bluuebunny/crossref_metadata_2025_split huggingface dataset:
Operative vs conservative treatment in distal radius fractures
Authors: Wu Meng , Li Xiongfeng , Li Jianyou , Chen Yonghua 
Published: July 2020

Abstract

Background:
Given this lack of conclusive outcome data, there are currently no clear guidelines to direct the treatment of displaced distal radius fractures in the elderly. This retrospective clinical trial was performed to compare the outcomes of two methods that were used for the treatment of displaced and unstable distal radial fractures in patients 65 years of age or older:

Methods:
This study was performed and reported in accordance with the Strengthening the Reporting of Observational studies in Epidemiology checklist. Between January 2017 and May 2018, a total of 184 patients who presented to Huzhou Traditional Chinese Medicine Hospital with distal radius fractures were extracted from the hospital database and evaluated for eligibility. This retrospective cohort study was approved by the institutional review board in our hospital. Outcome measures included Patient-Related Wrist Evaluation score, patient satisfaction, complications, and radiographic outcomes. SPSS software package (version 21.0; SPSS Inc, Chicago, IL) was used for all statistical analyses.

Results:
The hypothesis was that the two groups would achieve similar functional scores and complications in distal radial fractures.

Trial registration:
This study protocol was registered in Research Registry (researchregistry5689).
Predictors of all-cause 1-year mortality in myocardial infarction patients
Authors: Ye Qing , Zhang Jie , Ma Likun 
Published: July 2020

Abstract
Compared with the general population, myocardial infarction (MI) survivors have a higher risk of mortality in the first year after the index event.
The aim of this study was to determine the associations between variables obtained during the index admission and 1-year all-cause mortality on follow-up.
A cohort of 296 patients was enrolled in the study, with a median age of 63.8 ± 12.68 years. All patients received a coronary angiography and stent implantation by percutaneous coronary intervention. Each variable was tested for association with all-cause mortality, using chi-square tests for categorical and binary variables and t tests for continuous variables. The relative prognostic power of each significant variable was further evaluated by logistic regression before and after adjustment for differences in baseline characteristics.
Patients who were deceased after 1-year of MI had significantly higher mean age, increased prevalence of diabetes, and elevated heart rate as compared to those who were surviving. Univariate analysis indicated that patient mortality within 1-year of MI was strongly correlated with higher rates of pump failure on admission (P < .0001), bleeding complications (P = .02), the severity of coronary artery disease measured by Gensini score (P = .04), and decreased left ventricular ejection fraction (LVEF) (P < .0001). After adjustment of baseline variables, only pump failure (P = .006) and reduced LVEF (P < .0001) were independently associated with 1-year mortality.
Our study shows that LVEF dysfunction and pump failure are independent predictors of 1-year all-cause post-MI mortality, while the severity of coronary artery disease and bleeding did not qualify as independent predictors. Also, age, history of diabetes, and elevated heart rate may be used as markers for increased mortality rates.
Computed tomography-negative symptomatic intracerebral hemorrhage in a patient with cerebral small vessel disease
Authors: Han Jinhee , Yang Harin , Bae Jeong Hoon , Kim Hyun Young , Kim Young Seo 
Published: July 2020

Abstract

Rationale:
Computed tomography plays a key role in the initial evaluation of suspected acute stroke by ruling out the possibility of hemorrhage before thrombolysis. Recently, many reports have described cases of symptomatic microbleeds, and there may also have been a case of computed tomography- negative intracerebral hemorrhage.

Patient concerns:
A 70-year-old female patient who had a history of lacunar infarction and severe small vessel disease developed dysarthria. On brain non-contrast computed tomography there was no evidence of intracerebral hemorrhage. However, brain magnetic resonance imaging performed at 3 hours after the initial computed tomography showed cerebral hemorrhage.

Diagnoses:
The diagnosis was computed tomography-negative intracerebral hemorrhage.

Interventions:
The patient was treated with cilostazole 100 mg twice a day with blood pressure management.

Outcomes:
The dysarthria was fully recovered within 5 days and the patient did not suffer recurrent stroke symptoms over the following 2 years.

