bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphorylation of the Brome Mosaic Virus Capsid Regulates the Timing of Viral Infection
Authors: Hoover Haley S. , Wang Joseph Che-Yen , Middleton Stefani , Ni Peng , Zlotnick Adam , Vaughan Robert C. , Kao C. Cheng 
Published: June 2016

ABSTRACT
The four brome mosaic virus (BMV) RNAs (RNA1 to RNA4) are encapsidated in three distinct virions that have different disassembly rates in infection. The mechanism for the differential release of BMV RNAs from virions is unknown, since 180 copies of the same coat protein (CP) encapsidate each of the BMV genomic RNAs. Using mass spectrometry, we found that the BMV CP contains a complex pattern of posttranslational modifications. Treatment with phosphatase was found to not significantly affect the stability of the virions containing RNA1 but significantly impacted the stability of the virions that encapsidated BMV RNA2 and RNA3/4. Cryo-electron microscopy reconstruction revealed dramatic structural changes in the capsid and the encapsidated RNA. A phosphomimetic mutation in the flexible N-terminal arm of the CP increased BMV RNA replication and virion production. The degree of phosphorylation modulated the interaction of CP with the encapsidated RNA and the release of three of the BMV RNAs. UV cross-linking and immunoprecipitation methods coupled to high-throughput sequencing experiments showed that phosphorylation of the BMV CP can impact binding to RNAs in the virions, including sequences that contain regulatory motifs for BMV RNA gene expression and replication. Phosphatase-treated virions affected the timing of CP expression and viral RNA replication in plants. The degree of phosphorylation decreased when the plant hosts were grown at an elevated temperature. These results show that phosphorylation of the capsid modulates BMV infection.

IMPORTANCE
How icosahedral viruses regulate the release of viral RNA into the host is not well understood. The selective release of viral RNA can regulate the timing of replication and gene expression. Brome mosaic virus (BMV) is an RNA virus, and its three genomic RNAs are encapsidated in separate virions. Through proteomic, structural, and biochemical analyses, this work shows that posttranslational modifications, specifically, phosphorylation, on the capsid protein regulate the capsid-RNA interaction and the stability of the virions and affect viral gene expression. Mutational analysis confirmed that changes in modification affected virion stability and the timing of viral infection. The mechanism for modification of the virion has striking parallels to the mechanism of regulation of chromatin packaging by nucleosomes.
Psychological barriers to optimal insulin therapy: more concerns in adolescent females than males
Authors: Wisting Line , Bang Lasse , Skrivarhaug Torild , Dahl-Jørgensen Knut , Rø Øyvind 
Published: June 2016

ObjectiveThe aim of this study is to investigate psychological barriers (illness perceptions, insulin beliefs, and coping strategies) to optimal insulin therapy among adolescents with type 1 diabetes (T1D), with a specific focus on gender differences and mode of treatment (insulin pump vs pen).MethodsA total of 105 males and females (12–20 years) participated in this study. The Brief Illness Perception Questionnaire, the Beliefs about Medicines Questionnaire, and the Adolescent Coping Orientation for Problem Experiences were completed. Additionally, diabetes clinical data were collected by the Norwegian Childhood Diabetes Registry.ResultsFemales had significantly more negative illness perceptions than males on all dimensions (p<0.05), with moderate-to-large effect sizes. Regarding insulin beliefs, females scored significantly higher than males oninsulin concern(p<0.001), indicating more concerns about insulin. There were no significant gender differences on perceptions ofinsulin necessity. Finally, females scored significantly higher on the coping strategiesbeing socialandsolving family problems(p<0.01), indicating more positive coping among females than males for these subscales. In terms of treatment mode, the only statistically significant difference in the psychological aspects was for the illness perceptiontreatment control, with patients using insulin pen reporting more negative perceptions on this dimension than patients using insulin pump.ConclusionsAddressing psychological aspects may be a clinically important supplement to standard somatic T1D care. The consistent finding of gender differences across the psychological measures implies that a tailored treatment approach for males and females with T1D may be warranted.
Single-leg balance and core motor control in children: when does the risk for ACL injury occurs?
Authors: Hutchinson Allison B , Yao Paul , Hutchinson Mark R 
Published: June 2016

