cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10057116
title: Dataset related to article "Muscle quality and not quantity as a predictor of survival in head and neck squamous cell carcinoma "

description: This record contains raw data related to article "Muscle quality and not quantity as a predictor of survival in head and neck squamous cell carcinoma"
Abstract
Background: Sarcopenia is frequent in head and neck squamous cell carcinoma (HNSCC), as a consequence of malnutrition related to risk factors or tumoral mass. Treatment is associated with toxicities that lead to reduced calories intake and muscle mass wasting. Sarcopenia has been negatively associated with tumor control and survival outcomes.
Purpose: Our aim is to evaluate the prognostic impact of sarcopenia on overall survival (OS) and progression free survival (PFS) in HNSCC patients undergoing chemoradiation therapy within a prospective clinical trial of chemoradiation vs induction chemotherapy followed by radiation and cetuximab (INTERCEPTOR).
Materials and methods: On baseline CT or MRI, we investigated the association between OS and PFS with radiological markers of sarcopenia, measured at the third cervical vertebra level. We studied paravertebral skeletal muscles area (cm2), muscle density (HU), muscle index (cm2/m2), and intermuscular adipose tissue (IMAT) area (cm2).
Results: Imaging of 128 patients was evaluable. We found out that higher body mass index (BMI) was associated with better OS (p = 0.02), and PFS (p = 0.04). Skeletal muscle area (p = 0.02), and IMAT (p = 0.02) were negatively associated with PFS. IMAT was positively correlated with muscle area (Correlation coefficient 0.6, CI95% 0.47-0.7), and negatively associated with muscle density (Correlation coefficient -0.37, CI95% -0.53 - -0.18).
Conclusions: IMAT can be used as predictor of PFS in HNC patients undergoing chemoradiation therapy. The amount of intermuscular fat deposits induces alterations of muscle quality, without alterations of muscle quantity, influencing patients' prognosis.
DOI: 10.6084/m9.figshare.22580914
title: Five leguminosae species

description: this project contain the annotation files of five leguminosae species' genomes. 1. contig.gff.gz, contig.cds.gz, contig.pep.gz were the annotation files of the contig version genome assemblies that assembles by the nanopore long reads. 2. chr.gff.gz, chr.cds.gz, chr.pep.gz were the annotation files of the chromosomes version genome assemblies.
DOI: 10.17188/1316316
title: Materials Data on Zn3Co by Materials Project

description: Zn3Co is Uranium Silicide structured and crystallizes in the cubic Pm-3m space group. The structure is three-dimensional. Co is bonded to twelve equivalent Zn atoms to form CoZn12 cuboctahedra that share corners with twelve equivalent CoZn12 cuboctahedra, edges with twenty-four equivalent ZnZn8Co4 cuboctahedra, faces with six equivalent CoZn12 cuboctahedra, and faces with twelve equivalent ZnZn8Co4 cuboctahedra. All Co–Zn bond lengths are 2.64 Å. Zn is bonded to four equivalent Co and eight equivalent Zn atoms to form ZnZn8Co4 cuboctahedra that share corners with twelve equivalent ZnZn8Co4 cuboctahedra, edges with eight equivalent CoZn12 cuboctahedra, edges with sixteen equivalent ZnZn8Co4 cuboctahedra, faces with four equivalent CoZn12 cuboctahedra, and faces with fourteen equivalent ZnZn8Co4 cuboctahedra. All Zn–Zn bond lengths are 2.64 Å.
DOI: 10.17632/427xnk5wbg.1
title: aiming_strategy_DL

description: simulation data, GA benchmark datasets, training codes and validing codes for the article "A Method for Real-time Optimal Heliostat Aiming Strategy Generation via Deep Learning"
DOI: 10.5281/zenodo.4791679
title: Scaling of subcellular structures with cell length through decelerated growth

description: Data and imaging files for "Scaling of subcellular structures with cell length through decelerated growth."
DOI: 10.5281/zenodo.7795779
title: Dataset for the hVPS35 antibody screening study

description: This project contains the following underlying data included in a study aiming at characterizing antibodies for the hVPS35 protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.7671730).
DOI: 10.5281/zenodo.8407783
title: Assessment of general population knowledge, attitude, and practice on safe unused and expired drugs disposal: a cross-sectional study

description: Assessment of general population knowledge, attitude, and practice on safe unused and expired drugs disposal: a cross-sectional study
DOI: 10.6084/m9.figshare.21511401
title: Supplementary Material for: Local recurrence in choroidal melanomas following Robotic assisted Radiosurgery (CyberKnife)

