bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility and Validation of Corrected Left Ventricular Filling Time for Determining the Optimal AV Delay in Patients Receiving Cardiac Resynchronization Therapy
Authors: Higuchi Rumi , Tada Hiroshi , Okaniwa Hiroki , Nakajima Tsutomu , Takemura Naoki , Fuke Etsuko , Sato Chizuru , Hayashi Tatsuya , Miki Yuko , Sakamoto Tamotsu , Fukasawa Rie , Kumagai Koji , Naito Shigeto , Oshima Shigeru 
Published: August 2012

AbstractBackground: Optimizing the atrio‐ventricular delay (AVD) is important for increasing the left ventricular (LV) preload in patients receiving cardiac resynchronization therapy (CRT). The optimal AVD may be considered an AVD in which the maximum LV filling time (LVFT) is obtained. However, it is unclear whether or not the optimal AVD determined by Ritter's method (AVD‐Ritter) is identical to the AVD in which the maximum LVFT is obtained. The aim of this study was to clarify this point.Methods: In 17 patients who received CRT, the optimal AVD was determined by Ritter's method and the FT method. Eleven (65%) patients had 1° AV block. We measured the LVFT and R‐R time when the AVD was prolonged by 20 ms increments from 80 ms to 180 ms. In the FT method, the optimal AVD (AVD‐FT) was defined as the AVD in which the corrected LVFT (LVFTc) was maximally prolonged. The AVD‐Ritter and AVD‐FT were both determined during atrial pacing (Ap) and sensing (As). The LVFTc at each optimal AVD was also measured and compared.Results: During As, the AVD‐Ritter (114 ± 20 ms) showed a marginally significant difference when compared to the AVD‐FT (95 ± 18 ms; p = 0.053). However, during Ap, the AVD‐Ritter (138 ± 32 ms) was significantly longer than the AVD‐ET (113 ± 20 ms; p = 0.017). The LVFTc with the AVD‐Ritter was shorter than the AVD‐FT (As: 538 ± 40 vs. 557 ± 34 [ms], p = 0.002; Ap: 532 ± 37 vs. 563 ± 33 [ms], p = 0.023). These results were comparable with those obtained in the 11 patients with 1° AV block.Conclusions: The AVD‐Ritter during Ap may become shorter than that for the AVD‐FT because of the latency in patients receiving CRT. The FT method might be better than the AVD‐Ritter method to optimize the AVD in those patients.
Examination of the Effective Utilization of the CARELINK® Remote Monitoring System after its Introduction
Authors: Miyamoto Satoshi , Nakano Yukiko , Okahara Shigeyuki , Takahashi Hidenobu , Matsuzaki Hisayasu , Oda Noboru , Imai Katsuhiko , Sueda Taijirou , Kihara Yasuki 
Published: August 2012

AbstractBackground: Japan started using the CARELINK® (Medtronic, Inc, Minneapolis, MN, USA) remote monitoring system in April 2009. However, in some cases, the device failed to transmit a message after registration or according to schedule. We investigated the difference between patients who could make effective use of CARELINK® system and those who could not.Subjects and Method: Sixty patients who had registered until December 2009 at our institution were analyzed. These patients were divided into two groups: those who were able to use the device effectively (group G, n = 49) and those who were not (group F = 11). Patient background, automatic or manual telemetries, new or existing implant patient, presence of adverse events, and the use or non‐use of a checklist at the time of introduction were compared between the two groups.Results: In group G, more patients used a checklist at the time of introduction than that in group F (use of checklist/total, 31/49 in group G vs. 3/11 in group F; P, 0.029). No significant difference was observed in other factors between the two groups.Conclusion: We consider that the method used to explain the system are important to make the patients understand handling methods of CARELINK® system. The number of patients introduced to remote monitoring of implantable devices will continue to increase in the future; therefore, we must continue to develop innovative approaches for their effective us.
The QT Intervals in Infancy and Time for Infantile ECG Screening for Long QT Syndrome
Authors: Yoshinaga Masao , Kato Yoshiaki , Nomura Yuichi , Hazeki Daisuke , Yasuda Toshiaki , Takahashi Kazuhiro , Higaki Takashi , Tanaka Yuji , Wada Akihiro , Horigome Hitoshi , Takahashi Hideto , Ueno Kentaro , Suzuki Hiroshi , Nagashima Masami 
Published: August 2012

