bluuebunny/crossref_metadata_2025 huggingface dataset:
Incident Hepatitis C Virus Infections in the Swiss HIV Cohort Study: Changes in Treatment Uptake and Outcomes Between 1991 and 2013
Authors: Wandeler Gilles , Schlauri Marion , Jaquier Marie-Eve , Rohrbach Janine , Metzner Karin J. , Fehr Jan , Ambrosioni Juan , Cavassini Matthias , Stöckle Marcel , Schmid Patrick , Bernasconi Enos , Keiser Olivia , Salazar-Vizcaya Luisa , Furrer Hansjakob , Rauch Andri ,   The Swiss HIV Cohort Study, Aubert V. , Battegay M. , Bernasconi E. , Böni J. , Bucher H.C. , Burton-Jeangros C. , Calmy A. , Cavassini M. , Dollenmaier G. , Egger M. , Elzi L. , Fehr J. , Fellay J. , Furrer H. , Fux C.A. , Gorgievski M. , Günthard H. , Haerry D. , Hasse B. , Hirsch H.H. , Hoffmann M. , Hösli I. , Kahlert C. , Kaiser L. , Keiser O. , Klimkait T. , Kouyos R. , Kovari H. , Ledergerber B. , Martinetti G. , Martinez de Tejada B. , Metzner K. , Müller N. , Nadal D. , Nicca D. , Pantaleo G. , Rauch A. , Regenass S. , Rickenbach M. , Rudin C. , Schöni-Affolter F. , Schmid P. , Schüpbach J. , Speck R. , Tarr P. , Telenti A. , Trkola A. , Vernazza P. , Weber R. , Yerly S.
Published: February 2015

Background.  The hepatitis C virus (HCV) epidemic is evolving rapidly in patients infected with human immunodeficiency virus (HIV). We aimed to describe changes in treatment uptake and outcomes of incident HCV infections before and after 2006, the time-point at which major changes in HCV epidemic became apparent.

Methods.  We included all adults with an incident HCV infection before June 2012 in the Swiss HIV Cohort Study, a prospective nationwide representative cohort of individuals infected with HIV. We assessed the following outcomes by time period: the proportion of patients starting an HCV therapy, the proportion of treated patients achieving a sustained virological response (SVR), and the proportion of patients with persistent HCV infection during follow-up.

Results.  Of 193 patients with an HCV seroconversion, 106 were diagnosed before and 87 after January 2006. The proportion of men who have sex with men increased from 24% before to 85% after 2006 (P < .001). Hepatitis C virus treatment uptake increased from 33% before 2006 to 77% after 2006 (P < .001). Treatment was started during early infection in 22% of patients before and 91% after 2006 (P < .001). An SVR was achieved in 78% and 29% (P = .01) of patients treated during early and chronic HCV infection. The probability of having a detectable viral load 5 years after diagnosis was 0.67 (95% confidence interval [CI], 0.58–0.77) in the group diagnosed before 2006 and 0.24 (95% CI, 0.16–0.35) in the other group (P < .001).

Conclusions.  In recent years, increased uptake and earlier initiation of HCV therapy among patients with incident infections significantly reduced the proportion of patients with replicating HCV.
The Efficacy of Adjuvant Chemotherapy in Patients With Stage II/III Resected Rectal Cancer Treated With Neoadjuvant Chemoradiation Therapy
Authors: Ahn Daniel H. , Wu Christina , Wei Lai , Williams Terence M. , Wuthrick Evan , Abdel-Misih Sherif , Harzman Alan , Husain Syed , Schmidt Carl , Goldberg Richard M. , Bekaii-Saab Tanios
Published: February 2015

Introduction:

Patients with stage II/III rectal cancers are treated with neoadjuvant chemoradiation and surgical resection followed by adjuvant chemotherapy (CT) per practice guidelines. It is unclear whether adjuvant CT provides survival benefit, and the purpose of this study was to measure outcomes in patients who did and did not receive adjuvant CT.

Materials and Methods:

We used a prospectively collected database for patients treated at The Ohio State University, and analyzed overall survival (OS), time to recurrence, patient characteristics, tumor features, and treatments. Survival curves were estimated using Kaplan-Meier method and compared by the log-rank test. Age was compared using the Wilcoxon test, and other categorical variables were compared using the χ2 or Fisher exact test.

Results:

Between August 2005 and July 2011, 110 patients were identified and 71 patients had received adjuvant CT. There was no significant difference in sex, race, pathologic tumor stage, and pathologic complete response between the 2 patient groups. Although patient characteristics showed a difference in age (median age 54.3 vs. 62 y, P=0.01) and advanced pathologic nodal status (43% vs. 19%, P=0.02), there was a significant difference in OS. Median OS was 72.6 months with CT versus 36.4 months without CT (P=0.0003). Median time to recurrence has not yet been reached.

