bluuebunny/crossref_metadata_2025_split huggingface dataset:
MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data
Authors: Khakmardan Saman , Rezvani Mohsen , Pouyan Ali Akbar , Fateh Mansoor , Alinejad-Rokny Hamid 
Published: March 2020

Abstract
Background
Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and identify significant interactions. Each method receives its own Hi-C data structure and only work on specific operating systems.

Results
We introduce MHiC (Multi-function Hi-C data analysis tool), a tool to identify and visualize statistically signifiant interactions from Hi-C data. The MHiC tool (i) works on different operating systems, (ii) accepts various Hi-C data structures from different Hi-C analysis tools such as HiCUP or HiC-Pro, (iii) identify significant Hi-C interactions with GOTHiC, HiCNorm and Fit-Hi-C methods and (iv) visualizes interactions in Arc or Heatmap diagram. MHiC is an open-source tool which is freely available for download on https://github.com/MHi-C.

Conclusions
MHiC is an integrated tool for the analysis of high-throughput chromosome conformation capture (Hi-C) data.
Validation of END-of-life ScorING-system to identify the dying patient: a prospective analysis
Authors: Villa Gianluca , Amass Timothy , Giua Rosa , Lanini Iacopo , Chelazzi Cosimo , Tofani Lorenzo , McFadden Rory , De Gaudio A. Raffaele , OMahony Sean , Levy Mitchell M. , Romagnoli Stefano 
Published: March 2020

Abstract
Background
The “END-of-Life ScorING-System” (ENDING-S) was previously developed to identify patients at high-risk of dying in the ICU and to facilitate a practical integration between palliative and intensive care. The aim of this study is to prospectively validate ENDING-S in a cohort of long-term critical care patients.

Materials and methods
Adult long-term ICU patients (with a length-of-stay> 4 days) were considered for this prospective multicenter observational study. ENDING-S and SOFA score were calculated daily and evaluated against the patient’s ICU outcome. The predictive properties were evaluated through a receiver operating characteristic (ROC) analysis.

Results
Two hundred twenty patients were enrolled for this study. Among these, 21.46% died during the ICU stay. ENDING-S correctly predicted the ICU outcome in 71.4% of patients. Sensitivity, specificity, positive and negative predictive values associated with the previously identified ENDING-S cut-off of 11.5 were 68.1, 72.3, 60 and 89.3%, respectively. ROC-AUC for outcome prediction was 0.79 for ENDING-S and 0.88 for SOFA in this cohort.

Conclusions
ENDING-S, while not as accurately as in the pilot study, demonstrated acceptable discrimination properties in identifying long-term ICU patients at very high-risk of dying. ENDING-S may be a useful tool aimed at facilitating a practical integration between palliative, end-of-life and intensive care.

Trial registration
Clinicaltrials.gov Identifier: NCT02875912; First registration August 4, 2016.
Diagnostic accuracy and utility of three dengue diagnostic tests for the diagnosis of acute dengue infection in Malaysia
Authors: Chong Zhuo Lin , Sekaran Shamala Devi , Soe Hui Jen , Peramalah Devi , Rampal Sanjay , Ng Chiu-Wan 
Published: March 2020

Abstract
Background
Dengue is an emerging infectious disease that infects up to 390 million people yearly. The growing demand of dengue diagnostics especially in low-resource settings gave rise to many rapid diagnostic tests (RDT). This study evaluated the accuracy and utility of ViroTrack Dengue Acute - a new biosensors-based dengue NS1 RDT, SD Bioline Dengue Duo NS1/IgM/IgG combo - a commercially available RDT, and SD Dengue NS1 Ag enzyme-linked immunosorbent assay (ELISA), for the diagnosis of acute dengue infection.

Methods
This prospective cross-sectional study consecutively recruited 494 patients with suspected dengue from a health clinic in Malaysia. Both RDTs were performed onsite. The evaluated ELISA and reference tests were performed in a virology laboratory. The reference tests comprised of a reverse transcription-polymerase chain reaction and three ELISAs for the detection of dengue NS1 antigen, IgM and IgG antibodies, respectively. The diagnostic performance of evaluated tests was computed using STATA version 12.

