bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender Equality Issues, Perception and Divorce
Authors: Wandi Joni Indra , Reflianto Reflianto
Published: April 2021

Tujuan dari penelitian ini adalah untuk menganalisis fenomena perilaku, gugatan emosional dan perceraian oleh perempuan dalam keluarga masyarakat matrilineal di Padang. Penelitian ini menggunakan metode kualitatif dengan desain survei. Teknik pengumpulan data menggunakan formulir wawancara, lembar observasi dan dokumentasi. Analisis data dilakukan dengan mengklasifikasikan, mendapatkan interpretasi, membuat validitas dan menarik kesimpulan. Untuk menguji validitas data digunakan triangulasi dan diskusi dengan kolega. Hasil penelitian menunjukkan bahwa fenomena gugatan perilaku, emosi dan perceraian oleh perempuan dalam keluarga masyarakat matrilineal di Padang terjadi karena dampak kesetaraan gender. Di sisi positif, kesetaraan gender dapat dirasakan oleh perempuan dalam pendidikan, kepemimpinan dan kesempatan untuk mendapatkan pekerjaan. Sementara efek samping negatif dari kesetaraan gender dalam keluarga adalah menurunnya kematangan emosi, perubahan budaya dan nilai-nilai agama dalam perilaku sosial perempuan. Implementasi penelitian ini bermanfaat bagi ninik mamak, akademisi, ulama dan pemerintah daerah Padang untuk mensosialisasikan dan memberikan konsultasi untuk mengevaluasi penerapan nilai-nilai budaya, adat dan agama dalam perspektif jenis kelamin dan dengan demikian menciptakan kesetaraan gender harus sesuai dengan ajaran adat dan agama.Purposes of this study were to analyze the behavioral phenomenon, emotional and divorce lawsuit by women in the family of matrilineal society in Padang. This research used a qualitative method with survey design. Technique of collecting data used interview form, observation sheets and documentation. Data analysis was carried out by classifying, getting interpretation, making validity and drawing conclusions. To test the validity of the data used triangulation and discussions with colleagues. The results of research showed that phenomenon of behavioral, emotional and divorce lawsuit by women in the family of matrilineal society in Padang occur due to the impact of gender equality. On the positive side, gender equality could be felt by women in education, leadership and the opportunity to get a job. While the negative side effects of gender equality in the family was declining the emotional maturity, changing in culture and religious values in the social behavior of women. Implementation of this research to be useful for ninik mamak, academician, clergy and the local government of Padang to socialize and provide consultation to evaluate the application of cultural values, customs and religion in a gender perspective and thus creating gender equality should be in accordance with the customary and religious teachings.
Development of a core outcome set for the evaluation of interventions to enhance trial participation decisions on behalf of adults who lack capacity to consent: a mixed methods study (COnSiDER Study)
Authors: Shepherd Victoria , Wood Fiona , Robling Michael , Randell Elizabeth , Hood Kerenza
Published: April 2021

BackgroundTrials involving adults who lack capacity to provide consent for themselves rely on proxy or surrogate decision-makers, usually a family member, to make decisions about participation. Following decades of innovations to improve informed consent in trials, the first interventions to enhance proxy decisions about trial participation are now being developed. However, a lack of standardised outcome measurement in the evaluation of these novel interventions will impede comparisons between their effectiveness. The aim of this study was to establish an agreed standardised core outcome set (COS) for use when evaluating interventions to improve proxy decisions about trial participation on behalf of adults who lack capacity to consent.MethodsWe used established methods to develop the COS including a consensus study with key stakeholder groups comprising those who will use the COS in research (researchers and healthcare professionals) and patients or their representatives. Following a scoping review to identify candidate items, we used a modified two-round Delphi survey to achieve consensus on core outcomes, with equivocal items taken to a consensus meeting for discussion. The COS was finalised following an online consensus meeting in October 2020.ResultsA total of 28 UK stakeholders (5 researchers, 10 trialists, 3 patient/family representatives, 7 recruiters and 3 advisors/approvers) participated in the online Delphi survey to rank candidate items. Items were broadly grouped into three categories: how family members make decisions, their experiences of making decisions, and the personal aspects that influence the decision. Following the Delphi survey, 27 items were included and ten items exhibited no consensus which required discussion at the consensus meeting. Sixteen participants attended the meeting, including additional patient/family representatives invited to increase representation from this key group. We reached consensus for the inclusion of 28 outcome items, including one selected at the consensus meeting.ConclusionsThe study identified outcomes that should be measured as a minimum in all evaluations of interventions to enhance proxy decisions about trials. Further work is required to identify appropriate measures and timing of outcome measurement. Enhancing the quality of proxy decisions will help improve trial participation decisions for these vulnerable groups. Trial registration: The study is registered on the COMET database (https://www.comet-initiative.org/Studies/Details/1409)
Anthropogenic influence on extreme precipitation over global land areas seen in multiple observational datasets
Authors: Madakumbura Gavin D. , Thackeray Chad W. , Norris Jesse , Goldenson Naomi , Hall Alex
Published: April 2021

