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Ying Cui, Wen Chen, Jinfeng Chi, Lei Wang
BACKGROUND The aim of this study was to compare the transcriptome between impaired fasting glucose (IFG) and type 2 diabetes mellitus (T2DM), and further research their molecular mechanisms. MATERIAL AND METHODS The original microarray GSE21321, including miRNA and mRNA expression profiles, was downloaded from the GEO database. Data preprocessing was processed by limma package, and differentially expressed genes (DGs) and miRNA (DMs) were screened. Then, the regulatory relationships among miRNA, TF, and genes were screened and the regulatory network was constructed...
December 1, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Riccardo Delli Ponti, Stefanie Marti, Alexandros Armaos, Gian Gaetano Tartaglia
Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database)...
November 28, 2016: Nucleic Acids Research
Siân E Davies, Megan Rhys, Sarah E Voss, Rosemary Greenwood, Matthew Thomas, Jonathan R Benger
OBJECTIVE: To characterise psychological wellbeing in survivors of out-of-hospital cardiac arrest (OHCA), and examine its relationship to cognitive function. PATIENTS: Forty-one highly functioning cardiac arrest survivors were drawn from the follow-up cohort of a randomised controlled trial of initial airway management in OHCA (ISRCTN:18528625). DESIGN: Psychological wellbeing was assessed with a self-report questionnaire (the Depression Anxiety and Stress Scale; DASS) and cognitive function was examined using the Delayed Matching to Samples (DMS) test from the Cambridge Neuropsychological Test Automated Battery (CANTAB)...
November 24, 2016: Resuscitation
Joshua G Dunn, Jonathan S Weissman
BACKGROUND: Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis...
November 22, 2016: BMC Genomics
Bijuan Chen, Zheng Deng, Wenmin Li, Moran Gao, Qingqing Liu, C Z Gu, F X Hu, B G Shen, Benjamin Frandsen, Sky Cheung, Liu Lian, Yasutomo J Uemura, Cui Ding, Shengli Guo, Fanlong Ning, Timothy J S Munsie, Murray Neff Wilson, Yipeng Cai, Graeme Luke, Zurab Guguchia, Shingo Yonezawa, Zhi Li, Changqing Jin
We report the discovery of a new fluoride-arsenide bulk diluted magnetic semiconductor (Ba,K)F(Zn,Mn)As with the tetragonal ZrCuSiAs-type structure which is identical to that of the "1111" iron-based superconductors. The joint hole doping via (Ba,K) substitution &spin doping via (Zn,Mn) substitution results in ferromagnetic order with Curie temperature up to 30 K and demonstrates that the ferromagnetic interactions between the localized spins are mediated by the carriers. Muon spin relaxation measurements confirm the intrinsic nature of the long range magnetic order in the entire volume in the ferromagnetic phase...
November 22, 2016: Scientific Reports
Qizhi Hu, Jai Prakash, Cristianne J F Rijcken, Wim E Hennink, Gert Storm
Covalent entrapment of drug molecules within core-crosslinked polymeric micelles (CCPM) represents an attractive approach to improve their therapeutic index. As an alternative to the most commonly employed intravenous (i.v.) route, subcutaneous (s.c.) administration offers the possibility of self-administration and thereby may reduce healthcare costs. The aim of this work was to assess the pharmacokinetic profile and systemic availability of drug-containing CCPM following s.c. injection. We here derivatised dexamethasone (DMS) with three different linkers, which enabled covalent attachment of this drug to the core of CCPM...
September 26, 2016: International Journal of Pharmaceutics
Qizhi Hu, Jai Prakash, Cristianne J F Rijcken, Wim E Hennink, Gert Storm
Covalent entrapment of drug molecules within core-crosslinked polymeric micelles (CCPM) represents an attractive approach to improve their therapeutic index. As an alternative to the most commonly employed intravenous (i.v.) route, subcutaneous (s.c.) administration offers the possibility of self-administration and thereby may reduce healthcare costs. The aim of this work was to assess the pharmacokinetic profile and systemic availability of drug-containing CCPM following s.c. injection. We here derivatised dexamethasone (DMS) with three different linkers, which enabled covalent attachment of this drug to the core of CCPM...
