bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary function and radiological features 4 months after COVID-19: first results from the national prospective observational Swiss COVID-19 lung study
Authors: Guler Sabina A. , Ebner Lukas , Aubry-Beigelman Catherine , Bridevaux Pierre-Olivier , Brutsche Martin , Clarenbach Christian , Garzoni Christian , Geiser Thomas K. , Lenoir Alexandra , Mancinetti Marco , Naccini Bruno , Ott Sebastian R. , Piquilloud Lise , Prella Maura , Que Yok-Ai , Soccal Paula M. , von Garnier Christophe , Funke-Chambour Manuela 
Published: January 2021

BackgroundThe infectious coronavirus disease 2019 (COVID-19) pandemic is an ongoing global healthcare challenge. Up to one-third of hospitalised patients develop severe pulmonary complications and acute respiratory distress syndrome. Pulmonary outcomes following COVID-19 are unknown.MethodsThe Swiss COVID-19 lung study is a multicentre prospective cohort investigating pulmonary sequelae of COVID-19. We report on initial follow-up 4 months after mild/moderate or severe/critical COVID-19 according to the World Health Organization severity classification.Results113 COVID-19 survivors were included (mild/moderate n=47, severe/critical n=66). We confirmed several comorbidities as risk factors for severe/critical disease. Severe/critical disease was associated with impaired pulmonary function,i.e.diffusing capacity of the lung for carbon monoxide (DLCO) % predicted, reduced 6-min walk distance (6MWD) and exercise-induced oxygen desaturation. After adjustment for potential confounding by age, sex and body mass index (BMI), patients after severe/critical COVID-19 had aDLCO20.9% pred (95% CI 12.4–29.4% pred, p=0.01) lower at follow-up.DLCO% pred was the strongest independent factor associated with previous severe/critical disease when age, sex, BMI, 6MWD and minimal peripheral oxygen saturation at exercise were included in the multivariable model (adjusted odds ratio per 10% predicted 0.59, 95% CI 0. 37–0.87; p=0.01). Mosaic hypoattenuation on chest computed tomography at follow-up was significantly associated with previous severe/critical COVID-19 including adjustment for age and sex (adjusted OR 11.7, 95% CI 1.7–239; p=0.03).Conclusions4 months after severe acute respiratory syndrome coronavirus 2 infection, severe/critical COVID-19 was associated with significant functional and radiological abnormalities, potentially due to small-airway and lung parenchymal disease. A systematic follow-up for survivors needs to be evaluated to optimise care for patients recovering from COVID-19.
Tight association of genome rearrangements with gene expression in conifer plastomes
Authors: Wu Chung-Shien , Sudianto Edi , Chaw Shu-Miaw 
Published: January 2021

Abstract
Background
Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes.

Results
We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression.

Conclusions
Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.
Granulomatous interstitial nephritis in a patient with SARS-CoV-2 infection
Authors: Szajek Katarzyna , Kajdi Marie-Elisabeth , Luyckx Valerie A. , Fehr Thomas Hans , Gaspert Ariana , Cusini Alexia , Hohloch Karin , Grosse Philipp 
Published: January 2021

Abstract
Background
Acute kidney injury (AKI) associated with severe coronavirus disease 19 (COVID-19) is common and is a significant predictor of morbidity and mortality, especially when dialysis is required. Case reports and autopsy series have revealed that most patients with COVID-19 – associated acute kidney injury have evidence of acute tubular injury and necrosis - not unexpected in critically ill patients. Others have been found to have collapsing glomerulopathy, thrombotic microangiopathy and diverse underlying kidney diseases. A primary kidney pathology related to COVID-19 has not yet emerged. Thus far direct infection of the kidney, or its impact on clinical disease remains controversial. The management of AKI is currently supportive.

