bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term effects of a food pattern on cardiovascular risk factors and age-related changes of muscular and cognitive function
Authors: Wernicke Charlotte , Apostolopoulou Konstantina , Hornemann Silke , Efthymiou Andriana , Machann Jürgen , Schmidt Sein , Primessnig Uwe , Bergmann Manuela M. , Grune Tilman , Gerbracht Christiana , Herber Katharina , Pohrt Anne , Pfeiffer Andreas F.H. , Spranger Joachim , Mai Knut 
Published: September 2020

Abstract

Introduction:
The mean age of the German population increased over the last years, which resulted in a higher prevalence of cardiovascular diseases, type 2 diabetes, cognitive impairment, sarcopenia and bone fractures. Current evidence indicates a preservation of human wellbeing in the elderly by a healthy diet, although the recommended macronutrient composition and quality remains unclear and needs further long-term investigation. In this context we investigate the effect of a specific dietary pattern on age-related disorders in a randomized controlled multi-center trial (RCT).

Methods:
We assess the effect of a specific dietary pattern (NutriAct) with a high proportion of unsaturated fat, plant proteins and fibres (fat 35%–40% of total energy (%E) of which 15%E–20%E monounsaturated fatty acids (MUFA) and 10%E–15%E polyunsaturated fatty acids (PUFA), 15%E–25%E proteins, ≥30 g fibres per day and 35%E–45%E carbohydrates) on age-related impairment of health within a 36-months RCT conducted in the region of Berlin and Potsdam. 502 eligible men (n = 183) and women (n = 319), aged 50 to 80 years, with an increased risk to develop age-related diseases were randomly assigned to either an intervention group focusing on NutriAct dietary pattern or a control group focusing on usual care and dietary recommendations in accordance to the German Nutrition Society (DGE). In the intervention group, 21 nutrition counsellings as well as supplementation of rapeseed oil, oil cake and specific designed foods are used to achieve the intended NutriAct dietary pattern.
The primary outcome is a composite endpoint of age-related disorders, including cardiovascular morbidity, decline of cognitive function as well as clinical features of sarcopenia. Secondary outcomes include diet-induced effects on quality of life, depression, frailty, cardiovascular function, bone density, fat distribution pattern, glucose, lipid and energy metabolism, as well as the identification of biomarkers linked with age-related disorders.

Discussion:
The findings of this trial will provide clinically relevant information regarding dietary effects on age-related impairment of health and will contribute to the definition of the optimal macronutrient composition in the context of healthy aging in the German population.
Bullying experience of pupils in Nigerian primary schools
Authors: Umoke Prince C.I. , Umoke MaryJoy , Ugwuanyi Christian S. , Okeke Chinedu I.O. , Eseadi Chiedu , Onuorah Adaorah R. , Ugwu Gloria C. , Obiweluozo Patience Enuma , Uzodinma Uchenna Eugenia , Uwakwe Rowland C. , Uba Mercy Benedette Ifeoma , Ebizie Elizabeth N. , Onyeke Nkechi G. , Otu Mkpoikanke S. 
Published: September 2020

Abstract
Childhood bullying leads to life-long scars and hinders adult development. Schoolchildren involved in bullying are at risk of developing behavioural difficulties, physical health problems and suicidal ideation. This research aimed to evaluate the bullying experience of pupils in Nigerian primary schools.
The study is a cross-sectional analytic survey conducted from June to November 2019. A total of 1080 pupils in participated in the study. A self-report questionnaire containing 3 questions was used for collecting data. Analysis of the collected data was done using percentage and Chi-Squared at 0.05 probability level.
Results indicate that 51.4% of the male pupils and 50.8% of females reported being victims of bullying. 51.8% of the males and 49.5% of females were found to be perpetrators of bullying. 39.6% of the males and 42.9% of the females were bystanders of bullying. 35.1% of the males and 34.1% of females have experienced any 2 of the categories while 11.2% of the males and 12.4% of the females have experienced all the categories of bullying. Results show a non-significant difference between male and female pupils on bullying victimization (χ2 = .036, P = .849), bullying perpetration (χ2 = .589, P = .443), and bullying bystander problem (χ2 = 1.194, P = .275).
In conclusion, school bullying is an increasing problem among Nigerian schoolchildren. Initiatives must, therefore, be taken by the Nigerian government to further prevent and counter bullying problem in Nigerian primary schools. Interventions aimed at helping schools to develop effective policies to reduce bullying behaviour among pupils should be initiated.
Bronchiectasis with secondary pulmonary infection in a child
Authors: Zhu Ting , Gu Haoxiang , Vinturache Angela , Ding Guodong , Lu Min 
Published: September 2020

