bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Full-Length Carbon Fiber Insoles on Lower Limb Kinetics in Patients With Midfoot Osteoarthritis
Authors: Yi Taeim , Kim Jung Hyun , Oh-Park Mooyeon , Hwang Ji Hye 
Published: September 2017

Objectives
We investigated the effects of full-length carbon fiber (FCF) insoles on gait, muscle activity, kinetics, and pain in patients with midfoot osteoarthritis (OA).

Design
We enrolled 13 patients with unilateral midfoot OA (mild: Visual Analog Scale [VAS] range, 1–3; moderate, VAS range, 4–7) and healthy controls. All participants were asked to walk under two conditions: with and without FCF insole. The outcome measures were ground reaction force, quantitative gait parameters, electromyography activities and pain severity (VAS).

Results
In the patients with moderate midfoot OA, significantly longer gait cycle and higher muscle activity of lower limb during loading-response phase were observed while walking without FCF insoles. In the mild midfoot OA group, there was no significant difference in VAS score (without, 2.0 ± 1.0 vs. with, 2.0 ± 0.5) with FCF insole use. However, significantly reduced VAS score (without, 5.5 ± 1.4 vs. with, 2.0 ± 0.5) and muscle activity of the tibialis anterior and increased muscle activity of gastrocnemius were observed in the moderate midfoot OA group by using an FCF insole (P < 0.05).

Conclusions
Full-length carbon fiber insoles can improve pain in individuals with moderate midfoot OA, which might be associated with changes in the kinetics and muscle activities of the lower limb. Taken together, the results of the present study suggest that FCF insoles may be used as a helpful option for midfoot OA.
Minimally Invasive Laparoscopically Dissected Deep Inferior Epigastric Artery Perforator Flap: An Anatomical Feasibility Study and a First Clinical Case
Authors: Hivelin Mikael , Soprani Antoine , Schaffer Nathaniel , Hans Stéphane , Lantieri Laurent 
Published: September 2017

Summary:
The deep inferior epigastric perforator (DIEP) flap is a workhorse of breast reconstruction. Risks of herniation derive from violation of the rectus abdominis muscle anterior rectus sheath and might be reduced by minimally invasive laparoscopic dissection (“MILD”) of the deep inferior epigastric vessels. The authors performed a feasibility study on five anatomical subjects and performed a secondary right breast reconstruction on a 67-year-old woman. A 30-degree laparoscope was used with laparoscopy ports inset to preserve the flap. Blunt preperitoneal dissection followed by carbon dioxide insufflation allowed the deep inferior epigastric pedicle to be dissected and clip-sectioned. The anterior rectus sheath was opened around the perforating vessels, and the flap was anastomosed on the internal mammary vessels. The length of incision in the anterior rectus sheath was compared between laparoscopic and conventional approaches. The mean incision length in the anterior rectus sheath was 3 cm versus 12 cm in the classic approach. Average duration of laparoscopic flap harvest was 50 minutes, including a mean of 30 minutes for deep inferior epigastric dissection. Adhesions led to a 1-cm peritoneal laceration in our first anatomical subject. There were no preoperative or postoperative complications in the clinical case. The clinical procedure duration was 8 hours 15 minutes, with the anterior rectus sheath incision reduced from the conventional 12 cm to 5 cm. Flap ischemia lasted 50 minutes. The patient was discharged on postoperative day 5. This anatomical study and first successful laparoscope-assisted DIEP flap harvest prove that reduced trauma to the anterior rectus sheath is feasible and promising.
Role of Brain Structure in Predicting Adherence to a Physical Activity Regimen
Authors: Gujral Swathi , McAuley Edward , Oberlin Lauren E. , Kramer Arthur F. , Erickson Kirk I. 
Published: September 2017

ABSTRACT

Objective
Physical activity (PA) is important for maintaining health throughout the lifespan. However, adherence to PA regimens is poor with approximately 50% of older adults terminating activity intervention programs within 6 months. In this study, we tested whether gray matter volume and white matter microstructural integrity before the initiation of a PA intervention predicts PA adherence.

