bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence of Chlamydia trachomatis in Inner-City Children and Adolescents—Implications for Vaccine Development
Authors: Banniettis Natalie , Thumu Sirisha , Weedon Jeremy , Chotikanatis Kobkul , Szigeti Aviva , Hammerschlag Margaret R. , Kohlhoff Stephan A. 
Published: July 2017

Background
Prevention of Chlamydia trachomatis infection is an ideal application for a vaccine program, which should optimally be administered before sexual debut. However, there are limited epidemiologic studies of C. trachomatis infection in an unselected pediatric population since routine screening and treatment of pregnant women was implemented in the United States in 1993.

Methods
Anonymized serum samples were obtained from children younger than 21 years in 2 medical centers in Brooklyn, New York, from 2013 to 2015. Anti–C. trachomatis IgG antibody was determined by a validated enzyme immunoassay. Infants younger than 1 year were excluded from the final analysis due to interference of maternal antibody.

Results
One thousand two sera were included in the final analysis. Fifty-seven percent were females. No antibody was detected at younger than 11 years. Anti–C. trachomatis IgG antibody was detected in 11.4% and 5.6% of female and male subjects, respectively, older than 11 years (P = 0.0027), and seropositivity increased with age. There was no significant difference in the distribution of age at infection between the centers (P = 0.432), but a difference was detected between genders (P = 0.012) with a higher percentage of female subjects testing positive.

Conclusions
Antibody was first detected at 11 years of age, likely coinciding with sexual debut. The prevalence of antibody was higher and appeared earlier in females, mirroring national surveillance trends based on nucleic acid amplification testing. The delay in male antibody detection may be due to biological or behavioral differences between genders. These data are critical in informing potential C. trachomatis vaccine strategies.
A 5-Minute Interval between Two Dilating Eye Drops Increases Their Effect
Authors: Denion Eric , Charlot Frédérique , Béraud Guillaume 
Published: July 2017

PURPOSE
Patients are usually advised to wait 5 minutes between eye drops. This delay supposedly allows the first drop not to be washed out by the second one, thereby increasing the combined effect. However, in the only experimental study conducted in humans on the concurrent administration of two different eye drops, the authors concluded that a 10-minute time interval between eye drops did not increase their combined effect. Our study was designed to address this puzzling observation.

METHODS
Using digital photographs shot in photopic conditions in 40 eyes of 20 healthy volunteers, we compared relative pupil surface (i.e., pupil to iris surface area ratios) before and after the administration of one drop of 10% phenylephrine and one drop of 0.5% tropicamide either immediately or after a 5-minute time interval.

RESULTS
Waiting 5 minutes yielded a 5.6% relative pupil surface gain (observer 1: P = .003, observer 2: P = .005) indicating an additional combined effect with a 5-minute time interval.

CONCLUSIONS
These results show a detectable additive effect that is probably the result of methodological refinements including the challenging of the mydriasis by photopic conditions and the use of pupil and iris surface areas, which may show differences that would be undetectable in terms of diameter.
Cancer Immunotherapy in Older Patients
Authors: Marrone Kristen A. , Forde Patrick M. 
Published: July 2017

Abstract
Advancing age remains one of the most significant risk factors for cancer development. Changes in the immune system occur with aging, and likely play a role in the increased incidence of malignancy in older patients. With the advent of immune checkpoint inhibitors, and their use in a variety of malignancies, there has been an explosion of clinical trials evaluating their use. Unfortunately, these trials have not shown consistent results in elderly patients, nor have age-specific outcomes been consistently reported. Further evaluation of the efficacy and toxicity of these agents in the elderly is needed, as they are now in frequent clinical use. By investigating how age-related changes in the immune system occur and intersect with use of immune checkpoint inhibitors, their use can be optimized in a clear and safe manner. Further study of age-related changes in the immune system can also lead to effective combination immunotherapeutic approaches, maximizing the efficacy of immune checkpoint inhibitors across tumor types and across the age spectrum of cancer patients.
The Biology of Aging and Cancer
Authors: Zhang Xinwen , Meng Xin , Chen Yiyin , Leng Sean X. , Zhang Haiyan 
Published: July 2017

