bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal epigenome-wide association studies of three male military cohorts reveal multiple CpG sites associated with post-traumatic stress disorder
Authors:   PGC PTSD EWAS Consortium, Snijders Clara , Maihofer Adam X. , Ratanatharathorn Andrew , Baker Dewleen G. , Boks Marco P. , Geuze Elbert , Jain Sonia , Kessler Ronald C. , Pishva Ehsan , Risbrough Victoria B. , Stein Murray B. , Ursano Robert J. , Vermetten Eric , Vinkers Christiaan H. , Smith Alicia K. , Uddin Monica , Rutten Bart P. F. , Nievergelt Caroline M. 
Published: January 2020

Abstract
Background
Epigenetic mechanisms have been suggested to play a role in the development of post-traumatic stress disorder (PTSD). Here, blood-derived DNA methylation data (HumanMethylation450 BeadChip) collected prior to and following combat exposure in three cohorts of male military members were analyzed to assess whether DNA methylation profiles are associated with the development of PTSD. A total of 123 PTSD cases and 143 trauma-exposed controls were included in the analyses. The Psychiatric Genomics Consortium (PGC) PTSD EWAS QC pipeline was used on all cohorts, and results were combined using a sample size weighted meta-analysis in a two-stage design. In stage one, we jointly analyzed data of two new cohorts (N = 126 and 78) for gene discovery, and sought to replicate significant findings in a third, previously published cohort (N = 62) to assess the robustness of our results. In stage 2, we aimed at maximizing power for gene discovery by combining all three cohorts in a meta-analysis.

Results
Stage 1 analyses identified four CpG sites in which, conditional on pre-deployment DNA methylation, post-deployment DNA methylation was significantly associated with PTSD status after epigenome-wide adjustment for multiple comparisons. The most significant (intergenic) CpG cg05656210 (p = 1.0 × 10−08) was located on 5q31 and significantly replicated in the third cohort. In addition, 19 differentially methylated regions (DMRs) were identified, but failed replication. Stage 2 analyses identified three epigenome-wide significant CpGs, the intergenic CpG cg05656210 and two additional CpGs located in MAD1L1 (cg12169700) and HEXDC (cg20756026). Interestingly, cg12169700 had an underlying single nucleotide polymorphism (SNP) which was located within the same LD block as a recently identified PTSD-associated SNP in MAD1L1. Stage 2 analyses further identified 12 significant differential methylated regions (DMRs), 1 of which was located in MAD1L1 and 4 were situated in the human leukocyte antigen (HLA) region.

Conclusions
This study suggests that the development of combat-related PTSD is associated with distinct methylation patterns in several genomic positions and regions. Our most prominent findings suggest the involvement of the immune system through the HLA region and HEXDC, and MAD1L1 which was previously associated with PTSD.
Atypical hemolytic uremic syndrome: a case report
Authors: Basnayake B. M. D. B. , Wazil A. W. M. , Nanayakkara N. , Samarakoon S. M. D. K. , Senavirathne E. M. S. K. , Thangarajah B. U. E. W. D. R. , Karunasena N. , Mahanama R. M. B. S. S. 
Published: January 2020

Abstract
Background
Thrombotic microangiopathy is a pathological condition comprised of microvascular thrombosis involving any organ of the body leading to thrombocytopenia, Coombs-negative hemolytic anemia, and end-organ damage. The most common forms of thrombotic microangiopathies are Shiga toxin-producing Escherichia coli-mediated hemolytic uremic syndrome, thrombotic thrombocytopenic purpura, and atypical hemolytic uremic syndrome. The atypical hemolytic uremic syndrome occurs due to genetic and acquired mutations in complement regulatory factors and to complement activation factors in the immune system, mainly the alternative pathway. Clinical manifestations and outcomes differ with the prevalent mutations of the patient. Currently, available treatment modalities are therapeutic plasma exchange and a monoclonal antibody against C5, eculizumab. We report a case of a Sri Lankan girl diagnosed with atypical hemolytic uremic syndrome complicated with septicemia, hemolytic anemia, acute kidney injury, pulmonary hemorrhage with respiratory failure, and hypertension who had a complete remission following long-term (30 months) therapeutic plasma exchange.

