bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitamin D and COVID-19 severity and related mortality: a prospective study in Italy
Authors: Campi Irene , Gennari Luigi , Merlotti Daniela , Mingiano Christian , Frosali Alessandro , Giovanelli Luca , Torlasco Camilla , Pengo Martino F. , Heilbron Francesca , Soranna Davide , Zambon Antonella , Di Stefano Marta , Aresta Carmen , Bonomi Marco , Cangiano Biagio , Favero Vittoria , Fatti Letizia , Perego Giovanni Battista , Chiodini Iacopo , Parati Gianfranco , Persani Luca 
Published: June 2021

AbstractBackgroundVitamin D deficiency has been suggested to favor a poorer outcome of Coronavirus disease-19 (COVID-19). We aimed to assess if 25-hydroxyvitamin-D (25OHD) levels are associated with interleukin 6 (IL-6) levels and with disease severity and mortality in COVID-19.MethodsWe prospectively studied 103 in-patients admitted to a Northern-Italian hospital (age 66.1 ± 14.1 years, 70 males) for severely-symptomatic COVID-19. Fifty-two subjects with SARS-CoV-2 infection but mild COVID-19 symptoms (mildly-symptomatic COVID-19 patients) and 206 subjects without SARS-CoV-2 infection were controls. We measured 25OHD and IL-6 levels at admission and focused on respiratory outcome during hospitalization.ResultsSeverely-symptomatic COVID-19 patients had lower 25OHD levels (18.2 ± 11.4 ng/mL) than mildly-symptomatic COVID-19 patients and non-SARS-CoV-2-infected controls (30.3 ± 8.5 ng/mL and 25.4 ± 9.4 ng/mL, respectively,p < 0.0001 for both comparisons). 25OHD and IL-6 levels were respectively lower and higher in severely-symptomatic COVID-19 patients admitted to intensive care Unit [(ICU), 14.4 ± 8.6 ng/mL and 43.0 (19.0–56.0) pg/mL, respectively], than in those not requiring ICU admission [22.4 ± 1.4 ng/mL,p = 0.0001 and 16.0 (8.0–32.0) pg/mL,p = 0.0002, respectively]. Similar differences were found when comparing COVID-19 patients who died in hospital [13.2 ± 6.4 ng/mL and 45.0 (28.0–99.0) pg/mL] with survivors [19.3 ± 12.0 ng/mL,p = 0.035 and 21.0 (10.5–45.9) pg/mL,p = 0.018, respectively). 25OHD levels inversely correlated with: i) IL-6 levels (ρ − 0.284,p = 0.004); ii) the subsequent need of the ICU admission [relative risk, RR 0.99, 95% confidence interval (95%CI) 0.98–1.00,p = 0.011] regardless of age, gender, presence of at least 1 comorbidity among obesity, diabetes, arterial hypertension, creatinine, IL-6 and lactate dehydrogenase levels, neutrophil cells, lymphocytes and platelets count; iii) mortality (RR 0.97, 95%CI, 0.95–0.99, p = 0.011) regardless of age, gender, presence of diabetes, IL-6 and C-reactive protein and lactate dehydrogenase levels, neutrophil cells, lymphocytes and platelets count.ConclusionIn our COVID-19 patients, low 25OHD levels were inversely correlated with high IL-6 levels and were independent predictors of COVID-19 severity and mortality.
Evaluation of Geenius HIV-1/2 Confirmatory Assay for the confirmatory and differential diagnosis of HIV-1/HIV-2 in Japan and reliability of the Geenius Reader in the diagnosis of HIV-2
Authors: Kusagawa Shigeru , Kawana-Tachikawa Ai , Matsubayashi Keiji , Hoshi Yuji , Ishimaru Ken , Hamaguchi Isao 
Published: June 2021

Abstract
Background
NEW LAV BLOT I and II (LAV I and LAV II), they were only option for human immunodeficiency virus (HIV) confirmatory test, following HIV screening test using HIV Ag/Ab combination test in Japan. We evaluated the performance of Geenius HIV-1/2 Confirmatory Assay (Geenius), both as a confirmatory test and for differentiation between HIV-1 and HIV-2, in comparison with LAV I and LAV II.

Methods
Eighty-nine HIV-1-positive plasma specimens, one anti-HIV-1 low-titer performance panel, 10 seroconversion panels, and two anti-HIV-1/2 combo performance panels were tested. The results were read with the Geenius Reader and by visual reading.

