bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species or local environment, what determines the infection of rodents by Toxoplasma gondii?
Authors: GOTTELAND CÉCILE , CHAVAL YANNICK , VILLENA ISABELLE , GALAN MAXIME , GEERS RÉGINE , AUBERT DOMINIQUE , POULLE MARIE-LAZARINE , CHARBONNEL NATHALIE , GILOT-FROMONT EMMANUELLE 
Published: October 2013

SUMMARYToxoplasmosis is largely present in rural areas but its spatial distribution in this environment remains poorly known. In particular, it is unclear if areas of high density of cats, the only hosts excreting Toxoplasma gondii, constitute foci of high prevalence. To improve our understanding of the spatial distribution of T. gondii in rural areas, we performed a serological survey in rodents from two villages in France. We trapped 710 rodents including commensal rats and meadow or forest voles and mice. The presence of T. gondii was examined using PCR, mice inoculation and modified agglutination test for antibodies (MAT). We conducted multivariate and discriminant analyses to identify biological, ecological or spatial variables that could explain T. gondii serology in rodents. We then used a logistic regression to assess the relative influence of each explanatory variable. Overall seroprevalence was 4·1%. Commensal-rats were more infected (12·5%) than non-commensal species (3·7%). However, the major determinant of the risk of infection was the distance to the nearest farm (OR = 0·75 for 100 m), which explained the risk in all species or non-commensal species only. We contrast the role of species characteristics and that of the local environment, and discuss the risk of environmental contamination for humans.
Integrating environmental policies towards a network of protected and quiet areas
Authors: VOTSI NEFTA-ELEFTHERIA P. , KALLIMANIS ATHANASIOS S. , MAZARIS ANTONIOS D. , PANTIS JOHN D. 
Published: October 2013

SummaryEnvironmental policy integration is an acknowledged principle of sustainable development. Spatial planning may be a useful means of integrating two policies with differing objectives. The Birds and Habitats Directives of the European Union (EU) aim at preserving biodiversity through the conservation of the Natura 2000 protected areas network, while the EU's Environmental Noise Directive aims at improving human health and wellbeing by controlling environmental noise, through the preservation of Quiet Areas (QAs). Using Greece as an example, an integrated network of Natura 2000 sites and QAs permitted the identification of potential spatial overlaps. The established Natura 2000 network incorporates more than 30% of the QAs located in the open countryside of Greece, and the combined network includes 17 out of the 19 conservation priority habitat types. Flagship species (like bear, wolf and wild goat) show a preference for sites containing QAs. It may be possible to combine these two EU policies efficiently, as protected and quiet areas appear to be mutually beneficial.
Idris, a general-purpose dependently typed programming language: Design and implementation
Authors: BRADY EDWIN 
Published: October 2013

AbstractMany components of a dependently typed programming language are by now well understood, for example, the underlying type theory, type checking, unification and evaluation. How to combine these components into a realistic and usable high-level language is, however, folklore, discovered anew by successive language implementors. In this paper, I describe the implementation ofIdris, a new dependently typed functional programming language.Idrisis intended to be ageneral-purposeprogramming language and as such provides high-level concepts such as implicit syntax, type classes anddonotation. I describe the high-level language and the underlying type theory, and present a tactic-based method forelaboratingconcrete high-level syntax with implicit arguments and type classes into a fully explicit type theory. Furthermore, I show how this method facilitates the implementation of new high-level language constructs.
Factors influencing the resilience of carers of individuals with dementia
Authors: Cherry MG , Salmon P , Dickson JM , Powell D , Sikdar S , Ablett J 
Published: October 2013

SummaryMost individuals with dementia live in the community, receiving care from family or lay carers. Carers’ wellbeing, and the quality of the care they provide, depends on their resilience in the face of the challenges associated with caring for someone with dementia. However, factors associated with carers’ resilience are not yet fully understood. The aim of this review is to present a narrative synthesis of factors, materials and resources associated with carers’ resilience. Electronic and hand searches identified relevant published literature, which was narratively synthesized. A framework consisting of three inter-related domains of factors influencing carers’ resilience emerged, encompassing: social and cultural factors; properties of the care relationship; and carers’ psychological factors. Holistic assessment based on this framework can help practitioners to identify vulnerable carers and to target help on factors that help to make them vulnerable but that are amenable to change.
Gamete quality of streaked prochilod Prochilodus lineatus (Characiformes) after GnRHa and dopamine antagonist treatment
Authors: Viveiros Ana T.M. , Gonçalves Antônio C.S. , Di Chiacchio Isabela M. , Nascimento Ariane F. , Romagosa Elizabeth , Leal Marcelo C. 
Published: October 2013

