bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving compliance to clinical practice guidelines with a multifaceted quality improvement program for the prevention of venous thromboembolic disease in nonsurgical patients
Authors: Ruiz-Talero Paula , Cerón-Perdomo Daniela , Hernández-Flórez Catalina , Gutiérrez-gómez Santiago , Muñoz-Velandia Oscar 
Published: April 2020

Abstract

Objective
To evaluate the change in compliance to thromboprophylaxis guidelines before and after the implementation of a multifaceted patient safety program.

Design
Longitudinal before and after study.

Setting
Teaching hospital, Hospital Universitario San Ignacio, Bogotá (Colombia).

Participants
Adult nonsurgical hospitalized patients.

Intervention
A multifaceted program for the prevention of venous thromboembolic (VTE) disease among adult nonsurgical hospitalized patients. The strategies of the program included (i) update and communication of thromboprophylaxis guidelines, (ii) the implementation of risk-assessment tools in electronic medical records, (iii) nursing staff activities and (iv) education to health personnel and patients for maintenance of the program.

Main Outcome Measure
Appropriate use of thromboprophylaxis.

Results
221 and 236 patients were evaluated in the pre- and postimplementation periods, respectively. Global appropriate thromboprophylaxis prescription went from 74.66 to 82.6% (P = 0.064). Adequate thromboprophylaxis in high-risk patients did not increase significantly (77.70 vs 80.62%, P = 0.528), but a significant reduction in inappropriate thromboprophylaxis formulation in low-risk patients was found, decreasing from 20.55 to 5.26% (P = 0.005).

Conclusions
Implementing a quality improvement multifaceted program improves the formulation of adequate thromboprophylaxis. Reducing the inappropriate prescription of VTE prophylaxis in patients at low risk of thrombosis can lead to a reduction in bleeding complications and a better use of economic and human resources.
From Threat to Risk? Exceptionalism and Logics of Health Security
Authors: Kirk Jessica 
Published: April 2020

AbstractThe logic of “risk” is increasingly important in the study of global health politics. One recent contribution has even argued that risk is beginning to replace security as the defining logic of health governance and policy. Others dispute this on the basis that risk and security have always operated together in the “securitization” of disease. This article constitutes a theoretical intervention into this burgeoning debate. Does a stronger appreciation of risk warrant the diminishment of security? Are we looking at the “riskification” of health rather than “securitization”? Or would this miss the way these two logics might be complimentary or intertwined in ways that we are yet to theorize? I argue that the global health and securitization literatures are better served by an explicit consideration of risk and security logics in interplay, or never entirely encompassed by the other, nor in complete alignment, yet never truly separate. To do this, I propose a reconceptualization of the central problem—exceptionalism—that allows for risk to be understood as a form of exceptionalist politics. I demonstrate the validity of this approach through an otherwise “easy case” of securitization: the US response to the 2014–2016 Ebola outbreak in West Africa.
OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment
Authors: Passaro Marco , Martinovic Martina , Bevilacqua Valeria , Hershberg Elliot A , Rossetti Grazisa , Beliveau Brian J , Bonnal Raoul J P , Pagani Massimiliano 
Published: April 2020

Abstract
Fluorescence in situ hybridization (FISH) is a powerful single-cell technique that harnesses nucleic acid base pairing to detect the abundance and positioning of cellular RNA and DNA molecules in fixed samples. Recent technology development has paved the way to the construction of FISH probes entirely from synthetic oligonucleotides (oligos), allowing the optimization of thermodynamic properties together with the opportunity to design probes against any sequenced genome. However, comparatively little progress has been made in the development of computational tools to facilitate the oligos design, and even less has been done to extend their accessibility. OligoMiner is an open-source and modular pipeline written in Python that introduces a novel method of assessing probe specificity that employs supervised machine learning to predict probe binding specificity from genome-scale sequence alignment information. However, its use is restricted to only those people who are confident with command line interfaces because it lacks a Graphical User Interface (GUI), potentially cutting out many researchers from this technology. Here, we present OligoMinerApp (http://oligominerapp.org), a web-based application that aims to extend the OligoMiner framework through the implementation of a smart and easy-to-use GUI and the introduction of new functionalities specially designed to make effective probe mining available to everyone.
Recurrence of Plasmodium malariae and P. falciparum Following Treatment of Uncomplicated Malaria in North Sumatera With Dihydroartemisinin-Piperaquine or Artemether-Lumefantrine
Authors: Lubis Inke Nadia D , Wijaya Hendri , Lubis Munar , Lubis Chairuddin P , Beshir Khalid B , Staedke Sarah G , Sutherland Colin J 
Published: April 2020

Abstract

Background
We assessed the efficacy of artemisinin-based combination therapies for treatment of uncomplicated falciparum malaria, with or without co-infecting Plasmodium spp., in Sumatera, Indonesia.

