bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antidepressants strongly influence the relationship between depression and heart rate variability: findings from The Irish Longitudinal Study on Ageing (TILDA)
Authors: O'Regan C. , Kenny R. A. , Cronin H. , Finucane C. , Kearney P. M. 
Published: July 2014

BackgroundHeart rate variability (HRV) is known to be reduced in depression; however, is unclear whether this is a consequence of the disorder or due to antidepressant medication.MethodsWe analysed data on 4750 participants from the first wave of The Irish Longitudinal Study on Ageing (TILDA). Time [standard deviation of normal to normal intervals (SDNN ms2)] and frequency domain [low frequency (LF) and high frequency (HF)] measures of HRV were derived from 3-lead surface electrocardiogram records obtained during 10 min of supine rest. Depression was assessed using the Center for Epidemiologic Studies – Depression scale.ResultsParticipants on antidepressants [with (n = 80) or without depression (n = 185)] differed significantly from controls (not depressed and not taking antidepressants n = 4107) on all measures of HRV. Depressed participants not taking antidepressants (n = 317) did not differ from controls on any measures of HRV. In linear regression analysis adjusted for relevant factors all antidepressants were associated with lower measures HRV. Participants on selective serotonin reuptake inhibitors (SSRIs) had higher measures of HRV relative to participants on tricyclic antidepressants or serotonin–norepinephrine reuptake inhibitors respectively.ConclusionsOur results suggest that reductions in HRV observed among depressed older adults are driven by the effects of antidepressant medications. SSRIs have less impact on HRV than other antidepressants but they are still associated with lower measures of HRV. Study limitations include the use of a self-report measure of depression and floor effects of age on HRV could have limited our ability to detect an association between HRV and depression.
Joint dynamic analysis of space manipulator with planetary gear train transmission
Authors: Yang Tianfu , Yan Shaoze , Ma Wei , Han Zengyao 
Published: July 2014

SUMMARYJoints of space manipulators are usually simplified as torsional springs in modeling motion equations, and the nonlinear behaviors of the reducer in the joints are generally neglected. In this study, a dynamic model of a space manipulator that considers the joints that are transmitted through a typical 2K-H planetary gear reducer is developed using the Lagrangian method. The backlash clearances, gear tooth profile error, and time-variant meshing stiffness are integrated into the process. The simulation results show that the backlash clearances lead to the accumulation of positioning errors in the space manipulator when the joints rotate back and forth. The tooth profile error is the main cause of severe acceleration fluctuations and meshing force impacts. These fluctuations influence torque instability, which may accelerate gear system failure.
Losing a language in childhood: a longitudinal case study on language attrition
Authors: FLORES CRISTINA 
Published: July 2014

ABSTRACTThis paper is based upon a longitudinal study of L2 attrition in a bilingual child who grew up in an L2 migration background (Germany) and moved to the country of origin (Portugal) at the age of nine, experiencing adominance shift from theL2 totheL1. The study aims to analyze the effects of language loss in L2 German. Data collection started 3 weeks after the child's immersion in the Portuguese setting and ended 18 months later. Results show first effects of language attrition after 5 months of reduced exposure to German; 18 months later the informant showed severe word retrieval difficulties and was unable to produce complete sentences in her L2. The findings thus confirm the conclusions of other studies on child language attrition, which attest to strong effects of attrition when the loss of contact with the target language occurs in childhood.
The impact of restaurant consumption among US adults: effects on energy and nutrient intakes
Authors: Nguyen Binh T , Powell Lisa M 
Published: July 2014

AbstractObjectiveTo examine the effect of fast-food and full-service restaurant consumption on adults’ energy intake and dietary indicators.DesignIndividual-level fixed-effects regression model estimation based on two different days of dietary intake data was used.SettingParallel to the rising obesity epidemic in the USA, there has been a marked upward trend in total energy intake derived from food away from home.SubjectsThe full sample included 12 528 respondents aged 20–64 years who completed 24 h dietary recall interviews for both day 1 and day 2 in the National Health and Nutrition Examination Survey (NHANES) 2003–2004, 2005–2006, 2007–2008 and 2009–2010.ResultsFast-food and full-service restaurant consumption, respectively, was associated with an increase in daily total energy intake of 813·75 kJ (194·49 kcal) and 858·04 kJ (205·21 kcal) and with higher intakes of saturated fat (3·48 g and 2·52 g) and Na (296·38 mg and 451·06 mg). Individual characteristics moderated the impacts of restaurant food consumption with adverse impacts on net energy intake being larger for black adults compared with their white and Hispanic counterparts and greater for middle-income v. high-income adults.ConclusionsAdults’ fast-food and full-service restaurant consumption was associated with higher daily total energy intake and poorer dietary indicators.
Televised obesity-prevention advertising across US media markets: exposure and content, 2010–2011
Authors: Kornfield Rachel , Szczypka Glen , Powell Lisa M , Emery Sherry L 
Published: July 2014