The intensification of extreme precipitation under anthropogenic forcing is robustly projected by global climate models, but highly challenging to detect in the observational record. Large internal variability distorts this anthropogenic signal. Models produce diverse magnitudes of precipitation response to anthropogenic forcing, largely due to differing schemes for parameterizing subgrid-scale processes. Meanwhile, multiple global observational datasets of daily precipitation exist, developed using varying techniques and inhomogeneously sampled data in space and time. Previous attempts to detect human influence on extreme precipitation have not incorporated model uncertainty, and have been limited to specific regions and observational datasets. Using machine learning methods that can account for these uncertainties and capable of identifying the time evolution of the spatial patterns, we find a physically interpretable anthropogenic signal that is detectable in all global observational datasets. Machine learning efficiently generates multiple lines of evidence supporting detection of an anthropogenic signal in global extreme precipitation.
Efficacy and safety of Qi-Jing Hui-Xin Decoction in the treatment of coronary microvascular angina: Study protocol for a randomized, controlled, multi-center clinical trial
Authors: Sun Yuanlong , Huang Chengxin , Huo Li , Li Yin , Chen Jun , Zhang Zixiu , Jia Meijun , Jiang Meixian , Ruan Xiaofen
Published: April 2021

Background: With the increased understanding of heart disease, microvascular angina (MVA) is receiving greater attention from clinicians. Studies have shown that patients with MVA have significantly higher major cardiovascular events and all-cause mortality than the control population, and the search for effective treatments is of great clinical importance. Both basic and clinical studies have shown that Qi-Jing Hui-Xin Decoction (QJHX) can relieve angina symptoms and improve clinical efficacy, but there is a lack of high-quality clinical studies to provide a research basis. This article introduces the evaluation protocol of QJHX for the adjunctive treatment of MVA.Methods/design: This is a prospective randomized controlled trial. The trial will enroll 150 patients with MVA. On the basis of Western drug treatment, patients will be randomized into two groups, and the experimental group will receive QJHX treatment for 12 weeks, and follow up at 24 week. The primary indicators are the clinical efficacy of angina pectoris and the evidence of Traditional Chinese Medicine (TCM) efficacy. Secondary indicators are Seattle Angina Scale score, serum lipid levels, electrocardiogram and echocardiogram diagnosis. Additional indicators are endothelial function and immunoinflammatory factors. Adverse events will be monitored throughout the trial.Discussion: Integrated traditional Chinese and Western medicine is commonly used for angina in China. This study will evaluate the clinical effectiveness and safety of adding QJHX on the basis of standardized Western medications. The results of the trial will provide high-level clinical research-based evidence for the application of QJHX in MVA.Trial registration: This study protocol was registered on 28 October 2019. The registration number is ChiCTR1900027015 at the Chinese Clinical Trial Registry.
Large-strain and Full-color Change Photonic Crystal Films Used as Mechanochromic Strain Sensors
Authors: Zhang Rui , Yang Zhiyu , Zheng Xu , Zhang Yanju , Wang Qing
Published: April 2021

Mechanochromic strain sensors based on photonic crystals, which can change structural color upon mechanical deformation, are promising for many applications including health monitoring and damage detection. Here, a large-strain and full-color change photonic crystal film as a mechanochromic strain sensor is reported. The mechanochromic photonic crystal (MPC) film with grating nanostructure is achieved by a fast and low-cost inverted nanoimprint lithography. The film enables bright and reversible color shift in the full visible range as it is stretched up to a large strain, which is proven in strain direction parallel and perpendicular to the grating. It is demonstrated that the MPC film can be used as a mechanochromic strain sensor able to visualize strain evolution and strain range of low carbon steel in tensile test, which brings a significant step toward visualizing strain monitoring.
Nicotinamide Riboside as a Neuroprotective Therapy for Glaucoma Study Protocol for a Randomized, Double-blind, Placebo-control Trial
Authors: Leung Christopher Kai-shun , Ren Seraph Tianmin , Chan Poemen Pui-man , Wan Kelvin H , Kam Aziz , Lai Gilda , Chiu Vivian , Ko Match , Yiu Cedric , Yu Marco
Published: April 2021

Background Whereas lowering the intraocular pressure (IOP) can slow optic nerve degeneration in glaucoma, many patients with glaucoma continue to develop progressive loss in vision despite significant reduction in IOP. No treatment has been shown to be effective for neuroprotection in glaucoma. We set out to conduct a randomized controlled trial to investigate whether nicotinamide riboside (NR), a nicotinamide adenine dinucleotide precursor, is effective to slow optic nerve degeneration in patients with primary open-angle glaucoma (POAG). We hypothesize that patients treated with NR have a slower rate of progressive retinal nerve fiber layer (RNFL) thinning compared with those treated with placebo. Methods This is a randomized, double blind, placebo controlled, parallel group, multi-center study including 125 patients with POAG. Patients will be randomized to receive 300mg NR or placebo for 24 months. Clinical examination, optical coherence tomography imaging of the RNFL, and visual field (VF) test will be performed at the baseline, 1 month, 4 months, and then at 2-month intervals until 24 months. The primary outcome measure is the rate of RNFL thinning measured over 24 months. The secondary outcome measures include (1) time to VF progression, (2) time to progressive RNFL/ganglion cell inner plexiform layer (GCIPL) thinning, and (3) the rate of change of VF sensitivity over 24 months (to investigate neuroprotection) and 1 month (to investigate neuroenhancement). The rates of RNFL thinning and VF sensitivity decline between treatment groups will be compared with linear mixed modeling. Survival analysis will be performed to compare the differences in time from baseline to VF progression and time from baseline to progressive RNFL/GCIPL thinning between treatment groups using Cox proportional hazards models. Discussion Outcome measures in glaucoma neuroprotection trials have been predicated on detection of VF progression, which may take years to develop and confirm. In addition to addressing whether NR has a neuroprotective/neuroenhancement effect in glaucoma patients, this study will demonstrate the feasibility of studying neuroprotection in a relatively short trial period (24 months) by comparing the rates of progressive RNFL thinning, a more reproducible and objective outcome measure compared with VF endpoints, between treatment groups.
The Thalamus in Trigeminal Neuralgia: Structural and Metabolic Abnormalities, and Influence on Surgical Response
Authors: Danyluk Hayden , Andrews Jennifer , Kesarwani Rohit , Seres Peter , Broad Robert , Wheatley Matt , Sankar Tejas
Published: April 2021

