bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced Glycation End Product Accumulation Is Associated With Low Skeletal Muscle Mass, Weak Muscle Strength, and Reduced Bone Density: The Nagahama Study
Authors: Tabara Yasuharu , Ikezoe Tome , Yamanaka Mikihiro , Setoh Kazuya , Segawa Hiroaki , Kawaguchi Takahisa , Kosugi Shinji , Nakayama Takeo , Ichihashi Noriaki , Tsuboyama Tadao , Matsuda Fumihiko ,   The Nagahama Study Group
Published: October 2018

Abstract

Background
The accumulation of advanced glycation end product (AGE) might exert deleterious effects on musculoskeletal properties. Our study aims to clarify this possible association in a large general population.

Methods
This study investigated a general population of 9,203 patients (mean age, 57.8 years). Skeletal muscle mass was measured by bioelectrical impedance analysis, whereas accumulation of AGEs was assessed by skin autofluorescence (SAF-AGE). The muscle strength of upper and lower limbs and usual gait speed were measured in a portion of older (≥60 years of age) participants (n = 1,934). The speed of sound (SOS) in the calcaneal bone was assessed via a quantitative ultrasound technique.

Results
In the total population, the frequency of low skeletal muscle mass linearly increased with the SAF-AGE quartiles (Q1: 14.2%, Q2: 16.1%, Q3: 21.1%, Q4: 24.8%; p < .001), and this association was independent of covariates including glycemic traits (Q4: odds ratio [OR] = 1.48, p < .001). The association between the highest SAF-AGE quartile and low skeletal muscle mass remained significant in the older subpopulation (OR = 1.85, p = .002). A similar but weak association was observed for low SOS (Q1: 8.9%, Q2: 8.3%, Q3: 10.4%, Q4: 12.2%; p < .001). Similar inverse associations were also observed with grip strength (OR = 1.98, p = .003), hip flexion strength (OR = 1.50, p = .012), and hip abduction strength (OR = 1.78, p = .001), but not with usual gait speed.

Conclusion
Accumulation of AGEs might be a deleterious factor for musculoskeletal properties.
Do universities generate spatial spillovers? Evidence from US counties between 1930 and 2010
Authors: Cermeño Alexandra L 
Published: October 2018

Abstract
This paper explores the impact of new universities established in the USA between 1931 and 1980 on population density, GDP and market size measured from 1930 to 2010. The analysis is based on differences in differences on counties selected through propensity score matching, as well as an instrumental variable approach. The evidence suggests that counties hosting a university for the first time grew by between 1% and 3% annually on top of the general trends of population density and GDP growth, and that this effect expanded to neighboring counties. Controlling for research intensity and interstate road infrastructure shows that the potential gains from these new universities were severely constrained by the ease of access, which eventually resulted in higher congestion costs. These results point to a situation where new universities create spillover effects that eventually fade away if not accompanied by additional investments.
Identification of Functioning Domains in the Presurgical Period and Their Relationships with Opioid Use and Pain Catastrophizing
Authors: Travaglini Letitia E , Highland Krista B , Rojas Winifred , Buckenmaier Chester C , Kent Michael 
Published: October 2018

AbstractObjectivesThe National Institutes of Health Patient-Reported Outcomes Measurement Information System (PROMIS) is a multidimensional screening system evaluating biopsychosocial factors affecting pain and functioning. Using a military sample, the current study 1) examined the structure and domains of the PROMIS, the Defense and Veterans Pain Rating Scale 2.0 (DVPRS), and the Pain Catastrophizing Scale (PCS) within a presurgical setting and 2) examined the relationship of these variables to pre- and postsurgical opioid use.MethodsThis cross-sectional study included 279 adult patients scheduled for surgery at the Walter Reed National Military Medical Center and a validation sample of 79 additional patients from the Naval Medical Center, San Diego. PROMIS, DVPRS, PCS, and opioid use data were collected before surgery. Exploratory factor analysis and confirmatory factor analysis identified the latent structure for the measures. A structural equation model (SEM) examined their relationship to pre- and postsurgical opioid use.ResultsTwo latent factors represented Psychosocial Functioning (PROMIS Depression, PROMIS Anxiety, and PROMIS Social Isolation) and Pain Impact (DVPRS, PROMIS Pain Interference, PROMIS Physical Functioning). The remaining PROMIS scales did not load onto a single factor. In the SEM, the two latent factors and PCS were significantly related to pre- and postsurgical opioid use.ConclusionsThis study highlights the utility and relative ease of using a convenient multidimensional assessment in presurgical settings. Using such an assessment can help provide targeted interventions for individuals who may be at greatest risk for negative postsurgical outcomes.
Epidemiological Trends of Anterior Cruciate Ligament Reconstruction in a Canadian Province
Authors: Zhang Yiyang , McCammon James , Martin Richard Kyle , Prior Heather J. , Leiter Jeff , MacDonald Peter B. 
Published: October 2018

Objective:
To determine epidemiological trends of anterior cruciate ligament reconstruction (ACL-R) in a Canadian province, estimate the national incidence, and compare with internationally published data.