Case presentation
A 15-year-old Sri Lankan girl was transferred from a local hospital with the features of septicemia and acute kidney injury for specialized management. She had high blood pressure (180/100 mmHg) on admission. She underwent appendicectomy based on suspicion of acute appendicitis as the cause of sepsis. Following surgery, her condition deteriorated, and intensive care unit management was warranted because she developed pulmonary hemorrhages and respiratory failure requiring mechanical ventilation and renal replacement therapy in the form of hemodialysis. Her blood investigations showed microangiopathic hemolytic anemia, thrombocytopenia, elevated lactate dehydrogenase, and reduced human complement C3 levels, together with a normal coagulation profile. She was diagnosed with atypical hemolytic uremic syndrome and was initiated on therapeutic plasma exchange and other supportive therapy, including corticosteroids. Following a lengthy course of plasma exchange, complete recovery was achieved.

Conclusion
The atypical hemolytic uremic syndrome is a rare disease entity requiring a high index of suspicion to diagnose. It is a diagnosis of exclusion. Early diagnosis with prompt treatment will render a better outcome. The atypical hemolytic uremic syndrome needs to be considered in all patients with thrombotic microangiopathy.
Combining lexical and context features for automatic ontology extension
Authors: Althubaiti Sara , Kafkas Şenay , Abdelhakim Marwa , Hoehndorf Robert 
Published: January 2020

AbstractBackgroundOntologies are widely used across biology and biomedicine for the annotation of databases. Ontology development is often a manual, time-consuming, and expensive process. Automatic or semi-automatic identification of classes that can be added to an ontology can make ontology development more efficient.ResultsWe developed a method that uses machine learning and word embeddings to identify words and phrases that are used to refer to an ontology class in biomedical Europe PMC full-text articles. Once labels and synonyms of a class are known, we use machine learning to identify the super-classes of a class. For this purpose, we identify lexical term variants, use word embeddings to capture context information, and rely on automated reasoning over ontologies to generate features, and we use an artificial neural network as classifier. We demonstrate the utility of our approach in identifying terms that refer to diseases in the Human Disease Ontology and to distinguish between different types of diseases.ConclusionsOur method is capable of discovering labels that refer to a class in an ontology but are not present in an ontology, and it can identify whether a class should be a subclass of some high-level ontology classes. Our approach can therefore be used for the semi-automatic extension and quality control of ontologies. The algorithm, corpora and evaluation datasets are available athttps://github.com/bio-ontology-research-group/ontology-extension.
Inter-rater reliability and concurrent validity of ROBINS-I: protocol for a cross-sectional study
Authors: Jeyaraman Maya M. , Rabbani Rasheda , Al-Yousif Nameer , Robson Reid C. , Copstein Leslie , Xia Jun , Pollock Michelle , Mansour Samer , Ansari Mohammed T. , Tricco Andrea C. , Abou-Setta Ahmed M. 
Published: January 2020

Abstract
Background
The Cochrane Bias Methods Group recently developed the “Risk of Bias (ROB) in Non-randomized Studies of Interventions” (ROBINS-I) tool to assess ROB for non-randomized studies of interventions (NRSI). It is important to establish consistency in its application and interpretation across review teams. In addition, it is important to understand if specialized training and guidance will improve the reliability of the results of the assessments. Therefore, the objective of this cross-sectional study is to establish the inter-rater reliability (IRR), inter-consensus reliability (ICR), and concurrent validity of ROBINS-I. Furthermore, as this is a relatively new tool, it is important to understand the barriers to using this tool (e.g., time to conduct assessments and reach consensus—evaluator burden).

Methods
Reviewers from four participating centers will appraise the ROB of a sample of NRSI publications using the ROBINS-I tool in two stages. For IRR and ICR, two pairs of reviewers will assess the ROB for each NRSI publication. In the first stage, reviewers will assess the ROB without any formal guidance. In the second stage, reviewers will be provided customized training and guidance. At each stage, each pair of reviewers will resolve conflicts and arrive at a consensus. To calculate the IRR and ICR, we will use Gwet’s AC1 statistic.
For concurrent validity, reviewers will appraise a sample of NRSI publications using both the New-castle Ottawa Scale (NOS) and ROBINS-I. We will analyze the concordance between the two tools for similar domains and for the overall judgments using Kendall’s tau coefficient.
To measure the evaluator burden, we will assess the time taken to apply the ROBINS-I (without and with guidance), and the NOS. To assess the impact of customized training and guidance on the evaluator burden, we will use the generalized linear models. We will use Microsoft Excel and SAS 9.4 to manage and analyze study data, respectively.