Methods
One hundred fifty-nine adults aged 60 to 80 years were randomly assigned to a moderate-intensity aerobic walking condition or a nonaerobic stretching and toning condition. Participants engaged in supervised exercise 3 times per week for 12 months. Data were collected for a period of 1 year. Voxel-based morphometry and tract-based spatial statistics protocols were used to process neuroimaging data, and ordinary least squares regression models with bootstrapping were used to analyze voxelwise neural predictors of PA adherence.

Results
Greater volume in several regions predicted greater PA adherence, including prefrontal, motor, somatosensory, temporal, and parietal regions (p < .01). We also found that higher fractional anisotropy in several white matter tracts predicted greater PA adherence (p
FDR-corrected < .05), including the superior longitudinal fasciculus, anterior thalamic radiation, forceps minor, and body of the corpus callosum.

Conclusions
These findings provide preliminary support for macro- and microstructural neural predictors of PA adherence and may translate to other health behaviors and behavioral goal pursuit more broadly.
Risk Factors and Oncologic Outcomes of Anastomosis Leakage After Laparoscopic Right Colectomy
Authors: Kwak Han Deok , Kim Seon-Hahn , Kang Dong Woo , Baek Se-Jin , Kwak Jung Myun , Kim Jin 
Published: September 2017

Purpose:
We estimated the incidence of anastomosis leakage and explore possible risk factors and oncologic outcomes following laparoscopic right-side colon resection among colon cancer patients.

Materials and Methods:
We retrospectively analyzed 423 patients who were diagnosed with appendiceal, cecal, ascending, or hepatic flexure colon cancer who underwent laparoscopic colonic resection and anastomosis between September 2006 and July 2014. We compared short-term and long-term outcomes between no-leakage and leakage groups.

Results:
There were 16 cases of right-side anastomosis leakage in a total 423 colon cancer cases (3.78%). The risk of leakage was increased in smokers (odds ratio=6.592, P=0.007) and with a longer operating time (odds ratio=1.024, P<0.001). There were no significant differences between the groups in local recurrence (P=0.106), overall survival (P=0.055), or cancer-specific survival (P=0.235).

Conclusions:
Smoking and long operating time are risk factors for right-side colon anastomosis. There were no significant differences in oncologic outcomes.
Laparoscopic Mesh-Less Cervicosacropexy for Uterovaginal Prolapse
Authors: Seracchioli Renato , Raimondo Diego , Arena Alessandro , Gava Giulia , Parmeggiani Clara , Martelli Valentina , Moro Elisa , Zanello Margherita , Paradisi Roberto , Mabrouk Mohamed 
Published: September 2017

Objectives
This study aimed to evaluate surgical and clinical outcomes of laparoscopic mesh-less cervicosacropexy for the treatment of uterovaginal prolapse.

Methods
This single institutional review board–approved prospective cohort study enrolled 46 consecutive, sexually active symptomatic women requiring surgical correction of uterovaginal prolapse, from July 2013 to March 2016. After supracervical laparoscopic hysterectomy, the cervix was suspended to the anterior longitudinal ligament of the sacral promontory through a continuous suture with plication and shortening of the right uterosacral ligament. Pelvic organs' function was evaluated through validated questionnaires during preoperative and postoperative follow-up evaluations. The anatomical recurrences of genital prolapse with a Pelvic Organ Prolapse Quantitative stage 2 or higher, in particular of central compartment (Pelvic Organ Prolapse Quantitative score C ≥−1), were recorded.

