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https://www.readbyqxmd.com/read/28641402/ec-tagging-allows-cell-type-specific-rna-analysis
#1
Naoki Hida, Mohamed Y Aboukilila, Dana A Burow, Rakesh Paul, Marc M Greenberg, Michael Fazio, Samantha Beasley, Robert C Spitale, Michael D Cleary
Purification of cell type-specific RNAs remains a significant challenge. One solution involves biosynthetic tagging of target RNAs. RNA tagging via incorporation of 4-thiouracil (TU) in cells expressing transgenic uracil phosphoribosyltransferase (UPRT), a method known as TU-tagging, has been used in multiple systems but can have limited specificity due to endogenous pathways of TU incorporation. Here, we describe an alternative method that requires the activity of two enzymes: cytosine deaminase (CD) and UPRT...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641399/compannotate-a-comparative-approach-to-annotate-base-pairing-interactions-in-rna-3d-structures
#2
Shahidul Islam, Ping Ge, Shaojie Zhang
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641392/alcohol-is-not-protective-against-mortality-following-traumatic-brain-injury
#3
Jennifer S Albrecht, Majid Afshar, Deborah M Stein, Gordon S Smith
Alcohol exposure results in reduced mortality following traumatic brain injury (TBI) in animal models, yet clinical studies reported conflicting results and clinical trials based on proposed mechanisms have been disappointing. Methodological issues common to many of the clinical studies may have contributed to spurious results. Our objective was to evaluate the association between blood alcohol concentration (BAC) and in-hospital mortality following TBI, overcoming methodological problems of prior studies. We conducted a retrospective cohort study on individuals treated for isolated TBI at the R Adams Cowley Shock Trauma Center between 1997-2012 (n = 1,084)...
June 21, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28641385/development-of-an-electronic-medical-record-based-child-physical-abuse-alert-system
#4
Rachel P Berger, Richard A Saladino, Janet Fromkin, Emily Heineman, Srinivasan Suresh, Tom McGinn
Objective: Physical abuse is a leading cause of pediatric morbidity and mortality. Physicians do not consistently screen for abuse, even in high-risk situations. Alerts in the electronic medical record may help improve screening rates, resulting in early identification and improved outcomes. Methods: Triggers to identify children < 2 years old at risk for physical abuse were coded into the electronic medical record at a freestanding pediatric hospital with a level 1 trauma center...
June 21, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28641384/acute-testosterone-deficiency-alters-adipose-tissue-fatty-acid-storage
#5
Sylvia Santosa, Nikki C Bush, Michael D Jensen
Context: Although the long-term effects of testosterone on adipose tissue lipid metabolism in men have been defined, the short-term regulation of these effects is not well understood. Objective: We examined the effects of acute testosterone withdrawal on subcutaneous abdominal and femoral adipose tissue fatty acid (FA) storage and cellular mechanisms. Design: This was a prospective, randomized trial. Setting: Mayo Clinic Clinical Research Unit...
June 21, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28641369/markers-of-inflammation-and-incident-breast-cancer-risk-in-the-women-s-health-study
#6
Deirdre K Tobias, Akintunde O Akinkuolie, Paulette D Chandler, Patrick R Lawler, JoAnn E Manson, Julie E Buring, Paul M Ridker, Lu Wang, I-Min Lee, Samia Mora
Chronic inflammation may be a risk factor for breast cancer development and progression, yet which inflammatory biomarkers and pathways are relevant is unknown. The study included 27,071 Women's Health Study participants (mean, 54.5 years old) free of cancer and cardiovascular disease at enrollment (1992 to 1995) with baseline measures of four inflammatory biomarkers: high sensitivity C-reactive protein (hsCRP), fibrinogen, N-acetyl side-chains of acute phase proteins (GlycA), and soluble intercellular adhesion molecule-1 (sICAM-1)...
