bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic differences between cultivated soybean, G. max and its wild relative G. soja
Authors: Joshi Trupti , Valliyodan Babu , Wu Jeng-Hung , Lee Suk-Ha , Xu Dong , Nguyen Henry T 
Published: January 2013

Abstract

Background

Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomics studies between the two varieties.

Results
We have further analysed the sequences and identified the 425 genes that are unique to G. max and unavailable in G. soja. We further studied the genes with significant number of non-synonymous SNPs in their upstream regions. 12 genes involved in seed development, 3 in oil and 6 in protein concentration are unique to G. max. A significant number of unique genes are seen to overlap with the QTL regions of the three traits including seed, oil and protein. We have also developed a graphical chromosome visualizer as part of the Soybean Knowledge Base (SoyKB) tools for molecular breeding, which was used in the analysis and visualization of overlapping QTL regions for multiple traits with the deletions and SNPs in G. soja.

Conclusions
The comparisons between genome sequences of G. max and G. soja show significant differences between the genomic compositions of the two. The differences also highlight the phenotypic differences between the two in terms of seed development, oil and protein traits. These significant results have been integrated into the SoyKB resource and are publicly available for users to browse at http://soykb.org/GSoja.
Genome reassembly with high-throughput sequencing data
Authors: Parrish Nathaniel , Sudakov Benjamin , Eskin Eleazar 
Published: January 2013

Abstract

Motivation
Recent studies in genomics have highlighted the significance of structural variation in determining individual variation. Current methods for identifying structural variation, however, are predominantly focused on either assembling whole genomes from scratch, or identifying the relatively small changes between a genome and a reference sequence. While significant progress has been made in recent years on both de novo assembly and resequencing (read mapping) methods, few attempts have been made to bridge the gap between them.

Results
In this paper, we present a computational method for incorporating a reference sequence into an assembly algorithm. We propose a novel graph construction that builds upon the well-known de Bruijn graph to incorporate the reference, and describe a simple algorithm, based on iterative message passing, which uses this information to significantly improve assembly results. We validate our method by applying it to a series of 5 Mb simulation genomes derived from both mammalian and bacterial references. The results of applying our method to this simulation data are presented along with a discussion of the benefits and drawbacks of this technique.
Ferromagnetism and semiconducting of boron nanowires
Authors: Li Jiling L , He Tao , Yang Guowei 
Published: January 2013

Abstract
More recently, motivated by extensively technical applications of carbon nanostructures, there is a growing interest in exploring novel non-carbon nanostructures. As the nearest neighbor of carbon in the periodic table, boron has exceptional properties of low volatility and high melting point and is stronger than steel, harder than corundum, and lighter than aluminum. Boron nanostructures thus are expected to have broad applications in various circumstances. In this contribution, we have performed a systematical study of the stability and electronic and magnetic properties of boron nanowires using the spin-polarized density functional calculations. Our calculations have revealed that there are six stable configurations of boron nanowires obtained by growing along different base vectors from the unit cell of the bulk α-rhombohedral boron (α-B) and β-rhombohedral boron (β-B). Well known, the boron bulk is usually metallic without magnetism. However, theoretical results about the magnetic and electronic properties showed that, whether for the α-B-based or the β-B-based nanowires, their magnetism is dependent on the growing direction. When the boron nanowires grow along the base vector [001], they exhibit ferromagnetism and have the magnetic moments of 1.98 and 2.62 μB, respectively, for the α-c [001] and β-c [001] directions. Electronically, when the boron nanowire grows along the α-c [001] direction, it shows semiconducting and has the direct bandgap of 0.19 eV. These results showed that boron nanowires possess the unique direction dependence of the magnetic and semiconducting behaviors, which are distinctly different from that of the bulk boron. Therefore, these theoretical findings would bring boron nanowires to have many promising applications that are novel for the boron bulk.
Correlation between matrix structural order and compressive stress exerted on silicon nanocrystals embedded in silicon-rich silicon oxide
Authors: Zatryb Grzegorz , Podhorodecki Artur , Misiewicz Jan , Cardin Julien , Gourbilleau Fabrice 
Published: January 2013

Abstract

Abstract
Silicon nanocrystals embedded in a silicon oxide matrix were deposited by radio frequency reactive magnetron sputtering. By means of Raman spectroscopy, we have found that a compressive stress is exerted on the silicon nanocrystal cores. The stress varies as a function of silicon concentration in the silicon-rich silicon oxide layers varies, which can be attributed to changes of nanocrystal environment. By conducting the Fourier transform infrared absorption experiments, we have correlated the stresses exerted on the nanocrystal core to the degree of matrix structural order.