Background
Medically-refractory trigeminal neuralgia (TN) can be treated successfully with operative intervention, but a significant proportion of patients are non-responders despite undergoing technically successful surgery. The thalamus is a key component of the trigeminal sensory pathway involved in transmitting facial pain, but the role of the thalamus in TN, and its influence on durability of pain relief after TN surgery, are relatively understudied. We aimed to test the hypothesis that variations in thalamic structure and metabolism are related to surgical non-response in TN.
Methods
We performed a longitudinal, peri-operative neuroimaging study of the thalamus in medically-refractory TN patients undergoing microvascular decompression or percutaneous balloon compression rhizotomy. Patients underwent structural MRI and MR spectroscopy scans pre-operatively and at 1-week following surgery, and were classified as responders or non-responders based on 1-year post-operative pain outcome. Thalamus volume, shape, and metabolite concentration (choline/creatine [Cho/Cr] and N-acetylaspartate/creatine [NAA/Cr]) were evaluated at baseline and 1-week, and compared between responders, non-responders, and healthy controls.
Results
Twenty healthy controls and 23 patients with medically-refractory TN treated surgically (17 responders, 6 non-responders) were included. Pre-operatively, TN patients as a group showed significantly larger thalamus volume contralateral to the side of facial pain. However, vertex-wise shape analysis showed significant contralateral thalamus volume reduction in non-responders compared to responders in an axially-oriented band spanning the outer thalamic circumference (peak p = 0.019). Further, while pre-operative thalamic metabolite concentrations did not differ between responders and non-responders, as early as 1-week after surgery, every single long-term non-responder showed a distinct decrease in contralateral thalamic Cho/Cr and NAA/Cr, irrespective of surgery type, which was not observed in responders.
Conclusions
Atrophy of the contralateral thalamus is a consistent feature across patients with medically-refractory TN. Regional alterations in preoperative thalamic structure, and very early post-operative metabolic changes in the thalamus, both appear to influence the durability of pain relief after TN surgery.
Cortical Cyclin A controls spindle orientation during asymmetric cell division
Authors: Darnat Pénélope , Burg Angelique , Sallé Jérémy , Lacoste Jérôme , Louvet-Vallée Sophie , Gho Michel , Audibert Agnes
Published: April 2021

Cell proliferation and cell polarity need to be precisely coordinated to orient the asymmetric cell divisions crucial for generating cell diversity in epithelia. In many instances, the Frizzled/Dishevelled planar cell polarity pathway is involved in mitotic spindle orientation, but how this is spatially and temporally coordinated with cell cycle progression has remained elusive. Using Drosophila sensory organ precursor cells as a model system, we show that Cyclin A, the main Cyclin driving the transition to M-phase of the cell cycle, is recruited to the apical-posterior cortex in prophase by the Frizzled/Dishevelled complex. This cortically localized Cyclin A then regulates the orientation of the division by recruiting Mud, a homologue of NuMA, the well-known spindle-associated protein. The observed non-canonical subcellular localization of Cyclin A reveals this mitotic factor as a direct link between cell proliferation, cell polarity and spindle orientation.
Coarse-Grained Geological Porous Media Structure Modeling Using Heuristic Algorithm and Evaluation of Porosity, Hydraulic Conductivity, and Pressure Drop with Experimental Results
Authors: Bezaatpour Javad , Fatehifar Esmaeil , Rasoulzadeh Ali
Published: April 2021

