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Sora Yoon, Hai C T Nguyen, Yun J Yoo, Jinhwan Kim, Bukyung Baik, Sounkou Kim, Jin Kim, Sangsoo Kim, Dougu Nam
Pathway-based analysis in genome-wide association study (GWAS) is being widely used to uncover novel multi-genic functional associations. Many of these pathway-based methods have been used to test the enrichment of the associated genes in the pathways, but exhibited low powers and were highly affected by free parameters. We present the novel method and software GSA-SNP2 for pathway enrichment analysis of GWAS P-value data. GSA-SNP2 provides high power, decent type I error control and fast computation by incorporating the random set model and SNP-count adjusted gene score...
March 19, 2018: Nucleic Acids Research
Manami Yamashita, Shin-Ya Kawaguchi, Tetsuya Hori, Tomoyuki Takahashi
Synaptic efficacy plays crucial roles in neuronal circuit operation and synaptic plasticity. Presynaptic determinants of synaptic efficacy are neurotransmitter content in synaptic vesicles and the number of vesicles undergoing exocytosis at a time. Bursts of presynaptic firings depress synaptic efficacy, mainly due to depletion of releasable vesicles, whereas recovery from strong depression is initiated by endocytic vesicle retrieval followed by refilling of vesicles with neurotransmitter. We washed out presynaptic cytosolic GABA to induce a rundown of IPSCs at cerebellar inhibitory cell pairs in slices from rats and then allowed fast recovery by elevating GABA concentration using photo-uncaging...
March 20, 2018: Cell Reports
Martin Köhler, Christoph Neff, Camilo Perez, Cyrill Brunner, Els Pardon, Jan Steyaert, Gisbert Schneider, Kaspar P Locher, Renato Zenobi
The application of nanobodies as binding partners for structure stabilization in protein x-ray crystallography is taking an increasingly important role in structural biology. However, the addition of nanobodies to the crystallization matrices might complicate the optimization of the crystallization process, which is why analytical techniques to screen and characterize suitable nanobodies are useful. Here, we show how chemical cross-linking combined with high-mass matrix-assisted laser/desorption ionization mass spectrometry can be employed as a fast screening technique to determine binding specificities of intact nanobody•membrane protein complexes...
March 21, 2018: Analytical Chemistry
Jayanta Paul, Raj Vigna Venugopal, Lorance Peter, Kula Naresh Kumar Shetty, Mohit P Shetti
BACKGROUND: Liver biopsy is a gold standard method for hepatic steatosis assessment. However, liver biopsy is an invasive and painful procedure and can cause severe complications therefore it cannot be frequently used in case of follow-up of patients. Non-invasive assessment of steatosis and fibrosis is of growing relevance in non-alcoholic fatty liver disease (NAFLD). To evaluate hepatic steatosis, transient elastography with controlled attenuation parameter (CAP) measurement is an option now days...
January 2018: Arquivos de Gastroenterologia
Francesca Bagnato, Simon Hametner, Emma Boyd, Verena Endmayr, Yaping Shi, Vasiliki Ikonomidou, Guanhua Chen, Siddharama Pawate, Hans Lassmann, Seth Smith, E Brian Welch
T2*-weighted multi-echo gradient-echo magnetic resonance imaging and its reciprocal R2* are used in brain imaging due to their sensitivity to iron content. In patients with multiple sclerosis who display pathological alterations in iron and myelin contents, the use of R2* may offer a unique way to untangle mechanisms of disease. Coronal slices from 8 brains of deceased multiple sclerosis patients were imaged using a whole-body 7.0 Tesla MRI scanner. The scanning protocol included three-dimensional (3D) T2*-w multi-echo gradient-echo and 2D T2-w turbo spin echo (TSE) sequences...
2018: PloS One
Tracey Ann Cuin, Ingo Dreyer, Erwan Michard
Fast responses to an external threat depend on the rapid transmission of signals through a plant. Action potentials (APs) are proposed as such signals. Plant APs share similarities with their animal counterparts; they are proposed to depend on the activity of voltage-gated ion channels. Nonetheless, despite their demonstrated role in (a)biotic stress responses, the identities of the associated voltage-gated channels and transporters remain undefined in higher plants. By demonstrating the role of two potassium-selective channels in Arabidopsis thaliana in AP generation and shaping, we show that the plant AP does depend on similar Kv -like transport systems to those of the animal signal...