AbstractObjectiveTo examine levels of exposure and content characteristics for recent televised obesity-prevention campaigns sponsored by state and community health departments, federal agencies, non-profit organizations and television stations in the USA.DesignNielsen television ratings for obesity-prevention advertising were collected for the top seventy-five US media markets and were used to calculate household exposure levels for 2010 and 2011. Governmental advertisements were coded for content.SettingUnited States.ResultsAverage household exposure to obesity-prevention campaigns was 2·6 advertisements per month. Exposure increased by 31 % between 2010 and 2011, largely driven by increases in federal advertisements. In 2011, the federal government accounted for 62 % of obesity-prevention exposure, non-profit organizations for 9 %, community departments for 8 %, state departments for 3 %, and television station-sponsored public-service announcements for 17 %. The greatest percentage increase between 2010 and 2011 was in community advertising, reflecting efforts funded by the Communities Putting Prevention to Work (CPPW) programme. Among thirty-four state and community campaigns, the majority advocated both healthy eating and physical activity (53 %). Campaigns typically had positive or neutral emotional valence (94 %). Obesity or overweight was mentioned in 47 % of campaigns, but only 9 % specifically advocated weight loss.ConclusionsExposure to televised obesity-prevention advertising increased from 2010 to 2011 and was higher than previously found in 1999–2003, apart from in 2003 during the federal VERB campaign. Nevertheless, exposure remains low relative to advertising for unhealthy foods. New federal campaigns have increased exposure to obesity-prevention advertising nationally, while CPPW grants have increased exposure for targeted areas.
Clinical Translation in the Virtual Liver Network
Authors: Kuepfer L , Kerb R , Henney AM 
Published: July 2014

The liver is the central detoxifying organ, continuously removing xenobiotics from the vascular system. Given its role in drug metabolism, a functional understanding of liver physiology is crucial to optimizing drug efficacy and patient safety. The Virtual Liver Network (VLN), a German national flagship research program, focuses on producing validated computer models of human liver physiology. These models are used to analyze patient‐derived data and thereby gain mechanistic insights in the processes underlying drug pharmacokinetics (PK).CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e127; doi:10.1038/psp.2014.25; published online 30 July 2014
Fingerprinting of hydroxyl radical-attacked polysaccharides byN-isopropyl-2-aminoacridone labelling
Authors: Vreeburg Robert A. M. , Airianah Othman B. , Fry Stephen C. 
Published: July 2014

Hydroxyl radicals (•OH) cause non-enzymic scission of polysaccharides in diverse biological systems. Such reactions can be detrimental (e.g. causing rheumatic and arthritic diseases in mammals) or beneficial (e.g. promoting the softening of ripening fruit, and biomass saccharification). Here we present a method for documenting •OH action, based on fluorescent labelling of the oxo groups that are introduced as glycosulose residues when •OH attacks polysaccharides. The method was tested on several polysaccharides, especially pectin, after treatment with Fenton reagents. 2-Aminoacridone plus cyanoborohydride reductively aminated the oxo groups in treated polysaccharides; the product was then reacted with acetone plus cyanoborohydride, forming a stable tertiary amine with the carbohydrate linked to N-isopropyl-2-aminoacridone (pAMAC). Digestion of labelled pectin with ‘Driselase’ yielded several fluorescent products which on electrophoresis and HPLC provided a useful ‘fingerprint’ indicating •OH attack. The most diagnostic product was a disaccharide conjugate of the type pAMAC·UA-GalA (UA=unspecified uronic acid), whose UA-GalA bond was Driselase-resistant (product 2A). 2A was clearly distinguishable from GalA-GalA–pAMAC (disaccharide labelled at its reducing end), which was digestible to GalA–pAMAC. The methodology is applicable, with appropriate enzymes in place of Driselase, for detecting natural and artificial •OH attack in diverse plant, animal and microbial polysaccharides.
Fabrication of size‐tunable hierarchical CrN nanohole arrays for two‐dimensional nanomould using modified nanosphere lithography
Authors: Wu Hung‐Chun , Bao MingDong , Ma Kung‐Jeng 
Published: July 2014