Results
The sensitivity and specificity of ViroTrack were 62.3% (95%CI 55.6–68.7) and 95.0% (95%CI 91.7–97.3), versus 66.5% (95%CI 60.0–72.6) and 95.4% (95%CI 92.1–97.6) for SD NS1 ELISA, and 52.4% (95%CI 45.7–59.1) and 97.7% (95%CI 95.1–99.2) for NS1 component of SD Bioline, respectively. The combination of the latter with its IgM and IgG components were able to increase test sensitivity to 82.4% (95%CI 76.8–87.1) with corresponding decrease in specificity to 87.4% (95%CI 82.8–91.2). Although a positive test on any of the NS1 assays would increase the probability of dengue to above 90% in a patient, a negative result would only reduce this probability to 23.0–29.3%. In contrast, this probability of false negative diagnosis would be further reduced to 14.7% (95%CI 11.4–18.6) if SD Bioline NS1/IgM/IgG combo was negative.

Conclusions
The performance of ViroTrack Dengue Acute was comparable to SD Dengue NS1 Ag ELISA. Addition of serology components to SD Bioline Dengue Duo significantly improved its sensitivity and reduced its false negative rate such that it missed the fewest dengue patients, making it a better point-of-care diagnostic tool. New RDT like ViroTrack Dengue Acute may be a potential alternative to existing RDT if its combination with serology components is proven better in future studies.
Scalp eschar and neck lymphadenopathy after tick bite (SENLAT) caused by Bartonella henselae in Korea: a case report
Authors: Seo Jun-Won , Kim Choon-Mee , Yun Na Ra , Kim Dong-Min , Kim Sung Soon , Choi Sangho , Chu Hyuk 
Published: March 2020

Abstract
Background
Tick-borne lymphadenopathy (TIBOLA) is an infectious disease, mainly caused by species from the spotted fever group rickettsiae and is characterized by enlarged lymph nodes following a tick bite. Among cases of TIBOLA, a case of scalp eschar and neck lymphadenopathy after tick bite (SENLAT) is diagnosed when an eschar is present on the scalp, accompanied by peripheral lymphadenopathy (LAP). Only a few cases of SENLAT caused by Bartonella henselae have been reported.

Case presentation
A 58-year-old male sought medical advice while suffering from high fever and diarrhea. Three weeks before the visit, he had been hunting a water deer, and upon bringing the deer home discovered a tick on his scalp area. Symptoms occurred one week after hunting, and a lump was palpated on the right neck area 6 days after the onset of symptoms. Physical examination upon presentation confirmed an eschar-like lesion on the right scalp area, and cervical palpation revealed that the lymph nodes on the right side were non-painful and enlarged at 2.5 × 1.5 cm. Fine needle aspiration of the enlarged lymph nodes was performed, and results of nested PCR for the Bartonella internal transcribed spacer (ITS) confirmed B. henselae as the causative agent.

Conclusion
With an isolated case of SENLAT and a confirmation of B. henselae in Korea, it is pertinent to raise awareness to physicians in other Asian countries that B. henselae could be a causative agent for SENLAT.
The WHO Safe Childbirth Checklist implementation: impact on the prescription of magnesium sulphate through a one-year longitudinal study
Authors: da Silva Gama Zenewton André , Medeiros Wilton Rodrigues , Saturno-Hernández Pedro Jesus , de Meneses Sousa Kelienny , Mello Matheus Silva , de Lima Vale Érico , de Souza Rosendo Tatyana Maria Silva , da Silva Edna Marta Mendes , de Freitas Marise Reis 
Published: March 2020

Abstract
Background
Preeclampsia is a relatively frequent condition during pregnancy and childbirth. The administration of magnesium sulphate as a prophylactic and treatment measure is an evidence-based practice for eclampsia; however, it is not consistently used, compromising the health of pregnant women. This study aimed to assess compliance with recommendations of the International Society for the Study of Hypertension in Pregnancy (ISSHP) for the use of MgSO4 in pregnant women with preeclampsia, before and after the implementation of the World Health Organization Safe Childbirth Checklist (SCC).

