bluuebunny/crossref_metadata_2025_split huggingface dataset:
Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism
Authors: Jeanne Nicolas , Saliou Adrien , Carcenac Romain , Lefebvre Caroline , Dubois Martine , Cazabat Michelle , Nicot Florence , Loiseau Claire , Raymond Stéphanie , Izopet Jacques , Delobel Pierre 
Published: November 2015

AbstractHIV-1 coreceptor usage must be accurately determined before starting CCR5 antagonist-based treatment as the presence of undetected minor CXCR4-using variants can cause subsequent virological failure. Ultra-deep pyrosequencing of HIV-1 V3 env allows to detect low levels of CXCR4-using variants that current genotypic approaches miss. However, the computation of the mass of sequence data and the need to identify true minor variants while excluding artifactual sequences generated during amplification and ultra-deep pyrosequencing is rate-limiting. Arbitrary fixed cut-offs below which minor variants are discarded are currently used but the errors generated during ultra-deep pyrosequencing are sequence-dependant rather than random. We have developed an automated processing of HIV-1 V3 env ultra-deep pyrosequencing data that uses biological filters to discard artifactual or non-functional V3 sequences followed by statistical filters to determine position-specific sensitivity thresholds, rather than arbitrary fixed cut-offs. It allows to retain authentic sequences with point mutations at V3 positions of interest and discard artifactual ones with accurate sensitivity thresholds.
Adipose-derived Stem Cell Conditioned Media Extends Survival time of a mouse model of Amyotrophic Lateral Sclerosis
Authors: Fontanilla Christine V. , Gu Huiying , Liu Qingpeng , Zhu Timothy Z. , Zhou Changwei , Johnstone Brian H. , March Keith L. , Pascuzzi Robert M. , Farlow Martin R. , Du Yansheng 
Published: November 2015

AbstractAdipose stromal cells (ASC) secrete various trophic factors that assist in the protection of neurons in a variety of neuronal death models. In this study, we tested the effects of human ASC conditional medium (ASC-CM) in human amyotrophic lateral sclerosis (ALS) transgenic mouse model expressing mutant superoxide dismutase (SOD1G93A). Treating symptomatic SOD1G93A mice with ASC-CM significantly increased post-onset survival time and lifespan. Moreover, SOD1G93A mice given ASC-CM treatment showed high motor neuron counts, less activation of microglia and astrocytes at an early symptomatic stage in the spinal cords under immunohistochemical analysis. SOD1G93A mice treated with ASC-CM for 7 days showed reduced levels of phosphorylated p38 (pp38) in the spinal cord, a mitogen-activated protein kinase that is involved in both inflammation and neuronal death. Additionally, the levels of α-II spectrin in spinal cords were also inhibited in SOD1G93A mice treated with ASC-CM for 3 days. Interestingly, nerve growth factor (NGF), a neurotrophic factor found in ASC-CM, played a significant role in the protection of neurodegeneration inSOD1G93A mouse. These results indicate that ASC-CM has the potential to develop into a novel and effective therapeutic treatment for ALS.
Antitumor potential of a synthetic interferon-alpha/PLGF-2 positive charge peptide hybrid molecule in pancreatic cancer cells
Authors: Yin Hongmei , Chen Naifei , Guo Rui , Wang Hong , Li Wei , Wang Guanjun , Cui Jiuwei , Jin Haofan , Hu Ji-Fan 
Published: November 2015

AbstractPancreatic cancer is the most aggressive malignant disease, ranking as the fourth leading cause of cancer-related death among men and women in the United States. Interferon alpha (IFNα) has been used to treat pancreatic cancer, but its clinical application has been significantly hindered due to the low antitumor activity. We used a “cDNA in-frame fragment library” screening approach to identify short peptides that potentiate the antitumor activity of interferons. A short positively charged peptide derived from the C-terminus of placental growth factor-2 (PLGF-2) was selected to enhance the activity of IFNα. For this, we constructed a synthetic interferon hybrid molecule (SIFα) by fusing the positively charged PLGF-2 peptide to the C-terminus of the human IFNα. Using human pancreatic cell lines (ASPC and CFPAC1) as a model system, we found that SIFα exhibited a significantly higher activity than did the wild-type IFNα in inhibiting the tumor cell growth. The enhanced activity of the synthetic SIFα was associated with the activation of interferon pathway target genes and the increased binding of cell membrane receptor. This study demonstrates the potential of a synthetic SIFα as a novel antitumor agent.
Substrate-based inhibitors exhibiting excellent protective and therapeutic effects against Botulinum Neurotoxin A intoxication
Authors: Guo Jiubiao , Wang Jinglin , Gao Shan , Ji Bin , Waichi Chan Edward , Chen Sheng 
Published: November 2015

