bluuebunny/crossref_metadata_2025_split huggingface dataset:
NORMAL CYCLIC POLYTOPES AND CYCLIC POLYTOPES THAT ARE NOT VERY AMPLE
Authors: HIBI TAKAYUKI , HIGASHITANI AKIHIRO , KATTHÄN LUKAS , OKAZAKI RYOTA 
Published: September 2013

AbstractLet $d$ and $n$ be positive integers such that $n\geq d+ 1$ and ${\tau }_{1} , \ldots , {\tau }_{n} $ integers such that ${\tau }_{1} \lt \cdots \lt {\tau }_{n} $. Let ${C}_{d} ({\tau }_{1} , \ldots , {\tau }_{n} )\subset { \mathbb{R} }^{d} $ denote the cyclic polytope of dimension $d$ with $n$ vertices $({\tau }_{1} , { \tau }_{1}^{2} , \ldots , { \tau }_{1}^{d} ), \ldots , ({\tau }_{n} , { \tau }_{n}^{2} , \ldots , { \tau }_{n}^{d} )$. We are interested in finding the smallest integer ${\gamma }_{d} $ such that if ${\tau }_{i+ 1} - {\tau }_{i} \geq {\gamma }_{d} $ for $1\leq i\lt n$, then ${C}_{d} ({\tau }_{1} , \ldots , {\tau }_{n} )$ is normal. One of the known results is ${\gamma }_{d} \leq d(d+ 1)$. In the present paper a new inequality ${\gamma }_{d} \leq {d}^{2} - 1$ is proved. Moreover, it is shown that if $d\geq 4$ with ${\tau }_{3} - {\tau }_{2} = 1$, then ${C}_{d} ({\tau }_{1} , \ldots , {\tau }_{n} )$ is not very ample.
Accelerating materials property predictions using machine learning
Authors: Pilania Ghanshyam , Wang Chenchen , Jiang Xun , Rajasekaran Sanguthevar , Ramprasad Ramamurthy 
Published: September 2013

AbstractThe materials discovery process can be significantly expedited and simplified if we can learn effectively from available knowledge and data. In the present contribution, we show that efficient and accurate prediction of a diverse set of properties of material systems is possible by employing machine (or statistical) learning methods trained on quantum mechanical computations in combination with the notions of chemical similarity. Using a family of one-dimensional chain systems, we present a general formalism that allows us to discover decision rules that establish a mapping between easily accessible attributes of a system and its properties. It is shown that fingerprints based on either chemo-structural (compositional and configurational information) or the electronic charge density distribution can be used to make ultra-fast, yet accurate, property predictions. Harnessing such learning paradigms extends recent efforts to systematically explore and mine vast chemical spaces and can significantly accelerate the discovery of new application-specific materials.
Redefining the dynamics of intergenerational family solidarity in spain
Authors: Caïs Jordi , Folguera Laia 
Published: September 2013

ABSTRACT
This article analyses the dynamics of family solidarity in Spain. The existing literature so far has defined the Spanish caring model as familistic due to the primacy of the family in the protection of dependants. However, this article shows that recent data on Spaniards' preferences concerning the care of their family dependents might question the sustainability of the bases of such model. This is consistent with the results of the OASIS Project, according to which societal changes may be leading to family care becoming less duty-driven and more dependent on personal affection and attachment. 1 The Spanish welfare state is labelled as familistic because family makes up for the lack of public benefits dampening adverse economic cycles and the problems of its more fragile members: children, young people and, especially, the elderly. Family solidarity is considered beneficial because it contains public spending and generates positive effects of solidarity and security in the population. Moreover, the expectations of the dependent elderly are focused on family, not on social services that always have been scarce in Spain and they are worsening with the economic crisis. But the Spanish welfare state based on familist values appears to be increasingly ineffective and more difficult to sustain. This article explains how changes in family structure and dynamics, along with the high rates of female labour force that Spain has recently achieved, affect family caregiving preferences and strategies.
ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses
Authors: Huntley Melanie A. , Larson Jessica L. , Chaivorapol Christina , Becker Gabriel , Lawrence Michael , Hackney Jason A. , Kaminker Joshua S. 
Published: September 2013

