared to be brain region-specific suggesting that differential phosphorylation adaptations might underlie the different neuronal activity responses to general anaesthesia between the CC and SON. Conclusion: In summary, these data suggest that rapid posttranslational modifications in proteins involved in cytoskeleton remodelling and synaptic signalling events might mediate the central mechanisms mediating general anaesthesia.
DOI: 10.6084/m9.figshare.23180150.v1
title: Supplementary Material for: The introduction of an MR-conditional prototype for cardiopulmonary bypass support – technical aspects and system requirements

description: Abstract Introduction: The use of cardiopulmonary bypass (CBP; also known as a heart-lung machine) in newborns with complex congenital heart defects may result in brain damage. Magnetic resonance imaging (MRI) assessments cannot be performed safely because the metal components used to construct CBP devices may elicit adverse effects on patients when they are placed in a magnetic field. Thus, this project aimed to develop a prototype MR-conditional circulatory support system that could be used to perform cerebral perfusion studies in animal models. Methods: The circulatory support device includes a roller pump with two rollers. The ferromagnetic and most of the metal components of the roller pump were modified or replaced and the drive was exchanged by an air-pressure motor. All materials used to develop the prototype device were tested in the magnetic field according to the American Society for Testing and Materials (ASTM) Standard F2503-13. The technical performance parameters, including runtime/durability as well as achievable speed and pulsation behavior, were evaluated and compared to standard requirements. The behavior of the prototype device was compared with a commercially available pump. Results: The MRI-conditional pump system produced no image artifacts and could be safely operated in the presence of the magnetic field. The system exhibited minor performance-related differences when compared to a standard CPB pump, feature testing revealed that the prototype meets the requirements (i.e., operability, controllability, and flow range) needed to proceed with the planned animal studies.
DOI: 10.6084/m9.figshare.23622735.v1
title: Supplementary Material for: Hydroxychloroquine Attenuates <i>hERG</i> Channel by Promoting the Membrane Channel Degradation: Computational Simulation and Experimental Evidence for QT-Interval Prolongation with Hydroxychloroquine Treatment

description: <b><i>Introduction:</i></b> The coronavirus disease 2019 (COVID-19) pandemic has led to millions of confirmed cases and deaths worldwide and has no approved therapy. Currently, more than 700 drugs are tested in the COVID-19 clinical trials, and full evaluation of their cardiotoxicity risks is in high demand. <b><i>Methods:</i></b> We mainly focused on hydroxychloroquine (HCQ), one of the most concerned drugs for COVID-19 therapy, and investigated the effects and underlying mechanisms of HCQ on <i>hERG</i> channel via molecular docking simulations. We further applied the HEK293 cell line stably expressing <i>hERG</i>-wild-type channel (<i>hERG</i>-HEK) and HEK293 cells transiently expressing <i>hERG</i>-p.Y652A or <i>hERG</i>-p.F656A mutants to validate our predictions. Western blot analysis was used to determine the <i>hERG</i> channel, and the whole-cell patch clamp was utilized to record <i>hERG</i> current (<i>I</i><sub>hERG</sub>). <b><i>Results:</i></b> HCQ reduced the mature <i>hERG</i> protein in a time- and concentration-dependent manner. Correspondingly, chronic and acute treatment of HCQ decreased the <i>hERG</i> current. Treatment with brefeldin A (BFA) and HCQ combination reduced <i>hERG</i> protein to a greater extent than BFA alone. Moreover, disruption of the typical <i>hERG</i> binding site (<i>hERG</i>-p.Y652A or <i>hERG</i>-p.F656A) rescued HCQ-mediated <i>hERG</i> protein and <i>I</i><sub>hERG</sub> reduction. <b><i>Conclusion:</i></b> HCQ can reduce the mature <i>hERG</i> channel expression and <i>I</i><sub>hERG</sub> via enhancing channel degradation. The QT prolongation effect of HCQ is mediated by typical <i>hERG</i> binding sites involving residues Tyr652 and Phe656.
DOI: 10.6084/m9.figshare.23151098
title: Supplementary Material for: Reduced Growth Hormone Predicts Worsening Adipose Tissue Insulin Resistance in Adults with Obesity

description: Objectives: Adipose tissue distribution and glucose metabolism differ from normal weight to adults with obestiy. Growth hormone (GH) is closely related to obesity. Few studies have investigated the role of GH in adipose tissue insulin resistance (Adipo-IR). Herein, we investigated GH level and Adipo-IR in adults ranging from normal weight to obesity and the potential association between GH and Adipo-IR. Methods: A total of 1017 participants had their body mass index (BMI), GH and Adipo-IR evaluated. Based on the BMI, participants were assigned to five groups from normal weight to class Ⅲ obesity; based on the GH level tertiles, participants were divided into low-, medium- and high-GH groups. Results: In total, the GH level was negatively correlated with the BMI and Adipo-IR index (r =-0.32 and -0.22, respectively; both p&lt;0.001). The GH level gradually decreased and Adipo-IR progressively increased from normal weight to class Ⅲ obesity (all p&lt;0.001). Compared with the low-GH group, the reductions in the BMI, homeostasis model assessment of insulin resistance index and homeostasis model assessment of β-cell function were more significant in both medium-GH and high-GH groups (all p&lt;0.05). Additionally, the Adipo-IR index in the high-GH group was significantly lower than that in the low-GH group (p&lt;0.001). For the multivariate regression analysis, serum GH concentration was an independent protective factor against Adipo-IR (β= -0.013 [95% CI -0.025 to -0.001], p=0.028). Conclusions: A marked suppression of GH level occurs in the adults with severe obesity. GH might be an important metabolic regulator associated with Adipo-IR.
DOI: 10.5281/zenodo.8147198
title: sarracenia_minor_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8147197
title: sarracenia_minor_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23274599
title: Supplementary Material for: Case Report Contraversive ocular tilt reaction with contralesional pseudo-abducens palsy in a patient with thalamomesencephalic stroke

