bluuebunny/crossref_metadata_2025_split huggingface dataset:
A giant peritoneal loose body impacted in the pelvic cavity, a rare and interesting finding during laparotomy
Authors: Mohammed Ayad A. 
Published: October 2020

Background:
Peritoneal loose bodies (sometimes termed as peritoneal mice) are rare findings that may be discovered incidentally during laparotomy or at autopsy. They consist of densely hyalinized, laminated, fibrous tissue which is arranged in multiple concentric layers. They arise from epiploic appendices which undergo torsion, ischemia and necrosis, saponification and then calcification. In most patients they cause no symptoms or nonspecific symptoms.

Case Presentation:
A 67-year-old male presented with lower abdominal pain and constipation for 3 months. Abdominal examination showed a fixed palpable mass in the lower abdomen arising from the pelvic cavity, the mass was firm, not tender and not mobile.
Magnetic resonance imaging of the pelvis showed a large lobulated 10×70 cm abdominal mass with no significant enhancement. During laparotomy there was a large smooth and firm intraperitoneal mass which was attached by small pedicle to the omentum. Extraction of the mass was performed. The cut surface of the mass showed multiple concentric layers with a central stone like structure. Histopathologic evaluation revealed extensive fibrous tissue with mild inflammatory cells infiltration and areas of calcifications.

Conclusion:
The most important critical step in the management of peritoneal loose bodies is to distinguish them from other intraperitoneal masses particularly tumors which is sometimes very difficult and may require some invasive procedures including surgery, surgery may also be required for large symptomatic masses.
Assessment of Cerebral Vasomotor Reactivity in Patients With Primary Open-angle Glaucoma and Ocular Hypertension Using the Breath-Holding Index
Authors: Arslan Gurcan D. , Olgun Ali , Ozcan Delil , Gökcal Elif , Guven Dilek , Asil Talip 
Published: October 2020

Précis:
Patients with ocular hypertension (OHT) do not show impaired cerebral vasodilation responses to hypercapnia but patients with primary open-angle glaucoma (POAG) do. Impaired vasoreactivity in patients with POAG may have neuronal or vascular origins and increase stroke risk.

Purpose:
To investigate changes in cerebral blood flow and cerebral vasomotor reactivity using the breath-holding index in patients with POAG and OHT, to examine whether these parameters contribute to the risk of ischemic stroke.

Methods:
Thirty patients with POAG, 30 patients with OHT, and 30 age- and sex-matched healthy control subjects were included in this university hospital-based, cross-sectional, and observational study. Eyes with a greater degree of visual field loss and/or more severe optic disc damage were selected for the study in patients with POAG, whereas in patients with OHT and controls, the study eye was chosen randomly. The mean blood flow velocity and breath-holding index were measured in the middle cerebral artery ipsilaterally in patient and control groups, by using transcranial Doppler ultrasonography.

Results:
The mean blood flow velocity and breath-holding indexes were significantly lower in patients with POAG than in the control group (all P<0.05). In the OHT group, the mean blood flow velocity and breath-holding indexes were not different from those in the control group.

Conclusions:
Patients with POAG have impaired vasodilation response to hypercapnia. Presumably, the neuronal changes and deterioration of the endothelium-mediated vasodilatation in patients with glaucoma may disrupt the regulation of arteries and potentially present functional insufficiency on vasoreactivity. Moreover, impaired cerebral vascular regulation may contribute to the increased risk of stroke in patients with POAG.
Health-related Quality of Life for Children With Leukemia: Child and Parental Perceptions
Authors: Ocak Ece , Yozgat Ayca K. , Kacar Dilek , Sucakli Iclal A. , Ozbek Namik Y. , Uneri Ozden S. , Yarali Nese 
Published: October 2020

Background:
The importance of health-related quality of life (HRQoL) in patients with acute lymphoblastic leukemia (ALL) has increased in recent years. This study aimed to assess HRQoL in children with ALL, affecting factors, and the relationship between parent proxy-report and child self-report HRQoL.

Materials and Methods:
A total of 59 children and their parents (both mother and father) were enrolled in this cross-sectional study. Turkish version of the Pediatric Quality of Life Inventory (PedsQL) 3.0 Cancer Modules were used to determine HRQoL.