description: Background: Tumor recurrence in choroidal melanoma has been associated with decreased overall survival due to metastatic spreading. To detect risk factors of local recurrence and side effects, we analyzed tumor planning and treatment parameters in patients with recurrence of choroidal melanoma after treatment with robotic-assisted radiosurgery (CyberKnife). Methods: 694 patients treated with CyberKnife between 2005 and 2019 were retrospectively reviewed. Age, gender, best-corrected visual acuity (BCVA), tumor height and diameter were recorded. Treatment planning and radiation doses were reviewed. Salvage therapy, overall survival, metastasis, and complications were recorded. Results: 74 patients showed local recurrence. Local recurrence occurred after 42.1 months post CyberKnife treatment (mean; range: 5 – 100 months). 14 out of 74 patients (18.9%) died during follow-up. Recurrence treatment included enucleation in 51 patients (68.9%) and radiosurgery in 19 patients (25.7%). Treatment planning without contrast medium MRI, radiation dose of less than 21 Gy and insufficient margin delineation were identified as risk factors incrementing local control. Discussion: Robotic assisted radiosurgery (CyberKnife) is a suitable treatment option for large choroidal melanoma up to 12mm. Patients with significantly better visual acuity received repeat Cyberknife treatment as salvage therapy and showed an eye retention rate of 81%.
DOI: 10.6084/m9.figshare.22325074
title: Supplementary Material for: Factors associated with mortality and long-term outcomes of Paediatric acute kidney injury in a resource-limited setting

description: Introduction Despite being a leading cause of morbidity and mortality globally, Acute Kidney Injury (AKI) is worse in resource-limited areas. This study explores AKI incidence, in-hospital mortality, and long-term outcomes in resource-limited settings. Methods This was a prospective study of children with AKI from 2014 to 2019. KDIGO 2012 defined AKI. We assessed the aetiology, in-hospital mortality, and long-term outcome of AKI in a mission hospital. Results Only 169 of 201 AKI patients had complete data. The ages ranged from 1.08 months to 17.5 years; 65.7% were male and 65.1% were from socio-economic class. The incidence of AKI was 59.6 cases per 1000 persons (95% CI 5.42, 47.1). Most patients had stage 1 KDIGO AKI (91; 53.8%). 1-5 years old had the highest incidence of AKI (65; 38.5%) Sepsis (26.6%), severe malaria (15.4%), and nephrotic syndrome (14.8%) were common AKI causes. Fever (72.8%), pallor (52.1%), and vomiting (45.6%) were the most common symptoms. Thirty-two (27.8%) patients had high blood pressure. In-hospital mortality was 14.8% (95% CI 9.8, 21.1). The cumulative incidence of AKI-related mortality was 93, 2 per 1000 person-years. Poor outcome was associated with breathlessness, hyponatraemia, and leucocytosis. Kaplan-Meier survival curve showed 80% (CI 74-87%) survival after 5-year of AKI. On Cox proportional-hazards analysis, the absence of breathlessness (HR 2.537, 95% CI 1.210 to 5.317) and hyponatremia (HR 2.914, 95% CI 1.343 to 6.324) were associated with increased survival. Discussion/Conclusion In resource-limited settings, infectious diseases and nephrotic syndrome are common causes of AKI. Factors associated with mortality include breathlessness and hyponatremia.
DOI: 10.6084/m9.figshare.22331638
title: Supplementary Material for: Defining current patterns of blood product use during intensive induction chemotherapy in newly diagnosed acute myeloid leukemia patients

