bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preoperative prediction of the individualized risk of early fetal death after laser therapy in twin‐to‐twin transfusion syndrome
Authors: Eixarch Elisenda , Valsky Dan , Deprest Jan , Baschat Ahmet A. , Lewi Liesbeth , Ortiz Javier U. , Martinez‐Crespo Josep Maria , Gratacos Eduard 
Published: June 2013

ABSTRACTObjectiveThe aim of this study is to evaluate the independent and combined value of gestational age, fetal weight, fetoplacental Doppler, and myocardial performance index for the prediction of individual risk of early (≤7 days) intrauterine fetal death (IUFD) after laser therapy in twin‐to‐twin transfusion syndrome (TTTS).Material and MethodsA consecutive series of 215 cases of TTTS treated with laser therapy in three centers was prospectively studied. Ultrasound evaluation within 24 h of surgery included estimated fetal weight discordance, umbilical artery, pulsatility index (PI) and diastolic flow evaluation, middle cerebral artery PI and middle cerebral artery peak systolic velocity, ductus venosus PI and atrial flow assessment, and modified myocardial performance index. Logistic regression analysis was used to explore the association of preoperative parameters with IUFD.ResultsIntrauterine fetal death occurred in 17 (7.9%) of the recipients and 33 (15.3%) donors (p = 0.016). The only independent predictors of IUFD in recipients was the middle cerebral artery peak systolic velocity >1.5 MoM (OR = 22, p = 0.015), but this event was present in only 3% of recipients. In donors, reverse end diastolic flow in the umbilical artery (OR = 14.748, p = 0.033), estimated fetal weight discordance (OR = 1.054, p = 0.036), and gestational age (OR = 0.757, p = 0.046) were independent predictors.ConclusionIn TTTS, preoperative fetal assessment can identify independent risk factors for early post‐operative IUFD, particularly in donors. © 2013 John Wiley & Sons, Ltd.
Octahydrogenated retinoic acid‐conjugated glycol chitosan nanoparticles as a novel carrier of azadirachtin: Synthesis, characterization, and in vitro evaluation
Authors: Lu Wei , Lu Meng‐Ling , Zhang Qing‐Peng , Tian Yong‐Qing , Zhang Zhi‐Xiang , Xu Han‐Hong 
Published: June 2013

ABSTRACTEnvironment‐friendly and controlled release formulation is highly promising for reducing environmental pollution and achieving the most effective utilization of pesticides. As a novel “green” nanocarrier of pesticides, amphiphilic self‐assembled nanoparticles were prepared by chemical conjugation of octahydrogenated retinoic acid (OR) to the backbone of glycol chitosan (GC). In aqueous media, the synthesized OR‐GC conjugates formed nanosized particles with a diameter of 257 nm. Hydrophobic azadirachtin (AZA) was efficiently loaded into the OR‐GC nanoparticles at a feed weight ratio of up to 1:4 using a simple dialysis method, the maximum drug‐loading efficiency of which was 74%. AZA‐OR‐GC (25 wt %) nanoparticles also showed sustained release of the incorporated AZA (65% of the loaded dose was released in 7 days at 27 °C in phosphate‐buffered saline; pH 7.2). Cytotoxicity tests and cell cycle arrest assays confirmed that OR‐GC exhibits good biocompatibility; AZA‐OR‐GC (25 wt %) nanoparticles also showed favorable inhibition of cell proliferation in Sl‐1 cells compared with free AZA in organic solvents. Overall, controlled release AZA‐OR‐GC may be a promising environment‐friendly formulation for integrated pest management. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3932–3940
Resistance and behavioural response of Plutella xylostella (Lepidoptera: Plutellidae) populations to Bacillus thuringiensis formulations
Authors: Zago Hugo B , Siqueira Herbert ÁA , Pereira Eliseu JG , Picanço Marcelo C , Barros Reginaldo 
Published: June 2013

