bluuebunny/crossref_metadata_2025_split huggingface dataset:
T372R Mutation Status in Yin Yang 1 Gene in Insulinoma Patients
Authors: Irshad Khushboo , Jyotsna Viveka , Agarwal Shipra , Chosdol Kunzang , Pal Sujoy , Deepak Rakesh 
Published: May 2017

AbstractInsulinomas are rare pancreatic neuroendocrine tumors. The genetic causes underlying insulinoma are still being investigated. Recently, 3 independent studies reported a recurrent somatic mutation in YY1 gene (C>G; Thr372Arg) among insulinoma patients belonging to Chinese and Western Caucasian populations, which was found to increase insulin secretion by β-cells. However, the status of this key gene variation remains unknown in patients of other ethnicities. We, therefore, screened Indian sporadic insulinoma patients for YY1 T372R mutation in the present study. Seventeen patients diagnosed with insulinoma were recruited retrospectively and their records of family history and clinical parameters were collected. Formalin-fixed paraffin-embedded tumor tissues were used to extract genomic DNA, which was subjected to PCR amplification of YY1 exon 5, followed by Sanger sequencing. Nucleotide sequences thus obtained were aligned against the documented sequence of YY1 exon 5. We found absence of C to G mutation at YY1 codon 372 in all 17 (100%) insulinoma tissues analyzed. On comparison with the mutation frequency observed in the Chinese patients, our results point to genetic heterogeneity in the pathogenesis of insulinoma. This is the first report on the status of YY1 T372R in insulinoma cases of Indian origin. This also warrants analysis of other documented as well as novel mutations in genes in insulinoma tumorigenesis.
CAEPs in non-habilitated congenitally deaf adults
Authors: Abraham Aju , Palaniswamy Hari Prakash , Yerraguntla Krishna , Rajashekhar Bellur 
Published: May 2017

Objective:
Most evidences from animal models and human subjects with auditory deprivation report that the children rehabilitated later than 5–6 years of age show abnormal CAEPs (absence of N1) even after a long period of cochlear implant usage and attributed to cortical decoupling. The current study aims to explore the auditory cortical activation in congenitally deaf adults who never received any rehabilitation.

Design:
Aided CAEPs were elicited using 1000 Hz pure tone at 30 dB SL from 11 congenitally deaf adults and age/gender matched controls aged between 17 and 45 years. The latencies and amplitudes of the P1–N1–P2 obligatory responses were measured and compared using topographic ANOVA (TANOVA).

Results:
The morphology of CAEP responses from the deaf group was similar to that of the normal hearing group except the presence of a broader P2. The amplitude measures between the groups did not reveal statistical significance; however, P2 latency revealed a significant difference between the groups. TANOVA revealed that the topographic maps between the groups did not significantly differ.

Conclusions:
The matured cortical response for acoustic stimulus, especially the presence of N1, clearly signifies the activation of auditory cortex. The presence of matured CAEPs might be due to the abnormal synaptogenesis of auditory neurons transforming into multisensory neurons and continues the normal course of maturation. These matured CAEP responses will be an indication of closure of critical period and limited benefit with rehabilitation.
Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
Authors: Kleffner Robert , Flatten Jeff , Leaver-Fay Andrew , Baker David , Siegel Justin B , Khatib Firas , Cooper Seth 
Published: May 2017

Abstract

Summary
Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter.

Availability and Implementation
Foldit Standalone is available for download at https://fold.it/standalone, under the Rosetta license, which is free for academic and non-profit users. It is implemented in cross-platform C ++ and binary executables are available for Windows, macOS and Linux.
Quantized minimax estimation over Sobolev ellipsoids
Authors: Zhu Yuancheng , Lafferty John 
Published: May 2017

