cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22683235
title: Supplementary Material for: A novel intronic deletion in PDE6B causes autosomal recessive retinitis pigmentosa by interfering with RNA splicing

description: Introduction: Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ~30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigate a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6, in association with recessive RP. Methods: Three unrelated consanguineous families were recruited from the North-Western part of Pakistan. Whole exome sequencing was performed for the probands of each family and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. Results: The clinical phenotype for all patients was compatible with rod cone degeneration, with onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3: c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In-vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and likely to disease. Discussion/Conclusion: Our findings further expand the mutational spectrum of the PDE6B gene.
DOI: 10.6084/m9.figshare.22683592
title: Supplementary Material for: Life-threatening hyperkalemia following low-dose trimethoprim-sulfamethoxazole: a case report

description: Hyperkalemia is a known adverse effect of trimethoprim-sulfamethoxazole, usually occurring at high doses. However, fatal hyperkalemia at low doses has rarely been reported. We present the case of an 80-year-old Japanese woman who experienced a cardiac arrest due to severe hyperkalemia after starting low-dose trimethoprim-sulfamethoxazole. This case suggests that trimethoprim-sulfamethoxazole can cause severe hyperkalemia and sudden death, even at low doses. When trimethoprim-sulfamethoxazole is administered, even at low doses, periodic monitoring of electrolyte levels is necessary, with the interval depending on concomitant medications and renal function.
DOI: 10.6084/m9.figshare.22820714
title: Supplementary Material for: New Miniaturized System for Ultrafiltration: Rationale and Design of a Single-Center, Crossover, Randomized, Open-Label, Pilot Study Protocol

description: Introduction: Fluid overload and congestion are common features in patients with heart failure and are associated with negative clinical outcomes. Therapies for these conditions are diuretic-centered but frequently failure to achieve patient adequate hydration status, prompting the use of extracorporeal ultrafiltration. Artificial Diuresis 1, AD1, is a miniaturized, portable, and wearable system designed to deliver isolated ultrafiltration with the finest degree of simplicity and practicality. Methods/Design: Single-center, crossover, randomized, open-label pilot study to investigate the safety and the efficacy (concerning ultrafiltration accuracy) of extracorporeal ultrafiltration with the device AD1 in comparison to isolated ultrafiltration with a traditional machine (PrisMaX. Patients with chronic kidney disease stage 5D (on hemodialysis) or intensive care patients presenting acute kidney injury stage 3D (requiring hemodialysis) will carry out a single session of isolated ultrafiltration with each of the machines. The safety primary outcomes will be the occurrence of adverse events. The efficacy primary outcome will be the accuracy of ultrafiltration rate (delivered/prescribed) on each of the devices. Discussion/Conclusion: AD1 is a novel miniaturized device for extracorporeal ultrafiltration. This study will be the first-in-human use of AD1 in patients with fluid overload. Trial registration number: CESC Provincia di Vicenza_6.9.22(n.54/22)_1575_29.9.22
DOI: 10.6084/m9.figshare.23051339
title: Supplementary Material for: Necrosis of Pedunculated Lipofibroma by Nab-Paclitaxel

description: We present a rare phenomenon of a soft tumor hanging on the woman’s left upper arm that underwent necrosis from the distal aspect during chemotherapy for pancreatic cancer. The benign tumor, pedunculated lipofibroma, originally had normal color for 10 years and then became necrotic when she was treated with gemcitabine and nab-paclitaxel. Necrosis stopped in conjunction with chemotherapy cessation. Dermatologists must remember that nab-paclitaxel could develop necrosis of a skin tumor.
DOI: 10.6084/m9.figshare.23276744
title: Supplementary Material for: Olaparib-Induced Purpuric Drug Eruption in a Patient with Castration-Resistant Prostate Cancer

description: Olaparib is recently approved as an anti-tumor agent for several cancers, including castration-resistant prostate cancer, which inhibits poly (adenosine diphosphate-ribose) polymerase, a DNA repair factor. Since olaparib is a newly approved drug, there are few reports of skin disorders that may be triggered by olaparib administration. In this report, we present a case with an olaparib-induced drug eruption presenting multiple purpuras on the patient’s fingers and fingertips. The present case suggests that olaparib might induce purpura as nonallergic drug eruption.
DOI: 10.5281/zenodo.4033811
title: Binder H33 - diffraction images for PDB record 8BDU

