bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Vitamin D Receptor TaqI and ApaI Genetic Polymorphisms with Nephrolithiasis and End Stage Renal Disease: A Meta-Analysis and an Investigation into Latitudinal Effect on Disease Penetrance
Authors: Hussain Tajamul , Naushad Shaik M. , Ahmed Anwar , Alamery Salman , Mohammed Arif A. , Abdelkader Mohamed O. 
Published: October 2019

Abstract
Background: The deficiency of vitamin D receptor (VDR) or its ligand, vitamin D3, is linked to the development of renal diseases. The TaqI (rs731236) and ApaI (rs7975232) polymorphisms of VDR gene are widely studied for their association with renal disease risk. However, studies have largely been ambiguous. Objectives: Here, a meta-analysis comprising 2669 renal disease cases and 3342 controls was carried out to clarify the association of TaqI and ApaI polymorphisms with nephrolithiasis (NL), diabetic nephropathy (DN) and end stage renal disease (ESRD). Methods and Results: The VDR TaqI C-allele under allele contrast and fixed effect models was significantly associated with NL and ESRD, and Apal T-allele with ESRD only under fixed effect model. Cochrane Q-test showed no evidence of heterogeneity for TaqI polymorphism and a significant heterogeneity for Apa I polymorphism. No publication bias was observed for both the polymorphisms. Interestingly, increased disease penetrance with an increase in latitude from south to north across the globe was found only in the case of Taql polymorphism but not with Apal. Conclusions and Implications: The present meta-analysis identifies TaqI and ApaI polymorphisms of VDR gene as significant risk factors for renal diseases. Besides, increased disease penetrance with Taql polymorphism from south to north may corroborate with combined effect of defective VDR expression and decreased vitamin D synthesis due shorter durations of sun exposure with increasing latitude. On the other hand, possibility of Apal polymorphism in linkage disequilibrium with an adjacent functional polymorphism and lack of their co-segregation may have resulted in reduced disease penetrance. Present findings may have implications in understanding the role of gene-environmental interaction in renal disease risk.
Comprehensive network analysis of integrin α11 expressed in human breast cancer
Authors: Fu Yun , Sun Xiaoyin , Zhuang Zhigang 
Published: October 2019

Abstract
Background: Breast cancer is the most common malignancy in women worldwide, but few genes have been reported to be involved in breast cancer development.
Methods: We constructed a co-expression network to expand upon the knowledge of the various molecular biomarkers in breast cancer development. Transcriptome data for the tissues of all breast cancer and para-carcinoma types were retrieved from The Cancer Genome Atlas (TCGA) database. We performed a co-expression analysis of breast cancer transcriptome data using Pearson’s correlation coefficient (PCC) for inter-sequence mutual rank (MR)-based cutoffs using 11 guide genes and employed Kaplan-Meier survival analyses to assess the prognostic values of hub genes.
Results: A co-expression network centered on the Integrin α 11 (ITGA11) of the extracellular matrix (including 11 guide genes and 72 edge genes) was extracted for breast cancer. The gene ontology (GO) analysis showed that various genes may also be included in the breast cancer network. Among them, CEMIP, COL11A1, CTHRC1, ITGA11, LUM and P4HA3 were negatively associated with the overall survival, and ADAMTS12 and LOXL1 were positively associated with the overall survival at early stage. However, there was no significant difference between the eight gene expressions and Disease-free survival.
Conclusions: Our co-expression analysis includes the isolated transcriptome of breast cancer, which is a useful resource for breast cancer researchers, as it enables them to elucidate important and complex biological events to prevent and predict cancer.
Two-dimensional speckle tracking echocardiography in goats: repeatability, variability, and validation of the technique using an exercise test and an experimentally induced acute ischemic cardiomyopathy.
Authors: Leroux Aurelia A , Moonen Marie , Farnir Frédéric , Deleuze Stefan , Sandersen Charlotte , Amory Hélène 
Published: October 2019