Knowledge of porous media structure is an essential part of the hydrodynamic investigation of fluid flow in porous media. To study soil behavior (as a granular porous media) and water and contaminant movement in the vadose zone, appropriate estimation of soil water retention curve (SWRC) and soil hydraulic conductivity curve (SHCC) has a pivotal role and is one of the most challenging topics for researchers and engineers in soil and water science. The SWCR can be approximated using an accurate particle size distribution (PSD) function. In this study by applying random close packing (RCP) method as an encouraging method for predicting and studying particle configuration, an optimal particle size distribution is developed for coarse-grained soils (0.025 mm < PSD < 3.35mm). The mentioned RCP is generated using heuristic algorithm with merging applicable equations of soil science. For porous media modeling, MATLAB software is used and the predicted results by the optimal model for the parameters of porosity, pressure drop, and saturated hydraulic conductivity are compared with laboratory measurements. Experimental design is conducted by MINITAB and predicted coarse-grained soils structure by the model is compared with 4 sifted soils. The results of the sensitivity analysis showed that the porosity obtained from the model is strongly sensitive to the resolution factor and should be chosen with a sufficiently large amount (higher than 250). Results showed good consistency (up to 95%) between predicted porosity and only 10% difference in pressure drop and permeability with observed measurements.
Exploring the Barriers Related to the Healthcare System and Healthcare Professionals in Implementing Quality Intravenous Chemotherapy: A Qualitative Study
Authors: salarvand shahin , Mousavi Masoumeh Sadat , Almasian Mohammad
Published: April 2021

Purpose: This study aimed to explore barriers related to the healthcare system (HCS) and healthcare providers (HCPs) in implementing quality intravenous (IV) chemotherapy (CT) from the perspectives of cancer patients, family caregivers, and healthcare professionals.Methods: Using an explanatory descriptive qualitative method, this study was conducted in 2019. Forty-one participants (6 patients, 5 family caregivers, 12 oncologists, and 18 nurses) were selected through purposive sampling. In-depth semi-structured interviews were conducted to collect the data, which were analyzed using qualitative content analysis. Lincoln and Guba’s criteria of rigor were employed to ensure the trustworthiness of the study.Results: Data analysis showed two categories, each with three subcategories: Barriers related to HCPs that contains “educational and communication barriers”, “failure to establish trust” and “unskilled healthcare professionals”; Barriers related to the HCS, which consists of “inadequate physical and care infrastructures to provide services”, “lack of support in the disease trajectory from diagnosis to rehabilitation” and “mismanagement of CT wards/procedures”.Conclusion: The identification and removal of the barriers related to HCPs and HCS from routine care are crucial. Education of and communication with cancer patients and their family caregivers are two important pillars in the quality of intravenous chemotherapy (IV CT) and this education and communication should be based on individualized care and tailored to the unique needs of each patient.
Iron(III) hydroxocomplex - methyl viologen dication system as a prospective tool for determination of hydroxyl radical reaction rate constants with environmental pollutants
Authors: Tyutereva Yuliya , Grivin Vyacheslav P. , Xu Jing , Wu Feng , Plyusnin Victor , Pozdnyakov Ivan
Published: April 2021

Reactivity of oxidative species with target pollutants is one of the crucial parameters for application of any system based on advanced oxidation processes (AOPs). This work presents new useful approach how to determine the hydroxyl radical reaction rate constants (kOH) using UVA laser flash photolysis technique. Fe(III) hydroxocomplex at pH 3 was applied as a standard source of hydroxyl radicals and methyl viologen dication (MV2+) was used as selective probe for •OH radical. Application of MV2+ allows to determine kOH values even for compounds which do not generate themselves optically detectable transient species in reaction with hydroxyl radicals. Validity of this approach was tested on a wide range of different persistent pesticides and its main advantages and drawbacks in comparison with existing steady-state and time-resolved techniques were discussed.
Association between absolute eosinopenia and mortality in SARS-COV-2 infection on the 70+, a discussed observation
Authors: Baudouin Edouard , Kosowki Jill , Mesinele Lea , Pujol Tom , Brunetti Nicoletta , Colas Marion , Neiss Marie , Simon Pauline , Trivalle Christophe , Tiramine Soraya , Laraaj Fahd , Vetillard Anne-Laure , Houenou-Quenum Nadège , Souques Cecile , Verdier Sébastien , Houdre Julie , Sorrel-Dejerine Adrien , Sanchez Joge , Jean-Sebastien Vidal , Guichardon Magali , Jean-Emmanuel Kahn , Collarino Rocca , Duron Emmanuelle
Published: April 2021

Background: This study aimed to seek for an association between absolute eosinopenia (eosinophils count < 10 /mm3) and mortality in an older adults suffering from COVID-19 hospitalized in a specific geriatric ward. Methods: This observational retrospective study was conducted in a French geriatric ward from March 17 to April 18, 2020. All 118 patients hospitalized for COVID-19 over 70 yo in acute stay care were enrolled. Patients with a treatment or a pathology which could interfere with eosinophil count were excluded. Results: No statistical difference was found between surviving or deceased patient regarding age (mean age (SD): 87 years (7)) and sex (34% of males). Differences for the most frequent acute events were statically different: Quick Sepsis-related Organ Failure Assessment (qSOFA) score was ≥ 2 at admission for 23% in the survivor group vs. 23 (72%) in the deceased (p < .001); acute kidney injury concerned 17% of the survivors vs. 69% of the decease (p< .001). Eosinopenia < 10/mm3 was significantly associated with mortality (OR (CI95%)) = 3.5 (1.2-11.4) after adjustment on age, gender, and activity of daily living. Conclusion: Absolute eosinopenia was associated with in hospital mortality in older adults. This result, if confirmed in other study, may help to predict the outcome of a SARS-COV-2 infection on geriatric patients and calls for immunologist to explore more globally the impact of inflammaging on the SARS-CoV-2 infection.
Exploring the Inclusion of Under-Served Groups in Trials Methodology Research: An Example from Ethnic Minority Populations’ Views on Deferred Consent
Authors: Raven-Gregg Timia , Shepherd Victoria
Published: April 2021