description: Binder H33 - diffraction data.
DOI: 10.6084/m9.figshare.21989222
title: Supplementary Material for: Mandibular metastasis as the first manifestation of hepatocellular carcinoma: Case report

description: Metastatic malignancies of the oral cavity are rare lesions, accounting for only 1–4% of all oral malignancies and can occur in the jaw bones, the oral soft tissues or even both. Although hepatocellular carcinoma is the most common primary hepatic tumor, in no more than 1% of the cases is there oral involvement. When metastatic tumor involves the oral cavity, the most frequent site is the posterior angle of the mandible. Histologically, hence, immunohistochemical markers are used for diagnosis. Glypican-3, HepPar1, CD34 are the markers that can be used to confirm the microscopic diagnosis of HCC. Very rarely, Hepatocellular carcinoma (HCC) metastasize to the oral cavity, and such cases have a poor prognosis due to delay in diagnosis. We present a 74-year-old male with a metastasis of HCC in left mandibular body as the first manifestation. Histologic examination confirmed metastatic hepatocellular carcinoma in the oral mucosa with immunohistochemical (IHC) markers. A review of pertinent literature was performed. Given the rarity of the disease, treatment principles are based mainly on retrospective series and case reports. We report an exceptionally unusual presentation with few cases (&lt;70) reported in the literature, thus representing a diagnostic challenge.
DOI: 10.6084/m9.figshare.23522799
title: Supplementary Material for: Encephalitis as a clinical manifestation of COVID-19: A Case Series

description: COVID-19 is a novel virus which causes a variety of clinical manifestations in the body some of which are still yet to be discovered. The main aim of our study is to highlight the neurological manifestations of COVID-19 as it is still new to the medical world and to emphasize the fact that the physicians have to be vary of the possibility that patients affected with COVID-19 can present with encephalitis. Only a few studies are available so far regarding the neurological manifestations of this novel virus which highlights the need of this study. We present a case series of four patients who were found to have COVID-19 encephalitis. There is still no disease defining test for diagnosis so the mainstay of diagnosis is exclusion of all the common causes of encephalitis. Brain MRI and CSF analysis performs an ancillary in the diagnostic tools. Our study also supports the use of IV Tocilizumab (4-8 mg/kg) and IV methylprednisolone (0.5-2 mg/kg) as possible treatment options with good results as the patients described in our case series responded well to these medications.
DOI: 10.6084/m9.figshare.22146836
title: Supplementary Material for: Cushing’s Syndrome in Adenocarcinoma of Lung Responding to Osilodrostat

description: Cushing syndrome (CS), secondary to paraneoplastic syndrome, is more commonly seen in small cell lung cancer (SCLC) but never before reported in EGFR-mutated adenocarcinoma of the lung. Here, we present a case of a patient whose symptoms of hypokalemia, hypertension and progressive abnormal glucose levels led to further workup that revealed ACTH-dependent hypercortisolism. Her cortisol levels dropped after one month of osilodrostat treatment while lung cancer was treated with osimertinib. The use of osilodrostat in paraneoplastic CS has been previously reported in only 3 patients.
DOI: 10.6084/m9.figshare.22189357
title: Supplementary Material for: Insulin Resistance, but Not Obstructive Sleep Apnea Is Associated with Hepatic Steatosis in Chinese Patients with Severe Obesity