Results:
According to subscales of the self-report form, nausea and operational anxiety scores differed significantly by the treatment status; communication score varied considerably by the hospitalization length of stay; pain and hurt, cognitive problems, and perceived physical appearance scores differed significantly by the maternal chronic disease status (P<0.05). The presence of maternal chronic disease was significantly related to the total score of the parent-proxy report (mother) (P<0.05). There was a moderate correlation between total scores of child and mother (P<0.05, r=0.419) but not with the father.

Conclusion:
Children on-treatment had significant problems in nausea and procedural anxiety subscales; however, children who were hospitalized more had fewer issues in the communication subscale. Also, children whose mother had chronic disease had poorer HRQoL regarding pain and hurt cognitive problems and treatment anxiety. Given the importance of assessment and monitoring HRQoL in children with ALL, health professionals should be aware of how parents’ chronic disease affects HRQoL. Psychosocial support should be provided to children and their parents, especially for those whose parents have a chronic illness.
Thyroid Metastasis From Cutaneous Melanoma on an 18F-FDG PET/CT Study
Authors: León-Asuero-Moreno Ignacio , García-Gómez Francisco Javier , Ríos-Martín Juan José , Álamo-de-la-Gala María del Carmen , Calvo-Morón María Cinta 
Published: October 2020

Abstract
The thyroid gland is an uncommon location for metastasis. We report a 59-year-old woman with a history of cutaneous malignant melanoma. A unique hypermetabolic mass on the left thyroid lobe was identified by control 18F-FDG PET/CT scan, leading to dysphagia and stridor clinic. Total thyroidectomy and lymphadenectomy were performed with histopathological results concordant with metastasis from melanoma. Despite its rarity, finding focal thyroid lesions in patients with an oncological history should alert us, recommending that its metastatic etiology be ruled out.
Geriatric Risk Prediction Models for Major Gastroenterological Surgery Using the National Clinical Database in Japan
Authors: Kofunato Yasuhide , Takahashi Arata , Gotoh Mitsukazu , Kakeji Yoshihiro , Seto Yasuyuki , Konno Hiroyuki , Kumamaru Hiraku , Miyata Hiroaki , Marubashi Shigeru 
Published: October 2020

Objectives:
To investigate the effect of geriatric variables on 5 newly added outcomes and create risk models for predicting these outcomes.

Summary of Background Data:
Because there is a current lack of geriatric research focusing on geriatric outcomes using a national surgical database in Japan, there is a need to investigate outcomes associated with major gastro-enterological surgery using these data.

Methods:
This multicenter prospective cohort study was conducted at 26 surgery departments across 21 institutions in Japan using the NCD surgical registry. in total, 22 new geriatric variables were imported from the ACS National Surgical Quality Improvement Program geriatric pilot study. The following 5 geriatric outcomes were defined: (1) postoperative delirium, (2) physical function on postoperative day 30, (3) fall risk on discharge, (4) discharge other than home with social service, and (5) functional decline on discharge, and geriatric risk prediction models for major gastroenterological surgery were created.

Results:
Between January 2018 and December 2018, data on 3981 procedures from 7 major gastroenterological surgeries were collected and analyzed. Older age and preoperative geriatric variables (Origin status from home, History of dementia, Use of mobility aid, fall history, and not competent on admission) were strongly associated with postoperative outcomes. Geriatric risk prediction models for these outcomes were created, with C-statistic values ranging from 0.74 to 0.90, demonstrating model validity and sufficiency of fit.

Conclusions:
The risk models for the newly defined 5 geriatric outcomes that we created can be used in the decision-making process or provision of care in geriatric patients.
Cost-effectiveness of Restrictive Strategy Versus Usual Care for Cholecystectomy in Patients With Gallstones and Abdominal Pain (SECURE-trial)
Authors: Latenstein Carmen S.S. , Wennmacker Sarah Z. , van Dijk Aafke H. , Drenth Joost P.H. , Westert Gert P. , van Laarhoven Cornelis J.H.M. , Boermeester Marja A. , de Reuver Philip R. , Dijkgraaf Marcel G.W. ,   on behalf of the SECURE trial collaborators
Published: October 2020

Objective:
To perform a cost-effectiveness analysis of restrictive strategy versus usual care in patients with gallstones and abdominal pain.