Abstract
The majority of patients with common malignancies are older adults. Intrinsic complex biological changes of aging along with inflammation, immunosenescence, age-associated chronic diseases, and extrinsic environmental and psychosocial factors have significant impact on not only development and behavior of individual malignancies, but also physiologic reserve and vulnerability of older patients who suffer from them. As a result, clinical practice of geriatric oncology demands integration of careful geriatric assessment and management. This article provides an overview of basic biology of aging and its relationship with cancer. After a brief introduction about the definition and mechanisms of aging, as well as age-related biological and physiological changes, the discussion mainly focuses on recent development and insights into the relationship of frailty, inflammation, and immunity with cancer, highlighting how the new knowledge can help further improve assessment and treatment of older patients with malignancies and promote cancer research.
Laparoscopic Intragastric Surgery With Endoscopic Assistance: A 2 Gastrostomy Approach With Multiple Applications
Authors: Gabriel Emmanuel , Rosso Kelly , Shahab Danish , Shah Rupen , Bain Andrew , Kukar Moshim , Hochwald Steven N. 
Published: July 2017

Purpose:
Laparoscopic intragastric resection is a surgical modality with acceptable oncologic outcomes for gastrointestinal stromal tumors and leiomyomas, particularly for masses located near the gastroesophageal junction (GEJ). We describe our technique of 2 gastrostomy laparoscopic, intragastric resection with endoscopic assistance.

Methods:
We detail our technique and report a unique application of this versatile approach.

Results:
Between December 2015 and July 2016, 4 patients underwent our combined technique of intragastric surgery. Complete resection was performed in the 2 patients who had gastrointestinal stromal tumors and 1 patient with a leiomyoma without complications. One patient had the unique diagnosis of gastritis cystica profunda. This mass could not be resected, but an effective Tru-cut core needle biopsy was obtained, and the mass was able to be diagnosed and decompressed.

Conclusions:
Our technique of 2 gastrostomy laparoscopic intragastric surgery is feasible and offers an effective oncologic approach for resection of tumors near the GEJ.
Revelation of the Genetic Basis for Convergent Innovative Anal Fin Pigmentation Patterns in Cichlid Fishes
Authors: Gu Langyu , Xia Canwei 
Published: July 2017

AbstractDetermining whether convergent novelties share a common genetic basis is vital to understanding the extent to which evolution is predictable. The convergent evolution of innovative anal fin pigmentation patterns in cichlid fishes is an ideal model for studying this question. Here, we focused on two patterns: 1) egg-spots, circular pigmentation patterns with different numbers, sizes and positions; and 2) the blotch, irregular pattern with no variation among species. How these two novelties originate and evolve remains unclear. Based on a thorough comparative transcriptomic and genomic analysis, we observed a common genetic basis with high evolutionary rates and similar expression levels between egg-spots and the blotch. But the associations of common genes with transcription factors and signalling pathways in the core gene network, as well as the integration of advantageous genes were observed specifically for egg-spots. Focusing on the whole transcriptomic level instead of limited numbers of candidate genes can explain the opposite conclusion between our study and the one from Santos et al. (2016), which suggested that no common genetic basis is shared between the blotch and egg-spots. Here, we propose that the re-use of the common genetic basis indicates important conservative functions (e.g., toolkit genes) for the origin of these convergent novel phenotypes, whereas independently evolved associations of common genes with transcription factors and signalling pathways (intrinsic factor) can free the evolution of egg-spots, and together with the integration of advantageous genes (extrinsic factor) can provide a clue to link egg-spots as a key innovation to the adaptive radiation in cichlid fishes. This hypothesis will further illuminate the mechanism of the origin and evolution of novelties in a broad sense.
Causal Role of Beta Oscillations in Time Estimation
Authors: Wiener Martin , Parikh Alomi , Krakow Arielle , Coslett H. Branch 
Published: July 2017