Abstract
We formulate the notion of minimax estimation under storage or communication constraints, and prove an extension to Pinsker's theorem for non-parametric estimation over Sobolev ellipsoids. Placing limits on the number of bits used to encode any estimator, we give tight lower and upper bounds on the excess risk due to quantization in terms of the number of bits, the signal size and the noise level. This establishes the Pareto optimal tradeoff between storage and risk under quantization constraints for Sobolev spaces. Our results and proof techniques combine elements of rate distortion theory and minimax analysis. The proposed quantized estimation scheme, which shows achievability of the lower bounds, is adaptive in the usual statistical sense, achieving the optimal quantized minimax rate without knowledge of the smoothness parameter of the Sobolev space. It is also adaptive in a computational sense, as it constructs the code only after observing the data, to dynamically allocate more codewords to blocks where the estimated signal size is large. Simulations are included that illustrate the effect of quantization on statistical risk.
Integrated Tuberculosis/Human Immunodeficiency Virus Community-Based Case Finding in Rural South Africa: Implications for Tuberculosis Control Efforts
Authors: Shenoi Sheela V , Moll Anthony P. , Brooks Ralph P. , Kyriakides Tassos , Andrews Laurie , Kompala Teja , Upadhya Devesh , Altice Frederick L. , Eksteen Francois J. , Friedland Gerald 
Published: May 2017

Abstract

Background
Intensive case finding is endorsed for tuberculosis (TB) control in high-risk populations. Novel case-finding strategies are needed in hard-to-reach rural populations with high prevalence of TB and human immunodeficiency virus (HIV).

Methods
We performed community-based integrated HIV and TB intensive case finding in a rural South African subdistrict from March 2010 to June 2012. We offered TB symptom screening, sputum collection for microbiologic diagnosis, rapid fingerstick HIV testing, and phlebotomy for CD4 cell count. We recorded number of cases detected and calculated population-level rates and number needed to screen (NNS) for drug-susceptible and -resistant TB.

Results
Among 5615 persons screened for TB at 322 community sites, 91.2% accepted concurrent HIV testing, identifying 510 (9.9%) HIV-positive individuals with median CD4 count of 382 cells/mm3 (interquartile range = 260–552). Tuberculosis symptoms were reported by 2049 (36.4%), and sputum was provided by 1033 (18.4%). Forty-one (4.0%) cases of microbiologically confirmed TB were detected for an overall case notification rate of 730/100000 (NNS = 137); 11 (28.6%) were multidrug-resistant or extensively drug-resistant TB. Only 5 (12.2%) TB cases were HIV positive compared with an HIV coinfection rate of 64% among contemporaneously registered TB cases (P = .001).

Conclusion
Community-based integrated intensive case finding is feasible and is high yield for drug-susceptible and -resistant TB and HIV in rural South Africa. Human immunodeficiency virus–negative tuberculosis predominated in this community sample, suggesting a distinct TB epidemiology compared with cases diagnosed in healthcare facilities. Increasing HIV/TB integrated community-based efforts and other strategies directed at both HIV-positive and HIV-negative tuberculosis may contribute to TB elimination in high TB/HIV burden regions.
Technology-Based Interventions for Substance Use and Comorbid Disorders: An Examination of the Emerging Literature
Authors: Sugarman Dawn E. , Campbell Aimee N.C. , Iles Brittany R. , Greenfield Shelly F. 
Published: May 2017

AbstractAmong individuals with substance use disorders (SUDs), comorbidity with other psychiatric disorders is common and often noted as the rule rather than the exception. Standard care that provides integrated treatment for comorbid diagnoses simultaneously has been shown to be effective. Technology-based interventions (TBIs) have the potential to provide a cost-effective platform for, and greater accessibility to, integrated treatments. For the purposes of this review, we defined TBIs as interventions in which the primary targeted aim was delivered by automated computer, Internet, or mobile system with minimal to no live therapist involvement. A search of the literature identified nine distinct TBIs for SUDs and comorbid disorders. An examination of this limited research showed promise, particularly for TBIs that address problematic alcohol use, depression, or anxiety. Additional randomized, controlled trials of TBIs for comorbid SUDs and for anxiety and depression are needed, as is future research developing TBIs that address SUDs and comorbid eating disorders and psychotic disorders. Ways of leveraging the full capabilities of what technology can offer should also be further explored.
Immunohistochemical Profiling of Corneas With Fuchs Endothelial Corneal Dystrophy
Authors: De Roo An-Katrien , Janssens Thomas , Foets Beatrijs , van den Oord Joost J. 
Published: May 2017

Purpose:
Fuchs endothelial corneal dystrophy (FECD) is the leading indication for endothelial keratoplasty. Further insight into its pathophysiology is needed to develop alternative therapies.

