bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Putative Cell Wall Synthesis Genes in Betula pendula
Authors: Chen Song , Zhao Xiyang , Chen Su 
Published: June 2020

Abstract
Cellulose is an essential structural component of the plant cell wall and is an important resource for the production of paper, textiles, bioplastics and other biomaterials. The synthesis of cellulose is among the most important but poorly understood biochemical processes, which is precisely regulated by internal and external cues. Here we identified 46 gene models in 7 gene families which encoding cellulose synthase and related enzymes of Betula pendula , and the transcript abundance of these genes in xylem, root, leaf and flower tissues also be determined. Based on these RNA-seq data, we have identified 8 genes that most likely participate in cell wall synthesis. In parallel, a gene co-expression network was also constructed based on transcriptome sequencing.
Response surface methodology to optimize inulinase production by a newly isolated Penicillium amphipolaria strain by solid-state fermentation of Saccharum arundinaceum
Authors: Das Deblina , Bhat Ramananda M , Selvaraj Raja 
Published: June 2020

Abstract
In the present investigation, a new fungal inulinase producer Penicillium amphipolaria KAS 2555 has been isolated from the soil of dead mangroves litter area, followed by the inulinase production and optimization by solid-state fermentation using a low-cost substrate – hardy sugarcane (Saccharum arundinaceum). While screening, only Penicillium amphipolaria KAS 2555 showed the hydrolysis zone on the plate containing inulin media. The exoinulolytic nature of inulinase and its form of action was confirmed by thin-layer chromatography (TLC). After 96 h of the fermentation period, an activity of 2.45 U/gds was obtained. The I/S ratio of 0.59 proved that the enzyme is inulolytic in nature. Media optimization was performed to obtain a regression model using Central Composite Design (CCD). For optimization, five significant media components viz., inulin, (NH4)2SO4, K2HPO4, KH2PO4 and, NaCl were used. A 3.10-fold increase in activity of inulinase (7.59 U/gds) was obtained under the optimal settings of (g/gds) inulin- 0.1, (NH4)2SO4- 0.002, K2HPO4- 0.1, KH2PO4- 0.02 and NaCl- 0.02.
Comparison of Methylation Capture Sequencing and Infinium EPIC Methylation Array in Peripheral Blood Mononuclear Cells
Authors: Shu Chang , Zhang Xinyu , Aouizerat Bradley E. , Xu Ke 
Published: June 2020

Abstract
Background: Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium Methylation EPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. Methods: Epienome-wide DNA methylation in four peripheral blood mononuclear cell samples was profiled by using SureSelectXT Methyl-Seq for MC-seq and EPIC platforms separately. CpG site-based reproducibility of MC-seq was assessed with DNA sample inputs ranging in quantity of high (> 1000ng), medium (300-1000ng), and low (150ng-300ng). To compare the performance of MC-seq and the EPIC arrays, we conducted a Pearson correlation and methylation value difference at each CpG site that was detected by both MC-seq and EPIC. We compared the percentage and counts in each CpG island and gene annotation between MC-seq and the EPIC array.Results: After quality control, an average of 3,708,550 CpG sites per sample was detected by MC-seq with DNA quantity >1000ng. Reproducibility of MC-seq detected CpG sites was high with strong correlation estimates for CpG methylation among samples with high, medium, and low DNA inputs (r > 0.96). The EPIC array captured an average of 846,464 CpG sites per sample. Compared with the EPIC array, MC-seq detected more CpGs in coding regions and CpG islands. Among the 472,540 CpG sites captured by both platforms, methylation of a majority of CpG sites was highly correlated in the same sample (r: 0.98~0.99). However, methylation for a small proportion of CpGs (N=235) differed significantly between the two platforms, with differences in beta values of greater than 0.5.Conclusions: Our results show that MC-seq is an efficient and reliable platform for methylome profiling with a broader coverage of the methylome than the array-based platform. Although methylation measurements in majority of CpGs are highly correlated, a number of CpG sites show large discrepancy between the two platforms, which warrants further investigation and needs cautious interpretation.
Incidence and Outcome of Acute Kidney Injury In Hospitalized Children
Authors: Paudel Rajan , Shah Gauri Shankar , chaudhary Shipra , Timilsina Anuradha 
Published: June 2020

