bluuebunny/crossref_metadata_2025_split huggingface dataset:
Farmer use of intermediated market channels: a review
Authors: Dimitri Carolyn , Gardner Karen 
Published: April 2018

AbstractIntermediated markets are relatively new market channels that have the potential to expand local and regional food systems while increasing the viability of small- and medium-sized farms. The intermediated channels comprise a short supply chain linking farmers with consumers through the use of intermediary such as a distributor or supermarket. In many instances, these supply chains embed social or environmental values, such as supporting local farming. In this paper, we examine the current state of knowledge about the intermediated market channel. The first source of knowledge consists of data from federal and private sources. Next, we review a selection of the published literature focusing on farmer use of intermediated market channels in the USA. The main intermediated channels include direct to institutions, such as schools and hospitals; food hubs; and direct to retail. The paper finishes by raising questions about future of intermediated markets, based on the findings of the literature review and data.
Cover crops use in Midwestern US agriculture: perceived benefits and net returns
Authors: Plastina Alejandro , Liu Fangge , Miguez Fernando , Carlson Sarah 
Published: April 2018

AbstractDespite being generally accepted as a promising conservation practice to reduce nitrate pollution and promote soil sustainability, cover crop adoption in Midwestern US agriculture is low. Based on focus groups, surveys and partial budgets, we calculated the annual net returns to cover crop use for farmers in Illinois, Iowa and Minnesota; and elicited farmers’ perceptions about the pros and cons of incorporating cover crops to their row cropping systems. The novelty of our methodology resides in comparing each farmer's practices in the portion of their cropping system with cover crops (typically small), against their practices in the other portion of their cropping system without cover crops. The resulting comparisons, accounting for farmer heterogeneity, are more robust than the typical effects calculated by comparing indicators across cover crop users and unrelated non-adopters. Our results highlight the complicated nature of integrating cover crops into the crop production system and show that cover crops affect whole farm profitability through several channels besides establishment and termination costs. Despite farmers’ positive perceptions about cover crops and the availability of cost-share programs, calculated annual net returns to cover crops use were negative for most participants.
Browning‐Related Decreases in Water Transparency Lead to Long‐Term Increases in Surface Water Temperature and Thermal Stratification in Two Small Lakes
Authors: Pilla Rachel M. , Williamson Craig E. , Zhang Jing , Smyth Robyn L. , Lenters John D. , Brentrup Jennifer A. , Knoll Lesley B. , Fisher Thomas J. 
Published: May 2018

AbstractSurface water temperatures are warming in many lakes across the globe, and this is widely attributed to warming air temperatures. Yet two lakes in Pennsylvania (USA) have shown long‐term increases in surface water temperatures over the past 27 summers during a period with no significant increase in regional air temperature. We examined the relationship between long‐term trends in seven metrics of whole‐lake thermal structure in two lakes and several potential driver variables. Driver variables included water transparency, lake pH, and meteorological variables. Both lakes exhibited significant surface warming and hypolimnetic cooling, resulting in stronger thermal stratification that further reduced mixing and heat transfer to deep waters. During this time period, there were no long‐term trends in solar radiation or in thawing degree days, but annual precipitation and lake pH increased. Water transparency greatly decreased due to increased dissolved organic matter quantity and color, most likely due to increased precipitation and recovery from anthropogenic acidification. In both lakes, the changes in lake thermal structure and heat distribution were strongly related to the decreases in water transparency and increases in dissolved organic matter. This transparency‐mediated mechanism may augment the effects of air temperature‐driven lake warming in other regions where decreasing transparency is also prevalent, further enhancing increases in surface water temperature and thermal stratification. These results have important ecological and biogeochemical implications, highlighting the need for investigations of multiple drivers to fully understand how lakes will respond to future climate change.
Author Correction: Role of hypoxia in Diffuse Large B-cell Lymphoma: Metabolic repression and selective translation of HK2 facilitates development of DLBCL
Authors: Bhalla Kavita , Jaber Sausan , Nahid M. Nanaji , Underwood Karen , Beheshti Afshin , Landon Ari , Bhandary Binny , Bastian Paul , Evens Andrew M. , Haley John , Polster Brian , Gartenhaus Ronald B. 
Published: May 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Continuous, semi-automatic monitoring of ground deformation using Sentinel-1 satellites
Authors: Raspini Federico , Bianchini Silvia , Ciampalini Andrea , Del Soldato Matteo , Solari Lorenzo , Novali Fabrizio , Del Conte Sara , Rucci Alessio , Ferretti Alessandro , Casagli Nicola 
Published: May 2018