Methods:
Sixteen genes from a previous microarray expression experiment (FECD vs. normal) were validated using immunohistochemistry on paraffin-embedded corneas (n = 6 FECD, n = 6 normal). The results were quantified manually and semiautomatically.

Results:
A higher percentage of corneal endothelial cells stained for alpha–smooth muscle actin (αSMA), cytokeratin 7, and superoxide dismutase 3 in FECD versus normal [odds ratios (ORs) of 60.90, 41.70, and 15.16, respectively, P < 0.001]. Dot-like staining for major histocompatibility complex, class II, DR alpha was present in FECD, but not in normal. Higher percentages of stromal cells in FECD versus normal stained for αSMA (OR = 864.26, P < 0.001), brain-derived neurotrophic factor (BDNF, OR = 6.34, P = 0.005), fibroblast growth factor 7 (FGF-7, OR = 2.76, P = 0.011), FGF-9 (OR = 5.97, P < 0.001), receptor FGFR-3 (OR = 13.90, P = < 0.001), and serum amyloid A1 (OR = 3.45, P = 0.023). Higher percentages of corneal epithelial cells stained for αSMA (OR = 2.20, P = 0.006) and BDNF (OR = 3.94, P < 0.001) in FECD versus normal.

Conclusions:
These results support a role for epithelial–mesenchymal transition (αSMA), oxidative stress (superoxide dismutase 3), and major histocompatibility complex, class II, DR alpha+ cells with dendritic morphology in the pathophysiology of FECD. Furthermore, corneal stromal cells express trophic molecules (BDNF and FGFs) and markers of chronic inflammation (serum amyloid A1) in FECD.
Serious Bacterial Infections in Hospitalized Febrile Infants in the First and Second Months of Life
Authors: Carmon Lior , Goldbart Aviv , Greenberg David , Ben-Shimol Shalom 
Published: May 2017

Objective:
Most protocols evaluating serious bacterial infection (SBI) risk in febrile infants classify neonates <30 days of age as high risk (HR), while other protocols do not distinguish between infants <30 and 30–60 days of age. We compared SBI rates in febrile infants at the first and the second months of life.

Methods:
This was a retrospective, population-based, cohort study. All febrile infants ≤60 days of age hospitalized in southern Israel, January 2013 through May 2014, were included. SBI risk assessment included medical history, physical examination, blood count and dipstick urine analysis.

Results:
Overall, 623 infants were identified; 142 HR infants <30 days of age, 95 low-risk (LR) infants <30 days of age, 232 HR infants 30–60 days of age and 154 LR infants 30–60 days of age. Urinary tract infection comprised 84.7% (133/157) of all SBIs. Among HR infants, higher SBI rates were observed in <30 versus 30–60 days (45.0% vs. 29.3%; P = 0.003), while respective rates were similar among LR infants (8.4% vs. 11.0%; P = 0.66). SBI rates in HR infants 0–14 versus 15–60 days of age were 45.3% versus 33.6% (P = 0.12), and 19.2% versus 8.9% (P = 0.15) in LR infants. Among HR infants, SBI rates were 52.8% and 39.5% in infants <30 days of age with temperature ≥39°C and <39°C, respectively, while in infants ≥30 days of age, respective rates were 31.2% and 26.7% (P = 0.005, comparing the 4 groups). Among LR infants, rates were not affected by temperature degree. Thrombocytopenia was associated with higher SBI rates in HR, but not in LR.

