bluuebunny/crossref_metadata_2025_split huggingface dataset:
New assessment based on the use of principal factor analysis to investigate corn silage quality from nutritional traits, fermentation end products and mycotoxins
Authors: Gallo Antonio , Bertuzzi Terenzio , Giuberti Gianluca , Moschini Maurizio , Bruschi Sara , Cerioli Carla , Masoero Francesco 
Published: January 2015

AbstractBACKGROUNDA survey on 68 dairy farms was carried out to evaluate the ensiling procedures adopted to store corn silage. Samples from core, lateral and apical zones of the feed‐out face of silos were analysed. A principal factor analysis (PFA) was carried out on the entire database (196 silage samples and 36 variables) and 11 principal factor components (PCs) were retained and interpreted.RESULTSEnsiling procedures influenced the area exposed to risk of air penetration. Cores had higher dry matter, starch and lactic acid content or lower pH, fibre, propionate and butyrate concentrations than peripheral samples (P < 0.05). The highest (P < 0.05) mycophenolic acid and roquefortina C concentrations were detected in lateral samples. Chemical and digestibility variables loaded on two PCs; four PCs were characterized by end‐products associated with clostridia, heterolactic, homolactic and aerobic fermentations; two PCs were associated with mycotoxins, whereas three PCs explained ensiling procedures.CONCLUSIONThe main quality traits of corn silages differed throughout the entire silo face. Minimization of the area exposed to risk of air penetration represents the best strategy to preserve the nutritional value and safety of corn silages. PFA allowed a clusterization of original variables into 11 PCs, appearing able to discriminate well and poorly preserved corn silages. © 2015 Society of Chemical Industry
The differentiation of tuna (family: Scombridae) products through the PCR‐based analysis of the cytochrome b gene and parvalbumin introns
Authors: Abdullah Asadatun , Rehbein Hartmut 
Published: January 2015

AbstractBACKGROUNDIn spite of the many studies performed over the years, there are still problems in the authentication of closely related tuna species, not only for canned fish but also for raw products. With the aim of providing screening methods to identify different tuna species and related scombrids, segments of mitochondrial cytochrome b (cyt b) and nuclear parvalbumin genes were amplified and sequenced or subjected to single‐strand conformation polymorphism (SSCP) and restriction fragment length polymorphism (RFLP) analyses.RESULTSThe nucleotide diagnostic sites in the cyt b gene of five tuna species from Indonesia were determined in this study and used to construct a phylogenetic tree. In addition, the suitability of the nuclear gene that encodes parvalbumin for the differentiation of tuna species was determined by SSCP and RFLP analyses of an intron segment. RFLP differentiated Thunnus albacares and from T. obesus, and fish species in the Thunnus genus could be distinguished from bullet tuna (Auxis rochei) by SSCP.CONCLUSIONSParvalbumin‐based polymerase chain reaction systems could serve as an additional tool in the detection and identification of tuna and other Scombridae fish species for routine seafood control. This reaction can be performed in addition to the cyt b analysis as previously described. © 2015 Society of Chemical Industry
The effect of oat β‐glucan on in vitro glucose diffusion and glucose transport in rat small intestine
Authors: Zhang Yu , Zhang Hui , Wang Li , Qian Haifeng , Qi Xiguang , Ding Xiangli , Hu Bo , Li Jiajia 
Published: January 2015

AbstractBACKGROUNDMany previous studies have reported the role of oat β‐glucan (OBG) in the reduction of postprandial glucose, and hypothesised that OBG may form a protective layer along the intestinal wall, acting as a viscous barrier to decrease glucose transportation. This study examined whether the molecular weight (MW) and concentration of OBG affected the diffusion of glucose in vitro. The effect of OBG on glucose transportation in vitro and sodium–potassium adenosine triphosphatase (Na+/K+‐ATPase) activity in the everted small intestines of normal rats was also examined.RESULTSIn vitro, higher MWs and concentrations of OBG increased the inhibitory effects on glucose diffusion and glucose adsorption. The transport of glucose by glucose transporters and Na+/K+‐ATPase activity in the small intestinal mucosa of rats were significantly lower following the addition of OBG than those in the absence of OBG at the same time‐points throughout glucose transportation (P < 0.05). In the OBG‐treated group, the Na+/K+‐ATPase activity decreased with increasing OBG MW. However, as the concentration of OBG in the solution increased, the Na+/K+‐ATPase activity in the small intestine increased due to stronger gastrointestinal motility. We also found that higher MWs of OBG had a greater inhibitory effect on intestinal disaccharidase activities in vitro.CONCLUSIONOat β‐glucan is able to adsorb glucose molecules, inhibit glucose transport, decrease the concentration of available glucose and suppress disaccharidase activities in the small intestine. © 2015 Society of Chemical Industry
Omega‐3 fatty acids protect from diet‐induced obesity, glucose intolerance, and adipose tissue inflammation through PPARγ‐dependent and PPARγ‐independent actions
Authors: Belchior Thiago , Paschoal Vivian A. , Magdalon Juliana , Chimin Patricia , Farias Talita M. , Chaves‐Filho Adriano B. , Gorjão Renata , St.‐Pierre Philippe , Miyamoto Sayuri , Kang Jing X. , Deshaies Yves , Marette André , Festuccia William 
Published: January 2015