Summary of Background Data:
A restrictive selection strategy for surgery in patients with gallstones reduces cholecystectomies, but the impact on overall costs and cost-effectiveness is unknown.

Methods:
Data of a multicentre, randomized-controlled trial (SECURE-trial) were used. Adult patients with gallstones and abdominal pain were included. Restrictive strategy was economically evaluated against usual care from a societal perspective. Hospital-use of resources was gathered with case-report forms and out-of-hospital consultations, out-of-pocket expenses, and productivity loss were collected with questionnaires. National unit costing was applied. The primary outcome was the cost per pain-free patient after 12 months.

Results:
All 1067 randomized patients (49.0 years, 73.7% females) were included. After 12 months, 56.2% of patients were pain-free in restrictive strategy versus 59.8% after usual care. The restrictive strategy significantly reduced the cholecystectomy rate with 7.7% and reduced surgical costs with €160 per patient, €162 was saved from a societal perspective. The cost-effectiveness plane showed that restrictive strategy was cost saving in 89.1%, but resulted in less pain-free patients in 88.5%. Overall, the restrictive strategy saved €4563 from a societal perspective per pain-free patient lost.

Conclusions:
A restrictive selection strategy for cholecystectomy saves €162 compared to usual care, but results in fewer pain-free patients. The incremental cost per pain-free patient are savings of €4563 per pain-free patient lost. The higher societal willingness to pay for 1 extra pain-free patient, the lower the probability that the restrictive strategy will be cost-effective.

Trial registration:
The Netherlands National Trial Register NTR4022. Registered on 5 June 2013.
The Surge in Deceased Liver Donors Due to the Opioid Epidemic: Is It Time to Split the Difference?
Authors: Yoeli Dor , Choudhury Rashikh A. , Nydam Trevor L. , Pomposelli James J. , Goss John A. , Pomfret Elizabeth A. , Wachs Michael E. , Adams Megan A. 
Published: October 2020

Background.
This study aimed to compare trends in use of drug overdose (DO) donors in adult versus pediatric liver transplants and the utilization of split liver transplantation in this donor population.

Methods.
The United Network for Organ Sharing database was reviewed for deceased donor liver transplants from March 2002 to December 2017. Recipients were categorized by donor mechanism of death. Donor splitting criteria was defined as age <40 y, single vasopressor or less, transaminases no >3 times the normal limit, and body mass index ≤ 28 kg/m2.

Results.
Adult liver transplants from DO donors increased from 2% in 2002 to 15% in 2017, while pediatric liver transplants from DO donors only increased from <1% to 3% in the same time. While 28% of DO donors met splitting criteria, only 3% of those meeting splitting criteria were used as a split graft. Both pediatric and adult recipients of DO donor livers achieved excellent patient and graft survival.

Conclusions.
DO donors are underutilized in pediatric liver transplantation. Increased splitting of DO donor livers could significantly decrease, if not eliminate, the pediatric liver waiting list.
Understanding the value of clinical symptoms of COVID-19. A logistic regression model
Authors: Fleitas Pedro E. , Paz Jorge A. , Simoy Mario I. , Vargas Carlos , Cimino Rubén O. , Krolewiecki Alejandro J. , Aparicio Juan P. 
Published: October 2020

