bluuebunny/crossref_metadata_2025_split huggingface dataset:
How does the WHO Surgical Safety Checklist fit with existing perioperative risk management strategies? An ethnographic study across surgical specialties
Authors: Wæhle Hilde Valen , Haugen Arvid Steinar , Wiig Siri , Søfteland Eirik , Sevdalis Nick , Harthug Stig 
Published: February 2020

Abstract
Background
The World Health Organization (WHO) Surgical Safety Checklist (SSC) has demonstrated beneficial impacts on a range of patient- and team outcomes, though variation in SSC implementation and staffʼs perception of it remain challenging. Precisely how frontline personnel integrate the SSC with pre-existing perioperative clinical risk management remains underexplored – yet likely an impactful factor on how SSC is being used and its potential to improve clinical safety. This study aimed to explore how members of the multidisciplinary perioperative team integrate the SSC within their risk management strategies.

Methods
An ethnographic case study including observations (40 h) in operating theatres and in-depth interviews of 17 perioperative team members was carried out at two hospitals in 2016. Data were analysed using content analysis.

Results
We identified three themes reflecting the integration of the SSC in daily surgical practice: 1) Perceived usefullness; implying an intuitive advantage assessment of the SSCʼs practical utility in relation to relevant work; 2) Modification of implementation; reflecting performance variability of SSC on confirmation of items due to precence of team members; barriers of performance; and definition of SSC as performance indicator, and 3) Communication outside of the checklist; including formal- and informal micro-team formations where detailed, specific risk communication unfolded.

Conclusion
When the SSC is not integrated within existing risk management strategies, but perceived as an “add on”, its fidelity is compromised, hence limiting its potential clinical effectiveness. Implementation strategies for the SSC should thus integrate it as a risk-management tool and include it as part of risk-management education and training. This can improve team learning around risk comunication, foster mutual understanding of safety perspectives and enhance SSC implementation.
Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy
Authors: Tarca Adi L. , Romero Roberto , Pique-Regi Roger , Pacora Percy , Done Bogdan , Kacerovsky Marian , Bhatti Gaurav , Jaiman Sunil , Hassan Sonia S. , Hsu Chaur-Dong , Gomez-Lopez Nardhy 
Published: February 2020

Abstract
Background
The amniotic fluid (AF) cell-free transcriptome is modulated by physiologic and pathologic processes during pregnancy. AF gene expression changes with advancing gestation reflect fetal development and organ maturation; yet, defining normal expression and splicing patterns for biomarker discovery in obstetrics requires larger heterogeneous cohorts, evaluation of potential confounding factors, and novel analytical approaches.

Methods
Women with a normal pregnancy who had an AF sample collected during midtrimester (n = 30) or at term gestation (n = 68) were included. Expression profiling at exon level resolution was performed using Human Transcriptome Arrays. Differential expression was based on moderated t-test adjusted p < 0.05 and fold change > 1.25; for differential splicing, a splicing index > 2 and adjusted p < 0.05 were required. Functional profiling was used to interpret differentially expressed or spliced genes. The expression of tissue-specific and cell-type specific signatures defined by single-cell genomics was quantified and correlated with covariates. In-silico validation studies were performed using publicly available datasets.

Results
1) 64,071 genes were detected in AF, with 11% of the coding and 6% of the non-coding genes being differentially expressed between midtrimester and term gestation. Expression changes were highly correlated with those previously reported (R > 0.79, p < 0.001) and featured increased expression of genes specific to the trachea, salivary glands, and lung and decreased expression of genes specific to the cardiac myocytes, uterus, and fetal liver, among others. 2) Single-cell RNA-seq signatures of the cytotrophoblast, Hofbauer cells, erythrocytes, monocytes, T and B cells, among others, showed complex patterns of modulation with gestation (adjusted p < 0.05). 3) In 17% of the genes detected, we found differential splicing with advancing gestation in genes related to brain development processes and immunity pathways, including some that were missed based on differential expression analysis alone.