IntroductionWhile numerous publications have demonstrated the correlation of poor single-leg balance and core motor control with an increased risk of anterior cruciate ligament (ACL) injuries in skeletally mature female athletes, few have analysed the preadolescent population regarding when indeed comparative deficits in balance and core control actually occur. The purpose of this study was to assess whether the neuromotor factors that place mature females at increased risk of ACL injury actually are present in preadolescents and if so when.MethodsThis study used simplified modifications of classic drop-jump testing as well as single-leg balance tests performed on stable and unstable surfaces to assess balance and core motor control. 84 children (males and females) ranging in age from 6 to 13 years were divided into 4 equally sized groups based on their academic classes. Each group was compared with each other, and compared with a cohort of 205 collegiate athletes. The latter served as a comparative norm of mature athletes who had performed the same or similar testing.ResultsOutcomes revealed that the preadolescent population performed poorly on the tests when compared with the collegiate population but the children matured with age until the eldest subgroups compared more favourably with the college-aged athletes. Girls appear to mature at a slightly earlier pace than boys. This study focusing on preadolescent children concluded that the neuromuscular changes that place females at greater risk of injury do not appear to occur prior to adolescence.ConclusionsBased on the outcomes of this study, it is suggested that sex differences regarding balance and core control deficits that can increase risk of ACL injuries likely occur after grade school (age 12–13).
Extension of Standard Model in multi-spinor field formalism — Visible and dark sectors
Authors: Sogami Ikuo S. 
Published: June 2016

With multi-spinor fields which behave as triple-tensor products of the Dirac spinors, the Standard Model is extended so as to embrace three families of ordinary quarks and leptons in the visible sector and an additional family of exotic quarks and leptons in the dark sector of our Universe. Apart from the gauge and Higgs fields of the Standard Model symmetry G, new gauge and Higgs fields of a symmetry isomorphic to G are postulated to exist in the dark sector. It is the bi-quadratic interaction between visible and dark Higgs fields that opens a main portal to the dark sector. Breakdowns of the visible and dark electroweak symmetries result in the Higgs boson with mass 125 GeV and a new boson which can be related to the diphoton excess around 750 GeV. Subsequent to a common inflationary phase and a reheating period, the visible and dark sectors follow weakly-interacting paths of thermal histories. We propose scenarios for dark matter in which no dark nuclear reaction takes place. A candidate for the main component of the dark matter is a stable dark hadron with spin 3/2, and the upper limit of its mass is estimated to be 15.1 GeV/c2.
Molecular Pathways: Cachexia Signaling—A Targeted Approach to Cancer Treatment
Authors: Miyamoto Yuji , Hanna Diana L. , Zhang Wu , Baba Hideo , Lenz Heinz-Josef 
Published: June 2016

Abstract
Cancer cachexia is a multifactorial syndrome characterized by an ongoing loss of skeletal muscle mass, which negatively affects quality of life and portends a poor prognosis. Numerous molecular substrates and mechanisms underlie the dysregulation of skeletal muscle synthesis and degradation observed in cancer cachexia, including proinflammatory cytokines (TNFα, IL1, and IL6), and the NF-κB, IGF1/AKT/mTOR, and myostatin/activin–SMAD pathways. Recent preclinical and clinical studies have demonstrated that anti-cachexia drugs (such as MABp1 and soluble receptor antagonist of myostatin/activin) not only prevent muscle wasting but also may prolong overall survival. In this review, we focus on the significance of cachexia signaling in patients with cancer and highlight promising drugs targeting tumor cachexia in clinical development. Clin Cancer Res; 22(16); 3999–4004. ©2016 AACR.
КЛІНІКО-ЛАБОРАТОРНА ХАРАКТЕРИСТИКА ПРОЯВІВ ІНФЕКЦІЙНОГО МОНОНУКЛЕОЗУ У ДІТЕЙ
Authors: Nezhoda I. I. , Bobruk S. V. 
Published: June 2016