Case Presentation
The patient presented here was positive for SARS-CoV-2, had severe acute respiratory distress syndrome and multi-organ failure. Within days of admission to the intensive care unit he developed oliguric acute kidney failure requiring dialysis. Acute kidney injury developed in the setting of hemodynamic instability, sepsis and a maculopapular rash. Over the ensuing days the patient also developed transfusion-requiring severe hemolysis which was Coombs negative. Schistocytes were present on the peripheral smear. Given the broad differential diagnoses for acute kidney injury, a kidney biopsy was performed and revealed granulomatous tubulo-interstitial nephritis with some acute tubular injury. Based on the biopsy findings, a decision was taken to adjust medications and initiate corticosteroids for presumed medication-induced interstitial nephritis, hemolysis and maculo-papular rash. The kidney function and hemolysis improved over the subsequent days and the patient was discharged to a rehabilitation facility, no-longer required dialysis.

Conclusions
Acute kidney injury in patients with severe COVID-19 may have multiple causes. We present the first case of granulomatous interstitial nephritis in a patient with COVID-19. Drug-reactions may be more frequent than currently recognized in COVID-19 and are potentially reversible. The kidney biopsy findings in this case led to a change in therapy, which was associated with subsequent patient improvement. Kidney biopsy may therefore have significant value in pulling together a clinical diagnosis, and may impact outcome if a treatable cause is identified.
Thyroid cancer overdiagnosis and overtreatment: a cross- sectional study at a thyroid cancer referral center in Ecuador
Authors: Solis-Pazmino Paola , Salazar-Vega Jorge , Lincango-Naranjo Eddy , Garcia Cristhian , Koupermann Gabriela Jaramillo , Ortiz-Prado Esteban , Ledesma Tannya , Rojas Tatiana , Alvarado-Mafla Benjamin , Carcamo Cesar , Ponce Oscar J. , Brito Juan P. 
Published: January 2021

AbstractBackgroundIn contrast to the rapid increase in thyroid cancer incidence, the mortality has remained low and stable over the last decades. In Ecuador, however, thyroid cancer mortality has increased. The objective of this study is to determine possible drivers of high rates of thyroid cancer mortality, through a cross-sectional analysis of all patients attending a thyroid cancer referral center in Ecuador.MethodsFrom June 2014 to December 2017, a cross-sectional study was conducted at the Hospital de Especialidades Eugenio Espejo, a regional reference public hospital for endocrine neoplasia in adults in Quito, Ecuador. We identified the mechanism of detection, histopathology and treatment modalities from a patient interview and review of clinical records.ResultsAmong 452 patients, 74.8% were young adults and 94.2% (426) were female. 13.7% had a family history of thyroid cancer, and patients’ median tumor size was 2 cm. The incidental finding was 54.2% whereas 45.8% was non-incidental. Thyroid cancer histology reported that 93.3% had papillary thyroid cancer (PTC), 2.7% follicular, 1.5% Hurtle cells, 1.6% medullary, 0.7% poor differentiated, and 0.2% anaplastic carcinoma. The mean MACIS (metastasis, age, completeness, invasion, and size) score was 4.95 (CI 4.15–5.95) with 76.2% of the thyroid cancer patients having MACIS score less than or equal to 6. The very low and low risk of recurrence was 18.1% (79) and 62% (271) respectively. An analysis of 319 patients with non-metastatic thyroid cancer showed that 10.7% (34) of patients had surgical complications. Moreover, around 62.5% (80 from 128 patients with thyroglobulin laboratory results) of TC patients had a stimulated-thyroglobulin value equal or higher than 2 ng/ml. Overall, a poor surgical outcome was present in 35.1% (112) patients. Out of 436 patients with differentiated thyroid carcinoma, 86% (375) received radioactive iodine.ConclusionThyroid cancer histological characteristics and method of diagnosis are like those described in other reports without any evidence of the high frequency of aggressive thyroid cancer histology. However, we observed evidence of overtreatment and poor surgical outcomes that demand additional studies to understand their association with thyroid cancer mortality in Ecuador.
Orbital aspergillosis: a case report and review of the literature
Authors: Lever Mael , Wilde Benjamin , Pförtner Roman , Deuschl Cornelius , Witzke Oliver , Bertram Stefanie , Eckstein Anja , Rath Peter-Michael 
Published: January 2021

Abstract
Background
Orbital aspergillosis is a rare sight- and life-threatening fungal infection affecting immunocompromised or otherwise healthy patients. It is often misdiagnosed due to its unspecific clinical and radiologic appearance. Therapeutic delay can have dramatic consequences. However, progress in microbiological diagnostic techniques and therapeutic experience from case series help improve the management of this disease.