Background: Deferred consent is used to recruit patients in emergency research, when informed consent cannot be obtained prior to enrolment. This model of consent allows studies to recruit larger numbers of participants, especially where a surrogate-decision maker may be unavailable to provide consent. Whilst deferred consent offers the potential to promote trial diversity by including under-served groups, it is ethically complex and views about its use amongst these populations requires further exploration. The aim of this article is to build upon recent initiatives to improve inclusivity in trials, such as the NIHR INCLUDE project, and consider whether trials methodology research is inclusive, focusing on ethnic minority populations’ attitudes towards the use of deferred consent.Main text: Findings from the literature suggest that research regarding attitudes toward recruitment methods like deferred consent largely fail to adequately represent ethnic minorities. Many studies fail to report the composition of patient samples or conduct analyses on any differences between specific patient groups. In those that do, the categorisation of ethnic groups is ambiguous. Frequently diversely different groups are considered as more homogenous than they are. Whilst deferred consent is deemed generally acceptable, analysis of patient sub-groups shows that this attitude is not universal. Those from racial and ethnic minority backgrounds reported higher levels of unacceptability, which was impacted by previous first or second-hand experience of its use and historical mistrust in research. However, whilst deferred consent was found to increase the numbers of black participants enrolled in some trials, their over-enrolment in other trials may raise further concerns. Conclusions: Inclusivity in clinical trials is important, as highlighted by the COVID-19 pandemic. To improve this, we must ensure that methodological studies such as those exploring attitudes to research are inclusive. More effort is needed to understand the views of under-served groups, such as ethnic minorities, toward research in order to improve participation in clinical trials. Our findings echo those from the INCLUDE project, in that better reporting is needed and increasing the confidence of ethnic minority groups in research requires improving representation throughout the research process. This will involve diversifying research teams and ethics committees.
Concentration of Selected Elements in the Hair of Malagasy Girls in Relation to Their Nutritional Status and Environmental Exposure
Authors: Zielińska-Dawidziak Magdalena , Człapka-Matyasik Magdalena , Wojciechowska Zofia , Proch Jędrzej , Niedzielski Przemysław
Published: April 2021

Although the children malnutrition in Madagascar and the environmental pollution of this country has been widely discussed, there is no research on the susceptibility of malnourished Malagasy to toxic elements. Nine elements concentration (Al, As, Cd, Cr, Hg, Ni, Pb, Sn, Sb) was determined in 103 samples of schoolgirls scalp hair (8–15 years old), and in twenty samples of water and soil, from two areas: Antananarivo (UR) and Berevo (RU). Samples were analysed by an inductively coupled plasma-optical emission spectrometer using a microwave-induced nitrogen plasma atomic emission spectrometer. The nutritional status was evaluated by Cole’s Index. The recommended level of Sb was exceeded in the soil samples, while the Al and Ni in the water. Underweight was related to higher accumulation of Al, Cd, Cr, Pb, and Ni in the hair and more common among girls living in RU than UR region (42% vs 28%). . Two-factor analysis of variance showed differences in the Al and Cr content in the girls’ hair depending both on their place of residence and nutritional status. This indicate that the malnourished girls may be more susceptible to soil and water pollution with toxic elements than girls with adequate nutritional status.
Probability Assessment of Slope Instability in Seasonally Cold Regions under Climate Change
Authors: Zhu Yulong , Ishikawa Tatsuya , Yamada Tomohito J. , Subramanian Srikrishnan Siva
Published: April 2021

This paper proposes an effective approach for evaluating the influences of climate change on slope stability in seasonally cold regions. Firstly, to semi-quantitatively assess the effects of climate changes on the uncertainty of climate factors, this study analyzes the trend of the two main climate factors (precipitation and air temperature) by the regression analysis using the meteorological monitoring data of the past 120 years in different scales (e.g., world, country (Japan), and city (Sapporo)), and the meteorological simulation data obtained by downscaling the outputs of three different regional atmospheric models (RAMs) with lateral boundary conditions from three different general circulation models (GCMs). Next, to discuss the effects of different climate factors (air temperature, precipitation, etc.) and to determine the key climate factors on the slope instability, an assessment approach for evaluating the effects of climate changes on slope instability is proposed through the water content simulation and slope stability analysis using a 2-dimensional (2D) finite element method (FEM) homogeneous conceptual slope model with considering freeze-thaw action. Finally, to check the effectiveness of the above assessment approach, assessment of instability of an actual highway embankment slope with the local layer geometry is done by applying the past and predicted future climate data. The results indicate that affected by global warming, the air temperature rise in some cold cities is more serious. The predicted future weather will affect the shape of the normal density curve (NDC) of the distribution of slope failures in one year. The climate changes (especially the increase in precipitation) in the future will increase the infiltration during the Spring season. It will lengthen the time that the highway slope is in an unstable state due to high volumetric water content, thereby enhancing the instability of the slopes and threatening more slopes in the future.
Selenium Enriched Bacillus Subtilis Yb-1114246 Improved Growth and Immunity of Broiler Chickens Through Modified Ileal Bacterial Composition
Authors: Yang Jiajun , Wang Jiang , Huang Kehe , Liu Qingxin , Xu Xiaozhou , Liu Guofang , Zhang Hao , Zhu Mengling
Published: April 2021