Results
Mean ± SD age was 55.5 ± 10.9 years. Mean ± SD operating time was 97.4 ± 25.6 (range, 60–180) minutes. Mean ± SD hospitalization length was 3.6 ± 0.9 (range, 2–6) days. No intraoperative complications were recorded. Median length of follow-up was 24 (range, 12–38) months. During the follow-up period, the objective success rates for central compartment prolapse and for all compartments were 93.5% and 89.1%, respectively. No woman presented dyspareunia at follow-up. Thirty-nine women (84.8%) reported very high satisfaction related to surgery and 6 (13%) a moderate satisfaction. Overall Female Sexual Function Index, Knowles-Eccersley-Scott Symptom, and Bristol Female Lower Urinary Tract scores improved significantly after surgery, except for incontinence score domain.

Conclusions
Laparoscopic mesh-less cervicosacropexy represents an effective and feasible option for the surgical treatment of uterovaginal prolapse in sexually active women, avoiding postoperative complications due to the mesh use.
Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors
Authors: Mannakee Brian K , Balaji Uthra , Witkiewicz Agnieszka K. , Gutenkunst Ryan N. , Knudsen Erik S. 
Published: September 2017

AbstractMotivationTumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts (PDXs). Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, MAPEX, to identify and filter out spurious calls from both these sources.ResultsWhen calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms. When applied to any tumor, MAPEX also automatically flags calls that potentially arise from paralogous sequences. Our implementation, mapexr, runs quickly and easily on a desktocomputer. MAPEX is thus a useful addition to almost any pipeline for calling genetic variants in tumors.
Parallel natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize
Authors: Yan Lang , Kenchanmane Raju Sunil Kumar , Lai Xianjun , Zhang Yang , Dai Xiuru , Rodriguez Oscar , Mahboub Samira , Roston Rebecca L. , Schnable James C. 
Published: September 2017

ABSTRACTArtificial selection has produced varieties of domesticated maize which thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and sub-tropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read isoseq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation on other cold adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes which were targets of artificial selection during the adaptation of maize to temperate climates and those which were targets of natural selection in temperate adapted T. dactyloides. This overlap between the targets of natural and artificial selection suggests genetic changes in crop-wild relatives associated with adaptation to new environments may be useful guides for identifying genetic targets for breeding efforts aimed at adapting crops to a changing climate.
dBBQs : dataBase of Bacterial Quality scores
Authors: Wanchai Visanu , Patumcharoenpol Preecha , Nookaew Intawat , Ussery David 
Published: September 2017

AbstractBackgroundIt is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and put them in a fast and easy-to-use database.ResultsProkaryotic genomic data from all sources were collected and combined to make a non-redundant set of bacterial genomes. The genome quality score for each was calculated by four different measurements: assembly quality, number of rRNA and tRNA genes, and the occurrence of conserved functional domains. The dataBase of Bacterial Quality scores (dBBQs) was designed to store and retrieve quality scores. It offers fast searching and download features which the result can be used for further analysis. In addition, the search results are shown in interactive JavaScript chart framework using DC.js. The analysis of quality scores across major public genome databases find that around 68% of the genomes are of acceptable quality for many uses.ConclusionsdBBQs (available athttp://arc-gem.uams.edu/dbbqs) provides genome quality scores for all available prokaryotic genome sequences with a user-friendly Web-interface. These scores can be used as cut-offs to get a high-quality set of genomes for testing bioinformatics tools or improving the analysis. Moreover, all data of the four measurements that were combined to make the quality score for each genome, which can potentially be used for further analysis. dBBQs will be updated regularly and is freely use for non-commercial purpose.
Application of Polymersomes Engineered to Target P32 Protein for Detection of Small Breast Tumors in Mice
Authors: Simón-Gracia Lorena , Scodeller Pablo , Salazar Fuentes Sergio , Gómez Vallejo Vanessa , Ríos Xabier , San Sebastián Eneko , Sidorenko Valeria , Di Silvio Desirè , Suck Meina , De Lorenzi Federica , Yokota Rizzo Larissa , von Stillfried Saskia , Kilk Kalle , Lammers Twan , Moya Sergio E , Teesalu Tambet 
Published: September 2017