November 30, 2016: International Journal of Pharmaceutics
Jendai Richards, Henry Ato Ogoe, Wenzhi Li, Oguljahan Babayewa, Wei Xu, Tameka Bythwood, Minerva Garcia-Barrios, Li Ma, Qing Song
Vascular smooth muscle cell (VSMC) accumulation in the neointimal is a common feature in vascular diseases such as atherosclerosis, transplant arteriosclerosis and restenosis. In this study, we isolated the neointimal cells and uninjured residential vascular smooth muscle cells by laser micro dissection and carried out single-cell whole-genome methylation sequencing. We also sequenced the bisulfite converted genome of circulating bone-marrow-derived cells such as peripheral blood mononuclear cells (PBMC) and bone marrow mononuclear cells (BMMC)...
July 2016: Molecular Biology (Los Angeles, Calif.)
D Sevastos, E Kotsalos, A Koliadima
In the present work the evaporation retardation of SO2 and (CH3)2S (=DMS) from water by soluble surfactants was studied by the Reversed-Flow Gas Chromatography (R.F.G.C.) technique. Using suitable mathematical analysis, rate coefficients, kc, for the transfer of SO2 and DMS from pure or artificial sea water to the atmospheric environment were determined in the presence or the absence of surfactants. The efficiency of the three surfactants used (CTAB, TRITON X-100 and SDS) to retard the evaporation rate of SO2 and DMS from water was estimated by the decrease of the kc values in the presence of the three surfactants, compared to those in the absence of surfactants...
November 8, 2016: Science of the Total Environment
K P Divya, Ramshekhar N Menon, Ravi Prasad Varma, P N Sylaja, Bejoy Thomas, C Kesavadas, J Sunitha, V S Lekha, S Deepak
PURPOSE: To elucidate the cognitive profiles of post-stroke vascular mild cognitive impairment (VaMCI) in comparison to MCI of non-vascular etiology and cognitively normal healthy controls at a tertiary-care hospital in southern India. RESULTS: Logistic regression analysis adjusted for age and sex comparing VaMCI [N=50] with controls [N=27] revealed significant impairment in visual, verbal learning-recall and executive function scores. As compared to the MCI group [N=36], VaMCI had significantly higher scores on Weschler's Memory Scale (WMS) verbal subset delayed recall scores (p=0...
October 24, 2016: Journal of the Neurological Sciences
Woosuk Kim, Hee Sun Yim, Dae Young Yoo, Hyo Young Jung, Jong Whi Kim, Jung Hoon Choi, Yeo Sung Yoon, Dae Won Kim, In Koo Hwang
BACKGROUND: Cadmium leads to learning and memory impairment. Dendropanax morbifera Léveille stem extract (DMS) reduces cadmium-induced oxidative stress in the hippocampus. We investigated the effects of DMS on cadmium-induced impairments in memory in rats. METHODS: Cadmium (2 mg/kg), with or without DMS (100 mg/kg), was orally administered to 7-week-old Sprague-Dawley rats for 28 days. Galantamine (5 mg/kg), an acetylcholinesterase inhibitor, was intraperitoneally administered as a positive control...
November 9, 2016: BMC Complementary and Alternative Medicine
Pai-Shan Chen, Shu-Hua Chen, Jung-Hsuan Chen, Wan-Yun Haung, Hsin-Tung Liu, Po-Hsin Kong, Olivia Hsu-Yuan Yang
An advantage of differential mobility spectrometry (DMS) is it provides an orthogonal mechanism to mass spectrometry (MS). The DMS-MS/MS detects analytes in the gas phase on the basis of differences in ion mobility in low and high electric fields, which makes DMS-MS/MS an alternative to chromatographic separation-MS. One drawback of DMS is its limited resolution and sensitivity, especially for detecting small molecules when using a nonpolar inert gas as the carrier gas. The present work has evaluated the effects on peak capacity of adding chemical modifiers to inert carrier gases (nitrogen, helium, argon and carbon dioxide)...