Conclusions:
In HR infants, higher SBI rates were associated with younger age, higher body temperature and thrombocytopenia. In contrast, SBI (mostly urinary tract infection) rates among LR infants (approximately 10%) were not associated with these factors.
Interacting influences of gender and chronic pain status on parasympathetically mediated heart rate variability in adolescents and young adults
Authors: Walker Lynn S. , Stone Amanda L. , Smith Craig A. , Bruehl Stephen , Garber Judy , Puzanovova Martina , Diedrich André 
Published: May 2017

Abstract
Considerable research links chronic pain to autonomic nervous system (ANS) dysfunction, specifically low heart rate variability (HRV) mediated by reduced parasympathetic activity. However, little is known about factors that influence ANS function in chronic pain. The ANS is the primary pathway for brain–gut communication, making it of particular interest in gastrointestinal disorders, such as irritable bowel syndrome, characterized by functional abdominal pain (FAP). We evaluated the relation of sex, pain severity, and psychological stress to ANS function in adolescents/young adults from a database of pediatric FAP and control participants enrolled 8 years earlier in a prospective study of pain. At follow-up in adolescence/young adulthood (Mean age = 19.46, SD = 3.48), we classified participants as Pain-Remit (n = 130), Pain-Persist (n = 96), and pain-free controls (n = 123). We recorded electrocardiogram data at rest and during laboratory stressors. Results demonstrated significantly lower HRV in Pain-Persist females compared with Pain-Remit females, female controls, and all males regardless of pain category. Spectral analysis of electrocardiogram showed that Pain-Persist females had reduced power in the high frequency domain of cardiac activity, ie, reduced parasympathetic “braking” of sympathetic activity, both at rest and during stress. Pain-Remit females exhibited levels of autonomic imbalance intermediate between those of females with persistent FAP and all other participants. Parasympathetically mediated low HRV in young women with persistent FAP may reflect a peripheral mechanism (eg, gut dysfunction) or a central nervous system mechanism (eg, pain amplification or poor emotion self-regulation) involving prolonged sympathetic activation.
UPS-indel: a Universal Positioning System for Indels
Authors: Hasan Mohammad Shabbir , Wu Xiaowei , Watson Layne T. , Li Zhiyi , Zhang Liqing 
Published: May 2017

AbstractBackgroundIndels, though differing in allele sequence and position, are biologically equivalent when they lead to the same altered sequences. Storing biologically equivalent indels as distinct entries in databases causes data redundancy, and may mislead downstream analysis and interpretations. About 10% of the human indels stored in dbSNP are redundant. It is thus desirable to have a unified system for identifying and representing equivalent indels in publically available databases. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare indel calling results produced by different tools.ResultsUPS-indel identifies nearly 15% indels in dbSNP (version 142) as redundant across all human chromosomes, higher than previously reported. When applied to COSMIC coding and noncoding indel datasets, UPS-indel identifies nearly 29% and 13% indels as redundant, respectively. Comparing the performance of UPS-indel with existing variant normalization tools vt normalize, BCFtools, and GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly by these tools. Moreover, comparing UPS-indel to other state-of-the-art approaches for indel call set comparison demonstrates that UPS-indel is clearly superior to other approaches in finding indels in common among call sets.ConclusionsUPS-indel is theoretically proven to find all equivalent indels, and is thus exhaustive. UPS-indel is written in C++ and the command line version is freely available to download athttp://ups-indel.sourceforge.net. The online version of UPS-indel is available athttp://bench.cs.vt.edu/ups-indel/.
MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra
Authors: Liu Youzhong , Mrzic Aida , Meysman Pieter , Vijlder Thomas De , Romijn Edwin P. , Valkenborg Dirk , Bittremieux Wout , Laukens Kris 
Published: May 2017