Conclusions
This represents the largest AF transcriptomics study in normal pregnancy, reporting for the first time that single-cell genomic signatures can be tracked in the AF and display complex patterns of expression during gestation. We also demonstrate a role for alternative splicing in tissue-identity acquisition, organ development, and immune processes. The results herein may have implications for the development of fetal testing to assess placental function and fetal organ maturity.
Haemosporidioses in wild Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos): an in situ hybridization study with emphasis on exo-erythrocytic parasite burden
Authors: Himmel Tanja , Harl Josef , Pfanner Simone , Nedorost Nora , Nowotny Norbert , Weissenböck Herbert 
Published: February 2020

Abstract
Background
Passerine birds are frequently infected with diverse haemosporidian parasites. While infections are traditionally considered benign in wild birds, recent studies demonstrated mortalities of passerine species due to exo-erythrocytic development of the parasites, which can damage organs in affected hosts. However, exo-erythrocytic development remains insufficiently investigated for most haemosporidian species and thus little is known about the virulence of tissue stages in wild passerine birds. The aim of the present study was to investigate natural haemosporidian infections in deceased Eurasian blackbirds (Turdus merula) and song thrushes (Turdus philomelos) and to determine parasite burden and associated histological effects.

Methods
For molecular analysis, blood and tissue samples from 306 thrushes were screened for Plasmodium, Haemoproteus and Leucocytozoon parasites by nested PCR. For the detection of parasite stages in organ samples, tissue sections were subjected to chromogenic in situ hybridization (CISH) using genus- and species-specific probes targeting the rRNAs of parasites. Exo-erythrocytic parasite burden was semi-quantitatively assessed and histological lesions were evaluated in haematoxylin–eosin-stained sections.

Results
By PCR, 179 of 277 Eurasian blackbirds and 15 of 29 song thrushes were positive for haemosporidians. Parasites of all three genera were detected, with Plasmodium matutinum LINN1 and Plasmodium vaughani SYAT05 showing the highest prevalence. CISH revealed significant differences in exo-erythrocytic parasite burden between lineages in Eurasian blackbirds, with P. matutinum LINN1 frequently causing high exo-erythrocytic parasite burdens in various organs that were associated with histological alterations. Song thrushes infected with P. matutinum LINN1 and birds infected with other haemosporidian lineages showed mostly low exo-erythrocytic parasite burdens. Two Eurasian blackbirds infected with Leucocytozoon sp. TUMER01 showed megalomeronts in various organs that were associated with inflammatory reactions and necroses.

Conclusion
This study suggests that P. matutinum LINN1, a common lineage among native thrushes, regularly causes high exo-erythrocytic parasite burdens in Eurasian blackbirds, which may result in disease and mortalities, indicating its high pathogenic potential. The findings further illustrate that the same parasite lineage may show different levels of virulence in related bird species which should be considered when assessing the pathogenicity of haemosporidian parasite species. Finally, the study provides evidence of virulent Leucocytozoon sp. TUMER01 infections in two Eurasian blackbirds caused by megalomeront formation.
Angiotensin II blockade had no effect on range of motion after total knee arthroplasty: a retrospective review
Authors: Langston Joseph R. , Ramsey Duncan C. , Skoglund Kathryn , Schabel Kathryn 
Published: February 2020

Abstract
Background
Stiffness and pain from arthrofibrosis following total knee arthroplasty (TKA) is a challenging problem, and investigating methods to prevent or reduce the incidence of postoperative arthrofibrosis is critical. Studies have shown that angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) are efficacious at preventing fibrotic disorders in the lungs, liver, kidneys, and eyes. Our aim was to determine if ACEI or ARB use postoperatively reduces the incidence of arthrofibrosis in TKA patients.

