bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a novel PDE10APET radioligand, [11C]T‐773, in nonhuman primates: Brain and whole body PET and brain autoradiography
Authors: Takano Akihiro , Stepanov Vladimir , Gulyás Balázs , Nakao Ryuji , Amini Nahid , Miura Shotaro , Kimura Haruhide , Taniguchi Takahiko , Halldin Christer 
Published: April 2015

ABSTRACTPhosphodiesterase 10A (PDE10A) is considered to be a key target for the treatment of several neuropsychiatric diseases. The characteristics of [11C]T‐773, a novel positron emission tomography (PET) radioligand with high binding affinity and selectivity for PDE10A, were evaluated in autoradiography and in nonhuman primate (NHP) PET. Brain PET measurements were performed under baseline conditions and after administration of a selective PDE10A inhibitor, MP‐10. Total distribution volume (VT) and binding potential (BPND) were calculated using various kinetic models. Whole body PET measurements were performed to calculate the effective dose of [11C]T‐773. Autoradiography studies in postmortem human and monkey brain sections showed high accumulation of [11C]T‐773 in the striatum and substantia nigra which was blocked by MP‐10. Brain PET showed high accumulation of [11C]T‐773 in the striatum, and the data could be fitted using a two tissue compartment model. BPND was approximately 1.8 in the putamen when the cerebellum was used as the reference region. Approximately 70% of PDE10A binding was occupied by 1.8 mg/kg of MP‐10. Whole body PET showed high accumulation of [11C]T‐773 in the liver, kidney, heart, and brain in the initial phase. The radioligand was partly excreted via bile and the gastrointestinal tract, and partly excreted through the urinary tract. The calculated effective dose was 0.007 mSv/MBq. In conclusion, [11C]T‐773 was demonstrated to be a promising PET radioligand for PDE10A with favorable brain kinetics. Dosimetry results support multiple PET measurements per person in human studies. Further research is required with [11C]T‐773 in order to test the radioligand's potential clinical applications. Synapse 69:345–355, 2015. © 2015 Wiley Periodicals, Inc.
Optimizing collection methods for noninvasive genetic sampling of neotropical felids
Authors: Wultsch Claudia , Waits Lisette P. , Hallerman Eric M. , Kelly Marcella J. 
Published: April 2015

ABSTRACTField‐sampling methods for molecular scatology studies must be optimized, especially when working on elusive species in challenging tropical environments where rates of DNA degradation are elevated because of hot and humid weather conditions. To maximize polymerase chain reaction (PCR) amplification success and genotyping accuracy rates and to minimize genotyping error rates for fecal DNA samples of jaguars (Panthera onca) and co‐occurring Neotropical felids collected in Belize, Central America, we evaluated the performance of two fecal DNA storage techniques (dimethyl sulfoxide saline solution [DETs buffer] and 95% ethanol [EtOH]) suitable for long‐term preservation at remote tropical sites. Additionally, we tested fecal samples collected from 4 different locations on the scat (top, side, bottom, inside) at 2 different tropical forest types (tropical broadleaf and tropical pine forests). DETs buffer was the superior fecal DNA preservation method, with 44% higher PCR amplification success (P = 0.009) and 17% higher genotyping accuracy (P = 0.021) than 95% EtOH‐stored samples. Polymerase chain reaction amplification success of fecal DNA collected at the more open, pine‐forest (Pinus sp.) site differed significantly across locations on the scat, with highest mean success rates obtained from the top (85% ± 6.5% SD), followed by the side (79% ± 9.4% SD), bottom (76% ± 11.9% SD), and inside (69% ± 10.3% SD) of scat samples. Scat samples collected at the more closed‐canopy broadleaf site did not show any significant differences in amplification success rates across scat locations. We recommend that researchers optimize field‐sampling methods, including collection and storage protocols, by conducting a pilot study prior to their molecular scatology research efforts. © 2015 The Wildlife Society.
Ready-to-eat cereals improve nutrient, milk and fruit intake at breakfast in European adolescents
Authors: Michels Nathalie , De Henauw Stefaan , Beghin Laurent , Cuenca-García Magdalena , Gonzalez-Gross Marcela , Hallstrom Lena , Kafatos Anthony , Kersting Mathilde , Manios Yannis , Marcos Ascensión , Molnar Denes , Roccaldo Romana , Santaliestra-Pasías Alba M. , Sjostrom Michael , Reye Béatrice , Thielecke Frank , Widhalm Kurt , Claessens Mandy 
Published: April 2015

Abstract

Purpose

Breakfast consumption has been recommended as part of a healthy diet. Recently, ready-to-eat cereals (RTEC) became more popular as a breakfast item. Our aim was to analyse the dietary characteristics of an RTEC breakfast in European adolescents and to compare them with other breakfast options.

