bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of a CALM Buoy Moored Vessel in Squall Condition
Authors: Paalvast Mark , Kymmell Jelte , Gorter Ward , Brown Alison 
Published: October 2016

This paper reviews the response of a hawser moored vessel to squalls and addresses a novel method for obtaining statistically reliable design loads. Industry paradigms related to squall selection for analysis input are reviewed and renewed.
A benchmark database consisting of more than 15,000 unique squall-wave-current induced extreme values enables the validation of a range of less computationally demanding analysis and squall selection methods.
Extreme values are extrapolated to a design value using a Peak Over Threshold (POT) method to fit a Generalized Pareto Distribution (GPD). The influence of associated metocean conditions and squall characteristics on the vessel response is presented. By means of bootstrapping a satisfactory population size for design purposes is studied. The findings challenge common design practices currently employed throughout the industry.
Stochastic Linearization and its Application in Motion Analysis of Cylindrical Floating Structure With Bilge Boxes
Authors: Shao Yan-Lin , You Jikun , Glomnes Einar Bernt 
Published: October 2016

To account for the viscous effects of damping devices, for instance, bilge keels or bilge boxes, on the motions of ships and offshore structures, Morison’s equation is often adopted as an empirical but practical approach in the design process. In order to combine the standard engineering panel method with the drag term in Morison’s equation, and remain in the frequency domain, the drag term has to be linearized based on, for instance, stochastic linearization. In this paper, the stochastic linearization scheme is implemented in an in-house code and verified through the comparison with the DNV GL software WADAM.
The model test results of a large cylindrical FPSO with bilge box are used to calibrate the drag coefficients in the Morison’s equation. When the linearized drag forces are included, heave motion RAOs correspond better to the model test results. However, the predicted natural periods of heave motions are seen to be smaller than those obtained from model tests. It is suspected that the viscous flow separation around the bilge box increases the added mass of the unit beyond what is predicted by potential flow alone. Discussions are made on the effect of viscous added mass on the heave natural period.
It is quite common to only include the damping effects in the motion analysis for large offshore structures and ignore the contribution of the viscous effects on the excitation force. For the considered cylindrical FPSO, this paper demonstrates that the viscous excitation force can be important in survival conditions.
Factors influencing the performance of patient specific quality assurance for pencil beam scanning IMPT fields
Authors: Trnková P. , Bolsi A. , Albertini F. , Weber D. C. , Lomax A. J. 
Published: October 2016

PurposeA detailed analysis of 2728 intensity modulated proton therapy (IMPT) fields that were clinically delivered to patients between 2007 and 2013 at Paul Scherrer Institute (PSI) was performed. The aim of this study was to analyze the results of patient specific dosimetric verifications and to assess possible correlation between the quality assurance (QA) results and specific field metrics.MethodsDosimetric verifications were performed for every IMPT field prior to patient treatment. For every field, a steering file was generated containing all the treatment unit information necessary for treatment delivery: beam energy, beam angle, dose, size of air gap, nuclear interaction (NI) correction factor, number of range shifter plates, number of Bragg peaks (BPs) with their position and weight. This information was extracted and correlated to the results of dosimetric verification of each field which was a measurement of two orthogonal profiles using an orthogonal ionization chamber array in a movable water column.ResultsThe data analysis has shown more than 94% of all verified plans were within defined clinical tolerances. The differences between measured and calculated dose depend critically on the number of BPs, total thickness of all range shifter plates inserted in the beam path, and maximal range. An increase of the dose difference was observed with smaller number of BPs (i.e., smaller tumor) and smaller ranges (i.e., superficial tumors). The results of the verification do not depend, however, on the prescribed dose, NI correction, or the size of the air gap. There is no dependency of the transversal and longitudinal spot position precision on the beam angle. The value of NI correction depends on the number of spots and number of range shifter plates.ConclusionsThe presented study has shown that the verification method used at Centre for Proton Therapy at Paul Scherrer Institute is accurate and reproducible for performing patient specific QA. The results confirmed that the dose discrepancy is dependent on the size and location of the tumor.
Antibodies Damage the Resilience of Fimbriae, Causing Them To Be Stiff and Tangled
Authors: Singh Bhupender , Mortezaei Narges , Savarino Stephen J. , Uhlin Bernt Eric , Bullitt Esther , Andersson Magnus 
Published: October 2016