Methods
This quasi-experimental study was conducted between July 2015 and July 2016 at a third-level maternity hospital in northeastern Brazil, where the SCC was implemented. Compliance (underuse and overuse of MgSO4) was assessed in biweekly samples of 30 deliveries assessed 6 months before and 6 months after SCC implementation, using indicators based on international guidelines. A total of 720 deliveries were assessed over 1 year using an ad hoc application for reviewing medical records. Aggregated adequate use was estimated for the study period, and the time series measurements were compared to a control chart to assess change.

Results
The incidence of preeclampsia was 39.9% (287/720). Among these, 64.8% (186/287) had severe signs or symptoms and needed MgSO4. Underuse (no prescription when needed) of MgSO4 was observed in 74.7% (139/186) of women who needed the drug. Considering all women, non-compliance with the prescription protocol (underuse and overuse) was 20.0% (144/720). After introducing the SCC, the use of MgSO4 in women with preeclampsia with severe features increased from 19.1 to 34.2% (p = 0.025). Longitudinal analysis showed a significant (p < 0.05) ascending curve of adequate use of MgSO4 after the SCC was implemented.

Conclusions
Compliance with recommendations for the use of MgSO4 in preeclampsia was low, but improved after implementation of the SCC. Interventions to improve compliance based on diagnosis and treatment reminders may help in the implementation of this good practice.
Estimating racial health disparities among adverse birth outcomes as deviations from the population rates
Authors: Thompson James A. , Suter Melissa A. 
Published: March 2020

Abstract
Background
Despite significant research, the reasons for racial health disparities among adverse birth outcomes (ABO) remain largely unknown. The bulk of research into racial health disparities among ABO in the United States has concentrated on the risk of race and ethnic groups relative to the specific sub-population of non-Hispanic white women and their children. The objective of this study was to estimate the racial and ethnic risks among a set of neonatal and maternal health disparities while minimizing bias attributable to how the baseline risk was established.

Methods
All birth records were obtained from the United States Natality database for the years 2014 to 2017. A Bayesian modeling approach was used to estimate the risk disparity for disorders by race. The estimation of the race-specific risks used a sum-to-zero constraint for the race regression coefficients.

Results
Estimating racial health disparities relative to the overall population rate yielded novel results and identified perinatal health disparities for all the race groups studied.

Conclusions
Unbiased risk estimates for racial disparities among ABO are now available for stimulating and initiating more complex causal modeling that can lead to understanding how racial health disparities for ABO are mediated and how they can be prevented.
Alteration in the sensitivity to crizotinib by Na+/H+ exchanger regulatory factor 1 is dependent to its subcellular localization in ALK-positive lung cancers
Authors: Yang Fenglian , Hu Mu , Chang Siyuan , Huang Jing , Si Yang , Wang Jinghui , Cheng Shan , Jiang Wen G. 
Published: March 2020

Abstract
Background
Na+/H+ exchanger regulatory factor 1 (NHERF1) is an important scaffold protein participates in the modulation of a variety of intracellular signal pathways. NHERF1 was able to enhance the effects of chemo-drugs in breast and cervical cancer cells. Anaplastic lymphoma kinase (ALK) fusion mutations are validated molecules targeted therapy in lung cancers, where crizotinib can be used as the specific inhibitor to suppress tumor progression. However, due to the less frequent occurrence of ALK mutations and the complexity for factors to determine drug responses, the genes that could alter crizotinib sensitivity are unclear.

Methods
Both ALK-translocated and ALK-negative lung adenocarcinoma specimens in tissue sections were collected for immunohistochemistry. The possible mechanisms of NHERF1 and its role in the cell sensitivity to crizotinib were investigated using an ALK-positive and crizotinib-sensitive lung adenocarcinoma cell line H3122. Either a NHERF1 overexpression vector or agents for NHERF1 knockdown was used for crizotinib sensitivity measures, in association with cell viability and apoptosis assays.

Results
The expression level of NHERF1 in ALK-translocated NSCLC was significantly higher than that in other lung cancer tissues. NHERF1 expression in ALK positive lung cancer cells was regulated by ALK activities, and was in return able to alter the sensitivity to crizotinib. The function of NHERF1 to influence crizotinib sensitivity was depending on its subcellular distribution in cytosol instead of its nucleus localized form.

