bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-Year Clinical and Radiological Outcomes in Patients With Diabetes Undergoing Single-Level Anterior Cervical Discectomy and Fusion
Authors: Arnold Paul M. , Vaccaro Alexander R. , Sasso Rick C. , Goulet Benoit , Fehlings Michael G. , Heary Robert F. , Janssen Michael E. , Kopjar Branko 
Published: April 2020

Study Design: Secondary analysis of data from the multicenter, randomized, parallel-controlled Food and Drug Administration (FDA) investigational device exemption study. Objective: Studies on outcomes following anterior cervical discectomy and fusion (ACDF) in individuals with diabetes are scarce. We compared 24-month radiological and clinical outcomes in individuals with and without diabetes undergoing single-level ACDF with either i-FACTOR or local autologous bone. Methods: Between 2006 and 2013, 319 individuals with single-level degenerative disc disease (DDD) and no previous fusion at the index level underwent ACDF. The presence of diabetes determined the 2 cohorts. Data collected included radiological fusion evaluation, neurological outcomes, Neck Disability Index (NDI), Visual Analog Scale (VAS) scores, and the 36-Item Short Form Survey Version 2 (SF-36v2) Physical and Mental component summary scores. Results: There were 35 individuals with diabetes (11.1%; average body mass index [BMI] = 32.99 kg/m2; SD = 5.72) and 284 without (average BMI = 28.32 kg/m2; SD = 5.67). The number of nondiabetic smokers was significantly higher than diabetic smokers: 73 (25.70%) and 3 (8.57%), respectively. Preoperative scores of NDI, VAS arm pain, and SF-36v2 were similar between the diabetic and nondiabetic participants at baseline; however, VAS neck pain differed significantly between the cohorts at baseline ( P = .0089). Maximum improvement for NDI, VAS neck and arm pain, and SF-36v2 PCS and MCS scores was seen at 6 months in both cohorts and remained stable until 24 months. Conclusions: ACDF is effective for cervical radiculopathy in patients with diabetes. Diabetes is not a contraindication for patients requiring single-level surgery for cervical DDD.
Effect of total dissolved gas supersaturation on the tolerance of grass carp (Ctenopharyngodon idellus)
Authors: Fan Zequn , Deng Yuxuan , Yuan Quan , Liu Xiaoqing , Shi Haoran , Feng Cuixia , Yang Yao , Xu Liangfang 
Published: April 2020

Abstract
Background
Total dissolved gas (TDG) caused by the rapid outflow of water from dams may threaten the survival of fish. However, few studies have assessed the impact of fish size on their tolerance to TDG supersaturation in the Yangtze River. To investigate the influences of fish size on the TDG supersaturation tolerance of fish, juvenile grass carp (Ctenopharyngodon idellus) of two sizes were subjected to TDG-supersaturated water at high levels (125%, 130%, 135% and 140%). Furthermore, varying flood flows may cause different TDG levels during the flood season. Fish may be subjected to low, chronic exposure to TDG before peak flooding occurs. However, TDG tolerance in fish subjected to high levels of TDG-supersaturated water after chronic exposure is rare. To further investigate the tolerance of juvenile grass carp subjected to acute exposure after chronic TDG exposure, juvenile grass carp were exposed to high levels of TDG-supersaturated water (125–140%) after receiving 96 h of chronic exposure (115% TDG).

Results
In the single acute exposure and multiple exposures (acute exposure after chronic exposure), similar abnormal behaviours and symptoms of gas bubble disease (GBD) were observed in the juvenile grass carp subjected to the TDG-supersaturated water. No abnormal behaviour or mortality was observed in fish in the first chronic exposure of the multiple-exposure treatment. As the TDG level increased, the mortality of the large and small juvenile grass carp increased. The median lethal time (LT50) for the large juvenile grass carp was 36.55, 21.75 and 6.37 h at 130%, 135% and 140% TDG levels, respectively, while the LT50 value of the small juvenile grass carp was 88.13, 61.49 and 35.88 h at the same TDG levels, respectively. In addition, the LT50 value of juvenile grass carp during acute TDG exposure after chronic exposure was 26.22, 7.54 and 5.34 h at 130%, 135% and 140% TDG levels, respectively.

Conclusion
The tolerance of juvenile grass carp decreased with increasing TDG levels. The large juvenile grass carp had weaker tolerance to TDG-supersaturated water than the small juvenile grass carp. In addition, compared with juvenile grass carp subjected to single acute exposure, juvenile grass carp subjected to multiple exposures exhibited lower tolerance and were more vulnerable to the adverse effects of TDG.
A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Authors: Wu Leilei , Deng Qinfang , Xu Ze , Zhou Songwen , Li Chao , Li Yi-Xue 
Published: April 2020

Abstract
Background
Hybrid capture-based next-generation sequencing of DNA has been widely applied in the detection of circulating tumor DNA (ctDNA). Various methods have been proposed for ctDNA detection, but low-allelic-fraction (AF) variants are still a great challenge. In addition, no panel-wide calling algorithm is available, which hiders the full usage of ctDNA based ‘liquid biopsy’. Thus, we developed the VBCALAVD (Virtual Barcode-based Calling Algorithm for Low Allelic Variant Detection) in silico to overcome these limitations.

