bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of bacterial core communities in the central Baltic by comparative RNA–DNA-based fingerprinting provides links to structure–function relationships
Authors: Brettar Ingrid , Christen Richard , Höfle Manfred G 
Published: June 2011

Abstract
Understanding structure–function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.
SEAL: a distributed short read mapping and duplicate removal tool
Authors: Pireddu Luca , Leo Simone , Zanetti Gianluigi 
Published: June 2011

Abstract
Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode.
Availability: SEAL is available online at http://biodoop-seal.sourceforge.net/.
Contact: luca.pireddu@crs4.it
JSBML: a flexible Java library for working with SBML
Authors: Dräger Andreas , Rodriguez Nicolas , Dumousseau Marine , Dörr Alexander , Wrzodek Clemens , Le Novère Nicolas , Zell Andreas , Hucka Michael 
Published: June 2011

Abstract
Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java™ programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend.
Availability: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.
Contact: jsbml-team@sbml.org
Supplementary information: Supplementary data are available at Bioinformatics online.
GeneNetWeaver:in silicobenchmark generation and performance profiling of network inference methods
Authors: Schaffter Thomas , Marbach Daniel , Floreano Dario 
Published: June 2011

AbstractMotivation: Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate benchmarks and the lack of tools for a differentiated analysis of network predictions on such benchmarks.Results: Here, we describe a novel and comprehensive method for in silico benchmark generation and performance profiling of network inference methods available to the community as an open-source software called GeneNetWeaver (GNW). In addition to the generation of detailed dynamical models of gene regulatory networks to be used as benchmarks, GNW provides a network motif analysis that reveals systematic prediction errors, thereby indicating potential ways of improving inference methods. The accuracy of network inference methods is evaluated using standard metrics such as precision-recall and receiver operating characteristic curves. We show how GNW can be used to assess the performance and identify the strengths and weaknesses of six inference methods. Furthermore, we used GNW to provide the international Dialogue for Reverse Engineering Assessments and Methods (DREAM) competition with three network inference challenges (DREAM3, DREAM4 and DREAM5).Availability: GNW is available at http://gnw.sourceforge.net along with its Java source code, user manual and supporting data.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: dario.floreano@epfl.ch
Human Subthalamic Neuron Spiking Exhibits Subtle Responses to Sedatives
Authors: MacIver M. Bruce , Bronte-Stewart Helen M. , Henderson Jaimie M. , Jaffe Richard A. , Brock-Utne John G. 
Published: June 2011

Background
During deep brain stimulation implant surgery, microelectrode recordings are used to map the location of targeted neurons. The effects produced by propofol or remifentanil on discharge activity of subthalamic neurons were studied intraoperatively to determine whether they alter neuronal activity.

Methods
Microelectrode recordings from 11 neurons, each from individual patients, were discriminated and analyzed before and after administration of either propofol or remifentanil. Subthalamic neurons in rat brain slices were recorded in patch-clamp to investigate cellular level effects.

Results
Neurons discharged at 42 ± 9 spikes/s (mean ± SD) and showed a common pattern of inhibition that lasted 4.3 ms. Unique discharge profiles were evident for each neuron, seen using joint-interval analysis. Propofol (intravenous bolus 0.3 mg/kg) produced sedation, with minor effects on discharge activity (less than 2.0% change in frequency). A prolongation of recurrent inhibition was evident from joint-interval analysis, and propofol's effect peaked within 2 min, with recovery evident at 10 min. Subthalamic neurons recorded in rat brain slices exhibited inhibitory synaptic currents that were prolonged by propofol (155%) but appeared to lack tonic inhibitory currents. Propofol did not alter membrane potential, membrane resistance, current-evoked discharge, or holding current during voltage clamp. Remifentanil (0.05 mg/kg) had little effect on overall subthalamic neuron discharge activity and did not prolong recurrent inhibition.