ABSTRACT

As adhesion fimbriae are a major virulence factor for many pathogenic Gram-negative bacteria, they are also potential targets for antibodies. Fimbriae are commonly required for initiating the colonization that leads to disease, and their success as adhesion organelles lies in their ability to both initiate and sustain bacterial attachment to epithelial cells. The ability of fimbriae to unwind and rewind their helical filaments presumably reduces their detachment from tissue surfaces with the shear forces that accompany significant fluid flow. Therefore, the disruption of functional fimbriae by inhibiting this resilience should have high potential for use as a vaccine to prevent disease. In this study, we show that two characteristic biomechanical features of fimbrial resilience, namely, the extension force and the extension length, are significantly altered by the binding of antibodies to fimbriae. The fimbriae that were studied are normally expressed on enterotoxigenic
Escherichia coli
, which are a major cause of diarrheal disease. This alteration in biomechanical properties was observed with bivalent polyclonal antifimbrial antibodies that recognize major pilin subunits but not with the Fab fragments of these antibodies. Thus, we propose that the mechanism by which bound antibodies disrupt the uncoiling of natural fimbria under force is by clamping together layers of the helical filament, thereby increasing their stiffness and reducing their resilience during fluid flow. In addition, we propose that antibodies tangle fimbriae via bivalent binding, i.e., by binding to two individual fimbriae and linking them together. Use of antibodies to disrupt physical properties of fimbriae may be generally applicable to the large number of Gram-negative bacteria that rely on these surface-adhesion molecules as an essential virulence factor.

IMPORTANCE
Our study shows that the resiliency of colonization factor antigen I (CFA/I) and coli surface antigen 2 (CS2) fimbriae, which are current targets for vaccine development, can be compromised significantly in the presence of antifimbrial antibodies. It is unclear how the humoral immune system specifically interrupts infection after the attachment of enterotoxigenic
Escherichia coli
(ETEC) to the epithelial surface. Our study indicates that immunoglobulins, in addition to their well-documented role in adaptive immunity, can mechanically damage the resilience of fimbriae of surface-attached ETEC, thereby revealing a new mode of action. Our data suggest a mechanism whereby antibodies coat adherent and free-floating bacteria to impede fimbrial resilience. Further elucidation of this possible mechanism is likely to inform the development and refinement of preventive vaccines against ETEC diarrhea.
Development and Characterization of Recombinant Virus Generated from a New World Zika Virus Infectious Clone
Authors: Weger-Lucarelli James , Duggal Nisha K. , Bullard-Feibelman Kristen , Veselinovic Milena , Romo Hannah , Nguyen Chilinh , Rückert Claudia , Brault Aaron C. , Bowen Richard A. , Stenglein Mark , Geiss Brian J. , Ebel Gregory D. 
Published: October 2016

ABSTRACT

Zika virus (ZIKV; family
Flaviviridae
, genus
Flavivirus
) is a rapidly expanding global pathogen that has been associated with severe clinical manifestations, including devastating neurological disease in infants. There are currently no molecular clones of a New World ZIKV available that lack significant attenuation, hindering progress toward understanding determinants of transmission and pathogenesis. Here we report the development and characterization of a novel ZIKV reverse genetics system based on a 2015 isolate from Puerto Rico (PRVABC59). We generated a two-plasmid infectious clone system from which infectious virus was rescued that replicates in human and mosquito cells with growth kinetics representative of wild-type ZIKV. Infectious clone-derived virus initiated infection and transmission rates in
Aedes aegypti
mosquitoes comparable to those of the primary isolate and displayed similar pathogenesis in AG129 mice. This infectious clone system provides a valuable resource to the research community to explore ZIKV molecular biology, vaccine development, antiviral development, diagnostics, vector competence, and disease pathogenesis.