AbstractBACKGROUNDInsecticide resistance is probably the major cause of control failure of Plutella xylostella (L.) in Brazil. In most production regions, the use of chemicals has been the prevalent method of control, with reduced efficacy through cropping seasons, even for the most recent use of products based on Bacillus thuringiensis (Bt). The current status of the resistance to these products was assessed, as well as the behavioural response of P. xylostella populations to Bt sprays.RESULTSMost populations of P. xylostella were resistant to Bt products, particularly to Xentari®WDG (2–54‐fold). Differences in walking characteristics of larvae were variable for most populations, for both Dipel®WP and Xentari®WDG, but not associated with resistance. Most females preferred to lay eggs on untreated surfaces and showed a reduced proportion of oviposition on treated surfaces that only correlated with resistance to Dipel®WP (r = −0.74, P = 0.02).CONCLUSIONBroad and indiscriminate use of Bt‐based products has selected Brazilian P. xylostella populations to resistance. Larval movement appears to be a resistance‐independent mechanism. Most populations of P. xylostella preferred to lay eggs on Bt‐free surfaces, which might be a result of growers' practice of spraying the cabbage head. Reduced oviposition on treated surfaces correlated with physiological resistance, suggesting a behavioural response among the Bt‐resistant colonies to Dipel®WP. © 2013 Society of Chemical Industry
A unified framework for testing linear‐invariant properties
Authors: Bhattacharyya Arnab , Grigorescu Elena , Shapira Asaf 
Published: June 2013

AbstractIn the study of property testing, a particularly important role has been played by linear invariant properties, i.e., properties of Boolean functions on the hypercube which are closed under linear transformations of the domain. Examples of such properties include linearity, Reed‐Muller codes, and Fourier sparsity. In this work, we describe a framework that can lead to a unified analysis of the testability of all linear‐invariant properties, drawing on techniques from additive combinatorics and from graph theory.Our main contributions here are the following:

We introduce a simple combinatorial condition, which we call subspace‐heredity, and conjecture that any property of Boolean functions satisfying it can be efficiently tested. Verifying this conjecture will unify many individual results in this area.
We show that if our conjecture holds, then one can obtain a simple combinatorial characterization of properties of Boolean functions that can be efficiently tested with one‐sided error, thus addressing a challenge posed by Sudan recently.
We introduce a new technique for proving the testability of Boolean functions. The main tool we develop is an extension of Green's arithmetic regularity lemma. Using it, we verify a special case of the conjecture.

Our approach here is motivated by techniques that proved to be very successful previously in studying the testability of graph properties.© 2013 Wiley Periodicals, Inc. Random Struct. Alg., 46, 232–260, 2015
Genotoxicity of cadmium chloride in the marine gastropod Nerita chamaeleon using comet assay and alkaline unwinding assay
Authors: Sarkar Anupam , Bhagat Jacky , Ingole Baban S. , Rao Durga P. , Markad Vijaykumar L. 
Published: June 2013

ABSTRACTThis paper presents an evaluation of the genotoxic effects of cadmium chloride (CdCl2) on marine gastropod, Nerita chamaeleon following the technique of comet assay and the DNA alkaline unwinding assay (DAUA). In this study, the extent of DNA damage in gill cells of N. chamaeleon was measured after in vivo exposure to four different concentrations (10, 25, 50, and 75 µg/L) of CdCl2. In vitro exposure of hydrogen peroxide (H2O2; 1, 10, 25, and 50 µM) of the gill cells showed a significant increase in the percentage tail DNA, Olive tail moment, and tail length (TL). Significant changes in percentage tail DNA by CdCl2 exposure were observed in all exposed groups of snails with respect to those in control. Exposure to 75 µg/L of CdCl2 produced significant decrease in DNA integrity as measured by DAUA at all duration with respect to control. In vivo exposure to different concentrations of CdCl2 (10, 25, 50, and 75 µg/L) to N. chamaeleon showed considerable increase in DNA damage as observed by both alkaline comet assay and the DAUA. The extent of DNA damage in marine gastropods determined by the application of alkaline comet assay and DAUA clearly indicated the genotoxic responses of marine gastropod, N. chamaeleon to a wide range of cadmium concentration in the marine environment. © 2013 Wiley Periodicals, Inc. Environ Toxicol 30: 177–187, 2015.
Large Normal and Intermediate Alleles in the Context of SCA2 Prenatal Diagnosis
Authors: Cruz‐Mariño Tania , Laffita‐Mesa Jose Miguel , Gonzalez‐Zaldivar Yanetza , Velazquez‐Santos Miguel , Aguilera‐Rodriguez Raul , Estupinan‐Rodriguez Annelie , Vazquez‐Mojena Yaime , Macleod Patrick , Paneque Milena , Velazquez‐Perez Luis 
Published: June 2013