description: Introduction: Blood product transfusion retains a critical role in the supportive care of patients with acute myeloid leukemia (AML). Whereas previous studies have shown increased transfusion dependency to portend inferior outcome, predictive factors of an increased transfusion burden and the prognostic impact of transfusion support have not been assessed recently. Methods/Patients: We performed a retrospective analysis of a recent cohort of patients given intensive induction chemotherapy in 2014-2022. Results: The analysis comprised 180 patients with a median age of 57 years with 80% designated as de novo AML. Fifty-four patients (31%) were FLT3-ITD mutated and 73 patients (42%) harbored NPM1. Favorable risk and intermediate risk ELN 2017 patients accounted for 43% and 34% of patients, respectively. The median number of red blood cell (RBC) and platelet units given during induction were 9 units and 7, respectively. Seventeen patients (9%) received cryoprecipitate and fresh frozen plasma (FFP) was given to 12 patients (7%). Lower initial hemoglobin and platelet levels were predictive of increased use of RBC (p&lt;0.0001) and platelet transfusions (p&lt;0.0001). FFP was significantly associated with induction related mortality (42% versus 5%; p&lt;0.0001) and with FLT3-ITD (72% versus 28%; p=0.004). Blood group AB experienced improved mean overall survival compared to blood group O patients (4.1 years versus 2.8 years; p=0.025). In multivariate analysis, increased number of FFP [hazard ratio (HR), 4.23; 95% confidence interval (CI), 2.1-8.6; p&lt;0.001) and RBC units (HR, 1.8; 95% CI, 1.2-2.8; p=0.008) given was associated with inferior survival. Conclusion: Transfusion needs during induction crucially impact the clinical trajectory of AML patients.
DOI: 10.6084/m9.figshare.23584689
title: Supplementary Material for: Exhaled Breath Condensate and Respiratory Sequelae in Children Post-COVID-19

description: <b><i>Background:</i></b> Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an acute respiratory illness. A substantial proportion of adults experience persistent symptoms. There is a paucity of data on respiratory sequelae in children. Exhaled breath condensate (EBC) is a non-invasive tool used to assess airway inflammation. <b><i>Objectives:</i></b> This study aimed to evaluate EBC parameters, respiratory, mental and physical ability among children post COVID-19 infection. <b><i>Methods:</i></b> Observational study of confirmed SARS-CoV-2 infection cases among children, aged 5–18 years, evaluated once, 1–6 months post positive SARS-CoV-2 PCR testing. All subjects performed spirometry, 6-min walk test (6MWT), EBC (pH, interleukin-6), and completed medical history questionnaires, Depression, Anxiety, and Stress Scale (DASS-21), and physical activity scores. Severity of COVID-19 disease was classified according to WHO criteria. <b><i>Results:</i></b> Fifty-eight children were included and classified asymptomatic (<i>n</i> = 14), mild (<i>n</i> = 37), and moderate (<i>n</i> = 7) disease. The asymptomatic group included younger patients compared to the mild and moderate groups (8.9 ± 2.5y vs. 12.3 ± 3.6y and 14.6 ± 2.5y, respectively, <i>p</i> = 0.001), as well as lower DASS-21 total scores (3.4 ± 4 vs. 8.7 ± 9.4 and 8.7 ± 0.6 respectively, <i>p</i> = 0.056), with higher scores in proximity to positive PCR (<i>p</i> = 0.011). No differences were found between the 3 groups regarding EBC, 6MWT, spirometry, body mass index percentile, and activity scores. <b><i>Conclusions:</i></b> COVID-19 is an asymptomatic-mild disease in most young healthy children, with gradually diminishing emotional symptoms. Children without prolonged respiratory symptoms revealed no significant pulmonary sequelae as evaluated by EBC markers, spirometry, 6MWT, and activity scores. Larger studies are required to assess long-term pediatric consequences of post SARS‐CoV‐2 infection, to assess the need for pulmonology surveillance.
DOI: 10.6084/m9.figshare.23634729
title: Supplementary Material for: Complete Blood Count Markers and C-Reactive Protein as Predictors of Testicular Viability in the Event of Testicular Torsion in Adults

description: <b><i>Introduction:</i></b> The association between blood markers and testicular viability after testicular torsion (TT) is not well known. We evaluated the role of complete blood count markers and C-reactive protein (CRP) in predicting testicular viability after TT. <b><i>Methods:</i></b> Fifty men, ≥18 years of age, operated for TT between the years 2015–2020 were enrolled. Blood markers including neutrophil-, lymphocyte-, and platelet count, and CRP were obtained. Neutrophil-lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR) were calculated. The study outcome was testicular salvage. <b><i>Results:</i></b> Median age was 23 years (interquartile range [IQR]: 21, 31). Median duration of torsion was 10 h (IQR: 6, 42). Sonographic texture of the testis was homogenous in 27 (56%) patients and heterogenous in 21 (44%). During scrotal exploration, 36 patients (72%) underwent orchiopexy and 14 (28%) underwent orchiectomy. Patients who underwent orchiopexy were younger (22 years vs. 31 years, <i>p</i> = 0.009), had a shorter duration of torsion (median 8 h vs. 48 h, <i>p</i> &lt; 0.001), and a homogenous texture on scrotal ultrasound (76.5 vs. 7.1%, <i>p</i> &lt; 0.001). Median NLR, PLR, and CRP were higher among patients who underwent orchiectomy; however, these differences did not reach statistical significance. Patients with heterogenous echotexture were significantly more likely to undergo orchiectomy (odds ratio = 42, 95% confidence interval: 7, 831, adjusted <i>p</i> value = 0.009). <b><i>Conclusions:</i></b> We found no association between blood-based biomarkers and testicular viability after TT; however, testicular echotexture significantly predicted outcome.
DOI: 10.5281/zenodo.8408349
title: Assessment of general population knowledge, attitude, and practice on safe unused and expired drugs disposal: a cross-sectional study [questionnaire]