Results
All 89 HIV-1-positive plasma specimens were identified as HIV-1-positive using Geenius; this 100% success rate was superior to that with LAV I (95.5% using WHO criteria, 98.9% using CDC criteria). The HIV-1-positive specimens showed low cross-reactivity with HIV-2 lines in Geenius. The sensitivity of Geenius for HIV-1 detection was the same as or greater than that of LAV I, but less than that of Genscreen HIV Ag-Ab ULT, in our analysis of the commercial performance and seroconversion panels. In contrast, five of the 13 HIV-2-positive specimens that had been identified as HIV-positive untypable by visual reading because of their cross-reactivity to HIV-1 lines were successfully identified by the Geenius Reader as HIV-2-positive with cross-reactivity.

Conclusions
Geenius provides strong performance for HIV confirmatory tests and HIV-1 differentiation tests. However, when visual reading is used, its performance in HIV-2 differentiation is less reliable. Because HIV-2 infection has been sporadically reported in Japan, the use of the Geenius Reader is preferable to ensure more reliable HIV-1/HIV-2 differentiation.
Long-term prognosis in patients with acute myocardial infarction and newly detected glucose abnormalities: predictive value of oral glucose tolerance test and HbA1c
Authors: Karayiannides Stelios , Djupsjö Catarina , Kuhl Jeanette , Hofman-Bang Claes , Norhammar Anna , Holzmann Martin J. , Lundman Pia 
Published: June 2021

Abstract
Background
Disturbances of glucose metabolism can be diagnosed by an oral glucose tolerance test (OGTT) and by glycated haemoglobin (HbA1c). The aim of this study was to investigate the association between newly detected disturbances of glucose metabolism and long-term prognosis after acute myocardial infarction (AMI) and to compare the predictive value of an OGTT and HbA1c.

Methods
Patients under the age of 80 years with no known history of diabetes admitted for AMI at the Department of Cardiology, Danderyd University Hospital, Stockholm, Sweden, from January 1st, 2006 until December 31st, 2013, were investigated with an OGTT and a HbA1c before discharge and were classified as having normal glucose tolerance (NGT), prediabetes or diabetes according to American Diabetes Association (ADA) criteria. Using nationwide, all-inclusive registers, patients were followed for the incidence of combined event [CE (first of myocardial infarction, heart failure, ischaemic stroke or mortality)] for a mean follow-up time of 4.8 years. Cox regression analysis was used to calculate Hazard Ratios (HR) and their 95% confidence intervals (CI).

Results
Of the 841 patients who were investigated with both an OGTT and a HbA1c, 139 (17%) patients had NGT, 398 (47%) had prediabetes and 304 (36%) had diabetes according to OGTT. The corresponding figures using HbA1c were 320 (38%), 461 (55%) and 60 (7%). Patients with newly discovered diabetes were older and had a higher body mass index compared to those with NGT. OGTT was not predictive for CE. In contrast, prediabetes identified by a HbA1c was associated with an increased risk for CE (HR 1.31; 95% CI 1.05–1.63) compared to normoglycaemia. When comparing the prognostic value of different glucose and HbA1c cut-offs, only a HbA1c ≥ 39 mmol/mol was significantly associated with CE (HR 95% CI; 1.30:1.05–1.61).

Conclusion
In this single-centre study, in a recent contemporary cohort, we found that around two thirds of the patients admitted with AMI with no known history of diabetes had disturbed glucose metabolism, in accordance with previous studies. HbA1c in the prediabetes range, but not OGTT, added predictive value on the long-term outcome, in a cohort to whom a pathologic OGTT result was communicated with lifestyle advice.
Using deep learning to identify recent positive selection in malaria parasite sequence data
Authors: Deelder Wouter , Benavente Ernest Diez , Phelan Jody , Manko Emilia , Campino Susana , Palla Luigi , Clark Taane G. 
Published: June 2021

Abstract
Background
Malaria, caused by Plasmodium parasites, is a major global public health problem. To assist an understanding of malaria pathogenesis, including drug resistance, there is a need for the timely detection of underlying genetic mutations and their spread. With the increasing use of whole-genome sequencing (WGS) of Plasmodium DNA, the potential of deep learning models to detect loci under recent positive selection, historically signals of drug resistance, was evaluated.

