bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to Infer Relative Fitness from a Sample of Genomic Sequences
Authors: Dayarian Adel , Shraiman Boris I 
Published: April 2014

Abstract
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman’s coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright–Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1–0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks.
The Lengths of Admixture Tracts
Authors: Liang Mason , Nielsen Rasmus 
Published: April 2014

Abstract
The distribution of admixture tract lengths has received considerable attention, in part because it can be used to infer the timing of past gene flow events between populations. It is commonly assumed that these lengths can be modeled as independently and identically distributed (iid) exponential random variables. This assumption is fundamental for many popular methods that analyze admixture using hidden Markov models. We compare the expected distribution of admixture tract lengths under a number of population-genetic models to the distribution predicted by the Wright–Fisher model with recombination. We show that under the latter model, the assumption of iid exponential tract lengths does not hold for recent or for ancient admixture events and that relying on this assumption can lead to false positives when inferring the number of admixture events. To further investigate the tract-length distribution, we develop a dyadic interval-based stochastic process for generating admixture tracts. This representation is useful for analyzing admixture tract-length distributions for populations with recent admixture, a scenario in which existing models perform poorly.
Chromosomal Evolution and Patterns of Introgression inHelianthus
Authors: Barb Jessica G , Bowers John E , Renaut Sebastien , Rey Juan I , Knapp Steven J , Rieseberg Loren H , Burke John M 
Published: April 2014

AbstractKnowledge of the nature and extent of karyotypic differences between species provides insight into the evolutionary history of the genomes in question and, in the case of closely related species, the potential for genetic exchange between taxa. We constructed high-density genetic maps of the silverleaf sunflower (Helianthus argophyllus) and Algodones Dune sunflower (H. niveus ssp. tephrodes) genomes and compared them to a consensus map of cultivated sunflower (H. annuus) to identify chromosomal rearrangements between species. The genetic maps of H. argophyllus and H. niveus ssp. tephrodes included 17 linkage groups each and spanned 1337 and 1478 cM, respectively. Comparative analyses revealed greater divergence between H. annuus and H. niveus ssp. tephrodes (13 inverted segments, 18 translocated segments) than between H. annuus and H. argophyllus (10 inverted segments, 8 translocated segments), consistent with their known phylogenetic relationships. Marker order was conserved across much of the genome, with 83 and 64% of the H. argophyllus and H. niveus ssp. tephrodes genomes, respectively, being syntenic with H. annuus. Population genomic analyses between H. annuus and H. argophyllus, which are sympatric across a portion of the natural range of H. annuus, revealed significantly elevated genetic structure in rearranged portions of the genome, indicating that such rearrangements are associated with restricted gene flow between these two species.
Duodenogastrojejunum Annular Internal Drainage for Superior Mesenteric Artery Syndrome: A Modified Staveley’s Surgery
Authors: Liu Wen 
Published: April 2014

INTRODUCTION: Superior mesenteric artery syndrome (SMAS) is caused by acute or chronic compression of the third part of the duodenum in the aortomesenteric angle. Staveley’s duodenojejunostomy (DJ) is an option when conservative management fails. In current case study, we reported a modified technique in treating the young patients who presented with a long-term history of intractable SMAS.
METHODS: Twelve patients presented with history of supper abdominal pain, nausea, distension and postprandial vomiting as well as weight loss. The finding of a significant narrowing of aortomesenteric angle and substantial duodenal compression established by endoscopic ultrasound and contrast-enhanced spiral CT, was in good agreement with a diagnosis of SMAS. Conservative treatment including enteral feeding failed to relieve the symptoms. Five cases were performed by traditional DJ and the other seven patients were applied with a modified DJ by duodenum-gastro-jejunum annular internal drainage. The patient health-related quality of life was evaluated by EQ-5D and SF-12 in all the cases within 1-yr and 3-yr follow ups.
RESULTS: There was no marked intra-abdominal hemorrhage, anastomotic leakage, postoperative infection and stromal hemorrhage / ulcers in all cases. There was no difference with respect to the intraoperative blood loss and urine output, and postoperative emerging time of negative fluid balance between the DJ and modified DJ groups. Compared to the traditional DJ, the modified procedure had an increased operation time (2.67 ± 0.29 vs 1.83 ± 0.29, P=0.03) and surgical stress score (SSS) (0.19 ± 0.02 vs 0.14 ± 0.01, P=0.02). Within postoperative one-month, sixty percent (3 cases) of DJ group had recurrent vomiting and epigastric pain and one patient need reoperation. During the 1-year and 3-year follow-ups, the recurrence cases of intermittent abdominal pain, distension and nausea were two and one respectively in DJ group. The patients in both groups showed increased weight gains in the follow ups. The patients with the modified DJ surgery showed not reflux gastritis, anastomotic ulcer and stricture with a complete relief of symptoms and a relatively higher SF-12 (PCS) compared to the DJ surgery (1-yr: 30.5 ± 3.1 vs 36.9 ± 3.2, P=0.04; 3-yr: 32.1 ± 3.1 vs 38.9 ± 3.2, P=0.04).
CONCLUSION: The case study showed that the modified procedure with duodenum annular internal drainage is feasible in relieving the symptoms when conservative treatment fails in young adults with SMAS. The new procedure increases surgery time and SSS. However, it potentially reduces the recurrence rate and postoperative complications of duodenal obstruction and antiperistalsis and improves quality of life. Further study will be required for effectiveness and safety of the modified procedure in the people with SMAS with longstanding history.
Morphology and thermal stability of bacterial cellulose/collagen composites
Authors: Albu Mădălina , Vuluga Zina , Panaitescu Denis , Vuluga Dumitru , Căşărică Angela , Ghiurea Marius 
Published: April 2014