AbstractPotent inhibitors to reverse Botulinum neurotoxins (BoNTs) activity in neuronal cells are currently not available. A better understanding of the substrate recognition mechanism of BoNTs enabled us to design a novel class of peptide inhibitors which were derivatives of the BoNT/A substrate, SNAP25. Through a combination of in vitro, cellular based and in vivo mouse assays, several potent inhibitors of approximately one nanomolar inhibitory strength both in vitro and in vivo have been identified. These compounds represent the first set of inhibitors that exhibited full protection against BoNT/A intoxication in mice model with undetectable toxicity. Our findings validated the hypothesis that a peptide inhibitor targeting the two BoNT structural regions which were responsible for substrate recognition and cleavage respectively could exhibit excellent inhibitory effect, thereby providing insight on future development of more potent inhibitors against BoNTs.
High-frequency and high-quality silicon carbide optomechanical microresonators
Authors: Lu Xiyuan , Lee Jonathan Y. , Lin Qiang 
Published: November 2015

AbstractSilicon carbide (SiC) exhibits excellent material properties attractive for broad applications. We demonstrate the first SiC optomechanical microresonators that integrate high mechanical frequency, high mechanical quality and high optical quality into a single device. The radial-breathing mechanical mode has a mechanical frequency up to 1.69 GHz with a mechanical Q around 5500 in atmosphere, which corresponds to a fm · Qm product as high as 9.47 × 1012 Hz. The strong optomechanical coupling allows us to efficiently excite and probe the coherent mechanical oscillation by optical waves. The demonstrated devices, in combination with the superior thermal property, chemical inertness and defect characteristics of SiC, show great potential for applications in metrology, sensing, and quantum photonics, particularly in harsh environments that are challenging for other device platforms.
Evolution of the statistical distribution in a topological defect network
Authors: Xue Fei , Wang Xueyun , socolenco Ion , Gu Yijia , Chen Long-Qing , Cheong Sang-Wook 
Published: November 2015

AbstractThe complex networks of numerous topological defects in hexagonal manganites are highly relevant to vastly different phenomena from the birth of our cosmos to superfluidity transition. The topological defects in hexagonal manganites form two types of domain networks: type-I without and type-II with electric self-poling. A combined phase-field simulations and experimental study shows that the frequencies of domains with N-sides, i.e. of N-gons, in a type-I network are fitted by a lognormal distribution, whereas those in type-II display a scale-free power-law distribution with exponent ∼2. A preferential attachment process that N-gons with a larger N have higher probability of coalescence is responsible for the emergence of the scale-free networks. Since the domain networks can be observed, analyzed and manipulated at room temperature, hexagonal manganites provide a unique opportunity to explore how the statistical distribution of a topological defect network evolves with an external electric field.
Energy savings and operation improvement of rotating cement kiln by the implementation of a unique new drive system
Authors: Christopoulos George A. , Safacas Athanasios N. , Zafiris Athanasios 
Published: November 2015

Analysis, simulation, implementation and results of a new kiln drive system consisting of two AC motors of 315 kW each, on an existing common tooth gear, as a new contribution for the operational optimisation of rotating kilns, are presented in this study. Two separate inverter units control the two asynchronous motors with a common rectifier. This study also illustrates how backlash problems on tooth gear and maintenance needs are eliminated while reducing operational costs, down‐times and energy consumption, by applying contemporary technology, including power electronics and dynamic performance in control systems.
Circulating current losses analysis and improved incomplete transposition for stator bars in large hydro‐generators
Authors: Liang Yanping , Chen Yuanqi 
Published: November 2015