PACS
78.67.Bf, 78.67.Pt, 73.63.Bd, 78.47.D, 74.25.Nd
Kinetic study of H-terminated silicon nanowires oxidation in very first stages
Authors: Bashouti Muhammad Y , Sardashti Kasra , Ristein Jürgen , Christiansen Silke 
Published: January 2013

Abstract
Oxidation of silicon nanowires (Si NWs) is an undesirable phenomenon that has a detrimental effect on their electronic properties. To prevent oxidation of Si NWs, a deeper understanding of the oxidation reaction kinetics is necessary. In the current work, we study the oxidation kinetics of hydrogen-terminated Si NWs (H-Si NWs) as the starting surfaces for molecular functionalization of Si surfaces. H-Si NWs of 85-nm average diameter were annealed at various temperatures from 50°C to 400°C, in short-time spans ranging from 5 to 60 min. At high temperatures (T ≥ 200°C), oxidation was found to be dominated by the oxide growth site formation (made up of silicon suboxides) and subsequent silicon oxide self-limitation. Si-Si backbond oxidation and Si-H surface bond propagation dominated the process at lower temperatures (T < 200°C).
Development of a multi-electrode array for spinal cord epidural stimulation to facilitate stepping and standing after a complete spinal cord injury in adult rats
Authors: Gad Parag , Choe Jaehoon , Nandra Mandheerej Singh , Zhong Hui , Roy Roland R , Tai Yu-Chong , Edgerton V Reggie 
Published: January 2013

Abstract

Background
Stimulation of the spinal cord has been shown to have great potential for improving function after motor deficits caused by injury or pathological conditions. Using a wide range of animal models, many studies have shown that stimulation applied to the neural networks intrinsic to the spinal cord can result in a dramatic improvement of motor ability, even allowing an animal to step and stand after a complete spinal cord transection. Clinical use of this technology, however, has been slow to develop due to the invasive nature of the implantation procedures, the lack of versatility in conventional stimulation technology, and the difficulty of ascertaining specific sites of stimulation that would provide optimal amelioration of the motor deficits. Moreover, the development of tools available to control precise stimulation chronically via biocompatible electrodes has been limited. In this paper, we outline the development of this technology and its use in the spinal rat model, demonstrating the ability to identify and stimulate specific sites of the spinal cord to produce discrete motor behaviors in spinal rats using this array.

Methods
We have designed a chronically implantable, rapidly switchable, high-density platinum based multi-electrode array that can be used to stimulate at 1–100 Hz and 1–10 V in both monopolar and bipolar configurations to examine the electrophysiological and behavioral effects of spinal cord epidural stimulation in complete spinal cord transected rats.

Results
In this paper, we have demonstrated the effectiveness of using high-resolution stimulation parameters in the context of improving motor recovery after a spinal cord injury. We observed that rats whose hindlimbs were paralyzed can stand and step when specific sets of electrodes of the array are stimulated tonically (40 Hz). Distinct patterns of stepping and standing were produced by stimulation of different combinations of electrodes on the array located at specific spinal cord levels and by specific stimulation parameters, i.e., stimulation frequency and intensity, and cathode/anode orientation. The array also was used to assess functional connectivity between the cord dorsum to interneuronal circuits and specific motor pools via evoked potentials induced at 1 Hz stimulation in the absence of any anesthesia.

Conclusions
Therefore the high density electrode array allows high spatial resolution and the ability to selectively activate different neural pathways within the lumbosacral region of the spinal cord to facilitate standing and stepping in adult spinal rats and provides the capability to evoke motor potentials and thus a means for assessing connectivity between sensory circuits and specific motor pools and muscles.
An alternative high output tissue microarray technique
Authors: Shi Yuan , He Deming , Hou Yingyong , Hu Qin , Xu Chen , Liu Yalan , Jiang Dongxian , Su Jieakesu , Zeng Haiying , Tan Yunshan 
Published: January 2013

Abstract

Background
Tissue microarray (TMA) is a high throughput research tool, which has greatly facilitated and accelerated in situ tissue analyses. However, its productivity has been restricted due to the confined thickness of traditional donor block. Here, we introduce an improved high output TMA method that is applicable to a broader range of tissue samples.