Methods
In a retrospective review, we analyzed 141 consecutive TKAs performed at a single institution by a single surgeon from December 2010 to December 2014. Range of motion (ROM) in patients already taking ACEI, ARB, or neither medication was compared. Independent variables recorded were gender, age, BMI, presence of diabetes or preoperative opioid or statin use, preoperative ROM, and use of ACEIs or ARBs. Dependent variables recorded were postoperative knee flexion, extension, and total arc of motion. The primary outcome variable was success or failure of achieving 118o total arc of motion postoperatively, based on a study that found significant compromise of function in TKA patients who failed to obtain this goal. Secondary endpoints were postoperative knee flexion, extension, and total arc of motion.

Results
The use of neither ACEIs nor ARBs showed a significant difference in attaining greater than 118° of motion postoperatively compared to controls at 6 months. Significant predictors of obtaining > 118° motion were BMI (p < 0.05), preoperative flexion (p < 0.001), and preoperative total arc of motion (p < 0.002). Significant predictors of secondary ROM outcomes were preoperative ROM and BMI.

Conclusions
Our study demonstrated that the principle predictor of postoperative ROM is BMI and preoperative ROM. The use of ACEIs or ARBs did not result in a greater likelihood of obtaining satisfactory ROM postoperatively.
Is supported self-management for depression effective for adults in community-based settings in Vietnam?: a modified stepped-wedge cluster randomized controlled trial
Authors: Murphy Jill K. , Xie Hui , Nguyen Vu Cong , Chau Leena W. , Oanh Pham Thi , Nhu Tran Kieu , O’Neil John , Goldsmith Charles H. , Van Hoi Nguyen , Ma Yue , Lou Hayami , Jones Wayne , Minas Harry 
Published: February 2020

AbstractBackgroundThis study tested the effectiveness of a supported self-management (SSM) intervention to reduce symptoms of depression among adults compared with enhanced treatment as usual in community-based and primary care settings in Vietnam.MethodsThe cluster randomized trial included 376 adults in 32 communes in eight provinces. Eligible participants scored > 7 on the SRQ-20 depression scale. Patients with severe symptoms were excluded and referred to tertiary care. Randomization took place at the commune level. The immediate intervention group included 16 communes with 190 participants and the delayed group included 16 communes with 186 participants. Participants in communes randomized to the immediate intervention group received a two-month course of SSM, consisting of a workbook and supportive coaching. Those in communes randomized to the delayed group received enhanced treatment as usual and, for ethical purposes, received the SSM intervention after 4 months. The primary outcome is the effect of SSM on reduction in depression scores as indicated by a reduced proportion of participants with SRQ-20 scores > 7 at 2 months after commencement of SSM intervention. Blinding was not possible during intervention delivery but outcome assessors were blinded. Analysis was intention-to-treat.ResultsAt 2 months, 26.4% of the intervention group and 42.3% of the delayed group had SRQ-20 scores > 7. The adjusted odds ratio of having depression between the intervention and control was 0.42 (p < 0.0001), 95% CI (0.28, 0.63). Receiving the intervention thus reduces the odds of having depression by 58%, compared with receiving the control after 2 months of treatment. No adverse events were reported.ConclusionsResults suggest that SSM is effective for decreasing depression symptoms among adults in community-based settings in Vietnam.Trial RegistrationThis trial is registered at ClinicalTrials.gov, number NCT03001063.
Tumour necrosis factor alpha promotes secretion of 14-3-3η by inducing necroptosis in macrophages
Authors: Trimova Gulzhan , Yamagata Kaoru , Iwata Shigeru , Hirata Shintaro , Zhang Tong , Uemura Fumi , Satoh Minoru , Biln Norma , Nakayamada Shingo , Maksymowych Walter P. , Tanaka Yoshiya 
Published: February 2020

Abstract
Background
14-3-3η is an intracellular protein also detected in the serum and synovial fluid of patients with rheumatoid arthritis (RA). It is closely related to disease activity and anti-cyclic citrullinated peptide antibody levels. However, the main source of 14-3-3η and the mechanism of its release into the extracellular space remain unclear. Addressing these two points was the main goal of the current study.

Methods
The source of 14-3-3η was investigated by immunostaining RA synovial tissue. Fibroblast-like synoviocytes, CD4+ cells, and macrophages were selected as candidates among the various cell types in the synovial tissue. Phosphorylation of mixed-lineage kinase domain-like pseudokinase (MLKL) and cell death of macrophages were studied by phalloidin staining and electron microscopy after stimulation with an oxidative stress inducer (diamide) or tumour necrosis factor (TNF)-α. Extracellular 14-3-3η protein levels were examined by western blotting.

Results
Macrophages from the synovial tissue from RA, but not osteoarthritis, showed dense and widespread cytoplasmic staining for the 14-3-3η protein, co-localized with peptidylarginine deiminase 4. Swelling and membrane rupture of macrophages were induced by treatment with TNF-α, but not interleukin (IL) 6/soluble IL-6 receptor (sIL-6R). Increased MLKL phosphorylation followed by necroptosis was also induced in TNF-α-stimulated macrophages. Necrostatin-1, a necroptosis inhibitor, antagonized MLKL phosphorylation. High levels of 14-3-3η were detected in the culture supernatants of macrophages stimulated with diamide and TNF-α, but not IL-6/sIL-6R.

Conclusions
Macrophages that highly express 14-3-3η undergo TNF-α-induced necroptosis with damage to the cellular structure, resulting in the secretion of 14-3-3η into the extracellular space. The current study provides a novel mechanism for 14-3-3η level increase in the RA synovial fluid.
Maize genomes to fields (G2F): 2014–2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets
Authors: McFarland Bridget A. , AlKhalifah Naser , Bohn Martin , Bubert Jessica , Buckler Edward S. , Ciampitti Ignacio , Edwards Jode , Ertl David , Gage Joseph L. , Falcon Celeste M. , Flint-Garcia Sherry , Gore Michael A. , Graham Christopher , Hirsch Candice N. , Holland James B. , Hood Elizabeth , Hooker David , Jarquin Diego , Kaeppler Shawn M. , Knoll Joseph , Kruger Greg , Lauter Nick , Lee Elizabeth C. , Lima Dayane C. , Lorenz Aaron , Lynch Jonathan P. , McKay John , Miller Nathan D. , Moose Stephen P. , Murray Seth C. , Nelson Rebecca , Poudyal Christina , Rocheford Torbert , Rodriguez Oscar , Romay Maria Cinta , Schnable James C. , Schnable Patrick S. , Scully Brian , Sekhon Rajandeep , Silverstein Kevin , Singh Maninder , Smith Margaret , Spalding Edgar P. , Springer Nathan , Thelen Kurt , Thomison Peter , Tuinstra Mitchell , Wallace Jason , Walls Ramona , Wills David , Wisser Randall J. , Xu Wenwei , Yeh Cheng-Ting , de Leon Natalia 
Published: February 2020

Abstract
Objectives
Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F’s genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014–2017.

Data description
Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.
A greedy stacking algorithm for model ensembling and domain weighting
Authors: Kurz Christoph F. , Maier Werner , Rink Christian 
Published: February 2020

Abstract
Objective
Because it is impossible to know which statistical learning algorithm performs best on a prediction task, it is common to use stacking methods to ensemble individual learners into a more powerful single learner. Stacking algorithms are usually based on linear models, which may run into problems, especially when predictions are highly correlated. In this study, we develop a greedy algorithm for model stacking that overcomes this issue while still being very fast and easy to interpret. We evaluate our greedy algorithm on 7 different data sets from various biomedical disciplines and compare it to linear stacking, genetic algorithm stacking and a brute force approach in different prediction settings. We further apply this algorithm on a task to optimize the weighting of the single domains (e.g., income, education) that build the German Index of Multiple Deprivation (GIMD) to be highly correlated with mortality.

Results
The greedy stacking algorithm provides good ensemble weights and outperforms the linear stacker in many tasks. Still, the brute force approach is slightly superior, but is computationally expensive. The greedy weighting algorithm has a variety of possible applications and is fast and efficient. A python implementation is provided.
Combining PRNU and noiseprint for robust and efficient device source identification
Authors: Cozzolino Davide , Marra Francesco , Gragnaniello Diego , Poggi Giovanni , Verdoliva Luisa 
Published: February 2020

AbstractPRNU-based image processing is a key asset in digital multimedia forensics. It allows for reliable device identification and effective detection and localization of image forgeries, in very general conditions. However, performance impairs significantly in challenging conditions involving low quality and quantity of data. These include working on compressed and cropped images or estimating the camera PRNU pattern based on only a few images. To boost the performance of PRNU-based analyses in such conditions, we propose to leverage the image noiseprint, a recently proposed camera-model fingerprint that has proved effective for several forensic tasks. Numerical experiments on datasets widely used for source identification prove that the proposed method ensures a significant performance improvement in a wide range of challenging situations.
Evolutionary understanding of the conditions leading to estimation of behavioral properties through system dynamics
Authors: Park Chulwook 
Published: February 2020

AbstractOne of the basic approaches in science views behavioral products as a process within a dynamic system. The mechanism might be seen as a representation of many instances of centralized control in real time. Many real systems, however, exhibit autonomy by denying statically treated mechanisms. This study addresses the issues related to the identification of dynamic systems and suggests how determining the basic principles of a collective structure may be the key to understanding complex behavioral processes. A fundamental model is derived to assess the advantages of this perspective using a basic methodology. The connection between perspective and technique demonstrates certain aspects within their actual context while also clearly including the framework of actual dynamic system identification.
The efficacy of DNA mismatch repair enzyme immunohistochemistry as a screening test for hypermutated gliomas
Authors: McCord Matthew , Steffens Alicia , Javier Rodrigo , Kam Kwok-Ling , McCortney Kathleen , Horbinski Craig 
Published: February 2020

AbstractA subset of gliomas has DNA repair defects that lead to hypermutated genomes. While such tumors are resistant to alkylating chemotherapies, they may also express more mutant neoantigens on their cell surfaces, and thus be more responsive to immunotherapies. A fast, inexpensive method of screening for hypermutated gliomas would therefore be of great clinical value. Since immunohistochemistry (IHC) for the DNA mismatch repair (MMR) proteins Msh2, Msh6, Mlh1, and Pms2 is already used to screen for hypermutated colorectal cancers, we sought to determine whether that panel might have similar utility in gliomas. MMR IHC was scored in 100 WHO grade I-IV gliomas (from 96 patients) with known tumor mutation burden (TMB), while blinded to TMB data. Cases included 70 grade IV GBMs, 13 grade III astrocytomas, 4 grade II astrocytomas (3 diffuse astrocytomas and 1 pleomorphic xanthoastrocytoma), 1 grade I pilocytic astrocytoma, 2 grade III oligodendrogliomas, 7 grade II oligodendrogliomas, and 3 grade I glioneuronal tumors. Eight of 100 tumors showed loss of one or more MMR proteins by IHC, and all 8 were hypermutated. Among the remaining 92 gliomas with intact MMR IHC, only one was hypermutated; that tumor had an inactivating mutation in another DNA repair gene, ATM. Overall accuracy, sensitivity, and specificity for DNA MMR IHC compared to the gold standard of TMB were 99, 89, and 100%, respectively. The strongest correlates with hypermutation were prior TMZ treatment, MGMT promoter methylation, and IDH1 mutation. Among the 8 MMR-deficient hypermutated gliomas, 4 (50%) contained both MMR-lost and MMR-retained tumor cells. Together, these data suggest that MMR IHC could be a viable front-line screening test for gliomas in which immunotherapy is being considered. They also suggest that not all cells in a hypermutated glioma may actually be MMR-deficient, a finding that might need to be considered when treating such tumors with immunotherapies.