Methods
A deep learning-based approach (called “DeepSweep”) was developed, which can be trained on haplotypic images from genetic regions with known sweeps, to identify loci under positive selection. DeepSweep software is available from https://github.com/WDee/Deepsweep.

Results
Using simulated genomic data, DeepSweep could detect recent sweeps with high predictive accuracy (areas under ROC curve > 0.95). DeepSweep was applied to Plasmodium falciparum (n = 1125; genome size 23 Mbp) and Plasmodium vivax (n = 368; genome size 29 Mbp) WGS data, and the genes identified overlapped with two established extended haplotype homozygosity methods (within-population iHS, across-population Rsb) (~ 60–75% overlap of hits at P < 0.0001). DeepSweep hits included regions proximal to known drug resistance loci for both P. falciparum (e.g. pfcrt, pfdhps and pfmdr1) and P. vivax (e.g. pvmrp1).

Conclusion
The deep learning approach can detect positive selection signatures in malaria parasite WGS data. Further, as the approach is generalizable, it may be trained to detect other types of selection. With the ability to rapidly generate WGS data at low cost, machine learning approaches (e.g. DeepSweep) have the potential to assist parasite genome-based surveillance and inform malaria control decision-making.
Urothelial carcinoma of the graft kidney with molecular analyses: a rare case report
Authors: Chen Joyce M. , Kenneth Haines G. , Lam William , Reddy Asha , Mehrotra Meenakshi , Houldsworth Jane , Si Qiusheng 
Published: June 2021

Abstract
Background
Malignancy after transplantation is a leading cause of death among kidney transplant recipients. However, donor-derived malignancies are rare. We report a case of a high grade papillary urothelial carcinoma arising in a transplanted kidney.

Case presentation
A 62-year-old female who received a kidney transplantation more than 30 years ago presented with urinary tract infection, acute renal failure, and hydronephrosis of the transplant kidney. Anterograde nephrostogram showed a large filling defect in the lower pole of the transplant kidney and in the proximal 3–4 cm of the ureter. A biopsy from the renal pelvic mass showed a high grade urothelial carcinoma. She underwent an anterior exenteration, resection of both transplant and native kidneys and bilateral pelvic lymph node dissection. Pathologic examination showed a high grade papillary urothelial carcinoma which appeared to arise in the pelvis of the graft kidney, involve the graft ureter and native urinary bladder. The tumor had metastasized to one left obturator lymph node but spared the two native kidneys and ureters. Short tandem repeat (STR) analysis confirmed the tumor to be of donor origin. Next-generation sequencing identified amplification of TERT and loss of CDKN2A/CDKN2B in the primary tumor.

Conclusion
While it is known that transplant recipients have an increased risk of urothelial carcinoma compared to the general population, the lack of the well-documented risk factors, such as older age at transplantation, BK polyomavirus infection, and prolonged post-transplantation history and dissemination of the tumor in this case shed light on the de novo tumorigenesis of the graft kidney within the host microenvironment. Amplification of Telomerase reverse transcriptase (TERT) and loss of cyclin dependent kinase inhibitor 2A/2B (CDKN2A/CDKN2B) detected in the tumor by next gene sequencing suggests that they may play an important role in this case.
Mental healthcare for asylum-seekers and refugees residing in the United Kingdom: a scoping review of policies, barriers, and enablers
Authors: Pollard Teresa , Howard Natasha 
Published: June 2021

Abstract
Background
Since 2011, a large influx of asylum-seekers and refugees has put pressure on the UK’s under-resourced national health services and mental health services. Asylum-seekers and refugees (ASR) may experience traumatic events pre-departure, life-threating circumstances on their journeys, and difficulties integrating into host countries related to immigration policies, social isolation, poor living conditions, and unemployment, all of which can significantly affect their mental health. This topic is increasingly important due to the numbers of people seeking asylum and growing concern for their mental health on resettlement. This study examined UK-wide policies and guidance, healthcare practices, barriers, and enablers of mental healthcare for ASR residing in the UK.

Methods
We conducted a scoping review using Arksey and O’Malley’s 2005 framework, which included semi-structured interviews with stakeholders from non-governmental organisations, academia, UK National Health Service, and community groups. We synthesised and analysed literature and interview data thematically to examine current barriers and potential enablers of ASR mental health support in the UK.