June 21, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28641362/estimating-the-potential-cost-of-a-high-dose-immune-tolerance-induction-iti-therapy-relative-to-the-cost-of-a-combined-therapy-of-a-low-dose-iti-therapy-with-bypassing-agent-prophylaxis
#7
G Kenet, A Oladapo, J D Epstein, C Thompson, A Novack, D J Nugent
INTRODUCTION: The International Immune Tolerance Study (I-ITI) demonstrated comparable success rates between low (FVIII 50 IU/kg/TIW) and high dose (FVIII 200 IU/kg/day) regimens. While costlier, the high dose ITI regimen achieved shorter time-to-treatment success with fewer bleeding episodes compared to the low dose ITI regimen. Adding bypassing agent prophylaxis (BAP) to a low dose ITI regimen may reduce bleeding while still being less costly than high dose ITI. AIM AND METHODS: An economic model was developed to compare high dose ITI to low dose ITI with BAP...
June 22, 2017: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/28641312/impact-of-novel-mir-145-3p-regulatory-networks-on-survival-in-patients-with-castration-resistant-prostate-cancer
#8
Yusuke Goto, Akira Kurozumi, Takayuki Arai, Nijiro Nohata, Satoko Kojima, Atsushi Okato, Mayuko Kato, Kazuto Yamazaki, Yasuo Ishida, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
BACKGROUND: Despite recent advancements, metastatic castration-resistant prostate cancer (CRPC) is not considered curative. Novel approaches for identification of therapeutic targets of CRPC are needed. METHODS: Next-generation sequencing revealed 945-1248 miRNAs from each lethal mCRPC sample. We constructed miRNA expression signatures of CRPC by comparing the expression of miRNAs between CRPC and normal prostate tissue or hormone-sensitive prostate cancer (HSPC)...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28641308/detection-of-phosphatidylserine-positive-exosomes-for-the-diagnosis-of-early-stage-malignancies
#9
Raghava Sharma, Xianming Huang, Rolf A Brekken, Alan J Schroit
BACKGROUND: There has been increasing interest in the detection of tumour exosomes in blood for cancer diagnostics. Most studies have focussed on miRNA and protein signatures that are surrogate markers for specific tumour types. Because tumour cells and tumour-derived exosomes display phosphatidylserine (PS) in their outer membrane leaflet, we developed a highly sensitive ELISA-based system that detects picogram amounts of exosomal phospholipid in plasma as a cancer biomarker. METHODS: This report describes the development of a highly specific and sensitive ELISA for the capture of PS-expressing tumour exosomes in the blood of tumour-bearing mice...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28641297/factor-analysis-and-psychometric-properties-of-the-minnesota-nicotine-withdrawal-scale-and-the-minnesota-nicotine-withdrawal-scale-revised-italian-version
#10
Andrea Svicher, Agnese Beghè, Giacomo Mangiaracina, Fiammetta Cosci
BACKGROUND/AIMS: We run Exploratory and Confirmatory Factor Analyses of the Minnesota Nicotine Withdrawal Scale (MNWS) and of the MNWS-Revised (MNWS-R). Psychometric properties were also explored. METHODS: Adult Italian smokers, 366 in all, were assessed via the MNWS-R together with rating scales measuring cigarette dependence, alcohol use, anxiety sensitivity and negative affect at baseline and after 3 months. RESULTS: The MNWS showed good psychometric properties (α = 0...
June 23, 2017: European Addiction Research
https://www.readbyqxmd.com/read/28641286/effect-of-bexarotene-on-platelet-activation-and-apoptosis
#11
Hang Cao, Rosi Bissinger, Anja T Umbach, Meinrad Gawaz, Florian Lang
BACKGROUND/AIMS: The retinoid X receptor (RXRs) stimulator Bexarotene ((4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl] benzoic acid) is used for the treatment of several malignancies. Bexarotene is at least in part effective by stimulation of apoptosis of tumor cells. Moreover, Bexarotene triggers eryptosis, the suicidal death of erythrocytes. Similar to erythrocytes, blood platelets lack nuclei but are nevertheless able to enter an apoptosis-like phenotype, characterized by caspase activation, cell shrinkage and cell membrane scrambling with phospha-tidylserine translocation to the cell surface...