Abstract
Background: Acute kidney injury (AKI) is now increasingly common in hospitalized children with adverse short and long term outcomes. The objective of this study is to know the incidence, etiology and short term outcome of AKI in developing nation.Methods: This prospective observational study is done in pediatric wards and pediatric intensive care unit (PICU) of tertiary center of eastern Nepal, between age group 2 months to 14 years. AKI is defined according to pRIFLE criteria.Results: From May 2015 to March 2016 942 patient enrolled in Pediatric wards and PICU are evaluated. The incidence of AKI was 5.9% and 21.76% in PICU. AKI was commonest among cases having infectious etiology compromising 73.2% (n=41), 16.1%(n=9) due to primary renal disease , 5.35%(n=3) secondary to congenital heart disease, and 5.35% due to other causes. Inotropes was required in 55.4% (n=31) cases, nineteen(33.9%)required mechanical ventilator while 3 (5.36%) underwent hemodialysis. Out of 56 AKI patients 71.4% (n=40) improved and 28.6% (n=16) expired. Patient with AKI had significant longer duration of hospital stay as compared to Non AKI (7 day vs 3 days , P< 0.001). Mortality was high in AKI patient who required mechanical ventilation, inotropes (p<0.001) and AKI Injury and Failure stage(p=0.003) .Conclusion: The incidence of AKI is high in pediatric patients. Patients with AKI increases the duration of hospital stay and mortality is more in patients requiring mechanical ventilation and inotropes.
The Impact of Choice Architecture on Clinical Decision-Making in Sepsis: A Proof of Concept Study
Authors: Mansoori Jason , Clark Brendan , Havranek Edward , Douglas Ivor 
Published: June 2020

Abstract
Background: Despite improved survival and increasing hospital mandates, discordance with sepsis resuscitation guidelines is common. We sought to determine whether choice architecture can promote faster or slower decision-making among physicians and the associated risk of guideline-discordance in sepsis.Methods: We conducted an electronic, survey-based time-to-event analysis using a sepsis clinical vignette and multivariable Cox proportional hazards regression. Respondents included physicians from multiple specialties and levels of training at an academic tertiary-care hospital and academic safety-net hospital. Respondents were randomized to one of three distinct answer sets: control (6 options with no time limit), time constraint (10 seconds, intended to promote faster thinking) or choice overload (24 options, intended to promote slower thinking). The primary outcomes were response time and discordance with Surviving Sepsis Campaign 2016 fluid resuscitation guidelines, adjusting for physician characteristics. Physician risk tolerance and predisposition towards intuitive or analytical thinking were assessed for effect modification.Results: 189 of 624 (30.3%) physicians completed the survey. Total response time was lower in time constraint (45.8s, IQR 38.3s-56.6s, P<0.001) and higher in choice overload (94.2s, IQR 73.0s-142.6s, P=0.005) groups compared to control (71.5s, IQR 52.6s-100.6s). In contrast, relative hazard for guideline discordance was increased in time constraint (3.38, 1.97-5.79, P<0.001) and decreased in choice overload (0.52, 0.30-0.93, P=0.03) groups dependent on Cognitive Reflection Test (7.87, 1.80-34.44, P=0.006) and risk tolerance scores (JPI-RTS 2.00, 1.05-3.84, P=0.04 and MFS 0.42, 0.20-0.88, P=0.02), respectively.Conclusions: Choice architecture may impact clinical decisions and guideline discordance in sepsis, warranting further investigation in real-world contexts.
Nurse Home Visit Program to Promote Parenting In Brazil: Premises And Planning
Authors: siqueira luciola , Chiesa Anna Maria , Miguel Euripedes , Silva Leticia , Vadakattu Sharonya , Alarcao Fernanda , Fracolli Lislaine 
Published: June 2020