This Letter presents a low‐cost, high‐throughput strategy for fabricating size‐tunable hierarchical CrN nanohole arrays for a nanomould using a magnetron sputtering approach with nanosphere lithography (NIL)‐based technology. The size of the polystyrene nanospheres has a direct inﬂuence on the diameter and period of the CrN nanohole structure. The reactive ion etching and magnetron sputtering process can easily control the nanohole size and depth. The hole depth generally depends on the ﬁlm thickness. The contact angles were measured by the sessile drop method using distilled water, ethylene glycol and diiodomethane. The surface‐free energy of the CrN nanomould was calculated using the Owens–Wendt geometric mean approach. This Letter reports the successful fabrication of a series of nanoholes with diameters decreased from 347 ± 9.6 to approximately 166 ± 11.8 nm with a depth of 100 ± 5.6 nm. The corresponding surface‐free energy decreased from 40.83 to approximately 24.58 mN/m. The diameter of nanoholes has an obvious effect on the surface‐free energy and there is tendency for the surface‐free energy to decrease with the decrease in the diameter of the nanoholes. This new approach of ordered CrN nanohole array structures can be used to create a two‐dimensional nanomould for NIL.
Origin of myofibroblasts in the fibrotic liver in mice
Authors: Iwaisako Keiko , Jiang Chunyan , Zhang Mingjun , Cong Min , Moore-Morris Thomas Joseph , Park Tae Jun , Liu Xiao , Xu Jun , Wang Ping , Paik Yong-Han , Meng Fanli , Asagiri Masataka , Murray Lynne A. , Hofmann Alan F. , Iida Takashi , Glass Christopher K. , Brenner David A. , Kisseleva Tatiana 
Published: July 2014

Significance
Liver resident activated hepatic stellate cells (aHSCs), and activated portal fibroblasts (aPFs) are the major source of the fibrous scar in the liver. aPFs have been implicated in liver fibrosis caused by cholestatic liver injury, whereas fibrosis in hepatotoxic liver injury is attributed to aHSCs. However, the contribution of aPFs to cholestatic fibrosis is not well characterized because of difficulties in cell purification and the lack of identified aPF-specific markers. We have developed a novel flow cytometry-based method of aPFs purification from the nonparenchymal cell fraction of collagen-α1(I)-GFP mice and have identified potential aPF-specific markers. The goal of this study is to determine whether aPFs contribute to cholestatic liver fibrosis and identify the mechanism(s) of their activation.
Trowel: a fast and accurate error correction module for Illumina sequencing reads
Authors: Lim Eun-Cheon , Müller Jonas , Hagmann Jörg , Henz Stefan R. , Kim Sang-Tae , Weigel Detlef 
Published: July 2014

Abstract
Motivation: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections.
Result: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k -mer spectrum. With high-quality k -mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size.
Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net .
Contact: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Prehabilitation versus Rehabilitation
Authors: Gillis Chelsia , Li Chao , Lee Lawrence , Awasthi Rashami , Augustin Berson , Gamsa Ann , Liberman A. Sender , Stein Barry , Charlebois Patrick , Feldman Liane S. , Carli Francesco 
Published: July 2014

Abstract

Background:
The preoperative period (prehabilitation) may represent a more appropriate time than the postoperative period to implement an intervention. The impact of prehabilitation on recovery of function al exercise capacity was thus studied in patients undergoing colorectal resection for cancer.

Methods:
A parallel-arm single-blind superiority randomized controlled trial was conducted. Seventy-seven patients were randomized to receive either prehabilitation (n = 38) or rehabilitation (n = 39). Both groups received a home-based intervention of moderate aerobic and resistance exercises, nutritional counseling with protein supplementation, and relaxation exercises initiated either 4 weeks before surgery (prehabilitation) or immediately after surgery (rehabilitation), and continued for 8 weeks after surgery. Patients were managed with an enhanced recovery pathway. Primary outcome was functional exercise capacity measured using the validated 6-min walk test.