SummaryThe efficiency of Ovaprim™ salmon gonadotropin-releasing hormone agonist (GnRHa) and dopamine antagonist on the induction of spawning and spermiation in Prochilodus lineatus in comparison with the commonly used method using pituitary extract (PE) was evaluated. Females received PE at 0.5 + 5.0 mg/kg and Ovaprim™ at 0.05 + 0.45 ml/kg or at 0.125 + 0.375 ml/kg. All males received a first dose of PE at 0.4 mg/kg and then PE at 4.0 mg/kg or Ovaprim™ at 0.25 ml/kg. Oocyte, egg, larvae and sperm quality were evaluated. All females spawned and oocyte, egg and larvae quality were similar between Ovaprim™-treated (both doses) and PE-treated females. Data from females were pooled and the mean values were: 242 g ova weight, 15% ova index, 1209 oocytes/g ova, 284,539 oocytes/female, 183 oocytes/g body weight, 1.18 mm oocyte diameter, 49% fertilization rate, 43% hatching rate and 89% normal larvae. Sperm quality was similar between Ovaprim™-treated and PE-treated males. Data from males were pooled and the mean values of semen were: volume of 3.0 ml, 14.9 × 109 sperm/ml, osmolality of 283 mOsm/kg, pH of 7.4, 71% motile sperm, 217 μm/s curvilinear velocity, 102 μm/s straight-line velocity and 189 μm/s average path velocity. Ovaprim™ treatment can be used for commercial reproduction of P. lineatus, without any loss of gamete quality in comparison with PE treatment.
A novel DYRK1B inhibitor AZ191 demonstrates that DYRK1B acts independently of GSK3β to phosphorylate cyclin D1 at Thr286, not Thr288
Authors: Ashford Anne L. , Oxley David , Kettle Jason , Hudson Kevin , Guichard Sylvie , Cook Simon J. , Lochhead Pamela A. 
Published: October 2013

DYRK1B (dual-specificity tyrosine phosphorylation-regulated kinase 1B) is amplified in certain cancers and may be an oncogene; however, our knowledge of DYRK1B has been limited by the lack of selective inhibitors. In the present study we describe AZ191, a potent small molecule inhibitor that selectively inhibits DYRK1B in vitro and in cells. CCND1 (cyclin D1), a key regulator of the mammalian G1–S-phase transition, is phosphorylated on Thr286 by GSK3β (glycogen synthase kinase 3β) to promote its degradation. DYRK1B has also been proposed to promote CCND1 turnover, but was reported to phosphorylate Thr288 rather than Thr286. Using in vitro kinase assays, phospho-specific immunoblot analysis and MS in conjunction with AZ191 we now show that DYRK1B phosphorylates CCND1 at Thr286, not Thr288, in vitro and in cells. In HEK (human embryonic kidney)-293 and PANC-1 cells (which exhibit DYRK1B amplification) DYRK1B drives Thr286 phosphorylation and proteasome-dependent turnover of CCND1 and this is abolished by AZ191 or DYRK1B RNAi, but not by GSK3β inhibitors or GSK3β RNAi. DYRK1B expression causes a G1-phase cell-cycle arrest, but overexpression of CCND1 (wild-type or T286A) fails to overcome this; indeed, DYRK1B also promotes the expression of p21CIP1 (21 kDa CDK-interacting protein 1) and p27KIP1 (CDK-inhibitory protein 1). The results of the present study demonstrate for the first time that DYRK1B is a novel Thr286-CCND1 kinase that acts independently of GSK3β to promote CCND1 degradation. Furthermore, we anticipate that AZ191 may prove useful in defining further substrates and biological functions of DYRK1B.
Exocytosis acts as a modulator of the ILT4-mediated inhibition of neutrophil functions
Authors: Baudhuin Jeremy , Migraine Julie , Faivre Valerie , Loumagne Laure , Lukaszewicz Anne-Claire , Payen Didier , Favier Benoit 
Published: October 2013