ScopeWe tested herein the hypothesis that peroxisome proliferator activated receptor γ (PPARγ) is a major mediator of omega‐3 (n‐3) protective actions against high‐fat diet (HFD) induced obesity, glucose intolerance, and adipose tissue inflammation.Methods and resultsC57BL6 wild‐type and fat‐1 transgenic (fat‐1) mice were fed a low‐fat diet (LFD) or HFD, treated or not with PPARγ antagonist, and evaluated for energy balance, adiposity, glucose tolerance, and adipose tissue inflammation. Fat‐1 mice were protected from obesity, fasting hyperglycemia, glucose intolerance, and adipose tissue inflammation. PPARγ inhibition completely abolished fat‐1 protection against HFD‐induced glucose intolerance, but not obesity or adipose tissue inflammation. To investigate the role of myeloid cell as mediator of n‐3 beneficial metabolic actions, mice with deletion (LyzM‐PPARγKO) or nondeletion (LyzM‐PPARγWT) of PPARγ in myeloid cells were fed either LFD or HFD (lard) or an HFD rich in n‐3 (fish oil). Our findings indicate that myeloid cell associated PPARγ is not involved in the attenuation of HFD‐induced glucose intolerance and adipose tissue inflammation induced by n‐3.ConclusionHigh endogenous n‐3 fatty acid levels protect from HFD obesity, glucose intolerance, and adipose tissue inflammation. Among these, only protection against glucose intolerance is mediated by non‐myeloid cell PPARγ.
Automated analysis of hip joint cartilage combining MR T2 and three‐dimensional fast‐spin‐echo images
Authors: Chandra Shekhar S. , Surowiec Rachel , Ho Charles , Xia Ying , Engstrom Craig , Crozier Stuart , Fripp Jurgen 
Published: January 2015

PurposeTo validate a fully automated scheme to extract biochemical information from the hip joint cartilages using MR T2 mapping images incorporating segmentation of co‐registered three‐dimensional Fast‐Spin‐Echo (3D‐SPACE) images.MethodsManual analyses of unilateral hip (3 Tesla) MR images of 24 asymptomatic volunteers were used to validate a 3D deformable model method for automated cartilage segmentation of SPACE scans, partitioning of the individual femoral and acetabular cartilage plates into clinically defined sub‐regions and propagating these results to T2 maps to calculate region‐wise T2 value statistics. Analyses were completed on a desktop computer (∼10 min per case).ResultsThe mean voxel overlap between automated A and manual M segmentations of the cartilage volumes in the (clinically based) SPACE images was 73%
. The automated and manual analyses demonstrated a relative difference error <10% in the median “T2 average signal” for each cartilage plate. The automated and manual analyses showed consistent patterns between significant differences in T2 data across the hip cartilage sub‐regions.ConclusionThe good agreement between the manual and automatic analyses of T2 values indicates the use of structural 3D‐SPACE MR images with the proposed method provides a promising approach for automated quantitative T2 assessment of hip joint cartilages. Magn Reson Med 75:403–413, 2016. © 2015 Wiley Periodicals, Inc.
Molecular insights into the binding of coenzyme F420 to the conserved protein Rv1155 from Mycobacterium tuberculosis
Authors: Mashalidis Ellene H. , Gittis Apostolos G. , Tomczak Aurelie , Abell Chris , Barry Clifton E. , Garboczi David N. 
Published: January 2015