<p class="1"><em>Висвітлено клініко-лабораторні особливості перебігу інфекційного мононуклеозу у дітей у період з березня по липень 2015 р., з урахуванням етіологічного чинника, клініки та даних імунологічних досліджень слизової оболонки орофарингеальної зони.</em></p>
Large-Scale Controls on Atlantic Tropical Cyclone Activity on Seasonal Time Scales
Authors: Lim Young-Kwon , Schubert Siegfried D. , Reale Oreste , Molod Andrea M. , Suarez Max J. , Auer Benjamin M. 
Published: June 2016

AbstractInterannual variations in seasonal tropical cyclone (TC) activity (e.g., genesis frequency and location, track pattern, and landfall) over the Atlantic are explored by employing observationally constrained simulations with the NASA Goddard Earth Observing System, version 5 (GEOS-5), atmospheric general circulation model. The climate modes investigated are El Niño–Southern Oscillation (ENSO), the North Atlantic Oscillation (NAO), and the Atlantic meridional mode (AMM).The results show that the NAO and AMM can strongly modify and even oppose the well-known ENSO impacts, like in 2005, when a strong positive AMM (associated with warm SSTs and a negative SLP anomaly over the western tropical Atlantic) led to a very active TC season with enhanced TC genesis over the Caribbean Sea and a number of landfalls over North America, under a neutral ENSO condition. On the other end, the weak TC activity during 2013 (characterized by weak negative Niño index) appears caused by a NAO-induced positive SLP anomaly with enhanced vertical wind shear over the tropical North Atlantic. During 2010, the combined impact of the three modes produced positive SST anomalies across the entire low-latitudinal Atlantic and a weaker subtropical high, leading to more early recurvers and thus fewer landfalls despite enhanced TC genesis. The study provides evidence that TC number and track are very sensitive to the relative phases and intensities of these three modes and not just to ENSO alone. Examination of seasonal predictability reveals that the predictive skill of the three modes is limited over tropics to subtropics, with the AMM having the highest predictability over the North Atlantic, followed by ENSO and NAO.
New approach for modeling the quality of the bagging date using desirability functions
Authors: Guedri W , Jaouadi M , Msahli S 
Published: June 2016

The date palm, especially the variety Deglet Nour, produces some dates of high quality. The crop is increasingly attacked by insects while ripening on the palm and damaged by autumnal rains. Various forms of covers have been tried commercially. In this study we considered common materials used worldwide and tested under laboratory conditions. These products require the satisfaction of several properties at the same time. On this basis, the product’s requirements can be identified and converted into a physical element, that is, quality index “QI”, which measures the overall satisfaction of the bagging product. Its value ranges from 0 to l. Hence, “QI” can be used to detect the lack of effectiveness of one of the properties, and thus it should serve as an important measure in quality assurance. It includes the following eight parameters with their ranges: overall migration of toxicological specific substances; solar absorption coefficient; air permeability; resistance to water penetration; breaking load; tear strength; thickness; and weight. The results show that the highest quality index reached is 0.5. It is concluded that the “QI” can evaluate and classify the existing date bunch bags and it can effectively identify the property that should be improved.
Simultaneous bilingualism: Early developments, incomplete later outcomes?
Authors: Silva-Corvalán Carmen 
Published: June 2016

