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https://www.readbyqxmd.com/read/28734826/biophysical-constraints-arising-from-compositional-context-in-synthetic-gene-networks
#1
Enoch Yeung, Aaron J Dy, Kyle B Martin, Andrew H Ng, Domitilla Del Vecchio, James L Beck, James J Collins, Richard M Murray
Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes...
July 18, 2017: Cell Systems
https://www.readbyqxmd.com/read/28734549/habitual-versus-goal-driven-attention
#2
REVIEW
Yuhong V Jiang
Recent research has expanded the list of factors that control spatial attention. Beside current goals and perceptual salience, statistical learning, reward, motivation and emotion also affect attention. But do these various factors influence spatial attention in the same manner, as suggested by the integrated framework of attention, or do they target different aspects of spatial attention? Here I present evidence that the control of attention may be implemented in two ways. Whereas current goals typically modulate where in space attention is prioritized, search habits affect how one moves attention in space...
July 4, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/28733282/differentiating-botulinum-neurotoxin-producing-clostridia-with-a-simple-multiplex-pcr-assay
#3
Charles H D Williamson, Adam J Vazquez, Karen Hill, Theresa J Smith, Roxanne Nottingham, Nathan E Stone, Colin J Sobek, Jill H Cocking, Rafael A Fernández, Patricia A Caballero, Owen P Leiser, Paul Keim, Jason W Sahl
Diverse members of the genus clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum Groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This study introduces a multiplex polymerase chain reaction (PCR) assay for differentiating members of C. botulinum Group I, C...
July 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28733087/unobtrusive-assessment-of-neonatal-sleep-state-based-on-heart-rate-variability-retrieved-from-electrocardiography-used-for-regular-patient-monitoring
#4
Jan Werth, Xi Long, Elly Zwartkruis-Pelgrim, Hendrik Niemarkt, Wei Chen, Ronald M Aarts, Peter Andriessen
As an approach of unobtrusive assessment of neonatal sleep state we aimed at an automated sleep state coding based only on heart rate variability obtained from electrocardiography used for regular patient monitoring. We analyzed active and quiet sleep states of preterm infants between 30 and 37weeks postmenstrual age. To determine the sleep states we used a nonlinear kernel support vector machine for sleep state separation based on known heart rate variability features. We used unweighted and weighted misclassification penalties for the imbalanced distribution between sleep states...
July 18, 2017: Early Human Development
https://www.readbyqxmd.com/read/28731893/validity-of-administrative-data-in-identifying-cancer-related-events-in-adolescents-and-young-adults-a-population-based-study-using-the-impact-cohort
#5
Sumit Gupta, Paul C Nathan, Nancy N Baxter, Cindy Lau, Corinne Daly, Jason D Pole
BACKGROUND: Despite the importance of estimating population level cancer outcomes, most registries do not collect critical events such as relapse. Attempts to use health administrative data to identify these events have focused on older adults and have been mostly unsuccessful. We developed and tested administrative data-based algorithms in a population-based cohort of adolescents and young adults with cancer. METHODS: We identified all Ontario adolescents and young adults 15-21 years old diagnosed with leukemia, lymphoma, sarcoma, or testicular cancer between 1992-2012...
July 20, 2017: Medical Care
https://www.readbyqxmd.com/read/28730685/tex15-a-dna-repair-gene-associated-with-prostate-cancer-risk-in-han-chinese
#6
Xiaoling Lin, Zhongzhong Chen, Peng Gao, Zhimei Gao, Haitao Chen, Jun Qi, Fang Liu, Dingwei Ye, Haowen Jiang, Rong Na, Hongjie Yu, Rong Shi, Daru Lu, Siqun Lilly Zheng, Zengnan Mo, Yinghao Sun, Qiang Ding, Jianfeng Xu
BACKGROUND: Both common and rare genetic variants may contribute to risk of developing prostate cancer. Genome-wide association studies (GWASs) have identified ∼100 independent, common variants associated with prostate cancer risk. However, little is known about the association of rare variants (minor allele frequency [MAF] <1%) in the genome with prostate cancer risk. METHODS: A two-stage study was used to test the association of rare, deleterious coding variants, annotated using predictive algorithms, with prostate cancer risk in Chinese men...
July 21, 2017: Prostate
https://www.readbyqxmd.com/read/28730284/a-novel-interplay-between-hotair-and-dna-methylation-in-osteosarcoma-cells-indicates-a-new-therapeutic-strategy
#7
Xingang Li, Hongming Lu, Guilian Fan, Miao He, Yu Sun, Kai Xu, Fengjun Shi
PURPOSE: Osteosarcoma (OS) is one of the most prevalent primary malignant bone tumors in adolescent. HOTAIR is highly expressed and associated with the epigenetic modifications, especially DNA methylation, in cancer. However, the regulation mechanism between HOTAIR and DNA methylation and the biological effects of them in the pathogenesis of osteosarcoma remains elusive. METHOD: Through RNA-sequencing and computational analysis, followed by a variety of experimental validations, we report a novel interplay between HOTAIR, miR-126, and DNA methylation in OS...