Results
Based on the understanding of the nature of ctDNA fragmentation, a novel platform-independent virtual barcode strategy was established to eliminate random sequencing errors by clustering sequencing reads into virtual families. Stereotypical mutant-family-level background artifacts were polished by constructing AF distributions. Three additional robust fine-tuning filters were obtained to eliminate stochastic mutant-family-level noises. The performance of our algorithm was validated using cell-free DNA reference standard samples (cfDNA RSDs) and normal healthy cfDNA samples (cfDNA controls). For the RSDs with AFs of 0.1, 0.2, 0.5, 1 and 5%, the mean F1 scores were 0.43 (0.25~0.56), 0.77, 0.92, 0.926 (0.86~1.0) and 0.89 (0.75~1.0), respectively, which indicates that the proposed approach significantly outperforms the published algorithms. Among controls, no false positives were detected. Meanwhile, characteristics of mutant-family-level noise and quantitative determinants of divergence between mutant-family-level noises from controls and RSDs were clearly depicted.

Conclusions
Due to its good performance in the detection of low-AF variants, our algorithm will greatly facilitate the noninvasive panel-wide detection of ctDNA in research and clinical settings. The whole pipeline is available at https://github.com/zhaodalv/VBCALAVD.
Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms
Authors: Tretina Kyle , Pelle Roger , Orvis Joshua , Gotia Hanzel T. , Ifeonu Olukemi O. , Kumari Priti , Palmateer Nicholas C. , Iqbal Shaikh B. A. , Fry Lindsay M. , Nene Vishvanath M. , Daubenberger Claudia A. , Bishop Richard P. , Silva Joana C. 
Published: April 2020

AbstractBackgroundThe apicomplexan parasiteTheileria parvacauses a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution ofT. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage ofT. parvato update structural and functional gene annotations across the entire nuclear genome.ResultsThe re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized.ConclusionsThe process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites.
Are interventions effective at improving driving in older drivers?: A systematic review
Authors: Castellucci H. I. , Bravo G. , Arezes P. M. , Lavallière M. 
Published: April 2020

AbstractBackgroundWith the aging of the population, the number of older drivers is on the rise. This poses significant challenges for public health initiatives, as older drivers have a relatively higher risk for collisions. While many studies focus on developing screening tools to identify medically at-risk drivers, little research has been done to develop training programs or interventions to promote, maintain or enhance driving-related abilities among healthy individuals. The purpose of this systematic review is to synopsize the current literature on interventions that are tailored to improve driving in older healthy individuals by working on components of safe driving such as: self-awareness, knowledge, behaviour, skills and/or reducing crash/collision rates in healthy older drivers.MethodsRelevant databases such as Scopus and PubMed databases were selected and searched for primary articles published in between January 2007 and December 2017. Articles were identified using MeSH search terms: (“safety” OR “education” OR “training” OR “driving” OR “simulator” OR “program” OR “countermeasures”) AND (“older drivers” OR “senior drivers” OR “aged drivers” OR “elderly drivers”). All retrieved abstracts were reviewed, and full texts printed if deemed relevant.ResultsTwenty-five (25) articles were classified according to: 1) Classroom settings; 2) Computer-based training for cognitive or visual processing; 3) Physical training; 4) In-simulator training; 5) On-road training; and 6) Mixed interventions. Results show that different types of approaches have been successful in improving specific driving skills and/or behaviours. However, there are clear discrepancies on how driving performance/behaviours are evaluated between studies, both in terms of methods or dependent variables, it is therefore difficult to make direct comparisons between these studies.ConclusionsThis review identified strong study projects, effective at improving older drivers’ performance and thus allowed to highlight potential interventions that can be used to maintain or improve older drivers’ safety behind the wheel. There is a need to further test these interventions by combining them and determining their effectiveness at improving driving performance.
Altered Achilles tendon morphology in individuals with chronic post-stroke hemiparesis: a case report
Authors: Liang Jing Nong , Ho Kai-Yu 
Published: April 2020

Abstract
Background
Individuals post-stroke walk slowly and with more effort, which puts them at higher risks for falls. The slow walking speed results from insufficient propulsive forces generated by the paretic leg. Current rehabilitative efforts to improve walking function target increasing propulsive forces, but overlook the muscle-tendon unit.