Methods
Febrile patients aged &gt;6 months with uncomplicated P. falciparum were randomized to receive dihydroartemisinin-piperaquine or artemether-lumefantrine, plus single-dose primaquine, and were followed for 42 days. Mixed Plasmodium infections were included; P. vivax infections received 14 days of primaquine. We retrospectively restricted the analysis to cases with polymerase chain reaction (PCR)–confirmed parasitemia. Recurrent parasitemia in follow-up was identified by species-specific nested PCR.

Results
Of the 3731 participants screened, 302 were enrolled and randomized. In the dihydroartemisinin-piperaquine arm, P. falciparum infections were confirmed by PCR in 59 participants, with mixed infections in 23 (39.0%). In the artemether-lumefantrine arm, P. falciparum infections were confirmed by PCR in 55 participants, with mixed infections in 16 (29.0%). Both regimens were well tolerated, and symptoms improved rapidly in all treated participants. In the dihydroartemisinin-piperaquine arm, 1 P. falciparum recurrence (on day 7) and 6 P. malariae recurrences (1 had a mixed infection with P. falciparum) were identified during days 3–42 of follow-up. In the artemether-lumefantrine arm, 1 P. falciparum/P. malariae/P. vivax recurrence occurred on day 35. Submicroscopic persistence occurred during follow-up in 21 (37%) of 57 receiving dihydroartemisinin-piperaquine and 20 (39%) of 51 receiving artemether-lumefantrine.

Conclusions
In Sumatera, both regimens effectively cleared initial parasitemia, but P. falciparum and P. malariae persisted in some individuals. Molecular species detection should be deployed in antimalarial efficacy trials in Indonesia.

Trial registration
NCT02325180.
Partner Abuse Among Treatment-Seeking Individuals with Chronic Pain: Prevalence, Characteristics, and Association with Pain-Related Outcomes
Authors: Craner Julia R , Lake Eric S , Bancroft Kimberly E , Hanson Karen M 
Published: April 2020

Abstract

Objective
This study assessed the prevalence of abusive partner relationships among individuals presenting for chronic pain treatment. In addition, this study examined the association between partner abuse histories and pain-relevant outcome variables.

Design
Cross-sectional.

Setting
This study took place at a specialty pain rehabilitation treatment center in the Midwestern United States.

Subjects
Participants in this study (N = 108) included adults (Mage = 45.73 [15.95] years) presenting for chronic pain treatment who consented to participate in a research study on stress, relationships, and chronic pain.

Methods
Participants completed self-report measures about relationship and abuse histories, physical and mental health, and demographic information. Participants were categorized into the following groups: no intimate partner violence (IPV), past IPV (&gt;12 months ago), or current/recent IPV (≤12 months ago).

Results
Results indicated that over half (56%) of the sample endorsed a history of partner abuse and around one-third (29%) of the sample had experienced abuse within the past year. Psychological/emotional abuse was the most common form of abuse reported. Those with current/recent abuse histories reported greater impairment in pain interference, post-traumatic stress symptoms, mental health functioning, and pain self-efficacy compared with those who had not experienced abuse in the past year.