description: Introduction Severe obesity often present with nonalcoholic fatty liver disease (NAFLD) and obstructive sleep apnea (OSA). Emerging researches suggest OSA plays an important role in NAFLD development and progression while the relationship between OSA and NAFLD is still conflicting . The interaction of OSA and NAFLD should be further evaluated as obesity surges. The purpose of this study was to assess the prevalence of OSA and NAFLD in patients with obesity undergoing bariatric surgery, and evaluate the association between OSA and severity of NAFLD. Methods 141 patients with severe obesity undergoing preoperative polysomnography and intraoperative liver biopsy during bariatric surgery was investigated. Clinical, anthropometric variables, liver enzymes, fasting blood glucose, fasting serum insulin, and homeostasis model assessment (HOMA-IR) were measured. The severity of NAFLD was assessed by degree of steatosis, ballooning, intralobular inflammation and NAFLD activity score (NAS). The diagnosis and severity assessment of OSA was based on an apnea/hypopnea index (AHI). Results OSA was diagnosed in 127 (90.07%), NAFLD in 124 (87.94%), and non-alcoholic steatohepatitis (NASH) in 72 (51.06%) patients. There was a statistically difference in body mass index (BMI), waist circumstance, neck circumstance, high-density lipoprotein-cholesterol (HDL), fasting insulin, and HOMA-IR among the three groups divided by the severity of AHI. In addition, the distribution of hepatic steatosis grades among the three groups was statistically different (P=0.025). AHI was significantly associated with HOMA-IR and hepatic steatosis when assessing the association between OSA parameters and liver histology in NAFLD(P&lt; 0.05). Patients with steatosis of grade 1-3 had significantly elevated aspartate aminotransferase(AST), alanine aminotransferase(ALT), gamma glutamyl transferase (GGT),triglycerides (TG), fasting insulin, fasting glucose, HOMA-IR, and AHI compared with the patients with steatosis of grade 0. In a multivariable logistic analysis, the positive association between AHI and hepatic steatosis attenuated after adjusting for HOMA-IR. Conclusion Prevalence of OSA and NAFLD was high in patients with obesity eligible for bariatric procedures. HOMA-IR, but not AHI, was an independent risk factor for hepatic steatosis in this population.
DOI: 10.6084/m9.figshare.22242247
title: Supplementary Material for: Primary Ovarian Neuroendocrine Carcinoid Tumor Arising in a Mature Cystic Teratoma

description: Primary ovarian neuroendocrine carcinoid tumors are extremely rare. However, their clinical course is good, and hence, fertility-sparing surgery is a feasible treatment option in cases of unilateral localized lesions. In this report, we present the case of a 20-year-old nulliparous woman who was diagnosed as having a primary ovarian neuroendocrine carcinoid tumor arising from a mature cystic teratoma. She underwent laparoscopic right ovarian cystectomy and her postoperative recovery was uneventful. The patient has been under close observation over a 1-year follow-up period and has shown no evidence of tumor recurrence.
DOI: 10.6084/m9.figshare.22586119
title: Supplementary Material for: Durable response to maintenance treatment comprised of viagenpumatucel-L, nivolumab, ramucirumab, and docetaxel in a PD-L1-low advanced stage non-small cell lung cancer: A case report

description: Checkpoint inhibitors are now standard of care for late-stage non-small cell lung cancer (NSCLC); however, only a minority of patients treated with a checkpoint inhibitor show clinical benefit compared to platinum-based chemotherapy alone, regardless of PD-L1 expression levels. We describe a case of durable tumor response and disease stabilization in a patient with advanced pretreated squamous NSCLC given a maintenance treatment comprised of nivolumab, docetaxel, and ramucirumab combined with the allogeneic cellular cancer vaccine viagenpumatucel-L over a period of 28 months. Our case suggests that cancer vaccine strategies may sensitize tumors to checkpoint inhibition, even in patients refractory to available treatment, and lead to improved efficacy.
DOI: 10.5281/zenodo.3924770
title: IoT-deNAT: Outbound flow-based network traffic data of IoT and non-IoT devices behind a home NAT

