bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops
Authors: Cao Ke , Zheng Zhijun , Wang Lirong , Liu Xin , Zhu Gengrui , Fang Weichao , Cheng Shifeng , Zeng Peng , Chen Changwen , Wang Xinwei , Xie Min , Zhong Xiao , Wang Xiaoli , Zhao Pei , Bian Chao , Zhu Yinling , Zhang Jiahui , Ma Guosheng , Chen Chengxuan , Li Yanjun , Hao Fengge , Li Yong , Huang Guodong , Li Yuxiang , Li Haiyan , Guo Jian , Xu Xun , Wang Jun 
Published: July 2014

Abstract
Background
Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution.

Results
We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis.
We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.

Conclusions
Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.
DawnRank: discovering personalized driver genes in cancer
Authors: Hou Jack P , Ma Jian 
Published: July 2014

AbstractLarge-scale cancer genomic studies have revealed that the genetic heterogeneity of the same type of cancer is greater than previously thought. A key question in cancer genomics is the identification of driver genes. Although existing methods have identified many common drivers, it remains challenging to predict personalized drivers to assess rare and even patient-specific mutations. We developed a new algorithm called DawnRank to directly prioritize altered genes on a single patient level. Applications to TCGA datasets demonstrated the effectiveness of our method. We believe DawnRank complements existing driver identification methods and will help us discover personalized causal mutations that would otherwise be obscured by tumor heterogeneity. Source code can be accessed at http://bioen-compbio.bioen.illinois.edu/DawnRank/.
Epigenetics of discordant monozygotic twins: implications for disease
Authors: Castillo-Fernandez Juan E , Spector Tim D , Bell Jordana T 
Published: July 2014

AbstractMonozygotic (MZ) twins share nearly all of their genetic variants and many similar environments before and after birth. However, they can also show phenotypic discordance for a wide range of traits. Differences at the epigenetic level may account for such discordances. It is well established that epigenetic states can contribute to phenotypic variation, including disease. Epigenetic states are dynamic and potentially reversible marks involved in gene regulation, which can be influenced by genetics, environment, and stochastic events. Here, we review advances in epigenetic studies of discordant MZ twins, focusing on disease. The study of epigenetics and disease using discordant MZ twins offers the opportunity to control for many potential confounders encountered in general population studies, such as differences in genetic background, early-life environmental exposure, age, gender, and cohort effects. Recently, analysis of disease-discordant MZ twins has been successfully used to study epigenetic mechanisms in aging, cancer, autoimmune disease, psychiatric, neurological, and multiple other traits. Epigenetic aberrations have been found in a range of phenotypes, and challenges have been identified, including sampling time, tissue specificity, validation, and replication. The results have relevance for personalized medicine approaches, including the identification of prognostic, diagnostic, and therapeutic targets. The findings also help to identify epigenetic markers of environmental risk and molecular mechanisms involved in disease and disease progression, which have implications both for understanding disease and for future medical research.
Equine mesenchymal stromal cells and embryo-derived stem cells are immune privileged in vitro
Authors: Paterson Yasmin Z , Rash Nicola , Garvican Elaine R , Paillot Romain , Guest Deborah J 
Published: July 2014

Abstract
Introduction
Autologous mesenchymal stem cells (MSCs) are an attractive concept in regenerative medicine, but their mechanism of action remains poorly defined. No immune response is reported after in vivo injection of allogeneic equine MSCs or embryo-derived stem cells (ESCs) into the equine tendon, which may be due to the cells’ immune-privileged properties. This study further investigates these properties to determine their potential for clinical application in other tissues.

