bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal trends in oropharyngeal cancer treatment and survival: 1998–2009
Authors: Chen Amy Y. , Zhu Jason , Fedewa Stacey 
Published: July 2013

Objectives/HypothesisTo describe temporal trends of surgical and nonsurgical treatment for advanced oropharyngeal cancer, and to report contemporary survival estimates and factors associated with survival.Study DesignPatients diagnosed between 1998 and 2009 with a first primary, invasive, advanced‐stage squamous cell carcinoma of the oropharynx were selected from the National Cancer Database (N = 67,239). The outcomes of this study were first primary treatment and survival. Treatment was defined as chemotherapy with concurrent radiation (ChemoRT), radiation alone (RT), and surgery.MethodsTwo‐tailed t tests were used to evaluate the statistical significance of treatment type by sociodemographic variables. Multivariate log binomial regression models were used to estimate risk ratio and 95% confidence interval of select treatments (ChemoRT vs. RT and ChemoRT vs. surgery). For survival analysis, all variables were entered into a single model to test for violations in the proportional hazards (PH) assumption. All PH analyses were stratified by stage and age at diagnosis, and insurance status.ResultsThe total analytic cohort included 43,983 patients. Sociodemographic variables predicted type of treatment and survival. In addition, chemoradiation was increasingly used during this time period and was associated with improved survival. There was no decrease in mean or median age of patients during this time period to explain the improved survival.ConclusionsThese results confirmed previously reported trends of increasing use of nonsurgical therapy in the treatment of advanced oropharyngeal cancers. In addition, this analysis describes numerous factors that were predictive of overall survival including race, insurance, increasing use of chemoradiation, and socioeconomic status.Level of Evidence2b Laryngoscope, 124:131–138, 2014
Improved imaging of Cochlear nerve hypoplasia using a 3‐tesla variable flip‐angle turbo spin‐echo sequence and a 7‐cm surface coil
Authors: Giesemann Anja M. , Raab Peter , Lyutenski Stefan , Dettmer Sabine , Bültmann Eva , Frömke Cornelia , Lenarz Thomas , Lanfermann Heinrich , Goetz Friedrich 
Published: July 2013

Objective/HypothesisMagnetic resonance imaging of the temporal bone has an important role in decision making with regard to cochlea implantation, especially in children with cochlear nerve deficiency. The purpose of this study was to evaluate the usefulness of the combination of an advanced high‐resolution T2‐weighted sequence with a surface coil in a 3‐Tesla magnetic resonance imaging scanner in cases of suspected cochlear nerve aplasia.Study DesignProspective study.MethodsSeven patients with cochlear nerve hypoplasia or aplasia were prospectively examined using a high‐resolution three‐dimensional variable flip‐angle turbo spin‐echo sequence using a surface coil, and the images were compared with the same sequence in standard resolution using a standard head coil. Three neuroradiologists evaluated the magnetic resonance images independently, rating the visibility of the nerves in diagnosing hypoplasia or aplasia.ResultsEight ears in seven patients with hypoplasia or aplasia of the cochlear nerve were examined. The average age was 2.7 years (range, 9 months–5 years). Seven ears had accompanying malformations. The inter‐rater reliability in diagnosing hypoplasia or aplasia was greater using the high‐resolution three‐dimensional variable flip‐angle turbo spin‐echo sequence (fixed‐marginal kappa: 0.64) than with the same sequence in lower resolution (fixed‐marginal kappa: 0.06).ConclusionsExamining cases of suspected cochlear nerve aplasia using the high‐resolution three‐dimensional variable flip‐angle turbo spin‐echo sequence in combination with a surface coil shows significant improvement over standard methods.Level of EvidenceNA. Laryngoscope, 124:751–754, 2014
External branch of the superior laryngeal nerve monitoring during thyroid and parathyroid surgery: International Neural Monitoring Study Group standards guideline statement
Authors: Barczyński Marcin , Randolph Gregory W. , Cernea Claudio R. , Dralle Henning , Dionigi Gianlorenzo , Alesina Piero F. , Mihai Radu , Finck Camille , Lombardi Davide , Hartl Dana M. , Miyauchi Akira , Serpell Jonathan , Snyder Samuel , Volpi Erivelto , Woodson Gayle , Kraimps Jean Louis , Hisham Abdullah N. ,   with the International Neural Monitoring Study Group
Published: July 2013

