bluuebunny/crossref_metadata_2025_split huggingface dataset:
Productivity costs decrease after endoscopic sinus surgery for refractory chronic rhinosinusitis
Authors: Rudmik Luke , Smith Timothy L. , Mace Jess C. , Schlosser Rodney J. , Hwang Peter H. , Soler Zachary M. 
Published: September 2015

Objectives/HypothesisThe primary objective of this pilot study was to define the change in productivity costs following endoscopic sinus surgery (ESS) for chronic rhinosinusitis (CRS). Secondary objectives were to identify CRS‐related characteristics that may influence the degree of productivity improvement after ESS.Study DesignProspective, multi‐institutional, observational cohort study.MethodsThe human capital approach was used to define productivity costs. Annual absenteeism, presenteeism, and lost leisure time were quantified to define annual lost productive time (LPT). LPT was monetized using the annual daily wage rates obtained from the 2012 US Census and the 2013 US Department of Labor statistics.ResultsTwenty‐seven patients with refractory CRS who underwent ESS were followed for a mean of 15 months (range, 8–25 months). Following ESS, there were improvements in annual absenteeism (22 days reduced to 3 days), annual presenteeism (41 days reduced to 19 days), and annual household days lost (12 days reduced to 6 days). Overall, the preoperative productivity costs were reduced after ESS ($9,190 vs. $3,373, respectively; P < .001).ConclusionsDaily productivity is negatively impacted by the presence of CRS. The outcomes from this study provide the first insights into the reduced productivity costs associated with receiving ESS for refractory CRS. Future studies with larger sample sizes will need to validate the results from this pilot study.Level of Evidence2c Laryngoscope, 126:570–574, 2016
Outcomes and complications in superior semicircular canal dehiscence surgery: A systematic review
Authors: Gioacchini Federico Maria , Alicandri‐Ciufelli Matteo , Kaleci Shaniko , Scarpa Alfonso , Cassandro Ettore , Re Massimo 
Published: September 2015

ObjectiveSuperior semicircular canal dehiscence (SSCD) represents a rare condition that may be associated to some particular symptoms as vertigo, autophony, and Tullio phenomenon. In those patients who present severe symptoms surgical treatment is required. Middle fossa craniotomy and transmastoid approaches are both described. Concerning repairing techniques, plugging and/or resurfacing are typically used to close the defect. Our aim was first to analyze the overall outcomes and complications of this surgery. Our second aim was to make a comparison between the different surgical modalities to investigate the eventual advantages and disadvantages.Review MethodsA search through Ovid MEDLINE was organized in January 2015 to include all eligible articles. A statistical analysis of the obtained data was performed.ResultsTwenty studies comprising a total of 150 procedures were included. Four modalities of canal repair were described (plugging, capping, resurfacing, plugging with resurfacing). The overall rate of success resulted in 94% (95% confidence interval: 87%‐97%). No statistically significant differences were observed among the different modalities of canal repair concerning both success rate and surgical complications. Differences observed between the middle fossa approach and transmastoid approach in terms of outcome were not statistically significant.ConclusionsThis review showed that surgical treatment for SSCD represents a safe option for those patients with severe symptoms of this condition. Differences observed in terms of success rate or complications were analyzed between the different surgical techniques with results that were not statistically significant.Level of EvidenceNA Laryngoscope, 126:1218–1224, 2016
Differential expression of HDAC and HAT genes in atrophying skeletal muscle
Authors: Beharry Adam W. , Judge Andrew R. 
Published: September 2015

ABSTRACTIntroduction: Histone deacetylase (HDAC) proteins, which counter the activity of histone acetyltransferases (HATs), are necessary for normal muscle atrophy in response to several pathophysiological conditions. Despite this, it remains unknown whether a common or unique transcriptional profile of HDAC and HAT genes exist during the progression of muscle atrophy. Methods: Muscles were harvested from cast immobilized, denervated, or nutrient deprived animals for quantitative reverse transcriptase‐polymerase chain reaction analysis of HDAC and HAT gene expression. Results: The mRNA levels of Hdac2, Hdac4, Hdac6, Sirt1, p300, Cbp, and Pcaf increased, and Hdac7 decreased in skeletal muscle in each experimental model of muscle atrophy. Hdac1 and Hdac3 were increased only in cast immobilized and denervated muscles. Conclusions: While specific HDACs and HATs are increased in multiple models of muscle atrophy, increased expression of class I HDACs was unique to muscle disuse, reinforcing that specific HDAC inhibitors may be more effective than pan‐HDAC inhibitors at countering muscle atrophy. Muscle Nerve 52: 1098–1101, 2015
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11
Authors: Cao Renzhi , Bhattacharya Debswapna , Adhikari Badri , Li Jilong , Cheng Jianlin 
Published: September 2015