Abstract

Rationale:
Although bronchiectasis is conventionally considered a chronic pulmonary disease of adulthood, knowledge of pediatric bronchiectasis not related to cystic fibrosis started to emerge. Limited information in this field is available and the management is based on expert opinion.

Patient concerns:
An 8-year-old girl admitted for 7 days history of wet cough, purulent fetid sputum, shortness of breath and low-grade fever. The wet cough has presented for the past 4 years, during which she had frequent hospitalization for recurrent lower respiratory tract infections.

Diagnosis:
Chest high-resolution computerized tomography revealed diffuse bronchial dilations accompanied by inflammation in the bilateral lung fields. Microbiologic investigation for bronchoalveolar lavage fluid was positive for Pseudomonas aeruginosa.

Interventions:
With a working diagnosis of bronchiectasis with secondary pulmonary infection, sensitive cefoperazone-sulbactam was administrated for 14 days with gradual improvement of clinical symptoms. Bronchoscopy washing substantially soothed the symptoms, reducing the cough and sputum volumes.

Outcomes:
The child was discharged after 14 days, and treated on long-term prophylactic antibiotic use (amoxicillin-clavulanic acid, 20 mg/kg/d, ≥ 4 weeks).

Lessons:
Although bronchiectasisis are condition in childhood, the diagnosis is suspected in children with persistent wet or productive cough, and should be confirmed by a chest high-resolution computerized tomography scan. Antibiotics and airway clearance techniques represent the milestones of bronchiectasis management although there are only a few guidelines in children.
Using a cervical ripening balloon to penetrate the placenta and quickly reduce bleeding by pressing against the placenta during pregnancy termination for patients with placenta previa in the second trimester
Authors: Su Chang , Chen Danqing 
Published: September 2020

Abstract

Introduction:
The clinical treatment is complicated for patients with placenta previa who must terminate pregnancy due to fetal malformation, death, or inevitable abortion in the second trimester. It is difficult to manage excessive bleeding during pregnancy termination; and those patients face risks of removing the uterus, infection and other complications.

Patient concerns:
Two patients had placenta previa in the second trimester. Both cases had to terminate pregnancy. Case 1 patient had intrauterine fetal death. Case 2 patient had life-threatening vaginal bleeding. Both patients had bleeding and their cervix was not mature during vaginal delivery.

Diagnosis:
After hospitalization, placenta previa was confirmed by magnetic resonance imaging for case 1 patient. Placenta previa was confirmed by ultrasound examination for case 2 patient. Both patients had to terminate pregnancy.

Interventions:
We designed a new procedure using a cervical ripening balloon to reduce the risks during pregnancy termination for patients with placenta previa. A cervical ripening balloon was inserted through the placenta and placed between the fetus and placenta; external force was applied to keep the cervical ripening balloon pressing against the placenta that covers the cervical os. The cervical ripening balloon dilated the cervix, quickly reduced bleeding, and induced vaginal delivery during pregnancy termination for patients with placenta previa. This method was applied to 2 patients with placenta previa who must terminate pregnancy.

Outcomes:
Using the new method, both patients had a successful pregnancy termination and vaginal delivery with minimal bleeding. Total time from the balloon placement to the end of the delivery was about 3 hours. The procedure only used a cervical ripening balloon without uterine artery embolization needed. The fetus was delivered through the vagina; and the uterus was fully retained. There was no postpartum infection.