Purpose: Research on the language of heritage speakers has shown that in situations of societal bilingualism the functionally restricted language evidences the simplification of some grammatical domains. A frequent question is whether this stage of grammatical simplification is due to incomplete or interrupted acquisition in the early years of a bilingual’s life, or a result of processes of attrition of acquired knowledge of the underused language. This article considers the issue of incompleteness through an examination of the relationship between bilingual children’s developing grammars and the more or less changed bilingual systems of adult second and third generation immigrants (“heritage speakers”) in the USA. Methodology: The issue of incompleteness is examined in two corpora: (1) Recordings of 50 Spanish-English adult Mexican-American bilinguals; and (2) Longitudinal data obtained during the first six years of life of two Spanish-English bilingual siblings. Data analysis: Qualitative and quantitative analyses of the grammar of subjects, verbal clitics, and verb tenses of the Spanish of the bilinguals under study. Findings: The outcome of reduced exposure and production of a minority language in simultaneous bilingual acquisition reflects the incomplete acquisition by age 6;0 of some aspects of the input language. The bilingual siblings’ unequal control of the minority language is shown to parallel the range of proficiencies identified across the adult heritage speakers. Significance: Some linguists argue that heritage speakers’ grammars are less restrictive or “different” in some respects but not incomplete. In contrast, this article demonstrates that at least some of the reduced grammars of heritage speakers result from a halted process of acquisition in the early years of life. Furthermore, while difference is not an explanatory construct, incomplete acquisition due to interrupted development caused by restricted exposure and production offers an explanation for the range of proficiencies attested among adult heritage speakers.
Blood pressure, arterial stiffness and endogenous lithium clearance in relation to AGTR1 A1166C and AGTR2 G1675A gene polymorphisms
Authors: Cwynar Marcin , Gąsowski Jerzy , Głuszewska Anna , Królczyk Jarosław , Bartoń Henryk , Słowik Agnieszka , Grodzicki Tomasz 
Published: June 2016

Introduction: Although recently a matter of epidemiologic controversy, sodium overload and its interaction with genetic factors predispose to hypertension and related target organ complications. Methods: In 131 (66 male) treated hypertensives, we measured peripheral and central arterial pressures and pulse wave augmentation indexes (AIxP, AIxC1, AIxC2), pulse wave velocity (PWV), daily urinary sodium excretion and did genetic studies of AGTR1 A1166C and AGTR2 G1675A polymorphisms. Proximal (FELi) and distal (FDRNa) sodium reabsorption measurements were performed using endogenous lithium clearance. Results: In men, we found interaction between FDRNa and AGTR2 G1675A polymorphism with respect to AIxC1 ( pINT=0.01), AIxC2 ( pINT=0.05) and AIxP ( pINT=0.006). Arterial stiffness increased with higher sodium reabsorption in the distal tubule, in the presence of AGTR2 G allele with the opposite tendency in A allele carriers. In the subgroup with FDRNa below median, as compared to those with FDRNa above median, the AIxC1 (139.6±3.8 vs 159.1±5.7%; p=0.009), AIxC2 (26.3±1.8 vs 33.3±1.7%; p=0.016) and AIxP (83.4±2.5 vs 96.5±2.6%; p<0.0001) were lower, in the G allele carrying men and GG homozygous women. Conclusions: The relation between sodium reabsorption in the distal tubule and the development of arterial stiffness depends on the AGTR2 G1675A polymorphism in blood pressure independent fashion.
Recruitment Into a Pediatric Continuous Glucose Monitoring RCT
Authors: Volkening Lisa K. , Gaffney Kaitlin C. , Katz Michelle L. , Laffel Lori M. 
Published: June 2016