AbstractIn 2001 a program for predictive testing of Spinocerebellar Ataxia type 2 was developed in Cuba, based on the detection of an abnormal CAG trinucleotide repeat expansion in the ATXN2 gene. A descriptive study was designed to assess the implications of ATXN2 large normal and intermediate alleles in the context of the SCA2 Prenatal Diagnosis Program. Four clinical scenarios were selected based upon the behaviour of large normal and intermediate alleles when passing from one generation to the next, showing expansions, contractions, or stability in the CAG repeat size. In some populations, traditional Mendelian risk figures of 0 % or 50 % may not be applicable due to the high frequency of unstable large normal alleles. Couples with no family history of SCA2 may have a >0 % risk of having an affected offspring. Similarly, couples in which there is both an expanded and a large normal allele may have a recurrence risk >50 %. It is imperative that these issues be addressed with these couples during genetic counseling. These recurrence risks have to be carefully estimated in the presence of such alleles (particularly alleles ≥27 CAG repeats), carriers need to be aware of the potential risk for their descendants, and programs for prenatal diagnosis must be available for them.
The protective role of endogenous bacterial communities in chironomid egg masses and larvae
Authors: Senderovich Yigal , Halpern Malka 
Published: June 2013

Abstract
Insects of the family Chironomidae, also known as chironomids, are distributed worldwide in a variety of water habitats. These insects display a wide range of tolerance toward metals and organic pollutions. Bacterial species known for their ability to degrade toxicants were identified from chironomid egg masses, leading to the hypothesis that bacteria may contribute to the survival of chironomids in polluted environments. To gain a better understanding of the bacterial communities that inhabit chironomids, the endogenous bacteria of egg masses and larvae were studied by 454-pyrosequencing. The microbial community of the egg masses was distinct from that of the larval stage, most likely due to the presence of one dominant bacterial Firmicutes taxon, which consisted of 28% of the total sequence reads from the larvae. This taxon may be an insect symbiont. The bacterial communities of both the egg masses and the larvae were found to include operational taxonomic units, which were closely related to species known as toxicant degraders. Furthermore, various bacterial species with the ability to detoxify metals were isolated from egg masses and larvae. Koch-like postulates were applied to demonstrate that chironomid endogenous bacterial species protect the insect from toxic heavy metals. We conclude that chironomids, which are considered pollution tolerant, are inhabited by stable endogenous bacterial communities that have a role in protecting their hosts from toxicants. This phenomenon, in which bacteria enable the continued existence of their host in hostile environments, may not be restricted only to chironomids.
Conservation Treatments: Cleaning, Consolidation and Protection
Authors: Dei L. 
Published: June 2013

In this chapter some general remarks dealing with cleaning, consolidation and protection will be given, in order to make the reader aware of the “practical” operations occurring during conservation and restoration. This contribution serves thus as a basis before introducing, in the following chapters, the new materials developed by nanoscience and nanotechnology.Some main principles concerning meanings, purposes and strategies of both conservation and restoration will be enunciated in the first part, highlighting the difference between these two terms. The chapter will then treat the two fundamental rules of scientific conservation and restoration: reversibility and physic-chemical compatibility. These two meaningful guidelines will be discussed in detail, showing how the history of the last 50 years of conservation and restoration evidenced the importance of taking into account both rules, emphasizing compatibility against reversibility. In particular, the physico-chemical compatibility of new materials with respect to original artworks materials will be highlighted as a new and modern golden rule. The chapter concludes by stating some general criteria for modern conservation and restoration, individuating in materials science and materials chemistry the research fields with strong potential to develop new art-compatible materials, and widely discussing some possible new educational profiles to inform conservation scientists to face the challenges of the third millennium in the field of science and technology as applied to the world's cultural heritage.
Emotional Facial and Vocal Expressions During Story Retelling by Children and Adolescents With High-Functioning Autism
Authors: Grossman Ruth B. , Edelson Lisa R. , Tager-Flusberg Helen 
Published: June 2013

Purpose
People with high-functioning autism (HFA) have qualitative differences in facial expression and prosody production, which are rarely systematically quantified. The authors' goals were to qualitatively and quantitatively analyze prosody and facial expression productions in children and adolescents with HFA.