Lessons:
In patients with underlying severe small vessel disease and microbleeds, there could be computed tomography-negative hemorrhage and susceptibility weighted magnetic resonance image could be needed. More attention is required before applying thrombolysis therapy because there is a possibility of cerebral hemorrhage in those patients.
Progressive worsening of the respiratory and gut microbiome in children during the first two months of COVID-19
Authors: Xu Rong , Liu Pengcheng , Zhang Tao , Wu Qunfu , Zeng Mei , Ma Yingying , Jin Xia , Xu Jin , Zhang Zhigang , Zhang Chiyu 
Published: July 2020

AbstractChildren are less susceptible to COVID-19 and manifests lower morbidity and mortality after infection, for which a multitude of mechanisms may be proposed. Whether the normal development of gut-airway microbiome is affected by COVID-19 has not been evaluated. We demonstrate that COVID-19 alters the respiratory and gut microbiome of children. Alteration of the microbiome was divergent between the respiratory tract and gut, albeit the dysbiosis was dominated by genus Pseudomonas and sustained for up to 25-58 days in different individuals. The respiratory microbiome distortion persisted in 7/8 children for at least 19-24 days after discharge from the hospital. The gut microbiota showed early dysbiosis towards later restoration in some children, but not others. Disturbed development of both gut and respiratory microbiomes, and prolonged respiratory dysbiosis in children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to an increased health risk in the post-COVID-19 era.
Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia
Authors: Komissarov Andrey B. , Safina Ksenia R. , Garushyants Sofya K. , Fadeev Artem V. , Sergeeva Mariia V. , Ivanova Anna A. , Danilenko Daria M. , Lioznov Dmitry , Shneider Olga V. , Shvyrev Nikita , Spirin Vadim , Glyzin Dmitry , Shchur Vladimir , Bazykin Georgii A 
Published: July 2020

AbstractThe ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions came from non-Chinese sources, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-4) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.7 (2.5-5.0).
The assessment of Computer Vision Algorithms for the Diagnosis of Prostatic Adenocarcinoma in Surgical Specimens
Authors: Bukhari Syed Usama Khalid , Mehtab Ubeer , Hussain Syed Shahzad , Syed Asmara , Armaghan Syed Umar , Shah Syed Sajid Hussain 
Published: July 2020

AbstractIntroductionProstatic malignancy is a major cause of morbidity and fatality among men around the globe. More than a million new cases of prostatic cancer are diagnoses annually. The incidence of prostatic malignancy is rising and it is expected that more than two million new cases of prostatic carcinoma will be diagnosed in 2040. The application of machine learning to assist the histopathologists could be a very valuable adjunct tool for the histological diagnosis of prostatic malignant tumors.Aim & ObjectivesTo evaluate the effectiveness of artificial intelligence for the histopathological diagnosis of prostatic carcinoma by analyzing the digitized pathology slides.Materials & MethodsEight hundred and two (802) images in total, were obtained from the anonymised slides stained with hematoxylin and eosin which included anonymised 337 images of prostatic adenocarcinoma and 465 anonymised images of nodular hyperplasia of prostate. Eighty percent (80%) of the total digital images were used for training and 20% for testing. Three ResNet architectures ResNet-18, ResNet-34, and ResNet-50 were employed for the analysis of these images.ResultsThe evaluation of digital images by ResNet-18, ResNet-34, and ResNet-50 revealed the diagnostic accuracy of 97.1%, 98 % and 99.5 % respectively.DiscussionThe application of artificial intelligence is being considered as a very useful tool which may improve the patient care by improving the diagnostic accuracy and reducing the cost. In radiology, the application of deep learning to interpret radiological images has revealed excellent results. In the present study, the analysis of pathology images by convolutional neural network architecture revealed the diagnostic accuracy of 97.1%, 98 % and 99.5 % with by ResNet-18, ResNet-34, and ResNet-50 respectively. The findings of the present study are in accordance with the other published series, which were carried out to determine the accuracy of machine learning for the diagnosis of cancers of lung, breast and prostate. The application of deep learning for the histological diagnosis of malignant tumors could be quite helpful in improving the patient care.ConclusionThe findings of the present study suggest that intelligent vision system possibly a worthwhile tool for the histopathological evaluation of prostatic tissue to differentiate between the benign and malignant disorders.
Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations
Authors: Quistrebert Jocelyn , Orlova Marianna , Kerner Gaspard , Ton Le Thi , Luong Nguyễn Trong , Danh Nguyễn Thanh , Jabot-Hanin Fabienne , Seeleuthner Yoann , Bustamante Jacinta , Boisson-Dupuis Stéphanie , Huong Nguyen Thu , Ba Nguyen Ngoc , Casanova Jean-Laurent , Delacourt Christophe , Hoal Eileen G. , Alcaïs Alexandre , Thai Vu Hong , Thành Lai The , Abel Laurent , Schurr Erwin , Cobat Aurélie 
Published: July 2020