AbstractWe present the continuous monitoring of ground deformation at regional scale using ESA (European Space Agency) Sentinel-1constellation of satellites. We discuss this operational monitoring service through the case study of the Tuscany Region (Central Italy), selected due to its peculiar geological setting prone to ground instability phenomena. We set up a systematic processing chain of Sentinel-1 acquisitions to create continuously updated ground deformation data to mark the transition from static satellite analysis, based on the analysis of archive images, to dynamic monitoring of ground displacement. Displacement time series, systematically updated with the most recent available Sentinel-1 acquisition, are analysed to identify anomalous points (i.e., points where a change in the dynamic of motion is occurring). The presence of a cluster of persistent anomalies affecting elements at risk determines a significant level of risk, with the necessity of further analysis. Here, we show that the Sentinel-1 constellation can be used for continuous and systematic tracking of ground deformation phenomena at the regional scale. Our results demonstrate how satellite data, acquired with short revisiting times and promptly processed, can contribute to the detection of changes in ground deformation patterns and can act as a key information layer for risk mitigation.
Essential role of connective tissue growth factor (CTGF) in transforming growth factor-β1 (TGF-β1)-induced myofibroblast transdifferentiation from Graves’ orbital fibroblasts
Authors: Tsai Chieh-Chih , Wu Shi-Bei , Kau Hui-Chuan , Wei Yau-Huei 
Published: May 2018

AbstractConnective tissue growth factor (CTGF) associated with transforming growth factor-β (TGF-β) play a pivotal role in the pathophysiology of many fibrotic disorders. However, it is not clear whether this interaction also takes place in GO. In this study, we investigated the role of CTGF in TGF-β-induced extracellular matrix production and myofibroblast transdifferentiation in Graves’ orbital fibroblasts. By Western blot analysis, we demonstrated that TGF-β1 induced the expression of CTGF, fibronectin, and alpha-smooth muscle actin (α-SMA) in Graves’ orbital fibroblasts. In addition, the protein levels of fibronectin and α-SMA in Graves’ orbital fibroblasts were also increased after treatment with a recombinant human protein CTGF (rhCTGF). Moreover, we transfected the orbital fibroblasts with a small hairpin RNA of CTGF gene (shCTGF) to knockdown the expression levels of CTGF, which showed that knockdown of CTGF significantly diminished TGF-β1-induced expression of CTGF, fibronectin and α-SMA proteins in Graves’ orbital fibroblasts. Furthermore, the addition of rhCTGF to the shCTGF-transfected orbital fibroblasts could restore TGF-β1-induced expression of fibronectin and α-SMA proteins. Our findings demonstrate that CTGF is an essential downstream mediator for TGF-β1-induced extracellular matrix production and myofibroblast transdifferentiation in Graves’ orbital fibroblasts and thus may provide with a potential therapeutic target for treatment of GO.
Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer
Authors: Srirattana Kanokwan , St. John Justin C. 
Published: May 2018