AbstractCoenzyme F420 is a deazaflavin hydride carrier with a lower reduction potential than most flavins. In Mycobacterium tuberculosis (Mtb), F420 plays an important role in activating PA‐824, an antituberculosis drug currently used in clinical trials. Although F420 is important to Mtb redox metabolism, little is known about the enzymes that bind F420 and the reactions that they catalyze. We have identified a novel F420‐binding protein, Rv1155, which is annotated in the Mtb genome sequence as a putative flavin mononucleotide (FMN)‐binding protein. Using biophysical techniques, we have demonstrated that instead of binding FMN or other flavins, Rv1155 binds coenzyme F420. The crystal structure of the complex of Rv1155 and F420 reveals one F420 molecule bound to each monomer of the Rv1155 dimer. Structural, biophysical, and bioinformatic analyses of the Rv1155–F420 complex provide clues about its role in the bacterium.
Evaluation of a model community‐wide bed bug management program in affordable housing
Authors: Cooper Richard A , Wang Changlu , Singh Narinderpal 
Published: January 2015

AbstractBACKGROUNDLow‐income apartment communities in the United States are suffering from disproportionally high bed bug, Cimex lectularius L., infestations owing to lack of effective monitoring and treatment. Studies examining the effectiveness of integrated pest management (IPM) for the control of bed bugs in affordable housing have been limited to small subsets of bed‐bug‐infested apartments, rather than at the apartment community level. We developed, implemented and evaluated a complex‐wide IPM program for bed bugs in an affordable housing community. Proactive inspections and biweekly treatments using a combination of non‐chemical and chemical methods until bed bugs were not detected for three biweekly monitoring visits were key elements of the IPM program.RESULTSA total of 55 bed‐bug‐infested apartments were identified during the initial inspection. Property management was unaware of 71% of these infestations. Over the next 12 months, 14 additional infested apartments were identified. The IPM program resulted in a 98% reduction in bed bug counts among treated apartments and reduced infestation rates from 15 to 2.2% after 12 months.CONCLUSIONSAdopting a complex‐wide bed bug IPM program, incorporating proactive monitoring, and biweekly treatments of infested apartments utilizing non‐chemical and chemical methods can successfully reduce infestation rates to very low levels. © 2015 Society of Chemical Industry
miR-135a Inhibits Cancer Stem Cell-Driven Medulloblastoma Development by Directly Repressing Arhgef6 Expression
Authors: Hemmesi Katayoun , Squadrito Mario Leonardo , Mestdagh Pieter , Conti Valentina , Cominelli Manuela , Piras Ignazio S. , Sergi Lucia Sergi , Piccinin Sara , Maestro Roberta , Poliani Pietro L. , Speleman Frank , De Palma Michele , Galli Rossella 
Published: January 2015

Abstract
microRNAs (miRNAs) are short noncoding RNAs, which regulate gene expression post-transcriptionally and play crucial roles in relevant biological and pathological processes. Here, we investigated the putative role of miRNAs in modulating the tumor-initiating potential of mouse medulloblastoma (MB)-derived cancer stem cells (CSCs). We first subjected bona fide highly tumorigenic (HT) CSCs as well as lowly tumorigenic MB CSCs and normal neural stem cells to miRNA profiling, which identified a HT CSC-specific miRNA signature. Next, by cross-checking CSC mRNA/miRNA profiles, we pinpointed miR-135a as a potential tumor suppressor gene, which was strongly downregulated in HT CSCs as well as in the highly malignant experimental tumors derived from them. Remarkably, enforced expression of miR-135a in HT CSCs strongly inhibited tumorigenesis by repressing the miR-135a direct target gene Arhgef6. Considering the upregulation of Arhgef6 in human MBs and its involvement in mediating experimental medulloblastomagenesis, its efficient suppression by miR-135a might make available an effective therapeutic strategy to selectively impair the tumorigenic potential of MB CSCs. Stem Cells 2015;33:1377–1389
Perturbations of Heart Development and Function in Cardiomyocytes from Human Embryonic Stem Cells with Trisomy 21
Authors: Bosman Alexis , Letourneau Audrey , Sartiani Laura , Del Lungo Martina , Ronzoni Flavio , Kuziakiv Rostyslav , Tohonen Virpi , Zucchelli Marco , Santoni Federico , Guipponi Michel , Dumevska Biljana , Hovatta Outi , Antonarakis Stylianos E. , Jaconi Marisa E. 
Published: January 2015