Conclusions
Partner abuse appears common among individuals with chronic pain and is associated with pain-relevant outcomes, warranting additional clinical attention and research in this area.
Extracellular DNA controls expression of Pseudomonas aeruginosa genes involved in nutrient utilization, metal homeostasis, acid pH tolerance and virulence
Authors: Lewenza Shawn , Johnson Lori , Charron-Mazenod Laetitia , Hong Mia , Mulcahy-O'Grady Heidi 
Published: April 2020

Introduction.Pseudomonas aeruginosagrows in extracellular DNA (eDNA)-enriched biofilms and infection sites. eDNA is generally considered to be a structural biofilm polymer required for aggregation and biofilm maturation. In addition, eDNA can sequester divalent metal cations, acidify growth media and serve as a nutrient source.Aim.We wanted to determine the genome-wide influence on the transcriptome of planktonicP. aeruginosaPAO1 grown in the presence of eDNA.Methodology.RNA-seq analysis was performed to determine the genome-wide effects on gene expression of PAO1 grown with eDNA. Transcriptionalluxfusions were used to confirm eDNA regulation and to validate phenotypes associated with growth in eDNA.Results.The transcriptome of eDNA-regulated genes included 89 induced and 76 repressed genes (FDR<0.05). A large number of eDNA-induced genes appear to be involved in utilizing DNA as a nutrient. Several eDNA-induced genes are also induced by acidic pH 5.5, and eDNA/acidic pH promoted an acid tolerance response inP. aeruginosa. ThecyoABCDEterminal oxidase is induced by both eDNA and pH 5.5, and contributed to the acid tolerance phenotype. Quantitative metal analysis confirmed that DNA binds to diverse metals, which helps explain why many genes involved in a general uptake of metals were controlled by eDNA. Growth in the presence of eDNA also promoted intracellular bacterial survival and influenced virulence in the acute infection model of fruit flies.Conclusion.The diverse functions of the eDNA-regulated genes underscore the important role of this extracellular polymer in promoting antibiotic resistance, virulence, acid tolerance and nutrient utilization; phenotypes that contribute to long-term survival.
Remdesivir inhibits renal fibrosis in obstructed kidneys
Authors: Wu Ming , Xu Lin , Tan Bo , Huang Di , Yuan Meijie , Ye Chaoyang 
Published: April 2020

AbstractAimKidney impairment is observed in patients with COVID-19. We aimed to demonstrate the effect of anti-COVID-19 agent remdesivir on renal fibrosis.MethodsRemdesivir and its active nucleoside metabolite GS-441524 were used to treat TGF-β stimulated renal fibroblasts (NRK-49F) and human renal epithelial cells (HK2). Cell viability was determined by CCK8 assay, and fibrotic markers were measured by Western blotting. Vehicle or remdesivir were given by intraperitoneal injection or renal injection through the left ureter in unilateral ureteral obstruction (UUO) mice. Serum and kidneys were harvested. The concentrations of remdesivir and GS-441524 were measured using LC-MS/MS. Renal and liver function were assessed. Renal fibrosis was evaluated by Masson’s trichrome staining and Western blotting.ResultsRemdesivir and GS-441524 inhibited cell proliferation and the expression of fibrotic markers (fibronectin, pSmad3, and aSMA) in NRK-49F and HK2 cells. Intraperitoneal injection or renal injection of remdesivir attenuated renal fibrosis of UUO kidneys. Renal and liver function were not changed in remdesivir treated UUO mice. Remdesivir can not be detected, but two remdesivir metabolites were detected after injection.ConclusionRemdesivir inhibits renal fibrosis in obstructed kidneys.
Correspondence: RecurrentGNAQmutation encoding T96S in natural killer/T cell lymphoma
Authors: Lim Jing Quan , Lim Soon Thye , Ong Choon Kiat 
Published: April 2020

AbstractRecurrentGNAQmutation encoding p.T96S in natural-killer/T cell lymphoma (NKTCL) was recently reported in 8.7% (11/127) of NKTCL patients. At the time of publication, this phenomenon was not observed in preceding genomic studies of NKTCL. We suspected that p.T96S was a false-positive somatic call due to misaligned sequencing reads that originated from the highly similar GNAQ-pseudogene (GNAQP) chr2q21.1 locus. Linkage disequilibrium analysis also revealed thatGNAQPhas high frequencies of co-occurring polymorphic mismatches which led to the preferential misalignment of sequencing reads to theGNAQchr9q21.2 locus instead. This correspondence implicates our interpretation of true-positive somatic variants and many other studies which could be affected by similar suboptimal interpretation of somatic mutations.
G2S3: a gene graph-based imputation method for single-cell RNA sequencing data
Authors: Wu Weimiao , Dai Qile , Liu Yunqing , Yan Xiting , Wang Zuoheng 
Published: April 2020