Case presentations
Two individuals with chronic post-stroke hemiparesis are presented. In both individuals post-stroke, paretic ankle plantarflexors presented with increased muscle tone. Gait kinetics revealed asymmetric propulsive forces, specifically, insufficient propulsive forces by the paretic legs, consistent with previous literature. Sonography revealed increased thickness of paretic Achilles tendon at the calcaneal insertion, in both stroke cases, in contrast to comparable Achilles tendon thickness between limbs in the non-neurologically impaired controls.

Conclusion
Tendon unit integrity should be considered in individuals post-stroke who demonstrate abnormal muscle tone and insufficient propulsion during gait.
Exons deletion of CNKSR2 gene identified in X-linked syndromic intellectual disability
Authors: Daoqi Mei , Guohong Chen , Yuan Wang , Zhixiao Yang , Kaili Xu , Shiyue Mei 
Published: April 2020

Abstract
Background
The Houge type of X-linked syndromic mental retardation is an X-linked intellectual disability (XLID) recently recorded in the Online Mendelian Inheritance in Man (OMIM) and only 8 cases have been reported in literature thus far.

Case presentation
We present two brothers with intractable seizures and syndromic intellectual disability with symptoms consisting of delayed development, intellectual disability, and speech and language delay. The mother was a symptomatic carrier with milder clinical phenotype. Whole exome sequencing identified a small fragment deletion spanning four exons, about 9.5 kilobases (kb) in length in the CNKSR2 gene in the patients. The mutation co-segregation revealed that exon deletions occurred de novo in the proband’s mother.

Conclusion
Although large deletions have been reported, no small deletions have yet been identified. In this case report, we identified a small deletion in the CNKSR2 gene. This study enhances our knowledge of the CNKSR2 gene mutation spectrum and provides further information about the phenotypic characteristics of X-linked syndromic intellectual disability.
Prevalence and risk factors of chronic kidney disease and diabetic kidney disease in a central Chinese urban population: a cross-sectional survey
Authors: Duan Jia-Yu , Duan Guang-Cai , Wang Chong-Jian , Liu Dong-Wei , Qiao Ying-Jin , Pan Shao-Kang , Jiang Deng-Ke , Liu Yong , Zhao Zi-Hao , Liang Lu-Lu , Tian Fei , Liu Zhang-Suo 
Published: April 2020

Abstract
Background
This study was conducted to evaluate and update the current prevalence of and risk factors for chronic kidney disease (CKD) and diabetic kidney disease (DKD) in a central Chinese urban population.

Methods
From December 2017 to June 2018, a total of 5231 subjects were randomly enrolled from 3 communities in 3 districts of Zhengzhou. CKD was defined as estimated glomerular filtration rate (eGFR) < 60 mL/min.1.73m2 or urinary albumin to creatinine ratio ≥ 30 mg/g (albuminuria). Diabetic subjects with systolic blood pressure > 140 mmHg, albuminuria or an eGFR less than 60 mL/min/1.73 m2 were classified as having DKD. Participants completed a questionnaire assessing lifestyle and relevant medical history, and blood and urine specimens were taken. Serum creatinine, uric acid, total cholesterol, triglycerides, low-density lipoprotein, high-density lipoprotein and urinary albumin were assessed. The age- and sex-adjusted prevalences of CKD and DKD were calculated, and risk factors associated with the presence of reduced eGFR, albuminuria, DKD, severity of albuminuria and progression of reduced renal function were analyzed by binary and ordinal logistic regression.

Results
The overall adjusted prevalence of CKD was 16.8% (15.8–17.8%) and that of DKD was 3.5% (3.0–4.0%). Decreased renal function was detected in 132 participants (2.9, 95% confidence interval [CI]: 2.5–3.2%), whereas albuminuria was found in 858 participants (14.9, 95% CI: 13.9–15.9%). In all participants with diabetes, the prevalence of reduced eGFR was 6.3% (95% CI = 3.9–8.6%) and that of albuminuria was 45.3% (95% CI = 40.4–50.1%). The overall prevalence of CKD in participants with diabetes was 48.0% (95% CI = 43.1–52.9%). The results of the binary and ordinal logistic regression indicated that the factors independently associated with a higher risk of reduced eGFR and albuminuria were older age, sex, smoking, alcohol consumption, overweight, obesity, diabetes, hypertension, dyslipidemia and hyperuricemia.