Methods
Mitomycin C-treated MSCs, ESCs, or differentiated ESCs (dESCs) were cultured with allogeneic equine peripheral blood mononuclear cells (PBMCs), and their effect on PBMC proliferation, in the presence or absence of interferon-gamma (IFN-γ) was determined. MSCs and super-antigen (sAg)-stimulated PBMCs were co-cultured directly or indirectly in transwells, and PBMC proliferation examined. Media from MSC culture were harvested and used for PBMC culture; subsequent PBMC proliferation and gene expression were evaluated and media assayed for IFN-γ, tumor necrosis factor alpha (TNF-α), and interleukin (IL)-10 and IL-6 proteins with enzyme-linked immunosorbent assay (ELISA).

Results
Co-culture of PBMCs with ESCs or dESCs did not affect baseline proliferation, whereas co-culture with MSCs significantly suppressed baseline proliferation. Stimulation of PBMC proliferation by using super-antigens (sAgs) was also suppressed by co-culture with MSCs. Inhibition was greatest with direct contact, but significant inhibition was produced in transwell culture and by using MSC-conditioned media, suggesting that soluble factors play a role in MSC-mediated immune suppression. The MSCs constitutively secrete IL-6, even in the absence of co-culture with PBMCs. MSC-conditioned media also brought about a change in the cytokine-expression profile of sAg-stimulated PBMCs, significantly reducing PBMC expression of IL-6, IFN-γ, and TNF-α.

Conclusions
Equine MSCs and ESCs possess a degree of innate immune privilege, and MSCs secrete soluble factors that suppress PBMC proliferation and alter cytokine expression. These properties may make possible the future clinical use of allogeneic stem cells to help standardize and broaden the scope of treatment of tissue injuries.
Epigenetic Regulation of Uterine Biology by Transcription Factor KLF11 via Posttranslational Histone Deacetylation of Cytochrome p450 Metabolic Enzymes
Authors: Zheng Ye , Tabbaa Zaid M. , Khan Zaraq , Schoolmeester John K. , El-Nashar Sherif , Famuyide Abimbola , Keeney Gary L. , Daftary Gaurang S. 
Published: July 2014

AbstractEndocrine regulation of uterine biology is critical for embryo receptivity and human reproduction. Uterine endometrium depends on extrinsic sex steroid input and hence likely has mechanisms that enable adaptation to hormonal variation. Emerging evidence suggests that sex steroid bioavailability in the endometrium is determined by adjusting their metabolic rate and fate via regulation of cytochrome (CYP) p450 enzymes. The CYP enzymes are targeted by ubiquitously expressed Sp/Krüppel-like (Sp/KLF) transcription factors. Specifically, KLF11 is highly expressed in reproductive tissues, regulates an array of endocrine/metabolic pathways via epigenetic histone-based mechanisms and, when aberrantly expressed, is associated with diabetes and reproductive tract diseases, such as leiomyoma and endometriosis. Using KLF11 as a model to investigate epigenetic regulation of endometrial first-pass metabolism, we evaluated the expression of a comprehensive array of metabolic enzymes in Ishikawa cells. KLF11 repressed most endometrial CYP enzymes. To characterize KLF11-recruited epigenetic regulatory mechanisms, we focused on the estrogen-metabolizing enzyme CYP3A4. KLF11 expression declined in secretory phase endometrial epithelium associated with increased CYP3A4 expression. Additionally, KLF11 bound to CYP3A4 promoter GC elements and thereby repressed promoter, message, protein as well as enzymatic function. This repression was epigenetically mediated, because KLF11 colocalized with and recruited the corepressor SIN3A/histone deacetylase resulting in selective deacetylation of the CYP3A4 promoter. Repression was reversed by a mutation in KLF11 that abrogated cofactor recruitment and binding. This repression was also pharmacologically reversible with an histone deacetylase inhibitor. Pharmacological alteration of endometrial metabolism could have long-term translational implications on human reproduction and uterine disease.
Phagosome maturation during endosome interaction revealed by partial rhodopsin processing in retinal pigment epithelium
Authors: Wavre-Shapton Silène T. , Meschede Ingrid P. , Seabra Miguel C. , Futter Clare E. 
Published: July 2014