description: This dataset is comprised of NetFlow records, which capture the outbound network traffic of 8 commercial IoT devices and 5 non-IoT devices, collected during a period of 37 days in a lab at Ben-Gurion University of The Negev. The dataset was collected in order to develop a method for telecommunication providers to detect vulnerable IoT models behind home NATs. Each NetFlow record is labeled with the device model which produced it; for research reproducibilty, each NetFlow is also allocated to either the "training" or "test" set, in accordance with the partitioning described in: Y. Meidan, V. Sachidananda, H. Peng, R. Sagron, Y. Elovici, and A. Shabtai, A novel approach for detecting vulnerable IoT devices connected behind a home NAT, Computers & Security, Volume 97, 2020, 101968, ISSN 0167-4048, https://doi.org/10.1016/j.cose.2020.101968. (http://www.sciencedirect.com/science/article/pii/S0167404820302418) Please note: The dataset itself is free to use, however users are requested to cite the above-mentioned paper, which describes in detail the research objectives as well as the data collection, preparation and analysis. Following is a brief description of the features used in this dataset. # NetFlow features, used in the related paper for analysis 'FIRST_SWITCHED': System uptime at which the first packet of this flow was switched<br> 'IN_BYTES': Incoming counter for the number of bytes associated with an IP Flow<br> 'IN_PKTS': Incoming counter for the number of packets associated with an IP Flow<br> 'IPV4_DST_ADDR': IPv4 destination address<br> 'L4_DST_PORT': TCP/UDP destination port number<br> 'L4_SRC_PORT': TCP/UDP source port number<br> 'LAST_SWITCHED': System uptime at which the last packet of this flow was switched<br> 'PROTOCOL': IP protocol byte (6: TCP, 17: UDP)<br> 'SRC_TOS': Type of Service byte setting when there is an incoming interface<br> 'TCP_FLAGS': Cumulative of all the TCP flags seen for this flow # Features added by the authors 'IP': Prefix of the destination IP address, representing the network (without the host)<br> 'DURATION': Time (seconds) between first/last packet switching # Label<br> 'device_model': &lt;type&gt;.&lt;manufacturer&gt;.&lt;model number&gt; # Partition<br> 'partition': Training or test # Additional NetFlow features (mostly zero-variance)<br> 'SRC_AS': Source BGP autonomous system number<br> 'DST_AS': Destination BGP autonomous system number<br> 'INPUT_SNMP': Input interface index<br> 'OUTPUT_SNMP': Output interface index<br> 'IPV4_SRC_ADDR': IPv4 source address<br> 'MAC': MAC address of the source # Additional data<br> 'category': IoT or non-IoT<br> 'type': IoT, access_point, smartphone, laptop<br> 'date': Datepart of FIRST_SWITCHED<br> 'inter_arrival_time': Time (seconds) between successive flows of the same device (identified by its MAC address)
description: {"references": ["Meidan et al. (2020). A Novel Approach for Detecting Vulnerable IoT Devices Connected Behind a Home NAT. Computers & Security"]}
DOI: 10.5281/zenodo.6410935
title: Computational validation of clonal and subclonal copy number alterations from bulk tumour sequencing

description: Somatic variant identification from WGS data is a crucial step in the analysis of cancer genomes. Several tools are available to perform mutations calling, however, the noisiness of data requires appropriate quality control assessment. In the preprint work available at https://doi.org/10.1101/2021.02.13.429885 we present CNAqc, an R package devised to assess the quality of allele-specific Copy Number Alterations (CNA), somatic mutations, and tumor purity estimates. In order to test the model, we ran CNAqc on 2778 single-sample PCAWG whole-genomes and 48 TCGA whole-exomes. We uploaded the results of our analysis using the release of the tool available at https://github.com/caravagnalab/CNAqc/releases/tag/rr_22_0.1 in the form of .rds files. All the necessary details for the reproduction of our results are reported in the Supplementary Materials of the above-mentioned manuscript.
DOI: 10.6084/m9.figshare.21989192
title: Supplementary Material for: Hypoglycemic encephalopathy manifesting with cortical hemichorea-hemiballismus syndrome: a case report

description: Hyper-/hypoglycemic states are a rare but well-established cause of hyperkinetic movements, including chorea and ballismus, usually associated with brain lesions in the basal ganglia. We report a case of hemichorea-hemiballismus (HCHB) syndrome that developed after a severe hypoglycemic episode in a 71-year-old man with poorly controlled type 2 diabetes mellitus. Uncommonly, brain MRI showed contralateral cortical-subcortical T2 and T2-FLAIR- hyperintense frontoparietal lesions, with cingulate gyrus involved, while the basal ganglia were unaffected. In patients with hypoglycemic encephalopathy associated with cortical lesions, the long-term prognosis is usually poor. Nevertheless, in our patient, the dyskinesias and the cerebral lesions progressively regressed by achieving good glycemic control. After four and twelve months, the patient’s neurological examination was normal. To our knowledge, this is the first evidence of hypoglycemic etiology of cortical HCHB syndrome, supporting recent theories that cortical circuitries may independently contribute to the pathogenesis of chorea and ballismus. This is also the first report of cingulate gyrus involvement in hypoglycemic encephalopathy. Finally, this case may indicate that a subset of patients with cortical lesions due to hypoglycemia could present a good clinical outcome, likely, depending on the size of the lesions and the duration and severity of the hypoglycemic episode.
DOI: 10.6084/m9.figshare.22004798
title: Supplementary Material for: Repositioning of In-the-Bag Dislocated Intraocular Lenses. A Randomized Clinical Trial Comparing Two Surgical Methods