Background: The purpose was to identify patient/family characteristics and recruitment process characteristics associated with the decision to participate in a 2-year continuous glucose monitoring (CGM) RCT for youth with type 1 diabetes and their families. Method: Study staff approached patients who were conditionally eligible according to medical record review or referred by a provider. We categorized families according to participation decision (agree vs decline) and timing of decision (day of approach vs later [“thinkers”]). Results: Over 18 months, we approached 456 eligible patients; 19% agreed on the day of approach, 10% agreed later, 42% declined on the day of approach, and 30% declined later. Agreers were younger ( P = .002), had shorter diabetes duration ( P = .0003), had a lower insulin dose ( P = .02), checked blood glucose levels more often ( P = .002), and were more likely to use pump therapy ( P = .009) than decliners. Patients/families were more likely to agree in fall/winter (41%) than spring/summer (19%, P < .0001). Of decliners, 50% cited no interest in CGM as the reason for nonparticipation. Among thinkers, 49% of patients who made a decision within 2 weeks of being approached agreed; only 15% of thinkers who made a decision >2 weeks after being approached agreed to participate ( P < .0001). Conclusions: Recruitment is a critical and often challenging phase of clinical trials. Recruitment to pediatric CGM studies may be especially challenging due to youths’ reluctance to use CGM. These data provide an opportunity to better understand and possibly optimize recruitment into future pediatric CGM studies and other studies of advanced diabetes technologies.
A Longitudinal Observational Study of Developmental Defects of Enamel from Birth to 6 Years of Age
Authors: Seow W.K. , Leishman S.J. , Palmer J.E. , Walsh L.J. , Pukallus M. , Barnett A.G. 
Published: June 2016

Developmental defects of the enamel (DDE) commonly occur in the primary dentition. Although several cross-sectional studies have shown the association of DDE with caries, there is a paucity of longitudinal studies demonstrating that teeth with DDE are at greater risk of caries than are normal teeth. Therefore, the aim of the present study was to longitudinally track a total of 14,220 primary teeth in 725 children from a large birth cohort study, who were interviewed by telephone or home visits at 6-mo intervals. There were 74 children with at least 1 tooth with DDE. We compared teeth with and without DDE by calculating hazard ratios for caries using a Cox proportional hazards model and by plotting caries-free probabilities by child’s age for DDE categories in a Kaplan-Meier plot. Our results show that teeth with DDE had a much higher risk for caries and developed caries earlier than did teeth without DDE. The hazard ratios (95% confidence intervals) for caries were 6.0 (2.4 to 14.6; P < 0.001) for pits, 5.5 (3.8 to 7.8; P < 0.001) for missing enamel, and 4.5 (1.8 to 11.3; P < 0.002) for hypoplasia occurring with yellow-brown opacities. Kaplan-Meier survival plots of caries-free probabilities by age, depending on DDE type, suggest that all types of enamel hypoplasia are associated with a statistically significant increased risk for caries. The study provides longitudinal evidence that DDE are a strong determinant for caries in the primary dentition (ACTRN No. 012606000356561). Knowledge Transfer Statement: The study provides longitudinal evidence that developmental defects of enamel of the primary dentition are strongly associated with increased risk of early childhood caries.
A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue
Authors: Kovacheva Violeta N. , Snead David , Rajpoot Nasir M. 
Published: June 2016

Abstract
Background
There have been great advancements in the field of digital pathology. The surge in development of analytical methods for such data makes it crucial to develop benchmark synthetic datasets for objectively validating and comparing these methods. In addition, developing a spatial model of the tumour microenvironment can aid our understanding of the underpinning laws of tumour heterogeneity.

Results
We propose a model of the healthy and cancerous colonic crypt microenvironment. Our model is designed to generate synthetic histology image data with parameters that allow control over cancer grade, cellularity, cell overlap ratio, image resolution, and objective level.

Conclusions
To the best of our knowledge, ours is the first model to simulate histology image data at sub-cellular level for healthy and cancerous colon tissue, where the cells have different compartments and are organised to mimic the microenvironment of tissue in situ rather than dispersed cells in a cultured environment. Qualitative and quantitative validation has been performed on the model results demonstrating good similarity to the real data. The simulated data could be used to validate techniques such as image restoration, cell and crypt segmentation, and cancer grading.
PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics
Authors: Fernandez-Ricaud Luciano , Kourtchenko Olga , Zackrisson Martin , Warringer Jonas , Blomberg Anders 
Published: June 2016

Abstract
Background
Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology.

Results
To automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics.
Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis.

Conclusions
PRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases.