bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of immunoglobulin transcripts and hypermutation following SHIVAD8 infection and protein-plus-adjuvant immunization
Authors: Francica Joseph R. , Sheng Zizhang , Zhang Zhenhai , Nishimura Yoshiaki , Shingai Masashi , Ramesh Akshaya , Keele Brandon F. , Schmidt Stephen D. , Flynn Barbara J. , Darko Sam , Lynch Rebecca M. , Yamamoto Takuya , Matus-Nicodemos Rodrigo , Wolinsky David ,   NISC Comparative Sequencing Program, Barnabas Betty , Blakesley Robert , Bouffard Gerry , Brooks Shelise , Coleman Holly , Dekhtyar Mila , Gregory Michael , Guan Xiaobin , Gupta Jyoti , Han Joel , Ho Shi-ling , Legaspi Richelle , Maduro Quino , Masiello Cathy , Maskeri Baishali , McDowell Jenny , Montemayor Casandra , Mullikin James , Park Morgan , Riebow Nancy , Schandler Karen , Schmidt Brian , Sison Christina , Stantripop Mal , Thomas James , Thomas Pamela , Vemulapalli Meg , Young Alice , Nason Martha , Valiante Nicholas M. , Malyala Padma , De Gregorio Ennio , Barnett Susan W. , Singh Manmohan , O’Hagan Derek T. , Koup Richard A. , Mascola John R. , Martin Malcolm A. , Kepler Thomas B. , Douek Daniel C. , Shapiro Lawrence , Seder Robert A. 
Published: April 2015

AbstractDeveloping predictive animal models to assess how candidate vaccines and infection influence the ontogenies of Envelope (Env)-specific antibodies is critical for the development of an HIV vaccine. Here we use two nonhuman primate models to compare the roles of antigen persistence, diversity and innate immunity. We perform longitudinal analyses of HIV Env-specific B-cell receptor responses to SHIVAD8 infection and Env protein vaccination with eight different adjuvants. A subset of the SHIVAD8-infected animals with higher viral loads and greater Env diversity show increased neutralization associated with increasing somatic hypermutation (SHM) levels over time. The use of adjuvants results in increased ELISA titres but does not affect the mean SHM levels or CDR H3 lengths. Our study shows how the ontogeny of Env-specific B cells can be tracked, and provides insights into the requirements for developing neutralizing antibodies that should facilitate translation to human vaccine studies.
Regulation of autophagy and the ubiquitin–proteasome system by the FoxO transcriptional network during muscle atrophy
Authors: Milan Giulia , Romanello Vanina , Pescatore Francesca , Armani Andrea , Paik Ji-Hye , Frasson Laura , Seydel Anke , Zhao Jinghui , Abraham Reimar , Goldberg Alfred L. , Blaauw Bert , DePinho Ronald A. , Sandri Marco 
Published: April 2015

AbstractStresses like low nutrients, systemic inflammation, cancer or infections provoke a catabolic state characterized by enhanced muscle proteolysis and amino acid release to sustain liver gluconeogenesis and tissue protein synthesis. These conditions activate the family of Forkhead Box (Fox) O transcription factors. Here we report that muscle-specific deletion of FoxO members protects from muscle loss as a result of the role of FoxOs in the induction of autophagy–lysosome and ubiquitin–proteasome systems. Notably, in the setting of low nutrient signalling, we demonstrate that FoxOs are required for Akt activity but not for mTOR signalling. FoxOs control several stress–response pathways such as the unfolded protein response, ROS detoxification, DNA repair and translation. Finally, we identify FoxO-dependent ubiquitin ligases including MUSA1 and a previously uncharacterised ligase termed SMART (Specific of Muscle Atrophy and Regulated by Transcription). Our findings underscore the central function of FoxOs in coordinating a variety of stress-response genes during catabolic conditions.
Multinuclear metal-binding ability of a carotene
Authors: Horiuchi Shinnosuke , Tachibana Yuki , Yamashita Mitsuki , Yamamoto Koji , Masai Kohei , Takase Kohei , Matsutani Teruo , Kawamata Shiori , Kurashige Yuki , Yanai Takeshi , Murahashi Tetsuro 
Published: April 2015