Abstract
Background : Two-dimensional speckle tracking (2DST) technique has been validated in numerous animal species, but neither studies of repeatability, nor measurements after exercise or in animals with cardiac disease have been reported in goats. Therefore, the aim of this study was to validate this technique in goats for further clinical and experimental applications in this species. This study was divided into several steps. First, a standardized echocardiographic protocol including several right parasternal short-axis views at papillary muscles level was performed three times at one-day intervals in ten healthy adult unsedated Saanen goats to test repeatability and variability of 2DST measurements. Then, the same measurements were performed immediately before and after a standardized exercise on treadmill in seven of the goats, and at 24h after induction of an experimental ischemic cardiomyopathy in five of the goats, to test the reliability of the technique to assess physiological and pathological changes.
Results: Global and regional measurements of radial and circumferential strain and strain rate, radial displacement, rotation and rotation rate were obtained. Comparisons were performed using ANOVA II (p<0.05). Caprine 2DST measurements demonstrated a good repeatability for global measurements except for the late diastolic peak of the circumferential and radial strain rate. Segmental 2DST measurements were also repeatable except for the anteroseptal segment diastolic peaks and several rotation and rotation rate measurements. Overall variability was moderate to high. Segmental and global peak values obtained after exercise and after myocardial ischemia were significantly different than curves obtained at baseline.
Conclusions: The results of this study are consistent with those previously described in other animal species and humans. 2DST echocardiography is a valid technique to evaluate physiological and pathological changes in myocardial function in goats, despite the technical limitations observed in this species.
A 2x2 factorial, randomised, open-label trial to determine the clinical and cost- effectiveness of hypertonic saline (HTS 6%) and carbocisteine for airway clearance versus usual care over 52 weeks in adults with bronchiectasis: A protocol for the CLEAR clinical trial
Authors: Bradley Judy , Anand Rohan , O'Neill Brenda , Ferguson Kathryn , Clarke Mike , Carroll Mary , Chalmers James , de-Soyza Anthony , Duckers Jamie , Hill Adam T , Loebinger Michael R , Copeland Fiona , Gardner Evie , Campbell Christina , Agus Ashley , Maguire Alistair , Boyle Roisin , McKinney Fionnuala , Dickson Naomi , McAuley Danny , Elborn Stuart 
Published: October 2019

Abstract
Background Current guidelines for the management of bronchiectasis (BE) highlight the lack of evidence to recommend mucoactive agents, such as hypertonic saline (HTS) and carbocisteine, to aid sputum-removal as part of standard care. We hypothesise that mucoactive agents (HTS or cabocisteine, or a combination) are effective in reducing exacerbations over a 52-week period, compared to usual care. Methods A 52-week, 2x2 factorial randomised open label trial to determine the clinical and cost-effectiveness of HTS 6% and carbocisteine for airway clearance versus usual care: CLEAR (clinical and cost-effectiveness of hypertonic saline (HTS 6%) and carbocisteine for airway clearance versus usual care). Patients will be randomised to either (i) Standard care and twice daily nebulised HTS (6%), (ii) Standard care and carbocisteine (750mg three times per day until visit 3 reducing to 750mg twice per day), (iii) Standard care and combination of twice-daily nebulised HTS and carbocisteine, or (iv) Standard care. The primary outcome is the mean number of exacerbations over 52 weeks. Key inclusion criteria: adults with a diagnosis of BE on computed tomography scans, BE as the primary respiratory diagnosis, two or more pulmonary exacerbations in the last year requiring antibiotics and production of daily sputum. Discussion This trial’s pragmatic research design avoids the significant costs associated with double-blind trials whilst optimising rigor in other areas of trial-delivery. CLEAR will provide evidence as to whether HTS, carbocisteine or both are effective and cost-effective for BE patients.
Farmer Participatory Research Advances Sustainable Agriculture: Lessons from Michigan and Malawi
Authors: Snapp Sieglinde S. , DeDecker James , Davis Adam S. 
Published: October 2019