Methods
In this method, a 3.6 cm long and 2.7 cm wide recipient block with 88 square lattices (3 mm in width) was first prepared using several commercial instruments. A 2 mm wide and 6 mm long tissue rod was then prepared using a self-made blade-shaped knife from each paraffin embedded donor block of gastrointestinal stromal tumors. These rods were manually arrayed one by one into the corresponding lattices of the 60°C pre-softened recipient block with the guide of holes drilled with a steel needle. A 70-rod TMA was made to testify this method.

Results
The prepared TMA had well defined array configurations, good tissue morphology and fully preserved proteins and DNA. A total of 500–1000 TMA sections could be easily obtained from a TMA block.

Conclusion
This low-cost and time-saving method provides an alternative sampling tool for high output TMA.

Virtual Slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1979605867857990
REVIEWS
Authors: Collard Christophe , Hand Richard J. , Raw Laurence 
Published: January 2013

FILM AND LITERATURE: AN INTRODUCTION AND READER – SECOND EDITION, TIMOTHY CORRIGAN (ED.) (2012) London: Routledge, 470 pp., ISBN: 978-0-415-56010-8, p/bk, £24.99
IN THE PEANUT GALLERY WITH MYSTERY SCIENCE THEATER 3000: ESSAYS ON FILM, FANDOM, TECHNOLOGY AND THE CULTURE
OF RIFFING, ROBERT G. WEINER AND SHELLEY E. BARBA (EDS) (2011) Jefferson, NC: McFarland, 265 pp., ISBN: 0786445327, 9780786445325, p/bk, $40.00
WILLIAM GILLETTE: AMERICA’S SHERLOCK HOLMES, HENRY ZECHER (2011) New York: XLibris Corporation, 733 pp., ISBN: 978-1-4535-5580-4,
p/bk, $22.50
Algebraic points on Shimura curves of Γ0(p)-type
Authors: Arai Keisuke , Momose Fumiyuki 
Published: January 2013

Abstract.

In this article,
we classify the characters associated to algebraic points
on Shimura curves of Γ0(p)-type, and over a quadratic field
we show that
there are at most elliptic points on such a Shimura curve
for every sufficiently large prime number p.
This is an analogue of the study of rational points or points over a quadratic field
on the modular curve

X
0

(
p
)

$X_0(p)$

by Mazur and the second author.
We also apply the result to a finiteness conjecture on abelian varieties
with constrained prime power torsion by Rasmussen–Tamagawa.
Weight gain in an eating disorders day program
Authors: deGraft-Johnson Ama , Fisher Martin , Rosen Lisa , Napolitano Barbara , Laskin Emma 
Published: January 2013

Abstract
Background: Day treatment programs have increasingly become an important level of care in the medical and psychiatric management of patients with eating disorders, yet there is little in the literature describing the weight gain patterns of patients in these programs.
Methods: Weight gain accomplished by 198 patients admitted to a day program over a 2-year period was studied. Weight gain was analyzed by demographic, diagnostic and program-related variables and was compared for weekdays and weekends.
Results: The mean length of stay was 2.6 weeks and patients gained a mean of 2.1 pounds (0.95 kg) in the program. Approximately one-quarter of patients lost weight, one-quarter gained 0 to <2 pounds (0.9 kg), one-quarter gained 2–4 pounds (0.9–1.8 kg), and one-quarter gained more than 4 pounds (1.8 kg). Weight gain was greater in those with a diagnosis of anorexia nervosa or eating disorder not otherwise specified (compared to bulimia nervosa), a longer time in the program, and a lower body mass index on admission. Patients gained more on weekdays, while in the program, than on weekends, when they were home.
Conclusions: The data showed that most patients accomplished modest weight gains during a relatively short stay in an eating disorders day program, demonstrating what can be expected for this level of care in the current healthcare environment.
Color science of nanocrystal quantum dots for lighting and displays
Authors: Erdem Talha , Demir Hilmi Volkan 
Published: January 2013

