bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nasopharyngeal Acid Reflux and Eustachian Tube Dysfunction in Adults
Authors: Brunworth Joseph D. , Mahboubi Hossein , Garg Rohit , Johnson Brandon , Brandon Bryan , Djalilian Hamid R. 
Published: March 2014

Objective: This study aimed to evaluate the relationship between nasopharyngeal pH and Eustachian tube dysfunction (ETD) in adults. Study Design: Unmatched case-control study. Methods: Forty-one subjects, 20 adults with a diagnosis of ETD and 21 healthy adults as controls, were enrolled from an outpatient clinic. All subjects had a Dx–pH probe placed near the torus tubarius in the posterior nasopharynx for 24 hours. The pH values were recorded every 0.5 second. Decreases in pH were considered as reflux events if the pH dropped below 5.5. Results: The average nasopharyngeal pH value was 6.90 (range, 5.33-7.73) in the subjects with ETD and 7.07 (range, 5.99-7.94) in the controls. The difference between the 2 groups was not statistically significant ( P = .30). The ETD group, on average, had a higher number of nasopharyngeal reflux events (2.3 ± 1.6 vs 0.8 ± 1.2, respectively; P = .002) and higher reflux finding score (3.6 ± 2.7 vs 0.4 ± 1.4, respectively; P < .001) than the control group. Conclusion: By using a novel pH probe that allows detection of acidity in a nonliquid environment, a comparison of nasopharyngeal pH between control patients and those with ETD was performed. Eustachian tube dysfunction was more likely to be associated with a higher number of nasopharyngeal reflux events and higher reflux finding score. Nasopharyngeal reflux may have a role in the pathogenesis of ETD.
Minimally Invasive Video-Assisted Thyroidectomy
Authors: Kania Romain , Hammami Hassene , Vérillaud Benjamin , Blancal Jean-Philippe , Sauvaget Elisabeth , Tran Hugo , Leclerc Nicolas , Al Tabaa Khaled , Herman Philippe , Pons Yoann 
Published: March 2014

Background: The objectives of this study were first to show principles of the minimally invasive video-assisted thyroidectomy (MIVAT), based on a video highlighting critical steps, and second to discuss tips and pearls to assist surgical teams that would like to start using this technique. Methods: Based on a video, we described tips and pearls of a MIVAT. Results: MIVAT includes 5 main steps: (1) skin incision and identification of the common carotid artery, (2) dissection and ligation of the upper pedicle, (3) identification of the inferior laryngeal nerve and parathyroid glands, (4) isthmectomy and lobe extraction, and (5) closure. Discussion: Coordination between the surgeon and the 2 assistants is of paramount importance for the performance of MIVAT. Appropriate material is also required. The magnification and tissue contrast emphasizes the identification of the vessels, the superior and inferior laryngeal nerves, and parathyroid glands, on a large-view screen.
Personally Modifiable Risk Factors Associated with Pediatric Hearing Loss: A Systematic Review
Authors: Vasconcellos Adam P. , Kyle Meghann E. , Gilani Sapideh , Shin Jennifer J. 
Published: March 2014

BackgroundPediatric hearing loss is an increasingly recognized problem with significant implications. Increasing our quantitative understanding of potentially modifiable environmental risk factors for hearing loss may form the foundation for prevention and screening programs.ObjectiveTo determine whether specific threshold exposure levels of personally modifiable risk factors for hearing loss have been defined, with the overarching goal of providing actionable guidance for the prevention of pediatric hearing loss.Data SourcesA systematic review was performed. Computerized searches of PubMed, EMBASE, and the Cochrane Library were completed and supplemented with manual searches.Review MethodsInclusion/exclusion criteria were designed to determine specific threshold values of personally modifiable risk factors on hearing loss in the pediatric population. Searches and data extraction were performed by independent reviewers.ResultsThere were 38 criterion‐meeting studies, including a total of 50,651 subjects. Threshold noise exposures significantly associated with hearing loss in youth included: (1) more than 4 hours per week or more than 5 years of personal headphone usage, (2) more than 4 visits per month to a discotheque, and (3) working on a mechanized farm. Quantified tobacco levels of concern included any level of in utero smoke exposure as well as secondhand exposure sufficient to elevate serum cotinine.ConclusionsSpecific thresholds analyses are limited. Future studies would ideally focus on stratifying risk according to clearly defined levels of exposure, in order to provide actionable guidance for children and families.
Effects of Type 2 Diabetes on Otoacoustic Emissions and the Medial Olivocochlear Reflex
Authors: Eren Erdem , Harman Ece , Arslanoğlu Seçil , Önal Kazım 
Published: March 2014