AbstractThe aim of this paper was to prepare composites of bacterial cellulose (BC) and collagen to evaluate both the effect of collagen on the morphological, mechanical and thermal properties of BC and the effect of BC on the thermal stability of collagen for designing composites with increased potential biomedical applications. Two series of composites were prepared, the first series by immersing BC pellicle in solutions of collagen obtained in three forms, collagen gel (CG), collagen solution (CS) and hydrolysed collagen (HC), followed by freeze drying; and the second series of composites by mixing BC powder in solutions of collagen (CG, CS and HC), also followed by freeze drying. The properties of obtained composites were evaluated by Fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), mechanical tests, scanning electron microscopy (SEM) and atomic force microscopy (AFM). The results revealed that BC acts as a thermal stabilizer for CS matrix, while with CG matrix it interacts synergistically leading to composites with improved properties. On the other hand, the BC sheet impregnated with collagen has a significantly improved thermal stability. Collagen (as HC, CS or CG) has also a positive influence on the mechanical properties of lyophilized BC sheet. A four times increase of modulus was observed in BC/HC and BC/CG composites. and an increase of 60 times for BC/CS. The spectacular increase of elastic modulus and tensile strength in the case of BC/CS composite was explained by the easier penetration of collagen solution in the BC network and impregnation of BC fibrils as revealed by SEM and AFM analyzes.
Thyroid function tests and its interpretation
Authors: Raj KC Shiva 
Published: April 2014

Abstract: Thyroid diseases are among the most prevalent of medical conditions. In the patients with obvious features of hypothyroidism or hyperthyroidism thyroid function tests only confirm the diagnosis. Though TSH is widely used as a screening test in suspicion with thyroid disorder, many times TSH alone may be misleading. In this situation TSH along with T4 and T3 should be performed which will resolve the problem. However, thyroid function tests may not concord with each other. Discordant results between TSH, T4 and T3 may be because of various conditions like subclinical hypo- or hyperthyroidism, non-thyroidal illness, drugs etc. Beside that antibody interference and special condition like pregnancy may alter the thyroid hormone concentration. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10318 Journal of Pathology of Nepal (2014) Vol. 4, 584-590
Effect of natal and colonised host species on female host acceptance and male joining behaviour of the mountain pine beetle (Coleoptera: Curculionidae) using pine and spruce
Authors: McKee Fraser R. , Huber Dezene P.W. , Lindgren B. Staffan , Hodgkinson Robert S. , Aukema Brian H. 
Published: April 2014

AbstractThe mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae), outbreak in British Columbia and Alberta, Canada, currently extends over 18.3 million ha of pine forest. The principal host of the insect is lodgepole pine, Pinus contorta var. latifolia Englemann (Pineaceae) although it is a generalist herbivore on pines. Mountain pine beetles do not typically colonise spruce. However, during the current outbreak, several instances of mountain pine beetle attack on interior hybrid spruce, Picea glauca (Moench) Voss×Picea engelmannii Parry ex. Engelmann (Pinaceae) have been noted in areas where severe lodgepole pine mortality has occurred. Occasionally, beetle reproduction within spruce has been successful. Reproductive behaviours of mountain pine beetles reared from pine and spruce, such as female host acceptance and male joining behaviour, were studied on bolts of pine and spruce in laboratory bioassays. Females more readily accepted spruce host material relative to pine. Females that developed in spruce had higher rates of host acceptance of both pine and spruce host material than females that had developed in pine. We interpret these latter results with caution, however, as inference is partially restricted by sourcing viable insects from one spruce in this study. Implications of these findings to the concepts of host adaptation and population dynamics of this eruptive herbivore are discussed.
Check MAIT
Authors: Gapin Laurent 
Published: May 2014