Conclusions
These results help to characterize the circuit properties and feedback inhibition of subthalamic neurons and demonstrate that both propofol and remifentanil produce only minor alterations of subthalamic neuron discharge activity that should not interfere with deep brain stimulation implant surgery.
Effect of Head Elevation on Passive Upper Airway Collapsibility in Normal Subjects during Propofol Anesthesia
Authors: Kobayashi Masato , Ayuse Takao , Hoshino Yuko , Kurata Shinji , Moromugi Shunji , Schneider Hartmut , Kirkness Jason P. , Schwartz Alan R. , Oi Kumiko 
Published: June 2011

Background
Head elevation can restore airway patency during anesthesia, although its effect may be offset by concomitant bite opening or accidental neck flexion. The aim of this study is to examine the effect of head elevation on the passive upper airway collapsibility during propofol anesthesia.

Method
Twenty male subjects were studied, randomized to one of two experimental groups: fixed-jaw or free-jaw. Propofol infusion was used for induction and to maintain blood at a constant target concentration between 1.5 and 2.0 μg/ml. Nasal mask pressure (PN) was intermittently reduced to evaluate the upper airway collapsibility (passive PCRIT) and upstream resistance (RUS) at each level of head elevation (0, 3, 6, and 9 cm). The authors measured the Frankfort plane (head flexion) and the mandible plane (jaw opening) angles at each level of head elevation. Analysis of variance was used to determine the effect of head elevation on PCRIT, head flexion, and jaw opening within each group.

Results
In both groups the Frankfort plane and mandible plane angles increased with head elevation (P < 0.05), although the mandible plane angle was smaller in the free-jaw group (i.e., increased jaw opening). In the fixed-jaw group, head elevation decreased upper airway collapsibility (PCRIT ~ -7 cm H₂O at greater than 6 cm elevation) compared with the baseline position (PCRIT ~ -3 cm H₂O at 0 cm elevation; P < 0.05).

Conclusion
: Elevating the head position by 6 cm while ensuring mouth closure (centric occlusion) produces substantial decreases in upper airway collapsibility and maintains upper airway patency during anesthesia.
Long‐term Follow‐up of Children With 6‐Thioguanine‐related Chronic Hepatoxicity Following Treatment for Acute Lymphoblastic Leukaemia
Authors: Rawat Dinesh , Gillett Peter M. , Devadason David , Wilson David C. , McKiernan Patrick J. 
Published: June 2011

ABSTRACT6‐Thioguanine (6‐TG) therapy in childhood acute lymphoblastic leukaemia results in chronic hepatotoxicity and portal hypertension. We report follow‐up data in a cohort of 10 children with acute lymphoblastic leukaemia and 6‐TG‐related hepatotoxicity described initially in 2006. Clinically significant portal hypertension was present in the majority of patients several years after cessation of 6‐TG treatment. These data reflect the natural history of noncirrhotic portal hypertension and emphasises the need to incorporate ongoing surveillance in the transition arrangement to adult services in this select group of patients.
Optimizing Early Nutritional Support Based on Recent Recommendations in VLBW Infants and Postnatal Growth Restriction
Authors: Senterre Thibault , Rigo Jacques 
Published: June 2011

ABSTRACTObjective:The aim of this study was to evaluate postnatal growth up to discharge in very low birth weight infants after optimizing nutritional support based on recent nutritional recommendations.Patients and Methods:A prospective, nonrandomized, consecutive, and observational study in infants weighing <1250 g.Results:One hundred two infants were included during a 2‐year period (birth weight 1005 ± 157 g, gestational age 28.5 ± 1.9 weeks). First‐day nutritional intake was 38 ± 6 kcal/kg/day with 2.4 ± 0.3 g/kg/day of protein. Mean intake during the first week of life was 80 ± 14 kcal/kg/day with 3.2 ± 0.5 g/kg/day of protein. On average from birth to discharge, 122 ± 10 kcal/kg/day and 3.7 ± 0.2 g/kg/day of protein were administered. Postnatal weight loss was limited to the first 3 days of life, and birth weight was regained after 7 days in average. Catch‐up occurred after the second week in all groups of very low birth weight infants. Small‐for‐gestational age infants demonstrated an earlier and higher weight gain, allowing a rapid catch‐up growth. The same proportion of infants was small‐for‐gestational age at birth and at discharge (20%, P = 0.74).Conclusions:This study confirmed that the first week of life is a critical period to promote growth and that early nutrition from the first day of life is essential. Postnatal weight loss may be limited and subsequent growth may be optimized with a dramatic reduction of postnatal growth restriction.
Elastic wave mode separation for tilted transverse isotropy media
Authors: Yan Jia , Sava Paul 
Published: June 2011

