bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis of polyethylene glycol recognition by antibody
Authors: Lee Cheng-Chung , Su Yu-Cheng , Ko Tzu-Ping , Lin Li-Ling , Yang Chih-Ya , Chang Stanley Shi-Chung , Roffler Steve R. , Wang Andrew H.-J. 
Published: January 2020

Abstract
Background
Polyethylene glycol (PEG) is widely used in industry and medicine. Anti-PEG antibodies have been developed for characterizing PEGylated drugs and other applications. However, the underlying mechanism for specific PEG binding has not been elucidated.

Methods
The Fab of two cognate anti-PEG antibodies 3.3 and 2B5 were each crystallized in complex with PEG, and their structures were determined by X-ray diffraction. The PEG-Fab interactions in these two crystals were analyzed and compared with those in a PEG-containing crystal of an unrelated anti-hemagglutinin 32D6-Fab. The PEG-binding stoichiometry was examined by using analytical ultracentrifuge (AUC).

Results
A common PEG-binding mode to 3.3 and 2B5 is seen with an S-shaped core PEG fragment bound to two dyad-related Fab molecules. A nearby satellite binding site may accommodate parts of a longer PEG molecule. The core PEG fragment mainly interacts with the heavy-chain residues D31, W33, L102, Y103 and Y104, making extensive contacts with the aromatic side chains. At the center of each half-circle of the S-shaped PEG, a water molecule makes alternating hydrogen bonds to the ether oxygen atoms, in a similar configuration to that of a crown ether-bound lysine. Each satellite fragment is clamped between two arginine residues, R52 from the heavy chain and R29 from the light chain, and also interacts with several aromatic side chains. In contrast, the non-specifically bound PEG fragments in the 32D6-Fab crystal are located in the elbow region or at lattice contacts. The AUC data suggest that 3.3-Fab exists as a monomer in PEG-free solution but forms a dimer in the presence of PEG-550-MME, which is about the size of the S-shaped core PEG fragment.

Conclusions
The differing amino acids in 3.3 and 2B5 are not involved in PEG binding but engaged in dimer formation. In particular, the light-chain residue K53 of 2B5-Fab makes significant contacts with the other Fab in a dimer, whereas the corresponding N53 of 3.3-Fab does not. This difference in the protein-protein interaction between two Fab molecules in a dimer may explain the temperature dependence of 2B5 in PEG binding, as well as its inhibition by crown ether.
Porcine versus bovine surfactant therapy for RDS in preterm neonates: pragmatic meta-analysis and review of physiopathological plausibility of the effects on extra-pulmonary outcomes
Authors: Foligno Silvia , De Luca Daniele 
Published: January 2020

AbstractBackgroundWhile porcine seems to be superior to bovine surfactants in terms of respiratory outcomes, it is unclear if a surfactant can improve extra-pulmonary outcomes in preterm neonates with respiratory distress syndrome and if there is any physiopathological/biological mechanism linking surfactant therapy to these outcomes. We aim to fill these knowledge gaps.MethodsSystematic and pragmatic review coupled with meta-analysis of randomized controlled trials of bovine or porcine surfactants administered to treat RDS in preterm neonates; common extra-pulmonary neonatal intensive care outcomes were considered. As additional analysis, animal or human translational studies about mechanisms linking surfactant replacement to extra-pulmonary neonatal outcomes were also systematically reviewed.ResultsPorcine surfactant is associated with lower incidence of patentductus arteriosus(OR:0.655; 95%CI:0.460–0.931);p = 0.018; 12 trials; 1472 patients); prenatal steroids (coeff.:-0.009, 95%CI:-0.03–0.009,p = 0.323) and gestational age (coeff.:0.079, 95%CI:-0.18–0.34,p = 0.554) did not influence this effect size. No significant differences were found between porcine and bovine surfactants on neonatal intensive care unit length of stay (mean difference (days):-2.977; 95%CI:-6.659–0.705;p = 0.113; 8 trials; 855 patients), intra-ventricular hemorrhage of any grade (OR:0.860; 95%CI:0.648–1.139);p = 0.293; 15 trials; 1703 patients), severe intra-ventricular hemorrhage (OR:0.852; 95%CI:0.624–1.163);p = 0.313; 15 trials; 1672 patients), necrotizing entero-colitis (OR:1.190; 95%CI:0.785–1.803);p = 0.412; 9 trials; 1097 patients) and retinopathy of prematurity (OR:0.801; 95%CI:0.480–1.337);p = 0.396; 10 trials; 962 patients).ConclusionsPhysiopathological mechanisms explaining the effect of surfactant have been found for patentductus arteriosusonly, while they are lacking for all other endpoints. Porcine surfactant is associated with lower incidence of PDA than bovine surfactants. As there are no differences in terms of other extra-pulmonary outcomes and no physiopathological plausibility, these endpoints should not be used in future trials.RegistrationPROSPERO n.CRD42018100906.
Factors associated with quality of life of adult patients with acute leukemia and their family caregivers in China: a cross-sectional study
Authors: Wang Chunfeng , Yan Jie , Chen Jingyi , Wang Ying , Lin Ying Chun , Hu Rong , Wu Yong 
Published: January 2020