Abstract
Congenital heart defects (CHD) occur in approximately 50% of patients with Down syndrome (DS); the mechanisms for this occurrence however remain unknown. In order to understand how these defects evolve in early development in DS, we focused on the earliest stages of cardiogenesis to ascertain perturbations in development leading to CHD. Using a trisomy 21 (T21) sibling human embryonic stem cell (hESC) model of DS, we show that T21-hESC display many significant differences in expression of genes and cell populations associated with mesodermal, and more notably, secondary heart field (SHF) development, in particular a reduced number of ISL1+ progenitor cells. Furthermore, we provide evidence for two candidate genes located on chromosome 21, ETS2 and ERG, whose overexpression during cardiac commitment likely account for the disruption of SHF development, as revealed by downregulation or overexpression experiments. Additionally, we uncover an abnormal electrophysiological phenotype in functional T21 cardiomyocytes, a result further supported by mRNA expression data acquired using RNA-Seq. These data, in combination, revealed a cardiomyocyte-specific phenotype in T21 cardiomyocytes, likely due to the overexpression of genes such as RYR2, NCX, and L-type Ca2+ channel. These results contribute to the understanding of the mechanisms involved in the development of CHD. Stem Cells 2015;33:1434–1446
Enhanced SMAD1 Signaling Contributes to Impairments of Early Development in CFC-iPSCs
Authors: Han Kyu-Min , Kim Seung-Kyoon , Kim Dongkyu , Choi Jung-Yun , Im Ilkyun , Hwang Kyu-Seok , Kim Cheol-Hee , Lee Beom Hee , Yoo Han-Wook , Han Yong-Mahn 
Published: January 2015

Abstract
Cardio-facio-cutaneous (CFC) syndrome is a developmental disorder caused by constitutively active ERK signaling manifesting mainly from BRAF mutations. Little is known about the role of elevated ERK signaling in CFC syndrome during early development. Here, we show that both SMAD1 and ERK signaling pathways may contribute to the developmental defects in CFC syndrome. Induced pluripotent stem cells (iPSCs) derived from dermal fibroblasts of a CFC syndrome patient (CFC-iPSCs) revealed early developmental defects in embryoid body (EB) development, β-catenin localization, and neuronal differentiation. Both SMAD1 and ERK signalings were significantly activated in CFC-iPSCs during EB formation. Most of the β-catenin was dissociated from the membrane and preferentially localized into the nucleus in CFC-EBs. Furthermore, activation of SMAD1 signaling recapitulated early developmental defects in wild-type iPSCs. Intriguingly, inhibition of SMAD1 signaling in CFC-iPSCs rescued aberrant EB morphology, impaired neuronal differentiation, and altered β-catenin localization. These results suggest that SMAD1 signaling may be a key pathway contributing the pathogenesis of CFC syndrome during early development. Stem Cells 2015;33:1447–1455
Universal Cardiac Induction of Human Pluripotent Stem Cells in Two and Three-Dimensional Formats: Implications for In Vitro Maturation
Authors: Zhang Miao , Schulte Jan Sebastian , Heinick Alexander , Piccini Ilaria , Rao Jyoti , Quaranta Roberto , Zeuschner Dagmar , Malan Daniela , Kim Kee-Pyo , Röpke Albrecht , Sasse Philipp , Araúzo-Bravo Marcos , Seebohm Guiscard , Schöler Hans , Fabritz Larissa , Kirchhof Paulus , Müller Frank Ulrich , Greber Boris 
Published: January 2015