AbstractCarotenes are naturally abundant unsaturated hydrocarbon pigments, and their fascinating physical and chemical properties have been studied intensively not only for better understanding of the roles in biological processes but also for the use in artificial chemical systems. However, their metal-binding ability has been virtually unexplored. Here we report that β-carotene has the ability to assemble and align ten metal atoms to afford decanuclear homo- and heterometal chain complexes. The metallo–carotenoid framework shows reversible metalation–demetalation reactivity with multiple metals, which allows us to control the size of metal chains as well as the heterobimetallic composition and arrangement of the carotene-supported metal chains.
A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human UDP-glucose Pyrophosphorylase, a Key Enzyme in Cell Metabolism
Authors: Führing Jana Indra , Cramer Johannes Thomas , Schneider Julia , Baruch Petra , Gerardy-Schahn Rita , Fedorov Roman 
Published: April 2015

AbstractIn mammals, UDP-glucose pyrophosphorylase (UGP) is the only enzyme capable of activating glucose-1-phosphate (Glc-1-P) to UDP-glucose (UDP-Glc), a metabolite located at the intersection of virtually all metabolic pathways in the mammalian cell. Despite the essential role of its product, the molecular basis of UGP function is poorly understood. Here we report the crystal structure of human UGP in complex with its product UDP-Glc. Beyond providing first insight into the active site architecture, we describe the substrate binding mode and intermolecular interactions in the octameric enzyme that are crucial to its activity. Importantly, the quaternary mechanism identified for human UGP in this study may be common for oligomeric sugar-activating nucleotidyltransferases. Elucidating such mechanisms is essential for understanding nucleotide sugar metabolism and opens the perspective for the development of drugs that specifically inhibit simpler organized nucleotidyltransferases in pathogens.
The natural compound chebulagic acid inhibits vascular endothelial growth factor A mediated regulation of endothelial cell functions
Authors: Lu Kai , Basu Sujit 
Published: April 2015

AbstractVascular endothelial growth factor A (VEGFA) plays an important role in tumour angiogenesis and its angiogenic action is mainly mediated through its VEGF receptor 2 (VEGFR-2). Therefore drugs targeting VEGFA/VEGFR-2 are being presently used in the clinics for treatment of several types of solid malignant tumours. We here in report that low dose of chebulagic acid (CA), a hydrolysable tannin found in myrobalan fruits can inhibit VEGFA induced vascular permeability, endothelial cell proliferation, migration, tube formation and thereby, angiogenesis by suppressing VEGFR-2 phosphorylation. CA may thus be an effective and useful natural inhibitor of VEGFA mediated angiogenesis.
Electronic transport in two-dimensional high dielectric constant nanosystems
Authors: Ortuño M. , Somoza A. M. , Vinokur V. M. , Baturina T. I. 
Published: April 2015

AbstractThere has been remarkable recent progress in engineering high-dielectric constant two dimensional (2D) materials, which are being actively pursued for applications in nanoelectronics in capacitor and memory devices, energy storage and high-frequency modulation in communication devices. Yet many of the unique properties of these systems are poorly understood and remain unexplored. Here we report a numerical study of hopping conductivity of the lateral network of capacitors, which models two-dimensional insulators and demonstrate that 2D long-range Coulomb interactions lead to peculiar size effects. We find that the characteristic energy governing electronic transport scales logarithmically with either system size or electrostatic screening length depending on which one is shorter. Our results are relevant well beyond their immediate context, explaining, for example, recent experimental observations of logarithmic size dependence of electric conductivity of thin superconducting films in the critical vicinity of superconductor-insulator transition where a giant dielectric constant develops. Our findings mark a radical departure from the orthodox view of conductivity in 2D systems as a local characteristic of materials and establish its macroscopic global character as a generic property of high-dielectric constant 2D nanomaterials.
Copper Salts Mediated Morphological Transformation of Cu2O from Cubes to Hierarchical Flower-like or Microspheres and Their Supercapacitors Performances
Authors: Chen Liang , Zhang Yu , Zhu Pengli , Zhou Fengrui , Zeng Wenjin , Lu Daoqiang Daniel , Sun Rong , Wong Chingping 
Published: April 2015