Conclusions:

In this retrospective analysis, adjuvant CT was associated with a longer OS despite more advanced pathologic nodal staging. Prospective randomized studies are warranted to determine whether adjuvant CT provides a survival benefit for patients across the spectrum of stage II and III rectal cancer.
Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor
Authors: de los Santos Emmanuel L. C. , Meyerowitz Joseph T. , Mayo Stephen L. , Murray Richard M.
Published: February 2015

The pursuit of circuits and metabolic pathways of increasing complexity and ro-bustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, variants of qacR, a tetR family repressor, were generated by computational protein design and screened in a cell-free transcription-translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from thein vitroscreen were further characterizedin vitroandin vivoin a gene circuit. The screen yielded two qacR mutants that respond to vanillin bothin vitroandin vivo. We believe this process, a combination of the generation of variants coupled within vitroscreening, can serve as a framework for designing new sensors for other target compounds.
Differential Evolution Approach to Detect Recent Admixture
Authors: Kozlov Konstantin , Chebotarov Dmitry , Hassan Mehedi , Triska Martin , Triska Petr , Flegontov Pavel , Tatarinova Tatiana
Published: February 2015

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals.reAdmixcan incorporate individual’s knowledge of ancestors (e.g. having some ancestors from Turkey or a Scottish grandmother).reAdmixis an online tool available athttp://chcb.saban-chla.usc.edu/reAdmix/.
SHAPE directed RNA folding
Authors: Luntzer Dominik , Lorenz Ronny , Hofacker Ivo L. , Stadler Peter F. , Wolfinger Michael T.
Published: February 2015

Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of theviennaRNA Packagewe compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure.

Availability and implementation

The capability for SHAPE directed RNA folding is part of the upcoming release of theviennaRNA Package 2.2, for which a preliminary release is already freely available athttp://www.tbi.univie.ac.at/RNA.

Contact

michael.wolfinger@univie.ac.at

Supplementary information

Supplementary data is attached.
A complete bacterial genome assembledde novousing only nanopore sequencing data
Authors: Loman Nicholas J. , Quick Joshua , Simpson Jared T.
Published: February 2015

A method forde novoassembly of data from the Oxford Nanopore MinION instrument is presented which is able to reconstruct the sequence of an entire bacterial chromosome in a single contig. Initially, overlaps between nanopore reads are detected. Reads are then subjected to one or more rounds of error correction by a multiple alignment process employing partial order graphs. After correction, reads are assembled using the Celera assembler. Finally, the assembly is polished using signal-level data from the nanopore employing a novel hidden Markov model. We show that this method is able to assemble nanopore reads fromEscherichia coliK-12 MG1655 into a single contig of length 4.6Mb permitting a full reconstruction of gene order. The resulting draft assembly has 98.4% nucleotide identity compared to the finished reference genome. After polishing the assembly with our signal-level HMM, the nucleotide identity is improved to 99.4%. We show that MinION sequencing data can be used to reconstruct genomes without the need for a reference sequence or data from other sequencing platforms.
Small Glycosylated Lignin Oligomers Are Stored in Arabidopsis Leaf Vacuoles
Authors: Dima Oana , Morreel Kris , Vanholme Bartel , Kim Hoon , Ralph John , Boerjan Wout
Published: February 2015

Lignin is an aromatic polymer derived from the combinatorial coupling of monolignol radicals in the cell wall. Recently, various glycosylated lignin oligomers have been revealed in Arabidopsis thaliana. Given that monolignol oxidation and monolignol radical coupling are known to occur in the apoplast, and glycosylation in the cytoplasm, it raises questions about the subcellular localization of glycosylated lignin oligomer biosynthesis and their storage. By metabolite profiling of Arabidopsis leaf vacuoles, we show that the leaf vacuole stores a large number of these small glycosylated lignin oligomers. Their structural variety and the incorporation of alternative monomers, as observed in Arabidopsis mutants with altered monolignol biosynthesis, indicate that they are all formed by combinatorial radical coupling. In contrast to the common believe that combinatorial coupling is restricted to the apoplast, we hypothesized that the aglycones of these compounds are made within the cell. To investigate this, leaf protoplast cultures were cofed with 13C6-labeled coniferyl alcohol and a 13C4-labeled dimer of coniferyl alcohol. Metabolite profiling of the cofed protoplasts provided strong support for the occurrence of intracellular monolignol coupling. We therefore propose a metabolic pathway involving intracellular combinatorial coupling of monolignol radicals, followed by oligomer glycosylation and vacuolar import, which shares characteristics with both lignin and lignan biosynthesis.
A Chaperone Function of NO CATALASE ACTIVITY1 Is Required to Maintain Catalase Activity and for Multiple Stress Responses in Arabidopsis
Authors: Li Jing , Liu Juntao , Wang Guoqiang , Cha Joon-Yung , Li Guannan , Chen She , Li Zhen , Guo Jinghua , Zhang Caiguo , Yang Yongqing , Kim Woe-Yeon , Yun Dae-Jin , Schumaker Karen S. , Chen Zhongzhou , Guo Yan
Published: February 2015