AbstractThe neural mechanisms underlying time perception are of vital importance to a comprehensive understanding of behavior and cognition. Recent work has pointed to a supramodal role for beta oscillations in coordinating endogenous timing mechanisms for the purpose of measuring temporal intervals. However, the majority of this work has employed paradigms relying on timed motor responses, which are confounded by beta’s established role in motor movement. Further, no study to date has tested if the alteration of beta oscillations subsequently impacts timing. Here, we address these concerns and demonstrate for the first time a causal connection between beta oscillations and timing. To accomplish this, we first re-analyzed two, separate EEG datasets from psychophysical experiments (Wiener, et al. 2012; 2015) demonstrating that beta oscillations are associated with the retention and comparison of a memory standard for duration, and that transcranial magnetic stimulation (TMS) of the right supramarginal gyrus leads to an increase in midline beta power during the encoding of a temporal interval, corresponding with a longer perceived interval of time. Next, we conducted a study of 20 healthy human participants using transcranial alternating current stimulation (tACS), over frontocentral cortex, at alpha (10Hz) and beta (20Hz) frequencies, during a visual temporal bisection task, demonstrating that beta stimulation exclusively shifts the perception of time such that stimuli are reported as longer in length, while preserving precision. Finally, we decomposed trial-by-trial choice data with a drift diffusion model of decision making and temporal encoding that reveals the shift in timing is caused by a change in the starting point of accumulation, rather than the drift rate or threshold. Our results provide causal evidence of beta’s involvement in the perception of time, and point to a specific role for beta oscillations in the encoding and retention of memory for temporal intervals.
Measurement Error Correction of Genome-Wide Polygenic Scores in Prediction Samples
Authors: Tucker-Drob Elliot M. 
Published: July 2017

Abstract/IntroductionDiPrete, Burik, & Koellinger (2017;http://dx.doi.org/10.1101/134197) propose using an instrumental variable (IV) framework to correct genome-wide polygenic scores (GPSs) for error, thereby producing disattenuated estimates of SNP heritability in predictions samples. They demonstrate their approach by producing two independent GPSs for Educational Attainment (“multiple indicators”) in a prediction sample (Health and Retirement Study; HRS) from independent sets of SNP regression weights, each computed from a different half of the discovery sample (EA2; Okbay et al. 2016), i.e. “by randomly splitting the GWAS sample that was used for [the GPS] construction.”Here, I elucidate how a structural equation modeling (SEM) framework that specifies true score variance in GPSs as a latent variable can be used to derive an equivalent correction to the IV approach proposed by DiPrete et al. (2017). This approach, which is rooted in a psychometric modeling tradition, has a number of advantages: (1) it formalizes the assumed data-generating model, (2) it estimates all parameters of interest in a single step, (3) is can be flexibly incorporated into a larger multivariate analysis (such as the “Genetic Instrumental Variable” approach proposed by DiPrete et al., 2017), (4) it can easily be adapted to relax assumptions (e.g. that the GPS indicators equally represent the true genetic factor score), and (5) it can easily be extended to include more than two GPS indicators. After describing how the multiple indicator approach to GPS correction can specified as a structural equation model, I demonstrate how a structural equation modeling approach can be used to correct GPSs for error using SNP heritability obtained using GREML or LD score regression to produce a correction that is equivalent to an approach recently proposed by Daniel Benjamin and colleagues. Finally, I briefly discuss what I view as some conceptual limitations surrounding the error correction approaches described, regardless of the estimation method implemented.
Systematic selection of reference genes for normalization of circulating RNA transcripts in pregnant women based on RNA-seq data
Authors: Chim Stephen S. C. , Wong Karen K. W. , Chung Claire Y. L. , Lam Stephanie K. W. , Kwok Jamie S. L. , Lai Chit-Ying , Cheng Yvonne K. Y. , Hui Annie S. Y. , Meng Meng , Chan Oi-Ka , Tsui Stephen K. W. , Lee Keun-Young , Chan Ting-Fung , Leung Tak-Yeung 
Published: July 2017