SignificanceNeutrophils are key components of inflammatory responses and immune defense against pathogens. Neutrophil functions are tightly controlled by surface receptors. Our study shows that the engagement of immunoglobulin-like transcript 4 (ILT4) inhibitory receptor impairs phagocytosis and respiratory burst of neutrophils. Moreover, we found that following induction of neutrophil granule exocytosis, ILT4 expression increases as a result of the rapid translocation of an intracellular pool to the cell surface. This increase of ILT4 expression enhances the ILT4-mediated inhibition of neutrophil activity. Finally, ILT4 up-regulation on neutrophils is impaired in sepsis patients. These results reveal a unique mechanism of regulation of neutrophil functions through ILT4 and its exocytosis that may have implications in inflammatory disorders and immune responses.
Chromosome missegregation rate predicts whether aneuploidy will promote or suppress tumors
Authors: Silk Alain D. , Zasadil Lauren M. , Holland Andrew J. , Vitre Benjamin , Cleveland Don W. , Weaver Beth A. 
Published: October 2013

Significance
Aneuploidy, an abnormal chromosome content that commonly occurs because of errors in chromosome segregation, can promote or suppress tumor formation. What determines how aneuploidy influences tumorigenesis has remained unclear. Here we show that the rate of chromosome missegregation, rather than the level of accumulated aneuploidy, determines the effect on tumors. Increasing the rate of chromosome missegregation beyond a certain threshold suppresses tumors by causing cell death. Increasing errors of chromosome segregation did not affect tumor formation caused by genetic mutations that do not themselves alter chromosome inheritance. These results suggest that accelerating chromosome missegregation in chromosomally unstable tumors may be a useful strategy therapeutically.
Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs
Authors: Tae Hongseok , Kim Dong-Yun , McCormick John , Settlage Robert E. , Garner Harold R. 
Published: October 2013

Abstract
Motivation: Inferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise caused by the repetitive nature of microsatellites and the technologies used to generate raw sequence data.
Results: We have developed a program, GenoTan, using a discretized Gaussian mixture model combined with a rules-based approach to identify inherited variation of microsatellite loci from short sequence reads without paired-end information. It effectively distinguishes length variants from noise including insertion/deletion errors in homopolymer runs by addressing the bidirectional aspect of insertion and deletion errors in sequence reads. Here we first introduce a homopolymer decomposition method which estimates error bias toward insertion or deletion in homopolymer sequence runs. Combining these approaches, GenoTan was able to genotype 94.9% of microsatellite loci accurately from simulated data with 40x sequence coverage quickly while the other programs showed &lt;90% correct calls for the same data and required 5∼30× more computational time than GenoTan. It also showed the highest true-positive rate for real data using mixed sequence data of two Drosophila inbred lines, which was a novel validation approach for genotyping.
Availability: GenoTan is open-source software available at http://genotan.sourceforge.net.
Contact: garner@vbi.vt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information
Authors: Li Yue , Goldenberg Anna , Wong Ka-Chun , Zhang Zhaolei 
Published: October 2013

Abstract
Motivation: Systematic identification of microRNA (miRNA) targets remains a challenge. The miRNA overexpression coupled with genome-wide expression profiling is a promising new approach and calls for a new method that integrates expression and sequence information.
Results: We developed a probabilistic scoring method called targetScore. TargetScore infers miRNA targets as the transformed fold-changes weighted by the Bayesian posteriors given observed target features. To this end, we compiled 84 datasets from Gene Expression Omnibus corresponding to 77 human tissue or cells and 113 distinct transfected miRNAs. Comparing with other methods, targetScore achieves significantly higher accuracy in identifying known targets in most tests. Moreover, the confidence targets from targetScore exhibit comparable protein downregulation and are more significantly enriched for Gene Ontology terms. Using targetScore, we explored oncomir–oncogenes network and predicted several potential cancer-related miRNA–messenger RNA interactions.
Availability and implementation: TargetScore is available at Bioconductor: http://www.bioconductor.org/packages/devel/bioc/html/TargetScore.html.
Contact: yueli@cs.toronto.edu or zhaolei.zhang@utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Novel NLRP3/cryopyrin mutations and pro-inflammatory cytokine profiles in Behçet’s syndrome patients
Authors: Yüksel Şahru , Eren Elif , Hatemi Gülen , Sahillioğlu Ali Can , Gültekin Yetiş , Demiröz Duygu , Akdiş Cezmi , Fresko İzzet , Özören Nesrin 
Published: October 2013