AbstractSingle-cell RNA sequencing provides an opportunity to study gene expression at single-cell resolution. However, prevalent dropout events result in high data sparsity and noise that may obscure downstream analyses. We propose a novel method, G2S3, that imputes dropouts by borrowing information from adjacent genes in a sparse gene graph learned from gene expression profiles across cells. We applied G2S3 and other existing methods to seven single-cell datasets to compare their performance. Our results demonstrated that G2S3 is superior in recovering true expression levels, identifying cell subtypes, improving differential expression analyses, and recovering gene regulatory relationships, especially for mildly expressed genes.
Background and Design of the Community Awareness Resources and Education (CARE) Project: Reducing Cervical Cancer in Appalachia
Authors: Hade Erinn M. , Ferketich Amy K. , Lehman Amy M. , Paskett Electra D. , Wewers Mary Ellen , Ruffin Mack , Tatum Cathy , Lemeshow Stanley 
Published: April 2020

AbstractObjectiveThe Community Awareness Resources and Education (CARE) project: Reducing Cervical Cancer in Appalachia is part of the NIH Centers for Population Health and Health Disparities initiative. It aims to increase screening rates for cervical cancer, to assist in tobacco cessation, and to determine the role of human papillomavirus (HPV) in contributing to the increased risk of cervical cancer.MethodsEligible subjects were recruited from 14 clinics in Appalachian Ohio. CARE’s cross sectional survey (CS) (571 participants) characterized social, behavioral, and environmental factors of Pap smear screening and smoking. The intervention projects tested programs to increase Pap smear screening (280 participants) or aid in smoking cessation (300 participants). A case control study (1360 participants) assessed social, behavioral, and biologic predictors of abnormal Pap tests.ResultsThe CS participants tended to be younger, more educated, and were more likely to be employed than the general population of Appalachian women 18 and over. They were similar to the other samples in terms of race, marital status, income level and smoking status.ConclusionsCARE will provide valuable information about the multi-level barriers to obtaining regular Pap smears and quitting smoking, as well as help to identify important biological and social risk factors related to abnormal Pap smears.
Reporting the life tracks of confirmed cases can effective prevent and control the COVID-19 outbreak in China
Authors: Zhang Jie , Wang Tianjing , Wang Jiaqi , Chen Jingjing , Yan Hongwei , Sun Lin 
Published: April 2020

AbstractBackgroundSince late December 2019, a novel coronavirus (COVID-19) has emerged in Wuhan and rapidly spread throughout China. Fears were raised higher, effective policies for prevention and control were concerned.MethodsTill March 3, 91273 confirmed COVID-19 cases were included in. Using Mann-Whitney U test, the provinces that reported the life tracks of confirmed cases to public had lower increased in daily new confirmed cases.ResultsCompared with the paired province, Tianjin, Jilin, Gansu, Shanxi, Hainan and Guizhou had significant differences in the number of new confirmed cases and have lower mean rank (P<0.05). Shanghai had a lower mean rank (P=0.175) but no significant difference. Besides, the successful prevention and control work need other effective strategies, such as real time media coverage, isolating the suspected cases or close contacts, delaying the return of work, closing schools, wearing facial masks, and disinfecting the communities, et.al.ConclusionsStrategies must be adjusted in real time according to the epidemic. Reporting the life tracks of confirmed cases was an effective way to control the epidemic. They may be suggestions to other counties with an outbreak of COVID-19.
Clinical Characteristics and Risk of Second Primary Lung Cancer After Cervix Cancer: A Population-Based Study
Authors: Qian Chengyuan , Liu Hong , Feng Yan , Meng Shenglan , Wang Dong , Xu Mingfang 
Published: April 2020