ObjectiveTo demonstrate if cochleopathy in patients with type 2 diabetes with normal audiometric hearing threshold can be detected with otoacoustic emissions or medial olivocochlear (MOC) reflex measurements.Study DesignCross‐sectional study.SettingTertiary university teaching hospital.MethodsThe study involved 40 type 2 diabetic patients and 24 healthy volunteers. All participants who showed normal otoscopic findings, hearing thresholds, and acoustic admittance were included. Cochlear activity of participants was evaluated by means of distortion product otoacoustic emissions (DPOAEs) and transient otoacoustic emissions (TOAEs). The MOC reflex was evoked with contralateral acoustic stimulation and recorded with DPOAEs and TOAEs.ResultA comparison of DPOAE and TOAE levels with a t test between patient and control groups revealed no significant difference (P >. 05). A comparison of the MOC reflex response between the 2 groups also revealed no statistically significant difference (P >. 05).ConclusionAlthough decreased OAE amplitude levels were found in diabetic patients, there was no statistically significant difference in OAEs and MOC reflex. Additional studies are needed to evaluate the role of OAEs and MOC reflex in normal‐hearing patients with diabetes.
Pediatric Exercise Stress Laryngoscopy following Laryngotracheoplasty: A Comparative Review
Authors: Sidell Douglas R. , Balakrishnan Karthik , Hart Catherine K. , Willging J. Paul , Knecht Sandra K. , de Alarcon Alessandro 
Published: March 2014

ObjectiveExercise‐induced airway obstruction in pediatric patients is a unique phenomenon with multiple potential etiologies. An accurate diagnosis can be challenging to establish in pediatric patients because they are frequently asymptomatic at rest. Exercise stress laryngoscopy (ESL) is a modality by which pediatric patients can be evaluated under physiologic conditions that produce their symptoms. The purpose of this study was to demonstrate (1) the diagnostic effectiveness of pediatric ESL and (2) the ability of ESL to guide treatment for “normal” and post–airway reconstruction patients with exercise intolerance.Study DesignCase series with chart review.SettingTertiary care children's hospital.Subjects and MethodsPatients undergoing ESL for exercise intolerance were reviewed. Demographics, surgical history, examination findings, and management recommendations were extracted.ResultsThirty‐seven patients (average age, 13.5 years; range, 5‐21 years) were included. There were 14 male and 23 female patients. Airway abnormalities became evident in 56% of patients. Of these, 24% had focal supraglottic collapse, 43% had evidence of paradoxical vocal fold motion, 24% had combined supraglottic and glottic dysfunction, and 9% had distal airway abnormalities. Overall, 18 patients had changes in management after ESL. Twelve patients in this review had histories of laryngotracheoplasty with equivocal findings on operative bronchoscopy. Of these patients, 10 (83%) received focal diagnoses after ESL.ConclusionESL is a contemporary modality by which complex patients with undiagnosed exercise intolerance can be effectively evaluated. ESL can be an important tool used to guide treatment in pediatric patients with exercise‐induced dyspnea after airway reconstruction.
Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation
Authors: Rönnerblad Michelle , Andersson Robin , Olofsson Tor , Douagi Iyadh , Karimi Mohsen , Lehmann Sören , Hoof Ilka , de Hoon Michiel , Itoh Masayoshi , Nagao-Sato Sayaka , Kawaji Hideya , Lassmann Timo , Carninci Piero , Hayashizaki Yoshihide , Forrest Alistair R. R. , Sandelin Albin , Ekwall Karl , Arner Erik , Lennartsson Andreas 
Published: March 2014

Key Points
In granulopoiesis, changes in DNA methylation preferably occur at points of lineage restriction in low CpG areas. DNA methylation is dynamic in enhancer elements and appears to regulate the expression of key transcription factors and neutrophil genes.
A fixed point theorem for preordered complete fuzzy quasi-metric spaces and an application
Authors: Castro-Company Francisco , Romaguera Salvador , Tirado Pedro 
Published: March 2014

Abstract
We obtain a fixed point theorem for a type of generalized contractions on preordered complete fuzzy quasi-metric spaces which is applied to deduce, among other results, a procedure to show in a direct and easy fashion the existence of solution for the recurrence equations that are typically associated to Quicksort and Divide and Conquer algorithms, respectively.