Abstract
Directed cardiac differentiation of human pluripotent stem cells (hPSCs) enables disease modeling, investigation of human cardiogenesis, as well as large-scale production of cardiomyocytes (CMs) for translational purposes. Multiple CM differentiation protocols have been developed to individually address specific requirements of these diverse applications, such as enhanced purity at a small scale or mass production at a larger scale. However, there is no universal high-efficiency procedure for generating CMs both in two-dimensional (2D) and three-dimensional (3D) culture formats, and undefined or complex media additives compromise functional analysis or cost-efficient upscaling. Using systematic combinatorial optimization, we have narrowed down the key requirements for efficient cardiac induction of hPSCs. This implied differentiation in simple serum and serum albumin-free basal media, mediated by a minimal set of signaling pathway manipulations at moderate factor concentrations. The method was applicable both to 2D and 3D culture formats as well as to independent hPSC lines. Global time-course gene expression analyses over extended time periods and in comparison with human heart tissue were used to monitor culture-induced maturation of the resulting CMs. This suggested that hPSC-CMs obtained with our procedure reach a rather stable transcriptomic state after approximately 4 weeks of culture. The underlying gene expression changes correlated well with a decline of immature characteristics as well as with a gain of structural and physiological maturation features within this time frame. These data link gene expression patterns of hPSC-CMs to functional readouts and thus define the cornerstones of culture-induced maturation. Stem Cells 2015;33:1456–1469
Chromatin Changes at thePPAR-γ2Promoter During Bone Marrow-Derived Multipotent Stromal Cell Culture Correlate With Loss of Gene Activation Potential
Authors: Lynch Patrick J. , Thompson Elaine E. , McGinnis Kathleen , Rovira Gonzalez Yazmin I. , Lo Surdo Jessica , Bauer Steven R. , Hursh Deborah A. 
Published: January 2015

AbstractBone marrow-derived multipotent stromal cells (BM-MSCs) display a broad range of therapeutically valuable properties, including the capacity to form skeletal tissues and dampen immune system responses. However, to use BM-MSCs in a clinical setting, amplification is required, which may introduce epigenetic changes that affect biological properties. Here we used chromatin immunoprecipitation to compare post-translationally modified histones at a subset of gene promoters associated with developmental and environmental plasticity in BM-MSCs from multiple donors following culture expansion. At many locations, we observed localization of both transcriptionally permissive (H3K4me3) and repressive (H3K27me3) histone modifications. These chromatin signatures were consistent among BM-MSCs from multiple donors. Since promoter activity depends on the relative levels of H3K4me3 and H3K27me3, we examined the ratio of H3K4me3 to H3K27me3 (K4/K27) at promoters during culture expansion. The H3K4me3 to H3K27me3 ratios were maintained at most assayed promoters over time. The exception was the adipose-tissue specific promoter for the PPAR-γ2 isoform of PPAR-γ, which is a critical positive regulator of adipogenesis. At PPAR-γ2, we observed a change in K4/K27 levels favoring the repressed chromatin state during culture. This change correlated with diminished promoter activity in late passage cells exposed to adipogenic stimuli. In contrast to BM-MSCs and osteoblasts, lineage-restricted preadipocytes exhibited levels of H3K4me3 and H3K27me3 that favored the permissive chromatin state at PPAR-γ2. These results demonstrate that locus-specific changes in H3K4me3 and H3K27me3 levels can occur during BM-MSC culture that may affect their properties. Stem Cells 2015;33:2169–2181
Gender, assets, and market-oriented agriculture: learning from high-value crop and livestock projects in Africa and Asia
Authors: Quisumbing Agnes R. , Rubin Deborah , Manfre Cristina , Waithanji Elizabeth , van den Bold Mara , Olney Deanna , Johnson Nancy , Meinzen-Dick Ruth 
Published: January 2015

Abstract
Strengthening the abilities of smallholder farmers in developing countries, particularly women farmers, to produce for both home and the market is currently a development priority. In many contexts, ownership of assets is strongly gendered, reflecting existing gender norms and limiting women’s ability to invest in more profitable livelihood strategies such as market-oriented agriculture. Yet the intersection between women’s asset endowments and their ability to participate in and benefit from agricultural interventions receives minimal attention. This paper explores changes in gender relations and women’s assets in four agricultural interventions that promoted high value agriculture with different degrees of market-orientation. Findings suggest that these dairy and horticulture projects can successfully involve women and increase production, income and the stock of household assets. In some cases, women were able to increase their control over production, income and assets; however in most cases men’s incomes increased more than women’s and the gender-asset gap did not decrease. Gender- and asset-based barriers to participation in projects as well as gender norms that limit women’s ability to accumulate and retain control over assets both contributed to the results. Comparing experiences across the four projects, especially where projects implemented adaptive measures to encourage gender-equitable outcomes, provides lessons for gender-responsive projects targeting existing and emerging value chains for high value products. Other targeted support to women farmers may also be needed to promote their acquisition of the physical assets required to expand production or enter other nodes of the value chain.