AbstractThe natural history of tuberculosis (TB) is characterized by a large inter-individual outcome variability after exposure to Mycobacterium tuberculosis. Specifically, some highly exposed individuals remain resistant to M. tuberculosis infection, as inferred by tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). We performed a genome-wide association study of resistance to M. tuberculosis infection in an endemic region of Southern Vietnam. We enrolled household contacts (HHC) of pulmonary TB cases and compared subjects who were negative for both TST and IGRA (n=185) with infected individuals (n=353) who were either positive for both TST and IGRA or had a diagnosis of TB. We found a genome-wide significant locus on chromosome 10q26.2 with a cluster of variants associated with strong protection against M. tuberculosis infection (OR=0.42, 95%CI 0.35-0.49, P = 3.71×10−8, for the genotyped variant rs17155120). The locus was replicated in a French multi-ethnic HHC cohort and a familial admixed cohort from a hyper-endemic area of South Africa, with an overall OR for rs17155120 estimated at 0.50 (95%CI 0.45-0.55, P = 1.26×10−9). The variants are located in intronic regions and upstream of C10orf90, a tumor suppressor gene which encodes an ubiquitin ligase activating the transcription factor p53. In silico analysis showed that the protective alleles were associated with a decreased expression in monocytes of the nearby gene ADAM12 which could lead to an enhanced response of Th17 lymphocytes. Our results reveal a novel locus controlling resistance to M. tuberculosis infection across different populations.
SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality
Authors: Fajnzylber Jesse , Regan James , Coxen Kendyll , Corry Heather , Wong Colline , Rosenthal Alexandra , Worrall Daniel , Giguel Francoise , Piechocka-Trocha Alicja , Atyeo Caroline , Fischinger Stephanie , Chan Andrew , Flaherty Keith T. , Hall Kathryn , Dougan Michael , Ryan Edward T. , Gillespie Elizabeth , Chishti Rida , Li Yijia , Jilg Nikolaus , Hanidziar Dusan , Baron Rebecca M. , Baden Lindsey , Tsibris Athe M. , Armstrong Katrina A. , Kuritzkes Daniel R. , Alter Galit , Walker Bruce D. , Yu Xu , Li Jonathan Z. ,   for the Massachusetts Consortium for Pathogen Readiness
Published: July 2020

ABSTRACTThe relationship between SARS-CoV-2 viral load and risk of disease progression remains largely undefined in coronavirus disease 2019 (COVID-19). We quantified SARS-CoV-2 viral load from participants with a diverse range of COVID-19 severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. SARS-CoV-2 plasma RNA was detected in 27% of hospitalized participants and 13% of outpatients diagnosed with COVID-19. Amongst the participants hospitalized with COVID-19, higher prevalence of detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. SARS-CoV-2 viral loads, especially plasma viremia, were associated with increased risk of mortality. SARS-CoV-2 viral load may aid in the risk stratification of patients with COVID-19 and its role in disease pathogenesis should be further explored.
Chronotropic Incompetence Limits Aerobic Exercise Capacity in Patients Taking Beta-Blockers
Authors: Tysarowski Maciej , Smarz Krzysztof , Zaborska Beata , Pilichowska-Paszkiet Ewa , Sikora-Frac Malgorzata , Budaj Andrzej , Jaxa-Chamiec Tomasz 
Published: July 2020