AbstractBackgroundThe new coronavirus SARS-CoV-2, the causative agent of COVID-19, is responsible for the current pandemic outbreak worldwide. However, there is limited information regarding the set of specific symptoms of COVID-19. Therefore, the objective of this study was to describe the main symptoms associated with COVID-19 to aid in the clinical diagnosis for the rapid identification of cases.Methods and findingsA cross sectional study of all those diagnosed by RT-PCR for SARS-CoV-2 between April 1 and May 24 in Argentina was conducted. The data includes clinical and demographic information from all subjects at the time of presentation, which were uploaded to the centralized national reporting system at health centers. A total of 67318 individuals were included in this study, where 12% tested positive for SARS-CoV-2. The study population was divided in two age groups, a group aged 0 to 55 years-old (<56 group), (median = 32, n=48748) and another group aged 56 to 103 years-old (≥56 group) (median =72, n=18570). Multivariate logistic regression analyses showed that out of a total of 23 symptoms, only five were found to have a positive association with COVID-19: anosmia (odds ratio [OR] 10.40, 95% confidence interval [CI] 8.20-13.10, <56 group; OR 6.09 CI 3.05-12.20, ≥56 group) dysgeusia (OR 3.67, CI 2.7-4.9, <56 group; OR 3.53 CI 1.52-8.18, ≥56 group), low grade fever (37.5-37.9° C) (OR 1.61, CI 1.20-2.05, <56 group; OR 1.80 CI 1.07-3.06, ≥56 group), cough (OR 1.20, CI 1.05-1.38, <56 group; OR 1.37 CI 1.04-1.80, ≥56 group) and headache only in <56 group (OR 1.71, CI 1.48-1.99). In turn, at the time of presentation, the symptoms associated with respiratory problems: chest pain, tachypnea, dyspnea, respiratory failure and use of accessory muscles for breathing, had a negative association with COVID-19 (OR <1) or did not present statistical relevance (OR = 1).With the intention of helping the clinical diagnosis, we designed a model to be able to identify possible cases of COVID-19. This model included 16 symptoms, the age and sex of the individuals, and was able to detect 80% of those infected with SARS-CoV-2 with a specificity of 46%.ConclusionsThe analysis of symptoms opens the opportunity for a guidance and improved symptoms based definition of suspected cases of COVID-19, where multiple factors (age, sex, symptoms and interaction between symptoms) are considered. We present a tool to help identify COVID-19 cases to provide quick information to aid decision-making by health personnel and program managers.
Recovery of monocyte exhaustion is associated with resolution of lung injury in COVID-19 convalescence
Authors: Scott N.A. , Knight S.B. , Pearmain L. , Brand O. , Morgan D.J. , Jagger C. , Khan S. , Hackney P. , Smith L. , Menon M. , Konkel J. E. , Shuwa H. A. , Franklin M. , Kästele V. , Harbach S. , Brij S. , Ustianowski A. , Uriel A. , Lindergard G. , Bakerly N. Diar , Dark P. , Mathioudakis A.G. , Gray K.J. , Lord G.M. , Felton T. , Brightling C. , Ho L-P ,   NIHR Respiratory TRC,   CIRCO, Hanley K. Piper , Simpson A. , Grainger J.R. , Hussell T. , Mann E.R. 
Published: October 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection resulting in the clinical syndrome COVID-19 is associated with an exaggerated immune response and monocyte infiltrates in the lungs and other peripheral tissues. It is now increasingly recognised that chronic morbidity persists in some patients. We recently demonstrated profound alterations of monocytes in hospitalised COVID-19 patients. It is currently unclear whether these abnormalities resolve or progress following patient discharge. We show here that blood monocytes in convalescent patients at their 12 week follow up, have a greater propensity to produce pro-inflammatory cytokines TNFα and IL-6, which was consistently higher in patients with resolution of lung injury as indicated by a normal chest X-ray and no shortness of breath (a key symptom of lung injury). Furthermore, monocytes from convalescent patients also displayed enhanced levels of molecules involved in leucocyte migration, including chemokine receptor CXCR6, adhesion molecule CD31/PECAM and integrins VLA-4 and LFA-1. Expression of migration molecules on monocytes was also consistently higher in convalescent patients with a normal chest X-ray. These data suggest persistent changes in innate immune function following recovery from COVID-19 and indicate that immune modulating therapies targeting monocytes and leucocyte migration may be useful in recovering COVID-19 patients with persistent symptoms.
CTCF-binding element regulates ESC differentiation via orchestrating long-range chromatin interaction between enhancers and HoxA
Authors: Su Guangsong , Wang Wenbin , Chen Jun , Liu Man , Zheng Jian , Guo Dianhao , Bi Jinfang , Zhao Zhongfang , Shi Jiandang , Zhang Lei , Lu Wange 
Published: October 2020