Conclusion:
This new method using a cervical ripening balloon could be a quick and effective way to reduce the risks during pregnancy termination for patients with placenta previa. It is especially helpful in emergency situations with minimal requirements of personnel and equipment. Our study showed great potential of this new utilization of a cervical ripening balloon, and is worthy of further research.
Health Care Failure Mode and Effect Analysis in the Operating Room Setting
Authors: Pirouzi Maryam , Gorji Hassan A. , Ravaghi Hamid , Afshari Atefeh 
Published: September 2020

Objectives:
Operating rooms (ORs) and surgical settings are potential sources of sentinel adverse events. To better understand the characteristics of errors in OR processes, we performed prospective risk analysis.

Methods:
The study was mixed qualitative and quantitative research. We used the Healthcare Failure Mode and Effect Analysis (HFMEA) method to analyze the selected perioperative, operative, and postoperative processes in the OR via a 2-round Delphi technique. We identified the most prominent failure modes according to a Hazard Decision Matrix, analyzed and categorized proposed possible causes, and provided solutions to mitigate hazard scores.

Results:
Ten important processes and 7 subprocesses within the OR were selected and mapped, and 187 failure modes were identified and scored on the basis of severity and probability. A total of 36 potential failure modes were highlighted as high-risk failures and moved to decision trees for further analyses.

Conclusion:
Developing policy for the familiarization of new personnel designing a checklist for accurate gases counting; drafting comprehensive presurgical posters; preparing all necessary equipment in difficult intubation; developing instruction for monthly checking of the OR equipment; and developing the evaluation criteria of staff performance are examples of solutions that are proposed to improve the quality of OR processes.
A high-throughput method for measuring critical thermal limits of leaves by chlorophyll imaging fluorescence
Authors: Arnold Pieter A. , Briceño Verónica F. , Gowland Kelli M. , Catling Alexandra A. , Bravo León A. , Nicotra Adrienne B. 
Published: September 2020

AbstractPlant thermal tolerance is a crucial research area as the climate warms and extreme weather events become more frequent. Leaves exposed to temperature extremes have inhibited photosynthesis and will accumulate damage to photosystem II (PSII) if tolerance thresholds are exceeded. Temperature-dependent changes in basal chlorophyll fluorescence (T-F0) can be used to identify the critical temperature at which PSII is inhibited. We developed and tested a high-throughput method for measuring the critical temperatures for PSII at low (CTMIN) and high (CTMAX) temperatures using a Maxi-Imaging fluorimeter and a thermoelectric Peltier plate heating/cooling system. We examined how experimental conditions: wetvsdry surfaces for leaves and heating/cooling rate, affectCTMINandCTMAXacross four species.CTMAXestimates were not different whether measured on wet or dry surfaces, but leaves were apparently less cold tolerant when on wet surfaces. Heating/cooling rate had a strong effect on bothCTMAXandCTMINthat was species-specific. We discuss potential mechanisms for these results and recommend settings for researchers to use when measuringT-F0. The approach that we demonstrated here allows the high-throughput measurement of a valuable ecophysiological parameter that estimates the critical temperature thresholds of leaf photosynthetic performance in response to thermal extremes.
Performance Assessment of First-Generation Anti-SARS-CoV-2 Serological Assays
Authors: Imam Mehjabeen , Khawaja Shabnum , Naz Arshi , Siddiqui Ahson , Nafees Tehmina S. , Younus Amber , Shamsi Usama , Shabir Imran , Ahmed Shakir , Tariq Naveen , Tariq Salman , Shamsi Tahir S. 
Published: September 2020