Background: Selenium-enriched Bacillus subtilis (SEBS) was made to add into the diets of broiler chickens to observe combined effects on the bacterial composition and immunity of ileum through its colonization on the site of intestinal mucous membrane to improve the body growth and immunity. Five hundred 1-d-old chickens were divided into five groups randomly: Control, inorganic Se, Bacillus subtilis (B. subtilis), SEBS, and antibiotic. The feed duration was 42 days (d). Growth performance was recorded and calculated. The strain of B. subtilis and SEBS colonizing in the gastrointestinal tract (GIT) were investigated using fluorescence in situ hybridization (FISH) assay and quantitative real-time polymerase chain reaction (qPCR). The V3-V4 hypervariable regions of the bacterial region of 16S rRNA gene were sequenced. Results: After 42 d of treatment, chicks feed SEBS or Bacillus subtilis had higher body weights than the control chicks or those given inorganic Se. SEBS colonized in distal segments of the ileum improved bacterial diversity, while reducing the number of endogenous pathogen and increasing the number of Lactobacillus sp. in ileal mucous membranes. Species of unclassified Lachnospiraceae, uncultured Anaerosporobacter, Peptococcus, Lactobacillus salivarius, and Ruminococcaceae_UCG-014, and unclassified Butyricicoccus in ileal mucous membranes played an important role in promoting immunity, such as tumor necrosis factor-α and interferon-β through spearman’s analysis. Dietary supplementary Se also improved bacterial composition of ileal mucous membranes. SEBS colonization in the ileal mucous membrane optimized bacterial composition, more enhanced the abundances of metabolic and immune genes on body growth and immunity. Conclusions: SEBS improved body growth performance and immunity of broiler chickens through colonization in the ileal mucous membrane and modified ileal bacterial composition.
Sex-stratified single-cell RNA-Seq analysis identifies sex-specific and cell type-specific transcriptional responses in Alzheimer’s disease across two brain regions.
Authors: Belonwu Stella , Li Yaqiao , Bunis Daniel , Rao Arjun , Solsberg Caroline Warly , Tang Alice , Fragiadakis Gabriela , Dubal Dena , Oskotsky Tomiko , Sirota Marina
Published: April 2021

Alzheimer’s disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can inform new therapeutic approaches for both sexes. Here, we utilized nearly 74,000 cells from human prefrontal and entorhinal cortex samples from the first two publicly available single-cell RNA sequencing AD datasets to study cell type-specific sex-stratified transcriptomic perturbations in AD. Our examination at the single-cell level revealed that sex-specific gene and pathway differences in AD were most prominently observed in glial cells of the prefrontal cortex. In the entorhinal cortex, we observed the same genes and pathways to be perturbed in opposing directions between sexes in AD relative to healthy state. Our findings contribute to growing evidence of sex differences in AD-related transcriptomic changes, which can fuel the development of therapies that may prove more effective at reversing AD pathophysiology.
Impact of Gene Annotation Choice on the Quantification of RNA-Seq Data
Authors: Chisanga David , Liao Yang , Shi Wei
Published: April 2021

Background: RNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to each gene. Gene annotation data, which include chromosomal coordinates of exons for tens of thousands of genes, are required for this quantification process. There are several major sources of gene annotations that can be used for quantification, such as Ensembl and RefSeq databases. However, there is very little understanding of the effect that the choice of annotation has on the accuracy of gene expression quantification in an RNA-seq analysis.Results: In this paper, we present results from our comparison of Ensembl and RefSeq human annotations on their impact on gene expression quantification using a benchmark RNA-seq dataset generated by the SEquencing Quality Control (SEQC) consortium. We show that the use of RefSeq gene annotation models led to better quantification accuracy, based on the correlation with ground truths including expression data from >800 real-time PCR validated genes, known titration ratios of gene expression and microarray expression data. We also found that the recent expansion of the RefSeq annotation has led to a decrease in its annotation accuracy. Finally, we demonstrated that the RNA-seq quantification differences observed between different annotations were not affected by the use of different normalization methods.Conclusion: In conclusion, our study found that the use of the conservative RefSeq gene annotation yields better RNA-seq quantification results than the more comprehensive Ensembl annotation. We also found that, surprisingly, the recent expansion of the RefSeq database, which was primarily driven by the incorporation of sequencing data into the gene annotation process, resulted in a reduction in the accuracy of RNA-seq quantification.
Multi-transcriptomic analysis points to early organelle dysfunction in human astrocytes in Alzheimer’s disease
Authors: Galea Elena , Weinstock Laura D. , Larramona-Arcas Raquel , Pybus Alyssa F. , Giménez-Llort Lydia , Escartin Carole , Wood Levi B.
Published: April 2021