Catalases are key regulators of reactive oxygen species homeostasis in plant cells. However, the regulation of catalase activity is not well understood. In this study, we isolated an Arabidopsis thaliana mutant, no catalase activity1-3 (nca1-3) that is hypersensitive to many abiotic stress treatments. The mutated gene was identified by map-based cloning as NCA1, which encodes a protein containing an N-terminal RING-finger domain and a C-terminal tetratricopeptide repeat-like helical domain. NCA1 interacts with and increases catalase activity maximally in a 240-kD complex in planta. In vitro, NCA1 interacts with CATALASE2 (CAT2) in a 1:1 molar ratio, and the NCA1 C terminus is essential for this interaction. CAT2 activity increased 10-fold in the presence of NCA1, and zinc ion binding of the NCA1 N terminus is required for this increase. NCA1 has chaperone protein activity that may maintain the folding of catalase in a functional state. NCA1 is a cytosol-located protein. Expression of NCA1 in the mitochondrion of the nca1-3 mutant does not rescue the abiotic stress phenotypes of the mutant, while expression in the cytosol or peroxisome does. Our results suggest that NCA1 is essential for catalase activity.
Nebula: reconstruction and visualization of scattering data in reciprocal space
Authors: Reiten Andreas , Chernyshov Dmitry , Mathiesen Ragnvald H.
Published: February 2015

Two-dimensional solid-state X-ray detectors can now operate at considerable data throughput rates that allow full three-dimensional sampling of scattering data from extended volumes of reciprocal space within second to minute timescales. For such experiments, simultaneous analysis and visualization allows for remeasurements and a more dynamic measurement strategy. A new software,Nebula, is presented. It efficiently reconstructs X-ray scattering data, generates three-dimensional reciprocal space data sets that can be visualized interactively, and aims to enable real-time processing in high-throughput measurements by employing parallel computing on commodity hardware.
X-ray micro Laue diffraction tomography analysis of a solid oxide fuel cell
Authors: Ferreira Sanchez Dario , Villanova Julie , Laurencin Jérôme , Micha Jean-Sébastien , Montani Alexandre , Gergaud Patrice , Bleuet Pierre
Published: February 2015

The relevance of micro Laue diffraction tomography (µ-LT) to investigate heterogeneous polycrystalline materials has been studied. For this purpose, a multiphase solid oxide fuel cell (SOFC) electrode composite made of yttria-stabilized zirconia and nickel oxide phases, with grains of about a few micrometres in size, has been analyzed. In order to calibrate the Laue data and to test the technique's sensitivity limits, a monocrystalline germanium sample of about 8 × 4 µm in cross-section size has also been studied through µ-LT. The SOFC and germanium Laue diffraction pattern analyses are compared and discussed. The indexing procedure has been successfully applied for the analysis of the germanium Laue data, and the depth-resolved two-dimensional cartographies of the full deviatoric strain tensor components were obtained. The development and application of an original geometrical approach to analyze the SOFC Laue data allowed the authors to resolve grains with sizes of about 3 µm and to identify their individual Laue patterns; by indexing those Laue patterns, the crystalline phases and orientations of most of the grains identified through the geometrical approach could be resolved.
Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)
Authors: Yates Luke A. , Durrant Benjamin P. , Barber Michael , Harlos Karl , Fleurdépine Sophie , Norbury Chris J. , Gilbert Robert J. C.
Published: February 2015

The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. InSchizosaccharomyces pombethe TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting them for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate microRNAs, altering their maturation. Cid1 has been studied as a model TUT that has provided insights into the larger and more complex metazoan enzyme system. In this paper, two strategies are described that led to improvements both in the crystallogenesis of Cid1 and in the resolution of diffraction by ∼1.5 Å. These advances have allowed high-resolution crystallographic studies of this TUT system to be initiated.
Crystal structure of bis[1-(2-hydroxyethyl)-2-methyl-5-nitro-1H-imidazole-κN3]silver(I) tetrafluoridoborate methanol monosolvate
Authors: Palmer Joshua H. , Upmacis Rita K.
Published: February 2015

1-(2-Hydroxyethyl)-2-methyl-5-nitro-1H-imidazole (metronidazole, MET) is a medication that is used to treat infections by a variety of anaerobic organisms, but there are relatively few reports of the structures of metal compounds that exhibit coordination of metronidazole. We have demonstrated that MET reacts with AgBF4to give [Ag(MET)2]BF4·CH3OH, in which the AgIcation is coordinated by two MET ligands with atransarrangement. The structure of [Ag(MET)2]BF4exhibits some interesting differences from its nitrate counterpart, [Ag(MET)2]NO3[Funet al.(2008).Acta Cryst.E64, m668]. For instance, although the two MET ligands of both [Ag(MET)2]BF4and [Ag(MET)2]NO3are almost coplanar, the former compound has ananti-like geometry with a molecular inversion center, but the latter has asyn-like arrangement. In the crystal, the BF4−anion is linked by an O—H...F hydrogen bond to the methanol solvent molecule, which is, in turn, linked to the cation by an O—H...O hydrogen bond; the components of the structure are linked by O—H...O hydrogen bonds, forming chains along [001]. One of the MET ligands and the BF4−anion are disordered over two sets of sites with ratios of refined occupancies 0.501 (17):0.499 (17) and 0.539 (19):0.461 (19), respectively.
Crystal structure of (18-crown-6)potassium(I) [(1,2,3,4,5-η)-cycloheptadienyl][(1,2,3-η)-cycloheptatrienyl]cobalt(I)
Authors: Brennessel William W. , Ellis John E.
Published: February 2015