June 23, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28641282/health-related-genetic-direct-to-consumer-tests-in-the-german-setting-the-available-offer-and-the-potential-implications-for-a-solidarily-financed-health-care-system
#12
Marika Plöthner, Mike Klora, Daniel Rudolph, Johann-Matthias Graf von der Schulenburg
BACKGROUND: The global genetic direct-to-consumer (DTC) market will reach a volume of USD 230 billion in 2018. The expenditures for this genetic analysis are borne by the customer, whereas consequential costs may arise for a solidarily financed system. In a first step, it is essential to gain an overview of the currently available offer in the German setting. METHODS: In April 2016, we conducted a systematic internet search in the Google search engine. In November 2016, we updated the information of the webpages in terms of country, language, types of health-related tests, additional offer of non-health-related DTC test, information about sensitivity and specificity, certification and accreditation, costs as well as reference to German Act on Genetic Testing...
June 23, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28641251/robust-face-recognition-with-kernelized-locality-sensitive-group-sparsity-representation
#13
Shoubiao Tan, Xi Sun, Wentao Chan, Lei Qu, Ling Shao
In this paper, a novel joint sparse representation method is proposed for robust face recognition. We embed both group sparsity and kernelized locality-sensitive constraints into the framework of sparse representation. The group sparsity constraint is designed to utilize the grouped structure information in the training data. The local similarity between test and training data is measured in the kernel space instead of the Euclidian space. As a result, the embedded nonlinear information can be effectively captured, leading to a more discriminative representation...
June 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641249/eit-imaging-regularization-based-on-spectral-graph-wavelets
#14
Bo Gong, Benjamin Schullcke, Sabine Krueger-Ziolek, Marko Vauhkonen, Gerhard Wolf, Ullrich Mueller-Lisse, Knut Moeller
The objective of Electrical Impedance Tomographic reconstruction is to identify the distribution of tissue conductivity from electrical boundary conditions. This is an ill-posed inverse problem usually solved under the finite element method framework. In previous studies, standard sparse regularization was used for difference EIT to achieve a sparse solution. However, regarding element-wise sparsity, standard sparse regularization interferes with the smoothness of conductivity distribution between neighboring elements and is sensitive to noise...
June 16, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28641234/improved-boundary-segmentation-of-skin-lesions-in-high-frequency-3d-ultrasound
#15
B Sciolla, P Delachartre, L Cowell, T Dambry, B Guibert
In this article, we propose a segmentation algorithm for skin lesions in 3D high-frequency ultrasound images. The segmentation is done on melanoma and Basal-cell carcinoma tumors, the most common skin cancer types, and could be used for diagnosis and surgical excision planning in a clinical context. Compared with previously proposed algorithms, which tend to underestimate the size of the lesion, we propose two new boundary terms which provide significant improvements of the accuracy. The first is a probabilistic boundary expansion (PBE) term designed to broaden the segmented area at the boundaries, which uses the feature asymmetry criterion...
June 15, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28641217/the-aggressor-at-the-mirror-psychiatric-correlates-of-deliberate-self-harm-in-male-prison-inmates
#16
N Verdolini, A Murru, L Attademo, R Garinella, I Pacchiarotti, C Del Mar Bonnin, L Samalin, L Pauselli, M Piselli, A Tamantini, R Quartesan, A F Carvalho, E Vieta, A Tortorella
BACKGROUND: Deliberate self-harm (DSH) causes important concern in prison inmates as it worsens morbidity and increases the risk for suicide. The aim of the present study is to investigate the prevalence and correlates of DSH in a large sample of male prisoners. METHODS: A cross-sectional study evaluated male prisoners aged 18+ years. Current and lifetime psychiatric diagnoses were assessed with the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders - DSM-IV Axis I and Axis II Disorders and with the Addiction Severity Index-Expanded Version...