Defects in phagocytosis and degradation of photoreceptor outer segments (POS) by the retinal pigment epithelium (RPE) are associated with aging and retinal disease.
The daily burst of rod outer segment (ROS) phagocytosis by the RPE provides a unique opportunity to analyse phagosome processing in vivo. In mouse retinae phagosomes containing stacked rhodopsin-rich discs were identified by immuno-electron microscopy. Early apical phagosomes stained with both cytoplasmic and intradiscal domain rhodopsin antibodies. During phagosome maturation a remarkably synchronised loss of the cytoplasmic epitope coincided with movement to the cell body and preceded phagosome:lysosome fusion and disc degradation. Loss of the intradiscal rhodopsin epitope and disc digestion occurred upon fusion with cathepsin D-positive lysosomes. The same sequential stages of phagosome maturation were identified in cultured RPE and macrophages challenged with isolated POS. Loss of the cytoplasmic rhodopsin epitope was insensitive to pH but sensitive to protease inhibition and co-incided with interaction of phagosomes with endosomes. Thus, during prelysosomal maturation of ROS-containing phagosomes limited rhodopsin processing occurs upon interaction with endosomes. This potentially provides a sensitive readout of phagosome:endosome interactions applicable to multiple phagocytes.
dendsort: modular leaf ordering methods for dendrogram representations in R
Authors: Sakai Ryo , Winand Raf , Verbeiren Toni , Moere Andrew Vande , Aerts Jan 
Published: July 2014

Dendrograms are graphical representations of binary tree structures resulting from agglomerative hierarchical clustering. In Life Science, a cluster heat map is a widely accepted visualization technique that utilizes the leaf order of a dendrogram to reorder the rows and columns of the data table. The derived linear order is more meaningful than a random order, because it groups similar items together. However, two consecutive items can be quite dissimilar despite proximity in the order. In addition, there are 2n-1 possible orderings given n input elements as the orientation of clusters at each merge can be flipped without affecting the hierarchical structure. We present two modular leaf ordering methods to encode both the monotonic order in which clusters are merged and the nested cluster relationships more faithfully in the resulting dendrogram structure. We compare dendrogram and cluster heat map visualizations created using our heuristics to the default heuristic in R and seriation-based leaf ordering methods. We find that our methods lead to a dendrogram structure with global patterns that are easier to interpret, more legible given a limited display space, and more insightful for some cases. The implementation of methods is available as an R package, named ”dendsort”, from the CRAN package repository. Further examples, documentations, and the source code are available at [https://bitbucket.org/biovizleuven/dendsort/].
A clinically novel AIP mutation in a patient with a very large, apparently sporadic somatotrope adenoma
Authors: Salvatori Roberto , Daly Adrian F , Quinones-Hinojosa Alfredo , Thiry Albert , Beckers Albert 
Published: July 2014

Summary
Heterozygous germline inactivating mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene lead to pituitary adenomas that most frequently present in the setting of familial isolated pituitary adenoma syndrome, usually as somatotropinomas and prolactinomas. More recently, they have been found in a significant percentage of young patients presenting with pituitary macroadenoma without any apparent family history. We describe the case of a 19-year-old man who presented with a gigantic somatotropinoma. His family history was negative. His peripheral DNA showed a heterozygous AIP mutation (p.I13N), while tumor tissue only had the mutated allele, showing loss of heterozygosity (LOH) and suggesting that the mutation caused the disease.

Learning points

AIP mutations may be observed in sporadic somatotrope adenomas occurring in young patients.

LOH is a strong indicator that an AIP variant is disease causing.