AbstractTriple negative breast cancer (TNBC) is the deadliest form of breast cancer and its successful treatment critically depends on early diagnosis and therapy. The multi-compartment protein p32 is overexpressed and present at cell surfaces in a variety of tumors, including TNBC, specifically in the malignant cells and endothelial cells, and in macrophages localized in hypoxic areas of the tumor. Herein we used polyethylene glycol-polycaprolactone polymersomes that were affinity targeted with the p32-binding tumor penetrating peptide LinTT1 (AKRGARSTA) for imaging of TNBC lesions. A tyrosine residue was added to the peptide to allow for124I labeling and PET imaging. In a TNBC model in mice, systemic LinTT1-targeted polymersomes accumulated in early tumor lesions more than twice as efficiently as untargeted polymersomes with up to 20% ID/cc at 24 h after administration. The PET-imaging was very sensitive, allowing detection of tumors as small as ∼20mm3. Confocal imaging of tumor tissue sections revealed a high degree of vascular exit and stromal penetration of LinTT1-targeted polymersomes and co-localization with tumor-associated macrophages. Our studies show that systemic LinTT1-targeted polymersomes can be potentially used for precision-guided tumor imaging and treatment of TNBC.
Age, sex, and puberty related development of the corpus callosum: a multi-technique diffusion MRI study
Authors: Genc Sila , Malpas Charles B , Ball Gareth , Silk Timothy J , Seal Marc L 
Published: September 2017

AbstractPurposeThe corpus callosum is integral to the central nervous system, and continually develops with age by virtue of increasing axon diameter and ongoing myelination. Magnetic resonance imaging (MRI) techniques offer a means to disentangle these two aspects of white matter development. We investigate the profile of microstructural metrics across the corpus callosum, and assess the impact of age, sex and pubertal development on these processes.MethodsThis study made use of two independent paediatric populations. Multi-shell diffusion MRI data were analysed to produce a suite of diffusion tensor imaging (DTI), neurite orientation density and dispersion imaging (NODDI), and apparent fibre density (AFD) metrics. A multivariate profile analysis was performed for each diffusion metric across 10 subdivisions of the corpus callosum.ResultsAll diffusion metrics significantly varied across the length of the corpus callosum. AFD exhibited a strong relationship with age across the corpus callosum (partialη2= .65), particularly in the posterior body of the corpus callosum (partialη2= .72). In addition, females had significantly higher AFD compared with males, most markedly in the anterior splenium (partialη2= .14) and posterior genu (partialη2= .13). Age-matched pubertal group differences were localised to the splenium.ConclusionWe present evidence of a strong relationship between apparent fibre density and age, sex, and puberty during development. These results are consistent withex vivostudies of fibre morphology, providing insights into the dynamics of axonal development in childhood and adolescence using diffusion MRI.Target journalsBrain Structure & Function; HBM; NeuroImage; Developmental Cognitive Neuroscience
Inferring critical points of ecosystem transitions from spatial data
Authors: Majumder Sabiha , Tamma Krishnapriya , Ramaswamy Sriram , Guttal Vishwesha 
Published: September 2017

AbstractEcosystems can undergo abrupt transitions from one state to an alternative stable state when the driver crosses a threshold or a critical point. Dynamical systems theory suggests that systems take long to recover from perturbations near such transitions. This leads to characteristic changes in the dynamics of the system, which can be used as early warning signals of imminent transitions. However, these signals are qualitative and cannot quantify the critical points. Here, we propose a method to estimate critical points quantitatively from spatial data. We employ a spatial model of vegetation that shows a transition from vegetated to bare state. We show that the critical point can be estimated as the ecosystem state and the driver values at which spatial variance and autocorrelation are maximum. We demonstrate the validity of this method by analysing spatial data from regions of Africa and Australia that exhibit alternative vegetation biomes.
Pleiotropy in enhancer function is encoded through diverse genetic architectures
Authors: Preger-Ben Noon Ella , Sabarís Gonzalo , Ortiz Daniela , Sager Jonathan , Liebowitz Anna , Stern David L. , Frankel Nicolas 
Published: September 2017