Abstract
BackgroundPromoting good parenting has been a challenge for public policies since child development became part of the Sustainable Development Goals until 2030. Home visitation programs have been proved to be effective in supporting the most vulnerable families, especially the vulnerable, first time pregnant’s teenagers, in acquiring skills and incorporating parenting practices that promote integral child development. The Young Mothers Caregivers is an innovative, experimental program, implemented in the context of a RCT. This paper aims to analyze the fidelity of the HVs, regarding the planning and the operative framework of the young Mothers Cargivers’ protocol.MethodsThis qualitative study was conducted by content analysis from nurse’s records of 390 HVs delivered for 39 teenagers, attended by YMCP. The software Wordart was used to visualize the frequency of themes. The analysis examined, 1) which priority areas were most focused on in HV records, and 2) which themes were prominent in each content priority area, according to the five axes that compose the bases of the interventions. ResultsThe first trimester of HV focused on “Care with Health” axis (specially “Nutrition”); along with “Life Course” axis, “Familiar&Social Network”, “Environment” and “Parenting”. In the second trimester of HV, again “Care with Health” axis (primarily focused on “Nutrition” and “Birth”) was identified in records, as was the concept of “Parenting” (“Praise”, “Attachment”, and “Expressing Feelings”). In the third trimester of HV, “Care with Health” axis (primarily through Breastfeeding and Birth) and “Parenting” axis(through Praise, Attachment, and Readiness to Address Concerns) were prominent. ConclusionsThe content priorities raised in each HV trimester, with different themes within each category, indicating the capacity to adjust the protocol according to the youth interest. At different times, some categories were more highlighted than others. The study found recurring emphasis on praise and the nurse’s ability to address concerns, underscoring the importance of a strong relationship among the nurse visitor and the young mother. Relevance to PracticeData highlights the role of responsive communication and participant’s centered needs as skills for nurses that delivers HV. This is a crucial aspect to structure the monitoring and supervision axes of the Program, for further scaling up.
Metabolites of Bacterial-Feeding Nematodes Stimulate Bacterial Indole-3-Acetic Acid (IAA) Synthesis
Authors: Li Mengsha , Li Mengdi , Zhou Ming , Zhao Yexin , Xu Jingjing , Hu Feng , Li Teng , Li Huixin 
Published: June 2020

Abstract
Interorganismal metabolites play significant roles in regulating behaviors and communications between organisms. Nematodes are the most abundant animals on earth, and function well in soil ecosystem due to their interactions with microbes. Bacterial-feeding nematodes stimulate the activity of indole-3-acetic acid (IAA)-producing bacteria and increase the content of IAA in soil. However, we do not fully understand how bacterial-feeding nematodes interact with bacteria and affect IAA synthesis. In this study, the model nematode Caenorhabditis elegans and three species of soil-dwelling IAA-producing bacteria ( Bacillus amyloliquefaciens JX1, Arthrobacter pascens ZZ21 and A. chlorphenolicus L4) were employed to determine the effect of nematodes on the IAA biosynthesis of bacteria. Then the metabolites and extracts of C. elegans were tested the effect on three bacterial IAA synthesis (but only A. pascens ZZ21 for the extracts). Lastly, two soil-dwelling bacterial-feeding nematodes ( Mesorhabditis sp. and Acrobeloides sp.) and two IAA-producing bacteria ( B. amyloliquefaciens JX1 and A. pascens ZZ21) were subsequently used to explore the universality of this interaction. Our results showed that the metabolites or extracts of nematodes could promote the IAA biosynthesis of IAA-producing bacteria, and implied this stimulatory effect maybe widely spread in metabolites of bacterial-feeding nematodes and IAA-producing bacteria, but vary with nematodes and bacteria species. Our findings indicate that bacterial-feeding nematodes could mediate the interaction between nematodes and bacteria by their metabolites, except for their feeding behavior, and offer insights into the ecological function of the metabolites of nematodes.
An experts’ opinion-based comparison and benefit cost analysis of post-mortem versus tuberculin skin test surveillance systems, Mpumalanga, South Africa
Authors: Marange Rudo , Fasina Folorunso , Reininghaus Bjorn , Morar-Leather Darshana 
Published: June 2020