November 23, 2016: Analytica Chimica Acta
Meghan Zubradt, Paromita Gupta, Sitara Persad, Alan M Lambowitz, Jonathan S Weissman, Silvi Rouskin
Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase...
November 7, 2016: Nature Methods
Sean B Ostlund, Angela T Liu, Kate M Wassum, Nigel T Maidment
The dorsomedial striatum (DMS) has been strongly implicated in flexible, outcome-based decision making, including the outcome-specific Pavlovian-to-instrumental transfer effect (PIT), which measures the tendency for a reward-predictive cue to preferentially motivate actions that have been associated with the predicted reward over actions associated with different rewards. Although the neurochemical underpinnings of this effect are not well understood, there is growing evidence that striatal acetylcholine signaling may play an important role...
November 4, 2016: European Journal of Neuroscience
Yuedong Yang, Xiaomei Li, Huiying Zhao, Jian Zhan, Jihua Wang, Yaoqi Zhou
As most RNA structures are elusive to structure determination, obtaining solvent accessible surface areas (ASA) of nucleotides in an RNA structure is an important first step to characterize potential functional sites and core structural regions. Here, we developed RNAsnap, the first machine-learning method trained on protein-bound RNA structures for solvent accessibility prediction. Built on sequence profiles from multiple sequence alignment (RNAsnap-prof), the method provided robust prediction in five-fold cross-validation and an independent test (Pearson correlation coefficients, r, between predicted and actual ASA values are 0...
November 2, 2016: RNA
Aimilia Gastounioti, Andrew Oustimov, Brad M Keller, Lauren Pantalone, Meng-Kang Hsieh, Emily F Conant, Despina Kontos
PURPOSE: With raw digital mammograms (DMs), which retain the relationship with x-ray attenuation of the breast tissue, not being routinely available, processed DMs are often the only viable means to acquire imaging measures. The authors investigate differences in quantitative measures of breast density and parenchymal texture, shown to have value in breast cancer risk assessment, between the two DM representations. METHODS: The authors report data from 8458 pairs of bilateral raw ("FOR PROCESSING") and processed ("FOR PRESENTATION") DMs acquired from 4278 women undergoing routine screening evaluation, collected with DM units from two different vendors...
November 2016: Medical Physics
Antonella Muscella, Carla Vetrugno, Luca Giulio Cossa, Giovanna Antonaci, Francesco De Nuccio, Sandra Angelica De Pascali, Francesco Paolo Fanizzi, Santo Marsigliante
Malignant pleural mesothelioma (MPM) is an aggressive malignancy highly resistant to chemotherapy. There is an urgent need for effective therapy inasmuch as resistance, intrinsic and acquired, to conventional therapies is common. Among Pt(II) antitumor drugs, [Pt(O,O'-acac)(γ-acac)(DMS)] (Ptac2S) has recently attracted considerable attention due to its strong in vitro and in vivo antiproliferative activity and reduced toxicity. The purpose of this study was to examine the efficacy of Ptac2S treatment in MPM...
2016: PloS One
Andrey Krokhotin, Anthony M Mustoe, Kevin M Weeks, Nikolay V Dokholyan
Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base pairing interactions. We recently introduced an approach for single-molecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP)...
November 1, 2016: RNA
Daniel J Peirano, Alberto Pasamontes, Cristina E Davis
Modern differential mobility spectrometers (DMS) produce complex and multi-dimensional data streams that allow for near-real-time or post-hoc chemical detection for a variety of applications. An active area of interest for this technology is metabolite monitoring for biological applications, and these data sets regularly have unique technical and data analysis end user requirements. While there are initial publications on how investigators have individually processed and analyzed their DMS metabolomic data, there are no user-ready commercial or open source software packages that are easily used for this purpose...
September 2016: International Journal for Ion Mobility Spectrometry
A V Sekridova, A M Varizhuk, O N Tatarinova, V V Severov, N A Barinov, I P Smirnov, V N Lazarev, D V Klinov, G E Pozmogova
In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome...
July 2016: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
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