AbstractDespite the increasing importance of non-targeted metabolomics to answer various life science questions, extracting biochemically relevant information from metabolomics spectral data is still an incompletely solved problem. Most computational tools to identify tandem mass spectra focus on a limited set of molecules of interest. However, such tools are typically constrained by the availability of reference spectra or molecular databases, limiting their applicability to identify unknown metabolites. In contrast, recent advances in the field illustrate the possibility to expose the underlying biochemistry without relying on metabolite identification, in particular via substructure prediction. We describe an automated method for substructure recommendation motivated by association rule mining. Our framework captures potential relationships between spectral features and substructures learned from public spectral libraries. These associations are used to recommend substructures for any unknown mass spectrum. Our method does not require any predefined metabolite candidates, and therefore it can be used for the partial identification of unknown unknowns. The method is called MESSAR (MEtabolite SubStructure Auto-Recommender) and is implemented in a free online web service available atmessar.biodatamining.be.Author SummaryMass spectrometry is one of most used techniques to detect and identify metabolites. However, learning metabolite structures directly from mass spectrometry data has always been a challenging task. Thousands of mass spectra from various biological systems still remain unanalyzed simply because no current bioinformatic tools are able to generate structural hypotheses. By manually studying mass spectra of standard compounds, chemists discovered that metabolites that share common substructures can also share spectral features. As data scientists, we believe that such relationships can be unraveled from massive structure and spectra data by machine learning. In this study, we adapted “association rule mining”, traditionally used in market basket analysis, to structural and spectral data, allowing us to investigate all spectral features - metabolite substructures relationships. We further collected all statistically sound relationships into a database and used them to assign substructral hypotheses to unexplored spectra. We named our approach MESSAR, MEtabolite SubStructure Auto-Recommender, available to the metabolomics and mass spectrometry community as a free and open web service.
Repetitive transcranial magnetic stimulation increases phase-amplitude coupling
Authors: Nakatani Chie , Mullin Caitlin , Wagemans Johan , Leeuwen Cees van 
Published: May 2017

AbstractA prominent feature of brain activity with relevance to cognitive processes is Phase-Amplitude Coupling (PAC) between slow and fast oscillatory signals. A newly developed neural mass model of cross-frequency coupling [1] predicts, counter-intuitively, that PAC shows sustained increases after repetitive Transcranial Magnetic Stimulation (rTMS). This is because rTMS leads to simultaneous neuronal firing in distinct regions, thereby enhancing the connectivity that, according to the model, is needed for PAC to be increased. We tested this prediction in healthy human volunteers. Two seconds of 10Hz rTMS were applied to the intraparietal sulcus, temporal-parietal junction, and lateral occipital complex. PAC in the subsequent electro-encephalogram was analyzed for two band pairs, theta-gamma and alpha-gamma, and compared to a sham condition. For all stimulation loci, PAC was higher in both band pairs after rTMS than in the sham condition. These results were found to be conform the model prediction. The perspective for using rTMS to modulate cross-band coupling is discussed.
Extinction rates in tumor public goods games
Authors: Gerlee Philip , Altrock Philipp M. 
Published: May 2017

AbstractCancer evolution and progression are shaped by cellular interactions and Darwinian selection. Evolutionary game theory incorporates both of these principles, and has been proposed as a framework to understand tumor cell population dynamics. A cornerstone of evolutionary dynamics is the replicator equation, which describes changes in the relative abundance of different cell types, and is able to predict evolutionary equilibria. Typically, the replicator equation focuses on differences in relative fitness. We here show that this framework might not be sufficient under all circumstances, as it neglects important aspects of population growth. Standard replicator dynamics might miss critical differences in the time it takes to reach an equilibrium, as this time also depends on cellular turnover in growing but bounded populations. As the system reaches a stable manifold, the time to reach equilibrium depends on cellular death and birth rates. These rates shape the timescales, in particular in co-evolutionary dynamics of growth factor producers and free-riders. Replicator dynamics might be an appropriate framework only when birth and death rates are of similar magnitude. Otherwise, population growth effects cannot be neglected when predicting the time to reach an equilibrium, and cell type specific rates have to be accounted for explicitly.