Background: Electrocardiographic and molecular studies have clarified an association between sudden infant death syndrome (SIDS) and long QT syndrome (LQTS), and few data are available for the QT interval in infancy from birth to 1 year of age. Appropriate time of electrocardiographic screening is not clarified. Medical examinations during infancy are mandatory in Japan.Methods and Results: The study population included 1,058 infants. Electrocardiograms were collected with information of infants at birth and at examination. The QT intervals of three consecutive beats were measured in lead V5. Statistical analysis revealed that the following formula was appropriate to minimize the effect of heart rate for infants: corrected QT interval; QTc = QT interval/RR interval 0.43. Subjects were divided into four groups as follows: 0–2, 3–6, 6–11, and 12–52 weeks of age. Tukey's multiple comparison showed that the QTc intervals were longest (p < 0:0001) in subjects who were 6–11 weeks of age.Conclusions: The QTc interval showed the highest peak at 6‐11 weeks of age in infancy. The peak period of occurrence of SIDS is at approximately 2 months of age. An appropriate time of electrocardiographic screening for QT prolongation will be one month of age, and follow‐up studies are needed.
Mediating Labour: An Introduction
Authors: Bosma Ulbe , van Nederveen Meerkerk Elise , Sarkar Aditya 
Published: August 2012

SummaryThe essays in this volume aim to explain the evolution and persistence of various practices of indirect labour recruitment. Labour intermediation is understood as a global phenomenon, present for many centuries in most countries of the world, and taking on a wide range of forms: varying from outright trafficking to job placement in the context of national employment policies. By focusing on the actual practices of different types of labour mediators in various regions of the world during the nineteenth and twentieth centuries, and by highlighting both the national as well as the international and translocal contexts of these practices, this volume intends to further a historically informed global perspective on the subject.
New species and new records of the lichen genusPorpidia(Lecideaceae) from western China
Authors: WANG Xin Yu , ZHANG Lu Lu , JOSHI Yogesh , WANG Hai Ying , HUR Jae Seoun 
Published: August 2012

AbstractA taxonomic study of the genusPorpidiain western China revealed two species hitherto unknown to science,Porpidia squamosaandP. shangrila, along with three new records for the country:P. flavicunda, P. soredizodesandP. thomsonii. Detailed taxonomic descriptions, ecological and chemical characters, and illustrations are provided for the new taxa, and brief taxonomic descriptions provided for the newly reported taxa. A key to all known ChinesePorpidiaspecies is also provided.
Presence of three distinct genotypes within the Paragonimus westermani complex in northeastern India
Authors: DEVI K. REKHA , NARAIN KANWAR , MAHANTA JAGADISH , NIRMOLIA TULIKA , BLAIR DAVID , SAIKIA SIDHARTHA P. , AGATSUMA TAKESHI 
Published: August 2012

SUMMARYThe name Paragonimus westermani (Kerbert, 1878) is commonly applied to members of a species complex that includes the well-known Asian lung fluke of medical and veterinary importance. Unambiguous molecular and morphological evidence showing the presence of a member of the complex in India has recently been published. In the present study we report the occurrence of 2 more members of the P. westermani complex in northeastern (NE) India. Surveys of the freshwater crabs Maydelliatelphusa lugubris in NE India revealed 2 morphologically distinct types of lung fluke metacercariae. Phylogenetic analyses, using DNA sequences from ITS2, 28S and cox1 gene regions indicate that these lung metacercariae belong to P. westermani complex. Type 1 metacercariae have a more basal position within the complex whereas type 2 metacercariae are closely related to the relatively derived forms of P. westermani from NE Asia (Japan, Korea, China) and Vietnam. A third type of metacercaria (type 3), detected in another crab host, Sartoriana spinigera in Assam, was phylogenetically close to P. siamensis, also a member of the P. westermani group. Molecular evidence has demonstrated the existence of 3 genotypes of lung flukes within the Paragonimus westermani complex in NE India. Two of these were previously unknown.
Towards a new, ecologically targeted approach to monitoring wild bird populations for avian influenza viruses
Authors: SCHOENE C. U. R. , STAUBACH C. , GRUND C. , GLOBIG A. , KRAMER M. , WILKING H. , BEER M. , CONRATHS F. J. , HARDER T. C. ,   the BL Monitoring Group
Published: August 2012

SUMMARYPrevalence monitoring of avian influenza in wild bird populations is important to estimate risks for the occurrence of potentially zoonotic and economically disastrous outbreaks of highly pathogenic avian influenza virus (AIV) in poultry worldwide. A targeted, cost-effective monitoring method for AIV in wild birds was developed, which is based on monitoring results for AIV in Germany and information on the distribution and abundance of wild bird species in selected habitat types. Spatial data were combined with virological and outbreak data for the period of 1 January 2006 to 31 December 2010. Using Germany as an example, we identified 11 indicator species. By concentrating monitoring efforts on these species in spatially confined locations, we propose a targeted and more cost-effective risk-based AIV monitoring approach that can be adapted universally for the identification of wild bird indicator species worldwide with the perspective of reducing sample sizes (and costs) without impairing the validity of the results.
Worldwide implementation of the WHO Child Growth Standards
Authors: de Onis Mercedes , Onyango Adelheid , Borghi Elaine , Siyam Amani , Blössner Monika , Lutter Chessa 
Published: August 2012