description: Introduction: To evaluate IOL tilt, IOL-induced astigmatism (IIA), refractive change and impact of capsular fibrosis on IOL position after scleral fixation of dislocated IOL using two methods: Ab Externo Scleral Suture Loop Fixation (Group A) and a modification, Embracing the Continuous Curvilinear Capsulorhexis (Group B). Methods: In this prospective randomized clinical trial conducted at St. Erik Eye Hospital, 117 patients with dislocated IOL were randomized to Group A (n = 61) or B (n = 56). Patients with ordinary pseudophakia (n = 60) served as controls. IOL tilt was measured three-dimensionally with anterior segment optical coherence tomography (AS-OCT). Results: The median IOL tilt was similar with both methods (A: 7.8°; B: 8.3°; p=0.51), but higher than in ordinary pseudophakia (5.4°; p&lt;0.001). Both groups showed a myopic shift, p&lt;0.001. In cases without capsular fibrosis, the median IOL tilt was 15.5° in Group A (n = 7) and 7.0° in Group B (n = 5), p=0.19. For each degree of IOL tilt, IIA increased by 0.075D (p&lt;0.001). IOL position could be measured with AS-OCT in all patients given that the IOL was visible in the pupil. Discussion/Conclusion: After IOL fixation surgery, IOL tilt is higher than in normal pseudophakia. A study involving more patients without capsular fibrosis could clarify whether IOL position is better with method B in this subgroup. IOL-induced astigmatism is low, but myopic shift is common. AS-OCT is useful for IOL tilt assessment after IOL fixation surgery. Trial registration number: NCT04150263
DOI: 10.6084/m9.figshare.22017584
title: Supplementary Material for: Cutaneous manifestations of Sarcoidosis seen in a patient with a history of Tuberous Sclerosis

description: This case report details a patient with a history of tuberous sclerosis presenting with new onset cutaneous lesions that turn out to be sarcoidosis. There may be a shared dysfunction of mTOR present in sarcoidosis and tuberous sclerosis. Both diseases have remarkably variable findings, as dermatologists, it is important to maintain a wide differential when new cutaneous lesions arise in a patient with a history of either disorder.
DOI: 10.6084/m9.figshare.22093631
title: Supplementary Material for: Primary pleural angiosarcoma treated with nivolumab and ipilimumab: a case report

description: Primary pleural angiosarcoma (PPA) is a rare and clinically fatal pleural tumor originating from vascular endothelial cells. Herein, we presented the case of a 73-year-old man who was referred to our emergency room with complaints of right chest and back pain for a few days. Chest computed tomography revealed massive pleural effusion and a large mass in the right chest cavity. Thoracoscopic examination demonstrated a large hemorrhagic tumor on the parietal pleura whose pathological analysis indicated PPA. The patient received immunotherapy combined with nivolumab and ipilimumab. A cycle of nivolumab and ipilimumab improved his hemorrhagic anemia and reduced the pleural effusion and tumor size. This treatment outcome suggests that nivolumab and ipilimumab comprise a vital treatment option for PPA.
DOI: 10.6084/m9.figshare.22242055
title: Supplementary Material for: Efficacy of Intravenous Immunoglobulins Against Chronic Lymphocytic Inflammation with Pontine Perivascular Enhancement Responsive to Steroids (CLIPPERS): A Case Report

description: Chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS) is an inflammatory disease of the central nervous system that predominantly affects the brainstem. Apart from corticosteroids, there are few reported treatment options for CLIPPERS, and there is no standard therapy. A 77-year-old man presented with diplopia that had persisted for 5 months. Dysarthria and numbness of the distal right upper extremity and right lips were also observed. Brain magnetic resonance imaging (MRI) revealed a hyperintense area around the brainstem. Symptoms were relieved immediately following intravenous methylprednisolone (IVMP) administration. However, after gradual tapering of oral prednisolone to 5 mg/day, the symptoms relapsed, and brain imaging revealed that the condition had worsened. Intravenous immunoglobulins (IVIg) were administered for recurrence, with no clinical improvement. After each IVMP treatment, the patient recovered promptly. Based on the patient’s symptoms and characteristic MRI findings, exclusion of other diseases, and the significant efficacy of corticosteroids, he was diagnosed with CLIPPERS. There was no recurrence at a maintenance prednisolone dose of 8 mg/day. IVIg had a poor effect on the acute phase of CLIPPERS symptoms. Compared with other immunosuppressants, IVIg is less effective in suppressing the relapse of CLIPPERS.