Abstract
Summary: It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API.
Availability: The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.
Contact: hackney.jason@gene.com or kaminker.josh@gene.com
STAR: an integrated solution to management and visualization of sequencing data
Authors: Wang Tao , Liu Jie , Shen Li , Tonti-Filippini Julian , Zhu Yun , Jia Haiyang , Lister Ryan , Whitaker John W. , Ecker Joseph R. , Millar A. Harvey , Ren Bing , Wang Wei 
Published: September 2013

Abstract
Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data.
Results: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data.
Availability and implementation: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.
Contact: wei-wang@ucsd.edu
A C library for retrieving specific reactions from the BioModels database
Authors: Neal M. L. , Galdzicki M. , Gallimore J. T. , Sauro H. M. 
Published: September 2013

Abstract
Summary: We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions.
Availability and implementation: The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder.
Contact: mneal@uw.edu
Outcomes of kidney allograft in recipients with kidney disease of unknown etiology
Authors: Kim Hyo Jin , Kim Hyunsuk , Cho Hyun Seop , Hwang Jin Ho , Jung In Mok , Ahn Curie , Ha Jongwon , Oh Yun Kyu , Lim Chun Soo , Chae Dong‐Wan , Kim Yon Su , Lee Jung Pyo 
Published: September 2013

AbstractThe etiology of renal disease is important because the primary renal pathology may affect the outcomes of kidney allograft with respect to recurrence, rejection, and survival. However, for a significant number of patients who undergo kidney transplantation, the disease etiology is unknown. Here, allograft outcomes for patients with kidney disease of unknown etiology (UEK) at three affiliated Korean hospitals were identified. The incidence of biopsy‐proven acute rejection (BPAR) for UEK was 22.9%, which was similar to the rates for diabetic nephropathy (DN, 24.4%) and IgA nephropathy (IgAN, 20.0%; p = 0.345). The cumulative incidence of post‐transplant glomerulonephritis (PTGN) among patients with UEK was significantly lower than that among patients with IgAN (p < 0.001). Overall graft survival of the UEK group was superior to that of the DN group (hazards ratio 0.39, 95% confidence interval 0.17–0.92, p = 0.030). Preemptive transplantation for UEK significantly reduced the incidence of BPAR (preemptive vs. non‐preemptive 9.6% vs. 30.3%, p = 0.001), but graft survival and recurrence were not affected by preemptive transplantation. The outcomes of kidney transplantation for patients with UEK were not inferior to those for patients with IgAN or DN. Preemptive kidney transplantation may be encouraged for UEK patients.
A novel zoometric index for assessing body composition in adult rabbits
Authors: Sweet H. , Pearson A. J. , Watson P. J. , German A. J. 
Published: September 2013

Obesity is an emerging problem in domesticated rabbits, and an easy‐to‐use measure of adipose tissue mass is needed. The current study aimed to develop a zoometric ratio, capable of estimating body condition in rabbits. Body weight (BW), body condition score (BCS), and zoometric measures (distal forelimb length, DFL; vertebral length, VL were measured in 150 pet rabbits. Zoometric formulae were created, combining BW with a zoometric measure, and these were tested for their ability to predict adipose tissue mass judged by BCS. Seventy‐five (50 per cent) of the rabbits were in ideal condition (BCS 2.5–3.5), 52 (35 per cent) were overweight (BCS>3.5), and 23 (15 per cent) were underweight (BCS<2.5). Median (range) DFL and VL measurements were 12.1 (8.8–16.4 cm) and 34.0 (26.5–50.5 cm), respectively. In rabbits of medium breed size, the BW/DFL ratio was most strongly associated with BCS (Kendall's τ 0.80, P<0.001). Using BW/DFL limits for optimum body condition (eg, minimum 0.16; maximum 0.21), all underweight and overweight rabbits were correctly classified, while only 2/61 (3 per cent) rabbits with an optimum BCS were incorrectly classified as overweight. This study provides preliminary evidence that the BW/DFL might be a useful indirect measure of adipose tissue mass in rabbits of medium breed size.
A Chinese Monk under a “Barbarian” Mask?
Authors: Chen Jinhua 
Published: September 2013