AbstractMonodisperse Cu2O of different microstructures, such as cubes, flower-like and microspheres, have been extensively synthesized by a simple polyol reduction method using different copper salts, i.e. (Cu(acac)2, Cu(OH)2 and Cu(Ac)2·H2O). The effects of copper salts on the morphology of Cu2O were investigated in details through various characterization methods, including X-ray diffraction, transmission electron microscopy, scanning electron microscopy and UV-Vis absorption spectra. The effects of morphology on the electrochemical properties were further studied. Among the different structures, Cu2O with the microspheric morphology shows the highest specific capacitance and the best cycling stability compared with those of the other two structures, thus bear larger volume charge during the electrochemical reaction due to the microspheres of small nanoparticles.
RETRACTED ARTICLE: Sirt7 promotes gastric cancer growth and inhibits apoptosis by epigenetically inhibiting miR-34a
Authors: Zhang Shun , Chen Ping , Huang Zuoan , Hu Xiaorong , Chen Mengting , Hu Shanshan , Hu Yixin , Cai Ting 
Published: April 2015

AbstractGastric cancer is the fourth most common cancer worldwide, with a low 5-year survival rate. Epigenetic modification plays pivotal roles in gastric cancer development. However, the role of histone-modifying enzymes in gastric cancer remains largely unknown. Here we report that Sirt7, a NAD+-dependent class III histone deacetylase, is over-expressed in human gastric cancer tissues. Sirt7 level is significantly correlated with disease stage, metastasis and survival. Knockdown of Sirt7 in gastric cancer cells inhibits cell proliferation and colony formation in vitro. In vivo subcutaneous xenograft results also show that Sirt7 knockdown can markedly repress gastric cancer cell growth. In addition, Sirt7 depletion induces apoptosis in gastric cancer cells via up-regulating expression of pro-apoptotic proteins and down-regulating anti-apoptotic proteins. Mechanically, Sirt7 binds to the promoter of miR-34a and deacetylases the H3K18ac, thus represses miR-34a expression. Reversely, depletion of miR-34a inhibits gastric cancer apoptosis induced by Sirt7 knockdown and restores cellular capacity of proliferation and colony formation. miR-34a depletion reduces Sirt7-knockdown-induced arrest of gastric growth. Finally, miR-34a is tightly associated with survival of patients with gastric cancer.
Inclusion bodies and pH lowering: as an effect of gold nanoparticles in Streptococcus pneumoniae
Authors: Ortiz-Benitez Edgar Augusto , Carrillo-Morales Mariana , Velázquez-Guadarrama Norma , Fandiño-Armas Jesús , Olivares-Trejo José de Jesús 
Published: April 2015

Abstract
Streptococcus pneumoniae is a human pathogen whose principal virulence factor is its capsule. This structure allows the bacterium to evade the human immune system. Treatment of infections caused by this bacterium is based on antibiotics; however, the emergence of antibiotic-resistant strains makes this task increasingly difficult. Therefore, it is necessary to investigate new therapies, such as those based on gold nanoparticles, for which unfortunately the mechanisms involved have not yet been investigated. As far as we know, this study is the first that attempts to explain how gold nanoparticles destroy the bacterium Streptococcus pneumoniae. We found that the mean particle size was an important issue, and that the effect on the bacterium was dose-dependent. Cellular growth was inhibited by the presence of the nanoparticles, as was cell viability. The pH of the bacterial growth media was acidified, but interestingly the reactive species were not affected. A transmission electron microscopy analysis revealed the presence of inclusion bodies of gold nanoparticles within the bacterium. We present the first findings that attempt to explain how gold nanoparticles lyse Gram-positive bacteria.
Impaired Statistical Learning in Developmental Dyslexia
Authors: Gabay Yafit , Thiessen Erik D. , Holt Lori L. 
Published: April 2015