Intraoperative neural monitoring (IONM) during thyroid surgery has gained widespread acceptance as an adjunct to the gold standard of visual identification of the recurrent laryngeal nerve (RLN). Contrary to routine dissection of the RLN, most surgeons tend to avoid rather than routinely expose and identify the external branch of the superior laryngeal nerve (EBSLN) during thyroidectomy or parathyroidectomy. IONM has the potential to be utilized for identification of the EBSLN and functional assessment of its integrity; therefore, IONM might contribute to voice preservation following thyroidectomy or parathyroidectomy. We reviewed the literature and the cumulative experience of the multidisciplinary International Neural Monitoring Study Group (INMSG) with IONM of the EBSLN. A systematic search of the MEDLINE database (from 1950 to the present) with predefined search terms (EBSLN, superior laryngeal nerve, stimulation, neuromonitoring, identification) was undertaken and supplemented by personal communication between members of the INMSG to identify relevant publications in the field. The hypothesis explored in this review is that the use of a standardized approach to the functional preservation of the EBSLN can be facilitated by application of IONM resulting in improved preservation of voice following thyroidectomy or parathyroidectomy. These guidelines are intended to improve the practice of neural monitoring of the EBSLN during thyroidectomy or parathyroidectomy and to optimize clinical utility of this technique based on available evidence and consensus of experts.Level of Evidence5 Laryngoscope, 123:S1–S14, 2013
Understanding the treatment of waves in atmospheric models. Part 1: The shortest resolved waves of the 1D linearized shallow‐water equations
Authors: Ullrich P. A. 
Published: July 2013

AbstractThis article provides an intercomparison of the dispersive and diffusive properties of several standard numerical methods applied to the 1D linearized shallow‐water equations without the Coriolis term, including upwind and central finite‐volume, spectral finite‐volume, discontinuous Galerkin, spectral element, and staggered finite‐volume. All methods are studied up to tenth‐order accuracy, where possible. A consistent framework is developed which allows for direct intercomparison of the ability of these methods to capture the behaviour of linear gravity waves. The Courant–Friedrichs–Lewy (CFL) condition is also computed, which is important for gauging the stability of these methods, and leads to a measure of approximate equal error cost. The goal of this work is threefold: first, to determine the shortest wavelength which can be considered ‘resolved’ for a particular method; second, to determine the effect of increasing the order of accuracy on the ability of a method to capture wave‐like motion; and third, to determine which numerical methods offer the best treatment of wave‐like motion.
Psychological distress in patients with an implantable cardioverter defibrillator
Authors: Shiga Tsuyoshi , Suzuki Tsuyoshi , Nishimura Katsuji 
Published: July 2013

AbstractDespite the effectiveness of an implantable cardioverter defibrillator (ICD), its implantation and concomitant therapies, including shocks, can induce psychological distress in patients. Depression has been observed in approximately 30% of ICD patients, and shocks may contribute to the persistence of depression. Anxiety is common, with reports of 24–87% of ICD patients experiencing symptoms of anxiety after implantation, and type D personality and ICD‐related concerns may play important roles in the level of anxiety in ICD patients. However, the association between ICD shocks and anxiety is controversial. The prevalence of posttraumatic stress disorder (PTSD) in ICD patients is approximately 20%, and type D personality, comorbidities, and frequent shocks may contribute to PTSD. It is also important to pay attention to the psychological distress in the partners of ICD patients.
SELLING THE PASS: HABEAS CORPUS, DIPLOMATIC RELATIONS AND THE PROTECTION OF LIBERTY AND SECURITY OF PERSONS DETAINED ABROAD
Authors: Eatwell Tatyana 
Published: July 2013