Zhihuilun (?-876) was not only a major advocate of Esoteric Buddhism in ninth-century China, he also played a crucial role in transmitting Esotericism to the rest of East Asia. Details of the life of this important figure have remained lost in the mists of uncertainty due to the lack of reliable data. Relying on long-hidden evidence, this article shows that almost all of the remarks made about Zhihuilun by Zanning (919-1001) in the Song gaoseng zhuan are contradicted by this body of new evidence and must be modified or simply rejected. In addition to reconstructing more accurately the life of a principal esoteric promoter, this article aims at exposing certain fundamental flaws inherent in monastic biographies. It also suggests that the nature and functions of Chinese Esoteric Buddhism might need to be reassessed in view of the newly revealed Chinese origin of this key promoter of that tradition. Zhihuilun (?-876) n’a pas seulement été l’un des grands représentants du bouddhisme ésotérique en Chine au ixe siècle, il a également joué un rôle crucial dans la transmission de l’ésotérisme vers le reste de l’Asie orientale. Les détails de la vie de cette importante personnalité restaient enveloppés de mystère en raison de l’absence de sources fiables. La présente étude s’appuie sur des données restées longtemps cachées pour montrer que presque toutes les indications données par Zanning (919-1001) sur Zhihuilun dans le Song gaoseng zhuan sont contredites par ces nouvelles données, et qu’elles doivent par conséquent être soit modifiées, soit rejetées purement et simplement. Outre qu’il propose une reconstruction plus exacte de la vie d’un des grands promoteurs de l’ésotérisme, l’article s’attache à exposer certains des problèmes fondamentaux soulevés par les biographies de moines. Il est également suggéré que la nature même et les fonctions du bouddhisme ésotérique chinois méritent peut-être d’être réévaluées à la lumière de l’origine chinoise, telle qu’elle est révélée ici, d’un des personnages clés de cette tradition.
Courtesan Editor
Authors: Berg Daria 
Published: September 2013

This article focuses on female editorship and sexual politics in late Ming and early Qing China, using Hua suo shi, an anthology edited by the courtesan poet Xue Susu, as a case study. It traces textual production and transmission, and reconstructs the literary and cultural contexts of this work to explore the courtesan’s editorial gaze and representation of gender through a close reading of it. The analysis of its two main themes—women as commodities, and women as agents—shows how the courtesan editor re-imagined China’s cultural landscape from her point of view. New examples of female agency are discovered in analyzing the cultural process of editing as a “web of discourses,” providing a window on the emergence of a new female editorial voice in early modern China’s cultural discourse. Cet article se concentre sur le rôle éditorial des femmes et sur les politiques sexuelles en Chine à la fin des Ming et au début des Qing. Une anthologie éditée par la courtisane et poétesse Xue Susu, le Hua suo shi, sert d’étude de cas. Le processus de production et de transmission textuelle est examiné et le contexte littéraire et culturel de l’ouvrage restitué, permettant d’explorer le regard éditorial et le jeu de genre de la courtisane à travers une lecture serrée du texte. L’analyse des deux thèmes dominants — la femme comme marchandise, la femme comme agent — démontre la façon dont la courtisane éditrice ré-imagine le paysage culturel chinois de son propre point de vue. D’autres exemples d’intervention féminine se révèlent lorsqu’on analyse le processus culturel d’édition en tant que “réseau de discours”. Ainsi s’ouvre une fenêtre sur l’émergence d’une nouvelle voix éditoriale féminine au sein du discours culturel chinois au début des temps modernes.
Visual Culture, Spectatorship and Humanitarian Disaster
Authors: Nair Gaana J. 
Published: September 2013

This article examines the dialogic encounter between the spectator and the spectacle in the context of war crimes and humanitarian disasters (in this context, the Sri Lankan civil war) in Vanni Eli, a short film by a Sri Lankan Tamizh diasporic filmmaker Tamiliam Subhas. The narrative introduces us not only to the military disaster that is war but also to the humanitarian disasters effected through war. The article studies the role of the spectator who ‘witnesses’ the torture, and thus complicates the ethics of both the act of torture and the viewing of it. By looking closely at the ingenious ways of narrating torture the article argues that the creative representation of war and disaster implicates within its discourse not merely the participants and the victims of the war alone but also the ‘peripheral’ subjects like the mice (the film’s lead ‘actors’), and by extension, the spectators participating in the discursive construction of the victimized. Despite the symbolic disembodiment and effacement of the tortured, their suffering is recognized as a humanitarian disaster with the shared grammar of suffering common to all.1
Imagining Bio-disaster, Reproducing Social Order
Authors: Sundaram Neeraja 
Published: September 2013