MSC:47H10, 54H25, 06A06, 68Q25.
Estimation of protein function using template-based alignment of enzyme active sites
Authors: Hanson Brett , Westin Charles , Rosa Mario , Grier Alexander , Osipovitch Mikhail , MacDonald Madolyn L , Dodge Greg , Boli Paule M , Corwin Cyprian W , Kessler Haeja , McKay Talia , Bernstein Herbert J , Craig Paul A 
Published: March 2014

Abstract

Background
The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function. Functional residues are critical components of predictively useful motifs. We have implemented a novel method, to complement current approaches, which detects motifs solely on the basis of distance restraints between catalytic residues.

Results
ProMOL is a plugin for the PyMOL molecular graphics environment that can be used to create active site motifs for enzymes. A library of 181 active site motifs has been created with ProMOL, based on definitions published in the Catalytic Site Atlas (CSA). Searches with ProMOL produce better than 50% useful Enzyme Commission (EC) class suggestions for level 1 searches in EC classes 1, 4 and 5, and produce some useful results for other classes. 261 additional motifs automatically translated from Jonathan Barker’s JESS motif set [Bioinformatics 19:1644–1649, 2003] and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search methods.

Conclusion
The ProMOL plugin for PyMOL provides ready access to template-based local alignments. Recent improvements to ProMOL, including the expanded motif library, RMSD calculations and output selection formatting, have greatly increased the program’s usability and speed, and have improved the way that the results are presented.
Prophage-like elements present in Mycobacteriumgenomes
Authors: Fan Xiangyu , Xie Longxiang , Li Wu , Xie Jianping 
Published: March 2014

Abstract

Background
Prophages, integral components of many bacterial genomes, play significant roles in cognate host bacteria, such as virulence, toxin biosynthesis and secretion, fitness cost, genomic variations, and evolution. Many prophages and prophage-like elements present in sequenced bacterial genomes, such as Bifidobacteria, Lactococcus and Streptococcus, have been described. However, information for the prophage of Mycobacterium remains poorly defined.

Results
In this study, based on the search of the complete genome database from GenBank, the Whole Genome Shotgun (WGS) databases, and some published literatures, thirty-three prophages were described in detail. Eleven of them were full-length prophages, and others were prophage-like elements. Eleven prophages were firstly revealed. They were phiMAV_1, phiMAV_2, phiMmcs_1, phiMmcs_2, phiMkms_1, phiMkms_2, phiBN42_1, phiBN44_1, phiMCAN_1, phiMycsm_1, and phiW7S_1. Their genomes and gene contents were firstly analyzed. Furthermore, comparative genomics analyses among mycobacterioprophages showed that full-length prophage phi172_2 belonged to mycobacteriophage Cluster A and the phiMmcs_1, phiMkms_1, phiBN44_1, and phiMCAN_1 shared high homology and could be classified into one group.

Conclusions
To our knowledge, this is the first systematic characterization of mycobacterioprophages, their genomic organization and phylogeny. This information will afford more understanding of the biology of Mycobacterium.
Pulmonary lymphangitic carcinomatosis in liver carcinoma: a rare case report and literature review
Authors: Zhuang Li , Liu Xiangyan , Hu Chen , Zhang Lin , Jiang Guoping , Wu Jian , Zheng Shusen 
Published: March 2014

Abstract
Primary liver carcinoma is the most important malignant disease. The nodular metastatic foci of liver carcinoma are usually found in the lung, adrenal gland or abdomen after resection or transplantation. Pulmonary lymphangitic carcinomatosis (PLC) accounts for approximately 6% to 8% of metastatic cancer in the lung. The occurrence of PLC is extremely rare in liver carcinoma. Herein we report the case of a patient with PLC after liver transplantation due to liver carcinoma. PLC was confirmed by clinical manifestations, imaging studies and cytologic examination of exfoliated cells in the pleural effusion.
Construct validity of the Chelsea critical care physical assessment tool: an observational study of recovery from critical illness
Authors: Corner Evelyn J , Soni Neil , Handy Jonathan M , Brett Stephen J 
Published: March 2014