Case presentation
A 78-year-old immunocompetent woman presented at an eye clinic for subacute swelling, reddening, and ptosis of her left upper eyelid. Based on radiologic and histologic considerations, she was treated for idiopathic orbital inflammation, but her condition worsened. After a second biopsy of the orbital mass, aspergillosis was diagnosed. Her condition improved promptly after initiation of an oral voriconazole treatment. Additionally, using a polymerase chain reaction (PCR) assay, A. fumigatus was identified on tissue of both biopsies and its azole susceptibility was examined simultaneously.

Conclusions
In the case described here, oral antifungal treatment was sufficient for the therapy of invasive orbital aspergillosis. Performing fungal PCR on orbital tissue can accelerate the diagnostic process and should be performed in ambiguous cases of slowly growing orbital mass. Finally, interdisciplinary management is the key to optimal treatment of orbital tumours and infections.
Identification of pathogenic genes and transcription factors in respiratory syncytial virus
Authors: Li Lei , Ni Yong An , Song Zhenfeng , Yi Zhi , Wang Fang 
Published: January 2021

AbstractBackgroundRespiratory syncytial virus (RSV) is a major cause of acute lower respiratory infections in children, especially bronchiolitis. Our study aimed to identify the key genes and upstream transcription factors in RSV.MethodsTo screen for RSV pathogenic genes, an integrated analysis was performed using the RSV microarray dataset in GEO. Functional annotation and potential pathways for differentially expressed genes (DEGs) were further explored by GO and KEGG enrichment analysis. We constructed the RSV-specific transcriptional regulatory network to identify key transcription factors for DEGs in RSV.ResultsFrom three GEO datasets, we identified 1059 DEGs (493 up-regulated and 566 down-regulated genes, FDR < 0.05 and |Combined.ES| > 0.8) between RSV patients and normal controls. GO and KEGG analysis revealed that ‘response to virus’ (FDR = 7.13E-15), ‘mitochondrion’ (FDR = 1.39E-14) and ‘Asthma’ (FDR = 1.28E-06) were significantly enriched pathways for DEGs. The expression of IFI27, IFI44, IFITM3, FCER1A, and ISG15 were shown to be involved in the pathogenesis of RSV.ConclusionsWe concluded that IFI27, IFI44, IFITM3, FCER1A, and ISG15 may play a role in RSV. Our finding may contribute to the development of new potential biomarkers, reveal the underlying pathogenesis and also identify novel therapeutic targets for RSV.
Establishing percentiles for blood pressure based on absolute height for children and adolescents
Authors: Cossio-Bolaños Marco , Vidal-Espinoza Rubén , de Campos Felipe Castelli Correia , Sulla-Torres José , Cossio-Bolaños Wilbert , Andruske Cynthia Lee , Albornoz Camilo Urra , Campos Rossana Gómez 
Published: January 2021

Abstract
Background
Evaluating blood pressure (BP) is one element for diagnosing and preventing disease in student populations. The objectives of this research were to (a) identify the range of height for measuring BP adjusted for student populations and (b) propose percentiles for evaluating BP based on height.

Methods
A cross-sectional study was carried out with 3,013 students. Weight, height, and diastolic (DBP) and systolic (SBP) blood pressure were evaluated. Body Mass Index (BMI) was calculated. Height ranges of 5 and 10 cm were generated.