AbstractBackgroundAcute leukemia (AL) not only impairs the quality of life (QOL) of patients, but also affects that of their family caregivers (FCs). Studies on QOL of AL patients and their FCs are limited. This study aimed to evaluate the QOL of AL patients and their FCs, and to explore the factors associated with QOL of patients and of FCs.MethodsA multicenter cross-sectional study was conducted. The QOL of 196 patient–FC dyads was assessed. The Functional Assessment of Cancer Therapy-Leukemia (FACT-Leu) was used for patients, and the 36-item Short-Form Health Survey (SF-36) was used for FCs. Independent-samples t-tests or one-way analysis of variance were used to compare QOL subscale scores between groups with different sociodemographic/clinical characteristics. Multiple regression analysis was conducted to identify the factors associated with QOL of AL patients and their FCs.ResultsThe total FACT-Leu score for AL patients was 76.80 ± 16.44, and the physical component summary (PCS) and mental component summary (MCS) scores for FCs were 64.67 ± 15.44 and 52.50 ± 13.49, respectively. All QOL subscales for patients (t = 12.96–34.73,p < 0.001) and FCs (t = 2.55–14.36,p < 0.05), except role emotional (t = − 0.01,p = 0.993), were lower than those reported in previous studies. Sex, employment, and chemotherapy were significantly associated with total FACT-Leu score in AL patients (p < 0.05). Age, sex, marital status, education, employment, and relationship to patients were significantly associated with SF-36 PCS or MCS (p < 0.05).ConclusionsAL patients and their FCs both have lower QOL than the population in previous studies. These findings suggest that not only AL patients’ physical and mental health but also overall family QOL should be assessed. Interventions supporting patient–FC dyads should be developed to improve their QOL.
Perforated and bleeding peptic ulcer: WSES guidelines
Authors: Tarasconi Antonio , Coccolini Federico , Biffl Walter L. , Tomasoni Matteo , Ansaloni Luca , Picetti Edoardo , Molfino Sarah , Shelat Vishal , Cimbanassi Stefania , Weber Dieter G. , Abu-Zidan Fikri M. , Campanile Fabio C. , Di Saverio Salomone , Baiocchi Gian Luca , Casella Claudio , Kelly Michael D. , Kirkpatrick Andrew W. , Leppaniemi Ari , Moore Ernest E. , Peitzman Andrew , Fraga Gustavo Pereira , Ceresoli Marco , Maier Ronald V. , Wani Imtaz , Pattonieri Vittoria , Perrone Gennaro , Velmahos George , Sugrue Michael , Sartelli Massimo , Kluger Yoram , Catena Fausto 
Published: January 2020

Abstract
Background
Peptic ulcer disease is common with a lifetime prevalence in the general population of 5–10% and an incidence of 0.1–0.3% per year. Despite a sharp reduction in incidence and rates of hospital admission and mortality over the past 30 years, complications are still encountered in 10–20% of these patients. Peptic ulcer disease remains a significant healthcare problem, which can consume considerable financial resources. Management may involve various subspecialties including surgeons, gastroenterologists, and radiologists. Successful management of patients with complicated peptic ulcer (CPU) involves prompt recognition, resuscitation when required, appropriate antibiotic therapy, and timely surgical/radiological treatment.