Design:
Retrospective review.

Setting:
All hospitals that performed ACL reconstructions in Manitoba between 1980 and 2015.

Participant:
All patients that underwent ACL-R in Manitoba between 1980 and 2015.

Intervention:
This is a retrospective review looking at deidentified, individual-level administrative records of health services used for the entire population of Manitoba (approximately 1.3 million). Codes for ACL and cruciate ligament reconstruction were searched from 1980 to 2015. Patient demographics included age, sex, geographic area of residence, and neighborhood income quintile.

Main Outcome Measures:
Trends of ACL reconstructions from 1980 to 2015.

Results:
A total of 10 114 ACL-R were performed during the 36-year study period and patients were predominantly male (63.1%). The mean age at ACL-R was 29.5 years (SD 10.0) for males and 28.5 years (SD 11.9) for females, whereas age younger than 40 years accounted for 81.7% of all ACL-R. The incidence of ACL-R increased from 7.56/100 000 inhabitants in 1980 to 48.45/100 000 in 2015. The proportion of females undergoing ACL-R has increased from 29.3% in 1980% to 41.9% in 2015, and female patients now comprise the majority of ACL-R in the under-20 age category.

Conclusion:
The incidence of ACL-R has significantly increased since 1980; female patients now make up a greater proportion than males of the ACL-R population younger than 20 years. This information can be used to guide resource allocation planning and focus injury prevention initiatives.
Smaller Inguinal Hernias are Independent Risk Factors for Developing Chronic Postoperative Inguinal Pain (CPIP)
Authors: Hoffmann Henry , Walther Daniela , Bittner Reinhard , Köckerling Ferdinand , Adolf Daniela , Kirchhoff Philipp 
Published: October 2018

Objective:
Impact of inguinal hernia defect size as stratified by the European Hernia Society (EHS) classification I to III on the rate of chronic postoperative inguinal pain (CPIP).

Background:
CPIP is the most important complication after inguinal hernia repair. The impact of hernia defect size according to the EHS classification on CPIP is unknown.

Methods:
In total, 57,999 male patients from the Herniamed registry undergoing primary unilateral inguinal hernia repair including a 1-year follow-up were selected between September 1, 2009 and November 30, 2016. Using multivariable analysis, the impact of EHS inguinal hernia classification (EHS I vs EHS II vs EHS III and/or scrotal) on developing CPIP was investigated.

Results:
Multivariable analysis revealed for smaller inguinal hernias a significant higher rate of pain at rest [EHS I vs EHS II: odds ratio, OR = 1.350 (1.180–1.543), P < 0.001; EHS I vs EHS III and/or scrotal: OR = 1.839 (1.504–2.249), P < 0.001; EHS II vs EHS III and/or scrotal: OR = 1.363 (1.125–1.650), P = 0.002], pain on exertion [EHS I vs EHS II: OR = 1.342 (1.223–1.473), P < 0.001; EHS I vs EHS III and/or scrotal: OR = 2.002 (1.727–2.321), P < 0.001; EHS II vs EHS III and/or scrotal: OR = 1.492 (1.296; 1.717), P < 0.001], and pain requiring treatment [EHS I vs EHS II: OR = 1.594 (1.357–1.874), P < 0.001; EHS I vs EHS III and/or scrotal: OR = 2.254 (1.774–2.865), P < 0.001; EHS II vs EHS III and/or scrotal: OR = 1.414 (1.121–1.783), P = 0.003] at 1-year follow-up. Younger patients (<55 y) revealed higher rates of pain at rest, pain on exertion, and pain requiring treatment (each P < 0.001) with a significantly trend toward higher rates of pain in smaller hernias.

Conclusions:
Smaller inguinal hernias have been identified as an independent patient-related risk factor for developing CPIP.
On the Concurrent Use of Self-System Therapy and Functional Magnetic Resonance Imaging–Guided Transcranial Magnetic Stimulation as Treatment for Depression
Authors: Neacsiu Andrada D. , Luber Bruce M. , Davis Simon W. , Bernhardt Elisabeth , Strauman Timothy J. , Lisanby Sarah H. 
Published: October 2018

Objectives
Despite the growing use of repetitive transcranial magnetic stimulation (rTMS) as a treatment for unipolar depression, its typical effect sizes have been modest, and methodological and conceptual challenges remain regarding how to optimize its efficacy. Linking rTMS to a model of the neurocircuitry underlying depression and applying such a model to personalize the site of stimulation may improve the efficacy of rTMS. Recent developments in the psychology and neurobiology of self-regulation offer a conceptual framework for identifying mechanisms of action in rTMS for depression, as well as for developing guidelines for individualized rTMS treatment. We applied this framework to develop a multimodal treatment for depression by pairing self-system therapy (SST) with simultaneously administered rTMS delivered to an individually targeted region of dorsolateral prefrontal cortex identified via functional magnetic resonance imaging (fMRI).