AbstractRNA transcripts circulating in peripheral blood represent an important source of non-invasive biomarkers. To accurately quantify the levels of a circulating transcript, one needs to normalize the data with internal control reference genes, which are detected at relatively constant levels across different blood samples. A few stably-expressed reference gene candidates have to be selected from transcriptome data before validation of their stable expression by reverse-transcription quantitative polymerase chain reaction. However, there is a lack of transcriptome, let alone whole-transcriptome, data from maternal blood. To overcome this shortfall, we performed RNA-seq on blood samples from women presented with preterm labor. Of 11215 exons detected in the maternal blood whole-transcriptome, we systematically identified a panel of 395 genes comprising exons that were detected at acoefficient of variation(CV) ranging from 7.75%-17.7%. Their levels were considerably less variable than anyGAPDHexon (minimumCV, 27.3%). Upon validation, selected genes from this panel remained as more stably expressed thanGAPDHin maternal blood. This panel is over-represented with genes involved with actin cytoskeleton, macromolecular complex and the integrin signaling pathway. This groundwork provides a starting point for systematically selecting reference gene candidates for normalizing the levels of circulating RNA transcripts in maternal blood.
Comment on “Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans”
Authors: Landler Lukas , Nimpf Simon , Hochstoeger Tobias , Nordmann Gregory Charles , Papadaki-Anastasopoulou Artemis , Keays David Anthony 
Published: July 2017

AbstractA diverse array of species on the planet employ the Earth’s magnetic field as a navigational aid. As the majority of these animals are migratory, their utility to interrogate the molecular and cellular basis of the magnetic sense is limited. Vidal-Gadea and colleagues recently argued that the wormC. eleganspossesses a magnetic sense that guides their vertical movement in soil. In making this claim they relied on three different behavioural assays that involved magnetic stimuli. Here, we set out to replicate their results employing blinded protocols and double wrapped coils that control for heat generation. We find no evidence supporting the existence of a magnetic sense inC. elegans. We further show that the Vidal-Gadea hypothesis is problematic as the adoption of a correction angle and a fixed trajectory relative to the Earth’s magnetic inclination does not necessarily result in vertical movement.
Wisdom of artificial crowds feature selection in untargeted metabolomics: An application to the development of a blood-based diagnostic test for thrombotic myocardial infarction
Authors: Trainor Patrick J. , Yampolskiy Roman V. , DeFilippis Andrew P. 
Published: July 2017

AbstractIntroductionHeart disease remains a leading cause of global mortality. While acute myocardial infarction (colloquially: heart attack), has multiple proximate causes, proximate etiology cannot be determined by a blood-based diagnostic test. We enrolled a suitable patient cohort and conducted an untargeted quantification of plasma metabolites by mass spectrometry for developing a test that can differentiate between thrombotic MI, non-thrombotic MI, and stable disease. A significant challenge in developing such a diagnostic test is solving the NP-hard problem of feature selection for constructing an optimal statistical classifier.ObjectiveWe employed a Wisdom of Artificial Crowds (WoAC) strategy for solving the feature selection problem and evaluated the accuracy and parsimony of downstream classifiers in comparison with embedded feature selection via the Lasso and Elastic Net.Materials and MethodsArtificial Crowd Wisdom was generated via aggregation of the best solutions from independent and diverse genetic algorithm populations that were initialized with bootstrapping and a random subspaces constraint.Results / ConclusionsWoAC feature selection performed favorably compared to Lasso and Elastic Net solutions. The classifier constructed following WoAC feature selection had a cross-validation estimated misclassification rate of 2.6% as compared to 26.3% via the Lasso and 18.5% via an Elastic Net. The classifier warrants further evaluation as a diagnostic test in an independent cohort.
Compositional shifts in the root microbiota track the life-cycle of field-grown rice plants
Authors: Edwards Joseph , Santos-Medellín Christian , Liechty Zachary , Nguyen Bao , Lurie Eugene , Eason Shane , Phillips Gregory , Sundaresan Venkatesan 
Published: July 2017