Purpose
Developmental dyslexia (DD) is commonly thought to arise from phonological impairments. However, an emerging perspective is that a more general procedural learning deficit, not specific to phonological processing, may underlie DD. The current study examined if individuals with DD are capable of extracting statistical regularities across sequences of passively experienced speech and nonspeech sounds. Such statistical learning is believed to be domain-general, to draw upon procedural learning systems, and to relate to language outcomes.

Method
DD and control groups were familiarized with a continuous stream of syllables or sine-wave tones, the ordering of which was defined by high or low transitional probabilities across adjacent stimulus pairs. Participants subsequently judged two 3-stimulus test items with either high or low statistical coherence as being the most similar to the sounds heard during familiarization.

Results
As with control participants, the DD group was sensitive to the transitional probability structure of the familiarization materials as evidenced by above-chance performance. However, the performance of participants with DD was significantly poorer than controls across linguistic and nonlinguistic stimuli. In addition, reading-related measures were significantly correlated with statistical learning performance of both speech and nonspeech material.

Conclusion
Results are discussed in light of procedural learning impairments among participants with DD.
Linguistic Feature Development Across Grades and Genre in Elementary Writing
Authors: Hall-Mills Shannon , Apel Kenn 
Published: April 2015

Purpose
As children develop skills in writing across academic contexts, clinicians and educators need to have a fundamental understanding of typical writing development as well as valid and reliable assessment methods. The purpose of this study was to examine the progression of linguistic elements in school-age children's narrative and expository writing development.

Method
Narrative and expository writing samples produced by 89 children in Grades 2 through 4 were analyzed at the microstructure and macrostructure levels. Measures of receptive vocabulary, word-level reading, and reading comprehension were obtained.

Results
Exploratory factor analyses revealed 4 microstructure factors (e.g., productivity, grammatical complexity, grammatical accuracy, and lexical density) and 1 macrostructure factor (e.g., a combination of organization, text structure, and cohesion). Multivariate analyses of covariance with reading comprehension as a covariate showed that productivity and macrostructure were sensitive to grade-level and genre differences and that expository grammatical complexity was sensitive to grade-level differences.

Conclusions
Findings are discussed in light of grade-level standards for narrative and expository writing and current practices in writing assessment. Multiple suggestions are offered for clinical and educational implications, and specific directions are provided for future research.
The future of transgenic farm animal production with emphasis on pigs.
Authors: Petersen B. , Niemann H. 
Published: April 2015

Abstract
Transgenic livestock already play an important role as models for human diseases, for producing recombinant pharmaceutical proteins, and in the future may serve as donors of organs for terminally ill patients and tissues and cells in regenerative medicine to cope with degenerative diseases and ultimately might contribute to satisfy the increasing demand for valuable animal derived proteins for an ever-increasing global human population. The first transgenic livestock were produced in 1985 by microinjection of foreign DNA into zygotic pronuclei. Since then, significant progress has been made with regard to methods that permit efficient and targeted insertion of precise modifications in the complex mammalian genomes. This in turn will further enhance the development of transgenic livestock with well-defined genetically engineered chromosomal loci that are not affected by neighbouring chromosomal sequences and without integration of undesired DNA sequences such as antibiotic resistant cassettes that hinder products of these animals to enter the market. Here, we review the recent advances of the methodologies for the production of transgenic farm animals which will be important in meeting global challenges in valuable animal protein production and will open new horizons for biomedicine.
Prediction of nitrogen efficiency in dairy cattle: a review.
Authors: Reed K. F. , Casper D. P. , France J. , Kebreab E. 
Published: April 2015