ABSTRACTSeismic waves propagate through the earth as a superposition of different wave modes. Seismic imaging in areas characterized by complex geology requires techniques based on accurate reconstruction of the seismic wavefields. A crucial component of the methods in this category, collectively known as wave‐equation migration, is the imaging condition that extracts information about the discontinuities of physical properties from the reconstructed wavefields at every location in space. Conventional acoustic migration techniques image a scalar wavefield representing the P‐wave mode, in contrast to elastic migration techniques, which image a vector wavefield representing both the P‐ and S‐waves. For elastic imaging, it is desirable that the reconstructed vector fields are decomposed into pure wave modes, such that the imaging condition produces interpretable images, characterizing, for example, PP or PS reflectivity. In anisotropic media, wave mode separation can be achieved by projection of the reconstructed vector fields on the polarization vectors characterizing various wave modes. For heterogeneous media, because polarization directions change with position, wave mode separation needs to be implemented using space‐domain filters. For transversely isotropic media with a tilted symmetry axis, the polarization vectors depend on the elastic material parameters, including the tilt angles. Using these parameters, we separate the wave modes by constructing nine filters corresponding to the nine Cartesian components of the three polarization directions at every grid point. Since the S polarization vectors in transverse isotropic media are not defined in the singular directions, e.g., along the symmetry axes, we construct these vectors by exploiting the orthogonality between the SV and SH polarization vectors, as well as their orthogonality with the P polarization vector. This procedure allows one to separate all three modes, with better preserved P‐wave amplitudes than S‐wave amplitudes. Realistic synthetic examples show that this wave mode separation is effective for both 2D and 3D models with strong heterogeneity and anisotropy.
Discontinuous Galerkin frequency domain forward modelling for the inversion of electric permittivity in the 2D case
Authors: El Bouajaji Mohamed , Lanteri Stéphane , Yedlin Matthew 
Published: June 2011

ABSTRACTWe have recently developed a discontinuous Galerkin frequency domain modelling algorithm for the solution of the 2D transverse magnetic Maxwell equations. This method is formulated on an unstructured triangular discretization of the computational domain and makes use of a high order polynomial interpolation of the electromagnetic field components within each triangular element. The discontinuous nature of the approximation naturally allows for a local definition of the interpolation order that is, in combination with a possibly non‐conforming local refinement of the mesh, a key ingredient for obtaining a flexible and accurate discretization method. Moreover, heterogeneity of the propagation media is easily dealt with by assuming element‐wise values of the electromagnetic parameters. In this paper, we propose the use of this discontinuous Galerkin frequency domain method as the forward modelling algorithm for solving the inverse problem for the electric permittivity in the 2D case. The inversion process is based on a gradient minimization technique developed by Pratt for seismological applications. Preliminary numerical results are presented for the imaging of a simplified subsurface model with the aim of assessing the performances of the proposed inversion methodology with regards to the number of frequencies, the number of recorded data and the number of sources.
Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information
Authors: Edsgärd D. , Scheel M. , Hansen N. T. , Ralfkiaer U. , Jensen T. S. , Skakkebæk N. E. , Brunak S. , Gupta R. , Rajpert‐De Meyts E. , Ottesen A. M. 
Published: June 2011

SummaryTo search for disease‐related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk‐associated genes among loci targeted by CNVs. The top‐ranked candidate, RLN1, encoding a Relaxin‐H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome‐wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed in both groups (p = 1). Immunohistochemistry for Relaxin‐H1 (RLN1), Relaxin‐H2 (RLN2) and their cognate receptor, RXFP1, detected one, and in some cases both, of the relaxins in Leydig cells, Sertoli cells and a subset of neoplastic germ cells, whereas the receptor was present in Leydig cells and spermatids. Collectively, the findings show that a heterozygous loss at the RLN1 locus is not a genetic factor mediating high population‐wide risk for testicular germ cell tumour, but do not exclude a contribution of this aberration in some cases of cancer. The preliminary expression data suggest a possible role of the relaxin peptides in spermatogenesis and warrant further studies.
Foetal exposure to phthalate esters and anogenital distance in male newborns
Authors: Suzuki Y. , Yoshinaga J. , Mizumoto Y. , Serizawa S. , Shiraishi H. 
Published: June 2011