Methods
In this proof-of-concept study, we examined the acceptability, feasibility, and preliminary efficacy of combining individually fMRI-targeted rTMS with SST. Using the format of a cognitive paired associative stimulation paradigm, the treatment was administered to 5 adults with unipolar depression in an open-label trial.

Results
The rTMS/SST combination was well tolerated, feasible, and acceptable. Preliminary evidence of efficacy also was promising. We hypothesized that both treatment modalities were targeting the same neural circuitry through cognitive paired associative stimulation, and observed changes in task-based fMRI were consistent with our model. These neural changes were directly related to improvements in depression severity.

Conclusions
The new combination treatment represents a promising exemplar for theory-based, individually targeted, multimodal intervention in mood disorders.
The design and evaluation of a Bayesian system for detecting and characterizing outbreaks of influenza
Authors: Millett Nicholas E. , Aronis John M. , Wagner Michael M. , Tsui Fuchiang , Ye Ye , Ferraro Jeffrey P. , Haug Peter J. , Gesteland Per H. , Cooper Gregory F. 
Published: October 2018

1AbstractThe prediction and characterization of outbreaks of infectious diseases such as influenza remains an open and important problem. This paper describes a framework for detecting and characterizing outbreaks of influenza and the results of testing it on data from ten outbreaks collected from two locations over five years. We model outbreaks with compartment models and explicitly model non-influenza influenza-like illnesses.
GeneHummus: A pipeline to define gene families and their expression in legumes and beyond
Authors: Die Jose V. , Elmassry Moamen Mahmoud , LeBlanc Kimberly Hathaway , Awe Olaitan I. , Dillman Allissa , Busby Ben 
Published: October 2018

AbstractDuring the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called ‘orphan crops’) is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. Analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool. Here, we present the GeneHummus pipeline, a step-by-step R-based pipeline for the identification, characterization and expression analysis of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes. We anticipate that our pipeline should be suitable for any plant gene family, and likely other gene families, vastly improving the speed and ease of genomic data processing.
Encoding of an engram for food location by satiety-promoting Drd2 hippocampal neurons
Authors: Azevedo Estefania P. , Pomeranz Lisa , Cheng Jia , Schneeberger Marc , Stern Sarah , Doerig Katherine , Greengard Paul , Friedman Jeffrey M. 
Published: October 2018

SUMMARYAssociative learning guides feeding behavior in mammals in part by using cues that link location in space to food availability. However, the elements of the top-down circuitry encoding the memory of the location of food is largely unknown, as are the high-order processes that control satiety. Here we report that hippocampal dopamine 2 receptor (D2R) neurons are specifically activated by food and that modulation of their activity reduce food intake in mice. We also found that activation of these neurons interferes with the valence of food and the acquisition of a spatial memory linking food to a location via projections from the hippocampus to the lateral septum. Finally, we showed that inputs from lateral entorhinal cortex (LEC) to the hippocampus can also drive satiety via activation of D2R cells. These data describe a previously unidentified function for hippocampal D2R cells to regulate feeding behavior and identifies a LEC->Hippocampus->Septal high-order circuit that encodes the memory of food location.
Ablation of NMDA receptors in dopamine neurons disrupts attribution of incentive salience to reward-paired stimuli
Authors: Cieślak Przemysław Eligiusz , Parkitna Jan Rodriguez 
Published: October 2018

AbstractMidbrain dopamine (DA) neurons play a crucial role in the formation of conditioned associations between environmental cues and appetitive events. Activation of N-methyl-D-aspartate (NMDA) receptors is a key mechanism responsible for the generation of conditioned responses of DA neurons to reward cues. Here, we tested the effects of the cell type-specific inactivation of NMDA receptors in DA neurons in adult mice on stimulus-reward learning. Animals were trained in a Pavlovian learning paradigm in which they had to learn the predictive value of two conditioned stimuli, one of which (CS+) was paired with the delivery of a water reward. Over the course of conditioning, mutant mice learned that the CS+ predicted reward availability, and they approached the reward receptacle more frequently during CS+ trials than CS− trials. However, conditioned responses to the CS+ were weaker in the mutant mice, possibly indicating that they did not attribute incentive salience to the CS+. To further assess whether the attribution of incentive salience was impaired by the mutation, animals were tested in a conditioned reinforcement test. The test revealed that mutant mice made fewer instrumental responses paired with CS+ presentation, confirming that the CS+ had a weaker incentive value. Taken together, these results indicate that reward prediction learning does occur in the absence of NMDA receptors in DA neurons, but the ability of reward-paired cues to invigorate and reinforce behavior is lost.
Gene Expression Correlates of the Cortical Network Underlying Sentence Processing
Authors: Kong Xiang-Zhen , Tzourio-Mazoyer Nathalie , Joliot Marc , Fedorenko Evelina , Liu Jia , Fisher Simon E. , Francks Clyde 
Published: October 2018