Somatotrope adenomas in carriers of AIP mutations are generally larger and more difficult to cure.
Improvement on Mechanical Properties of a Particle Board Made of Recycled Material Based on Tetra Brik®
Authors: Carrillo J.G. , Ventura D.A. Pool , Gamboa R.A. , Cruz-Estrada R.H. 
Published: July 2014

ABSTRACTThe topic of Urban Solid Waste (USW) has become increasingly controversial in our times due to the high volumes being produced and not disposed properly; one effective way to reduce the generation of USW is finding new ways to recycling. This study proposes a means of recycling Tetra Brik® (TBr) cartons and high density polyethylene recycled containers (HDPEr), by generating an agglomerate with optimal mechanical properties in comparison with other TBr-based agglomerates. For the analysis of this material’s mechanical properties, two types of evaluation tests are carried out; flexure and screw pull-out test. Results show significant mechanical advantages over other TBr-based laminates by the integration of an HDPEr matrix to the system, thereby improving mechanical properties.
Influence of the Reprocessing by Plasma Melting and Injection Molding on the Thermomechanical Properties of a Ni-Ti SMA Manufactured by VIM
Authors: Brito Simões Jackson de , Roberto Pereira Francisco Fernando , Otubo Jorge , de Araújo Carlos José 
Published: July 2014

ABSTRACTShape Memory Alloys (SMA) metallic materials that change their mechanical and physical properties with temperature variation and mechanical loading, surprising engineers and researchers. In this way, one can develop thermomechanical actuators capable, for example, of generating force by blocking the shape recovery or change the natural frequency of a mechanical system by blocking resonance. The processing of these SMA are countless, each one with its specific limitation and particularity. This study aims to evaluate the influence of rapid solidification of a Ni-Ti SMA that is originally manufactured by Vacuum Induction Melting (VIM) and reprocessed by Plasma Melting (PM) followed by injection molding into different metal molds (steel, brass, aluminum and copper). The influence of such a processing is analyzed through Differential Scanning Calorimetry (DSC) and Electrical Resistance as a function of Temperature (ERT) to determine the effects on transformation temperatures. The results demonstrate that by using the copper mold one can provide greater uniformity of the material properties. Thus, there is the possibility of obtaining different kinds of SMA mini-actuators by PM injection in a copper mold and that includes different shapes and sizes that can be studied further.
Mathematical modeling of aluminum degassing by the impeller injector technique validated by a physical modeling
Authors: Hernández-Hernández M. , Cruz-Mendez W. F. , Gonzalez-Rivera C. , Ramírez-Argáez M. A. 
Published: July 2014

ABSTRACTA mathematical model is developed to describe deoxidation of water in a physical model of a batch aluminum degassing reactor equipped with the rotor-injector technique, assuming that deoxidation kinetics of water is similar to dehydrogenization of liquid aluminum. Degassing kinetics is described by using mass transport and mass balance principles by assuming that degassing kinetics can be characterized by a mass transfer coefficient, which depends on the process variables. The transport coefficient and the average bubble diameter are estimated with correlations reported in the literature for similar gas-injection systems. The water physical model helped to validate the mathematical model and to perform a process analysis by varying: 1) Gas flow rate (20 and 40 l/min); and 2) Impeller’s angular velocity (290 and 573 rpm). Results from the model agree well with measurements of deoxidation kinetics at low impeller rotating speeds. At high rotating speeds the model is still valid but less reliable because it does not take into account the formation of the vortex at the free surface. Nevertheless, the model provides predictions of the influence of every operating parameter and it can be used as a good approximation for real systems.
The Effect of Silica Polymerization in Fly Ash on the Strength of Geopolymers
Authors: Koshukhova N. , Zhernovsky I. , Sobolev K. 
Published: July 2014