BackgroundOur understanding of the impact of astrocytes in Alzheimer’s disease (AD) is hindered by the lack of astrocyte-specific omics data from patients diagnosed with dementia due to AD. Studies aiming to profile human AD astrocytes—including single-nucleus RNA sequencing—were limited by the low number of differentially expressed genes detected, and by the small size of cohorts. We improved on prior studies with a novel systems-biology-based approach.Methods Human astrocytic and neuronal gene clusters were generated from RNA sequencing data from isolated healthy human brain cells using a cell-type enrichment score and clustering. The cell-specific gene clusters were localized in 766 subjects from three AD whole-brain transcriptomes generated by the Mount Sinai Hospital, the Mayo Clinic, and the Religious Order Study/Memory and Aging Project (ROSMAP), which also contains subjects with mild cognitive impairment (MCI). Gene clusters were organized into functional categories and subcategories using manual curation. Functional changes among subject groups were determined by gene set variation analysis (GSVA) and principal component analysis (PCA).Results Hierarchical clustering of transcriptomic data revealed molecular heterogeneity in individuals with the same clinical diagnosis. Particularly in the Mayo Clinic and ROSMAP cohorts, over 50% of Controls presented massive down-regulation of genes encoding for synaptic proteins, as widely documented in AD, suggesting that these subjects might have been at a preclinical stage at the time of death. Conversely, approximately 30% of AD patients showed preservation of neuronal genes as if they were non demented subjects, suggesting that they were resilient to AD pathology (present, according to CERAD and Braak scoring), but developed dementia due to comorbidities. The astrocytic gene profiles in AD patients presenting down-regulation of neuronal genes were termed ‘AD astrocytes’. According to GSVA and PCA, AD astrocytes showed down-regulation of genes encoding for mitochondrial and endolysosomal proteins, and up-regulation of genes related to perisynaptic astrocytic processes (PAP), and survival and stress responses.Discussion Astrocytes undergo a profound transcriptional change in a remarkable percentage of Control, MCI and AD subjects, affecting organelles and astrocyte-neuron interactions. We argue that therapies preventing organelle dysfunction in astrocytes may protect neural circuits in preclinical and clinical AD.
Effect of Supplemental Irrigation on Tuber Yield, Water Use Efficiency and Nitrogen Use Efficiency of Potato (Solanum Tuberosum L.) Grown in a Mollic Andosol
Authors: SATOGNON Felix , Owido Seth F.O. , Lelei Joyce J.
Published: April 2021

BackgroundThe yield of potato (8.86 tonnes/ha), the second staple food and cash crop in Kenya is remained low due to a reduction in seasonal precipitation and low soil fertility. Drought or dry periods between rainfall seasons and increased temperatures, which leads to high crop evapotranspiration, are experienced in 70-80% of the smallholder farms. Among major elements require by potato, nitrogen is the most important influential element but it is deficient in most potato-growing soils in Kenya because of nutrient depletion with inadequate nutrient replenishment results from continuous production. Hence the introduction of supplemental irrigation with an adequate application of this nutrient could increase crop yields. Therefore, this study was conducted in Nakuru, one of the major potato growing areas in Kenya, to determine the effects of full supplemental irrigation (FI) and four nitrogen levels, N0(0), N1(60), N2(90) and N3(130 kg N/ha) on tuber yield, water use efficiency (WUE) and nitrogen use efficiency (NUE) of potato grown in a mollic Andosol in Kenya compared to conventionnel rain-fed potato production. Results The results showed that tuber yield, marketable tuber yield and NUE significantly differed due to the interaction effect between irrigation and N-fertilization rate (P<0.001) whereas the WUE was statistically different due to the N-fertilization rate (P<0.001). The highest tuber yield 58.28 tonnes/ha was found in supplemental irrigation with an application of 130kg N/ha treatment. Full supplemental irrigation treatment increased marketable yield by 129.84, 94.63, 151.21 and 126.63% for 0, 60, 90 and 130 kg N/ha, respectively compared to rain-fed N-fertilization treatments. NUE increased statistically with an increase in N rate up to 90 kg N/ha, then tended to increase slightly as nitrogen rate increased further. An increase in potato tuber yield was positively correlated with number of tubers/plant (r=0.75), NUE (r=0.95), WUE (r=0.72) (P < 0.001).ConclusionsThe high potato yield and marketable tuber yield in mollic Andosol can be obtained when all water deficits of the growing season are eliminated with supplemental irrigation and an application of 130kg N/ha but it is essential to exploit water regimes for acceptable yield with water-saving.
The Correlation Between ATP Measurement and Microbial Contamination of Inanimate Surfaces
Authors: Arkel Andreas van , Willemsen Ina , Kluytmans Jan
Published: April 2021