description: Assessment of general population knowledge, attitude, and practice on safe unused and expired drugs disposal: a cross-sectional study [questionnaire]
DOI: 10.25919/5e30a9cf118cf
title: Anionic Graphene Oxide Data Set

description: This is a set of 20212 negatively charged graphene oxide nanoflake FINAL CONFIGURATIONS, for use in data-driven studies. These structures have been optimized and relaxed with an applied charge of -1, using density functional tight binding, as described in the attached Anionic_Header_list.pdf. The size ranges from 150 carbon atoms to 1014 carbon atoms, all with hexagonal, trigonal, rectangular or rhombic shapes. The edges are a combination of hydrogen passivated or unpassivated zig zag or armchair structure, and each parent size and shape includes a large number different concentrations of OH and O (in the ether configuration), all randomly distributed. All files are in XYZ format, and the naming convention is anionic_X, where X is the unique identifer, such that X={1,..., 20396}. These can be matched up with the correponding neutral nanoflakes using X. The neutral graphene oxide nanoflake collection can be found in the CSIRO Data Access Portal repository. Feature extraction has been conducted and a list of 830 features is included in the accompanying csv file, as described in the attached Anionic_Header_list.pdf. Note that this feature list is complete, and has not been optimized.
DOI: 10.4225/08/57998cc4d7891
title: Graphene Nanoflake Data Set

description: This is a set of graphene nanoflake FINAL CONFIGURATIONS, for use in data driven studies. These structures have been optimized (fully relaxed) using Density Functional Tight Binding.  Sizes range from 16 atoms to 2176 atoms, and shapes include trigons, hexagons and a matrix of rectangular structures defined by the number of graphene rings along the zigzag (zz) and armchair (ac) directions.  Hydrogen terminated versions of the structures are also provided.

All files are in XYZ format, and the naming convention is defined in the accompanying spreadsheet that lists all of the structural, statistical and energetic properties.  This spreadsheet is available in the Supporting Attachments (in two formats)
DOI: 10.6084/m9.figshare.21541566
title: Supplementary Material for: Antibiotic Prescribing Practices Differ between Patients with Penicillin Intolerance and Penicillin Allergy Labels

description: <b><i>Introduction:</i></b> Penicillin allergy labels are common. However, many penicillin allergy labels have been applied incorrectly and in fact represent penicillin intolerance. Patients with penicillin intolerance can receive penicillin antibiotics. The effect of penicillin intolerance labels on prescribing practices is uncertain. <b><i>Methods:</i></b> This multicenter retrospective cohort study included consecutive general medicine patients admitted to two tertiary hospitals over a 12-month period. Electronic medical records were reviewed for allergy and prescribing practices. Instances of penicillin prescription to patients with previously labeled penicillin allergies underwent case note review. <b><i>Results:</i></b> There were 12,134 individual hospital admissions included in the study. The number of admissions with a previous penicillin allergy label was 1,312 (10.8%) and with a penicillin intolerance label was 60 (0.5%). Penicillin allergy labels were associated with increased likelihood of being prescribed vancomycin (odds ratio 1.42, 95% confidence interval 1.16–1.75, <i>p</i> = 0.001) and moxifloxacin (odds ratio 20.0, 95% confidence interval 13.4–29.9, <i>p</i> &lt; 0.001). Penicillin intolerance was not associated with increased likelihood of receiving these antibiotics. There were 75 admissions during which an individual with a penicillin allergy label was prescribed one of the specified penicillins and only one adverse reaction in this group. These cases included eight deliberate challenges and 15 cases in which allergy history clarification was sufficient to delabel the allergy. <b><i>Conclusions:</i></b> This study supports that prescribing practices differ between patients with penicillin allergy labels and intolerance labels. Penicillin challenges may be undertaken safely in the inpatient setting. Further studies are required to investigate how best to interrogate penicillin allergy labels in this cohort.
DOI: 10.6084/m9.figshare.21805368
title: Supplementary Material for: Renal Autologous Cell Therapy in Type 2 Diabetes with Late Stage 4 Diabetes-Related Chronic Kidney Disease: Trial Design and Early Analysis