Sustainable production for field crops has proved to be a challenging proposition. Farmer participatory research (FPR) is an important approach to help ensure relevance and define locally adapted solutions for enhanced adoption of sustainable agriculture (SA) technologies. The mother and baby trial (MBT) design has proved effective as a FPR approach to address challenges on smallholder farms. The MBT systematically links long‐term “mother” trials, where slow and erratic processes can be monitored, to “baby” trials led by farmers to capture a wide range of farm practices and environmental contexts. Communication and learning is facilitated through MBTs as well. This distributed FPR approach documents the performance of technologies in diverse contexts and provides multiple opportunities for joint planning, observation, and reflection. We describe two MBT case studies, one within a developing country context (Malawi) and the other representing a novel application of MBT within an intensive agriculture context (Michigan). To explore tradeoffs in SA performance, multiple domains (productivity, environmental, and economic) are presented via radar charts as a visualization tool. In both FPR experiences, farmer perspectives and a wide range of practices were revealed. In Malawi, a mesic site was associated with steep SA tradeoffs compared with a marginal site. In Michigan, diversity in tillage practices, field crop performance, and soil health were found to be conditioned by the environment. Overall, the MBT approach supported the development of SA technologies adapted to local conditions.Core Ideas

Sustainable agricultural technologies are needed for environmental services.
Agricultural learning communities support joint learning and on‐farm adoption.
Case studies from Michigan and Malawi illustrate the mother and baby trial approach.
Farmer participatory research enhances stakeholder communication and adaptations.
Early Growth of Breadfruit in a Variety × Environment Trial
Authors: Lincoln Noa Kekuewa , Cho Alyssa , Dow Graham , Radovich Theodore 
Published: October 2019

Breadfruit [Artocarpus altilis (Parkinson) Fosberg] is growing in agronomic importance throughout the global tropics as a result of its potentially high yield and nutritious, carbohydrate‐rich fruit. A bottleneck to expanded production of breadfruit is the lack of agronomic performance metrics and growth parameters, including an understanding of variety × environment interactions among commonly grown varieties. To address this knowledge gap, four varieties of breadfruit (‘Otea, Fiti, Pua‘a, Ma‘afala) available at the commercial scale were established in a randomized complete block design at five diverse sites in Hawai'i. Soil, architectural, physiological, and climate data were collected on 18‐mo‐old trees in 2018. Growth rates varied considerably for height (0.44–2.78 m yr−1), diameter at breast height (0.85–5.19 cm yr−1), and canopy width (0.14–1.35 m yr−1). Diameter was significantly correlated to tree height (r2 = 0.88), canopy width (r2 = 0.83), and canopy volume (r2 = 0.94). Growth was significantly different between sites, and some variety × site interactions were significant. Univariate and multivariate linear regressions were used to explore relationships between growth and climate, soils, and architecture. Future work will focus on the continued evaluation of variety × environmental influence on fruit production and fruit quality and on promoting this network of sites as a valuable resource for the study of an underutilized crop species with substantial potential to be a major crop in the tropics.Core Ideas

Breadfruit, while rapidly growing in importance globally, suffers from a lack of agronomic study.
To our knowledge, the first variety × environment trial network of breadfruit was established in Hawai'i.
Examination of initial growth rates show considerably higher rates than represented in the literature.
Multiple climate and soil parameters significantly correlate to early growth.
An Economic and Biophysical Model of Deficit Irrigation
Authors: Trout Thomas J. , Manning Dale T. 
Published: October 2019

Competition for scarce water resources may lead to high water prices. Agricultural producers can adapt to increasing water price by adjusting irrigation management strategies. When water prices are high, deficit irrigation, the purposeful reduction of irrigation to reduce water use while accepting reduced yield, may increase net income. Deficit irrigation decisions depend on economic, biological, and physical conditions. A model based on relationships among the amount and cost of irrigation water applied, water productivity, and the value of water saved and crop yield was developed to assist farmers making deficit irrigation decisions. A model application for irrigated maize (Zia mays L.) production in northeast Colorado illustrates conditions under which deficit irrigation increases net income. High water costs and low crop prices favor deficit irrigation. When water has value for leasing, the combination of deficit irrigation production to reduce water use and water leasing may increase net income. Sufficiently high lease prices and low commodity prices favor rainfed production or fallowing.Core Ideas