Abstract
Increasing the efficiency of conversion of feed nitrogen (N) into milk and meat N in dairy cattle is an integral part of the effort to maintain or increase food production while decreasing agriculture's environmental impact. Mathematical models provide a means to assess and compare different strategies to increase N efficiency; however, their merit depends on the models' predictive capabilities. Evaluation of the currently available empirical models to predict faecal and urinary N excretion revealed low prediction accuracy and the presence of significant systematic biases. Application of more diverse and advanced model development techniques are needed to produce models whose precision and accuracy are sufficient for application in emissions mitigation protocols. Mechanistic models continue to advance and push the boundaries of knowledge in ruminant N metabolism; aided by advances in computer technology. However, improvement is required in the description of factors that influence microbial protein production and the use of metabolizable protein; this represents the greatest potential for increasing our prediction and understanding of N efficiency in dairy cattle. Attention to these two aspects of ruminant N metabolism in mechanistic models directed specifically at improving N efficiency and in the widely used nutrient requirement models will enhance our ability to meet dairy cattle's protein requirements in a sustainable manner.
Two-Body Scattering in (1 + 1) Dimensions by a Semi-relativistic Formalism and a Hulthén Interaction Potential
Authors: Hassanabadi S. , Ghominejad M. , Thylwe K.-E. 
Published: April 2015

Abstract
Scattering solutions of two-body Spinless Salpeter Equation (SSE) are investigated in the center of mass frame with a repulsive, symmetric Hulthén potential in one spatial dimension. Transmission and reflection coefficients are calculated and discussed.
Dynamic (2, 3) Threshold Quantum Secret Sharing of Secure Direct Communication*
Authors: Lai Hong , Mehmet Orgun A. , Xiao Jing-Hua , Josef Pieprzyk , Xue Li-Yin 
Published: April 2015

Abstract
In this paper, we show that a (2, 3) discrete variable threshold quantum secret sharing scheme of secure direct communication can be achieved based on recurrence using the same devices as in BB84. The scheme is devised by first placing the shares of smaller secret pieces into the shares of the largest secret piece, converting the shares of the largest secret piece into corresponding quantum state sequences, inserting nonorthogonal state particles into the quantum state sequences with the purpose of detecting eavesdropping, and finally sending the new quantum state sequences to the three participants respectively. Consequently, every particle can on average carry up to 1.5-bit messages due to the use of recurrence. The control codes are randomly prepared using the way to generate fountain codes with pre-shared source codes between Alice and Bob, making three participants can detect eavesdropping by themselves without sending classical messages to Alice. Due to the flexible encoding, our scheme is also dynamic, which means that it allows the participants to join and leave freely.
GS-align for glycan structure alignment and similarity measurement
Authors: Lee Hui Sun , Jo Sunhwan , Mukherjee Srayanta , Park Sang-Jun , Skolnick Jeffrey , Lee Jooyoung , Im Wonpil 
Published: April 2015

Abstract
Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner.
Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N-linked glycan library and PDB homologous/non-homologous N-glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility.
Availability and implementation: http://www.glycanstructure.org/gsalign.
Contact: wonpil@ku.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Recombination energy in double white dwarf formation
Authors: Nandez J. L. A. , Ivanova N. , Lombardi J. C. 
Published: April 2015

Abstract
In this Letter, we investigate the role of recombination energy during a common envelope event. We confirm that taking this energy into account helps to avoid the formation of the circumbinary envelope commonly found in previous studies. For the first time, we can model a complete common envelope event, with a clean compact double white dwarf binary system formed at the end. The resulting binary orbit is almost perfectly circular. In addition to considering recombination energy, we also show that between 1/4 and 1/2 of the released orbital energy is taken away by the ejected material. We apply this new method to the case of the double white dwarf system WD 1101+364, and we find that the progenitor system at the start of the common envelope event consisted of an ∼1.5 M⊙ red giant star in an ∼30 d orbit with a white dwarf companion.