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https://www.readbyqxmd.com/read/28220888/mintmap-fast-and-exhaustive-profiling-of-nuclear-and-mitochondrial-trna-fragments-from-short-rna-seq-data
#1
Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos
Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28176266/effects-on-the-torsional-vibration-behavior-in-the-investigation-of-dental-implant-osseointegration-using-resonance-frequency-analysis-a-numerical-approach
#2
Min Zhai, Bing Li, Dehua Li
Resonance frequency analysis (RFA) methods are widely used to assess implant stability, particularly the Osstell(®) device. The potential effects associated with this method have been discussed in the literature. Torsional RFA (T-RFA), mentioned in our previous study, could represent a new measurement method. The purpose of this study was to simulate T-shaped and Osstell(®) transducer-implant-bone system models; compare their vibration modes and corresponding resonance frequencies; and investigate the effects of their parameters, such as the effective implant length (EIL), bone quality, and osseointegration level, on the torsional resonance frequency (TRF) and bending resonance frequency (BRF) using three-dimensional finite element analysis...
February 7, 2017: Medical & Biological Engineering & Computing
https://www.readbyqxmd.com/read/28167310/change-trajectories-of-aggressive-behavior-among-children-in-long-term-residential-care
#3
Shalhevet Attar-Schwartz, Rami Benbenishty, Ilan Roziner
This study examined change trajectories of aggressive behaviors among children in long-term residential care in Israel and identified various child-, family-, and placement-related predictors of the change trajectories. Records of 799 children (average age at the beginning of the four years=10.4, 33.1% female) in their first four consecutive years in care were analyzed using the TRF aggressive behavior subscale (Achenbach, 1991) to measure the outcome variable. Children's and parents' characteristics and placement-related factors were used to explain variance in change trajectories...
February 3, 2017: Child Abuse & Neglect
https://www.readbyqxmd.com/read/28133587/non-radioactive-trf-assay-modifications-to-improve-telomeric-dna-detection-efficiency-in-plants
#4
Liliia R Nigmatullina, Margarita R Sharipova, Eugene V Shakirov
The length of telomeric DNA is often considered a cellular biomarker of aging and general health status. Several telomere length measuring assays have been developed, of which the most common is the Telomere Restriction Fragment (TRF) analysis, which typically involves the use of radioactively labeled oligonucleotide probes. While highly effective, this method potentially poses substantial health concerns and generates radioactive waste. Digoxigenin (DIG) alternatives to radioactive probes have been developed and used successfully in a number of assays...
December 2016: BioNanoScience
https://www.readbyqxmd.com/read/28129920/sex-dependent-telomere-shortening-telomerase-activity-and-oxidative-damage-in-marine-medaka-oryzias-melastigma-during-aging
#5
Bill Wp Yip, Helen Ol Mok, Drew R Peterson, Miles T Wan, Y Taniguchi, Wei Ge, Doris Wt Au
Marine medaka Oryzias melastigma at 4months (young), 8months (middle-aged) and 12months old (senior) were employed to determine age-associated change of sex ratios, sex hormones, telomere length (TL), telomerase activity (TA), telomerase transcription (omTERT) and oxidative damage in the liver. Overall, O. melastigma exhibited gradual senescence, sex differences in longevity (F>M), TL (F>M) and oxidative damage (F<M) during aging. In females, the plasma E2 level was positively correlated with TL (TRF>5kb), TA and omTERT expression (p≤0...
January 24, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28128550/an-ultrasensitive-sensing-material-based-on-opal-photonic-crystal-for-label-free-monitoring-of-transferrin
#6
Enqi Wu, Yuan Peng, Xihao Zhang, Jialei Bai, Yanqiu Song, Houluo He, Longxing Fan, Xiaochen Qu, Zhixian Gao, Ying Liu, Baoan Ning
A new opal photonic crystal (PC) sensing material, allowing label-free detection of transferrin (TRF) is proposed in the current study. This photonic crystal was prepared via a vertical convective self-assembly method with monodisperse microspheres polymerized by methyl methacrylate (MMA) and 3-acrylamidophenylboronic acid (AAPBA). FTIR, TG and DLS were used to characterize the components and particle size of the monodisperse microspheres. SEM was used to observe the morphology of the PC. The diffraction peaks intensity decreases as the TRF concentration increase...
January 27, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28124217/elemental-analysis-of-whole-and-protein-separated-blood-serum-of-patients-with-systemic-lupus-erythematosus-and-sj%C3%A3-gren-s-syndrome
#7
Csilla Noémi Tóth, Edina Baranyai, István Csípő, Tünde Tarr, Margit Zeher, József Posta, István Fábián
Systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS) are systemic autoimmune diseases with complex symptoms and pathogenesis that are still not completely understood. Several studies showed that the trace element homeostasis and also the levels of antioxidant plasma proteins are changed in autoimmune disorders; however, these results are controversial. In this study, the potassium (K), calcium (Ca), magnesium (Mg), copper (Cu), zinc (Zn), and iron (Fe) concentrations of the serum and proteins-immunoglobulin G (IgG), transferrin (Trf), albumin (Alb), and ceruloplasmin (Cp)-separated from serum samples by affinity chromatography were determined in patients with SLE and SS...