ABSTRACTModel evaluation and selection is an important step and a big challenge in template‐based protein structure prediction. Individual model quality assessment methods designed for recognizing some specific properties of protein structures often fail to consistently select good models from a model pool because of their limitations. Therefore, combining multiple complimentary quality assessment methods is useful for improving model ranking and consequently tertiary structure prediction. Here, we report the performance and analysis of our human tertiary structure predictor (MULTICOM) based on the massive integration of 14 diverse complementary quality assessment methods that was successfully benchmarked in the 11th Critical Assessment of Techniques of Protein Structure prediction (CASP11). The predictions of MULTICOM for 39 template‐based domains were rigorously assessed by six scoring metrics covering global topology of Cα trace, local all‐atom fitness, side chain quality, and physical reasonableness of the model. The results show that the massive integration of complementary, diverse single‐model and multi‐model quality assessment methods can effectively leverage the strength of single‐model methods in distinguishing quality variation among similar good models and the advantage of multi‐model quality assessment methods of identifying reasonable average‐quality models. The overall excellent performance of the MULTICOM predictor demonstrates that integrating a large number of model quality assessment methods in conjunction with model clustering is a useful approach to improve the accuracy, diversity, and consequently robustness of template‐based protein structure prediction. Proteins 2016; 84(Suppl 1):247–259. © 2015 Wiley Periodicals, Inc.
Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras‐GAP in hydrolysis of guanosine triphosphate?
Authors: Khrenova Maria G. , Grigorenko Bella L. , Mironov Vladimir A. , Nemukhin Alexander V. 
Published: September 2015

ABSTRACTInterpretation of the experiments showing that the Ras‐GAP protein complex maintains activity in guanosine triphosphate (GTP) hydrolysis upon replacement of Glu61 in Ras with its unnatural nitro analog, NGln, is an important issue for understanding details of chemical transformations at the enzyme active site. By using molecular modeling we demonstrate that both glutamine and its nitro analog in the aci‐nitro form participate in the reaction of GTP hydrolysis at the stages of proton transfer and formation of inorganic phosphate. The computed structures and the energy profiles for the complete pathway from the enzyme‐substrate to enzyme‐product complexes for the wild‐type and mutated Ras suggest that the reaction mechanism is not affected by this mutation. Proteins 2015; 83:2091–2099. © 2015 Wiley Periodicals, Inc.
Different combinations of atomic interactions predict protein‐small molecule and protein‐DNA/RNA affinities with similar accuracy
Authors: Dias Raquel , Kolazckowski Bryan 
Published: September 2015

ABSTRACTInteractions between proteins and other molecules play essential roles in all biological processes. Although it is widely held that a protein's ligand specificity is determined primarily by its three‐dimensional structure, the general principles by which structure determines ligand binding remain poorly understood. Here we use statistical analyses of a large number of protein−ligand complexes with associated binding‐affinity measurements to quantitatively characterize how combinations of atomic interactions contribute to ligand affinity. We find that there are significant differences in how atomic interactions determine ligand affinity for proteins that bind small chemical ligands, those that bind DNA/RNA and those that interact with other proteins. Although protein‐small molecule and protein‐DNA/RNA binding affinities can be accurately predicted from structural data, models predicting one type of interaction perform poorly on the others. Additionally, the particular combinations of atomic interactions required to predict binding affinity differed between small‐molecule and DNA/RNA data sets, consistent with the conclusion that the structural bases determining ligand affinity differ among interaction types. In contrast to what we observed for small‐molecule and DNA/RNA interactions, no statistical models were capable of predicting protein−protein affinity with >60% correlation. We demonstrate the potential usefulness of protein‐DNA/RNA binding prediction as a possible tool for high‐throughput virtual screening to guide laboratory investigations, suggesting that quantitative characterization of diverse molecular interactions may have practical applications as well as fundamentally advancing our understanding of how molecular structure translates into function. Proteins 2015; 83:2100–2114. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
The influence of Fe impurities on the annealing of OH–Li complexes in ZnO
Authors: Herklotz F. , Johansen K. M. , Galeckas A. , Sky T. N. , Svensson B. G. 
Published: September 2015