Methods
The present guidelines have been developed according to the GRADE methodology. To create these guidelines, a panel of experts was designed and charged by the board of the WSES to perform a systematic review of the available literature and to provide evidence-based statements with immediate practical application. All the statements were presented and discussed during the 5th WSES Congress, and for each statement, a consensus among the WSES panel of experts was reached.

Conclusions
The population considered in these guidelines is adult patients with suspected complicated peptic ulcer disease. These guidelines present evidence-based international consensus statements on the management of complicated peptic ulcer from a collaboration of a panel of experts and are intended to improve the knowledge and the awareness of physicians around the world on this specific topic. We divided our work into the two main topics, bleeding and perforated peptic ulcer, and structured it into six main topics that cover the entire management process of patients with complicated peptic ulcer, from diagnosis at ED arrival to post-discharge antimicrobial therapy, to provide an up-to-date, easy-to-use tool that can help physicians and surgeons during the decision-making process.
First detection of Enterocytozoon bieneusi in whooper swans (Cygnus cygnus) in China
Authors: Wang Yuexin , Zhang Kaihui , Zhang Yifan , Wang Ke , Gazizova Azhar , Wang Luyang , Cao Letian , Zhang Yajun , Huang Jianying , Cui Yuan , Zhang Yuxi , Zhang Longxian 
Published: January 2020

Abstract
Background
Enterocytozoon bieneusi is a parasite that infects humans and a wide range of other animals. The large migratory waterfowl, the whooper swan (Cygnus cygnus), travels through many cities during its migration and can spread parasites. Despite receiving increasing attention worldwide, there have been no reports of E. bieneusi infection occurring in C. cygnus. Therefore, this study aims to assess the prevalence and genetic characteristics of E. bieneusi in C. cygnus in Sanmenxia, China.

Methods
Altogether, 467 fresh fecal samples were collected in the Swan Wetland Park in Sanmenxia, China. Genomic DNA was extracted from fresh fecal samples (n = 467) and E. bieneusi was identified by nested PCR amplification of the internal transcribed spacer (ITS) region. ITS-positive sequences were aligned and phylogenetically analyzed to determine the genotypes of E. bieneusi.

Results
The overall prevalence of E. bieneusi in C. cygnus was 7.49% (35/467). Sequencing of the 35 positive samples revealed eight known genotypes (EbpA, EbpC, Henan-III, Henan-IV, BEB6, CD9, Peru6 and PtEb IX) and three novel genotypes (CSW1, CSW2 and CSW3). The phylogenetic tree constructed from the ITS sequences showed that seven genotypes (Peru6, EbpA, EbpC, Henan-III, CSW3, Henan-IV and CSW1) clustered within the zoonotic Group 1 while the remaining novel genotype CSW2 clustered within Group 5.

Conclusions
To our knowledge, this is the first report of E. bieneusi in C. cygnus. Of public health significance, our results suggest that migratory C. cygnus might play an important role in the water-borne transmission of E. bieneusi. Effective strategies will be necessary to control E. bieneusi infection in C. cygnus, other animals and humans.
DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)
Authors: Bhat R. S. , Rockey J. , Shirasawa Kenta , Tilak I. S. , Brijesh Patil M. P. , Reddy Lachagari V. B. 
Published: January 2020

Abstract
Objective
Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut.

Results
The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.
Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature
Authors: Ciolfi Andrea , Aref-Eshghi Erfan , Pizzi Simone , Pedace Lucia , Miele Evelina , Kerkhof Jennifer , Flex Elisabetta , Martinelli Simone , Radio Francesca Clementina , Ruivenkamp Claudia A. L. , Santen Gijs W. E. , Bijlsma Emilia , Barge-Schaapveld Daniela , Ounap Katrin , Siu Victoria Mok , Kooy R. Frank , Dallapiccola Bruno , Sadikovic Bekim , Tartaglia Marco 
Published: January 2020

Abstract
Background
We previously associated HIST1H1E mutations causing Rahman syndrome with a specific genome-wide methylation pattern.

Results
Methylome analysis from peripheral blood samples of six affected subjects led us to identify a specific hypomethylated profile. This “episignature” was enriched for genes involved in neuronal system development and function. A computational classifier yielded full sensitivity and specificity in detecting subjects with Rahman syndrome. Applying this model to a cohort of undiagnosed probands allowed us to reach diagnosis in one subject.