Abstract
Introduction
Intensive care unit-acquired weakness (ICU-AW) is common in survivors of critical illness, resulting in global weakness and functional deficit. Although ICU-AW is well described subjectively in the literature, the value of objective measures has yet to be established. This project aimed to evaluate the construct validity of the Chelsea Critical Care Physical Assessment tool (CPAx) by analyzing the association between CPAx scores and hospital-discharge location, as a measure of functional outcome.

Methods
The CPAx was integrated into practice as a service-improvement initiative in an 11-bed intensive care unit (ICU). For patients admitted for more than 48 hours, between 10 May 2010 and 13 November 2013, the last CPAx score within 24 hours of step down from the ICU or death was recorded (n = 499). At hospital discharge, patients were separated into seven categories, based on continued rehabilitation and care needs. Descriptive statistics were used to explore the association between ICU discharge CPAx score and hospital-discharge location.

Results
Of the 499 patients, 171 (34.3%) returned home with no ongoing rehabilitation or care input; 131 (26.2%) required community support; 28 (5.6%) went to inpatient rehabilitation for <6 weeks; and 25 (5.0%) went to inpatient rehabilitation for >6 weeks; 27 (5.4%) required nursing home level of care; 80 (16.0%) died in the ICU, and 37 (7.4%) died in hospital. A significant difference was found in the median CPAx score between groups (P < 0.0001). Four patients (0.8%) scored full marks (50) on the CPAx, all of whom went home with no ongoing needs; 16 patients (3.2%) scored 0 on the CPAx, all of whom died within 24 hours. A 0.8% ceiling effect and a 3.2% floor effect of the CPAx is found in the ICU. Compliance with completion of the CPAx stabilized at 78% of all ICU admissions.

Conclusion
The CPAx score at ICU discharge has displayed construct validity by crudely discriminating between groups with different functional needs at hospital discharge. The CPAx has a limited floor and ceiling effect in survivors of critical illness. A significant proportion of patients had a requirement for postdischarge care and rehabilitation.
Discriminative histogram taxonomy features for snake species identification
Authors: James Alex Pappachen , Mathews Bincy , Sugathan Sherin , Raveendran Dileep Kumar 
Published: March 2014

Abstract
Background
Incorrect snake identification from the observable visual traits is a major reason for death resulting from snake bites in tropics. So far no automatic classification method has been proposed to distinguish snakes by deciphering the taxonomy features of snake for the two major species of snakes i.e. Elapidae and Viperidae. We identify 38 different taxonomically relevant features to develop the Snake database from 490 sample images of Naja Naja (Spectacled cobra), 193 sample images of Ophiophagus Hannah (King cobra), 88 images of Bungarus caeruleus (Common krait), 304 sample images of Daboia russelii (Russell’s viper), 116 images of Echis carinatus (Saw scaled viper) and 108 images of Hypnale hypnale (Hump Nosed Pit Viper).

Results
Snake identification performances with 13 different types of classifiers and 12 attribute elevator demonstrate that 15 out of 38 taxonomically relevant features are enough for snake identification. Interestingly, these features were almost equally distributed from the logical grouping of top, side and body views of snake images, and the features from the bottom view of snakes had the least role in the snake identification.

Conclusion
We find that only few of the taxonomically relevant snake features are useful in the process of snake identification. These discriminant features are essential to improve the accuracy of snake identification and classification. The presented study indicate that automated snake identification is useful for practical applications such as in medical diagnosis, conservation studies and surveys by interdisciplinary practitioners with little expertise in snake taxonomy.
The Ability of Thyroid Hormone Receptors to Sense T4 as an Agonist Depends on Receptor Isoform and on Cellular Cofactors
Authors: Schroeder Amy , Jimenez Robyn , Young Briana , Privalsky Martin L. 
Published: March 2014