AbstractWe generated cattle embryos using mitochondrial supplementation and somatic cell nuclear transfer (SCNT), named miNT, to determine how additional mitochondrial DNA (mtDNA) modulates the nuclear genome. To eliminate any confounding effects from somatic cell mtDNA in intraspecies SCNT, donor cell mtDNA was depleted prior to embryo production. Additional oocyte mtDNA did not affect embryo development rates but increased mtDNA copy number in blastocyst stage embryos. Moreover, miNT-derived blastocysts had different gene expression profiles when compared with SCNT-derived blastocysts. Additional mtDNA increased expression levels of genes involved in oxidative phosphorylation, cell cycle and DNA repair. Supplementing the embryo culture media with a histone deacetylase inhibitor, Trichostatin A (TSA), had no beneficial effects on the development of miNT-derived embryos, unlike SCNT-derived embryos. When compared with SCNT-derived blastocysts cultured in the presence of TSA, additional mtDNA alone had beneficial effects as the activity of glycolysis may increase and embryonic cell death may decrease. However, these beneficial effects were not found with additional mtDNA and TSA together, suggesting that additional mtDNA alone enhances reprogramming. In conclusion, additional mtDNA increased mtDNA copy number and expression levels of genes involved in energy production and embryo development in blastocyst stage embryos emphasising the importance of nuclear-mitochondrial interactions.
Differences in Neuritogenic Activity and Signaling Activation of Madecassoside, Asiaticoside, and Their Aglycones in Neuro-2a cells
Authors: Nalinratana Nonthaneth , Meksuriyen Duangdeun , Ongpipattanakul Boonsri 
Published: May 2018

AbstractMadecassoside (MS) and asiaticoside (AS) along with their aglycones, madecassic acid (MA) and asiatic acid (AA), are considered the major neuroactive triterpenoid constituents of Centella asiatica. In this study, we aimed to compare MS, AS, MA, and AA for their neurite outgrowth activities and mechanisms in Neuro-2a cells. Immunofluorescent cell staining showed MS and AS significantly increased the percentage of neurite-bearing cells (%NBC) and the neurite length with higher potency than MA and AA. The triterpenoid glycosides induced sustained extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) phosphorylation, while their aglycones activated only transient signaling of ERK1/2. Suppression of ERK1/2 activation significantly abolished not only cAMP response element-binding protein (CREB) phosphorylation but also the increment of %NBC and neurite length in MS- and AS-treated cells. Inhibition of ERK phosphorylation did not produce similar blockage of CREB activation and neurite outgrowth in MA- and AA-treated cells. On the other hand, inactivation of protein kinase B (Akt) resulted in a suppression of neurite lengthening in all studied triterpenoids. This is the first study discerning the different signaling pathways of neurite outgrowth activity induced by C. asiatica triterpenoid glycosides and aglycones. Neurite outgrowth activity of the glycosides MS and AS was found to involve the activation of sustained ERK phosphorylation leading to CREB activation, while ERK activation was not associated with MA- and AA-induced neurite outgrowth. In addition, Akt activation was evident to be more involved in neurite elongation process.
Nursing Information Flow in Long-Term Care Facilities
Authors: Wei Quan , Courtney Karen 
Published: May 2018

Objective Long-term care (LTC), residential care requiring 24-hour nursing services, plays an important role in the health care service delivery system. The purpose of this study was to identify the needed clinical information and information flow to support LTC Registered Nurses (RNs) in care collaboration and clinical decision making.
Methods This descriptive qualitative study combines direct observations and semistructured interviews, conducted at Alberta's LTC facilities between May 2014 and August 2015. The constant comparative method (CCM) of joint coding was used for data analysis.
Results Nine RNs from six LTC facilities participated in the study. The RN practice environment includes two essential RN information management aspects: information resources and information spaces. Ten commonly used information resources by RNs included: (1) RN-personal notes; (2) facility-specific templates/forms; (3) nursing processes/tasks; (4) paper-based resident profile; (5) daily care plans; (6) RN-notebooks; (7) medication administration records (MARs); (8) reporting software application (RAI-MDS); (9) people (care providers); and (10) references (i.e., books). Nurses used a combination of shared information spaces, such as the Nurses Station or RN-notebook, and personal information spaces, such as personal notebooks or “sticky” notes. Four essential RN information management functions were identified: collection, classification, storage, and distribution. Six sets of information were necessary to perform RN care tasks and communication, including: (1) admission, discharge, and transfer (ADT); (2) assessment; (3) care plan; (4) intervention (with two subsets: medication and care procedure); (5) report; and (6) reference. Based on the RN information management system requirements, a graphic information flow model was constructed.
Conclusion This baseline study identified key components of a current LTC nursing information management system. The information flow model may assist health information technology (HIT) developers to consolidate the design of HIT solutions for LTC, and serve as a communication tool between nurses and information technology (IT) staff to refine requirements and support further LTC HIT research.
Embolized Guidewire into Central Aorta: A Nightmare in the Pediatric Intensive Care Unit
Authors: Nath R.K. , Sarowa Manoj , Pandit Neeraj , Agrawal Richa 
Published: April 2018