Conclusions
We demonstrate an epigenetic signature in subjects with Rahman syndrome that can be used to reach molecular diagnosis.
Replication and expansion of epigenome-wide association literature in a black South African population
Authors: Cronjé H. Toinét , Elliott Hannah R. , Nienaber-Rousseau Cornelie , Pieters Marlien 
Published: January 2020

Abstract
Background
DNA methylation is associated with non-communicable diseases (NCDs) and related traits. Methylation data on continental African ancestries are currently scarce, even though there are known genetic and epigenetic differences between ancestral groups and a high burden of NCDs in Africans. Furthermore, the degree to which current literature can be extrapolated to the understudied African populations, who have limited resources to conduct independent large-scale analysis, is not yet known. To this end, this study examines the reproducibility of previously published epigenome-wide association studies of DNA methylation conducted in different ethinicities, on factors related to NCDs, by replicating findings in 120 South African Batswana men aged 45 to 88 years. In addition, novel associations between methylation and NCD-related factors are investigated using the Illumina EPIC BeadChip.

Results
Up to 86% of previously identified epigenome-wide associations with NCD-related traits (alcohol consumption, smoking, body mass index, waist circumference, C-reactive protein, blood lipids and age) overlapped with those observed here and a further 13% were directionally consistent. Only 1% of the replicated associations presented with effects opposite to findings in other ancestral groups. The majority of these inconcistencies were associated with population-specific genomic variance. In addition, we identified eight new 450K array CpG associations not previously reported in other ancestries, and 11 novel EPIC CpG associations with alcohol consumption.

Conclusions
The successful replication of existing EWAS findings in this African population demonstrates that blood-based 450K EWAS findings from commonly investigated ancestries can largely be extrapolated to ethnicities for which epigenetic data are not yet available. Possible population-specific differences in 14% of the tested associations do, however, motivate the need to include a diversity of ethnic groups in future epigenetic research. The novel associations found with the enhanced coverage of the Illumina EPIC array support its usefulness to expand epigenetic literature.
Self-assembly into virus–like particles of the recombinant capsid protein of porcine circovirus type 3 and its application on antibodies detection
Authors: Wang Yu , Wang Gang , Duan Wei-Tong , Sun Ming-Xia , Wang Meng-Hang , Wang Shang-Hui , Cai Xue-Hui , Tu Ya-bin 
Published: January 2020

AbstractPCV3 capsid protein (Cap) is an important antigen for diagnosis and vaccine development. To achieve high-level expression of recombinant PCV3 Cap in Escherichia coli (E. coli), the gene of wild-type entire Cap (wt-eCap) was amplified from clinical samples, and three optimized entire Cap (opti-eCap) and one optimized Cap deleted nuclear location signal (NLS) (opti-dCap) gene fragments encoding the same amino acid sequence with wt-eCap were synthesized based on the codon bias of E. coli. Those gene fragments were inserted into the pET30a expression vector. One recombinant strain with the highest expressed soluble eCap from four entire Cap (one wt-eCap and three opti-eCap) and one recombinant strain expressed opti-dCap were selected for further purification. The purified eCap and dCap were identified by transmission electron microscopy (TEM), a large number of round hollow particles with a diameter of 10 nm virus-like particles (VLPs) were observed in eCap, whereas irregular aggregation of proteins observed in dCap. After formation the VLPs were applied as a coating antigen to establish an indirect ELISA (I-ELISA) for detection of PCV3-specific antibody in swine serum. 373 clinical swine serum samples from China collected in 2019 were tested utilizing the VLP-based I-ELISA method under optimized conditions. To the best of our knowledge, this is the first report of self-assembly into VLPs of PCV3 recombinant Cap. Our results demonstrated that the VLP-based I-ELISA will be a valuable tool for detecting the presence of PCV3 antibodies in serum samples and will facilitate screening of large numbers of swine serum for clinical purposes.
Health education programs for improving men’s engagement with health services in low- to middle-income countries: a scoping review protocol
Authors: Dzinamarira Tafadzwa , Kuupiel Desmond , Mashamba-Thompson Tivani Phosa 
Published: January 2020

Abstract
Background
Health education programs (HEPs) have been documented to increase individuals’ awareness toward their health and improve health outcomes. Given the reported poor health seeking behavior among men in low- to middle-income countries (LMICs), it is crucial for HEPs to be targeted toward men in order to improve health outcomes. Here, we outline a protocol for a scoping review aimed at mapping literature on HEPs for men in LMICs in order to reveal gaps to guide future research and practice.