AbstractOn 31 October 2012 the Supreme Court of England and Wales handed down its judgment in Rahmatullah v Secretary of State for Foreign Affairs and Secretary of State for Defence [2012] UKSC 48. The case concerns an application for habeas corpus brought by a citizen of Pakistan originally detained by the United Kingdom in Iraq before being transferred into the custody of the United States. Rahmatullah addresses important issues concerning the extraterritorial reach of habeas corpus under English law in respect of persons held in the custody of a foreign State, as well as the international rule of law. The case may be considered a legal victory for persons detained without trial by the US in facilities thought to be beyond the reach of the courts. However, in reality any strength in the arm of the law is drained by the priority given to the conduct of foreign affairs, ‘forbidden territory’ for the courts, over the Court's ruling and the UK's obligations under international law. The case is examined in the light of similar jurisprudence from US and Australian courts.
Does neuroticism make you old? Prospective associations between neuroticism and leukocyte telomere length
Authors: van Ockenburg S. L. , de Jonge P. , van der Harst P. , Ormel J. , Rosmalen J. G. M. 
Published: July 2013

BackgroundTelomere attrition, causing accelerated aging, might be one of the mechanisms through which neuroticism leads to somatic disease and increased all-cause mortality. In the current study we investigated whether neuroticism is prospectively associated with shorter telomere length (TL), a biological marker of aging.MethodParticipants were 3432 adults (mean age 52.9 years, range 32–79). Data were collected at baseline (T1) and at two follow-up visits after 4 years (T2) and 6 years (T3). Neuroticism was assessed using the 12-item neuroticism scale of the Revised Eysenck Personality Questionnaire (EPQ-R) at T2 and T3. TL was measured by a monochrome multiplex quantitative polymerase chain reaction (PCR) assay at T1, T2 and T3. A linear mixed model was used to assess whether neuroticism could predict TL prospectively after adjusting for age, sex, body mass index (BMI), frequency of sports, smoking status, presence of chronic diseases and level of education.ResultsNeuroticism was a significant negative predictor of TL at follow-up (B = −0.004,p = 0.044) after adjusting for sex, age, baseline TL and various biological and lifestyle factors.ConclusionsHigh neuroticism is significantly and prospectively associated with telomere attrition independent of lifestyle and other risk factors.
Population trends and breeding success of albatrosses and giant petrels at Gough Island in the face of at-sea and on-land threats
Authors: Cuthbert Richard J. , Cooper John , Ryan Peter G. 
Published: July 2013

AbstractSeveral factors threaten populations of albatrosses and giant petrels, including the impact of fisheries bycatch and, at some colonies, predation from introduced mammals. We undertook population monitoring on Gough Island of three albatross species (Tristan albatross Diomedea dabbenena L., sooty albatross Phoebetria fusca Hilsenberg, Atlantic yellow-nosed albatross Thalassarche chlororhynchos Gmelin) and southern giant petrels Macronectes giganteus (Gmelin). Over the study period, numbers of the Critically Endangered Tristan albatross decreased at 3.0% a year. Breeding success for this species was low (23%), and in eight count areas was correlated (r2 = 0.808) with rates of population decline, demonstrating chick predation by house mice Mus musculus L. is driving site-specific trends and an overall decline. Numbers of southern giant petrels were stable, contrasting with large increases in this small population since 1979. Significant population declines were not detected for either the Atlantic yellow-nosed or sooty albatross, however, caution should be applied to these results due to the small proportion of the population monitored (sooty albatross) and significant interannual variation in numbers. These trends confirm the Critically Endangered status of the Tristan albatross but further information, including a more accurate estimate of sooty albatross population size, is required before determining island wide and global population trends of the remaining species.
Mediengewaltkonsum und aggressives Verhalten
Authors: Möller Ingrid , Krahé Barbara , Busching Robert 
Published: July 2013

Eine Stichprobe von N = 1052 deutschen Jugendlichen mit und ohne Migrationshintergrund wurde im Abstand von jeweils 12 Monaten dreimal zu ihrem Gewaltmedienkonsum und ihrem aggressiven Verhalten befragt. Die Gruppen wurden hinsichtlich der Variablen Geschlecht, Alter, Schultyp und Schulleistung parallelisiert. Zu T1 besuchten die Teilnehmenden die 7. bzw. 8. Klasse. Die Jugendlichen mit Migrationshintergrund zeigten insgesamt einen höheren Gewaltmedienkonsum. Zu T3 berichteten sie mehr physische, aber weniger relationale Aggression als Jugendliche ohne Migrationshintergrund. Cross-Lagged Panel-Analysen ergaben parallele Zusammenhänge zwischen dem Konsum gewalthaltiger Medienangebote und Aggression für die beiden Gruppen: Habitueller Mediengewaltkonsum führte über die Zeit unabhängig vom Migrationsstatus zu einer erhöhten selbstberichteten physischen Aggression, umgekehrt ergab sich kein Pfad von der Aggressionsneigung zum späteren Konsum von Gewaltmedien. Zwischen Mediengewaltkonsum und relationaler Aggression fanden sich keine signifikanten Zusammenhänge über die Zeit.
Operation of inverter‐assisted wind‐driven slip‐ring induction generator for stand‐alone power supplies
Authors: Vijayakumar Krishnasamy , Kumaresan Natarajan , Gounden Nanjappa Gounder Ammasai 
Published: July 2013