IMPORTANCE
ZIKV is a rapidly spreading mosquito-borne pathogen that has been linked to Guillain-Barré syndrome in adults and congenital microcephaly in developing fetuses and infants. ZIKV can also be sexually transmitted. The viral molecular determinants of any of these phenotypes are not well understood. There is no reverse genetics system available for the current epidemic virus that will allow researchers to study ZIKV immunity, develop novel vaccines, or develop antiviral drugs. Here we provide a novel infectious clone system generated from a recent ZIKV isolated from a patient infected in Puerto Rico. This infectious clone produces virus with
in vitro
and
in vivo
characteristics similar to those of the primary isolate, providing a critical tool to study ZIKV infection and disease.
The reliability of the American Community Survey for injury surveillance
Authors: Bell Nathaniel , Cai Bo 
Published: October 2016

BackgroundTo evaluate the reliability and predictability of 49 socioeconomic indicators constructed from the annual and multiyear American Community Survey (ACS) data cycles for monitoring injury inequalities across the USA.MethodsCross-sectional analysis of the 2006–2013 annual and multiyear county-level ACS data cycles. Indicator reliability was assessed using the margin of error and coefficient of variation (CV). Overlapping multiyear data cycles were assessed for statistical dependence in the estimates. Negative binomial regression models were constructed from a selection of the most reliable indicators over time and across all data cycles using all-cause unintentional and homicide-related mortality records from the National Center for Health Statistics (NCHS).ResultsFewer than half of all indicators for each data cycle generated ‘high reliability’ CV estimates for at least 95% of all census counties. Indicator reliability did not linearly improve with increasing sample size afforded from the multiyear surveys. On average, changes in socioeconomic conditions for the same geographic areas were statistically significantly different (p<0.05) in 14% (rage 0–99%) to 16% (rage 0–93%) of all overlapping multiyear data cycles. ACS indicators that were among the most reliable across data cycles corroborated variable relationships derived using estimates from the 2000 decennial census and corresponding NCHS records for that year.ConclusionsFew of the socioeconomic indicators previously used to measure injury disparities are consistently reliable across all ACS data cycles. Researchers should be judicious when selecting consecutive multiyear data cycles to approximate changes in annual socioeconomic conditions. Among the indicators that are reliable, it is advisable to use estimates from the annual ACS data cycle as a crude barometer of injury inequalities and the multiyear files to confirm and add precedence to national trends every three and five years.
Exercise restrictions trigger psychological difficulty in active and athletic adults with hypertrophic cardiomyopathy
Authors: Luiten Rebecca C , Ormond Kelly , Post Lisa , Asif Irfan M , Wheeler Matthew T , Caleshu Colleen 
Published: October 2016

ObjectiveWe examined the extent and nature of the psychological difficulty experienced by athletic adults with hypertrophic cardiomyopathy (HCM), correlates of that difficulty and coping mechanisms.MethodsA survey assessed athletic history and psychological impact of exercise restrictions. LASSO penalised linear regression identified factors associated with psychological difficulty. Semistructured interviews provided deeper insight into the nature and origins of psychological difficulty.Results54 individuals (33% female, mean age 55.9) completed the survey. The majority were recreational athletes at the time of restriction (67%). There was a drop in athleticism after diagnosis, including time spent exercising (p=0.04) and identification as an athlete (p=0.0005). Most respondents (54%) found it stressful and/or difficult to adjust to exercise restrictions. Greater psychological morbidity was associated with history of elite or competitive athletics, athletic identity and decrease in time spent exercising. 16 individuals (44% female, mean age 52.4) were interviewed. Long-term effects included weight gain and uncertainty about exercising safely. The role of exercise in interviewees' lives contracted significantly after restriction, from multiple functions (eg, social, stress relief, fitness) to solely health maintenance. Interviewees reported a unique form of social support: having family and friends participate with them in lower intensity exercise. Lack of understanding from family or friends and avoiding exercise completely were detrimental to coping.ConclusionsAthletic adults with HCM experience multifaceted, lasting difficulty adjusting to exercise recommendations. These data can guide clinicians in identifying patients at highest risk for distress and in helping to bolster coping and adaptation.
Beat-to-beat control of human optokinetic nystagmus slow phase durations
Authors: Balaban Carey D. , Furman Joseph M. 
Published: October 2016

