bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term impacts of prenatal synthetic glucocorticoids exposure on functional brain correlates of cognitive monitoring in adolescence
Authors: Ilg Liesa , Klados Manousos , Alexander Nina , Kirschbaum Clemens , Li Shu-Chen 
Published: May 2018

AbstractThe fetus is highly responsive to the level of glucocorticoids in the gestational environment. Perturbing glucocorticoids during fetal development could yield long-term consequences. Extending prior research about effects of prenatally exposed synthetic glucocorticoids (sGC) on brain structural development during childhood, we investigated functional brain correlates of cognitive conflict monitoring in term-born adolescents, who were prenatally exposed to sGC. Relative to the comparison group, behavioral response consistency (indexed by lower reaction time variability) and a brain correlate of conflict monitoring (the N2 event-related potential) were reduced in the sGC exposed group. Relatedly, source localization analyses showed that activations in the fronto-parietal network, most notably in the cingulate cortex and precuneus, were also attenuated in these adolescents. These regions are known to subserve conflict detection and response inhibition as well as top-down regulation of stress responses. Moreover, source activation in the anterior cingulate cortex correlated negatively with reaction time variability, whereas activation in the precuneus correlated positively with salivary cortisol reactivity to social stress in the sGC exposed group. Taken together, findings of this study indicate that prenatal exposure to sGC yields lasting impacts on the development of fronto-parietal brain functions during adolescence, affecting multiple facets of adaptive cognitive and behavioral control.
Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin
Authors: Liakopoulos Apostolos , van der Goot Jeanet , Bossers Alex , Betts Jonathan , Brouwer Michael S. M. , Kant Arie , Smith Hilde , Ceccarelli Daniela , Mevius Dik 
Published: May 2018

AbstractThe blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12-encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization. We report here the first complete sequences of IncX3 plasmids of animal origin and show that IncX3 plasmids exhibit remarkable synteny in their backbone, while the major differences lie in their blaSHV-12-flanking region. Our findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host. These favourable features might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands, highlighting the epidemic potential of these plasmids.
Automatic emotion and attention analysis of young children at home: a ResearchKit autism feasibility study
Authors: Egger Helen L. , Dawson Geraldine , Hashemi Jordan , Carpenter Kimberly L. H. , Espinosa Steven , Campbell Kathleen , Brotkin Samuel , Schaich-Borg Jana , Qiu Qiang , Tepper Mariano , Baker Jeffrey P. , Bloomfield Richard A. , Sapiro Guillermo 
Published: May 2018

AbstractCurrent tools for objectively measuring young children’s observed behaviors are expensive, time-consuming, and require extensive training and professional administration. The lack of scalable, reliable, and validated tools impacts access to evidence-based knowledge and limits our capacity to collect population-level data in non-clinical settings. To address this gap, we developed mobile technology to collect videos of young children while they watched movies designed to elicit autism-related behaviors and then used automatic behavioral coding of these videos to quantify children’s emotions and behaviors. We present results from our iPhone study Autism & Beyond, built on ResearchKit’s open-source platform. The entire study—from an e-Consent process to stimuli presentation and data collection—was conducted within an iPhone-based app available in the Apple Store. Over 1 year, 1756 families with children aged 12–72 months old participated in the study, completing 5618 caregiver-reported surveys and uploading 4441 videos recorded in the child’s natural settings. Usable data were collected on 87.6% of the uploaded videos. Automatic coding identified significant differences in emotion and attention by age, sex, and autism risk status. This study demonstrates the acceptability of an app-based tool to caregivers, their willingness to upload videos of their children, the feasibility of caregiver-collected data in the home, and the application of automatic behavioral encoding to quantify emotions and attention variables that are clinically meaningful and may be refined to screen children for autism and developmental disorders outside of clinical settings. This technology has the potential to transform how we screen and monitor children’s development.
Repetitive stretching of giant liposomes utilizing the nematic alignment of confined actin
Authors: Tanaka Shunsuke , Takiguchi Kingo , Hayashi Masahito 
Published: May 2018