Method
Participants were 22 male children and adolescents with HFA and 18 typically developing (TD) controls (17 males, 1 female). The authors used a story retelling task to elicit emotionally laden narratives, which were analyzed through the use of acoustic measures and perceptual codes. Naïve listeners coded all productions for emotion type, degree of expressiveness, and awkwardness.

Results
The group with HFA was not significantly different in accuracy or expressiveness of facial productions, but was significantly more awkward than the TD group. Participants with HFA were significantly more expressive in their vocal productions, with a trend for greater awkwardness. Severity of social communication impairment, as captured by the Autism Diagnostic Observation Schedule (ADOS; Lord, Rutter, DiLavore, & Risi, 1999), was correlated with greater vocal and facial awkwardness.

Conclusions
Facial and vocal expressions of participants with HFA were as recognizable as those of their TD peers but were qualitatively different, particularly when listeners coded samples with intact dynamic properties. These preliminary data show qualitative differences in nonverbal communication that may have significant negative impact on the social communication success of children and adolescents with HFA.
Infection Prevention and Control in the Intensive Care Unit: Open versus Closed Models of Care
Authors: Daneman Nick , Scales Damon C. , Lawless Bernard , Muscedere John , Blount Vanessa , Fowler Robert A. 
Published: June 2013

In the intensive care unit (ICU), our sickest patients receive our most invasive treatments and are therefore highly vulnerable to hospital-acquired infection. Up to one-third of ICU patients develop infectious complications of care, with associated increases in morbidity, mortality, and healthcare costs. Earlier research has indicated substantial heterogeneity in uptake of infection prevention best practices in North American hospitals, and this variability may also exist in ICUs. We hypothesized that ICU system-level characteristics, including closed model of care, academic affiliation, and availability of a dedicated infection control practitioner (ICP), may be associated with improved infection prevention practices.During July 2011, we conducted a province-wide survey of nurse directors in ICUs across Ontario, Canada (population, 12 million). We developed a 77-item questionnaire to broadly capture ICU structures and processes relevant to infection prevention. The questionnaire was developed (item generation and reduction) by the authors and was further improved through pilot and sensibility testing by 3 ICU nurse directors and 2 ICPs. It was then distributed via e-mail by the Ontario Ministry of Health and Long-Term Care Critical Care Secretariat to nurse directors of all ICUs. A second email was sent to nonrespondents 2 weeks later. Approval was granted by the research ethics board at Sunnybrook Health Sciences Centre in Toronto, Canada.
Haplotype assembly in polyploid genomes and identical by descent shared tracts
Authors: Aguiar Derek , Istrail Sorin 
Published: June 2013

Abstract
Motivation: Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction.
Results: In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory–based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data.
Availability and Implementation: HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/.
Contact: Sorin_Istrail@brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Short read alignment with populations of genomes
Authors: Huang Lin , Popic Victoria , Batzoglou Serafim 
Published: June 2013

Abstract
Summary: The increasing availability of high-throughput sequencing technologies has led to thousands of human genomes having been sequenced in the past years. Efforts such as the 1000 Genomes Project further add to the availability of human genome variation data. However, to date, there is no method that can map reads of a newly sequenced human genome to a large collection of genomes. Instead, methods rely on aligning reads to a single reference genome. This leads to inherent biases and lower accuracy. To tackle this problem, a new alignment tool BWBBLE is introduced in this article. We (i) introduce a new compressed representation of a collection of genomes, which explicitly tackles the genomic variation observed at every position, and (ii) design a new alignment algorithm based on the Burrows–Wheeler transform that maps short reads from a newly sequenced genome to an arbitrary collection of two or more (up to millions of) genomes with high accuracy and no inherent bias to one specific genome.
Availability: http://viq854.github.com/bwbble.
Contact: serafim@cs.stanford.edu
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
Authors: Miwa Makoto , Ohta Tomoko , Rak Rafal , Rowley Andrew , Kell Douglas B. , Pyysalo Sampo , Ananiadou Sophia 
Published: June 2013

Abstract
Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge.
Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches.
Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText.
Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/.
Contact: makoto.miwa@manchester.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.