Abstract
Behçet’s syndrome (BS) is a systemic inflammatory disorder with unknown etiology. Features of both innate and adaptive immunity have been claimed in the pathogenesis of BS. To test the possible dysregulation of the NLRP3/cryopyrin (Nod-like receptor with a pyrin domain 3) inflammasome, as a result of mutation(s), we performed single-strand conformation polymorphism analyses and/or sequencing of all the coding regions and intron–exon boundaries of NLRP3/cryopyrin and ASC (apoptosis-associated speck-like protein containing CARD) genes from Turkish BS patients and healthy controls. At the same time, we determined pro-inflammatory cytokine secretion profiles of peripheral blood cells in response to LPS treatment using ELISA. BS patients with vascular involvement showed significantly increased levels of TNF-α release at 2-, 4- and 8-h post-treatment and significantly increased IL-1β levels were detected at 2h (P = 0.005) and 4h (P = 0.025) (n = 10). We identified four mutations in the NLRP3/cryopyrin gene, V200M (n = 3/104) and T195M (n = 1/104), in BS patients but none in control samples. No mutations were detected in the ASC gene. The effect of these NLRP3/cryopyrin mutants on ASC speck assembly and IL-1β secretion was tested and the V200M mutant was shown to induce IL-1β secretion. Thus, it is likely that certain mutations in NLRP3/cryopyrin in combination with yet unknown other factors may contribute to the pro-inflammatory cytokine profiles in BS patients.
The Tomato 14-3-3 Protein TFT4 Modulates H+ Efflux, Basipetal Auxin Transport, and the PKS5-J3 Pathway in the Root Growth Response to Alkaline Stress
Authors: Xu Weifeng , Jia Liguo , Shi Weiming , Balu¡ka Franti¡ek , Kronzucker Herbert J. , Liang Jiansheng , Zhang Jianhua 
Published: October 2013

Abstract
Alkaline stress is a common environmental stress, in particular in salinized soils. Plant roots respond to a variety of soil stresses by regulating their growth, but the nature of the regulatory pathways engaged in the alkaline stress response (ASR) is not yet understood. Previous studies show that PIN-FORMED2, an auxin (indole-3-acetic acid [IAA]) efflux transporter, PKS5, a protein kinase, and DNAJ HOMOLOG3 (J3), a chaperone, play key roles in root H+ secretion by regulating plasma membrane (PM) H+-ATPases directly or by targeting 14-3-3 proteins. Here, we investigated the expression of all 14-3-3 gene family members (TOMATO 14-3-3 PROTEIN1 [TFT1]–TFT12) in tomato (Solanum lycopersicum) under ASR, showing the involvement of four of them, TFT1, TFT4, TFT6, and TFT7. When these genes were separately introduced into Arabidopsis (Arabidopsis thaliana) and overexpressed, only the growth of TFT4 overexpressors was significantly enhanced when compared with the wild type under stress. H+ efflux and the activity of PM H+-ATPase were significantly enhanced in the root tips of TFT4 overexpressors. Microarray analysis and pharmacological examination of the overexpressor and mutant plants revealed that overexpression of TFT4 maintains primary root elongation by modulating PM H+-ATPase-mediated H+ efflux and basipetal IAA transport in root tips under alkaline stress. TFT4 further plays important roles in the PKS5-J3 signaling pathway. Our study demonstrates that TFT4 acts as a regulator in the integration of H+ efflux, basipetal IAA transport, and the PKS5-J3 pathway in the ASR of roots and coordinates root apex responses to alkaline stress for the maintenance of primary root elongation.
The adjudication of Shari'ah issues in Islamic financial contracts
Authors: Trakic Adnan 
Published: October 2013

Purpose
– This research aims to explore the possibility of raising and adjudicating Shari'ah issues in Islamic financial contracts before the secular courts with specific reference to the UK and Malaysia.