March 21, 2018: International Journal of Molecular Sciences
Cezar A Bizzi, Sandra M Cruz, Lucas Schmidt, Robert A Burrow, Juliano S Barin, Jose N G Paniz, Erico M M Flores
A new method for analytical applications based on the Maxwell-Wagner effect is proposed. Considering the interaction of carbonaceous materials with an electromagnetic field in the microwave frequency range, a very fast heating is observed due to interfacial polarization that results in localized microplasma formation. Such effect was evaluated in this work using a monomode microwave system, and temperature was recorded using an infrared camera. For analytical applications, a closed reactor under oxygen pressure was evaluated...
March 21, 2018: Analytical Chemistry
Karen E Elkind-Hirsch, Martha S Paterson, Donna Shaler, Hanh C Gutowski
OBJECTIVE: Our pilot study examined the effectiveness of sitagliptin-metformin (SITA-MET), metformin (MET), and placebo (P) therapy on fasting and post-glucose challenge glucose levels in postpartum women with prior gestational diabetes mellitus (GDM) and impaired glucose regulation. METHODS: Prediabetic women (N = 36, age 18 to 42 years) with recent GDM were randomized to P (one pill twice a day), MET (1,000 mg twice a day), or SITA-MET (50 mg SITA, 1,000 mg MET twice a day) for 16 weeks in a single-blind fashion...
March 21, 2018: Endocrine Practice
Susanna Mancini
Abortion is the object of a new, relatively efficient, denunciation campaign based on the defence of women's rights as well as that of the child to be born - ?love them both?. This movement, which started in the United States, is developing fast in Europe and spreading currently to contraception.
March 7, 2018: Journal International de Bioéthique et D'éthique des Sciences
S Varchanis, Y Dimakopoulos, C Wagner, J Tsamopoulos
Blood plasma has been considered a Newtonian fluid for decades. Recent experiments (Brust et al., Phys. Rev. Lett., 2013, 110) revealed that blood plasma has a pronounced viscoelastic behavior. This claim was based on purely elastic effects observed in the collapse of a thin plasma filament and the fast flow of plasma inside a contraction-expansion microchannel. However, due to the fact that plasma is a solution with very low viscosity, conventional rotational rheometers are not able to stretch the proteins effectively and thus, provide information about the viscoelastic properties of plasma...
March 21, 2018: Soft Matter
Tadanori Fukami, Takamasa Shimada, Bunnoshin Ishikawa
OBJECTIVE: In the current study, we tested a proposed method for fast spike detection in electroencephalography (EEG). APPROACH: We performed eigenvalue analysis in two-dimensional space spanned by gradients calculated from two neighboring samples to detect high-amplitude negative peaks. We extracted the spike candidates by imposing restrictions on parameters regarding spike shape and eigenvalues reflecting detection characteristics of individual medical doctors...
March 21, 2018: Journal of Neural Engineering
Doulaye Dembélé
High-throughput biological technologies are routinely used to generate gene expression profiling or cytogenetics data. To achieve high performance, methods available in the literature become more specialized and often require high computational resources. Here, we propose a new versatile method based on the data-ordering rank values. We use linear algebra, the Perron-Frobenius theorem and also extend a method presented earlier for searching differentially expressed genes for the detection of recurrent copy number aberration...
January 1, 2018: Statistical Methods in Medical Research
Digvijayini Bundhun, Sillma Rampadarath, Daneshwar Puchooa, Rajesh Jeewon
The purpose of the study was to explore the dietary intake, fruit, vegetable and energy intake and lifestyle behaviors among Mauritian children. A validated questionnaire was used, assessing dietary intake, mean energy intake, mean body mass index (BMI), lifestyle behaviors as well as nutritional knowledge (NK) among males and females. 336 children aged 6-12 years (165 males and 171 females) from 8 public primary schools were recruited. Statistical analyses revealed that children consumed less nutritious foods such as fruits, vegetables and whole grains and more of refined and calorie-laden foods, with no significant differences across genders...