The reaction of bis(anthracene)cobaltate(−I) with excess cycloheptatriene, C7H8, resulted in a new 18-electron cobaltate containing two different seven-membered ring ligands, based on single-crystal X-ray diffraction. The asymmetric unit of this structure contains two independent cation–anion pairs of the title complex, [K(18-crown-6)][Co(η3-C7H7)(η5-C7H9)], where 18-crown-6 stands for 1,4,7,10,13,16-hexaoxacyclooctadecane (C12H24O6), in general positions and well separated. Each (18-crown-6)potassium cation is in contact with the η3-coordinating ligand of one cobaltate complex. Each η3-coordinating ligand behaves as an allylic anion whoseexo-diene moiety is bent away from the allylic plane, and thus is not involved directly in the bonding. The metal-coordinating portions of the anionic η5ligands are planar and one of these ligands is modeled as disordered over two positions, with occupancy ratio 0.699 (5):0.301 (5), such that one orientation is rotated by one carbon atom with respect to the other. The diffraction intensities were integrated according to non-merohedral twin law [-1 0 0/0 -1 0/0.064 0 1], a 180° rotation about reciprocal lattice axis [001], and the masses of the twin domains refined to equal amounts. As both ligands are formally coordinated as anions, the cobalt atom is best considered to be CoI. This compound is of interest as the first to possess cycloheptatrienyl and cycloheptadienyl ligands in an anionic metal complex.
Editorial
Authors: Ogliastri Enrique
Published: February 2015

This issue includes six articles from ten universities in Chile, Colombia and Spain. The subjects are on entrepreneurship, public administration, management of intellectual capital marketing and also the immediate rejection policies of the journal's editor. The first study identifies different models of support programs in creating technology-based companies (spin‐offs) in universities from Spain and Great Britain, and the factors that determine their efficiency. The second one is on that factors that lead a person to entrepreneurship, particularly the impact of gender and the sociocultural aspects in regional entrepreneurships of Chile. The third studies the continuity of the entrepreneurial spirit in university students many years after graduating. The fourth makes an evaluation of the service portals available to the citizens of 19 countries in Latin America. The fifth is a study of the nets of scientific collaboration of the most prestigious Latin American business schools. The sixth is a study on the market orientation and obtained results in the business of rural tourism. An Editorial also deals with the criteria for immediate rejection of articles received by the journal. We plan a special issue on culture and art management, associated with the EURAM conference.

Este número incluye seis artículos provenientes de diez universidades de Chile, Colombia y España, sobre emprendimiento, administración pública, gestión del capital intelectual y mercadeo, así como la política de rechazo inmediato del editor de la revista. El primer estudio identifica diferentes modelos de programas de apoyo a la creación de empresas con base tecnológica (spin‐offs) en universidades de España y Gran Bretaña, y los factores que determinan su eficacia. El segundo sobre factores que llevan a una persona a emprender, en particular el impacto del género y aspectos socioculturales en los emprendimientos regionales en Chile. El tercero estudia la continuidad del espíritu empresarial de los universitarios varios años después de graduarse. El cuarto realiza una evaluación de los portales de servicio al ciudadano en 19 países de América Latina. El quinto es un estudio de las redes de colaboración científica de las escuelas de negocios más prestigiosas de América Latina. El sexto es un estudio sobre la orientación al mercado y los resultados obtenidos en el negocio de pequeñas firmas de servicios de turismo rural. Un Editorial trata sobre los criterios para rechazo inmediato de artículos recibidos en la revista. Planeamos un número especial sobre la gestión cultural y de arte, asociada a la conferencia de EURAM.
Empirical study of measuring supply chain performance
Authors: Sillanpää Ilkka
Published: February 2015

Purpose

– Supply chain (SC) performance measurement – the process of qualifying the efficiency and effectiveness of the SC. The purpose of this paper is to create a SC measurement framework for manufacturing industry, define which data should be measured and verify the measurement framework in the case company’s SC.

Design/methodology/approach

– There is a review of the current understanding of supply chain management and literature related to SC performance measurement and the study creates a framework for SC measurement. This research is qualitative case study research.

Findings

– This study presents the main theoretical framework of SC performance measurement. The key elements for the measurement framework were defined as time, profitability, order book analysis and managerial analysis. The measurement framework is tested by measuring case SC performance.

Research limitations/implications

– In the study, a performance measurement framework was created for the needs of manufacturing industry. Suggestions for future research are multiple case study in different manufacturing industry areas and positivistic-based SC performance research.

Practical implications

– The measurement framework in this study offers guidelines for measuring the SC in manufacturing industry but the measurement framework could be used in different areas of industry as well.

Originality/value

– The SC performance measurement framework is tested and a valid framework for SC performance measurement in manufacturing industry.
Applications of benchmarking and classification framework for supplier risk management
Authors: Phusavat Kongkiti , Anussornnitisarn Pornthep , Pongrakhananon Tatchapan , Pastuszak Zbigniew
Published: February 2015

Purpose

– The purpose of this paper is to develop a supplier risk framework. The framework provides the information about the risk level in which a supplier is classified. This study is part of the company’s one- department-one-improvement policy. This policy encourages all departments to look for way to improve process management. For this study, the Purchasing Department attempts to extend its supplier management practices by integrating the risk consideration.

Design/methodology/approach

– This work is considered as a case study. The study integrates the benchmarking and classification concepts for this extension. The involvement from the company’s purchasing department is critical. There are several steps that have been undertaken. Included are the selection of the supplies to be considered (i.e. packaging), the analysis of the formal complaints by the ratio-format indicator, the four criteria used for the classification, the risk level identification, and the next steps for improving supplier management. The results are verified by the use of cluster analysis. The data are from departmental staffs and manager.

Findings

– Based on the results, with the four agreed criteria (e.g. regional location, ownership type, joint venture, and registered capital and size), there are altogether four risk levels which are high, medium, low, and minimal.. For the packaging materials, most suppliers belong to the low and minimal risk levels (or 19 out of 27 suppliers). Future activities are then developed and added into the company’s ISO 9001: 2008 manual.

Practical implications

– The suppliers’ risk levels with corresponding future actions represent positive contributions to the purchasing department. Integrating supplier risk is based on the applications of benchmarking (i.e. the use of the ratio-format indicators) and classification (i.e. the need to understand the nature of the risk level) frameworks. Future actions to mitigate the risk are also proposed and incorporated into the purchasing department’s procedure.

Originality/value

– The project underlines the roles and importance of benchmarking in strengthening the supplier management processes. It also highlights the practicality and benefits of benchmarking when linking with the classification concept for addressing today business problems.
Domestic abuse victims’ perceptions of abuse and support: a narrative study
Authors: Spruin Elizabeth , Alleyne Emma , Papadaki Ioanna
Published: February 2015

Purpose

– While there is a large body of research exploring the various avenues of support for domestic abuse victims and the risk factors which put women at risk of victimization, there is little research exploring the perceptions of these women. The purpose of this paper is therefore to explore the personal views of victimized women; in particular, the risk factors that they believe put them at risk for abuse and what they feel support services should offer.

Design/methodology/approach

– In total, 12 women were interviewed about their experiences of domestic violence. Interviews were analyzed using thematic analysis which resulted in three themes: first intimate relationship; quality of life; and supporting services.

Findings

– The results from the analysis highlighted some prominent risk factors and, most importantly, emphasized the need for alternative forms of support. Overall, the findings provide an innovative way of viewing domestic violence by understanding it through victim ' s narratives, which can further aid to inform current support services within the UK and elsewhere.

Research limitations/implications

– The quality of life around the time of abuse is a factor that should be explored further in relation to the victimization of women.

Practical implications

– Ambivalent first sexual encounters may be an important risk factor for future relationship violence.

Social implications

– Support services for domestically abused women need to offer more internal support for vocational and educational services.

Originality/value

– There is little research exploring the personal views and perceptions of victimized women, in particular, the risk factors that they believe put them at risk for domestic abuse and what they feel support services should offer. The value of this research is therefore founded in the exploring this gap in literature and provide victims with a voice to aid researchers in understanding domestic abuse from another perspective. Investigating a victim ' s personal account is one pathway into beginning to understand the underlying thought processes and beliefs they attach to an event. If themes within a personal narrative account could be identified within victims of domestic abuse, it may allow a new aetiological perspective to develop in regard to the understanding and needs of abused women.
Housing Prices in Urban China as Determined by Demand and Supply
Authors: Chow Gregory C. , Niu Linlin
Published: February 2015

This paper studies the demand for and supply of residential housing in urban China since the late 1980s when the urban housing market became commercialized. Using aggregated annual data from 1987 to 2012 in a simultaneous equations framework we show that the rapid increase in the urban residential housing price can be well explained by the forces of demand and supply, with income determining demand and cost of construction affecting supply. We find the income elasticity of demand for urban housing to be approximately 1, the price elasticity of demand to be approximately −1.1 and the price elasticity of supply of the total housing stock to be approximately 0.5. The resulting long‐run effect of income on urban housing prices in elasticity terms is approximately 0.7, because the increase in income has shifted the demand curve outward more rapidly than the supply curve.
Evolution of the Interindustry Wage Structure in China Since the 1980s
Authors: Kwon Ohyun , Chang Simon , Fleisher Belton M.
Published: February 2015