Design/methodology/approach
– This is a legal research, and therefore, the paper uses the qualitative research methodology whereby a content analysis, in-depth case study, and library-based research were mainly used.

Findings
– Shari'ah issues raised before the UK courts, and arguably, before the secular courts in other Western jurisdictions, would not be adjudicated and enforced. English courts, in particular, would decide Islamic financial contracts according to the English law, disregarding Shari'ah issues. Conversely, Shari'ah issues raised before Malaysian civil courts would be duly adjudicated and enforced. The civil court is bound, by the new Central Bank of Malaysia Act 2009, to refer those issues to the Shari'ah Advisory Council of the Central Bank of Malaysia for them to be ascertained. The subsequent ruling of the SAC is binding on the courts.

Originality/value
– The Malaysian model for the adjudication of Shari'ah issues in Islamic financial contracts is very effective. Therefore, the research proposes to the parties in international Islamic financial contracts to choose Malaysian law as the law of reference and Malaysian courts as the forum for settlement of disputes. The Malaysian model, being already tested, can also be successfully exported to other countries wishing to introduce or develop Islamic finance.
Anomaly detection based on hybrid artificial immune principles
Authors: Salah Sobh Tarek 
Published: October 2013

Purpose– Anomaly detection of network attacks has become a high priority because of the need to guarantee security, privacy and reliability. This work aims to describe both intelligent immunological approaches and traditional monitoring systems for anomaly detection.Design/methodology/approach– Author investigated different artificial immune system (AIS) theories and proposes how to combine different ideas to solve problems of network security domain. An anomaly detection system that applies those ideas was built and tested in a real time environment, to test the pros and cons of AIS and clarify its applicability. Rather than building a detailed signature based model of intrusion detection system, the scope of this study tries to explore the principle in an immune network focusing on its self-organization, adaptive learning capability, and immune feedback.Findings– The natural immune system has its own intelligent mechanisms to detect the foreign bodies and fight them and without it, an individual cannot live, even just for several days. Network attackers evolved new types of attacks. Attacks became more complex, severe and hard to detect. This results in increasing needs for network defense systems, especially those with ability to extraordinary approaches or to face the dynamic nature of continuously changing network threats. KDD CUP'99 dataset are used as a training data to evaluate the proposed hybrid artificial immune principles anomaly detection. The average cost of the proposed model was 0.1195 where that the wining of KDD99 dataset computation had 0.233.Originality/value– It is original to introduce investigation on the vaccination biological process. A special module was built to perform this process and check its usage and how it could be formulated in artificial life.
Estimates on the effectiveness of web application firewalls against targeted attacks
Authors: Holm Hannes , Ekstedt Mathias 
Published: October 2013

Purpose– The purpose of this paper is to estimate the effectiveness of web application firewalls (WAFs) at preventing injection attacks by professional penetration testers given presence or absence of four conditions: whether there is an experienced operator monitoring the WAF; whether an automated black box tool has been used when tuning the WAF; whether the individual tuning the WAF is an experienced professional; and whether significant effort has been spent tuning the WAF.Design/methodology/approach– Estimates on the effectiveness of WAFs are made for 16 operational scenarios utilizing judgments by 49 domain experts participating in a web survey. The judgments of these experts are pooled using Cooke's classical method.Findings– The results show that the median prevention rate of a WAF is 80 percent if all measures have been employed. If no measure is employed then its median prevention rate is 25 percent. Also, there are no strong dependencies between any of the studied measures.Research limitations/implications– The results are only valid for the attacker profile of a professional penetration tester who prepares one week for attacking a WA protected by a WAF.Practical implications– The competence of the individual(s) tuning a WAF, employment of an automated black box tool for tuning and the manual effort spent on tuning are of great importance for the effectiveness of a WAF. The presence of an operator monitoring it has minor positive influence on its effectiveness.Originality/value– WA vulnerabilities are widely considered a serious concern. To manage them in deployed software, many enterprises employ WAFs. However, the effectiveness of this type of countermeasure under different operational scenarios is largely unknown.