Discussion
The quality of evidence from systematic reviews that include NRS depends partly on the study-level ROB assessments. The findings of this study will contribute to an improved understanding of the ROBINS-I tool and how best to use it.
Proportion of bacterial isolates, their antimicrobial susceptibility profile and factors associated with puerperal sepsis among post-partum/aborted women at a referral Hospital in Bahir Dar, Northwest Ethiopia
Authors: Admas Alemale , Gelaw Baye , BelayTessema  , Worku Amsalu , Melese Addisu 
Published: January 2020

AbstractBackgroundPuerperal sepsis is any bacterial infection of the genital tract that occurs after childbirth. It is among the leading causes of maternal morbidity and mortality especially in low-income countries including Ethiopia. The aim of this study was to determine the proportion of bacterial isolates, their antimicrobial susceptibility profile and factors associated with puerperal sepsis among post-partum/aborted women at a Referral Hospital in Bahir Dar, Northwest Ethiopia.MethodsA cross sectional study was conducted from January to May 2017 among 166 post-partum/aborted women admitted to Felege Hiwot Referral Hospital for medical services and suspected for puerperal sepsis.. Socio-demographic data and associated factors were collected using structured questionnaire. Bacteria were isolated and identified from blood samples on Trypton soya broth, blood, Chocolate and MacConkey agars following standard bacteriological procedures. The VITEK 2 identification and susceptibility testing system was used to determine the antimicrobial susceptibility profiles of bacterial isolates. Data were entered and analyzed using SPSS version 20. Factors associated with puerperal sepsis were considered statistically significant atP-value < 0.05.ResultsThe overall proportion of bacterial isolates among post-partum/aborted women was 33.7% (56/166); of which 55.4% was caused by Gram-negative and 44.6% was by Gram-positive bacteria. The most frequently isolated bacteria wereEscherichia coli(32.1%) from Gram-negatives andStaphylococcus aureus (33.9%) from Gram-positives. The proportion of other isolates was(7.2%) for Coagulase NegativeStaphylococci(CoNS), (12.5%) forKlebsiella pneumoniae,(10.7%) forAcinetobacter baumanniand(3.6%) forRaoultella ornithinolytica. All isolates of Gram-positive and Gram-negative bacteria were resistant to tetracycline (100%). The gram negatives show resistance to Cefazolin (72.7%), Tetracycline (93.9%) and Ampicillin (100%). The overall prevalence of multidrug resistance (MDR) was 84%. Women having multiparous parity were more likely to develop puerperal sepsis than primiparous parity (AOR 4.045; 95% CI: 1.479–11.061;P < 0.05). Other socio-demographic and clinical factors had no significant association with puerperal sepsis.ConclusionAbout one third of post-partum/aborted women suspected for puerperal sepsis were infected with one or more bacterial isolates. Significant proportion of bacterial isolates showed mono and multi-drug resistance for the commonly prescribed antibiotics. Women with multiparous parity were more likely to develop puerperal sepsis than primiparous parity.
Deep brain stimulation for Tourette’s syndrome
Authors: Xu Wenying , Zhang Chencheng , Deeb Wissam , Patel Bhavana , Wu Yiwen , Voon Valerie , Okun Michael S. , Sun Bomin 
Published: January 2020