The operation of wind‐driven single inverter‐battery‐assisted slip‐ring induction generator (SRIG) for stand‐alone power supplies has been proposed. For effective utilisation of wind energy, the proposed system will function as doubly fed induction generator (DFIG) or shorted stator induction generator (SSIG) depending upon the ac load requirement and available wind power, operating in four different modes. A method has been developed for the performance predetermination of such system. A supervisory control algorithm has been devised and implemented using TMS320LF2407A real time digital signal processor for the closed‐loop control of the proposed system. In this control algorithm, reliable and unambiguous feedback signals such as stator voltage, stator current and user command are used for decision making and for closed‐loop operation. The entire closed‐loop system with supervisory control algorithm has been tested in the laboratory with a 3.7 kW SRIG. The successful working of the proposed system with smooth changeover between the operating modes has been demonstrated with extensive experimental and simulation results. The advantage of the proposed wind energy system has also been brought out in comparison with classical back to back converter DFIG system for stand‐alone power supplies.
Electrical braking of synchronous generators for combined generator and water turbine bearings as well as stray‐load losses determination
Authors: Ćalasan Martin P. , Petrović Dragan S. , Ostojić Milutin M. 
Published: July 2013

This study describes a new method for determining combined synchronous generator and water turbine bearings losses as well as stray‐load losses of a generator, based on measurement of the speed change during electrical braking. In the electrical braking regime, the total braking torque of a hydrogenerator is made up of the torques defined by losses in the runner chamber of the hydraulic turbine, ventilation losses in the hydraulic‐turbine generator, bearings losses in the generator and the water turbine, as well as electromagnetic and stray‐load losses in the short‐circuit. In this study, the torque–speed curve is represented by the corresponding equations which describe all the torques occurring during electrical braking. By applying these equations to the measured results and using some numerical calculations, combined generator and water turbine bearings losses as well as stray‐load losses can be obtained. The proposed method is applied on a 190 MW generator at the Hydro Power Plant (HPP) Djerdap (in Serbia). The obtained results demonstrated a very high level of accuracy when compared with the values found in the manufacturer's technical documentation (Electrosila). The proposed method has the best and most economical use in large synchronous generators and generators in older power plants.
Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast
Authors: Dvir Shlomi , Velten Lars , Sharon Eilon , Zeevi Danny , Carey Lucas B. , Weinberger Adina , Segal Eran 
Published: July 2013

SignificanceThis study quantifies how protein levels are determined by the underlying 5′-UTR sequence of an mRNA. We accurately measured protein abundance in 2,041 5′-UTR sequence variants, differing only in positions −10 to −1. We show that a few nucleotide substitutions can significantly alter protein expression. We also developed a predictive model that explains two-thirds of the expression variation. We provide convincing evidence that key regulatory elements, including AUG sequence context, mRNA secondary structure, and out-of-frame upstream AUGs conjointly modulate protein levels. Our study can aid in synthetic biology applications, by suggesting sequence manipulations for fine-tuning protein expression in a predictable manner.
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data
Authors: Chen Wei-Ming , Danziger Samuel A. , Chiang Jung-Hsien , Aitchison John D. 
Published: July 2013