Background:The objective of this study was to determine the correlation between adenosine triphosphate (ATP) measurements and microbial contamination using a standardized method. Methods: ATP measurements and aerobic colony counts (ACC’s) were conducted on 10 pre-defined fomites in a hospital and nursing home setting. Per fomite two ATP measurements and two agar plate measurements were conducted, each measurement was conducted on a 25 cm2 surface. Both measurements were compared and analyzed for correlation. Results: In total 200 paired measurements were conducted, 200 ATP measurements and 200 ACC’s. The mean of all ATP measurements tested on the same surface was calculated, as was for all 200 ACC’s. There was a strong correlation between the mean of two ATP measurements on two different sites on the same fomite (R=0.800, p<0.001) as well as between two ACC measurements on the same fomite (R=0.667, p<0.001). A much weaker correlation was found between RLU values and ACC’s (R=0.244, p<0.001). Conclusions: Reproducibility of ATP measurements and ACC’s on the same fomite was good. However, the correlation between RLU values and ACC’s on hospital surfaces was much lower. This may be explained by the wide variety of biological material that is measured with ATP, of which the bacterial load is only one of many components. ATP measurement can be used to give a quantifiable outcome for the rating of cleanliness in health care facilities, however the results cannot be translated into the level of microbial contamination.
SFPQ Rescues F508del-CFTR Expression and Function in Cystic Fibrosis Bronchial Epithelial Cells
Authors: Kumar Parameet , Soni Dharmendra Kumar , Sen Chaitali , Larsen Mads B , Mazan-Mamczarz Krystyna , Piao Yulan , De Supriyo , Gorospe Myriam , Frizzell Raymond A. , Biswas Roopa
Published: April 2021

Cystic Fibrosis (CF) occurs as a result of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to misfolding, trafficking defects, and impaired function of the CFTR protein. Splicing factor proline/glutamine-rich (SFPQ) is a multifunctional nuclear RNA-binding protein (RBP) implicated in the regulation of gene expression pathways and intracellular trafficking. Here, we investigated the role of SFPQ in the regulation of the expression and function of F508del-CFTR in CF lung epithelial cells. We find that the expression of SFPQ is reduced in F508del-CFTR CF epithelial cells compared to WT-CFTR control cells. Interestingly, the overexpression of SFPQ in CF cells increases the expression as well as rescues the function of F508del-CFTR. Further, comprehensive transcriptome analyses indicate that SFPQ plays a key role in activating the mutant F508del-CFTR by modulating several cellular signaling pathways. This is the first report on the role of SFPQ in the regulation of expression and function of F508del-CFTR in CF lung disease. Our findings provide new insights into SFPQ-mediated molecular mechanisms and point to possible novel epigenetic therapeutic targets for CF and related pulmonary diseases.
Meta-QTLs, Ortho-MetaQTLs and Candidate Genes for Grain yield and Associated Traits in Wheat (Triticum aestivum L.)
Authors: Saini Dinesh Kumar , Srivast Puja , Pal Neeraj , Gupta P. K.
Published: April 2021

The present study involved meta-QTL analysis based on 8,998 QTLs, including 2,852 major QTLs for grain yield (GY) and its following ten component/related traits: (i) grain weight (GWei), (ii) grain morphology related traits (GMRTs), (iii) grain number (GN), (iv) spikes related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M) and (x) grain filling duration (GFD). The QTLs used for this study were retrieved from 230 reports involving 190 mapping populations (1999–2020), which also included 19 studies involving durum wheat. As many as 141 meta-QTLs were obtained with an average confidence interval of 1.37 cM (reduced 8.87 fold), the average interval in the original QTL being > 12.15 cM. As many as 63 MQTLs, each based on at least 10 original QTLs were considered to be the most stable and robust with thirteen identified as breeder’s meta-QTL. Meta-QTLs (MQTLs) were also utilized for identification of as many as 1,202 candidate genes (CGs), which also included 18 known genes. Based on a comparative genomics strategy, a total of 50 wheat homologues of 35 rice, barley and maize yield-related genes were also detected in these MQTL regions. Moreover, taking the advantage of synteny, a total of 24 ortho-MQTLs were detected at co-linear regions between wheat with barley, rice and maize. The present study is the most comprehensive till date, and first of its kind in providing stable and robust MQTLs and ortho-MQTLs, thus providing useful information for future basic studies and for marker-assisted breeding for yield and its component traits in wheat.
Characterization of the Gut Microbiota in Patients with Primary Sclerosing Cholangitis Compared to Inﬂammatory Bowel Disease and Healthy Controls
Authors: Ostadmohammadi Samaneh , Azimirad Masoumeh , Houri Hamidreza , Naseri Kaveh , Javanmard Ehsan , Mirjalali Hamed , Yadegar Abbas , Sadeghi Amir , Aghdaei Hamid Asadzadeh , Zali Mohammad Reza
Published: April 2021

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease. Its aetiology remains largely unknown, although frequent concomitant inﬂammatory bowel disease (IBD) hints towards common factors underlying intestinal and bile duct inﬂammation. Herein, we aimed to explore the relative abundance of fecal microbiota in PSC-IBD patients compared to IBD-only subjects and healthy controls.We included 14 PSC-IBD patients, 12 IBD patients, and 8 healthy controls (HCs). A quantitative real-time PCR (qPCR) assay was to determine a selection of bacterial phyla, families, and genera.Relative abundance of taxa showed that Bacteroidetes was the most abundant phylum among the patients with PSC-IBD (29.46%) and also HCs (39.34%), whereas the bacterial species belonging to the phylum Firmicutes was the most frequent group in IBD-only subjects (37.61%). The relative abundance of Enterobacteriaceae family was higher among PSC-IBD (3%) than HCs (0.5%), and thus, could be used as a PSC-associated microbial signature.Our findings showed that intestinal microbiota composition in PSC-IBD patients was completely different from that of IBD-only patients. Further studies using large-scale cohorts should be performed to better describe the contribution of the gut microbiota to PSC pathogenesis with underlying IBD.