This article studies the imagination and representation of biological disaster in contemporary popular cinema. The texts chosen are Steven Soderbergh’s 2011 film Contagion, Danny Boyle’s modern zombie-horror classic 28 Days Later (2002), Francis Lawrence’s I Am Legend (2007) and Alfonso Cuaron’s Children of Men (2006). This article is interested in the ‘sensual elaboration’, within filmic narrative, of biological disaster, and will argue that these films not only communicate with but organize their viewers’ perceptions of biological disaster. It studies the narrativizing of the onset and consequences of biological disaster, coded as an ‘invasion’ of the individual and social body in these films. It further argues that the individual and social body in these texts form the key site of negotiating anxieties surrounding their inevitable collapse in the wake of social, cultural and economic breakdown following biological disaster. The narrativizing of biological disaster in these films, this article will demonstrate, performs a crisis of reproducibility and reproductivity.
Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus
Authors: Patyshakuliyeva Aleksandrina , Jurak Edita , Kohler Annegret , Baker Adam , Battaglia Evy , de Bruijn Wouter , Burton Kerry S , Challen Michael P , Coutinho Pedro M , Eastwood Daniel C , Gruben Birgit S , Mäkelä Miia R , Martin Francis , Nadal Marina , van den Brink Joost , Wiebenga Ad , Zhou Miaomiao , Henrissat Bernard , Kabel Mirjam , Gruppen Harry , de Vries Ronald P 
Published: September 2013

Abstract

Background

Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present.

Results
In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies.

Conclusions
The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples.
A hierarchical spatial modelling approach to investigate MRSA transmission in a tertiary hospital
Authors: Kong Fiona , Paterson David L , Whitby Michael , Coory Michael , Clements Archie CA 
Published: September 2013

Abstract

Background
Most hospitals have a hierarchical design with beds positioned within cubicles and cubicles positioned within wards. Transmission of MRSA may be facilitated by patient proximity and thus the spatial arrangements of beds, cubicles and wards could be important in understanding MRSA transmission risk. Identifying high-risk areas of transmission may be useful in the design of more effective, targeted MRSA interventions.

Methods
Retrospective data on numbers of multi-resistant and non-multiresistant MRSA acquisitions were collected for 52 weeks in 2007 in a tertiary hospital in Brisbane, Australia. A hierarchical Bayesian spatio-temporal modelling approach was used to investigate spatial correlation in the hierarchically arranged datasets. The spatial component of the model decomposes cubicle-level variation into a spatially structured component and a spatially unstructured component, thereby encapsulating the influence of unmeasured predictor variables that themselves are spatially clustered and/or random. A fixed effect for the presence of another patient with the same type of MRSA in the cubicles two weeks prior was included.

Results
The best-fitting model for non-multiresistant MRSA had an unstructured random effect but no spatially structured random effect. The best-fitting model for multiresistant MRSA incorporated both spatially structured and unstructured random effects. While between-cubicle variability in risk of MRSA acquisition within the hospital was significant, there was only weak evidence to suggest that MRSA is spatially clustered. Presence of another patient with the same type of MRSA in the cubicles two weeks prior was a significant predictor of both types of MRSA in all models.

Conclusions
We found weak evidence of clustering of MRSA acquisition within the hospital. The presence of an infected patient in the same cubicle two weeks prior may support the importance of environmental contamination as a source of MRSA transmission.
Simultaneous display of two large proteins on the head and tail of bacteriophage lambda
Authors: Pavoni Emiliano , Vaccaro Paola , D’Alessio Valeria , De Santis Rita , Minenkova Olga 
Published: September 2013

Abstract

Background
Consistent progress in the development of bacteriophage lambda display platform as an alternative to filamentous phage display system was achieved in the recent years. The lambda phage has been engineered to display efficiently multiple copies of peptides or even large protein domains providing a powerful tool for screening libraries of peptides, proteins and cDNA.

Results
In the present work we describe an original method for dual display of large proteins on the surface of lambda particles. An anti-CEA single-chain antibody fragment and green fluorescent protein or alkaline phosphatase were simultaneously displayed by engineering both gpD and gpV lambda proteins.

Conclusions
Here we show that such modified phage particles can be used for the detection of target molecules in vitro and in vivo. Dual expression of functional moieties on the surface of the lambda phage might open the way to generation of a new class of diagnostic and therapeutic targeted nanoparticles.