ABSTRACTThe clinical and epidemiological use of SARS-CoV-2 antibody assays is under debate with urgent need to validate and verify the performance of SARS-CoV-2 serologic assays. We aim to assess the clinical and analytical performance of three commercial serological assays of SARS-CoV-2, comparing three anti-SARS-CoV-2-IgG ELISA and identifying the seroconversion and seroprevalence in our population.A cross sectional study conducted from April 2020 to July 2020 at National Institute of Blood disease and Bone Marrow Transplantation Karachi, Pakistan with sample size of 404, enrolled consecutively. Participants were categorized into four groups’ namely convalescent plasmadonors (CPDs n=239), health care professionals (HCPs n=44), healthy blood donors (HBDs n=70) and from community (n=51).We evaluated the performance of Elecsys anti-SARS-CoV-2 electrochemiluminescence (ECLIA) assay on Cobas-e411 by Roche, three qualitative anti-SARS-CoV-2-IgG enzyme linked imunosorbant assay (ELISA) by (Generic assays, Euroimmun & Omega diagnostics), one quantitative ELISA assay by AESKU Diagnostics and two immune chromatography(ICT) kits namely InstaTest™ by CORTEZ and TEST IT by TURKLAB.From total 404 subjects, 322 (83.5%) were males. Mean age was 36.79±11.95 years. Among 239 in CPDs group, 202(84.5%) showed positive antibodies by ECLIA. The qualitative anti-SARS-CoV-2 IgG ELISA was positive in 174 (72.8%) and quantitative IgG in 180(75.3%) with mean titer of 56.7 ±39.7 U/ml. Sensitivity and specificity of ECLIA were 97.44& 99%, ELISA by Generic assays were 67.85% and 89.9%; Euroimmun had 90.38% and 94.9%; Omega Diagnostics 96.4% and 95% and the AESKULISA 93.75% and 100% respectively. Seroconversion was found to be 53.8% and 77.77% within 7 -8 days and 12 to 14 days post onset of symptoms respectively. ICT had more specificity but less sensitivity. Seroprevalence was found to be 84.5%, 40.9% and 21.4% in CPDs, HCPs and HBDs respectively.The Roche ECLIA, qualitative ELISA by Omega Diagnostics & Euroimmun showed higher sensitivity as well as higher specificity. Quantitative ELISA has higher specificity and relatively high sensitivity. Significant numbers of COVID patients do not have detectable antibodies by all assays.
Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data
Authors: Johnson Kayla A , Krishnan Arjun 
Published: September 2020

AbstractBackgroundConstructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene prioritization. While optimal workflows for constructing coexpression networks – including good choices for data pre-processing, normalization, and network transformation – have been developed for microarray-based expression data, such well-tested choices do not exist for RNA-seq data. Almost all studies that compare data processing/normalization methods for RNA-seq focus on the end goal of determining differential gene expression.ResultsHere, we present a comprehensive benchmarking and analysis of 30 different workflows, each with a unique set of normalization and network transformation methods, for constructing coexpression networks from RNA-seq datasets. We tested these workflows on both large, homogenous datasets (Genotype-Tissue Expression project) and small, heterogeneous datasets from various labs (submitted to the Sequence Read Archive). We analyzed the workflows in terms of aggregate performance, individual method choices, and the impact of multiple dataset experimental factors. Our results demonstrate that between-sample normalization has the biggest impact, with trimmed mean of M-values or upper quartile normalization producing networks that most accurately recapitulate known tissue-naive and tissue-specific gene functional relationships.ConclusionsBased on this work, we provide concrete recommendations on robust procedures for building an accurate coexpression network from an RNA-seq dataset. In addition, researchers can examine all the results in great detail athttps://krishnanlab.github.io/norm_for_RNAseq_coexpto make appropriate choices for coexpression analysis based on the experimental factors of their RNA-seq dataset.
Structural biologists, let’s mind our colors
Authors: Saladi Shyam M. , Maggiolo Ailiena O. , Radford Kate , Clemons William M. 
Published: September 2020

AbstractIn structural biology, most figures of macromolecules are aimed at those well-versed in structure, requiring prior familiarity with scales and commonly used color schemes. Yet, as structural biology becomes democratized with the increasing pace of structure determination, the accessibility of structural data is paramount. Here, we identify three keys, and have written accompanying software plugins, for structural biologists to create figures truer to the hard-won data and clearer across different modes of color vision and to non-expert readers.Use perceptually uniform colormapsConsider readers with different modes of color visionBe explicit about scales and color usage
Clinical interpretation of integrative molecular profiles to guide precision cancer medicine
Authors: Reardon Brendan , Moore Nathaniel D , Moore Nicholas , Kofman Eric , Aldubayan Saud , Cheung Alexander , Conway Jake , Elmarakeby Haitham , Imamovic Alma , Kamran Sophia C. , Keenan Tanya , Keliher Daniel , Konieczkowski David J , Liu David , Mouw Kent , Park Jihye , Vokes Natalie , Dietlein Felix , Van Allen Eliezer M 
Published: September 2020