Methods
We will conduct a scoping review with guidance from the Arksey and O’Malley framework (Journal of Social Research Methodology 8(1):19–32, 2005), further enhanced by Levac et al. (Implementation Science 5(1):69, 2010). We will conduct a comprehensive keyword search for relevant studies presenting evidence on HEP for men in LMICs from PubMed, Google Scholar, EBSCOhost, and WEB of Science databases. In addition, we will search for relevant gray literature, dissertations, and theses from university repositories as well as international organizations such as the World Health Organization (WHO). We will include articles reporting evidence on health education programs for men in LMICs and published between January 2000 and March 2019. We will employ NVIVO version 12 software package to extract the relevant outcomes from the included articles using content thematic analysis. We will conduct quality appraisal of the included articles using the mixed methods appraisal tool (MMAT) 2018 version.

Discussion
We anticipate to find relevant studies reporting on health education programs for men in LMICs. The findings of this review will guide further implementation research on health education programs for men in LMICs. The results of the proposed scoping review will be disseminated electronically, in print, and through conference presentation as well as key stakeholder meetings.
Enhanced infection control interventions reduced catheter-related bloodstream infections in the neonatal department of Hung Vuong Hospital, Vietnam, 2011–2012: a pre- and post-intervention study
Authors: Phan Hang Thi , Vo Thuan Huu , Tran Hang Thi Thuy , Huynh Hanh Thi Ngoc , Nguyen Hong Thi Thu , Van Nguyen Truong 
Published: January 2020

Abstract
Background
Catheter-related bloodstream infections (CR-BSI) cause high neonatal mortality and are related to inadequate aseptic technique during the care and maintenance of a catheter. The incidence of CR-BSI among neonates in Hung Vuong Hospital was higher than that of other neonatal care centres in Vietnam.

Methods
An 18-month pre- and post-intervention study was conducted over three 6-month periods to evaluate the effectiveness of the intervention for CR-BSI and to identify risk factors associated with CR-BSI. During the intervention period, we trained all nurses in the Department of Neonatology on BSI preventive practices, provided auditing and feedback about aseptic technique during catheter care and maintenance, and reorganised preparation of total parenteral nutrition. All neonates with intravenous catheter insertion ≥48 h in the pre- and post-intervention period were enrolled. A standardised questionnaire was used to collect data. Blood samples were collected for cultures. We used Poisson regression to calculate rate ratio (RR) and 95% confidence interval (CI) for CR-BSI incidence rates and logistic regression to identify risk factors associated with CR-BSI.

Results
Of 2225 neonates enrolled, 1027 were enrolled in the pre-intervention period, of which 53 CR-BSI cases occurred in 8399 catheter-days, and 1198 were enrolled in the post-intervention period, of which 32 CR-BSI cases occurred in 8324 catheter-days. Incidence rates of CR-BSI significantly decreased after the intervention (RR = 0.61, 95% CI 0.39–0.94). Days of hospitalisation, episodes of non-catheter–related hospital-acquired infections, and the proportion of deaths significantly decreased after the intervention (p < 0.01). The CR-BSI was associated with days of intravenous catheter (odds ratio [OR] = 1.05, 95% CI 1.03–1.08), use of endotracheal intubation (OR = 2.27, 95% CI 1.27–4.06), and intravenous injection (OR = 8.50, 95% CI 1.14–63.4).

Conclusions
The interventions significantly decreased the incidence rate of CR-BSI. Regular refresher training and auditing and feedback about aseptic technique during care and maintenance of catheters are critical to reducing CR-BSI.
Active surveillance for highly resistant microorganisms in patients with prolonged hospitalization
Authors: Bastiaens Guido J. H. , Baarslag Tom , Pelgrum Corinne , Mascini Ellen M. 
Published: January 2020

AbstractWe evaluated a new hospital policy comprising active surveillance for highly resistant microorganisms (HRMO) in patients with prolonged hospitalization, including detection of nosocomial transmission after identification of HRMO carriers. Our findings raise the question of whether active surveillance should be extended from traditional risk groups to patients with prolonged hospitalization.