AbstractColloidal nanocrystals of semiconductor quantum dots (QDs) are gaining prominence among the optoelectronic materials in the photonics industry. Among their many applications, their use in artificial lighting and displays has attracted special attention thanks to their high efficiency and narrow emission band, enabling spectral purity and fine tunability. By employing QDs in color-conversion LEDs, it is possible to simultaneously accomplish successful color rendition of the illuminated objects together with a good spectral overlap between the emission spectrum of the device and the sensitivity of the human eye, in addition to a warm white color, in contrast to other conventional sources such as incandescent and fluorescent lamps, and phosphor-based LEDs, which cannot achieve all of these properties at the same time. In this review, we summarize the color science of QDs for lighting and displays, and present the recent developments in QD-integrated LEDs and display research. First, we start with a general introduction to color science, photometry, and radiometry. After presenting an overview of QDs, we continue with the spectral designs of QD-integrated white LEDs that have led to efficient lighting for indoor and outdoor applications. Subsequently, we discuss QD color-conversion LEDs and displays as proof-of-concept applications – a new paradigm in artificial lighting and displays. Finally, we conclude with a summary of research opportunities and challenges along with a future outlook.
Tautomers and polymorphs of pyrazolinone derivatives, generated from reactions of arylhydrazines, ArNHNH2, with 1,3-dicarbonyl compounds
Authors: Baddeley Thomas C. , Howie R. Alan , de Lima Geraldo M. , Wardell James L. , Wardell Solange M. S. V. 
Published: January 2013

Abstract
From reactions of arylhydrazines with R2COCH2CONHPh or R2COCH2CO2Me, different tautomeric pyrazolinone forms, 1-aryl-3-R2-4,5-dihydro-1H-pyrazol-5-ones (IIa), 1-aryl-3-R2-1H-pyrazol-5-ols (IIb) and 2-aryl-5-R2-1,2-dihydro-3H-pyrazol-3-ones (IIc)], can be isolated. The crystal structures of monoclinic- and triclinic-3-phenyl-1-(3-nitrophenyl)-4,5-dihydro-1H-pyrazol-5-one (IIa forms), tautomeric 1-(4-methylphenyl)-3-phenyl-4,5-dihydro-1H-pyrazol-5-one (IIa form), and 1-(4-methylphenyl)-3-phenyl-1H-pyrazol-5-ol (IIb form), as well as1-(4-methoxyphenyl)-3-phenyl-1H-pyrazo-5-ol (IIb form) and 2-(4-methoxyphenyl)-5-methyl-1,2-dihydro-3H-pyrazol-3-one (IIc form) are reported.
The data suggest thatthe most electron withdrawing aryl group [3-nitrophenyl] generates IIa forms, while the most electron releasing aryl group [4-methoxyphenyl] generates IIb and IIc forms and that the aryl group with the intermediate electronic effect [4-methylphenyl] provides both IIa and IIb forms. This trend is supported by the reported isolations of 1-(4-chlorophenyl)-3-phenyl-4,5-dihydro-1H-pyrazol-5-one and 1-(2,4-nitrophenyl)-3-methyl-4,5-dihydro-1H-pyrazol-5-one [both IIa-forms] with electron-withdrawing chloro and nitro groups respectively and by the isolation of IIb and co-crystallised IIb/IIc forms from use of phenylhydrazine as the reactant.
Synthesis and characterization of Tetrakis-μ-[N-phenylanthranilato](O,O′)-bis[(4-vinylpyridine copper(II)] complex
Authors: Taş Murat , Karabağ Elif , Titiz Abdullah , Kaya Mukadder , Ataseven Mehmet , Dal Hakan 
Published: January 2013

Abstract
The complex, tetrakis-μ-[2-(phenylamino)ben-zoato](O,O′)-bis[4-vinylpyridine copper(II)] (1) was synthesized by the reaction of N-phenylanthranilic acid and copper powder in the presence of 4-vinylpyridine and crystallized from ethanol-dichloromethane-n-hexane mixture (1 : 1 : 1). The crystal structure of 1 contains one binuclear cage complex and each dimer locate on a crystallographic inversion centre (triclinic, P-1 space group). In the compound, two Cu(II) ions are bridged by four µ2-O : O′ N-phenylanthranilato (NPA) ligands, forming a cage structure, and 4-vinylpyridine ligands are bonded through their N atoms to the Cu(II) ions in terminal positions to form square pyramidal environment around Cu(II) ions. The Cu(II) ions in apart of 2.6298(14) Å, are bridged by the carboxylate groups of four N-phenylanthranilate ligands. The complex molecules show three dimensional supramolecular networks by O—H···O, C—H···O, C—H···π and π···π interactions.
Distributed Storage Healthcare — The Basis of a Planet-Wide Public Health Care Network
Authors: Kakouros Nikolaos 
Published: January 2013