AbstractDevelopmental genes can have complex c/s-regulatory regions, with multiple enhancers scattered across stretches of DNA spanning tens or hundreds of kilobases. Early work revealed remarkable modularity of enhancers, where distinct regions of DNA, bound by combinations of transcription factors, drive gene expression in defined spatio-temporal domains. Nevertheless, a few reports have shown that enhancer function may be required in multiple developmental stages, implying that regulatory elements can be pleiotropic. In these cases, it is not clear whether the pleiotropic enhancers employ the same transcription factor binding sites to drive expression at multiple developmental stages or whether enhancers function as chromatin scaffolds, where independent sets of transcription factor binding sites act at different stages. In this work we have studied the activity of the enhancers of theshavenbabygene throughout D.melanogasterdevelopment. We found that all sevenshavenbabyenhancers drive gene expression in multiple tissues and developmental stages at varying levels of redundancy. We have explored how this pleiotropy is encoded in two of these enhancers. In one enhancer, the same transcription factor binding sites contribute to embryonic and pupal expression, whereas for a second enhancer, these roles are largely encoded by distinct transcription factor binding sites. Our data suggest that enhancer pleiotropy might be a common feature of c/s-regulatory regions of developmental genes and that this pleiotropy can be encoded through multiple genetic architectures.
A whole genome analysis of the red-crowned crane provides insight into avian longevity
Authors: Lee HyeJin , Chung Oksung , Cho Yun Sung , Jho Sungwoong , Jun JeHoon , Weber Jessica A. , Kim Jungeun , Lim Jeongheui , Edwards Jeremy S. , Paek Woon Kee , Bhak Jong 
Published: September 2017

AbstractThe red-crowned crane (Grus japonensis) is an endangered and large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is positively correlated with body size and negatively correlated with metabolic rate; although the genetic mechanisms for the red-crowned crane’s long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, we identified candidate genes that are correlated with longevity. Included among these are positively selected genes with known associations with longevity in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12 IL9R, SOD3, NUDT12, PNLIP, CTH, andRPA1). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and we hope this genome will provide a useful genetic resource for future conservation studies of this rare and iconic species.
Systematic Mendelian randomization framework elucidates hundreds of genetic loci which may influence disease through changes in DNA methylation levels
Authors: Richardson Tom G. , Haycock Philip C. , Zheng Jie , Timpson Nicholas J. , Gaunt Tom R. , Davey Smith George , Relton Caroline L. , Hemani Gibran 
Published: September 2017

AbstractWe have undertaken an extensive Mendelian randomization (MR) study using methylation quantitative trait loci (mQTL) as genetic instruments to assess the potential causal relationship between genetic variation, DNA methylation and 139 complex traits. Using two-sample MR, we observed 1,191 effects across 62 traits where genetic variants were associated with both proximal DNA methylation (i.e. cis-mQTL) and complex trait variation (P<1.39x10−08). Joint likelihood mapping provided evidence that the causal mQTL for 364 of these effects across 58 traits was also likely the causal variant for trait variation. These effects showed a high rate of replication in the UK Biobank dataset for 14 selected traits, as 121 of the attempted 129 effects replicated. Integrating expression quantitative trait loci (eQTL) data suggested that genetic variants responsible for 319 of the 364 mQTL effects also influence gene expression, which indicates a coordinated system of effects that are consistent with causality. CpG sites were enriched for histone mark peaks in tissue types relevant to their associated trait and implicated genes were enriched across relevant biological pathways. Though we are unable to distinguish mediation from horizontal pleiotropy in these analyses, our findings should prove valuable in identifying candidate loci for further evaluation and help develop mechanistic insight into the aetiology of complex disease.