Conclusion
Ectopically overexpressed NHERF1 could be a functional protein for consideration to suppress lung cancers. The determination of NHERF1 levels in ALK positive NSCLC tissues might be useful to predict crizotinib resistance, especially by distinguishing cytosolic or nuclear localized NHERF1 for the overexpressed molecules.
Outcomes of patients with initially locally advanced pancreatic adenocarcinoma who did not benefit from resection: a prospective cohort study
Authors: Garnier Jonathan , Ewald Jacques , Marchese Ugo , Gilabert Marine , Launay Simon , Moureau-Zabotto Laurence , Poizat Flora , Giovannini Marc , Delpero Jean-Robert , Turrini Olivier 
Published: March 2020

Abstract
Background
The current study aimed to evaluate the outcomes of patients with unresectable non-metastatic locally advanced pancreatic adenocarcinoma (LAPA) who did not benefit from resection considering the treatment strategy in the clinical settings.

Methods
Between 2010 and 2017, a total of 234 patients underwent induction chemotherapy for LAPA that could not be treated with surgery. After oncologic restaging, continuous chemotherapy or chemoradiation (CRT) was decided for patients without metastatic disease. The Kaplan–Meier method was used to determine overall survival (OS), and the Wilcoxon test to compare survival curves. Multivariate analysis was performed using the stepwise logistic regression method.

Results
FOLFIRINOX was the most common induction regimen (168 patients, 72%), with a median of 6 chemotherapy cycles and resulted in higher OS, compared to gemcitabine (19 vs. 16 months, hazard ratio (HR) = 1.2, 95% confidence interval: 0.86–1.6, P = .03). However, no difference was observed after adjusting for age (≤75 years) and performance status score (0–1). At restaging, 187 patients (80%) had non-metastatic disease: CRT was administered to 126 patients (67%) while chemotherapy was continued in 61 (33%). Patients who received CRT had characteristics comparable to those who continued with chemotherapy, with similar OS. They also had longer progression-free survival (median 13.3 vs. 9.6 months, HR = 1.38, 95% confidence interval: 1–1.9, P < .01) and limited short-term treatment-related toxicity.

Conclusions
The median survival of patients who could not undergo surgery was 19 months. Hence, CRT should not be eliminated as a treatment option and may be useful as a part of optimised sequential chemotherapy for both local and metastatic disease.
Bouldering psychotherapy is more effective in the treatment of depression than physical exercise alone: results of a multicentre randomised controlled intervention study
Authors: Karg Nina , Dorscht Lisa , Kornhuber Johannes , Luttenberger Katharina 
Published: March 2020

Abstract
Background
Recent scientific studies have suggested that climbing/bouldering is effective in alleviating depression when the comparison group was a waitlist control group, even when physical activity and other therapeutic approaches were controlled for. In the present study, we aimed to investigate the effectiveness of a manualised psychotherapeutic bouldering intervention for depressed individuals, compared with an active control group performing physical exercise alone.

Methods
In a multicentre randomised controlled intervention trial, 133 outpatients with depression were assigned to either a bouldering psychotherapy (BPT) group or a home-based supervised exercise programme (EP). Severity of depression as the primary outcome was assessed at baseline and directly after a ten-week intervention period using the Montgomery–Åsberg Depression Rating Scale (MADRS). Secondary outcomes included anxiety, coping skills, self-esteem, body image, and interpersonal sensitivity. We applied t-tests to test for differences within the groups (t0 vs. t1) and between the BPT and the EP and a multiple regression analysis with the post-intervention MADRS score as the dependent variable. The robustness of estimates was investigated with a sensitivity analyses.

Results
Patients in the BPT group showed a significantly larger decrease in depression scores compared with the EP on the MADRS (drop of 8.4 vs. 3.0 points, p = .002, Cohen’s d = 0.55). In the confounder-adjusted regression analyses, group allocation was found to be the only significant predictor of the post-intervention MADRS score (β = − 5.60, p = .001) besides the baseline MADRS score. Further significant differences in change scores between the BPT and the EP were found for anxiety (p = .046, d = 0.35), body image (p = .018, d = 0.42), and global self-esteem (p = .011, d = 0.45).