January 26, 2017: Biological Trace Element Research
https://www.readbyqxmd.com/read/28113290/dynamic-estimation-of-the-auditory-temporal-response-function-from-meg-in-competing-speaker-environments
#8
Sahar Akram, Jonathan Z Simon, Behtash Babadi
OBJECTIVE: A central problem in computational neuroscience is to characterize brain function using neural activity recorded from the brain in response to sensory inputs with statistical confidence. Most of existing estimation techniques, such as those based on reverse correlation, exhibit two main limitations: first, they are unable to produce dynamic estimates of the neural activity at a resolution comparable with that of the recorded data, and second, they often require heavy averaging across time as well as multiple trials in order to construct statistical confidence intervals for a precise interpretation of data...
November 15, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28109577/traditional-cardiovascular-risk-factors-or-inflammation-which-factors-accelerate-atherosclerosis-in-arthritis-patients
#9
A Dalbeni, A Giollo, A Tagetti, S Atanasio, G Orsolini, G Cioffi, F Ognibeni, M Rossini, P Minuz, C Fava, O Viapiana
: Patients with chronic inflammatory arthritis experience an increased incidence of cardiovascular (CV) events. In addition to visualizing atherosclerotic plaques, ultrasound examinations (USs) of the carotid arteries permit the measurement of subclinical markers of atherosclerosis, such as intima-media thickness (cIMT) and carotid segmental distensibility (cDC). The aims of the study were to identify the determinants of atherosclerosis acceleration (plaques, cIMT and cDC) in a sample of patients suffering from chronic arthritis and to compare these patients with a control group of people with ≤1 traditional risk factor (TRF) for CV disease...
January 14, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28091348/effects-of-intermittent-fasting-on-glucose-and-lipid-metabolism
#10
Rona Antoni, Kelly L Johnston, Adam L Collins, M Denise Robertson
Two intermittent fasting variants, intermittent energy restriction (IER) and time-restricted feeding (TRF), have received considerable interest as strategies for weight-management and/or improving metabolic health. With these strategies, the pattern of energy restriction and/or timing of food intake are altered so that individuals undergo frequently repeated periods of fasting. This review provides a commentary on the rodent and human literature, specifically focusing on the effects of IER and TRF on glucose and lipid metabolism...
January 16, 2017: Proceedings of the Nutrition Society
https://www.readbyqxmd.com/read/28053348/glucocorticoid-receptor-control-of-transcription-precision-and-plasticity-via-allostery
#11
REVIEW
Emily R Weikum, Matthew T Knuesel, Eric A Ortlund, Keith R Yamamoto
The glucocorticoid receptor (GR) is a constitutively expressed transcriptional regulatory factor (TRF) that controls many distinct gene networks, each uniquely determined by particular cellular and physiological contexts. The precision of GR-mediated responses seems to depend on combinatorial, context-specific assembly of GR-nucleated transcription regulatory complexes at genomic response elements. In turn, evidence suggests that context-driven plasticity is conferred by the integration of multiple signals, each serving as an allosteric effector of GR conformation, a key determinant of regulatory complex composition and activity...
March 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/27936807/trna-derived-rna-fragments-associate-with-human-multisynthetase-complex-msc-and-modulate-ribosomal-protein-translation
#12
Simon P Keam, Andrew Sobala, Sara Ten Have, Gyorgy Hutvagner
The functionality of small RNAs from abundant species of "housekeeping" noncoding RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, etc.) remains a highly studied topic. The current state of research on short RNAs derived from transfer RNA (tRNA), called tRNA-derived fragments (tRFs), has been restricted largely to expression studies and limited functional studies. 5' tRFs are known translational inhibitors in mammalian cells, yet little is known about their functionality. Here we report on the first experimental evidence of the tRF protein interactome, identifying the mammalian multisynthetase complex as the primary interactor of the 5' tRF Gln19...
December 12, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27919235/geographical-distribution-of-typhoid-risk-factors-in-low-and-middle-income-countries
#13
Jung-Seok Lee, Vijayalaxmi V Mogasale, Vittal Mogasale, Kangsung Lee
BACKGROUND: While the global burden of typhoid fever has been often brought up for attention, the detailed surveillance information has only been available for the limited number of countries. As more efficacious vaccines will be available in the near future, it is essential to understand the geographically diverse patterns of typhoid risk levels and to prioritize the right populations for vaccination to effectively control the disease. METHODS: A composite index called the typhoid risk factor (TRF) index was created based on data with the Global Positioning System (GPS)...
December 5, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27906949/pulsed-compared-to-thermal-radiofrequency-to-the-medial-calcaneal-nerve-for-management-of-chronic-refractory-plantar-fasciitis-a-prospective-comparative-study
#14
Ayman M Osman, Dina H El-Hammady, Mohamed M Kotb
BACKGROUND: Radiofrequency (RF) treatment is a minimally invasive procedure that has been used for more than 3 decades in treating various chronic pain syndromes. Conventional (continuous) RF treatment occasionally results in worsening or even initiating a new type of pain. The use of pulsed radiofrequency (PRF), which has a non- or minimally neurodestructive neuromodulatory effect, serves as an alternative to conventional RF therapy in many medical situations. OBJECTIVES: To evaluate the effect of applying PRF for 6 minutes vs...
November 2016: Pain Physician
https://www.readbyqxmd.com/read/27899576/the-nuclear-and-organellar-trna-derived-rna-fragment-population-in-arabidopsis-thaliana-is-highly-dynamic
#15
Valérie Cognat, Geoffrey Morelle, Cyrille Megel, Stéphanie Lalande, Jean Molinier, Timothée Vincent, Ian Small, Anne-Marie Duchêne, Laurence Maréchal-Drouard
In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27892839/influence-of-adhesive-type-and-placement-technique-on-postoperative-sensitivity-in-posterior-composite-restorations
#16
Trf Costa, M Rezende, A Sakamoto, B Bittencourt, P Dalzochio, A D Loguercio, A Reis
PURPOSE: This double blind, randomized clinical trial compared the postoperative sensitivity of the placement technique (incremental and bulk fill) in posterior composite resin restorations bonded with two different adhesive strategies (self-etch and etch-and-rinse). METHODS: Posterior dental cavities of 72 participants (n=236), with a cavity depth of at least 3 mm, were randomly divided into four groups. The restorations were bonded using either the etch-and-rinse Tetric N-Bond (Ivoclar Vivadent) or the self-etch Tetric N-Bond SE (Ivoclar Vivadent)...
November 28, 2016: Operative Dentistry
https://www.readbyqxmd.com/read/27892771/a-trna-derived-fragment-competes-with-mrna-for-ribosome-binding-and-regulates-translation-during-stress
#17
Jennifer Gebetsberger, Leander Wyss, Anna M Mleczko, Julia Reuther, Norbert Polacek
Posttranscriptional processing of RNA molecules is a common strategy to enlarge the structural and functional repertoire of RNomes observed in all three domains of life. Fragmentation of RNA molecules of basically all functional classes has been reported to yield smaller non-protein coding RNAs (ncRNAs) that typically possess different roles compared to their parental transcripts. Here we show that a valine tRNA-derived fragment (Val-tRF) that is produced under certain stress conditions in the halophilic archaeon Haloferax volcanii is capable of binding to the small ribosomal subunit...
November 28, 2016: RNA Biology
https://www.readbyqxmd.com/read/27875129/dynamic-estimation-of-the-auditory-temporal-response-function-from-meg-in-competing-speaker-environments
#18
Sahar Akram, Jonathan Z Simon, Behtash Babadi
OBJECTIVE: A central problem in computational neuroscience is to characterize brain function using neural activity recorded from the brain in response to sensory inputs with statistical confidence. Most of existing estimation techniques, such as those based on reverse correlation, exhibit two main limitations: first, they are unable to produce dynamic estimates of the neural activity at a resolution comparable with that of the recorded data, and second, they often require heavy averaging across time as well as multiple trials in order to construct statistical confidence intervals for a precise interpretation of data...
November 15, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27836746/trf2-recruits-orc-through-trfh-domain-dimerization
#19
Mitsunori Higa, Tatsunori Kushiyama, Seiichiro Kurashige, Daisuke Kohmon, Kouki Enokitani, Satoko Iwahori, Nozomi Sugimoto, Kazumasa Yoshida, Masatoshi Fujita
Telomeres are specialized chromatin structures that prevent the degradation and instability of the ends of linear chromosomes. While telomerase maintains long stretches of the telomeric repeat, the majority of telomeric DNA is duplicated by conventional DNA replication. A fundamental step in eukaryotic DNA replication involves chromatin binding of the origin recognition complex (ORC). In human cells, telomeric repeat binding factor 2 (TRF2) is thought to play a role in the recruitment of ORC onto telomeres...
January 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27832862/time-restricted-feeding-improves-insulin-resistance-and-hepatic-steatosis-in-a-mouse-model-of-postmenopausal-obesity
#20
Heekyung Chung, Winjet Chou, Dorothy D Sears, Ruth E Patterson, Nicholas J G Webster, Lesley G Ellies
BACKGROUND: Menopause is associated with significant hormonal changes that result in increased total body fat and abdominal fat, amplifying the risk for metabolic syndrome and diseases such as diabetes, cardiovascular disease and cancer in postmenopausal women. Intermittent fasting regimens hold significant health benefit promise for obese humans, however, regimens that include extreme daytime calorie restriction or daytime fasting are generally associated with hunger and irritability, hampering long-term compliance and adoption in the clinical setting...
December 2016: Metabolism: Clinical and Experimental
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