Methods
From the European multi-centre HELENA study, two 24-h dietary recalls of 3137 adolescents were available. Food items (RTEC or bread, milk/yoghurt, fruit) and macro- and micronutrient intakes at breakfast were calculated. Cross-sectional regression analyses were adjusted for gender, age, socio-economic status and city.

Results
Compared to bread breakfasts (39 %) and all other breakfasts (41.5 %), RTEC breakfast (19.5 %) was associated with improved nutrient intake (less fat and less sucrose; more fibre, protein and some micronutrients like vitamin B, calcium, magnesium and phosphorus) at the breakfast occasion. Exceptions were more simple sugars in RTEC breakfast consumers: more lactose and galactose due to increased milk consumption, but also higher glucose and fructose than bread consumers. RTEC consumers had a significantly higher frequency (92.5 vs. 50.4 and 60.2 %) and quantity of milk/yoghurt intake and a slightly higher frequency of fruit intake (13.4 vs. 10.9 and 8.0 %) at breakfast.

Conclusions
Among European adolescents, RTEC consumers showed a more favourable nutrient intake than consumers of bread or other breakfasts, except for simple sugars. Therefore, RTEC may be regarded as a good breakfast option as part of a varied and balanced diet. Nevertheless, more research is warranted concerning the role of different RTEC types in nutrient intake, especially for simple sugars.
Compression of the Celiac Artery by the Median Arcuate Ligament: Multidetector Computed Tomography Findings and Characteristics
Authors: Baskan Ozdil , Kaya Emre , Gungoren Fatma Zeynep , Erol Cengiz 
Published: April 2015

Purpose The prevalence of the celiac artery stenosis caused by median arcuate ligament (MAL) compression and its multidetector computed tomography (MDCT) characteristics were evaluated in patients who underwent abdominal MDCT procedures, retrospectively. Methods Totally 1121 patients who had abdominal MDCT with arterial phase or MDCT angiography of the abdominal aorta for various indications were analyzed for celiac artery compression by the MAL. Results Fifty (ie, 4.6%) patients showed typical MDCT features of MAL compression. Focal narrowing of the proximal celiac artery, a characteristic hooked appearance of the narrowed segment without calcification and atherosclerotic changes were diagnostic. Poststenotic dilatation was detected in 22 (44%) patients with MAL compression. The ratio of the stenosis of the celiac artery was between 35%-50% in 15 patients and 51%-80% in 35 patients. The gastroduodenal artery diameter of these patients was not significantly different from the asymptomatic control group. Conclusion MALS is an uncommon entity but it should be kept in mind in the presence of unexplained gastrointestinal symptoms. MDCT is a minimally invasive and plays a dominant role in the diagnosis of MAL compression especially with reformatted and 3-D reconstructed images.
Developmental stage‐dependent impact of midazolam on calbindin, calretinin and parvalbumin expression in the immature rat medial prefrontal cortex during the brain growth spurt
Authors: Osterop Samira F. , Virtanen Mari A. , Loepke Johanna R. , Joseph Bernadin , Loepke Andreas W. , Vutskits Laszlo 
Published: April 2015