How to reduce circulating current is extremely crucial to the design of stator windings. Many general transposition bars are used in AC machine to reduce circulating current losses, and incomplete transposition is widely used considering the level of reducing circulating current losses. However, the circulating current between strands with incomplete transposition will fluctuate to different extent when load current is changed. This study puts forward an improved incomplete transposition structure based on previous incomplete structure such that load current has little impact on circulating current, which could reduce circulating current losses in further. To validate the new structure, a 180 MW hydro‐generator is taken as an example, and circulating current losses in strands are calculated by three‐dimensional finite element method. The calculating results indicate that the improved incomplete transposition structure could reduce circulating current losses more effectively compared with previous structure.
Utility of Single-Channel Electronic Resistivity Counters for Monitoring River Herring Populations
Authors: Sheppard John J. , Bednarski Michael S. 
Published: November 2015

Abstract
Automated electronic counting systems are used to estimate river herring populations throughout New England. Measuring the accuracy of these counting systems is essential to understanding the limitations of counter-derived estimates, which comprise a vital component of river herring stock assessments. Our objective was to conduct a direct visual–electronic comparison of passage to evaluate the accuracy and biases of using single-channel electronic resistivity counting systems to monitor river herring. From 1999 to 2012, we conducted 1,189 direct comparisons. Of these, 555 occurred when river herring were actively migrating through the system. The counting system consistently underestimated passage, with 34–87% of seasonal observations recording fewer fish than were known to pass. Mixed-effects logistic regression indicated that the probability of an inexact count increased with increasing passage rate, which we attribute to simultaneous passage. We explored two techniques to correct for the biases observed during our sampling period and produce corrected estimates of run size. Although our results have limitations, the consistency of observed bias provides evidence that single-channel counters yield the resolution needed to infer population trend. Future monitoring should endeavor to correct the biases in single-channel counters and to explore alternative technologies that provide greater accuracy.
Received April 3, 2015; accepted August 10, 2015
Perioperative Dextromethorphan as an Adjunct for Postoperative Pain
Authors: King Michael R. , Ladha Karim S. , Gelineau Amanda M. , Anderson T. Anthony 
Published: November 2015

AbstractAbstract
This meta-analysis identified 21 studies describing the effects of dextromethorphan on postoperative pain and opioid consumption. Dextromethorphan was found to reduce pain from 1 to 24 h postoperatively and was found to reduce morphine requirements 24 to 48 h after surgery.

Background

N-methyl-d-aspartate receptor antagonists have been shown to reduce perioperative pain and opioid use. The authors performed a meta-analysis to determine whether the use of perioperative dextromethorphan lowers opioid consumption or pain scores.

Methods
PubMed, Web of Science, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Pubget, and EMBASE were searched. Studies were included if they were randomized, double-blinded, placebo-controlled trials written in English, and performed on patients 12 yr or older. For comparison of opioid use, included studies tracked total consumption of IV or intramuscular opioids over 24 to 48 h. Pain score comparisons were performed at 1, 4 to 6, and 24 h postoperatively. Difference in means (MD) was used for effect size.

Results
Forty studies were identified and 21 were eligible for one or more comparisons. In 848 patients from 14 trials, opioid consumption favored dextromethorphan (MD, −10.51 mg IV morphine equivalents; 95% CI, −16.48 to −4.53 mg; P = 0.0006). In 884 patients from 13 trials, pain at 1 h favored dextromethorphan (MD, −1.60; 95% CI, −1.89 to −1.31; P < 0.00001). In 950 patients from 13 trials, pain at 4 to 6 h favored dextromethorphan (MD, −0.89; 95% CI, −1.11 to −0.66; P < 0.00001). In 797 patients from 12 trials, pain at 24 h favored dextromethorphan (MD, −0.92; 95% CI, −1.24 to −0.60; P < 0.00001).

Conclusion
This meta-analysis suggests that dextromethorphan use perioperatively reduces the postoperative opioid consumption at 24 to 48 h and pain scores at 1, 4 to 6, and 24 h.
Practice environments and job satisfaction and turnover intentions of nurse practitioners
Authors: Poghosyan Lusine , Liu Jianfang , Shang Jingjing , D’Aunno Thomas 
Published: November 2015

Background:
Health care professionals, organizations, and policy makers are calling for expansion of the nurse practitioner (NP) workforce in primary care to assure timely access and high-quality care. However, most efforts promoting NP practice have been focused on state level scope of practice regulations, with limited attention to the organizational structures.

Purpose:
We examined NP practice environments in primary care organizations and the extent to which they were associated with NP retention measures.