ABSTRACTIndividual tumor molecular profiling is routinely used to detect single gene-variant (“first-order”) genomic alterations that may inform therapeutic actions -- for instance, a tumor with aBRAFp.V600E variant might be considered for RAF/MEK inhibitor therapy. Interactions between such first-order events (e.g., somatic-germline) and global molecular features (e.g. mutational signatures) are increasingly associated with clinical outcomes, but these “second order” alterations are not yet generally accounted for in clinical interpretation algorithms and knowledge bases. Here, we introduce the Molecular Oncology Almanac (MOAlmanac), a clinical interpretation algorithm paired with a novel underlying knowledge base to enable integrative interpretation of genomic and transcriptional cancer data for point-of-care treatment decision-making and translational hypothesis generation. We compared MOAlmanac to first-order interpretation methodology in multiple retrospective patient cohorts and observed that the inclusion of preclinical and inferential evidence as well as second-order molecular features increased the number of nominated clinical hypotheses. MOAlmanac also performed matchmaking between patient molecular profiles and cancer cell lines to further expand individualized clinical actionability. When applied to a prospective precision oncology trial cohort, MOAlmanac nominated a median of two therapies per patient and identified therapeutic strategies administered in 46% of patient profiles. Overall, we present a novel computational method to perform integrative clinical interpretation of individualized molecular profiles. MOAlmanc increases clinical actionability over conventional approaches by considering second-order molecular features and additional evidence sources, and is available as an open-source framework.
Assessing whitefly diversity to infer about begomovirus dynamics in cassava in Brazil
Authors: Xavier César A.D. , Nogueira Angélica M. , Bello Vinícius H. , Watanabe Luís F. M. , Alves-Júnior Miguel , Barbosa Leonardo F. , Beserra-Junior José E.A. , Boari Alessandra J. , Calegario Renata F. , Gorayeb Eduardo S. , Honorato-Júnior Jaime , Koch Gabriel , Lima Gaus S.A. , Lopes Cristian A. , Mello Raquel N. , Pantoja Késsia F. C. , Silva Fabio N. , Ramos-Sobrinho Roberto , Santana Enilton N. , Silva José W.P. , Krause-Sakate Renate , Zerbini F.M. 
Published: September 2020

AbstractPlant virus ecology is strongly dependent on that of its vector. The necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in promoting disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent begomoviruses vector that efficiently colonizes cassava is the reason why begomoviruses have not emerged in South America. To test this hypothesis, we performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields across twelve states representing the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on partial mitochondrial cytochrome oxidase I (mtCOI) sequences. A high species richness was observed, with five previously described species and two putative new ones. The most prevalent species wereTetraleurodes acaciaeandBemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence ofBemisia tabaciMiddle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process ofBtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop in the near future.
Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction
Authors: Torii Shiho , Ono Chikako , Suzuki Rigel , Morioka Yuhei , Anzai Itsuki , Fauzyah Yuzy , Maeda Yusuke , Kamitani Wataru , Fukuhara Takasuke , Matsuura Yoshiharu 
Published: September 2020

SummarySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the causative agent of coronavirus disease 2019 (COVID-19). While the development of specific treatments and a vaccine is urgently needed, functional analyses of SARS-CoV-2 have been limited by the lack of convenient mutagenesis methods. In this study, we established a PCR-based, bacterium-free method to generate SARS-CoV-2 infectious clones. Recombinant SARS-CoV-2 could be rescued at high titer with high accuracy after assembling 10 SARS-CoV-2 cDNA fragments by circular polymerase extension reaction (CPER) and transfection of the resulting circular genome into susceptible cells. Notably, the construction of infectious clones for reporter viruses and mutant viruses could be completed in two simple steps: introduction of reporter genes or mutations into the desirable DNA fragments (~5,000 base pairs) by PCR and assembly of the DNA fragments by CPER. We hope that our reverse genetics system will contribute to the further understanding of SARS-CoV-2.