Industry mean wages in China have exhibited sharply increased dispersion since the early1990s. Researchers have attributed this rising inequality within the industrial wage structure to: (i) increasingly competitive labour markets leading to better matches between worker pay, worker skills and employer demands; or (ii) residual government control in some industrial sectors that has generated high wages through monopoly rent sharing. We argue that the rise in China's industrial wage dispersion is primarily attributable to increasingly competitive labour markets, which have led to greater returns to schooling and to efficient redistribution of workers across major industry groups. We cannot reject the null hypothesis that the level or changes in government monopoly power has had negligible impact on China's rising industrial wage dispersion.
International Financial Flows in Low‐Income Countries
Authors: Lane Philip R.
Published: February 2015

For a sample of low‐income countries, we analyse the behaviour of international financial flows during three periods: (i) the 2003–2007 global boom; (ii) the 2008–2009 crisis; and (iii) the 2010–2012 recovery phase. In particular, we examine aid‐adjusted net financial inflows, debt inflows, foreign direct investment inflows and official reserve outflows. We highlight the role of country characteristics in explaining the cross‐country variation in international financial flows during these different phases.
Are Islamic Banks More Resilient During Financial Panics?
Authors: Farooq Moazzam , Zaheer Sajjad
Published: February 2015

Islamic banking is one of the fastest growing segments of the financial sector in developing countries. Rapid growth of this segment is accompanied with claims about its relative resilience to financial crises as compared to conventional banking. However, little empirical evidence is available to support such claims. Using data from Pakistan, where Islamic and conventional banks co‐exist, we compare the behaviour of Islamic and conventional banks during a financial panic. Our results show that Islamic bank branches are less prone to deposit withdrawals during financial panics, both unconditionally and after controlling for bank characteristics. The Islamic branches of banks that have both Islamic and conventional operations tend to attract (rather than lose) deposits during panics, which suggests a role for religious branding. We also find that Islamic bank branches grant more loans during financial panics and that their lending decisions are less sensitive to changes in deposits. Our findings suggest that greater financial inclusion of faith‐based groups may enhance the stability of the banking system.
Monetary Policy in Low Income Countries in the Face of The Global Crisis: A Structural Analysis
Authors: Baldini Alfredo , Benes Jaromir , Berg Andrew , Dao Mai C. , Portillo Rafael A.
Published: February 2015

We develop a dynamic stochastic general equilibrium model with a banking sector to analyse the impact of the financial crisis in developing countries and the role of the monetary policy response, with an application to Zambia. We view the crisis as a combination of three related shocks: a worsening in the terms of the trade, an increase in the country's risk premium and a decrease in the risk appetite of local banks. Model simulations broadly match the path of the economy during this period. We derive policy implications for central banks, and for dynamic stochastic general equilibrium modelling of monetary policy, in low‐income countries.
Role of Effective Composition on Antioxidant, Anti‐inflammatory, Sedative‐Hypnotic Capacities of 6 Common Edible Lilium Varieties
Authors: Wang Tingting , Huang Hanhan , Zhang Yao , Li Xia , Li Hongfa , Jiang Qianqian , Gao Wenyuan
Published: February 2015

Nine Lilium samples (belong to 6 different cultivars with different maturity stage) were qualitatively and quantitatively analyzed of total phenolics (TP), total flavonoids (TF), total saponins (TS), total carbohydrates (TC, polysaccharides), and soluble proteins contents (SP), and the monomeric components were quantified utilizing high‐performance liquid chromatography with photodiode array detector (HPLC‐PAD) associated with liquid chromatography–mass spectrometry (HPLC‐MS). Antioxidant activity (reducing power and DPPH radical scavenging activity), anti‐inflammatory (xylene‐induced mouse ear edema detumescent assay and carrageenan‐induced mouse paw edema detumescent assay), and sedative‐hypnotic capacities (sodium pentobarbital‐induced sleep assay) were comparatively evaluated in mouse model. Additionally, correlation analysis and principal component analysis were carried out to detect clustering and elucidate relationships between components’ concentrations and bioactivities to clarify the role of effective composition. Lilium bulbs in later maturity stage preliminary evidenced higher saponins content, and lower phenolic acids and flavonoids content. The result demonstrated that Lilium bulbs generally had distinct antioxidant, anti‐inflammatory, and sedative‐hypnotic capacities. Varieties statistically differed (P < 0.05) in chemical composition and bioactivities. Lilium varieties of Dongbei and Lanzhou presented potent sedative‐hypnotic effect and anti‐inflammatory activity. The antioxidant capacity was related to the phenolic acids and flavonoids contents, the anti‐inflammatory and sedative‐hypnotic capacities were related to the saponins content. This is first study presenting comprehensive description of common edible Lilium bulbs’ chemical compositions, sedative‐hypnotic, and anti‐inflammatory capacities grown in China. It would informatively benefit the genetic selection and cultivated optimization of Lilium varieties to improve nutritional quality, and promote Lilium bulbs as a therapeutic functional food worldwide.
A survey of genome‐wide single nucleotide polymorphisms through genome resequencing in the Périgord black truffle (Tuber melanosporum Vittad.)
Authors: Payen Thibaut , Murat Claude , Gigant Anaïs , Morin Emmanuelle , De Mita Stéphane , Martin Francis
Published: February 2015