AbstractA 4-month-old preterm, critically ill infant weighing 3.8 kg was admitted to our pediatric intensive care unit with congestive cardiac failure due to a large ventricular septal defect and its sequelae. During an attempt to insert a central line into the right subclavian vein at bedside, the guidewire inadvertently entered the subclavian artery and embolized distally. After multiple failed retrieval attempts, including surgical femoral cut-down to retrieve the wire, it was removed finally by fluoroscopic-guided percutaneous catheterization with the help of a cardiac bioptome and a gooseneck snare utilizing a novel maneuver.
Socioeconomic status and risk of kidney dysfunction: the Atherosclerosis Risk in Communities study
Authors: Vart Priya , Grams Morgan E , Ballew Shoshana H , Woodward Mark , Coresh Josef , Matsushita Kunihiro 
Published: May 2018

AbstractBackgroundThere is strong evidence of an association between socioeconomic status (SES) and end-stage renal disease (ESRD). However, the association of SES with the risk of chronic kidney disease (CKD) and the rate of change in kidney function is unclear.MethodsA cohort of 14 086 participants with an estimated glomerular filtration rate (eGFR) ≥60 mL/min/1.73 m2 at baseline in the Atherosclerosis Risk in Communities study (1987–89) were studied. The association of annual household income, educational attainment and neighborhood deprivation with incident ESRD, incident CKD and change in eGFR using four measurements over ∼23 years was assessed.ResultsA total of 432 participants developed ESRD and 3510 developed CKD over a median follow-up time of ∼23 years. After adjustment for demographics and baseline eGFR, the hazard ratio (HR) for incident ESRD compared with the high-income group was 1.56 [95% confidence interval (CI) 1.22–1.99 in the medium-income group and 2.30 (95% CI 1.75–3.02) in the low-income group (P-trend < 0.001), and for CKD was 1.10 (95% CI 1.01–1.20) in the medium-income group and 1.30 (95% CI 1.17–1.44) in the low-income group (P-trend < 0.001). After full adjustments, the HR for ESRD was 1.33 (95% CI 1.03–1.70) in the medium-income group and 1.50 (95% CI 1.14–1.98) in the low-income group (P-trend = 0.003) and for CKD was 1.01 (95% CI 0.92–1.10) in the medium-income group and 1.04 (95% CI 0.93–1.16) in the low-income group (P-trend = 0.50). The eGFR decline was 5% and 15% steeper in the medium- and low-income groups, respectively, after full adjustment (P-trend < 0.001). Results were similar, with lower educational attainment and higher neighborhood deprivation being associated with adverse outcomes.ConclusionsSES (annual household income, educational attainment or neighborhood deprivation) was associated not only with ESRD risk but also with eGFR decline, although the association with CKD appeared weaker.
BGEN: a binary file format for imputed genotype and haplotype data
Authors: Band Gavin , Marchini Jonathan 
Published: April 2018