AbstractA pivotal question in modern neuroscience is which genes regulate brain circuits that underlie cognitive functions. However, the field is still in its infancy. Here we report an integrated investigation of the high-level language network (i.e., sentence processing network) in the human cerebral cortex, combining regional gene expression profiles, task fMRI, large-scale neuroimaging meta-analysis, and resting-state functional network approaches. We revealed reliable gene expression-functional network correlations using three different network definition strategies, and identified a consensus set of genes related to connectivity within the sentence-processing network. The genes involved showed enrichment for neural development and actin-related functions, as well as association signals with autism, which can involve disrupted language functioning. Our findings help elucidate the molecular basis of the brain’s infrastructure for language. The integrative approach described here will be useful to study other complex cognitive traits.
Colocalization features for classification of tumors using desorption electrospray ionization mass spectrometry imaging
Authors: Inglese Paolo , Correia Gonçalo , Pruski Pamela , Glen Robert C , Takats Zoltan 
Published: October 2018

AbstractSupervised modeling of mass spectrometry imaging (MSI) data is a crucial component for the detection of the distinct molecular characteristics of cancerous tissues. Currently, two types of supervised analyses are mainly used on MSI data: pixel-wise segmentation of sample images, and whole-sample-based classification. A large number of mass spectra associated with each MSI sample can represent a challenge for designing models that simultaneously preserve the overall molecular content while capturing valuable information contained in the MSI data. Furthermore, intensity-related batch effects can introduce biases in the statistical models.Here we introduce a method based on ion colocalization features that allows the classification of whole tissue specimens using MSI data, which naturally preserves the spatial information associated the with the mass spectra and is less sensitive to possible batch effects. Finally, we propose data visualization strategies for the inspection of the derived networks, which can be used to assess whether the correlation differences are related to co-expression/suppression or disjoint spatial localization patterns and can suggest hypotheses based on the underlying mechanisms associated with the different classes of analyzed samples.
Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids
Authors: Chhabra Sapna , Liu Lizhong , Goh Ryan , Warmflash Aryeh 
Published: October 2018

AbstractDuring gastrulation, the pluripotent epiblast is patterned into the three germ layers, which form the embryo proper. This patterning requires a signaling cascade involving the BMP, WNT and NODAL pathways; however, how these pathways regulate one another in space and time to generate cell-fate patterns remains unknown. Using a human gastruloid model, we show that BMP signaling initiates a wave of WNT signaling, which, in turn, initiates a wave of NODAL signaling. While WNT propagation depends on continuous BMP activity, NODAL propagates independently of upstream signals. We further show that the duration of BMP signaling determines the position of mesodermal differentiation while WNT and NODAL synergize to achieve maximal differentiation. The waves of both WNT and NODAL signaling activity extend farther into the colony than mesodermal differentiation. Combining dynamic measurements of signaling activity with mathematical modeling revealed that the formation of signaling waves is inconsistent with WNT and NODAL forming a stable spatial pattern in signaling activities, and the final signaling state is spatially homogeneous. Thus, dynamic events in the BMP, WNT, and NODAL signaling cascade, in the absence of a signaling gradient, have the potential to mediate epiblast patterning.
Inferring demography and selection in organisms characterized by skewed offspring distributions
Authors: Sackman Andrew M. , Harris Rebecca , Jensen Jeffrey D. 
Published: October 2018

AbstractThe recent increase in time-series population genomic data from experimental, natural, and ancient populations has been accompanied by a promising growth in methodologies for inferring demographic and selective parameters from such data. However, these methods have largely presumed that the populations of interest are well-described by the Kingman coalescent. In reality, many groups of organisms, including viruses, marine organisms, and some plants, protists, and fungi, typified by high variance in progeny number, may be best characterized by multiple-merger coalescent models. Estimation of population genetic parameters under Wright-Fisher assumptions for these organisms may thus be prone to serious mis-inference. We propose a novel method for the joint inference of demography and selection under the Ψ-coalescent model, termed Multiple-Merger Coalescent Approximate Bayesian Computation, or MMC-ABC. We first quantify mis-inference under the Kingman and then demonstrate the superior performance of MMC-ABC under conditions of skewed offspring distribution. In order to highlight the utility of this approach, we re-analyzed previously published drug-selection lines of influenza A virus. We jointly inferred the extent of progeny-skew inherent to viral replication and identified putative drug-resistance mutations.