Abstract
The evolutionary conservation of T lymphocyte subsets bearing αβ TCRs using invariant α-chains is indicative of unique and important functions. Among these T lymphocytes, NKT cells that express an invariant TCRα-chain and recognize lipid Ags presented by the nonclassical MHC class I molecule CD1d are probably the most studied. However, a new population of evolutionarily conserved T cells with another invariant TCRα rearrangement was recently characterized. These cells, which are very abundant in humans, tend to reside in mucosal tissues and, therefore, were named mucosal-associated invariant T (MAIT) cells. Until recently, little was known about MAIT cells; however, several recent advances in our understanding of MAIT cell characteristics and functions secure their upcoming rise to fame in the immunology field and in clinical practice.
ICAM-1: Isoforms and Phenotypes
Authors: Ramos Theresa N. , Bullard Daniel C. , Barnum Scott R. 
Published: May 2014

Abstract
ICAM-1 plays an important role in leukocyte trafficking, immunological synapse formation, and numerous cellular immune responses. Although considered a single glycoprotein, there are multiple membrane-bound and soluble ICAM-1 isoforms that arise from alternative splicing and proteolytic cleavage during inflammatory responses. The function and expression of these isoforms on various cell types are poorly understood. In the generation of ICAM-1–deficient mice, two isoform-deficient ICAM-1 mutants were inadvertently produced as a result of alternative splicing. These mice, along with true ICAM-1–deficient mice and newly generated ICAM-1–transgenic mice, have provided the opportunity to begin examining the role of ICAM-1 isoforms (singly or in combination) in various disease settings. In this review, we highlight the sharply contrasting disease phenotypes using ICAM-1 isoform mutant mice. These studies demonstrate that ICAM-1 immunobiology is highly complex but that individual isoforms, aside from the full-length molecule, make significant contributions to disease development and pathogenesis.
Microsurgical training model for residents to approach to the orbit and the optic nerve in fresh cadaveric sheep cranium
Authors: Altunrende M. Emre , Hamamcioglu Mustafa Kemal , Hicdonmez Tufan , Akcakaya Mehmet Osman , Birgili Baris , Cobanoglu Sebahattin 
Published: April 2014

ABSTRACT
Background: Neurosurgery and ophthalmology residents need many years to improve microsurgical skills. Laboratory training models are very important for developing surgical skills before clinical application of microsurgery. A simple simulation model is needed for residents to learn how to handle microsurgical instruments and to perform safe dissection of intracranial or intraorbital nerves, vessels, and other structures. Materials and Methods: The simulation material consists of a one-year-old fresh cadaveric sheep cranium. Two parts (Part 1 and Part 2) were designed to approach structures of the orbit. Part 1 consisted of a 2-step approach to dissect intraorbital structures, and Part 2 consisted of a 3-step approach to dissect the optic nerve intracranially. Results: The model simulates standard microsurgical techniques using a variety of approaches to structures in and around the orbit and the optic nerve. Conclusions: This laboratory training model enables trainees to gain experience with an operating microscope, microsurgical instruments and orbital structures.
Supratentorial primitive neuroectodermal tumor presenting with intracranial hemorrhage in adult
Authors: Abuzayed Bashar , Khreisat Wiam , Maaiah William , Agailat Saoud 
Published: April 2014

ABSTRACTA 24-year-old female patient presented with complaints of nausea, vomiting and of loss of consciousness lasted for 15 minutes with left sided weakness. Neuroradiological evaluation revealed a hemorrhagic mass lesion in the right frontal lobe. The patient was operated and intraoperative findings showed a cortical-subcortical hematoma including hemorrhagic and disrupted tissue with a pathologic purple tissue on the periphery of the hematoma. Postoperative course was uneventful and postoperative histopathological examination revealed primitive neuroectodermal tumor. The patient was then referred to medical and radiation oncology clinics for further evaluation and treatment.
Validation of Analytic Methods for Combining Evidence Sources in Biosurveillance
Authors: Burkom Howard , Elbert Yevgeniy , Ramac-Thomas Liane , Cuellar Christopher 
Published: May 2014

To manage an increasingly complex data environment, a fusion module based on Bayesian networks (BN) was developed for the Dept. of Defense (DoD) Electronic Surveillance System for the Early Notification of Community-Based Epidemics (ESSENCE). Subsequent efforts have produced a full fusion-enabled version of ESSENCE for beta testing and further upgrades. The current presentation describes advances to formalize the network training, calibrate the component alerting algorithms and decision nodes together, and implement a validation strategy. A cross-validation strategy produced consistent threshold combinations yielding 88% sensitivity from reported events, a 10-15% improvement over the original demonstration module.
Imaging of Sub-retinal Pigment Epithelial Linear Structures in Patients with Age-Related Macular Degeneration
Authors: Inoue Maiko , Arakawa Akira , Yamane Shin , Kadonosono Kazuaki 
Published: April 2014