AbstractBackgroundHuman epidemiological data suggest a link between anesthesia exposure in early postnatal life and subsequent lasting neurocognitive alterations. Understanding the underlying mechanisms of this potential association is of paramount importance in an attempt to develop protective strategies. While general anesthetics are powerful modulators of GABAergic neurotransmission, little is known about the impact of these drugs on developing GABAergic networks. Here we addressed this issue by evaluating the impact of a 6‐h‐long midazolam exposure on the development of calbindin‐, calretinin‐ and parvalbumin‐expressing GABAergic interneurons.MethodsPhysiological expression patterns of calbindin‐, calretinin‐, and parvalbumin‐positive neurons as well as the impact of a 6‐h‐long midazolam exposure on these cell populations were evaluated in the medial prefrontal cortex of Wistar rats at defined stages of the brain growth spurt using stereological analysis. Activated caspase‐3 immunohistochemistry was used to quantify apoptotic death in controls and midazolam‐treated subjects.ResultsIn control animals, the number of parvalbumin expressing cells significantly (p < 0.01) increased while those of calbindin positive populations significantly (p < 0.01) decreased between postnatal day 10 and 20. Expression of calretinin remained constant during this period. Immediately following exposure, midazolam induced neuroapoptosis at both early (postnatal day 5, p = 0.016) and later (postnatal day 15, p = 0.025) stages of brain development. While this did not diminish overall neuronal density in the medial prefrontal cortex, exposure at P5 led to a subsequent increase in the number of parvalbumin positive neurons in lower cortical layers, and midazolam administration at P15 increased the number of both parvalbumin and calretinin expressing neurons 5 days following exposure.ConclusionThese observations demonstrate that midazolam exposure can impair the physiological differentiation patterns of GABAergic interneurons during the brain growth spurt. Considering the important role of GABAergic networks in neuronal physiology, these data provide us with one potential mechanism that could account for the lasting neurobehavioral and cognitive deficits observed in the context of anesthesia exposure in the early postnatal period.
Effect of prenatal stress on memory, nicotine withdrawal and 5HT1A expression in raphe nuclei of adult rats
Authors: Said N. , Lakehayli S. , Khachibi M. El , Ouahli M. El , Nadifi S. , Hakkou F. , Tazi A. 
Published: April 2015

AbstractMaternal distress has often been associated with cognitive deficiencies and drug abuse in rats. This study examined these behavioral effects in offspring of mothers stressed during gestation. To this end, pregnant dams were subjected to daily electric foot shocks during the last 10 days of pregnancy. We measured litter parameters and body weights of the descendants after weaning (21 days) and at adulthood (80 days). Afterwards, prenatally stressed and control rats' performances in the novel object recognition test were compared in order to evaluate their memory while others underwent the Water consumption test to assess the nicotine withdrawal intensity after perinatal manipulations. Meanwhile, another set of rats were sacrificed and 5HT1A receptors' mRNA expression was measured in the raphe nuclei by quantitative Real Time PCR. We noticed no significant influence of maternal stress on litter size and body weight right after weaning. However, control rats were heavier than the stressed rats in adulthood. The results also showed a significant decrease in the recognition score in rats stressed in utero compared to the controls. Moreover, a heightened anxiety symptom was observed in the prenatally stressed offspring following nicotine withdrawal. Additionally, the Real Time PCR method revealed that prenatal stress induced a significant decrease in 5HT1A receptors’ levels in the raphe nuclei. Nicotine had a similar effect on these receptors’ expression in both nicotine‐treated control and prenatally stressed groups. Taken together, these findings suggest that the cognitive functions and drug dependence can be triggered by early adverse events in rats.
GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach
Authors: Schmidt Ellen M. , Zhang Ji , Zhou Wei , Chen Jin , Mohlke Karen L. , Chen Y. Eugene , Willer Cristen J. 
Published: April 2015

Abstract
Motivation: The majority of variation identified by genome wide association studies falls in non-coding genomic regions and is hypothesized to impact regulatory elements that modulate gene expression. Here we present a statistically rigorous software tool GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) for evaluating enrichment of any set of genetic variants with any set of regulatory features. Using variants from five phenotypes, we describe a data-driven approach to determine the tissue and cell types most relevant to a trait of interest and to identify the subset of regulatory features likely impacted by these variants. Last, we experimentally evaluate six predicted functional variants at six lipid-associated loci and demonstrate significant evidence for allele-specific impact on expression levels. GREGOR systematically evaluates enrichment of genetic variation with the vast collection of regulatory data available to explore novel biological mechanisms of disease and guide us toward the functional variant at trait-associated loci.
Availability and implementation: GREGOR, including source code, documentation, examples, and executables, is available at http://genome.sph.umich.edu/wiki/GREGOR.
Contact: cristen@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PDIviz: analysis and visualization of protein–DNA binding interfaces
Authors: Ribeiro Judemir , Melo Francisco , Schüller Andreas 
Published: April 2015

Abstract
Summary: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction.
Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems.
Contact: aschueller@bio.puc.cl
Supplementary Information: Supplementary data are available at Bioinformatics online.
FastMotif: spectral sequence motif discovery
Authors: Colombo Nicoló , Vlassis Nikos 
Published: April 2015