ABSTRACTProper expressions of Homeobox A cluster genes (HoxA) are essential for embryonic stem cells (ESC) differentiation and individual development. However, the mechanisms underlying controlling precise spatiotemporal expressions ofHoxAduring early ESC differentiation remain poorly understood. Herein, we identified a functional CTCF-binding element (CBE+47) closest to the 3’-end ofHoxAwithin the same topologically associated domain (TAD) in ESC. CRISPR-Cas9 mediated the CBE+47deletion significantly promotes retinoic acid (RA)-inducedHoxAexpression and early ESC abnormal differentiation. In delineating its underlying mechanisms, we find that CBE+47can precisely organize chromatin interactions between its adjacent enhancers andHoxAby using chromosome conformation capture assay (Capture-C). Furthermore, we also find that its adjacent enhancers as enhancer-enhancer interaction complex (EEIC) are required for RA-inducedHoxAactivation. Collectively, these results provide a new insight for RA-inducedHoxAexpression, also highlight the unique and precise regulatory roles of CBE in ESC differentiation.
Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction
Authors: Lu Shuai , Li Yuguang , Wang Fei , Nan Xiaofei , Zhang Shoutao 
Published: October 2020

AbstractAntibodies consisting of variable and constant regions, are a special type of proteins playing a vital role in immune system of the vertebrate. They have the remarkable ability to bind a large range of diverse antigens with extraordinary affinity and specificity. This malleability of binding makes antibodies an important class of biological drugs and biomarkers. In this article, we propose a method to identify which amino acid residues of an antibody directly interact with its associated antigen based on the features from sequence and structure. Our algorithm uses convolution neural networks (CNNs) linked with graph convolution networks (GCNs) to make use of information from both sequential and spatial neighbors to understand more about the local environment of target amino acid residue. Furthermore, we process the antigen partner of an antibody by employing an attention layer. Our method improves on the state-of-the-art methodology.
MCM complexes are barriers that restrict cohesin-mediated loop extrusion
Authors: Dequeker Bart J. H. , Brandão Hugo B. , Scherr Matthias J. , Gassler Johanna , Powell Sean , Gaspar Imre , Flyamer Ilya M. , Tang Wen , Stocsits Roman , Davidson Iain F. , Peters Jan-Michael , Duderstadt Karl E. , Mirny Leonid A. , Tachibana Kikuё 
Published: October 2020

AbstractEukaryotic genomes are compacted into loops and topologically associating domains (TADs), which contribute to transcription, recombination and genomic stability. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered. Little is known about whether loop extrusion is impeded by DNA-bound macromolecular machines. We demonstrate that the replicative helicase MCM is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C of one-cell embryos revealed that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, suggesting loop extrusion is impeded before reaching CTCF. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocationin vitro.Simulations are consistent with MCMs as abundant, random barriers. We conclude that distinct loop extrusion barriers contribute to shaping 3D genomes.One Sentence SummaryMCM complexes are obstacles that impede the formation of CTCF-anchored loops.
An improved comprehensive strategy for deep and quantitative N-glycomics based on optimization of sample preparation, isotope-based data quality control and quantification, new N-glycan libraries and new algorithms
Authors: Guan Yudong , Hu Jiaxiang , Cao Weiqian , Cui Wencong , Yang Fan , Krisp Christoph , Lin Ling , Zhang Min , Voss Hannah , Schuster Raphael , Yan Guoquan , Fuh Marceline Manka , Thaysen-Andersen Morten , Packer Nicolle H. , Shen Huali , Yang Pengyuan , Schlüter Hartmut 
Published: October 2020

Withdrawal statement“The authors have withdrawn their manuscript because the authors need to re-organize the data and writing, meanwhile more experimental evidence from human cellular N-glycome will be added to support their viewpoints. In this preprint, only one human cell line, Acute Promyelocytic Leukemia (APL) cells, was deeply investigated to show the N-glycome landscape. To provide the shared features of human N-glycome, more human cells should be investigated. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.”
cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large whole genome sequencing datasets
Authors: Crawford Ryan D. , Snitkin Evan S. 
Published: October 2020

AbstractThe quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. We present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis. We applied this tool to generate core gene alignments for very large genomic datasets, including a dataset of over 11,000 genomes from the genusEscherichiacontaining 1,353 genes, which was constructed in less than 17 hours. We have released cognac as an R package (https://github.com/rdcrawford/cognac) with customizable parameters for adaptation to diverse applications.