AbstractTourette syndrome (TS) is a childhood-onset neuropsychiatric disorder characterized by the presence of multiple motor and vocal tics. TS usually co-occurs with one or multiple psychiatric disorders. Although behavioral and pharmacological treatments for TS are available, some patients do not respond to the available treatments. For these patients, TS is a severe, chronic, and disabling disorder. In recent years, deep brain stimulation (DBS) of basal ganglia-thalamocortical networks has emerged as a promising intervention for refractory TS with or without psychiatric comorbidities. Three major challenges need to be addressed to move the field of DBS treatment for TS forward: (1) patient and DBS target selection, (2) ethical concerns with treating pediatric patients, and (3) DBS treatment optimization and improvement of individual patient outcomes (motor and phonic tics, as well as functioning and quality of life). The Tourette Association of America and the American Academy of Neurology have recently released their recommendations regarding surgical treatment for refractory TS. Here, we describe the challenges, advancements, and promises of the use of DBS in the treatment of TS. We summarize the results of clinical studies and discuss the ethical issues involved in treating pediatric patients. Our aim is to provide a better understanding of the feasibility, safety, selection process, and clinical effectiveness of DBS treatment for select cases of severe and medically intractable TS.
Expert consensus on the diagnosis and treatment of heat stroke in China
Authors:   Expert Group of Heat Stroke Prevention and Treatment of the People’s Liberation Army, and People’s Liberation Army Professional Committee of Critical Care Medicine, Liu Shu-Yuan , Song Jing-Chun , Mao Han-Ding , Zhao Jin-Bao , Song Qing 
Published: January 2020

AbstractHeat stroke (HS) is a fatal disease caused by thermal damage in the body, and it has a very high mortality rate. In 2015, the People’s Liberation Army Professional Committee of Critical Care Medicine published the first expert consensus on HS in China, Expert consensus on standardized diagnosis and treatment for heat stroke. With an increased understanding of HS and new issues that emerged during the HS treatment in China in recent years, the 2015 consensus no longer meet the requirements for HS prevention and treatment. It is necessary to update the consensus to include the latest research evidence and establish a new consensus that has broader coverage, is more practical and is more in line with China’s national conditions. This new expert consensus includes new concept of HS, recommendations for laboratory tests and auxiliary examinations, new understanding of diagnosis and differential diagnosis, On-site emergency treatment and In-hospital treatment, translocation of HS patients and prevention of HS.
Surgery to avoid fatal complications and secure radicality after definitive chemoradiotherapy for clinical T4N2M0 stage IIIB non-small cell lung cancer: a case report
Authors: Yagi Yuriko , Kodama Ken , Momozane Toru , Kimura Yukio , Takeda Masashi , Kishima Hiroki 
Published: January 2020

Abstract
Background
Chemoradiotherapy (CRT) is the standard treatment for c-stage IIIB non-small cell lung cancer (NSCLC); however, patients who respond to CRT are at risk of developing fatal complications such as massive hemoptysis or infection. In such cases, surgery is an alternative option. Currently, there are limited reports on surgery for complications arising during definitive CRT for locally advanced NSCLC. We report a case of hemoptysis after definitive CRT for c-T4N2M0 stage IIIB NSCLC that was successfully treated with lower bilobectomy combined with left atrial resection.

Case presentation
A 72-year-old man with c-T4N2M0 stage IIIB NSCLC with left atrial invasion developed hemoptysis during CRT, which was discontinued to control hemoptysis. Chest computed tomography revealed a regressed and cavitated tumor. Three weeks after discontinuation of CRT, surgery was performed to avoid fatal complications and secure radicality. We performed lower bilobectomy combined with partial left atrial resection, which was performed using an automatic tri-stapler. The bronchial stump was covered with an omental flap. The resected specimen pathologically showed complete response with fistula between the intermediate bronchus and necrotic cavity in the tumor. His postoperative course was uneventful, and the patient was disease free at 10 months after surgery.

Conclusions
We successfully performed surgery after definitive CRT in a patient with c-T4N2M0 stage IIIB NSCLC. Partial left atrial resection was safely performed with an automatic tri-stapler. A complete pathological response to CRT was achieved. In a case with a chance of complete (R0) resection, when the risk of developing fatal complications might outweigh the risk of post-CRT surgery perioperative complications, surgery should be considered as a treatment option.
Successful removal of a giant esophageal lipoma by thoracoscopic enucleation: a case report
Authors: Goto Wataru , Sakurai Katsunobu , Kubo Naoshi , Tamamori Yutaka , Maeda Kiyoshi , Ohira Masaichi 
Published: January 2020

Abstract
Background
We report a rare case of giant esophageal lipoma treated with thoracoscopic enucleation successfully.