AbstractBackgroundLung cancer as a second primary malignancy is increasingly common, but the clinical characteristics of second primary non-small cell lung cancer after cervix cancer (CC-NSCLC) in comparison with first primary non-small cell lung cancer (NSCLC1) is unknown.MethodsThe Surveillance, Epidemiology and EndResults (SEER) cancer registry between 1998 and 2010 was used to conduct a large population-based cohort analysis. Demographic and clinical characteristics as well as prognostic data were systematically analyzed. We further compared overall survival (OS) in the two cohorts. Risk factors of secondary primary lung cancer in cervical cancer patients were also analyzed.Results557 (3.52%) had developed second primary lung cancer after cervix cancer and 451 were eligible for inclusion in the final analyses. In comparison to NSCLC1, patients with CC-NSCLC had a higher rate of squamous cell carcinoma (SCC) (36.59% vs. 19.07%, p<0.01). Median OS was longer for CC-NSCLC than for NSCLC1 before propensity score matching (PSM) (16 vs. 13months) but there was no significant difference after PSM. High-risk factors in cervical cancer to developing CC-NSCLC include: 50-79years old, black race (OR 1.417; 95%CI 1.095-1.834; p<0.05)and history of radiotherapy (OR 1.392; 95%CI 1.053-1.841; p<0.05).Conclusion50-79years old, black race and history of radiotherapy were independent risk factors of second primary lung cancer in cervical cancer patient. CC-NSCLC patients had distinctive clinical characteristics and a better prognosis compared with NSCLC1 patients.
Layer-specific Loss and Compensation of Parvocellular Response in Subcortical Pathways of Adult Human Amblyopia
Authors: Wen Wen , Wang Yue , He Sheng , Liu Hong , Zhao Chen , Zhang Peng 
Published: April 2020

AbstractAbnormal visual experience in critical period causes amblyopia or lazy eye, reducing visual abilities even with corrected optics. A long-standing question is where in the human visual system does the amblyopic deficit arise. In particular, whether amblyopia induces selective deficits of the magnocellular (M) or the parvocellular (P) geniculostriate pathways, and whether the more ancient retinotectal pathway is also affected. Technical limitations to non-invasively measure layer-specific activity in human lateral geniculate nucleus (LGN) and superior colliculus (SC) hampered efforts in addressing these questions. In the current study, using lamina-resolved 3T and 7T fMRI and visual stimuli selectively activating the M and P pathways, we investigated layer-specific response properties of the LGN and the SC of amblyopia patients and normal controls. With stimuli presented to the amblyopic eye, there was a stronger response loss in the P layers than in the M layers of the LGN. Compared to normal controls, amblyopic eye’s response to the P stimulus was selectively reduced in the superficial SC, while the fellow eye’s response was robustly increased in the deep SC. Selective P response deficits of amblyopia were also observed in the visual pulvinar, early visual cortex, and ventral but not dorsal visual streams. These results provide strong in vivo evidence in adult amblyopic patients for selective deficits of parvocellular functions in the visual thalamus, and additionally reveal response deficits to the amblyopic eye and neural compensation to the fellow eye in the retinotectal pathway.HighlightsParvocellular response loss in the LGN P layers, visual pulvinar and ventral visual streamSelective amblyopic deficits of the parvocellular pathwayAmblyopic eye’s response decreased in the superficial SCFellow eye’s response increased in the deep SCAmblyopic deficits and neural compensation in the retinotectal pathway
Assessing public health risk factors for internally displaced households in North Darfur, Sudan
Authors: Mahmoud Elfadil Mohammed , Pal Indraijt , Ahmad Mokbul Morshed 
Published: April 2020

PurposeThe purpose of this paper is to assess the public health risk factors of internally displaced households and suggest appropriate measures and strategies for health risk reduction in the context of IDPs.Design/methodology/approachThe composite Index (CI) method was used to compare the public health risk factors at the household level in three IDP camps. A set of 22 indicators were studied in 326 households. Households were selected by using a two-stage cluster sampling technique.FindingsThe findings indicate that the Shangil Tobaya camp is at the highest risk for communicable diseases (63.6%) followed by Zamzam (52.4%) and Abu Shouk (42.7%) at the household level. Eight indicators appeared to have made differential impacts between Abu Shouk and Shangil Tobaya, these include: level of education, walking time to health facilities, water source, latrines type, safe disposal of child feces, frequency of visit by pregnant women to antenatal care services, place of delivery and women delivering their children with the help of skilled birth attendants.Research limitations/implicationsSince the selection criteria of the camps were predefined; there are variations in the number of samples between the camps. Therefore, the generalizability may be compromised.Social implicationsIncreased access to healthcare services particularly reproductive health services to the most vulnerable groups (women). Community involvement in services management to promote ownership.Originality/valueThe methods used in this study is original and flexible and can be replicated for other emergency areas and risks.