Background:
As health providers move towards higher levels of information technology (IT) integration, they become increasingly dependent on the availability of the electronic health record (EHR). Current solutions of individually managed storage by each healthcare provider focus on efforts to ensure data security, availability and redundancy. Such models, however, scale poorly to a future of a planet-wide public health-care network (PWPHN). Our aim was to review the research literature on distributed storage systems and propose methods that may aid the implementation of a PWPHN.

Methods:
A systematic review was carried out of the research dealing with distributed storage systems and EHR. A literature search was conducted on five electronic databases: Pubmed/Medline, Cinalh, EMBASE, Web of Science (ISI) and Google Scholar and then expanded to include non-authoritative sources.

Results:
The English National Health Service Spine represents the most established country-wide PHN but is limited in deployment and remains underused. Other, literature identified and established distributed EHR attempts are more limited in scope. We discuss the currently available distributed file storage solutions and propose a schema of how one of these technologies can be used to deploy a distributed storage of EHR with benefits in terms of enhanced fault tolerance and global availability within the PWPHN.
We conclude that a PWPHN distributed health care record storage system is technically feasible over current Internet infrastructure. Nonetheless, the socioeconomic viability of PWPHN implementations remains to be determined.
Un autre regard sur les jeunes en situation d'inégalités sociales
Authors: Bordet Joëlle 
Published: January 2013

Résumé De façon dominante, les « jeunes des quartiers populaires » représentent pour la société et ses représentants un risque social. Ils sont appréhendés comme une entité globale sur le registre du déficit social ou du danger. Dans cet article, nous montrons comment cette posture des institutions et de leurs représentants a pour effet de mettre à distance l’inquiétude des adultes mais aussi les relations subjectives avec les jeunes. Afin de retrouver une confiance et de créer de nouveaux processus de subjectivation des jeunes, nous proposons, en référence aux travaux menés dans les municipalités, d’ouvrir de nouvelles perspectives de rencontres et d’action, en étayage sur leur désir de reconnaissance et d’avenir partagé.
Urgences psychiatriques et/ou centres de crise ?
Authors: Flavigny Henri 
Published: January 2013

Résumé Pour répondre adéquatement en urgence aux traumatismes psychiques et aux troubles du comportement de l’adolescent, il faut non seulement considérer l’exécution de l’acte, mais surtout son sens. C’est celui-ci qui impose la nécessité de disposer d’une gamme de solutions variées : les unes sont réalisées au niveau de la communauté sociale, représentées par les « centres de crise » pour adolescents, non psychiatriques, non médicalisés. Les autres par les « unités psychiatriques de réponse en urgence » aux besoins des adolescents. Ces dernières ne doivent pas fonctionner isolément, mais être articulées avec l’ensemble des éléments d’un intersecteur. C’est dans la mesure où nos réponses en urgence respecteront le sens de la question posée par l’expression diverse des traumatismes psychiques et des troubles du comportement de l’adolescent qu’elles se révéleront efficaces et que le moment de sa crise pourra constituer un élément positif pour son évolution.
La maison de Bernarda Alba : déni du féminin et refus du changement
Authors: Rosier Johanne 
Published: January 2013

Résumé Le drame théâtral de Frederico Garcia Lorca « La maison de Bernarda Alba » dévoile la vie de cinq filles maintenues dans un deuil de huit ans imposé par leur mère. Adela, la benjamine s’engagera dans un combat intime et violent contre sa mère, qui scellera le destin de sa féminité. La question centrale porte sur les aléas de la bipartition de la subjectivation féminine entre continuité et changement.
Immortality strategies
Authors: Triandafilidis Alexandra 
Published: January 2013

Résumé La création et l’investissement d’une image de soi à venir semblent nécessaires, à l’adolescent et à l’adulte, pour être (considérés comme) « normaux ». Autrement dit, ce qu’il est convenu d’appeler « projet » a un rôle central dans la vie psychique. Ce travail se propose de montrer que, si le projet est toujours à considérer comme « stratégie d’immortalité », sa fonction se trouve radicalement modifiée par la rencontre de l’adolescent avec le « mortifère » de la mort.