Results:
Median duration of prehabilitation was 24.5 days. While awaiting surgery, functional walking capacity increased (≥20 m) in a higher proportion of the prehabilitation group compared with the rehabilitation group (53 vs. 15%, adjusted P = 0.006). Complication rates and duration of hospital stay were similar. The difference between baseline and 8-week 6-min walking test was significantly higher in the prehabilitation compared with the rehabilitation group (+23.7 m [SD, 54.8] vs. −21.8 m [SD, 80.7]; mean difference 45.4 m [95% CI, 13.9 to 77.0]). A higher proportion of the prehabilitation group were also recovered to or above baseline exercise capacity at 8 weeks compared with the rehabilitation group (84 vs. 62%, adjusted P = 0.049).

Conclusion:
Meaningful changes in postoperative functional exercise capacity can be achieved with a prehabilitation program.
Minimizing Pedicle Screw Pullout Risks
Authors: Bianco Rohan-Jean , Arnoux Pierre-Jean , Wagnac Eric , Mac-Thiong Jean-Marc , Aubin Carl-Éric 
Published: July 2014

Study Design:
Detailed biomechanical analysis of the anchorage performance provided by different pedicle screw designs and placement strategies under pullout loading.

Objective:
To biomechanically characterize the specific effects of surgeon-specific pedicle screw design parameters on anchorage performance using a finite element model.

Summary of Background Data:
Pedicle screw fixation is commonly used in the treatment of spinal pathologies. However, there is little consensus on the selection of an optimal screw type, size, and insertion trajectory depending on vertebra dimension and shape.

Methods:
Different screw diameters and lengths, threads, and insertion trajectories were computationally tested using a design of experiment approach. A detailed finite element model of an L3 vertebra was created including elastoplastic bone properties and contact interactions with the screws. Loads and boundary conditions were applied to the screws to simulate axial pullout tests. Force-displacement responses and internal stresses were analyzed to determine the specific effects of each parameter.

Results:
The design of experiment analysis revealed significant effects (P<0.01) for all tested principal parameters along with the interactions between diameter and trajectory. Screw diameter had the greatest impact on anchorage performance. The best insertion trajectory to resist pullout involved placing the screw threads closer to the pedicle walls using the straightforward insertion technique, which showed the importance of the cortical layer grip. The simulated cylindrical single-lead thread screws presented better biomechanical anchorage than the conical dual-lead thread screws in axial loading conditions.

Conclusions:
The model made it possible to quantitatively measure the effects of both screw design characteristics and surgical choices, enabling to recommend strategies to improve single pedicle screw performance under axial loading.
QuASAR: Quantitative Allele Specific Analysis of Reads
Authors: Harvey Chris T. , Moyerbrailean Gregory A. , Davis Gordon O. , Wen Xiaoquan , Luca Francesca , Pique-Regi Roger 
Published: July 2014

AbstractMotivationExpression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls.ResultsWe present QuASAR, Quantitative Allele Specific Analysis of Reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available.Availabilityhttp://github.com/piquelab/QuASARContactfluca@wayne.edu;rpique@wayne.edu
Which genetic variants in DNase I sensitive regions are functional?
Authors: Moyerbrailean Gregory A. , Harvey Chris T. , Kalita Cynthia A. , Wen Xiaoquan , Luca Francesca , Pique-Regi Roger 
Published: July 2014

AbstractOngoing large experimental characterization is crucial to determine all regulatory sequences, yet we do not know which genetic variants in those regions are non-silent. Here, we present a novel analysis integrating sequence and DNase I footprinting data for 653 samples to predict the impact of a sequence change on transcription factor binding for a panel of 1,372 motifs. Most genetic variants in footprints (5,810,227) do not show evidence of allele-specific binding (ASB). In contrast, functional genetic variants predicted by our computational models are highly enriched for ASB (3,217 SNPs at 20% FDR). Comparing silent to functional non-coding genetic variants, the latter are 1.22-fold enriched for GWAS traits, have lower allele frequencies, and affect footprints more distal to promoters or active in fewer tissues. Finally, integration of the annotations into 18 GWAS meta-studies improves identification of likely causal SNPs and transcription factors relevant for complex traits.
Intraspecific Arabidopsis Hybrids Show Different Patterns of Heterosis Despite the Close Relatedness of the Parental Genomes
Authors: Groszmann Michael , Gonzalez-Bayon Rebeca , Greaves Ian K. , Wang Li , Huen Amanda K. , Peacock W. James , Dennis Elizabeth S. 
Published: July 2014

Abstract
Heterosis is important for agriculture; however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development.