AbstractGiant liposomes encapsulating cytoskeletons have been constructed to further understand the mechanisms of cell movement and develop cell-sized chemical machineries. Innovative studies demonstrating liposomal movements using microtubules and the molecular motors kinesin/dynein have been reported. However, no one has succeeded in generating repetitive motions controlled by external stimuli. Here we show that if the actin concentration in liposomes is comparable to that of cytoplasm of living cells, the liposomes can be deformed into spindle shapes by encapsulating only actin filaments, even without the molecular motor myosin. Furthermore, their shapes can be changed reversibly between spindle and sphere shapes by adjusting osmotic pressure or by light irradiation of fluorescent-labeled actin. In the latter case, the repetitive shape changes are accompanied with stretching and shrinking of filopodia- or acrosome projection-like extensions. Our results indicate that filamentous polymer of variable length like actin filament is a potential material for the reproduction of cell-like movement.
Advantages to a diverging Raman amplifier
Authors: Sadler James D. , Silva Luís O. , Fonseca Ricardo A. , Glize Kevin , Kasim Muhammad F. , Savin Alex , Aboushelbaya Ramy , Mayr Marko W. , Spiers Benjamin , Wang Robin H. W. , Bingham Robert , Trines Raoul M. G. M. , Norreys Peter A. 
Published: May 2018

AbstractThe plasma Raman instability can efficiently compress a nanosecond long high-power laser pulse to sub-picosecond duration. Although, many authors envisaged a converging beam geometry for Raman amplification, here we propose the exact opposite geometry; the amplification should start at the intense focus of the seed. We generalise the coupled laser envelope equations to include this non-collimated case. The new geometry completely eradicates the usual trailing secondary peaks of the output pulse, which typically lower the efficiency by half. It also reduces, by orders of magnitude, the initial seed pulse energy required for efficient operation. As in the collimated case, the evolution is self similar, although the temporal pulse envelope is different. A two-dimensional particle-in-cell simulation demonstrates efficient amplification of a diverging seed with only 0.3 mJ energy. The pulse has no secondary peaks and almost constant intensity as it amplifies and diverges.
Association between Insulin Resistance and Cardiovascular Risk Factors in Polycystic Ovary Syndrome Patients
Authors: Wanderley Miriam da Silva , Pereira Lara Cristina Ribeiro , Santos Carla Borges , Cunha Vinícius Santos da , Neves Mariam Viviane Jovino 
Published: May 2018

Objective To analyze the association between the indirect methods of evaluating insulin resistance (IR) and blood pressure, anthropometric and biochemical parameters in a population of polycystic ovary syndrome (PCOS) patients.
Methods Cross-sectional study performed at the Hospital Universitário de Brasília (HUB, in the Portuguese acronym) involving PCOS patients diagnosed from January 2011 to January 2013. Four indirect methods, namely, fasting blood insulin level, fasting glucose/insulin ratio (G/I), homeostatic model-assessment-insulin resistance (HOMA-IR), and the quantitative insulin sensitivity check index (QUICKI), were used to obtain the IR diagnosis. The data were analyzed using the test of proportions, the Chi-square test, and Fisher exact test, when indicated.
Results Out of the 83 patients assessed, aged 28.79 ± 5.85, IR was found in 51.81–66.2% of them using the G/I ratio and the QUICKI, respectively. The test of proportions did not show a significant difference between the methods analyzed. The proportion of IR diagnoses was statistically higher in obese women than in women with normal body mass index (BMI). We observed a statistically significant association between all the methods for diagnosing IR and BMI, waist circumference (WC) and lipid accumulation product (LAP). With regards to arterial hypertension (AH), we observed a significant association according to three methods, with the exception of the ratio G/I.
Conclusion Insulin resistance prevalence varied according to the diagnostic method employed, with no statistical difference between them. The proportion of IR diagnoses was statistically higher in obese women than in women with normal BMI. We observed a significant association between IR and WC, BMI, LAP, as well as dyslipidemia and AH in a high proportion of patients.
Endoscopic and Surgical Gastrostomy and Jejunostomy Tube Placement
Authors: El-Hayek Kevin , Bauman Marita 
Published: May 2018

AbstractEnteral access is a common request for consulting surgeons and interventionists. Prior to the 1980s, such a consultation often necessitated open surgical intervention whereas today, enteral access is often performed via several minimally invasive methods. Tools and techniques for minimally invasive enteral access have changed drastically due to advancements in the fields of endoscopy, laparoscopy, and interventional radiology. Percutaneous endoscopic gastrostomy tube placement is one such advancement. Since its first development, its basic principles have been applied to other minimally invasive techniques, which have resulted in an expansion of techniques for establishment of enteral access. In this article, we outline various endoscopic and surgical techniques for gastric and jejunal access.
Bacterial community analysis in three types of the fermented seafood, jeotgal, produced in South Korea
Authors: Song Eun-Ji , Lee Eun-Sook , Park So-Lim , Choi Hak-Jong , Roh Seong Woon , Nam Young-Do 
Published: May 2018