Case presentation
A 69-year-old woman was referred to our department with dysphagia. Computed tomography examination revealed a large hypoattenuating submucosal mass with dense fat in the middle and lower esophagus. Upper gastrointestinal endoscopy revealed a submucosal mass with normal mucosa on the middle and lower esophageal wall. On a diagnosis of esophageal lipoma, we performed a video-assisted thoracoscopic operation and the 14.0 × 6.5 × 3.0 cm in size submucosal tumor was completely enucleated. We could successfully avoid a subtotal esophagectomy with high invasiveness. The patient was discharged on the 36th day after operation, and no symptoms had been noted.

Conclusions
Video-assisted thoracoscopic enucleation with minimal invasiveness may be an appropriate treatment option even for such a huge benign esophageal submucosal tumor.
Cholecystohepatic duct detected during laparoscopic cholecystectomy: a case report
Authors: Maeda Koki , Tabata Masami , Sakamoto Tatsuya , Fujimura Yu , Takeuchi Taijiro , Desaki Ryosuke , Kobayashi Motoyuki , Ohsawa Ichiro , Kato Kenji , Iwata Makoto , Sanda Takayuki 
Published: January 2020

AbstractBackgroundThe cholecystohepatic duct is a rare form of an aberrant hepatic duct that connects to the gallbladder. Although cholecystohepatic duct is reported to be a very rare anomaly, injury of cholecystohepatic duct during cholecystectomy may result in serious complications. Herein, we present a case of cholecystohepatic duct in the ventral branch of the right posterior inferior segmental bile duct detected during laparoscopic cholecystectomy.Case presentationA 77-year-old woman with cholecystolithiasis had been referred to our hospital for surgery. Drip infusion cholecystocholangiography-computed tomography revealed a bile duct branch without communication between the intra- and extrabiliary systems, although the existence of this aberrant hepatic duct was not suspected preoperatively. A 4-port laparoscopic cholecystectomy was performed. After critical view of safety was confirmed, the cystic artery and duct were divided after double clipping. During antegrade mobilization of the gallbladder from the gallbladder bed, a thin, white cord-like material connecting the gallbladder neck and bed was detected. After clipping and dividing it, a cholecystohepatic duct injury was recognized through rechecking the results of the preoperative examinations. Biliary reconstruction was considered unnecessary because of the lesion’s small drainage area. The postoperative course was uneventful, and an enhanced computed tomography performed 6 months after the surgery revealed a dilation in the ventral branch of the right posterior inferior segmental bile duct. The patient’s liver function remained normal, and she had no symptoms of cholangitis 42 months after the surgery.ConclusionsAlthough cholecystohepatic duct is a rare anomaly compared to other aberrant hepatic ducts, surgeons performing cholecystectomy should always keep its existence in mind to avoid serious postoperative complications. Ideally, preoperative detection of cholecystohepatic duct is preferable, but even if it is detected during surgery, the appropriate management according to the drainage area is also important.
Surgery for Killian-Jamieson diverticulum: a report of two cases
Authors: Saisho Kohei , Matono Satoru , Tanaka Toshiaki , Mori Naoki , Hino Haruhiro , Fujisaki Masahiro , Nakagawa Masashi , Fujita Fumihiko , Akagi Yoshito 
Published: January 2020

Abstract
Background
Killian-Jamieson diverticulum (KJD) is a rare diverticulum arising from a muscular gap in the anterolateral wall of the proximal cervical esophagus. The first choice of treatment for KJD remains controversial due to its rare incidence. Here, we report two cases of KJD for which we performed different surgery: diverticulectomy in one case and diverticulopexy in the other.

Case presentation
Case 1 involved a 58-year-old woman presenting progressive pharyngeal discomfort for the past year. She was diagnosed as KJD using endoscopic and radiographic findings. She underwent diverticulectomy with cricopharyngeal and proximal esophageal myotomy. Staple line leakage developed at 1 month after surgery and was successfully treated conservatively. At 5 months after surgery, she was asymptomatic. Case 2 involved a 77-year-old woman presenting dysphagia for the past 2 years. She had a history of bilateral breast cancer and had hypertension, asthma, and osteoporosis. Taking her age and medical history into account, we selected diverticulopexy with cricopharyngeal and proximal esophageal myotomy. The postoperative course was uneventful. At 2 years after surgery, she remained free of dysphagia.

Conclusion
The first choice of surgery for KJD is diverticulectomy. In a high-risk patient, diverticulopexy is a reasonable treatment. We recommend the addition of myotomy as a part of any surgical treatment.