Abstract
Motivation: Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, most of the existing motif finding algorithms are computationally demanding, and they may not be able to support the increasingly large datasets produced by modern high-throughput sequencing technologies.
Results: We present FastMotif, a new motif discovery algorithm that is built on a recent machine learning technique referred to as Method of Moments. Based on spectral decompositions, our method is robust to model misspecifications and is not prone to locally optimal solutions. We obtain an algorithm that is extremely fast and designed for the analysis of big sequencing data. On HT-Selex data, FastMotif extracts motif profiles that match those computed by various state-of-the-art algorithms, but one order of magnitude faster. We provide a theoretical and numerical analysis of the algorithm’s robustness and discuss its sensitivity with respect to the free parameters.
Availability and implementation: The Matlab code of FastMotif is available from http://lcsb-portal.uni.lu/bioinformatics.
Contact: vlassis@adobe.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Accurate prediction of RNA nucleotide interactions with backbone k-tree model
Authors: Ding Liang , Xue Xingran , LaMarca Sal , Mohebbi Mohammad , Samad Abdul , Malmberg Russell L. , Cai Liming 
Published: April 2015

Abstract
Motivation: Given the importance of non-coding RNAs to cellular regulatory functions, it would be highly desirable to have accurate computational prediction of RNA 3D structure, a task which remains challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly resort to random sampling of conformations to achieve computational feasibility. However, native conformations may not be examined and prediction accuracy may be compromised due to sampling. State-of-the-art methods have yet to deliver satisfactory predictions for RNAs of length beyond 50 nucleotides.
Results: This paper presents a method to tackle a key step in the RNA 3D structure prediction problem, the prediction of the nucleotide interactions that constitute the desired 3D structure. The research is based on a novel graph model, called a backbone k-tree, to tightly constrain the nucleotide interaction relationships considered for RNA 3D structures. It is shown that the new model makes it possible to efficiently predict the optimal set of nucleotide interactions (including the non-canonical interactions in all recently revealed families) from the query sequence along with known or predicted canonical basepairs. The preliminary results indicate that in most cases the new method can predict with a high accuracy the nucleotide interactions that constitute the 3D structure of the query sequence. It thus provides a useful tool for the accurate prediction of RNA 3D structure.
Availability and Implementation: The source package for BkTree is available at http://rna-informatics.uga.edu/index.php?f=software&p=BkTree.
Contact: lding@uga.edu or cai@cs.uga.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo
Authors: Tang Yin , Bouvier Emil , Kwok Chun Kit , Ding Yiliang , Nekrutenko Anton , Bevilacqua Philip C. , Assmann Sarah M. 
Published: April 2015

Abstract
Motivation: RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise.
Results: We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform.
Availability and Implementation: StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/.
Contact: yxt148@psu.edu or sma3@psu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Antiseptic Body Washes for Reducing the Transmission of Methicillin-Resistant Staphylococcus aureus: A Cluster Crossover Study
Authors: Harris Patrick N. A. , Le Bich Diep , Tambyah Paul , Hsu Li Yang , Pada Surinder , Archuleta Sophia , Salmon Sharon , Mukhopadhyay Amartya , Dillon Jasmine , Ware Robert , Fisher Dale A. 
Published: April 2015

Abstract
Background.  Limiting the spread of methicillin-resistant Staphylococcus aureus (MRSA) within healthcare facilities where the organism is highly endemic is a challenge. The use of topical antiseptic agents may help interrupt the transmission of MRSA and reduce the risk of clinical infection. Octenidine dihydrochloride is a topical antiseptic that exhibits in vitro efficacy against a wide variety of bacteria, including S aureus.
Methods.  We conducted a prospective cluster crossover study to compare the use of daily octenidine body washes with soap and water in patients identified by active surveillance cultures to be MRSA-colonized, to prevent the acquisition of MRSA in patients with negative screening swabs. Five adult medical and surgical wards and 2 intensive care units were selected. The study involved an initial 6-month phase using octenidine or soap washes followed by a crossover in each ward to the alternative product. The primary and secondary outcomes were the rates of new MRSA acquisitions and MRSA clinical infections, respectively.
Results.  A total of 10 936 patients admitted for ≥48 hours was included in the analysis. There was a small reduction in MRSA acquisition in the intervention group compared with controls (3.0% vs 3.3%), but this reduction was not significant (odds ratio, 0.89; 95% confidence interval, .72–1.11; P = .31). There were also no significant differences in clinical MRSA infection or incidence of MRSA bacteremia.
Conclusions.  This study suggests that the targeted use of routine antiseptic washes may not in itself be adequate to reduce the transmission of MRSA in an endemic hospital setting.