ABSTRACT
Jeotgal is a traditional Korean seafood fermented by indigenous microbes. The bacterial community in five myeolchi-jeot (Engraulis japonica), five meongge-jeot (Halocynthia roretzi), and six saeu-jeot (Acetes japonicas) produced in South Korea was analyzed by barcoded pyrosequencing targeting the V1/V2 hyper-variable regions of the 16S rRNA gene. All samples were dominated by the phyla Firmicutes, which represented 67.7% (SD = 27.2%) of the population. Tetragenococcus halophilus and Tetragenococcus muriaticus were the predominant species in myeolchi-jeot. The LABs, Lactobacillus sakei, Lactobacillus curvatus, and Weissella koreensis were the predominant species in meongge-jeot. In myeolchi-jeot and meongge-jeot, the bacterial communities within samples were consistent in their predominance, however each of saeu-jeot samples had inter-individual variety in the bacterial community leading to the difficulties of standardization for the commercial production of saeu-jeot. The results of this study will conclusively help to expand our basic knowledge of jeotgal and the related microorganisms involved in food fermentation.
The modulation of corticospinal excitability and inhibition following acute resistance exercise in males and females
Authors: Latella Christopher , Hendy Ashlee , Vanderwesthuizen Dan , Teo Wei‐Peng 
Published: May 2018

AbstractObjective: The acute responses to resistance training (RT) between males and females are poorly understood, especially from a neural perspective. Therefore, we aimed to compare the corticospinal and intracortical responses during fatigue and recovery following RT.Methods: Twenty‐two participants (12M, 10F) completed one‐session of RT (3 × 12 repetition maximum) unilateral leg extensions with 60 s recovery. Single‐ and paired‐pulse transcranial magnetic stimulation measured changes in the motor‐evoked potential (MEP), corticospinal silent period (CSP), CSP/MEP ratio, and intracortical facilitation/inhibition (ICF, SICI). The maximal compound wave (MMAX) measured peripheral excitability of the rectus femoris (RF) and maximal voluntary isometric contraction (MVIC) neuromuscular function of the leg extensors. Measures were taken immediately post, 30 min, 1 and 6 h post‐training.Results: A significantly greater increase in MEP/MMAX ratio (p = .005) was observed for females immediately post‐training compared to males. While no sex differences in MEP/MMAX ratio was observed at 30 min and 1 h post‐training, a greater MEP/MMAX ratio for males was observed at 30 min (p < .001), which remained elevated up until 1 h post‐training for males when compared to baseline (p = .003). CSP trended to decrease for males compared to females immediately post‐training (d = 1.93). MVIC was decreased post‐training for males; 14.22% and females; 14.16% (P < .001), with MMAX reduced at 30 min for both groups (P < .001). No differences in the CSP/MEP ratio, SICI or ICF were observed (P > .05).Conclusion: The net output of corticospinal excitability is similar between males and females during fatigue. However, the mechanism in which this is modulated (increased MEP, decreased CSP) appears to be sex‐specific.
Application of network smoothing to glycan LC-MS profiling
Authors: Klein Joshua , Carvalho Luis , Zaia Joseph 
Published: May 2018

Abstract

Motivation
Glycosylation is one of the most heterogeneous and complex protein post-translational modifications. Liquid chromatography coupled mass spectrometry (LC-MS) is a common high throughput method for analyzing complex biological samples. Accurate study of glycans require high resolution mass spectrometry. Mass spectrometry data contains intricate sub-structures that encode mass and abundance, requiring several transformations before it can be used to identify biological molecules, requiring automated tools to analyze samples in a high throughput setting. Existing tools for interpreting the resulting data do not take into account related glycans when evaluating individual observations, limiting their sensitivity.

Results
We developed an algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans. Our algorithm optimizes a set of likelihood scoring functions based on glycan chemical properties but uses network Laplacian regularization and optionally prior information about expected glycan families to smooth the likelihood and thus achieve a consistent and more representative solution. Our method was able to identify as many, or more glycan compositions compared to previous approaches, and demonstrated greater sensitivity with regularization. Our network definition was tailored to N-glycans but the method may be applied to glycomics data from other glycan families like O-glycans or heparan sulfate where the relationships between compositions can be expressed as a graph.

Availability and implementation Built Executable
http://www.bumc.bu.edu/msr/glycresoft/ and Source Code: https://github.com/BostonUniversityCBMS/glycresoft.

Supplementary information
Supplementary data are available at Bioinformatics online.
ConSpeciFix: classifying prokaryotic species based on gene flow
Authors: Bobay Louis-Marie , Ellis Brian Shin-Hua , Ochman Howard 
Published: May 2018

Abstract

Summary
Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life.