July 20, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28729236/adolescents-perspectives-on-personalized-e-feedback-in-the-context-of-health-risk-behavior-screening-for-primary-care-qualitative-study
#8
Garret G Zieve, Laura P Richardson, Katherine Katzman, Heather Spielvogle, Sandy Whitehouse, Carolyn A McCarty
BACKGROUND: Electronic health screening tools for primary care present an opportunity to go beyond data collection to provide education and feedback to adolescents in order to motivate behavior change. However, there is limited research to guide feedback message development. OBJECTIVE: The aim of this study was to explore youth perceptions of and preferences for receiving personalized feedback for multiple health risk behaviors and reinforcement for health promoting behaviors from an electronic health screening tool for primary care settings, using qualitative methodology...
July 20, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28728070/feasibility-study-for-wax-deposition-imaging-in-oil-pipelines-by-pgnaa-technique
#9
Can Cheng, Wenbao Jia, Daqian Hei, Zhiyong Wei, Hongtao Wang
Wax deposition in pipelines is a crucial problem in the oil industry. A method based on the prompt gamma-ray neutron activation analysis technique was applied to reconstruct the image of wax deposition in oil pipelines. The 2.223MeV hydrogen capture gamma rays were used to reconstruct the wax deposition image. To validate the method, both MCNP simulation and experiments were performed for wax deposited with a maximum thickness of 20cm. The performance of the method was simulated using the MCNP code. The experiment was conducted with a (252)Cf neutron source and a LaBr3: Ce detector...
July 11, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28726721/identification-and-validation-of-new-alleles-of-falsiflora-and-compound-inflorescence-genes-controlling-the-number-of-branches-in-tomato-inflorescence
#10
Huan Zheng, Saneyuki Kawabata
The architecture of inflorescences shows extensive diversity in both branching frequency and flower number, which eventually, determines agricultural productivity. In this study, F₂ (second filial) populations derived from a cross between Solanum lycopersicum 10AS111A (highly-branched inflorescence) and the S. pimpinellifolium PI124039 (inflorescence having a single branch) were used to decipher the genetic control of branch number (BN) of inflorescence in plants bearing small-sized tomato fruits. The segregation ratio of single- and moderately-branched types to the highly-branched type was significantly different from 3:1 but not different from 15:1 at p < 0...
July 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28722290/development-of-a-cardiovascular-diseases-risk-prediction-model-and-tools-for-chinese-patients-with-type-2-diabetes-mellitus-a-population-based-retrospective-cohort-study
#11
Eric Yuk Fai Wan, Daniel Yee Tak Fong, Colman Siu Cheung Fung, Esther Yee Tak Yu, Weng Yee Chin, Anca Ka Chun Chan, Cindy Lo Kuen Lam
AIMS: Evidence-based cardiovascular diseases(CVD) risk prediction models and tools specific for Chinese patients with type 2 diabetes mellitus(T2DM) are currently unavailable. This study aimed to develop and validate a CVD risk prediction model for Chinese T2DM patients. MATERIALS AND METHODS: A retrospective cohort study was conducted on 137 935 Chinese patients aged 18-79 years with T2DM and without prior history of CVD, who had received public primary care services between 1 January 2010 and 31 December 2010...
July 19, 2017: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/28721517/vision-for-action-and-perception-elicit-dissociable-adherence-to-weber-s-law-across-a-range-of-graspable-target-objects
#12
Matthew Heath, Joseph Manzone, Michaela Khan, Shirin Davarpanah Jazi
A number of studies have reported that grasps and manual estimations of differently sized target objects (e.g., 20 through 70 mm) violate and adhere to Weber's law, respectively (e.g., Ganel et al. 2008a, Curr Biol 18:R599-R601)-a result interpreted as evidence that separate visual codes support actions (i.e., absolute) and perceptions (i.e., relative). More recent work employing a broader range of target objects (i.e., 5 through 120 mm) has laid question to this claim and proposed that grasps for 'larger' target objects (i...
July 18, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
https://www.readbyqxmd.com/read/28719649/differential-expression-of-small-rna-pathway-genes-associated-with-the-biomphalaria-glabrata-schistosoma-mansoni-interaction
#13
Fábio Ribeiro Queiroz, Luciana Maria Silva, Wander de Jesus Jeremias, Élio Hideo Babá, Roberta Lima Caldeira, Paulo Marcos Zech Coelho, Matheus de Souza Gomes
The World Health Organization (WHO) estimates that approximately 240 million people in 78 countries require treatment for schistosomiasis, an endemic disease caused by trematodes of the genus Schistosoma. In Brazil, Schistosoma mansoni is the only species representative of the genus whose passage through an invertebrate host, snails of the genus Biomphalaria, is obligatory before infecting a mammalian host, including humans. The availability of the genome and transcriptome of B. glabrata makes studying the regulation of gene expression, particularly the regulation of miRNA and piRNA processing pathway genes, possible...
2017: PloS One
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#14
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28718867/-defeated-by-life-validation-of-a-german-version-of-the-defeat-scale-ds-d
#15
Thomas Forkmann, Jana-Sophie Stenzel, Dajana Rath, Heide Glaesmer, Tobias Teismann
Introduction Defeat and entrapment are transdiagnostic constructs that play an important role in the development of depression, anxiety, suicidality and trauma-associated mental disorders. The present study aimed at presenting and validating a first German version of the Defeat-Scale (DS-d). Material and methods Through a web-based survey, N=480 participants were recruited (74% female; MAge=28.5, SDAge=11.1, Range: 18-80 years); 14.2% reported to currently suffer from a mental disorder, 8.5% reported at least one lifetime suicide attempt...
June 29, 2017: Psychotherapie, Psychosomatik, Medizinische Psychologie
https://www.readbyqxmd.com/read/28718770/benchmarking-gate-geant4-for-sup-16-sup-o-ion-beam-therapy
#16
Andreas Franz Resch, Hermann Fuchs, Dietmar Georg
Oxygen (<sup>16</sup>O) ions are a potential alternative to carbon ions in ion beam therapy. Their enhanced linear energy transfer indicates a higher relative biological effectiveness and a reduced oxygen enhancement ratio. Due to the limited availability of <sup>16</sup>O ion beams, Monte Carlo (MC) transport codes are important research tools to investigate their potential. The purpose of this study was to validate GATE/Geant4 for <sup>16</sup>O ion beam therapy on experimental data from literature...
July 18, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28718160/validity-of-claims-data-for-the-identification-of-male-infertility
#17
REVIEW
Yash S Khandwala, Chiyuan A Zhang, Shufeng Li, Mark R Cullen, Michael L Eisenberg
PURPOSE OF REVIEW: We sought to determine whether infertile men can accurately be identified within a large insurance claims database to validate its use for reproductive health research. RECENT FINDINGS: Prior literature suggests that men coded for infertility are at higher risk for chronic disease though it was previously unclear if these diagnostic codes correlated with true infertility. We found that the specificity of one International Classification of Disease (9th edition) code in predicting abnormal semen parameters was 92...
September 2017: Current Urology Reports
https://www.readbyqxmd.com/read/28717724/validation-and-quality-assessment-of-the-kilimanjaro-cancer-registry
#18
Leah L Zullig, Kristin Schroeder, Pilli Nyindo, Theresia Namwai, Elvis Silayo, Angelah Msomba, Michael Oresto Munishi, Francis Karia, Charles Muiruri, John Bartlett, Venance Maro, S Yousuf Zafar
PURPOSE: Global cancer burden has increasingly shifted to low- and middle-income countries and is particularly pronounced in Africa. There remains a lack of comprehensive cancer information as a result of limited cancer registry development. In Moshi, Tanzania, a regional cancer registry exists at Kilimanjaro Christian Medical Center. Data quality is unknown. Our objective was to evaluate the completeness and quality of the Kilimanjaro Cancer Registry (KCR). METHODS: In October 2015, we conducted a retrospective review of KCR by validating the internal consistency of registry records with medical and pathology records...
December 2016: Journal of Global Oncology
https://www.readbyqxmd.com/read/28716741/inferring-the-shallow-phylogeny-of-true-salamanders-salamandra-by-multiple-phylogenomic-approaches
#19
Ariel Rodríguez, James D Burgon, Mariana Lyra, Iker Irisarri, Denis Baurain, Leon Blaustein, Bayram Göcmen, Sven Künzel, Barbara Mable, Arne W Nolte, Michael Veith, Sebastian Steinfartz, Kathryn R Elmer, Hervé Philippe, Miguel Vences
The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduce the risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra. a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity...
July 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28716126/the-effects-of-potato-virus-y-derived-virus-small-interfering-rnas-of-three-biologically-distinct-strains-on-potato-solanum-tuberosum-transcriptome
#20
Lindani Moyo, Shunmugiah V Ramesh, Madhu Kappagantu, Neena Mitter, Vidyasagar Sathuvalli, Hanu R Pappu
BACKGROUND: Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions...
July 17, 2017: Virology Journal
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