description: We report a patient presenting with unique neuroophthalmological features of contraversive ocular tilt reaction and concomitant contralesional pseudo-abducens palsy. Magnetic resonance imaging confirmed the presence of an acute infarct in the right thalamomesencephalic region. We discuss the clinical topography of these unique neuroophthalmological findings.
DOI: 10.6084/m9.figshare.23274599.v1
title: Supplementary Material for: Case Report Contraversive ocular tilt reaction with contralesional pseudo-abducens palsy in a patient with thalamomesencephalic stroke

description: We report a patient presenting with unique neuroophthalmological features of contraversive ocular tilt reaction and concomitant contralesional pseudo-abducens palsy. Magnetic resonance imaging confirmed the presence of an acute infarct in the right thalamomesencephalic region. We discuss the clinical topography of these unique neuroophthalmological findings.
DOI: 10.6084/m9.figshare.23502045
title: Supplementary Material for: 30-year follow-up of early onset amyotrophic lateral sclerosis with a pathogenic variant in SPTLC1

description: Dominant mutations in serine palmitoyltransferase long chain base subunit 1 (SPTLC1), a known cause of hereditary sensory autonomic neuropathy type 1 (HSAN1), are a recently identified cause of juvenile amyotrophic lateral sclerosis (JALS) with slow progression. We present a case of SPTLC1-associated JALS followed for 30 years. She was initially evaluated at age 22 years for upper extremity weakness. She experienced gradual decline in muscle strength with development of weakness and hyperreflexia in lower extremities and diffuse fasciculations in the upper extremities at 26 years. She lost independent ambulation at age 45 years. Pulmonary function declined from a forced vital capacity of 94% predicted at 27 years to 49% predicted at 47 years, and she was hospitalized twice for respiratory failure. To our knowledge, this is the longest documented follow-up period of JALS caused by a de novo pathogenic variant in SPTLC1.
DOI: 10.6084/m9.figshare.23502045.v1
title: Supplementary Material for: 30-year follow-up of early onset amyotrophic lateral sclerosis with a pathogenic variant in SPTLC1

description: Dominant mutations in serine palmitoyltransferase long chain base subunit 1 (SPTLC1), a known cause of hereditary sensory autonomic neuropathy type 1 (HSAN1), are a recently identified cause of juvenile amyotrophic lateral sclerosis (JALS) with slow progression. We present a case of SPTLC1-associated JALS followed for 30 years. She was initially evaluated at age 22 years for upper extremity weakness. She experienced gradual decline in muscle strength with development of weakness and hyperreflexia in lower extremities and diffuse fasciculations in the upper extremities at 26 years. She lost independent ambulation at age 45 years. Pulmonary function declined from a forced vital capacity of 94% predicted at 27 years to 49% predicted at 47 years, and she was hospitalized twice for respiratory failure. To our knowledge, this is the longest documented follow-up period of JALS caused by a de novo pathogenic variant in SPTLC1.
DOI: 10.6084/m9.figshare.23668152
title: Manuscript Datasets

description: Seperate .csv files for research-grade and needs-id data used in manuscript.
DOI: 10.6084/m9.figshare.23668152.v1
title: Manuscript Datasets

description: Seperate .csv files for research-grade and needs-id data used in manuscript.
DOI: 10.6084/m9.figshare.23523366.v1
title: Supplementary Material for: Sequence Similarity Among Structural Repeats in the Piezo Family of Mechanosensitive Ion channels

description: Members of the Piezo family of mechanically activated cation channels are involved in multiple physiological processes including vascular development, cell differentiation, touch perception, hearing and more. Mutations in these proteins are associated with a variety of diseases, such as colorectal adenomatous polyposis, dehydrated hereditary stomacytosis, and hereditary xerocytosis. Available 3D structures for Piezo proteins show nine regions of four transmembrane segments each that have the same fold. Despite the remarkable similarity among the nine characteristic structural repeats in the family, no significant sequence similarity among them has been reported. Using a bioinformatics approach and the Transporter Classification Database (TCDB) as reference, we reliably identified sequence similarity among repeats based on four lines of evidence: (1) HMM-profile similarities across repeats at the family level, (2) pairwise sequence similarities between different repeats across Piezo homologs, (3) Piezo-specific conserved sequence signatures that consistently identify the same regions across repeats, and (4) conserved residues that maintain the same orientation and location in 3D space.
DOI: 10.25345/c5g44j16q
title: MassIVE MSV000092444 - Identification of Heavily Glycated Proteins at the Molecular Level
title: The data file contains the data for the glycation project.