AbstractThe annealing behavior of the center in ZnO, which leads to a local vibrational mode at , has been studied. Infrared absorption measurements confirm the previous findings that the center dissociates already at temperatures higher than about 500C and an apparent stability up to 1250C is due to efficient retrapping of H by Li. Secondary ion mass spectrometry data indicate that Fe impurities prevent a reformation of after dissociation. The formation of Fe −Li complexes is proposed as a prevailing mechanism for this behavior.
Retinoic Acid Induces Ubiquitination-Resistant RIP140/LSD1 Complex to Fine-Tune P
ax6 Gene in Neuronal Differentiation
Authors: Wu Cheng-Ying , Persaud Shawna D. , Wei Li-Na 
Published: September 2015

Abstract
Receptor-interacting protein 140 (RIP140) is a wide-spectrum coregulator for hormonal regulation of gene expression, but its activity in development/stem cell differentiation is unknown. Here, we identify RIP140 as an immediate retinoic acid (RA)-induced dual-function chaperone for LSD1 (lysine-specific demethylase 1). RIP140 protects LSD1's catalytic domain and antagonizes its Jade-2-mediated ubiquitination and degradation. In RA-induced neuronal differentiation, the increased RIP140/LSD1 complex is recruited by RA-elevated Pit-1 to specifically reduce H3K4me2 modification on the Pax6 promoter, thereby repressing RA-induction of Pax6. This study reveals a new RA-induced gene repressive mechanism that modulates the abundance, enzyme quality, and recruitment of histone modifier LSD1 to neuronal regulator Pax6, which provides a homeostatic control for RA induction of neuronal differentiation.
Developing nondestructive techniques for managing conflicts between fisheries and double‐crested cormorant colonies
Authors: Suzuki Yasuko , Roby Daniel D. , Lyons Donald E. , Courtot Karen N. , Collis Ken 
Published: September 2015

ABSTRACTDouble‐crested cormorants (Phalacrocorax auritus) have been identified as the source of significant mortality to juvenile salmonids (Oncorhynchus spp.) in the Columbia River Basin. Management plans for reducing the size of a large colony on East Sand Island (OR, USA) in the Columbia River estuary are currently being developed. We evaluated habitat enhancement and social attraction as nondestructive techniques for managing cormorant nesting colonies during 2004–2007. We tested these techniques on unoccupied plots adjacent to the East Sand Island cormorant colony. Cormorants quickly colonized these plots and successfully raised young. Cormorants also were attracted to nest and raised young on similar plots at 2 islands approximately 25 km from East Sand Island; 1 island had a history of successful cormorant nesting whereas the other was a site where cormorants had previously nested unsuccessfully. On a third island with no history of cormorant nesting or nesting attempts, these techniques were unsuccessful at attracting cormorants to nest. Our results suggest that some important factors influencing attraction of nesting cormorants using these techniques include history of cormorant nesting, disturbance, and presence of breeding cormorants nearby. These techniques may be effective in redistributing nesting cormorants away from areas where fish stocks of conservation concern are susceptible to predation, especially if sites with a recent history of cormorant nesting are available within their foraging or dispersal range. Published 2015. Wiley Periodicals, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.
High HER2 protein levels correlate with increased survival in breast cancer patients treated with anti‐HER2 therapy
Authors: Nuciforo Paolo , Thyparambil Sheeno , Aura Claudia , Garrido-Castro Ana , Vilaro Marta , Peg Vicente , Jimenez José , Vicario Rocio , Cecchi Fabiola , Hoos William , Burrows Jon , Hembrough Todd , Ferreres Juan Carles , Perez-Garcia José , Arribas Joaquin , Cortes Javier , Scaltriti Maurizio 
Published: September 2015