ABSTRACTThe formation of the structure of geopolymer binders based on low-calcium fly ash is a multifactorial process that depends on the degree of solubility of aluminosilicate components in the solution of alkali activator. It is observed that the geopolymer binders based on fly ash with an identical chemical and mineral composition, the same grain size, and also activated by the same alkalis can result in a different strength.This study is based on the assumption that there is dependence between the solubility of aluminosilicate components and the degree of polymerization of the silicates in glass phase. The degree of SiO2-polymerization is an integral parameter that is equal to the Si molar ratio (fSi) of the silicate component in the glass phase of fly ash. The degree of SiO2-polymerization can be estimated from the molar composition of glass phase, which is determined from the chemical composition and quantitative X-ray diffraction analysis including identification of the amorphous phase composition.The SiO2 polymerization rates of investigated fly ash specimens are confirmed by the IR results, specifically, by comparison of absorption bands of silicate fragments with varying levels of connectivity (Q0-4) in the range of wave numbers of 650–1350 cm-1.The comparative analysis of the correlation of 28-day strength of geopolymer binders based on fly ash from different sources and level of SiO2-polymerization demonstrated an inverse relationship with fSi molar ratio and compressive strength.
New Alumosilicate Fillers Based on Sedimentary Rocks for Asphalt Concrete
Authors: Strokova Valeria , Lebedev Mikhail , Potapova Irina , Sobolev Konstantin 
Published: July 2014

ABSTRACTAsphalt concrete is the most common material for highway and motorway construction. The quality of asphalt is determined, to a large extent, by properties of asphalt binder. Fillers, which are mineral powders from carbonate rocks and aggregates fines, such as limestone and dolomite, are often used in the composition of bitumen mastics affecting the performance of asphalt.This article explores the feasibility of using the fines of aluminosilicate sedimentary rocks as fillers. These materials are composed of clay minerals, which change their properties upon the contact with water. Normally, the use of such fillers is restricted because of poor water resistance and swelling of asphalt concrete. In order to improve the performance of these fillers, the thermal modification at moderate temperatures of 500–600 °C has been proposed. Such treatment provides sufficient structural stability of obtained materials and results in the reduction of water absorption of asphalt, improved water resistance (up to 2.5 times) and also, in reduced swelling (up to 9 times).It has been demonstrated that improvement in the filler performance can be achieved by a heat treatment. Such treatment induces changes in the mineral composition and converts the structure of clay minerals into the frame structure of zeolite, as confirmed by X-ray diffraction and infrared spectroscopy. Due to thermal treatment, there is a change in the acid-base properties of the surface of the filler, which is reflected in the profiles of the main adsorption centers. As a result, due to chemisorption, the modified aluminosilicate fillers are able to interact with bitumen. The application of new filler materials in asphalt concrete enables to enhance the performance.
Characterization and Utilization of Coconut Fibers of the Caribbean
Authors: Mathura Nadira , Cree Duncan , Mulligan Ryan P. 
Published: July 2014

ABSTRACTIn many tropical countries coconut (coir) fiber production is a major source of income for rural communities. The Caribbean has an abundance of coconuts but research into utilizing its by-products is limited. Environmentally friendly coir fibers are natural polymers generally discarded as waste material in this region. Research has shown that coir fiber from other parts of the world has successfully been recycled. This paper therefore investigates the mechanical properties of Caribbean coir fiber for potential applications in civil engineering.Approximately four hundred fibers were randomly taken from a coir fiber stack and subjected to retting in both distilled and saline water media. The mechanical properties of both the retted and unretted coir fibers were evaluated at weekly increments for a period of 3 months. Tensile strength test, x-ray diffraction analysis and scanning electron micrographs were used to assess trends and relationships between fiber gauge lengths, diameter, tensile strength and Young’s modulus. Diameters ranged between 0.11 mm-0.46 mm, while fiber samples were no longer than 250 mm in length. The tensile strength and strain at break decreased as the gauge length increased for both unretted and retted fibers. The opposite occurred for the relationship between the gauge length and Young’s modulus. Additionally, the tensile strength and modulus decreased as the fiber diameter increased. Neither distilled nor saline water improved the coir fiber’s crystalline index. Scanning electron micrographs qualitatively assessed fiber surfaces and captured necking and microfibril degradation at the fractured ends.The analysis revealed that the tensile strength, modulus, strain at break and crystallinity properties of the Caribbean coir fibers were comparable to commercially available coir fiber which are currently being used in many building applications.