ABSTRACTThe impact of modern technology on genetic epidemiology has been significant, with studies comprising millions of individuals assessed at tens of millions of genetic variants now becoming common. Studies on this scale provide logistical and analytic challenges starting with the issue of efficiently storing, transmitting, and accessing underlying data. Here we present a binary file format (the BGEN format) that can store both directly-typed and statistically imputed genotype data, and achieves substantial space savings by data compression and the use of an efficient representation for probabilities. We investigate the properties of this format using imputed data from the UK BiLEVE study, demonstrating both storage efficiency, and fast data loading performance on the order of hundreds of millions of imputed genotypes per second. To make using BGEN as easy as possible, we provide a detailed specification and a freely available reference implementation, and we leverage this by developing additional tools including an indexing tool (bgenix) and an R package (rbgen) that permits loading of BGEN-encoded data into the R statistical programming environment. The UK Biobank is one of a number of projects that have used BGEN for release of imputed data, and we expect the format to continue to be widely implemented and used.
A novel multi-perspective imaging platform (M-PIP) for phenotyping soybean root crowns in the field increases throughput and separation ability of genotype root properties
Authors: Seethepalli Anand , York Larry M. , Almtarfi Hussien , Fritschi Felix B. , Zare Alina 
Published: May 2018

AbstractBackgroundRoot crown phenotyping has linked root properties to shoot mass, nutrient uptake, and yield in the field, which increases the understanding of soil resource acquisition and presents opportunities for breeding. The original methods using manual measurements have been largely supplanted by image-based approaches. However, most image-based systems have been limited to one or two perspectives and rely on segmentation from grayscale images. An efficient high-throughput root crown phenotyping system is introduced that takes images from five perspectives simultaneously, constituting the Multi-Perspective Imaging Platform (M-PIP). A segmentation procedure using the Expectation-Maximization Gaussian Mixture Model (EM-GMM) algorithm was developed to distinguish plant root pixels from background pixels in color images and using hardware acceleration (CPU and GPU). Phenes were extracted using MatLab scripts. Placement of excavated root crowns for image acquisition was standardized and is ergonomic. The M-PIP was tested on 24 soybean [Glycine max (L.) Merr.] cultivars released between 1930 and 2005.ResultsRelative to previous reports of imaging throughput, this system provides greater throughput with sustained rates of 1.66 root crowns min-1. The EM-GMM segmentation algorithm with hardware acceleration was able to segment images in 10 s, faster than previous methods, and the output images were consistently better connected with less loss of fine detail. Image-based phenes had similar heritabilities as manual measures with the greatest effect sizes observed for Maximum Radius and Fine Radius Frequency. Correlations were also noted, especially among the manual Complexity score and phenes such as number of roots and Total Root Length. Averaging phenes across perspectives generally increased heritability, and no single perspective consistently performed better than others. Angle-based phenes, Fineness Index, Maximum Width, Holes, Solidity and Width-to-Depth Ratio were the most sensitive to perspective with decreased correlations among perspectives.ConclusionThe substantial heritabilities measured for many phenes suggest that they are potentially useful for breeding. Multiple perspectives together often produced the greatest heritabilities, and no single perspective consistently performed better than others. Thus, as illustrated here for soybean, multiple perspectives may be beneficial for root crown phenotyping systems. This system can contribute to breeding efforts that incorporate under-utilized root phenotypes to increase food security and sustainability.
Identifying high-priority proteins across the human diseasome using semantic similarity
Authors: Lau Edward , Venkatraman Vidya , Thomas Cody T , Van Eyk Jennifer E , Lam Maggie PY 
Published: April 2018

AbstractKnowledge of “popular proteins” has been a focus of multiple Human Proteome Organization (HUPO) initiatives and can guide the development of proteomics assays targeting important disease pathways. We report here an updated method to identify prioritized protein lists from the research literature, and apply it to catalog lists of important proteins across multiple cell types, sub-anatomical regions, and disease phenotypes of interest. We provide a systematic collection of popular proteins across 10,129 human diseases as defined by the Disease Ontology, 10,642 disease phenotypes defined by Human Phenotype Ontology, and 2,370 cellular pathways defined by Pathway Ontology. This strategy allows instant retrieval of popular proteins across the human “diseasome”, and further allows reverse queries from protein to disease, enabling functional analysis of experimental protein lists using bibliometric annotations.