Conclusions
Our study shows the current prevalence of CKD and DKD in residents of Central China. The high prevalence suggests an urgent need to implement interventions to relieve the high burden of CKD and DKD in China.
Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq
Authors: Yin Qinyan , Strong Michael J. , Zhuang Yan , Flemington Erik K. , Kaminski Naftali , de Andrade Joao A. , Lasky Joseph A. 
Published: April 2020

AbstractBackgroundNumerous publications suggest an association between herpes virus infection and idiopathic pulmonary fibrosis (IPF). These reports have employed immunohistochemistry, in situ hybridization and/or PCR, which are susceptible to specificity artifacts.MethodsWe investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K).ResultsWe identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs.ConclusionsTo the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
Daily fluctuating temperatures decrease growth and reproduction rate of a lethal amphibian fungal pathogen in culture
Authors: Lindauer Alexa L. , Maier Paul A. , Voyles Jamie 
Published: April 2020

Abstract
Background
Emerging infectious diseases (EIDs) are contributing to species die-offs worldwide. We can better understand EIDs by using ecological approaches to study pathogen biology. For example, pathogens are exposed to variable temperatures across daily, seasonal, and annual scales. Exposure to temperature fluctuations may reduce pathogen growth and reproduction, which could affect pathogen virulence, transmission, and environmental persistence with implications for disease. We examined the effect of a variable thermal environment on reproductive life history traits of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Bd causes chytridiomycosis, an emerging infectious disease of amphibians. As a pathogen of ectothermic hosts, Bd can be exposed to large temperature fluctuations in nature. To determine the effect of fluctuating temperatures on Bd growth and reproduction, we collected temperature data from breeding pools of the Yosemite toad (Anaxyrus canorus), a federally threatened species that is susceptible to chytridiomycosis. We cultured Bd under a daily fluctuating temperature regime that simulated Yosemite toad breeding pool temperatures and measured Bd growth, reproduction, fecundity, and viability.

Results
We observed decreased Bd growth and reproduction in a diurnally fluctuating thermal environment as compared to cultures grown at constant temperatures within the optimal Bd thermal range. We also found that Bd exhibits temperature-induced trade-offs under constant low and constant high temperature conditions.

Conclusions
Our results provide novel insights on variable responses of Bd to dynamic thermal conditions and highlight the importance of incorporating realistic temperature fluctuations into investigations of pathogen ecology and EIDs.
Elastography for the diagnosis of high-suspicion thyroid nodules based on the 2015 American Thyroid Association guidelines: a multicenter study
Authors: Hairu Li , Yulan Peng , Yan Wang , Hong Ai , Xiaodong Zhou , Lichun Yang , Kun Yan , Ying Xiao , Lisha Liu , Baoming Luo , Qiang Yong , Shuzhen Cong , Shuangquan Jiang , Xin Fu , Buyun Ma , Yi Li , Xixi Zhang , Xue Gong , Haitao Chen , Wenying Liu , Ling Tang , Xiaoyu Lv , Xinbao Zhao , Liang Li , Kehong Gan , Jiawei Tian 
Published: April 2020

AbstractBackgroundAn accurate diagnosis for high-suspicion nodules based on the 2015 American Thyroid Association (ATA) guidelines would reduce unnecessary invasive examinations. Elastography is a useful tool for discriminating benign and malignant thyroid nodules. The aim of this study is to investigate the diagnostic efficiency of elastography for high-suspicion thyroid nodules based on the 2015 ATA guidelines in the Chinese population.MethodsThyroid nodules with high-suspicion characteristics based on the 2015 ATA guidelines were subjected to conventional ultrasound (US) and ultrasound strain elastography (USE) examinations at 12 hospitals from 4 geographic regions across China. Cytology/histology of thyroid nodules was used as a reference method. Receiver operating characteristic (ROC) curves were plotted to evaluate the diagnostic performance of the elasticity score (ES) and strain ratio (SR). Logistic regression analysis was used to determine the predictors of malignancy.ResultsOverall, a total of 1445 thyroid nodules (834 malignant, 611 benign) from 12 centers were included in the final analysis. The areas under the curve of the ES and SR were 0.828 and 0.732, respectively. The sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the ES were 92.4, 60.7, 79.0, 76.3 and 85.5%, respectively, and those of the SR were 81.1, 50.1, 68.9, 65.9 and 67.9%, respectively. The combination of the Thyroid Imaging Reporting and Data System (TI-RADS) and ES led to a significant increase in the sensitivity and NPV (97.1 and 91.9%, respectively) compared with the TI-RADS alone. Logistic regression analysis showed that microcalcifications (OR = 5.290), taller than wide (OR = 12.710), irregular margins (OR = 10.117), extrathyroidal extension (ETE; OR = 6.412), the ES (OR = 3.741) and the SR (OR = 1.083) were independent predictors of malignant thyroid nodules. The sensitivity, specificity, accuracy, PPV and NPV of the ES were all superior in nodules ≥1 cm than in those < 1 cm (95.0% vs 90.4, 68.8% vs 56.8, 85.9% vs 74.4, 85.2% vs 69.9, and 87.8% vs 84.2%, respectively).ConclusionsElastography combined with the ES is a valuable tool for the assessment of high-suspicion thyroid nodules based on the 2015 ATA guidelines, especially in nodules ≥1 cm.