Results
We included 39 literature sources, of 1,638 identified, and 10 stakeholder interviews. Sources, most published in 2019 (n = 13), included data from England (n = 13), Scotland (n = 3), Wales (n = 3), and Northern Ireland (n = 2) and covered access to care (n = 16), mental health disorders (n = 7), impacts on health (n = 7), barriers to care (n = 13), policies and plans (n = 4), and clinical recommendations (n = 3). Synthesised themes from literature and interviews included existing barriers (i.e. communication difficulties and lack of funding, resources, and political will) and potential enablers (i.e. proposed provision practices, social needs of ASR, and policy changes).

Conclusions
There is a gap in the literature regarding UK-wide assessment of access and delivery of mental healthcare for ASR in the UK. Time sensitive and culturally appropriate approaches are needed, with greater funding and resource support from the UK Government. This study provides justification for a call to relax hostile environment policies, and for ASR-specific mental health services and support to be considered within the UK. Further research is needed to assess implementation of guidelines across the UK.
Serum uric acid, disease severity and outcomes in COVID-19
Authors: Dufour Inès , Werion Alexis , Belkhir Leila , Wisniewska Anastazja , Perrot Marie , De Greef Julien , Schmit Gregory , Yombi Jean Cyr , Wittebole Xavier , Laterre Pierre-François , Jadoul Michel , Gérard Ludovic , Morelle Johann ,   the CUSL COVID-19 Research Group, Beauloye Christophe , Collienne Christine , Dechamps Mélanie , Dupriez Florence , Hantson Philippe , Jacquet Luc-Marie , Kabamba Benoit , Larbaoui Fatima , Montiel Virginie , Penaloza Andrea , Pothen Lucie , Rodriguez-Villalobos Hector , Scohy Anais , Thoma Maximilien , Van Caeneghem Olivier , Yildiz Halil 
Published: June 2021

Abstract
Background
The severity of coronavirus disease 2019 (COVID-19) is highly variable between individuals, ranging from asymptomatic infection to critical disease with acute respiratory distress syndrome requiring mechanical ventilation. Such variability stresses the need for novel biomarkers associated with disease outcome. As SARS-CoV-2 infection causes a kidney proximal tubule dysfunction with urinary loss of uric acid, we hypothesized that low serum levels of uric acid (hypouricemia) may be associated with severity and outcome of COVID-19.

Methods
In a retrospective study using two independent cohorts, we investigated and validated the prevalence, kinetics and clinical correlates of hypouricemia among patients hospitalized with COVID-19 to a large academic hospital in Brussels, Belgium. Survival analyses using Cox regression and a competing risk approach assessed the time to mechanical ventilation and/or death. Confocal microscopy assessed the expression of urate transporter URAT1 in kidney proximal tubule cells from patients who died from COVID-19.

Results
The discovery and validation cohorts included 192 and 325 patients hospitalized with COVID-19, respectively. Out of the 517 patients, 274 (53%) had severe and 92 (18%) critical COVID-19. In both cohorts, the prevalence of hypouricemia increased from 6% upon admission to 20% within the first days of hospitalization for COVID-19, contrasting with a very rare occurrence (< 1%) before hospitalization for COVID-19. During a median (interquartile range) follow-up of 148 days (50–168), 61 (12%) patients required mechanical ventilation and 93 (18%) died. In both cohorts considered separately and in pooled analyses, low serum levels of uric acid were strongly associated with disease severity (linear trend, P < 0.001) and with progression to death and respiratory failure requiring mechanical ventilation in Cox (adjusted hazard ratio 5.3, 95% confidence interval 3.6–7.8, P < 0.001) or competing risks (adjusted hazard ratio 20.8, 95% confidence interval 10.4–41.4, P < 0.001) models. At the structural level, kidneys from patients with COVID-19 showed a major reduction in urate transporter URAT1 expression in the brush border of proximal tubules.

Conclusions
Among patients with COVID-19 requiring hospitalization, low serum levels of uric acid are common and associate with disease severity and with progression to respiratory failure requiring invasive mechanical ventilation.
Extracorporeal membrane oxygenation for COVID-19: a systematic review and meta-analysis
Authors: Ramanathan Kollengode , Shekar Kiran , Ling Ryan Ruiyang , Barbaro Ryan P. , Wong Suei Nee , Tan Chuen Seng , Rochwerg Bram , Fernando Shannon M. , Takeda Shinhiro , MacLaren Graeme , Fan Eddy , Brodie Daniel 
Published: June 2021

Abstract
Background
There are several reports of extracorporeal membrane oxygenation (ECMO) use in patients with coronavirus disease 2019 (COVID-19) who develop severe acute respiratory distress syndrome (ARDS). We conducted a systematic review and meta-analysis to guide clinical decision-making and future research.