Deficit irrigation may increase net farm income.
Expensive water, low crop prices, and high elasticity of water productivity favor deficit irrigation.
Combining economic with biophysical models improves applicability.
Response of Maize Productivity and Resource Use Efficiency to Combined Application of Controlled‐Release Urea and Normal Urea under Plastic Film Mulching in Semiarid Farmland
Authors: Tang Liang , Zhou Junxi , Zhai Xiaofang , Sun Haoran , Yue Shanchao , Guo Ning , Li Shiqing , Shen Yufang 
Published: October 2019

Controlled‐release urea is considered to enhance crop yields while reducing labor costs from fertilizer dressing, but the impacts can range widely depending on water availability in soil. Therefore, we conducted a 3‐yr field study to evaluate the potential role of controlled‐release urea in improving productivity and resource use efficiency of maize in semiarid areas in China. Treatments were established as two mulching modes (plastic film mulching [FM] and no mulching [NM]) and three nitrogen application modes (no nitrogen fertilizer [CK], a 1:2 ratio of controlled‐release urea to common urea [CRU], and common urea only [U]). Higher temperature and soil water content under FM treatments significantly accelerated maize growth and development, as indicated in terms of a larger leaf area index before silking, greater biomass accumulation, and greater grain yield. More robust plants with controlled‐release urea under mulching can better absorb and utilize deep soil water to increase water use efficiency (WUE). Mean shoot biomass, grain yield, and WUE during the three experimental years were 35.3, 19.0, and 12.4% higher in mulching with CRU treatments than in NM with controlled‐release urea treatments, respectively. Significant interactions existed for yield and WUE among surface mulching (SM), nitrogen fertilizer (NF), and sampling year (Y) in the three experimental years, except for SM × NF for WUE. These results demonstrate that a mixture of controlled‐release urea and U at an appropriate ratio under SM can provide a better water/temperature/nitrogen conditions for maize growth to realize relatively high yield with labor and time savings in semiarid farmland.Core Ideas

Film mulching benefits topsoil temperature, soil moisture, and utilization of deeper soil water.
Combining controlled‐release urea (CRU) and urea increased yield and resource use.
Combing CRU and urea under plastic film increased yield and WUE.
One‐time application of CRU + urea at an appropriate ratio will satisfy spring maize in dryland farming systems.
Effects of Cultivation Practices and Products on Bermudagrass Fairways in a Semiarid Region
Authors: Li Li , Young Joseph , Deb Sanjit 
Published: October 2019

High evapotranspirational demand combined with poor quality irrigation water increases salinity concerns in semiarid regions. Accumulated salts in the root zone may negatively affect bermudagrass (Cynodon spp.) growth and quality. The objective of this study was to examine the effectiveness of cultivation practices combined with products to enhance fairway conditions without applying leaching water levels. Two golf courses in Lubbock, TX, were selected for this research. Cultivation practices, including noncultivated control, core aerification, and slicing, were conducted in mid‐June of 2015 and 2016. Nine products recommended to enhance water movement or to disassociate sodium were applied within each cultivation treatment at label rates. Soil pH and electrical conductivity (EC) were determined from samples obtained in June, August, and October each year. Volumetric water content, visual turf quality, digital image analysis, normalized difference vegetation index, and ratio vegetation index were assessed from June to October in 2015 and 2016. Soil EC fluctuated with rainfall events. However, no treatment reduced soil EC. Gypsum‐based products increased soil EC but reduced pH at the conclusion of the research. Core aerification reduced aboveground parameters at Golf Course A because aerified holes remained visible throughout summer, whereas slicing and core aerification improved turf quality and ratio vegetation index at Golf Course B. These results emphasize the need to test irrigation water for the salinity hazard before implementing management strategies and the importance of leaching by rainfall or additional irrigation. Lastly, high surface disruption cultivation practices may inhibit bermudagrass recovery on higher clay content soils.Core Ideas

Rainfall and high ET fluctuated soil EC of bermudagrass golf fairways.
Gypsum products increased soil EC and reduced soil pH after 2 yr of applications.
Bermudagrass recovery from core aerification was slowed with higher clay content.
Cultivation practices improved parameters on high sand content soil after recovery.
Evaluation of the Simple Algorithm for Yield Estimate Model in Winter Wheat Simulation under Different Irrigation Scenarios
Authors: Zhang Chao , Liu Jiangui , Dong Taifeng , Shang Jiali , Tang Min , Zhao Lili , Cai Huanjie 
Published: October 2019