ABSTRACTBackgroundChronotropic incompetence in patients taking beta-blockers is associated with poor prognosis; however, its impact on exercise capacity (EC) remains unclear.MethodsWe retrospectively analyzed data from consecutive patients taking beta-blockers referred for cardiopulmonary exercise testing. EC was expressed as peak oxygen uptake (peak VO2; mL/kg/min). Chronotropic incompetence was defined as chronotropic index (CI) ≤ 62%. CI was calculated as [(HR at peak–HR at rest) / (maximum predicted HR–HR at rest)] × 100%.ResultsAmong 140 patients all taking beta-blockers (age 61 ± 9.7 years; 73% males), there were 113 (80.7%) patients with chronotropic incompetence. EC was lower in the group with chronotropic incompetence than the group without it, peak VO2 18.3 ± 5.7 vs. 24.0 ± 5.3 mL/kg/min, p < 0.001. In multivariate analysis EC correlated positively with CI (β = 0.14, p < 0.001) and male gender (β = 5.12, p < 0.001), and negatively with age (β = −0.17, p < 0.001) and presence of heart failure (β = −3.35, p < 0.001). Beta-blocker dose was not associated with EC. Partial correlation attributable to CI accounted for more than one-third of the variance in EC explained by the model.ConclusionsIn patients taking beta-blockers, presence of chronotropic incompetence was associated with lower EC, regardless of the beta-blocker dose. CI accounted for more than one-third of EC variance explained by our model.HIGHLIGHTSPatients on beta blockers with chronotropic incompetence have lower exercise capacityBeta-blocker dose is not associated with exercise capacityWe recommend incorporating chronotropic index into exercise stress testing
Sensitive alignment using paralogous sequence variants improves long read mapping and variant calling in segmental duplications
Authors: Prodanov Timofey , Bansal Vikas 
Published: July 2020

AbstractThe ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs) – sequence differences between paralogous sequences – to distinguish between multiple alignment locations. On simulated datasets, Duplomap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3% to 90.6%) and BLASR (82.9% to 90.7%) while maintaining high precision. Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8-21% of the reads in segmental duplications with high confidence relative to Minimap2. Using Duplomap aligned PacBio CCS reads, an additional 8.9 Mbp of DNA sequence was mappable, variant calling achieved a higher F1-score and 14,713 additional variants supported by linked-read data were identified. Finally, we demonstrate that a significant fraction of PSVs in segmental duplications overlap with variants and adversely impact short-read variant calling.
Bystander CD4+T cells infiltrate human tumors and are phenotypically distinct
Authors: Simoni Yannick , Li Shamin , Zhuang Summer , Heit Antja , Koo Si-Lin , Chow I-Ting , Kwok William W. , Tan Iain Beehuat , Tan Daniel S.W. , Newell Evan W. 
Published: July 2020

AbstractTumor-specific T cells likely underpin effective immune checkpoint-blockade therapies. Yet, most studies focus on Treg cells and CD8+tumor-infiltrating lymphocytes (TILs). Here we study CD4+TILs in human lung and colorectal cancers and observe that non-Treg CD4+TILs average more than 70% of total CD4+TILs in both cancer types. Leveraging high dimensional analyses including mass cytometry and single-cell sequencing, we reveal that CD4+TILs are heterogeneous at both gene and protein levels, within each tumor and across patients. Consistently, we find different subsets of CD4+TILs showing characteristics of effectors, tissue resident memory (Trm) or exhausted cells (expressing PD-1, CTLA-4 and CD39). In both cancer types, the frequencies of CD39−non-Treg CD4+TILs strongly correlate with frequencies of CD39−CD8+TILs, which we and others have previously shown to be enriched for cells specific for cancer-unrelated antigens (bystanders).Ex-vivo, we demonstrate that CD39−CD4+TILs can be specific for cancer unrelated antigens, such as HCMV epitopes. Overall, our findings highlight that CD4+TILs cells are not necessarily tumor-specific and suggest measuring CD39 expression as a straightforward way to quantify or isolate bystander CD4+T cells.Graphical abstract
Varying perivascular astroglial endfoot dimensions along the vascular tree maintain perivascular-interstitial flux through the cortical mantle
Authors: Wang Marie Xun , Ray Lori , Tanaka Kenji F. , Iliff Jeffrey J. , Heys Jeffrey 
Published: July 2020