Results
R2 values for height ranges of 5 cm consisted of [normotensive: DBP (R2 = 10 to 13%) and SBP (R2 = 14 to 20%), and for hypertensive: DBP (R2 = 0.07 to 15%) and for SBP (R2 = 29 to 32%)]. For height ranges of 10 cm, values included: [normotensive: DBP (R2 = 10 to 15%), and SBP (R2 = 15 to 21%) and for hypertensive: DBP (R2 = 0.07 to 16%) and SBP (R2 = 29 to 35%)]. For 5 cm height ranges, diferences occurred between both sexes for DBP (in 5 height ranges from 123 to 148 cm and 158 to 168 cm) and for the SBP (in 6 height ranges from 128 to 148 cm and from 158 to 168 cm). In the 10 cm categories, diferences appeared in DBP (from 138 to 148 cm) and in the SBP (from 158 to 168 cm).

Conclusions
Height is a determinant for evaluating blood pressure, and height ranges of 10 cm are more suitable for children and adolescents. The proposed percentiles based on height ranges allowed assessment of the DBP and SBP suggest their use in epidemiological and educational contexts.
Psychological distress among Italians during the 2019 coronavirus disease (COVID-19) quarantine
Authors: Bonati Maurizio , Campi Rita , Zanetti Michele , Cartabia Massimo , Scarpellini Francesca , Clavenna Antonio , Segre Giulia 
Published: January 2021

Abstract
Background
Quarantine as a preventive action to reduce people’s exposure to a contagious disease has substantial psychological impact. We aimed to collect information on psychologically distressing experiences of Italians living in quarantine during the COVID-19 pandemic.

Methods
From 6 to 20 April 2020 participants filled out an online questionnaire. Demographic and physical symptoms data from the prior 14 days of quarantine were collected. Psychological impact of quarantine was assessed by the COVID-19 Peritraumatic Distress Index (CPDI).

Results
In all, 20,158 participants completed the online survey. Of these, 11,910 (59.1%) were from Lombardy, the region with 37.7% of positive cases identified during the survey period. 30.1% of responders were male. About half (55.9%) of responders were 18–50 years old, 54.3% had a tertiary level of education, 69.5% were workers, 84.1% were living in houses with ≥3 rooms, and 13.7% were living alone. 9.7% had had contact with COVID-19 positive people. Of all responders, 9978 (48.6%) reported a psychological impact, 8897 (43.4%) of whom reported mild or moderate and 1081 (5.2%) severe psychological impact. The multivariate analysis, after adjustments, showed that an increasing CPDI score was associated with gender (female), first-second educational level, being unemployed, living in a ≤2 room house, having had new health problems during the previous 14 days, and not having been out of the house in the previous week. Concerning the type of psychological distress, 2003 responders (9.9%) reported moderate to severe depressive symptoms, 1131 (5.5%) moderate to severe anxiety symptoms, and 802 (3.9%) moderate to severe physical symptoms. A positive correlation was found between responder rate (per 10.000 residents) and positive COVID-19 cases (per 10.000 residents) by region (rs = + 0.83, p = < 0.0001), and between responder rate and region latitude (rs = + 0.91, p = < 0.0001), with a greater response rate in the north. Considering Lombardy Region responders, a negative correlation between CPDI score and distance from place of residence to the red zone (Nembro-Alzano) was found. Higher prevalence of psychological distress was found up to 25 km away from the red zone and, in particular, severe distress up to 15 km.

Conclusions
Policy makers and mental health professionals should be aware of quarantine’s adverse mental health consequences. Factors influencing the success of quarantine and infection control practices for both disease containment and community recovery should be identified and additional support to vulnerable persons at increased risk of adverse psychological and social consequences of quarantine should be guaranteed.
Is preoperative glenoid bone mineral density associated with aseptic glenoid implant loosening in anatomic total shoulder arthroplasty?
Authors: Mariaux Sandrine , Obrist Raphaël , Farron Alain , Becce Fabio , Terrier Alexandre 
Published: January 2021