The Périgord black truffle (Tuber melanosporum Vittad.), considered a gastronomic delicacy worldwide, is an ectomycorrhizal filamentous fungus that is ecologically important in Mediterranean French, Italian and Spanish woodlands. In this study, we developed a novel resource of single nucleotide polymorphisms (SNPs) for T. melanosporum using Illumina high‐throughput resequencing. The genome from six T. melanosporum geographical accessions was sequenced to a depth of approximately 20×. These geographical accessions were selected from different populations within the northern and southern regions of the geographical species distribution. Approximately 80% of the reads for each of the six resequenced geographical accessions mapped against the reference T. melanosporum genome assembly, estimating the core genome size of this organism to be approximately 110 Mbp. A total of 442 326 SNPs corresponding to 3540 SNPs/Mbps were identified as being included in all seven genomes. The SNPs occurred more frequently in repeated sequences (85%), although 4501 SNPs were also identified in the coding regions of 2587 genes. Using the ratio of nonsynonymous mutations per nonsynonymous site (pN) to synonymous mutations per synonymous site (pS) and Tajima's D index scanning the whole genome, we were able to identify genomic regions and genes potentially subjected to positive or purifying selection. The SNPs identified represent a valuable resource for future population genetics and genomics studies.
Candidates or Districts? Reevaluating the Role of Race in Voter Turnout
Authors: Fraga Bernard L.
Published: February 2015

Leading theories of race and participation posit that minority voters are mobilized by co‐ethnic candidates. However, past studies are unable to disentangle candidate effects from factors associated with the places from which candidates emerge. I reevaluate the links between candidate race, district composition, and turnout by leveraging a nationwide database of over 185 million individual registration records, including estimates for the race of every voter. Combining these records with detailed information about 3,000 recent congressional primary and general election candidates, I find that minority turnout is not higher in districts with minority candidates, after accounting for the relative size of the ethnic group within a district. Instead, Black and Latino citizens are more likely to vote in both primary and general elections as their share of the population increases, regardless of candidate race.
Confidence Intervals for Intraclass Correlation Coefficients in a Nonlinear Dose–Response Meta-Analysis
Authors: Demetrashvili Nino , Van den Heuvel Edwin R.
Published: February 2015

This work is motivated by a meta-analysis case study on antipsychotic medications. The Michaelis–Menten curve is employed to model the nonlinear relationship between the dose and receptor occupancy across multiple studies. An intraclass correlation coefficient (ICC) is used to quantify the heterogeneity across studies. To interpret the size of heterogeneity, an accurate estimate of ICC and its confidence interval is required. The goal is to apply a recently proposed generic beta-approach for construction the confidence intervals on ICCs for linear mixed effects models to nonlinear mixed effects models using four estimation methods. These estimation methods are the maximum likelihood, second-order generalized estimating equations and two two-step procedures. The beta-approach is compared with a large sample normal approximation (delta method) and bootstrapping. The confidence intervals based on the delta method and the nonparametric percentile bootstrap with various resampling strategies failed in our settings. The beta-approach demonstrates good coverages with both two-step estimation methods and consequently, it is recommended for the computation of confidence interval for ICCs in nonlinear mixed effects models for small studies.
Birds, Cattle, and Bracken Ferns: Bird Community Responses to a Neotropical Landscape Shaped by Cattle Grazing Activities
Authors: Maya‐Elizarrarás Elisa , Schondube Jorge E.
Published: February 2015

Large areas of tropical moist forests have been converted to cattle pastures, generating complex landscapes where different habitats are represented by small patches with an uneven spatial distribution. Here, we describe how bird communities respond to the different elements present in a livestock landscape that was originally dominated by tropical moist forest. We surveyed six habitats: open pastures, pastures with shrubs, early‐ and middle‐secondary forests, mature forest, and pastures invaded by bracken ferns (Pteridium aquilinum). Bird diversity was high in secondary and mature forests, and low in fern‐invaded sites and open pastures. Fern‐dominated sites had the lowest bird species richness, and trophic guild diversity of all habitats. Habitat structure affected both bird species richness and densities in similar ways. Tree species richness was the habitat attribute that had a bigger positive effect on bird species richness. Bird community structure varied among sampled habitats, separating habitats in two major groups (forests and pastures). Our data indicate that bracken fern‐invaded pastures were the worst habitat condition for avian communities. To increase bird diversity, we recommend to eliminate or manage bracken fern and to increase shrub and tree cover in open pastures to provide food resources and shelter for birds. Finally, we encourage the maintenance of secondary and mature forest remnants as a strategy to conserve resident birds within a landscape dominated by livestock activities.
High expression of interleukin‐11 is an independent indicator of poor prognosis in clear‐cell renal cell carcinoma
Authors: Pan Deng , Xu Le , Liu Haiou , Zhang Weijuan , Liu Weisi , Liu Yidong , Fu Qiang , Xu Jiejie
Published: February 2015