Abstract
Motivation: Protein phosphorylation is critical for regulating cellular activities by controlling protein activities, localization and turnover, and by transmitting information within cells through signaling networks. However, predictions of protein phosphorylation and signaling networks remain a significant challenge, lagging behind predictions of transcriptional regulatory networks into which they often feed.
Results: We developed PhosphoChain to predict kinases, phosphatases and chains of phosphorylation events in signaling networks by combining mRNA expression levels of regulators and targets with a motif detection algorithm and optional prior information. PhosphoChain correctly reconstructed ∼78% of the yeast mitogen-activated protein kinase pathway from publicly available data. When tested on yeast phosphoproteomic data from large-scale mass spectrometry experiments, PhosphoChain correctly identified ∼27% more phosphorylation sites than existing motif detection tools (NetPhosYeast and GPS2.0), and predictions of kinase–phosphatase interactions overlapped with ∼59% of known interactions present in yeast databases. PhosphoChain provides a valuable framework for predicting condition-specific phosphorylation events from high-throughput data.
Availability: PhosphoChain is implemented in Java and available at http://virgo.csie.ncku.edu.tw/PhosphoChain/ or http://aitchisonlab.com/PhosphoChain
Contact: john.aitchison@systemsbiology.org or jchiang@mail.ncku.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Trans-Golgi Network Localized ECHIDNA/Ypt Interacting Protein Complex Is Required for the Secretion of Cell Wall Polysaccharides inArabidopsis
Authors: Gendre Delphine , McFarlane Heather E. , Johnson Errin , Mouille Gregory , Sjödin Andreas , Oh Jaesung , Levesque-Tremblay Gabriel , Watanabe Yoichiro , Samuels Lacey , Bhalerao Rishikesh P. 
Published: July 2013

AbstractThe secretion of cell wall polysaccharides through the trans-Golgi network (TGN) is required for plant cell elongation. However, the components mediating the post-Golgi secretion of pectin and hemicellulose, the two major cell wall polysaccharides, are largely unknown. We identified evolutionarily conserved YPT/RAB GTPase Interacting Protein 4a (YIP4a) and YIP4b (formerly YIP2), which form a TGN-localized complex with ECHIDNA (ECH) in Arabidopsis thaliana. The localization of YIP4 and ECH proteins at the TGN is interdependent and influences the localization of VHA-a1 and SYP61, which are key components of the TGN. YIP4a and YIP4b act redundantly, and the yip4a yip4b double mutants have a cell elongation defect. Genetic, biochemical, and cell biological analyses demonstrate that the ECH/YIP4 complex plays a key role in TGN-mediated secretion of pectin and hemicellulose to the cell wall in dark-grown hypocotyls and in secretory cells of the seed coat. In keeping with these observations, Fourier transform infrared microspectroscopy analysis revealed that the ech and yip4a yip4b mutants exhibit changes in their cell wall composition. Overall, our results reveal a TGN subdomain defined by ECH/YIP4 that is required for the secretion of pectin and hemicellulose and distinguishes the role of the TGN in secretion from its roles in endocytic and vacuolar trafficking.
Structure of the Arabidopsis Glucan Phosphatase LIKE SEX FOUR2 Reveals a Unique Mechanism for Starch Dephosphorylation
Authors: Meekins David A. , Guo Hou-Fu , Husodo Satrio , Paasch Bradley C. , Bridges Travis M. , Santelia Diana , Kötting Oliver , Vander Kooi Craig W. , Gentry Matthew S. 
Published: July 2013

Abstract
Starch is a water-insoluble, Glc-based biopolymer that is used for energy storage and is synthesized and degraded in a diurnal manner in plant leaves. Reversible phosphorylation is the only known natural starch modification and is required for starch degradation in planta. Critical to starch energy release is the activity of glucan phosphatases; however, the structural basis of dephosphorylation by glucan phosphatases is unknown. Here, we describe the structure of the Arabidopsis thaliana starch glucan phosphatase LIKE SEX FOUR2 (LSF2) both with and without phospho-glucan product bound at 2.3Å and 1.65Å, respectively. LSF2 binds maltohexaose-phosphate using an aromatic channel within an extended phosphatase active site and positions maltohexaose in a C3-specific orientation, which we show is critical for the specific glucan phosphatase activity of LSF2 toward native Arabidopsis starch. However, unlike other starch binding enzymes, LSF2 does not possess a carbohydrate binding module domain. Instead we identify two additional glucan binding sites located within the core LSF2 phosphatase domain. This structure is the first of a glucan-bound glucan phosphatase and provides new insights into the molecular basis of this agriculturally and industrially relevant enzyme family as well as the unique mechanism of LSF2 catalysis, substrate specificity, and interaction with starch granules.