Abstract
BackgroundTuberculosis (TB) is a global health concern caused mostly by Mycobacterium bovis (M. bovis) and Mycobacterium tuberculosis (M. tuberculosis) in animals and humans respectively. As part of TB control strategies, most governments instituted test and slaughter policies for bovine TB (bTB) eradication with varied level of success.MethodsUsing the SurvCost® (http://www.cdc.gov/idsr/survcost.htm), we evaluated the postmortem surveillance (PMS) system as an alternative to the tuberculin skin test (TST). Experts’opinions survey was used to collect information on the perceived level of acceptability of PMS and TST, successes and challenges of both surveillance systems, economic and budget data. Benefit cost analysis of both systems were evaluated and the comparative economic benefit of PMS over TST was determined.ResultsTST implementation was challenging due to poor logistics, procurement challenge, poor feedback, inconsistency in testing and poor return rate for retesting. Experts agreed that PMS was cheaper but almost impracticable due to late detection and probable poor compliance rate but farmers were more open to PMS than TST. Personnel cost remains the largest part of the surveillance cost (47.8% of total costs). TST and PMS systems can be up to 4.40 and 5.96 times more beneficial that not tackling bTB respectively and PMS is 1.35 more cost beneficial that TST.ConclusionWhile TST is empirical, compliance by farmers was poor due to the associated inconveniences. In the alternative, PMS was convenient for farmers but experts believed that adherence will be poor unless increased manpower is available. We advocated for a blended approach between the two systems. Improved field surveillance and detailed economic data should benefit future economic assessment.Trial registrationNot applicable.
PFKFB4 Overexpression Facilitates Proliferation by Promoting the G1/S Transition and is Associated with a Poor Prognosis in Triple-Negative Breast Cancer
Authors: Cai Yu-Chen , Yang Hang , Shan Hong-Bo , Su Hui-Fang , Jiang Wen-Qi , Shi Yan-Xia 
Published: June 2020

Abstract
Background:6-Phosphofructo-2-kinase/fructose-2,6-biphosphate-4 (PFKFB4) is a key factor that plays an important role in tumorigenesis. However, its role in triple-negative breast cancer (TNBC) progression needs to be further validated.We investigated whether PFKFB4 is directly involved in the oncogenic signaling networks of TNBC.Methods: First, we assessed the expression level of PFKFB4 in tumor tissue specimens by immunohistochemistry and evaluated its prognostic value. Next, the effect of PFKFB4 on TNBC cell growth and associated mechanisms were investigated.Finally, the results were further verified in vivo. Results: We found that PFKFB4 overexpression was associated with an unfavorable prognosis in TNBC patients. PFKFB4 was overexpressed in TNBC cell lines in hypoxic environments, and its overexpression promoted tumor progression in vitro and in vivo. Further analyses demonstrated that the possible mechanism might be that PFKFB4 overexpression facilitates TNBC progression by enhancing the G1/S phase transition by increasing the proteinlevelof CDK6 and phosphorylation of Rb.Conclusions: These data suggest that PFKFB4 plays significant roles in the tumorigenesis and development of TNBC.Trial registration: Retrospectively registered.
Bringing to light a new energy path: the case of Minas Gerais State, Brazil
Authors: Ribeiro Ana Pimenta 
Published: June 2020

Abstract
Background

In Brazil, more than 60% of the energy comes from hydroelectricity, making the system highly vulnerable in the context of global climate change, with precipitation and temperature shifts over the years. Characterized by its multiple opportunities of sources and conversion technologies for energy, biomass has a high potential to become responsible for a relevant share on the renewable energy supply. Previous studies on biomass energy production in Brazil confirm promising results. This paper highlights possibilities for biomass power generation in Minas Gerais State. To estimate the energy productivity, a Sustainable Technical Coefficient was adopted: a conservative index that considerers the portion of residues that could be used maintaining the integrity of the soil.
Results

This index was applied, together with the data on the silviculture and selected crops yield. The local energy demand was also calculated and compared to the potential energy production. Results show that 78% of the municipalities could have their basic energy needs and 18% of the demand for productive uses met by residues of crops and silviculture production.
Conclusion