AbstractT4 (3,5,3′,5′-tetraiodo-l-thyronine) is classically viewed as a prohormone that must be converted to the T3 (3,5,3′-triiodo-l-thyronine) form for biological activity. We first determined that the ability of reporter genes to respond to T4 and to T3 differed for the different thyroid hormone receptor (TR) isoforms, with TRα1 generally more responsive to T4 than was TRβ1. The response to T4 vs T3 also differed dramatically in different cell types in a manner that could not be attributed to differences in deiodinase activity or in hormone affinity, leading us to examine the role of TR coregulators in this phenomenon. Unexpectedly, several coactivators, such as steroid receptor coactivator-1 (SRC1) and thyroid hormone receptor-associated protein 220 (TRAP220), were recruited to TRα1 nearly equally by T4 as by T3 in vitro, indicating that TRα1 possesses an innate potential to respond efficiently to T4 as an agonist. In contrast, release of corepressors, such as the nuclear receptor coreceptor NCoRω, from TRα1 by T4 was relatively inefficient, requiring considerably higher concentrations of this ligand than did coactivator recruitment. Our results suggest that cells, by altering the repertoire and abundance of corepressors and coactivators expressed, may regulate their ability to respond to T4, raising the possibility that T4 may function directly as a hormone in specific cellular or physiological contexts.
Intra-articular decorin influences the fibrosis genetic expression profile in a rabbit model of joint contracture
Authors: Abdel M. P. , Morrey M. E. , Barlow J. D. , Grill D. E. , Kolbert C. P. , An K. N. , Steinmann S. P. , Morrey B. F. , Sanchez-Sotelo J. 
Published: March 2014

Objectives The goal of this study was to determine whether intra-articular administration of the potentially anti-fibrotic agent decorin influences the expression of genes involved in the fibrotic cascade, and ultimately leads to less contracture, in an animal model. Methods A total of 18 rabbits underwent an operation on their right knees to form contractures. Six limbs in group 1 received four intra-articular injections of decorin; six limbs in group 2 received four intra-articular injections of bovine serum albumin (BSA) over eight days; six limbs in group 3 received no injections. The contracted limbs of rabbits in group 1 were biomechanically and genetically compared with the contracted limbs of rabbits in groups 2 and 3, with the use of a calibrated joint measuring device and custom microarray, respectively. Results There was no statistical difference in the flexion contracture angles between those limbs that received intra-articular decorin versus those that received intra-articular BSA (66° vs 69°; p = 0.41). Likewise, there was no statistical difference between those limbs that received intra-articular decorin versus those who had no injection (66° vs 72°; p = 0.27). When compared with BSA, decorin led to a statistically significant increase in the mRNA expression of 12 genes (p < 0.01). In addition, there was a statistical change in the mRNA expression of three genes, when compared with those without injection. Conclusions In this model, when administered intra-articularly at eight weeks, 2 mg of decorin had no significant effect on joint contractures. However, our genetic analysis revealed a significant alteration in several fibrotic genes. Cite this article: Bone Joint Res 2014;3:82–8.
From Pet-Making to High-Tech: Exploring the Dog‘s Role in the Media Environment
Authors: Rose Ellen 
Published: March 2014

Abstract
The purpose of this article is to broaden the media ecology perspective by considering the role of another creature, the dog, within the media environment. It is argued that the dog does not exist outside the media environment but is in fact a vital part its ecology. Its roles are formative (the dog’s presence in prehistoric human communities was arguably a precondition for the emergence of media and technology), compensatory (the dog’s presence helps us tolerate life in technological society), and moral (the dog communicates information about who we are as ethical beings that becomes vital in a society increasingly dominated by amoral technological imperatives). An acknowledgment of the dog’s roles is offered as a necessary step toward a truly ecological understanding of the nature and quality of interactions—both human and non-human—within the media environment.
The Computational Mind and the Digitized Society: A Question of Rules
Authors: Olson David R. 
Published: March 2014

Abstract
Information technology has allowed us to organize and coordinate actions to a degree unimaginable even a few decades ago—think of the man on the moon program— and to understand the rational workings of the human mind—think of Chomsky’s account of language as the product of rules and representations. I examine both of these ventures in terms of the increasing rationality of thought and action and the increasing rationality of social organization—the attempt to make both subject to explicit rules. I begin by commenting briefly on five domains where rules have a conspicuous place before advancing my arguments connecting rules, whether psychological or social, and literacy.