Introduction: Current methods to determine HER2 (human epidermal growth factor receptor 2) status are affected by reproducibility issues and do not reliably predict benefit from anti‐HER2 therapy. Quantitative measurement of HER2 may more accurately identify breast cancer (BC) patients who will respond to anti‐HER2 treatments.Methods: Using selected reaction monitoring mass spectrometry (SRM‐MS), we quantified HER2 protein levels in formalin‐fixed, paraffin‐embedded (FFPE) tissue samples that had been classified as HER2 0, 1+, 2+ or 3+ by immunohistochemistry (IHC). Receiver operator curve (ROC) analysis was conducted to obtain optimal HER2 protein expression thresholds predictive of HER2 status (by standard IHC or in situ hybridization [ISH]) and of survival benefit after anti‐HER2 therapy.Results: Absolute HER2 amol/μg levels were significantly correlated with both HER2 IHC and amplification status by ISH (p < 0.0001). A HER2 threshold of 740 amol/μg showed an agreement rate of 94% with IHC and ISH standard HER2 testing (p < 0.0001). Discordant cases (SRM‐MS‐negative/ISH‐positive) showed a characteristic amplification pattern known as double minutes. HER2 levels >2200 amol/μg were significantly associated with longer disease‐free survival (DFS) and overall survival (OS) in an adjuvant setting and with longer OS in a metastatic setting.Conclusion: Quantitative HER2 measurement by SRM‐MS is superior to IHC and ISH in predicting outcome after treatment with anti‐HER2 therapy.
Rethinking Judicial Independence in India and Sri Lanka
Authors: ABEYRATNE Rehan 
Published: September 2015

AbstractThe traditional narrative of judicial independence in India and Sri Lanka goes like this. The Indian Constitution established a strong and independent judiciary, which has become one of the most powerful in the world. By contrast, judicial independence was never entrenched in Sri Lanka due to insufficient constitutional safeguards and political interference. This paper seeks to challenge this narrative. It argues that despite important structural differences, India and Sri Lanka have followed similar judicial paths since the 1970s. Both judiciaries relaxed procedural requirements to allow sweeping public interest litigation; defined secularism and regulated religious practices in line with the dominant religious tradition; and largely deferred to the executive on the scope and necessity of emergency regulations. This remarkable convergence in jurisprudence demonstrates that (1) the Sri Lankan Supreme Court is more rights-protective and (2) its Indian counterpart is less willing to assert its independence on controversial issues than traditionally understood.
Can machine translation systems be evaluated by the crowd alone
Authors: GRAHAM YVETTE , BALDWIN TIMOTHY , MOFFAT ALISTAIR , ZOBEL JUSTIN 
Published: September 2015

AbstractCrowd-sourced assessments of machine translation quality allow evaluations to be carried out cheaply and on a large scale. It is essential, however, that the crowd's work be filtered to avoid contamination of results through the inclusion of false assessments. One method is to filter via agreement with experts, but even amongst experts agreement levels may not be high. In this paper, we present a new methodology for crowd-sourcing human assessments of translation quality, which allows individual workers to develop their own individual assessment strategy. Agreement with experts is no longer required, and a worker is deemed reliable if they are consistent relative to their own previous work. Individual translations are assessed in isolation from all others in the form of direct estimates of translation quality. This allows more meaningful statistics to be computed for systems and enables significance to be determined on smaller sets of assessments. We demonstrate the methodology's feasibility in large-scale human evaluation through replication of the human evaluation component of Workshop on Statistical Machine Translation shared translation task for two language pairs, Spanish-to-English and English-to-Spanish. Results for measurement based solely on crowd-sourced assessments show system rankings in line with those of the original evaluation. Comparison of results produced by the relative preference approach and the direct estimate method described here demonstrate that the direct estimate method has a substantially increased ability to identify significant differences between translation systems.
The critical mass approach to achieve a deal on green goods and services: what is on the table? How much should we expect?
Authors: de Melo Jaime , Vijil Mariana 
Published: September 2015