AbstractThe glymphatic system is a recently defined brain-wide network of perivascular spaces along which cerebrospinal fluid (CSF) and interstitial solutes exchange. Astrocyte endfeet encircling the perivascular space form a physical barrier in between these two compartments, and fluid and solutes that are not taken up by astrocytes move out of the perivascular space through the junctions in between astrocyte endfeet. However, little is known about the anatomical structure and the physiological roles of the astrocyte endfeet in regulating the local perivascular exchange. Here, visualizing astrocyte endfoot-endfoot junctions with immunofluorescent labeling against the protein megalencephalic leukoencephalopathy with subcortical cysts-1 (MLC1), we characterized endfoot dimensions along the mouse cerebrovascular tree. We observed marked heterogeneity in endfoot dimensions along vessels of different sizes, and of different types. Specifically, endfoot size was positively correlated with the vessel diameters, with large vessel segments surrounded by large endfeet and small vessel segments surrounded by small endfeet. This association was most pronounced along arterial, rather than venous segments. Computational modeling simulating vascular trees with uniform or varying endfeet dimensions demonstrates that varying endfoot dimensions maintain near constant perivascular-interstitial flux despite correspondingly declining perivascular pressures along the cerebrovascular tree through the cortical depth. These results describe a novel anatomical feature of perivascular astroglial endfeet and suggest that endfoot heterogeneity may be an evolutionary adaptation to maintain perivascular CSF-interstitial fluid exchange through deep brain structures.
Simultaneous Epigenetic Perturbation and Genome Imaging Reveal Distinct Roles of H3K9me3 in Chromatin Architecture and Transcription
Authors: Feng Ying , Wang Yao , Wang Xiangnan , He Xiaohui , Yang Chen , Naseri Ardalan , Pederson Thoru , Zheng Jing , Zhang Shaojie , Xiao Xiao , Xie Wei , Ma Hanhui 
Published: July 2020

AbstractDespite the long-observed correlation between H3K9me3, chromatin architecture and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cells remains unclear. Here we develop EpiGo (EpigeneticperturbationinducedGenomeorganization)-KRAB to introduce H3K9me3 at hundreds of loci spanning megabases on human chromosome 19 and simultaneously track genome organization. EpiGo-KRAB is sufficient to inducede novoheterochromatin-like domain formation, which requires SETDB1, a methyltransferase of H3K9me3. Unexpectedly, EpiGo-KRAB induced heterochromatin-like domain does not result in widespread gene repression except a small set of genes with concurrent loss of H3K4me3 and H3K27ac. Ectopic H3K9me3 appears to spread in inactive regions but is largely restricted to transcriptional initiation sites in active regions. Finally, Hi-C analysis showed that EpiGo-KRAB induced to reshape existing compartments. These results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression.
A Kmer-based paired-end read (KPR)de novoassembler and genotyper to genotype major histocompatibility complex class I (MHC-I) alleles for the dog
Authors: Feng Yuan , Hildebrand William H. , Tompkins Stephen M. , Zhao Shaying 
Published: July 2020

AbstractThe major histocompatibility complex class I (MHC-I) genes are highly polymorphic among individuals. MHC-I genotyping is required for determining the antigen-binding specificity of each MHC-I molecule in an individual. Numerous tools have been developed for human MHC-I genotyping using deep sequencing data such as RNA-seq; however they do not work for the dog, due to very limited information for canine alleles. To address this issue, we developed a Kmer-based paired-end read (KPR)de novoassembler and genotyper, which first assemble paired-end RNA-seq reads mapped to the MHC-I regions into contigsde novoand then genotype each contig. Our KPR tools are validated by Sanger sequencing, simulation and published genotype data. Applying our KPR tools on the published RNA-seq data of 158 tumor and 64 normal samples from 158 dogs, we have achieved a genotyping success rate of 86%, which includes 133 tumor and 57 normal samples from 142 dogs. We have identified 39 known alleles and 83 new alleles of high confidence in these dogs, yielding a more comprehensive MHC-I allele diversity landscape for the dog.