AbstractBacterial communities associated with roots impact the health and nutrition of the host plant. While a multitude of static factors are known to influence the composition of the root-associated microbiota, the dynamics of these microbial assemblies over the plant life cycle are poorly understood. Here, we use dense temporal sampling of spatial compartments to characterize the root-associated microbiota of field grown rice (Oryza sativa)over the course of three consecutive growing seasons and two sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth, then stabilizes compositionally for the remainder of the life cycle. Bacterial taxa conserved between field sites can be used as predictive features of rice plant age by modeling using a random forests approach. The age-prediction models were used to reveal that drought stressed plants have developmentally delayed microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.
Simulation of electrical machines: a FEM-BEM coupling scheme
Authors: Kielhorn Lars , Rüberg Thomas , Zechner Jürgen 
Published: July 2017

Purpose
Electrical machines commonly consist of moving and stationary parts. The field simulation of such devices can be demanding if the underlying numerical scheme is solely based on a domain discretization, such as in the case of the finite element method (FEM). This paper aims to present a coupling scheme based on FEM together with boundary element methods (BEMs) that neither hinges on re-meshing techniques nor deals with a special treatment of sliding interfaces. While the numerics are certainly more involved, the reward is obvious: the modeling costs decrease and the application engineer is provided with an easy-to-use, versatile and accurate simulation tool.

Design/methodology/approach
The authors present the implementation of a FEM-BEM coupling scheme in which the unbounded air region is handled by the BEM, while only the solid parts are discretized by the FEM. The BEM is a convenient tool to tackle unbounded exterior domains, as it is based on the discretization of boundary integral equations (BIEs) that are defined only on the surface of the computational domain. Hence, no meshing is required for the air region. Further, the BIEs fulfill the decay and radiation conditions of the electromagnetic fields such that no additional modeling errors occur.

Findings
This work presents an implementation of a FEM-BEM coupling scheme for electromagnetic field simulations. The coupling eliminates problems that are inherent to a pure FEM approach. In detail, the benefits of the FEM-BEM scheme are: the decay conditions are fulfilled exactly, no meshing of parts of the exterior air region is necessary and, most importantly, the handling of moving parts is incorporated in an intriguingly simple manner. The FEM-BEM formulation in conjunction with a state-of-the-art preconditioner demonstrates its potency. The numerical tests not only reveal an accurate convergence behavior but also prove the algorithm to be suitable for industrial applications.

Originality/value
The presented FEM-BEM scheme is a mathematically sound and robust implementation of a theoretical work presented a decade ago. For the application within an industrial context, the original work has been extended by higher-order schemes, periodic boundary conditions and an efficient treatment of moving parts. While not intended to be used under all circumstances, it represents a powerful tool in case that high accuracies together with simple mesh-handling facilities are required.
Thermo-electric simulation of battery-modules with reduced order modelling of linear electrical components
Authors: Pichler Franz , Koester Niels , Thaler Alexander 
Published: July 2017

Purpose
This paper aims to present a fully coupled thermo-electrical finite-element battery model with an applied model-order reduction. The model is used to analyse the thermal design of battery modules during typical drive-cycles of electric vehicles.

Design/methodology/approach
A model-order reduction is applied, in which the electrical linear bus-bars are analysed in an a-priori step. For these bus-bars, special distributed basis-functions are computed, which make the solution of differential Ohm's law unnecessary during the transient simulation. Furthermore, the distributed basis-functions are used to strongly couple the non-linear battery models, which reduces the iterations needed to simulate them.

Findings
Altogether, this results in a fast simulation scheme for coupled linear and non-linear electrical components and their thermal behaviour.

Originality/value
The presented method delivers an innovative approach, on how to systematically minimize the computational effort in a system of linear and non-linear electrical components, while keeping the full three-dimensional information of the original problem.