Methods
We searched MEDLINE, Embase, Cochrane and Scopus databases from 1 December 2019 to 10 January 2021 for observational studies or randomised clinical trials examining ECMO in adults with COVID-19 ARDS. We performed random-effects meta-analyses and meta-regression, assessed risk of bias using the Joanna Briggs Institute checklist and rated the certainty of evidence using the GRADE approach. Survival outcomes were presented as pooled proportions while continuous outcomes were presented as pooled means, both with corresponding 95% confidence intervals [CIs]. The primary outcome was in-hospital mortality. Secondary outcomes were duration of ECMO therapy and mechanical ventilation, weaning rate from ECMO and complications during ECMO.

Results
We included twenty-two observational studies with 1896 patients in the meta-analysis. Venovenous ECMO was the predominant mode used (98.6%). The pooled in-hospital mortality in COVID-19 patients (22 studies, 1896 patients) supported with ECMO was 37.1% (95% CI 32.3–42.0%, high certainty). Pooled mortality in the venovenous ECMO group was 35.7% (95% CI 30.7–40.7%, high certainty). Meta-regression found that age and ECMO duration were associated with increased mortality. Duration of ECMO support (18 studies, 1844 patients) was 15.1 days (95% CI 13.4–18.7). Weaning from ECMO (17 studies, 1412 patients) was accomplished in 67.6% (95% CI 50.5–82.7%) of patients. There were a total of 1583 ECMO complications reported (18 studies, 1721 patients) and renal complications were the most common.

Conclusion
The majority of patients received venovenous ECMO support for COVID-19-related ARDS. In-hospital mortality in patients receiving ECMO support for COVID-19 was 37.1% during the first year of the pandemic, similar to those with non-COVID-19-related ARDS. Increasing age was a risk factor for death. Venovenous ECMO appears to be an effective intervention in selected patients with COVID-19-related ARDS.

PROSPERO CRD42020192627.
An innovative training based on robotics for older people with subacute stroke: study protocol for a randomized controlled trial
Authors: Maranesi Elvira , Bevilacqua Roberta , Di Rosa Mirko , Pelliccioni Giuseppe , Di Donna Valentina , Luzi Riccardo , Morettini Micaela , Sbrollini Agnese , Casoni Elisa , Rinaldi Nadia , Baldoni Renato , Lattanzio Fabrizia , Burattini Laura , Riccardi Giovanni R. 
Published: June 2021

Abstract
Background
Stroke is a leading cause of disability, injury, and death in elderly people and represents a major public health problem with substantial medical and economic consequences. The incidence of stroke rapidly increases with age, doubling for each decade after age 55 years. Gait impairment is one of the most important problems after stroke, and improving walking function is often a key component of any rehabilitation program. To achieve this goal, a robotic gait trainer seems to be promising. In fact, some studies underline the efficacy of robotic gait training based on end-effector technology, for different diseases, in particular in stroke patients. In this randomized controlled trial, we verify the efficacy of the robotic treatment in terms of improving the gait and reducing the risk of falling and its long-term effects.

Methods
In this single-blind randomized controlled trial, we will include 152 elderly subacute stroke patients divided in two groups to receive a traditional rehabilitation program or a robotic rehabilitation using G-EO system, an end-effector device for the gait rehabilitation, in addition to the traditional therapy. Twenty treatment sessions will be conducted, divided into 3 training sessions per week, for 7 weeks. The control group will perform traditional therapy sessions lasting 50 min. The technological intervention group, using the G-EO system, will carry out 30 min of traditional therapy and 20 min of treatment with a robotic system. The primary outcome of the study is the evaluation of the falling risk. Secondary outcomes are the assessment of the gait improvements and the fear of falling. Further evaluations, such as length and asymmetry of the step, walking and functional status, and acceptance of the technology, will be carried.

Discussion
The final goal of the present study is to propose a new approach and an innovative therapeutic plan in the post-stroke rehabilitation, focused on the use of a robotic device, in order to obtain the beneficial effects of this treatment.

Trial registration
ClinicalTrials.gov NCT04087083. Registered on September 12, 2019