April 14, 2017: European Psychiatry: the Journal of the Association of European Psychiatrists
https://www.readbyqxmd.com/read/28641187/multi-criteria-decision-support-system-dss-for-optimal-locations-of-soil-aquifer-treatment-sat-facilities
#17
P Tsangaratos, A Kallioras, Th Pizpikis, E Vasileiou, I Ilia, F Pliakas
Managed Aquifer Recharge is a wide-spread well-established groundwater engineering method which is largely seen as sound and sustainable solution to water scarcity hydrologically sensitive areas, such as the Circum Mediterranean. The process of site selection for the installation of a MAR facility is of paramount importance for the feasibility and effectiveness of the project itself, especially when the facility will include the use of waters of impaired quality as a recharge source, as in the case of Soil-Aquifer-Treatment systems...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28641160/effects-of-hip-joint-centre-mislocation-on-gait-kinematics-of-children-with-cerebral-palsy-calculated-using-patient-specific-direct-and-inverse-kinematic-models
#18
Hans Kainz, Christopher P Carty, Sheanna Maine, Henry P J Walsh, David G Lloyd, Luca Modenese
Joint kinematics can be calculated by Direct Kinematics (DK), which is used in most clinical gait laboratories, or Inverse Kinematics (IK), which is mainly used for musculoskeletal research. In both approaches, joint centre locations are required to compute joint angles. The hip joint centre (HJC) in DK models can be estimated using predictive or functional methods, while in IK models can be obtained by scaling generic models. The aim of the current study was to systematically investigate the impact of HJC location errors on lower limb joint kinematics of a clinical population using DK and IK approaches...
June 4, 2017: Gait & Posture
https://www.readbyqxmd.com/read/28641145/lack-of-association-between-deletion-polymorphism-of-bim-gene-and-in-vitro-drug-sensitivity-in-b-cell-precursor-acute-lymphoblastic-leukemia
#19
Meixian Huang, Kunio Miyake, Keiko Kagami, Masako Abe, Tamao Shinohara, Atsushi Watanabe, Shinpei Somazu, Hiroko Oshiro, Kumiko Goi, Hiroaki Goto, Masayoshi Minegishi, Shotaro Iwamoto, Nobutaka Kiyokawa, Kanji Sugita, Takeshi Inukai
A deletion polymorphism in the BIM gene was identified as an intrinsic mechanism for resistance to tyrosine kinase inhibitor in chronic myeloid leukemia patients in East Asia. BIM is also involved in the responses to glucocorticoid and chemotherapy in acute lymphoblastic leukemia (ALL), suggesting a possible association between deletion polymorphism of BIM and the chemosensitivity of ALL. Thus, we analyzed 72 B-cell precursor (BCP)-ALL cell lines established from Japanese patients. Indeed, higher BIM gene expression was associated with good in vitro sensitivities to glucocorticoid and chemotherapeutic agents used in induction therapy...
June 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28641137/real-time-pcr-methods-for-the-detection-of-blown-pack-spoilage-causing-clostridium-species-c-estertheticum-c-gasigenes-and-c-ruminantium
#20
Rachael Reid, Catherine M Burgess, Evonne McCabe, Séamus Fanning, Paul Whyte, Joe Kerry, Declan Bolton
A set of real-time PCR methods for the detection of C. estertheticum, C. gasigenes and C. ruminantium, the causative agents of blown pack spoilage (BPS) in vacuum packaged beef, was developed. Robust validation of the sensitivity and specificity was carried out in the three matrices (beef meat drip, wet environmental swabs and dry environmental swabs) as encountered in our testing laboratory and against Clostridium strains (n=76) and non-Clostridium strains (n=36). It was possible to detect 4-5 spores per ml for C...
June 3, 2017: Meat Science
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