Purpose To evaluate hyperreflective linear structures (HLS), as assessed using spectral-domain optical coherence tomography (SD-OCT), identified under the retinal pigment epithelium (RPE) in patients with age-related macular degeneration (AMD). Methods This retrospective observational case study was conducted on 427 eyes of 408 consecutive patients who were scheduled to undergo anti-vascular endothelial growth factor (anti-VEGF) therapy for AMD. Patients with HLS under the RPE were investigated based on the SD-OCT findings at baseline or during the follow-up period. The associations between HLS and the lesion subtypes, localization in SD-OCT, clinical findings, and structural change after anti-VEGF treatment were also investigated. Results HLS were identified in 18 eyes of 16 patients. From the eyes with HLS, 12 eyes (66.7%) were diagnosed with retinal angiomatous proliferation (RAP), 4 eyes (22.2%) were diagnosed with occult choroidal neovascularization, and the remaining 2 eyes (11.1%) were diagnosed with polypoidal choroidal vasculopathy. HLS were multifocal and exhibited multilocalization under the RPE in all the eyes. Although it was difficult to identify these structures in the clinical findings at baseline, crystalline deposits correlated with the linear bands were observed during the follow-up period in 16 eyes (88.9%). After the anti-VEGF treatments, the HLS remained between the Bruch membrane and RPE or combined with the fibrovascular component. Conclusions HLS are rare SD-OCT findings found in patients with AMD, found in only 4.2% of the patients examined in this study. HLS were found especially in RAP lesions.
The Cementless Spotorno stem in THA: 10 year results
Authors: Yamasaki Takuma , Yasunaga Yuji , Mori Ryo , Hamanishi Michio , Shoji Takeshi , Ochi Mitsuo 
Published: April 2014

Background The clinical results of total hip arthroplasty (THA) with a cementless prosthesis have been constantly improving due to progress in the area of stem design and surface finish. Cementless Spotorno stem (CLS stem; Zimmer, Warsaw, USA) is a double-tapered rectangular straight stem. The purpose of this study is to investigate the mean 10 year results of CLS stem and to evaluate the press-fit stability of CLS stem. Methods One hundred and eighty-six consecutive patients (194 hips) were evaluated at more than five years after THA using CLS stems. The mean follow-up period was 111 months. The radiographic stability of the femoral stem was determined by Engh's criteria. The ascertained period of spot welds was noted by Gruen zones on the femoral side. The presence of stress shielding, and subsidence was also evaluated. Results A stable stem with bony on growth was identified in all cases. The mean period of expression of spot welds was 10.8 months in zone 2, 9.9 months in zone 3, 8.5 months in zone 5, and 8.8 months in zone 6. Stress shielding of more than grade 2 was observed in only three hips, which was non-progressive at one year after surgery. Subsidence of more than 2 mm was not observed in any of the hips. Conclusions Excellent stability of CLS stem has been maintained without abnormal bone reaction at the proximal femur. CLS stem is considered to achieve not only press-fit stability at trochanteric and subtrochanteric level, but bony fixation by osseointegration within one year after THA.
Periacetabular Osteotomy: Sporting, Social and Sexual Activity 9-12 Years Post Surgery
Authors: Klit Jakob , Hartig-Andreasen Charlotte , Jacobsen Steffen , Søballe Kjeld , Troelsen Anders 
Published: April 2014

Hip joint survivorship and functional outcome are traditional outcome measures applied after periacetabular osteotomy (PAO). Younger adults however have greater demands and expectations on the function of their hip joints and these demands are not expressed using traditional outcome assessment tools. The main purpose of this study was to explore alternative functional and quality of life measure after PAO. A cross sectional survey of preserved hip joints following PAO was performed. Fifty-two patients (68 hips), mean age 41 years (range 24-67), returned a questionnaire examining satisfaction, willingness to repeat surgery, quality of life, abilities in social activities, sports and sex-life, pain, limp, and stability of the hip. Median satisfaction was 5 (range 1-5) and 44 of 49 patients were willing to repeat surgery. Significant improvements were seen in quality of life, ability to do sports, participate in social activities and sex-life (p values <0.001) (although sex-life for males (p = 0.102)). Traditional outcomes (pain, stability and limp) showed significant improvements (p<0.001). Lasting improvements in patients’ sex life, social life and ability to do sports nine to 12 years following PAO were reported. Such factors are important measures of outcome in a younger adult cohort.