AbstractObjectiveTo describe the worldwide implementation of the WHO Child Growth Standards (‘WHO standards’).DesignA questionnaire on the adoption of the WHO standards was sent to health authorities. The questions concerned anthropometric indicators adopted, newly introduced indicators, age range, use of sex-specific charts, previously used references, classification system, activities undertaken to roll out the standards and reasons for non-adoption.SettingWorldwide.SubjectsTwo hundred and nineteen countries and territories.ResultsBy April 2011, 125 countries had adopted the WHO standards, another twenty-five were considering their adoption and thirty had not adopted them. Preference for local references was the main reason for non-adoption. Weight-for-age was adopted almost universally, followed by length/height-for-age (104 countries) and weight-for-length/height (eighty-eight countries). Several countries (thirty-six) reported newly introducing BMI-for-age. Most countries opted for sex-specific charts and the Z-score classification. Many redesigned their child health records and updated recommendations on infant feeding, immunization and other health messages. About two-thirds reported incorporating the standards into pre-service training. Other activities ranged from incorporating the standards into computerized information systems, to providing supplies of anthropometric equipment and mobilizing resources for the standards’ roll-out.ConclusionsFive years after their release, the WHO standards have been widely scrutinized and implemented. Countries have adopted and harmonized best practices in child growth assessment and established the breast-fed infant as the norm against which to assess compliance with children's right to achieve their full genetic growth potential.
Birth of ball lightning
Authors: Lowke J. J. , Smith D. , Nelson K. E. , Crompton R. W. , Murphy A. B. 
Published: August 2012

Many observations of ball lightning report a ball of light, about 10 cm in diameter, moving at about walking speed, lasting up to 20 s and frequently existing inside of houses and even aeroplanes. The present paper reports detailed observations of the initiation or birth of ball lightning. In two cases, navigation crew of aircraft saw ball lightning form at the windscreen inside the cockpit of their planes. In the first case, the ball lightning occurred during a thunderstorm, with much lightning activity outside of the plane. In the second case, large “horns” of electrical corona were seen outside of the plane at the surface of the radome, just prior to the formation of the ball lightning. A third case reports ball lightning formed inside of a house, during a thunderstorm, at a closed glass window. It is proposed, based on two‐dimensional calculations of electron and ion transport, that ball lightning in these cases is driven and formed by atmospheric ions impinging and collecting on the insulating surface of the glass or Perspex windows. This surface charge can produce electric fields inside of the cockpit or room sufficient to sustain an electric discharge. Charges of opposite sign to those outside of the window accumulate on the inside surface of the glass, leaving a ball of net charge moving inside of the cockpit or room to produce a pulsed discharge on a microsecond time scale.
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment
Authors: Ma Haisu , Zhao Hongyu 
Published: August 2012

Abstract
Motivation: It is well recognized that the effects of drugs are far beyond targeting individual proteins, but rather influencing the complex interactions among many relevant biological pathways. Genome-wide expression profiling before and after drug treatment has become a powerful approach for capturing a global snapshot of cellular response to drugs, as well as to understand drugs’ mechanism of action. Therefore, it is of great interest to analyze this type of transcriptomic profiling data for the identification of pathways responsive to different drugs. However, few computational tools exist for this task.
Results: We have developed FacPad, a Bayesian sparse factor model, for the inference of pathways responsive to drug treatments. This model represents biological pathways as latent factors and aims to describe the variation among drug-induced gene expression alternations in terms of a much smaller number of latent factors. We applied this model to the Connectivity Map data set (build 02) and demonstrated that FacPad is able to identify many drug–pathway associations, some of which have been validated in the literature. Although this method was originally designed for the analysis of drug-induced transcriptional alternation data, it can be naturally applied to many other settings beyond polypharmacology.
Availability and implementation: The R package ‘FacPad’ is publically available at: http://cran.open-source-solution.org/web/packages/FacPad/
Contact: hongyu.zhao@yale.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Positive-unlabeled learning for disease gene identification
Authors: Yang Peng , Li Xiao-Li , Mei Jian-Ping , Kwoh Chee-Keong , Ng See-Kiong 
Published: August 2012