For the state Minas Gerais, with its tradition of agriculture, the biomass residual energy is viable and should be considered by policymakers.
From qualitative to quantitative: a new approach for determining heat tolerance in cotton using triphenyl tetrazolium chloride
Authors: Jaconis Susan Yvonne , Conaty Warren C , Thompson Alan J. E. , Smith Shanna L , Trimarchi Chiara , Cottee Nicola S , Bange Michael P 
Published: June 2020

Abstract
Background

Susceptibility of cotton to heat stress in cotton production systems is a major concern for breeding programs. It is hypothesised that in order to maintain or improve cotton yields and quality in sub-optimal future climates, the negative effects of high temperature stress must be mitigated. To address this need, a fast and effect way of quantifying thermotolerant phenotypes is required. Triphenyl tetrazolium chloride (TTC) based enzyme viability testing following high temperature stress can be used as a heat tolerance phenotype. This is because when live cells encounter a TTC solution, TTC undergoes a chemical reduction producing a visible, insoluble red product called triphenyl formazan, that can be quantified spectrophotometrically. However, existing TTC based cell viability assays cannot easily be deployed at the scale required in a crop improvement program.
Results

In this study, a heat stress assay (HSA) based on the use of TTC enzyme viability testing has been refined and improved for efficiency, reliability, and ease of use through four experiments. Sampling factors which may influence assay results such as leaf age, plant water status, and short-term cold storage were also investigated. Experiments conducted in this study have successfully down scaled the assay and identified an optimal sampling regime, enabling measurement of large segregating populations for application in breeding programs. The optimal durations of leaf disc exposure to TTC and the subsequent extraction of the formazan product in ethanol were identified as 16 h and 13 h, respectively; leading to enhanced clarity of assay results.
Conclusions

These improvements in the methodology provide a new level of confidence in results, ensuring applicability of the assay to a breeding program. The improved HSA methodology is important as it is proposed that long-term improvements in cotton thermotolerance can be achieved through concurrent selection of superior phenotypes based on the HSA and yield performance in hot environments. Additionally, a new way of interpreting both heat tolerance and heat resistance were developed to differentiate genotypes that perform well at the time of a heat stress event and those that maintain a similar level of performance to a non-stressed control.
Corona Virus Disease 2019 (COVID-19): Intensive Care Admission Prediction Model
Authors: Hachim Mahomood Y. , Hachim Ibrahim Y. , Naeem Kashif Bin , Hannawi Haifa , Salmi Issa Al , Hannawi Suad 
Published: June 2020

Abstract
Background: Identifying clinical-features or a scoring-system to predict a benefit from hospital admission for patients with COVID-19 can be of great value for the decision-makers in the health-sector. We aim to identify differences in patients' demographic, clinical, laboratory and radiological findings of COVID-19 positive cases to develop and validate a diagnostic-model predicting who will develop severe-form and who will need critical-care in the future.Methodology: Patients were classified according to their clinical state into mild, moderate, severe, and critical. All their baseline clinical data, laboratory, and radiological results were used to construct a prediction-model that can predict if the COVID-19 patients will develop a severe condition that will necessitate their ICU-admission. An ensemble feature selection tool was used to identify the relative importance of each variable. The performance of the selected features compared to all features using logistic regression and area under curve test.Results: Patients with ICU admission showed a distinct clinical, demographic as well as laboratory features when compared to pattients that did not need ICU admission. This includes elder age group, male gender and presence of comorbidities like diabetis and history of hypertension.Out of the different demographic, clinical and laboratory charasteristics of these patients, Age at diagnosis, Lymphocyte count, C-reactive protein (CRP), lactate dehydrogenase (LDH), Albumin, Urea, and Procalcitonin levels were found to be able to predict which patients may need ICU admission. Conclusion: Higher CRP, LDH, Age at diagnosis, Urea, Procalcitonin, and lower Albumin, Lymphocyte count are significant determinant in ICU admission for COVID-19 patients.