AbstractIn July 2014 a group of 14 countries (the ‘Davos Group’) launched negotiations on liberalizing trade in ‘green goods’ (also known as environmental goods – EGs), focusing on the elimination of tariffs for a list of 54 products. With an average tariff of 1.8 per cent, this group has little to offer even if the list were extended to the 411 products on the ‘WTO list’. Taking into account tariff dispersion, their tariff structure on EGs would be equivalent to a uniform tariff of 3.4 per cent, about half the uniform tariff-equivalent for non EGs products. Enlarging the number of participants to low-income countries might be possible as, on average, their imports would not increase by more than 8 per cent. Because of the strong complementarities between trade in EGs and trade in environmental services, these should also be brought into the negotiation in spite of the likely difficulties in reaching agreement on their scope.
Cold Face Test-Induced Increases in Heart Rate Variability Are Abolished by Engagement in a Social Cognition Task
Authors: Iorfino Frank , Alvares Gail A. , Guastella Adam J. , Quintana Daniel S. 
Published: September 2015

Abstract. The vagus nerve is a major constituent in the bidirectional relationship between the heart and the prefrontal cortex. This study investigated the role of the vagus in social cognition using the cold face test (facial cooling) to stimulate the vagus nerve and increase prefrontal inhibitory control. Heart Rate Variability (HRV) was measured to index parasympathetic outflow while social cognition ability was tested using the Reading the Mind in the Eyes Test (RMET). Healthy males (n = 25) completed the RMET under two conditions: with and without facial cooling. Results indicated that although facial cooling increased HRV at rest, there was no improvement in the RMET during the facial cooling condition. Interestingly, completing the RMET with facial cooling abolished this increase in HRV, suggesting interference along the vagal reflex arc. These results are consistent with the involvement of a common cortico-subcortical circuit in autonomic and cognitive processes, important for emotion recognition.
Sonogenetics is a non-invasive approach to activating neurons in Caenorhabditis elegans
Authors: Ibsen Stuart , Tong Ada , Schutt Carolyn , Esener Sadik , Chalasani Sreekanth H. 
Published: September 2015

AbstractA major challenge in neuroscience is to reliably activate individual neurons, particularly those in deeper brain regions. Current optogenetic approaches require invasive surgical procedures to deliver light of specific wavelengths to target cells to activate or silence them. Here, we demonstrate the use of low-pressure ultrasound as a non-invasive trigger to activate specific ultrasonically sensitized neurons in the nematode, Caenorhabditis elegans. We first show that wild-type animals are insensitive to low-pressure ultrasound and require gas-filled microbubbles to transduce the ultrasound wave. We find that neuron-specific misexpression of TRP-4, the pore-forming subunit of a mechanotransduction channel, sensitizes neurons to ultrasound stimulus, resulting in behavioural outputs. Furthermore, we use this approach to manipulate the function of sensory neurons and interneurons and identify a role for PVD sensory neurons in modifying locomotory behaviours. We suggest that this method can be broadly applied to manipulate cellular functions in vivo.
Differential genomic imprinting regulates paracrine and autocrine roles of IGF2 in mouse adult neurogenesis
Authors: Ferrón S. R. , Radford E. J. , Domingo-Muelas A. , Kleine I. , Ramme A. , Gray D. , Sandovici I. , Constancia M. , Ward A. , Menheniott T. R. , Ferguson-Smith A. C. 
Published: September 2015

AbstractGenomic imprinting is implicated in the control of gene dosage in neurogenic niches. Here we address the importance of Igf2 imprinting for murine adult neurogenesis in the subventricular zone (SVZ) and in the subgranular zone (SGZ) of the hippocampus in vivo. In the SVZ, paracrine IGF2 is a cerebrospinal fluid and endothelial-derived neurogenic factor requiring biallelic expression, with mutants having reduced activation of the stem cell pool and impaired olfactory bulb neurogenesis. In contrast, Igf2 is imprinted in the hippocampus acting as an autocrine factor expressed in neural stem cells (NSCs) solely from the paternal allele. Conditional mutagenesis of Igf2 in blood vessels confirms that endothelial-derived IGF2 contributes to NSC maintenance in SVZ but not in the SGZ, and that this is regulated by the biallelic expression of IGF2 in the vascular compartment. Our findings indicate that a regulatory decision to imprint or not is a functionally important mechanism of transcriptional dosage control in adult neurogenesis.