Interleukin‐11 (IL‐11), a member of the IL‐6 family of cytokines, exerts pleiotropic oncogenic activities by stimulating angiogenesis and metastasis in many cancer types. The present study aims to evaluate the impact of IL‐11 expression on recurrence and mortality of patients with clear‐cell renal cell carcinoma (ccRCC). We retrospectively enrolled 193 ccRCC patients undergoing nephrectomy at a single center. Clinicopathologic features, recurrence‐free survival (RFS) and overall survival (OS) were recorded. IL‐11 intensity was assessed by immunohistochemistry in tumor specimens. The Kaplan–Meier method was applied to compare survival curves. Cox regression models were used to analyze the impact of prognostic factors on RFS and OS. The concordance index (C‐index) was calculated to assess predictive accuracy. High IL‐11 expression is associated with increased risk of recurrence and poor survival for ccRCC patients (P < 0.001 and P < 0.001, respectively), especially those with early‐stage disease (TNM stage I + II). Multivariate analyses confirmed that IL‐11 expression was an independent prognostic factor for RFS and OS (P = 0.006 and P = 0.008, respectively). The predictive accuracy of well‐established prognostic models was improved when IL‐11 expression was integrated. In conclusion, high IL‐11 expression is an independent predictor of poor prognosis in ccRCC patients. It may help identify patients who could benefit from additional treatments and closer follow up.
Advanced human T‐cell leukemia virus type 1 carriers and early‐stage indolent adult T‐cell leukemia‐lymphoma are indistinguishable based on CADM1 positivity in flow cytometry
Authors: Kobayashi Seiichiro , Watanabe Eri , Ishigaki Tomohiro , Ohno Nobuhiro , Yuji Koichiro , Nakano Kazumi , Yamochi Tadanori , Watanabe Nobukazu , Tojo Arinobu , Watanabe Toshiki , Uchimaru Kaoru
Published: February 2015

We previously reported that the cell adhesion molecule 1 (CADM1) versus CD7 plot in flow cytometry reflects disease progression in human T‐cell leukemia virus type 1 (HTLV‐1) infection. In CD4+ cells from peripheral blood, CADM1−CD7+ (P), CADM1+CD7dim (D) and CADM1+CD7− (N) subpopulations are observed. The D and N subpopulations increase as asymptomatic HTLV‐1 carriers (AC) progress to indolent adult T‐cell leukemia‐lymphoma (ATL) and the N subpopulation then expands in aggressive ATL. In the present study we examined whether the analysis can estimate the risk of developing ATL in advanced AC. Peripheral blood samples from AC (N = 41) and indolent ATL patients (N = 19) were analyzed by flow cytometry using the CADM1 versus CD7 plot for CD4+ cells and inverse long PCR (clonality analysis) of FACS‐sorted subpopulations. Almost all AC with a high HTLV‐1 proviral load (>4 copies/100 cells) had a CADM1+ (D + N) frequency of >10%. AC with 25% < CADM1+ ≤ 50% contained expanded clones similar to smoldering‐type ATL. In many patients in the 25% < CADM1+ ≤ 50% group, the proportion of abnormal lymphocytes was distributed around the 5% line, which divides AC and smoldering‐type ATL in Shimoyama's classification. In conclusion, the CADM1 versus CD7 plot is useful for selection of putative high‐risk AC. The characteristics of some AC and smoldering ATL are said to be similar; however, long‐term follow up is required and the clinical outcome (e.g. rate of transformation) of these cases should be used to determine whether to include them in the same clinical category.
The impact of a dedicated multidisciplinary team on the management of early rectal cancer
Authors: Vaughan‐Shaw P. G. , Wheeler J. M. D. , Borley N. R.
Published: February 2015

Aim

Local excision of early rectal cancer (ERCa) offers comparable survival and reduced operative morbidity compared with radical surgery, yet it risks an adverse oncological outcome if performed in the wrong setting. This retrospective review considers the impact of the introduction of a specialist early rectal cancer multidisciplinary team (ERCa MDT) on the investigation and management of ERCa.

Method

A retrospective comparative cohort study was undertaken. Patients with a final diagnosis of pT1 rectal cancer at our unit were identified for two 12‐month periods before and after the introduction of the specialist ERCa MDT. Data on investigations and therapeutic interventions were compared.

Results

Nineteen patients from 2006 and 24 from 2011 were included. In 2006, 12 patients underwent MRI and four transrectal ultrasound (TRUS) examination, while in 2011, 18 and 20, respectively, received MRI and TRUS. In 2006 four patients underwent incidental ERCa polypectomy, with all having a positive resection margin leading to anterior resection. In 2011 only one case with a positive margin following extended endoscopic mucosal resection was identified. Definitive local excision without subsequent resection occurred in two patients in 2006 and in 16 in 2011.

Conclusion

The study demonstrates an improvement in preoperative ERCa staging, a reduction in margin positivity and an increase in the use of local excision following the implementation of a specialist ERCa MDT. The increased detection of rectal neoplasms through screening and surveillance programmes requires further investigation and management. A specialist ERCa MDT will improve management and should be available to all practitioners involved with patients with ERCa.