February 2018: Heliyon
Jörn Grensemann
Routine use of cardiac output (CO) monitoring became available with the introduction of the pulmonary artery catheter into clinical practice. Since then, several systems have been developed that allow for a less-invasive CO monitoring. The so-called "non-calibrated pulse contour systems" (PCS) estimate CO based on pulse contour analysis of the arterial waveform, as determined by means of an arterial catheter without additional calibration. The transformation of the arterial waveform signal as a pressure measurement to a CO as a volume per time parameter requires a concise knowledge of the dynamic characteristics of the arterial vasculature...
2018: Frontiers in Medicine
Adrian Smedowski, Marita Pietrucha-Dutczak, Ruchi Maniar, Michael Ajeleti, Iwona Matuszek, Joanna Lewin-Kowalik
Preclinical toxicity screening of the new retinal compounds is an absolute requirement in the pathway of further drug development. Since retinal neuron cultivation and in vivo studies are relatively expensive and time consuming, we aimed to create a fast and reproducible ex vivo system for retinal toxicity screening. For this purpose, we used rat retinal explant culture that was retrogradely labeled with the FluoroGold before the isolation. Explants were exposed to a toxic concentration of gentamicin and ciliary neurotrophic factor (CNTF), a known neuroprotective agent...
2018: Oxidative Medicine and Cellular Longevity
Arjan van Zeijl, Titis A K Wardhani, Maryam Seifi Kalhor, Luuk Rutten, Fengjiao Bu, Marijke Hartog, Sidney Linders, Elena E Fedorova, Ton Bisseling, Wouter Kohlen, Rene Geurts
Parasponia represents five fast-growing tropical tree species in the Cannabaceae and is the only plant lineage besides legumes that can establish nitrogen-fixing nodules with rhizobium. Comparative analyses between legumes and Parasponia allows identification of conserved genetic networks controlling this symbiosis. However, such studies are hampered due to the absence of powerful reverse genetic tools for Parasponia . Here, we present a fast and efficient protocol for Agrobacterium tumefaciens -mediated transformation and CRISPR/Cas9 mutagenesis of Parasponia andersonii ...
2018: Frontiers in Plant Science
Xin Liu, Yichen Lu, Ege Iseri, Yuhan Shi, Duygu Kuzum
Electrophysiology is a decades-old technique widely used for monitoring activity of individual neurons and local field potentials. Optogenetics has revolutionized neuroscience studies by offering selective and fast control of targeted neurons and neuron populations. The combination of these two techniques is crucial for causal investigation of neural circuits and understanding their functional connectivity. However, electrical artifacts generated by light stimulation interfere with neural recordings and hinder the development of compact closed-loop systems for precise control of neural activity...
2018: Frontiers in Neuroscience
Stephanie C Cajigas-Loyola, Ricky L Miller, Bradley Spieler, Gregory Carbonella
Background: Mycotic aneurysms arising from the pulmonary arteries are rare; only a few cases have been reported. Staphylococcus and Streptococcus species are the most common causative pathogens. Mycotic aneurysms are seldom clinically apparent unless as a sequela of adverse procedural complications. They carry high morbidity and mortality if not treated expeditiously. Case Report: We present the case of a 37-year-old male with bacteremia and bronchopneumonia associated with a pulmonary artery mycotic aneurysm...
2018: Ochsner Journal
Bhumit Patel, Vipul D Yagnik
Background/aims: As increasing numbers of Crohn's disease (CD) cases are being recognized in India, so the differential diagnosis of CD and gastrointestinal tuberculosis (GITB) is becoming increasingly important. If patients are misdiagnosed with GITB, toxicity may result from unnecessary anti-TB therapy and treatment of the primary disease (ie, CD) gets delayed. We therefore aimed to assess the accuracy of various parameters that can be used to predict GITB diagnosis at index evaluation...
2018: Clinical and Experimental Gastroenterology
Jiabao Guo, Guo Tian, Qiyu Zhao, Tian'an Jiang
Introduction: Hemorrhage is a serious complication following percutaneous biopsy requiring detecting and immediate treatment of active bleeding. This study aimed to explore the potential benefits of ultrasound (US)-guided microwave ablation (MWA) to treat acute hemorrhage in risky locations. Materials and methods: We present seven patients (four males and three females) aged 19-69 years with solid-organ arterial hemorrhage treated by US-guided MWA and followed up with contrast-enhanced US (CEUS)...
2018: OncoTargets and Therapy
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