Methodology:
Data were collected through mail survey of NPs practicing in 163 primary care organizations in Massachusetts in 2012. NP practice environment was measured by the Nurse Practitioner Primary Care Organizational Climate Questionnaire, which has four subscales: Professional Visibility, NP–Administration Relations, NP–Physician Relations, and Independent Practice and Support. Two global items measured job satisfaction and NPs’ intent to leave their job. We aggregated NP level data to organization level to attain measures of practice environments. Multilevel logistic regression models were used.

Findings:
NPs rated the relationship between NPs and physicians favorably, contrary to the relationship between NPs and administrators. All subscales measuring NP practice environment had similar influence on the outcome variables. With every unit increase in each standardized subscale score, the odds of job satisfaction factors increased about 20% whereas the odds of intention of turnover decreased about 20%. NPs from organizations with higher mean scores on the NP–Administration subscale had higher satisfaction with their jobs (OR = 1.24, 95% CI [1.12, 1.39]) and had lower intent to leave (OR = 0.79, 95% CI [0.70, 0.90]).

Practice Implications:
NPs were more likely to be satisfied with their jobs and less likely to report intent to leave if their organizations support NP practice, favorable relations with physicians and administration, and clear role visibility. Creating productive practice environments that can retain NPs is a potential strategy for increasing the primary care workforce capacity.
Secondary Orbital Reconstruction in Patients with Prior Orbital Fracture Repair
Authors: Kim Jane S. , Lee Bradford W. , Scawn Richard L. , Korn Bobby S. , Kikkawa Don O. 
Published: November 2015

Purpose:
To evaluate clinical characteristics, preoperative imaging findings, pre- and post-operative outcomes, and satisfaction of patients requiring secondary reconstruction after inadequate primary orbital fracture repair.

Methods:
Retrospective review of 13 patients requiring secondary orbital reconstruction following unsatisfactory primary repair. Primary outcomes were postoperative changes in enophthalmos, hypo- or hyper-globus, superior sulcus deformity, and restrictive strabismus. Secondary outcomes included patient satisfaction.

Results:
Of 13 patients, 9 patients had primary orbital implants, and 4 patients did not. Of the 9 with implants, 6 had inferior displacement posteriorly, 2 had superior displacement posteriorly, and 1 had good position but had entrapped orbital tissues beneath it. Findings from primary surgery included enophthalmos (12/13), hypoglobus (10/13), hyperglobus (1/13), superior sulcus deformity (9/13), restricted supraduction (12/13), and restricted infraduction (7/13). Mean preoperative enophthalmos and hypoglobus were 4.4 ± 2.6 mm and 2.9 ± 1.4 mm, respectively. Secondary reconstruction resulted in mean reduction of enophthalmos by 3.4 ± 1.4 mm (p < 0.001), of hypoglobus by 2.9 ± 1.5 mm (p < 0.001), and of hyperglobus by 1 mm (n = 1). All 9 patients had resolution of their superior sulcus deformity. Of 12 cases with restricted ocular motility, all had improvements in postoperative motility following secondary surgery. Mean improvement in supraduction and infraduction was 1.8 ± 1.0 points (p < 0.001) and 1.4 ± 1.3 points (p = 0.025), respectively. Twelve patients reported being very satisfied or satisfied with secondary surgery; 1 patient was neutral.

Conclusions:
This study demonstrates that secondary orbital reconstruction can achieve excellent functional and cosmetic results with high patient satisfaction and minimal complications. Secondary reconstruction of previously repaired orbital fractures should be considered when clinically indicated.
Toxic‐metabolic Risk Factors in Pediatric Pancreatitis
Authors: Husain Sohail Z. , Morinville Veronique , Pohl John , Abu‐El‐Haija Maisam , Bellin Melena D. , Freedman Steve , Hegyi Peter , Heyman Melvin B. , Himes Ryan , Ooi Chee Y. , Schwarzenberg Sarah J. , Usatin Danielle , Uc Aliye 
Published: November 2015