Availability and implementation
ConSpeciFix’s webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML.
Complex integration of intrinsic and peripheral signaling is required for pituitary gland development†
Authors: Edwards Whitney , Raetzman Lori T 
Published: May 2018

AbstractThe coordination of pituitary development is complicated and requires input from multiple cellular processes. Recent research has provided insight into key molecular determinants that govern cell fate specification in the pituitary. Moreover, increasing research aimed to identify, characterize, and functionally describe the presumptive pituitary stem cell population has allowed for a better understanding of the processes that govern endocrine cell differentiation in the developing pituitary. The culmination of this research has led to the ability of investigators to recapitulate some of embryonic pituitary development in vitro, the first steps to developing novel regenerative therapies for pituitary diseases. In this current review, we cover the major players in pituitary stem/progenitor cell function and maintenance, and the key molecular determinants of endocrine cell specification. In addition, we discuss the contribution of peripheral hormonal regulation of pituitary gland development, an understudied area of research.
Effect of Aerobic Exercise Training and Essential Amino Acid Supplementation for 24 Weeks on Physical Function, Body Composition, and Muscle Metabolism in Healthy, Independent Older Adults: A Randomized Clinical Trial
Authors: Markofski Melissa M , Jennings Kristofer , Timmerman Kyle L , Dickinson Jared M , Fry Christopher S , Borack Michael S , Reidy Paul T , Deer Rachel R , Randolph Amanda , Rasmussen Blake B , Volpi Elena 
Published: May 2018

Abstract

Background
Essential amino acids (EAA) and aerobic exercise (AE) acutely and independently stimulate skeletal muscle protein anabolism in older adults.

Objective
In this Phase 1, double-blind, placebo-controlled, randomized clinical trial, we determined if chronic EAA supplementation, AE training, or a combination of the two interventions could improve muscle mass and function by stimulating muscle protein synthesis.

Methods
We phone-screened 971, enrolled 109, and randomized 50 independent, low-active, nonfrail, and nondiabetic older adults (age 72 ± 1 years). We used a 2 × 2 factorial design. The interventions were: daily nutritional supplementation (15 g EAA or placebo) and physical activity (supervised AE training 3 days/week or monitored habitual activity) for 24 weeks. Muscle strength, physical function, body composition, and muscle protein synthesis were measured before and after the 24-week intervention.

Results
Forty-five subjects completed the 24-week intervention. VO2peak and walking speed increased (p < .05) in both AE groups, irrespective of supplementation type, but muscle strength increased only in the EAA + AE group (p < .05). EAA supplementation acutely increased (p < .05) muscle protein synthesis from basal both before and after the intervention, with a larger increase in the EAA + AE group after the intervention. Total and regional lean body mass did not change significantly with any intervention.

Conclusions
In nonfrail, independent, healthy older adults AE training increased walking speed and aerobic fitness, and, when combined with EAA supplementation, it also increased muscle strength and EAA-stimulated muscle protein synthesis. These increases occurred without improvements in muscle mass.
De novo genome assembly of the red silk cotton tree (Bombax ceiba)
Authors: Gao Yong , Wang Haibo , Liu Chao , Chu Honglong , Dai Dongqin , Song Shengnan , Yu Long , Han Lihong , Fu Yi , Tian Bin , Tang Lizhou 
Published: May 2018

Abstract

Background
Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia as well as northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate further utilization of this plant resource, we present here the draft genome sequence for B. ceiba.

Findings
We assembled a relatively intact genome of B. ceiba by using PacBio single-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mb long, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively.

Conclusions
The high-quality draft genome assembly of B. ceiba will be a valuable resource enabling further genetic improvement and more effective use of this tree species.
Increased likelihood of induced seismicity in highly overpressured shale formations
Authors: Eaton David W , Schultz Ryan 
Published: May 2018

SUMMARYFluid-injection processes such as disposal of saltwater or hydraulic fracturing can induce earthquakes by increasing pore pressure and/or shear stress on faults. Natural processes, including transformation of organic material (kerogen) into hydrocarbon and cracking to produce gas, can similarly cause fluid overpressure. Here, we document two examples from the Western Canada Sedimentary Basin where earthquakes induced by hydraulic fracturing are strongly clustered within areas characterized by pore-pressure gradient in excess of 15 kPa m−1. Despite extensive hydraulic-fracturing activity associated with resource development, induced earthquakes are virtually absent in the Montney and Duvernay Formations elsewhere. Statistical analysis suggests a negligible probability that this spatial correlation developed by chance. This implies that, in addition to known factors such as anthropogenic pore-pressure increase and proximity to critically stressed faults, high in situ overpressure of shale formations may also represent a controlling factor for inducing earthquakes by hydraulic fracturing. On a geological timescale, natural pore-pressure generation may lead to fault-slip episodes that regulate the magnitude of formation overpressure.