This study provides the first clear evidence that the generation of optokinetic nystagmus fast phases (FPs) is a decision process that is influenced by performance of a concurrent disjunctive reaction time task (DRT). Ten subjects performed an auditory DRT during constant velocity optokinetic stimulation. Eye movements were measured in three dimensions with a magnetic search coil. Slow phase (SP) durations were defined as the interval between FPs. There were three main findings. Firstly, human optokinetic nystagmus SP durations are consistent with a model of a Gaussian basic interval generator (a type of biological clock), such that FPs can be triggered randomly at the end of a clock cycle (mean duration: 200–250 ms). Kolmogorov-Smirnov tests could not reject the modeled cumulative distribution for any data trials. Secondly, the FP need not be triggered at the end of a clock cycle, so that individual SP durations represent single or multiple clock cycles. Thirdly, the probability of generating a FP at the end of each interval generator cycle decreases significantly during performance of a DRT. These findings indicate that the alternation between SPs and FPs of optokinetic nystagmus is not purely reflexive. Rather, the triggering of the next FP is postponed more frequently if a recently presented DRT trial is pending action when the timing cycle expires. Hence, optokinetic nystagmus FPs show dual-task interference in a manner usually attributed to voluntary movements, including saccades. NEW & NOTEWORTHY This study provides the first clear evidence that the generation of optokinetic nystagmus (OKN) fast phases is a decision process that is influenced by performance of a concurrent disjunctive reaction time task (DRT). The slow phase (SP) durations are consistent with a Gaussian basic interval generator and multiple interval SP durations occur more frequently in the presence of the DRT. Hence, OKN shows dual-task interference in a manner observed in voluntary movements, such as saccades.
A Positive Feedback Loop of lncRNA-PVT1 and FOXM1 Facilitates Gastric Cancer Growth and Invasion
Authors: Xu Mi-die , Wang Yiqin , Weng Weiwei , Wei Ping , Qi Peng , Zhang Qiongyan , Tan Cong , Ni Shu-juan , Dong Lei , Yang Yusi , Lin Wanrun , Xu Qinghua , Huang Dan , Huang Zhaohui , Ma Yuqing , Zhang Wei , Sheng Weiqi , Du Xiang 
Published: October 2016

Abstract
Purpose: The long, noncoding RNA (lncRNA) PVT1 is an important epigenetic regulator with a critical role in human tumors. Here, we aimed to investigate the clinical application and the potential molecular mechanisms of PVT1 in gastric cancer tumorigenesis and progression.
Experimental Design: The expression level of PVT1 was determined by RT-qPCR analysis in 190 pairs of gastric cancer tissues and adjacent normal gastric mucosa tissues (ANT). The biologic functions of PVT1 were assessed by in vitro and in vivo functional experiments. RNA protein pull-down assays and LS/MS mass spectrometry analysis were performed to detect and identify the PVT1-interacting protein FOXM1. Protein–RNA immunoprecipitation assays were conducted to examine the interaction of FOXM1 and PVT1. Chromatin immunoprecipitation (ChIP) and luciferase analyses were utilized to identify the binding site of FOXM1 on the PVT1 promoter.
Results: The lncRNA PVT1 was significantly upregulated in gastric cancer tissues compared with ANTs. High expression of PVT1 predicted poor prognosis in patients with gastric cancer. PVT1 enhanced gastric cancer cell proliferation and invasion in vitro and in vivo. PVT1 directly bound FOXM1 protein and increased FOXM1 posttranslationally. Moreover, PVT1 is also a FOXM1-responsive lncRNA, and FOXM1 directly binds to the PVT1 promoter to activate its transcription. Finally, PVT1 fulfilled its oncogenic functions in a FOXM1-mediated manner.
Conclusions: Our study suggests that PVT1 promotes tumor progression by interacting with FOXM1. PVT1 may be a valuable prognostic predictor for gastric cancer, and the positive feedback loop of PVT1-FOXM1 could be a therapeutic target in pharmacologic strategies. Clin Cancer Res; 23(8); 2071–80. ©2016 AACR.
Few Disparities in Baseline Laboratory Testing After the Diuretic or Digoxin Initiation by Medicare Fee-For-Service Beneficiaries
Authors: Maciejewski Matthew L. , Mi Xiaojuan , Curtis Lesley H. , Ng Judy , Haffer Samuel C. , Hammill Bradley G. 
Published: October 2016