SummaryPhthalate esters, commonly used as plasticizers, show anti‐androgenic activity and cause male reproductive malformation in experimental animals. However, the effects of prenatal exposure to phthalate esters in humans have not been extensively studied. The purpose of this study was to examine the relationship between prenatal exposure to phthalate esters and the anogenital distance (AGD) as a reproductive endpoint in human male newborns. Spot urine samples were collected from 111 Japanese pregnant women after obtaining their informed consent. Seven urinary phthalate ester metabolites were determined by high performance liquid chromatography–tandem mass spectrometry. Urinary isoflavones concentrations were measured as possible covariates because their oestrogenicities and high exposure levels among Japanese have the potential to affect male genital development. Birth outcomes and AGD, the distance from the centre of the anus to external genitalia, were measured for their male newborns. In a multiple regression model, the log‐transformed mono‐2‐ethylhexyl phthalate concentration (specific gravity‐corrected) was negatively significant, and maternal smoking status was positively significant, in explaining anogenital index (AGI) when potential covariates were controlled for. Urinary isoflavones did not significantly contribute to AGI in any models. Our results suggest that prenatal exposure to di(2‐ethylhexyl) phthalate affects reproductive development in human males.
Mental health problems and medically unexplained physical symptoms in adult survivors of childhood sexual abuse: an integrative literature review
Authors: NELSON S. , BALDWIN N. , TAYLOR J. 
Published: June 2011

Accessible summaryPeople who were sexually abused as children are at higher risk than non‐abused people of suffering symptoms that doctors can't explain (e.g. irritable bowel syndrome), and to have mental ill health (e.g. anxiety and depression).Relations between themselves and doctors or nurses can often become strained and frustrating, bringing high healthcare costs without relief of their ‘medically unexplained symptoms’. The aim in the literature review was to find an evidence base that might contribute to more helpful treatment or support, to improving relationships with medical staff and revealing gaps in knowledge.Some theories about why sexual abuse survivors with mental ill health have these unexplained symptoms were found to stigmatize them. Other theories conflicted with each other. This increases the difficulty of identifying helpful interventions. Research focussed on finding out ‘risk factors’ rather than on improving people's health. It rarely involved survivors themselves, or staff who worked closely with them.Recommendations include consulting survivors themselves about their experiences, and about how doctors and nurses could work more sensitively with them; learning from patients' case histories and medical records; studying sexually abused children's health problems as they grow into adulthood; and supporting neurobiological research.AbstractPeople sexually abused in childhood are at higher risk than non‐abused people of medically unexplained symptoms such as irritable bowel syndrome or chronic pain, with mental ill health and high healthcare use. Friction and frustration, with high, unproductive healthcare costs, can often develop between these patients and health‐care professionals such as general practitioners and nursing staff. The aim of this integrative literature review was to seek a sound evidence base from which to develop helpful interventions, improve relationships and identify gaps in knowledge. It found some theories about interconnections among childhood sexual abuse mental health and medically unexplained symptoms, such as ‘somatization’ or ‘secondary gain’, were used prejudicially, stigmatizing survivors. Conflicting theories make more difficult the search for effective interventions. Researchers rarely collaborated with sexual abuse specialists. Emphasis on identifying key risk factors, rather than providing support or alleviating distress, and lack of studies where survivors voiced their own experiences, meant very few targeted interventions for this group were proposed. Recommendations to enable effective interventions include making abuse survivors the prime study focus; qualitative research with survivors, to assist doctors and nursing staff with sensitive care; case histories using medical records; prospective studies with sexually abused children; support for the growing field of neurobiological research.