Abstract
Background: Identifying disease genes from human genome is an important but challenging task in biomedical research. Machine learning methods can be applied to discover new disease genes based on the known ones. Existing machine learning methods typically use the known disease genes as the positive training set P and the unknown genes as the negative training set N (non-disease gene set does not exist) to build classifiers to identify new disease genes from the unknown genes. However, such kind of classifiers is actually built from a noisy negative set N as there can be unknown disease genes in N itself. As a result, the classifiers do not perform as well as they could be.
Result: Instead of treating the unknown genes as negative examples in N, we treat them as an unlabeled set U. We design a novel positive-unlabeled (PU) learning algorithm PUDI (PU learning for disease gene identification) to build a classifier using P and U. We first partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN and weak negative set WN. The weighted support vector machines are then used to build a multi-level classifier based on the four training sets and positive training set P to identify disease genes. Our experimental results demonstrate that our proposed PUDI algorithm outperformed the existing methods significantly.
Conclusion: The proposed PUDI algorithm is able to identify disease genes more accurately by treating the unknown data more appropriately as unlabeled set U instead of negative set N. Given that many machine learning problems in biomedical research do involve positive and unlabeled data instead of negative data, it is possible that the machine learning methods for these problems can be further improved by adopting PU learning methods, as we have done here for disease gene identification.
Availability and implementation: The executable program and data are available at http://www1.i2r.a-star.edu.sg/∼xlli/PUDI/PUDI.html.
Contact: xlli@i2r.a-star.edu.sg or yang0293@e.ntu.edu.sg
Supplementary information: Supplementary Data are available at Bioinformatics online.
RazerS 3: Faster, fully sensitive read mapping
Authors: Weese David , Holtgrewe Manuel , Reinert Knut 
Published: August 2012

Abstract
Motivation: During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that perform fast, with high sensitivity, and are able to deal with long reads and a large absolute number of insertions and deletions.
Results: RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work, we propose the successor RazerS 3, which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers’ bit-vector algorithm for verification, memory-saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular, long reads with many errors. We extensively compare RazerS 3 with other popular read mappers and show that its results are often superior to them in terms of sensitivity while exhibiting practical and often competitive run times. In addition, RazerS 3 works without a pre-computed index.
Availability and Implementation: Source code and binaries are freely available for download at http://www.seqan.de/projects/razers. RazerS 3 is implemented in C++ and OpenMP under a GPL license using the SeqAn library and supports Linux, Mac OS X and Windows.
Contact: david.weese@fu-berlin.de
Supplementary information: Supplementary data are available at Bioinformatics online.
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
Authors: Kumar Sudhir , Stecher Glen , Peterson Daniel , Tamura Koichiro 
Published: August 2012

Abstract
Summary: There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA’s graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis.
Availability: http://www.megasoftware.net/
Contact: s.kumar@asu.edu
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes
Authors: Kumar Narendra , Skolnick Jeffrey 
Published: August 2012

Abstract
Summary: High-quality enzyme function annotation is essential for understanding the biochemistry, metabolism and disease processes of organisms. Previously, we developed a multi-component high-precision enzyme function predictor, EFICAz2 (enzyme function inference by a combined approach). Here, we present an updated improved version, EFICAz2.5, that is trained on a significantly larger data set of enzyme sequences and PROSITE patterns. We also present the results of the application of EFICAz2.5 to the enzyme reannotation of 396 genomes cataloged in the ENSEMBL database.
Availability: The EFICAz2.5 server and database is freely available with a use-friendly interface at http://cssb.biology.gatech.edu/EFICAz2.5.
Contact: skolnick@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Optimal timepoint sampling in high-throughput gene expression experiments
Authors: Rosa Bruce A. , Zhang Ji , Major Ian T. , Qin Wensheng , Chen Jin 
Published: August 2012

Abstract
Motivation: Determining the best sampling rates (which maximize information yield and minimize cost) for time-series high-throughput gene expression experiments is a challenging optimization problem. Although existing approaches provide insight into the design of optimal sampling rates, our ability to utilize existing differential gene expression data to discover optimal timepoints is compelling.
Results: We present a new data-integrative model, Optimal Timepoint Selection (OTS), to address the sampling rate problem. Three experiments were run on two different datasets in order to test the performance of OTS, including iterative-online and a top-up sampling approaches. In all of the experiments, OTS outperformed the best existing timepoint selection approaches, suggesting that it can optimize the distribution of a limited number of timepoints, potentially leading to better biological insights about the resulting gene expression patterns.
Availability: OTS is available at www.msu.edu/∼jinchen/OTS.
Contact: wqin@lakeheadu.ca; jinchen@msu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.