Conclusions
The study provides evidence that the manualised BPT is not only effective in alleviating depressive symptoms but even goes beyond the effect of mere physical exercise. Based on these findings, the BPT should be considered as a complementary therapeutic approach.

Trial registration
Trial identification number: ISRCTN12457760: Study KuS (Klettern und Stimmung - Climbing and Mood) combined boulder and psychotherapy against depression, registered retrospectively on July 26th, 2017.
Emotion dysregulation in adults with attention deficit hyperactivity disorder: a meta-analysis
Authors: Beheshti Ashkan , Chavanon Mira-Lynn , Christiansen Hanna 
Published: March 2020

Abstract
Background
Emotional symptoms are increasingly considered a core feature of attention deficit/hyperactivity disorder (ADHD). We aimed to quantify the evidence of emotional dysregulation and its respective facets in individuals with adult ADHD compared to healthy controls using meta-analysis.

Methods
Two electronic databases (PubMed, PsycINFO) were reviewed to identify studies. Studies were eligible for inclusion that had reports on any measure of emotion (dys) regulation in adults (> 18 years of age) in clinically diagnosed patients with ADHD as well as healthy control participants. We included a total of 13 studies (N = 2535) to assess (1) the standardized mean difference in emotion dysregulation (ED) as a general factor and its specific facets (i.e., emotional lability, negative emotional responses, and emotion recognition) between adults with ADHD and healthy controls; and (2) the association between ADHD symptom severity and ED.

Results
Compared to healthy controls, adults with ADHD revealed significantly higher levels of general ED (Hedges’ g = 1.17, p < 0.001; Hedges’ g is the adjusted effect size). With regard to intermediate dimensions of ED, emotional lability exhibited the strongest weighted effect (Hedges’ g = 1.20, CI [0.57, 1.83], p < 0.001). Furthermore, symptom severity and general ED correlated significantly (r = 0.54, p < 0.001). Regarding intermediate dimensions of ED, negative emotional responses correlated closely with ADHD symptom severity (r = 0.63, p < 0.001) and emotional lability (r = 0.52, p < 0.001).

Conclusions
Our findings support ED symptoms as a core feature of ADHD’s psychopathology. With respect to dimensions of ED, emotional lability, and negative emotional responses play a more definitive role in the psychopathology of adults with ADHD. Due to insufficient statistical reports in the included studies, we could not perform meta-regressions to control the role of moderator variables.
The validation of organisational culture assessment instrument in healthcare setting: results from a cross-sectional study in Vietnam
Authors: Van Huy Nguyen , Thu Nguyen Thi Hoai , Anh Nguyen Le Tuan , Au Nguyen Thanh Hai , Phuong Nguyen The , Cham Nguyen Thi , Minh Pham Duc 
Published: March 2020

AbstractBackgroundOrganisational culture (OC) has increasingly become a crucial factor in defining healthcare practice and management. However, there has been little research validating and adapting OCAI (organisational culture assessment instrument) to assess OC in healthcare settings in developing countries, including Vietnam. The purpose of this study is to validate the OCAI in a hospital setting using key psychometric tests and confirmatory factor analysis (CFA).MethodsThis is a cross-sectional study. Self-administered structured questionnaire was completed by 566 health professionals from a Vietnamese national general hospital, the General Hospital of Quang Nam province. The psychometric tests and CFA were utilized to detect internal reliability and construct validity of the instrument.ResultsThe Cronbach’s alpha coefficients (α-reliability statistic) ranged from 0.6 to 0.8. In current culture, the coefficient was 0.80 for clan and 0.60 for adhocracy, hierarchy and market dimension, while in expected culture, the coefficient for clan, adhocracy, hierarchy, and market dimension was 0.70, 0.70, 0.70 and 0.60, respectively. The CFA indicated that most factor loading coefficients were of moderate values ranging from 0.30 to 0.60 in both current and expected culture model. These models are of marginal good fit.ConclusionsThe study findings suggest that the OCAI be of fairly good reliability and construct validity in measuring four types of organisational culture in healthcare setting in resource-constrained countries such as Vietnam. This result is a first step towards developing a valid Vietnamese version of the OCAI which can also provide a strong case for future research in the field of measuring and managing organisational culture.