AbstractBackgroundAseptic loosening of glenoid implants is the primary revision cause in anatomic total shoulder arthroplasty (aTSA). While supported by biomechanical studies, the impact of glenoid bone quality, more specifically bone mineral density (BMD), on aseptic glenoid loosening remains unclear. We hypothesized that lower preoperative glenoid BMD was associated with aseptic glenoid implant loosening in aTSA.MethodsWe retrospectively included 93 patients (69 females and 24 males; mean age, 69.2 years) who underwent preoperative non-arthrographic shoulder computed tomography (CT) scans and aTSA between 2002 and 2014. Preoperative glenoid BMD (CT numbers in Hounsfield unit) was measured in 3D using a reliable semi-automated quantitative method, in the following six contiguous volumes of interest (VOI): cortical, subchondral cortical plate (SC), subchondral trabecular, and three successive adjacent layers of trabecular bone. Univariate Cox regression was used to estimate the impact of preoperative glenoid BMD on aseptic glenoid implant loosening. We further compared 26 aseptic glenoid loosening patients with 56 matched control patients.ResultsGlenoid implant survival rates were 89% (95% confidence interval CI, 81–96%) and 57% (41–74%) at 5 and 10 years, respectively. Hazard ratios for the different glenoid VOIs ranged between 0.998 and 1.004 (95% CI [0.996, 1.007],p≥0.121). Only the SC VOI showed significantly lower CTn in the loosening group (622±104 HU) compared with the control group (658±88 HU) (p=0.048), though with a medium effect size (d=0.42). There were no significant differences in preoperative glenoid BMD in any other VOI between patients from the loosening and control groups.ConclusionsAlthough the preoperative glenoid BMD was statistically significantly lower in the SC region of patients with aseptic glenoid implant loosening compared with controls, this single-VOI difference was only moderate. We are thus unable to prove that lower preoperative glenoid BMD is clearly associated with aseptic glenoid implant loosening in aTSA. However, due to its proven biomechanical role in glenoid implant survival, we recommend extending this study to larger CT datasets to further assess and better understand the impact of preoperative glenoid BMD on glenoid implant loosening/survival and aTSA outcome.
Effects of unweighting on gait kinematics during walking on a lower-body positive-pressure treadmill in patients with hip osteoarthritis
Authors: Kataoka Yoshiaki , Shimizu Tomohiro , Takeda Ryo , Tadano Shigeru , Saito Yuki , Osuka Satoshi , Ishida Tomoya , Samukawa Mina , Irie Tohru , Takahashi Daisuke , Iwasaki Norimasa , Tohyama Harukazu 
Published: January 2021

AbstractBackgroundHip osteoarthritis (OA) is a musculoskeletal condition that makes walking difficult due to pain induced by weight-bearing activities. Treadmills that support the body weight (BW) reduce the load on the lower limbs, and those equipped with a lower-body positive-pressure (LBPP) device, developed as a new method for unweighting, significantly reduce pain in patients with knee OA. However, the effects of unweighting on gait kinematics remain unclear in patients with hip OA. Therefore, we investigated the effects of unweighting on kinematics in patients with hip OA during walking on a treadmill equipped with an LBPP device.MethodsA total of 15 women with hip OA and 15 age-matched female controls wore a three-dimensional (3-D) motion analysis system and walked at a self-selected speed on the LBPP treadmill. Data regarding self-reported hip pain using a numeric rating scale (NRS) in which the scores 0 and 10 represented no pain and the worst pain, respectively, under three different BW conditions (100, 75, and 50%) were collected. Moreover, 3-D peak joint angles during gait under each condition were calculated and compared.ResultsIn the hip OA group, the NRS pain scores at 50 and 75% BW conditions significantly decreased compared with that at 100% BW condition (50%,P = 0.002; 75%,P = 0.026), and the peak hip extension angle decreased compared with that in the healthy controls (P = 0.044). In both groups, unweighting significantly decreased the peak hip (P < 0.001) and knee (P < 0.001) flexion angles and increased the peak ankle plantar flexion angle (P < 0.001) during walking.ConclusionsUnweighting by the LBPP treadmill decreased pain in the hip OA group but did not drastically alter the gait kinematics compared with that in the control group. Therefore, regarding the use of the LBPP treadmill for patients with hip OA, clinicians should consider the benefits of pain reduction rather than the kinematic changes.