description: <b><i>Introduction:</i></b> Cell-based therapies potentially delay the trajectory toward end-stage kidney disease (ESKD) in late stage 4 diabetic chronic kidney disease (DKD). We describe the trial design, baseline patient characteristics, and early results of an IRB-approved phase II multicenter clinical trial, utilizing Renal Autologous Cell Therapy (REACT) in adults with pre-ESKD due to type 2 DKD. The trial objectives were safety and tolerability of REACT by assessment of the procedure, product administration, and renal-specific adverse events in addition to evaluate the impact on renal function following injection. <b><i>Methods:</i></b> Ten adults with an eGFR of 14–20 mL/min/1.73 m<sup>2</sup> were enrolled in a single-arm open-label trial. Following a percutaneous kidney biopsy, an ex vivo expansion of selected renal cells that form the REACT was injected into the cortex of the biopsied kidney with CT image guidance. Each participant received two doses of the REACT product at 6-month intervals. A 6-month observation pre-trial was required to establish patients’ “own” baseline and rate of DKD progression. <b><i>Results:</i></b> Five men and 5 women underwent 19 REACT injections (1 participant received only one injection). Their baseline characteristics were as follows: 3 Hispanic/Latino, 7 non-Hispanic, 7 white; mean (SD) age: 58.9 years (5.22), BMI 35.8 (8.2), eGFR (sCR) 15.5 (2.72), eGFR (sCR + Cys-C) 17.7 (3.67) mL/min/1.73 m<sup>2</sup>, sCr 3.6 mg/mL (0.73), Cys-C 2.6 mg/mL (0.52), and log random UACR 7.9 mg/g (1.01). The pre- and post-injection eGFR slope was −6.5 mL/min/1.73 m<sup>2</sup> and −3.9 mL/min/1.73 m<sup>2</sup>. No cell-related adverse events occurred, and two procedure-related hematomas required observation without transfusion or angiographic interventions. Dialysis was delayed a mean of 16 months (range 6–28 months). At 15 months, 2 patients (20%) have eGFR slope stability and have not commenced renal replacement therapy. <b><i>Conclusion:</i></b> Trials that include patients with an eGFR of &lt;20 mL/min/1.73 m<sup>2</sup> are uncommon, and none to date involve autologous homologous cell-based treatments. REACT has the potential to stabilize or delay dialysis in high-risk late stage 4 DKD.
DOI: 10.6084/m9.figshare.21856590
title: Supplementary Material for: Association of Torquetenovirus viremia with physical frailty and cognitive impairment in three independent European cohorts

description: Introduction: Immunosenescence and inflammaging have been implicated in the pathophysiology of frailty. Torquetenovirus (TTV), a single-stranded DNA anellovirus, the major component of the human blood virome, shows an increased replication rate with advancing age. An elevated TTV viremia has been associated with an impaired immune function and an increased risk of mortality in the older population. The objective of this study was to analyze the relation between TTV viremia, physical frailty and cognitive impairment Methods: TTV viremia was measured in 1131 nonfrail, 45 physically frail, and 113 cognitively impaired older adults recruited in the MARK-AGE study (overall mean age 64.7±5.9 years), then the results were checked in two other independent cohorts from Spain and Portugal, including 126 frail, 252 prefrail and 141 nonfrail individuals (overall mean age: 77.5±8.3 years). Results: TTV viremia ≥4log was associated with physical frailty (OR: 4.69; 95% CI: 2.06-10.67, p&lt;0.0001) and cognitive impairment (OR: 3.49, 95% CI : 2.14-5.69, p&lt;0.0001) in the MARK-AGE population. The association between TTV DNA load and frailty status was confirmed in the Spanish cohort, while a slight association with cognitive impairment was observed (OR: 1.33; 95% CI: 1.000-1.773), only in the unadjusted model. No association between TTV load and frailty or cognitive impairment was found in the Portuguese sample, although a negative association between TTV viremia and MMSE score was observed in Spanish and Portuguese females. Conclusions: These findings demonstrate an association between TTV viremia and physical frailty, while the association with cognitive impairment was observed only in the younger population from the MARK-AGE study. Further research is necessary to clarify TTV's clinical relevance in the onset and progression of frailty and cognitive decline in older individuals.