ABSTRACTPancreatitis in children can result from metabolic and toxic risk factors, but the evidence linking these factors is sparse. We review the evidence for association or causality of these risk factors in pancreatitis, discuss management strategies, and their rationale. We conducted a review of the pediatric pancreatitis literature with respect to the following risk factors: hyperlipidemia, hypercalcemia, chronic renal failure, smoking exposure, alcohol, and medications. Areas of additional research were identified. Hypertriglyceridemia of 1000 mg/dL or greater poses an absolute risk for pancreatitis; persistent elevations of calcium are predisposing. Further research is necessary to determine whether end‐stage renal disease leads to increased pancreatitis in children similar to adults. It is unknown whether cigarette smoking exposure, which clearly increases risk in adults, also increases risk in children. The role of alcohol in pediatric pancreatitis, whether direct or modifying, needs to be elucidated. The evidence supporting most cases of medication‐induced pancreatitis is poor. Drug structure, improper handling of drug by host, and bystander status may be implicated. Other pancreatitis risk factors must be sought in all cases. The quality of evidence supporting causative role of various toxic and metabolic factors in pediatric pancreatitis is variable. Careful phenotyping is essential, including search for other etiologic risk factors. Directed therapy includes correction/removal of any agent identified, and general supportive measures. Further research is necessary to improve our understanding of these pancreatitis risk factors in children.
Contrast-Enhanced Ultrasonography Diagnostic Evaluation of Esophageal Varices in Patients With Cirrhosis
Authors: Qiu Lanyan , Zhang Xiaoli , Liu Dong , Qian Linxue , Hu Xiangdong 
Published: November 2015

Abstract
The purpose of this study was to clarify the usefulness of contrast-enhanced ultrasonography (CEUS) for the diagnosis of esophageal varices (EVs) in patients with cirrhosis. A total of 81 cases (56 patients with EVs and 25 control subjects without EV) were examined by CEUS and by esophagogastroduodenoscopy. According to the esophagogastroduodenoscopy results, we divided the subjects into 3 groups: G0, G1, and G2. The G0 group had 25 patients who exhibited no liver abnormality other than liver cyst or hemangioma without EVs, G1 comprised 9 patients with small EVs and 13 with medium EVs. G2 was composed of 34 cases of severe EVs. Under CEUS, the following parameters were measured: the thickness of double-layer mucosa and submucosa in the lower esophagus (Tm), the maximum anteroposterior diameter of the lower esophagus (De), and the ratio of Tm to De (Tm/De). Time-intensity curves of the lower esophagus and aorta were drawn using QLAB software. One-factor analysis of variance was used to compare means between the 3 groups. The diagnostic value of CEUS was assessed by receiver operating characteristic curves. Bayes discriminant analysis was adopted for building discriminant equations. Tm, De, Tm/De, Tep, and Iep/Iap were greater in patients with EVs (G1 and G2) than in those without EVs (G0). The Tms for the G0, G1, and G2 groups were 4.16 ± 0.59 mm, 7.06 ± 0.89 mm, and 10.10 ± 1.77 mm (P < 0.01), respectively, with 7.65 mm being the best cutoff value for diagnosing ≥ G2 (sensitivity 96.9%, specificity 90.0%). The area under the receiver operating characteristic curve was 0.987. Three discriminant equations were obtained by Bayes discriminant analysis: y
0 = −6.2 + 2.5Tm, y
1 = −15.1 + 4.1Tm and y
2 = −31.7 + 6.0Tm, respectively. The equations correctly classified 91.7% of cases in the study, making an error rate of 8.3%. Tm attained from CEUS can be a new, convenient, noninvasive parameter for evaluating esophageal varices in patients with liver cirrhosis.
Beyond the Bifurcation
Authors: Deurdulian Corinne , Emmanuel Neelmini , Tchelepi Hisham , Grant Edward G. , Malhi Harshawn 
Published: November 2015

Abstract
Carotid ultrasonography (US) is most commonly performed to identify potential areas of flow-limiting stenosis in the internal carotid artery. Identification of stenosis and unstable plaque is important because these entities are leading predictors of stroke, the fourth most common cause of death in the United States. However, US can detect other important but less common vascular pathologies if proper techniques and nuances of these entities are understood.
In this article, we discuss the US appearance of abnormalities involving the carotid, vertebral, subclavian, and innominate arteries as well as the key clinical components of each diagnosis. These include congenital variants, dissection, stenosis, and vasculopathy. In addition, correlation of US findings with both magnetic resonance imaging and computed tomography more comprehensively demonstrates the complementary nature of these imaging modalities.