Background—
Despite the persistence of significant disparities, few evaluations examine disparities in laboratory testing by race/ethnicity, age, sex, Medicaid eligibility, and number of chronic conditions for Medicare fee-for-service beneficiaries’ newly prescribed medications. In Medicare beneficiaries initiating diuretics or digoxin, this study examined disparities in guideline-appropriate baseline laboratory testing and abnormal laboratory values.

Methods and Results—
To evaluate guideline-concordant testing for serum creatinine and serum potassium within 180 days before or 14 days after the index prescription fill date, we constructed retrospective cohorts from 10 states of 99 711 beneficiaries who had heart failure or hypertension initiating diuretic in 2011 and 8683 beneficiaries who had heart failure or atrial fibrillation initiating digoxin. Beneficiaries initiating diuretics were less likely to have testing if they were non-Hispanic Black (relative risk [RR], 0.99; 95% confidence interval [CI], 0.98–0.99) than non-Hispanic White. Beneficiaries initiating diuretics and beneficiaries initiating digoxin were more likely to have testing if they had multiple chronic conditions relative to 0 to 1 conditions. Beneficiaries initiating diuretics with laboratory values were more likely to have an abnormal serum creatinine value at baseline if they were non-Hispanic Black (RR, 2.57; 95% CI, 1.91–3.44), other race (RR, 2.11; 95% CI, 1.08–4.10), or male (RR, 2.75; 95% CI, 2.14–3.52) or an abnormal serum potassium value if they were aged ≥76 years (RR, 1.29; 95% CI, 1.09–1.51) or male (RR, 1.17; 95% CI, 1.03–1.33).

Conclusions—
Testing rates were consistently high, so there were negligible disparities in guideline-concordant testing of creatinine and potassium after the initiation of digoxin or diuretics by Medicare beneficiaries.
Inside Speech: Multisensory and Modality-specific Processing of Tongue and Lip Speech Actions
Authors: Treille Avril , Vilain Coriandre , Hueber Thomas , Lamalle Laurent , Sato Marc 
Published: October 2016

Abstract
Action recognition has been found to rely not only on sensory brain areas but also partly on the observer's motor system. However, whether distinct auditory and visual experiences of an action modulate sensorimotor activity remains largely unknown. In the present sparse sampling fMRI study, we determined to which extent sensory and motor representations interact during the perception of tongue and lip speech actions. Tongue and lip speech actions were selected because tongue movements of our interlocutor are accessible via their impact on speech acoustics but not visible because of its position inside the vocal tract, whereas lip movements are both “audible” and visible. Participants were presented with auditory, visual, and audiovisual speech actions, with the visual inputs related to either a sagittal view of the tongue movements or a facial view of the lip movements of a speaker, previously recorded by an ultrasound imaging system and a video camera. Although the neural networks involved in visual visuolingual and visuofacial perception largely overlapped, stronger motor and somatosensory activations were observed during visuolingual perception. In contrast, stronger activity was found in auditory and visual cortices during visuofacial perception. Complementing these findings, activity in the left premotor cortex and in visual brain areas was found to correlate with visual recognition scores observed for visuolingual and visuofacial speech stimuli, respectively, whereas visual activity correlated with RTs for both stimuli. These results suggest that unimodal and multimodal processing of lip and tongue speech actions rely on common sensorimotor brain areas. They also suggest that visual processing of audible but not visible movements induces motor and visual mental simulation of the perceived actions to facilitate recognition and/or to learn the association between auditory and visual signals.