Winter wheat (Triticum aestivum L.) is one of the major grain crops grown in Guanzhong Plain, China. Rapid and accurate crop growth and yield estimation are important for agricultural monitoring and policy decision‐making. Crop model simulation is an effective way to provide objective growth and yield forecast. In this study, we investigated the applicability of the Simple Algorithm for Yield Estimate (SAFY) model for estimating winter wheat dry shoot biomass (MS,d) and grain yield, using two growing seasons field data from different irrigation scenarios. Results showed that the leaf area index (LAI) could be reasonably well simulated, with a minimum root mean square estimate (RMSE) of 0.11. The water stress intensity of each irrigation scenario was well accounted for through stress factor of effective radiation use efficiency. Good accuracy were achieved for MS,d simulation in both calibration (RMSE = 0.054–0.183 kg m−2) and validation (RMSE = 0.146 kg m−2) datasets, but showed a general overestimation during later growth stages. The grain yield was well estimated with a relative error of 1.9% to 16.7% in 2013 to 2014 and 0.1% to 16.7% in 2014 to 2015. The comparison between estimated and measured yield of all irrigation scenarios were robust in both seasons, with the minimum RMSE and MRE of 35.0 g m−2 and 4.7%, respectively. This work demonstrates the potential of a simple crop model for estimating biomass and yield only by calibrate the LAI without further in situ data, and prefigures assimilation application with remote sensing data in future.Core Ideas

The SAFY model was evaluated in different irrigation scenarios.
The variation of LAI was highly sensitive to leaf partition parameters.
SAFY effectively simulated wheat biomass and yield under various irrigation scenarios.
A general overestimation on biomass was noted during later growth stages.
Combination of Humic Substances and Arbuscular Mycorrhizal Fungi Affecting Corn Plant Growth
Authors: Pinos Nadia Quevedo , Louro Berbara Ricardo Luis , Elias Sael Sanchez , van Tol de Castro Tadeu Augusto , García Andrés Calderín 
Published: October 2019

This study evaluates the interaction effects on corn (Zea mays L.) growth between intact humic substances (HS) extracted in an alkaline medium from three different origins (an Organosol [HS‐Org], an Andisol [HS‐And], and vermicompost [HS‐Vc]) and the arbuscular mycorrhizal fungus (AMF) Dentiscutata heterogama. The HS were characterized by spectroscopic techniques, and different biochemical, morphological, nutritional, and AMF colonization parameters were evaluated in corn plants. The experiment was conducted in a greenhouse, and low‐fertility soils sterilized after solarization were used as the substrate. Hybrid corn BR‐3025 was planted, and the HS concentrations used were 5, 10, and 20 mg carbon L−1 for HS‐And, HS‐Vc, and HS‐Org, respectively, applied 15, 25, and 45 d after emergence close to the roots. The results show that HS application and D. heterogama inoculation significantly stimulated the biomass in relation to the treatments without AMF. Carbohydrate and protein content were stimulated by HS–AMF interaction. A higher leaf content of nutrients was observed in the AMF‐ and HS‐inoculated plants. The HS‐Vc application and AMF inoculation resulted in intense stimulation, which was confirmed with a high mycorrhizal efficiency. The spore density and glomalin content were also stimulated by the three different HS applications independently of their source. The HS‐Vc has intermediate structural chemical characteristics in terms of polarity and aromaticity compared with HS‐Org and HS‐And. The HS‐Vc more strongly stimulated the plant physiological parameters when combined with the AMF inoculation. These results may indicate that the HS formed in soil and characterized by structures that are more balanced may function more effectively.Core Ideas
Balanced structural in humic substances (HS) exert greater bioactivity in plants.
HS and arbuscular mycorrhizal fungi (AMF) can stimulate plant growth and development.
Application of HS and AMF increase nutrient absorption and biomass production.
Spore density and glomalin were stimulated by HS applications independently of the source.