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https://www.readbyqxmd.com/read/29036546/crocoblast-running-blast-efficiently-in-the-age-of-next-generation-sequencing
#1
Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
Summary: CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29033805/musical-expertise-increases-top-down-modulation-over-hippocampal-activation-during-familiarity-decisions
#2
Pierre Gagnepain, Baptiste Fauvel, Béatrice Desgranges, Malo Gaubert, Fausto Viader, Francis Eustache, Mathilde Groussard, Hervé Platel
The hippocampus has classically been associated with episodic memory, but is sometimes also recruited during semantic memory tasks, especially for the skilled exploration of familiar information. Cognitive control mechanisms guiding semantic memory search may benefit from the set of cognitive processes at stake during musical training. Here, we examined using functional magnetic resonance imaging, whether musical expertise would promote the top-down control of the left inferior frontal gyrus (LIFG) over the generation of hippocampally based goal-directed thoughts mediating the familiarity judgment of proverbs and musical items...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/29031513/effective-cues-for-accelerating-young-drivers-time-to-transfer-control-following-a-period-of-conditional-automation
#3
Timothy J Wright, Ravi Agrawal, Siby Samuel, Yuhua Wang, Shlomo Zilberstein, Donald L Fisher
OBJECTIVE: During conditional automated driving, a transition from the automated driving suite to manual control requires the driver to take over control at a moment's notice. Thus, it is critical that a driver be made situationally aware as quickly as possible in those conditions where he or she may not be paying full attention. Recent research suggests that specific cues about upcoming hazards (e.g., "crosswalk ahead") can increase the drivers' situation awareness during these safety-critical take-over situations when compared with a general cue ("take over control")...
October 11, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/29029643/an-integrated-methodology-for-assessing-the-impact-of-food-matrix-and-gastrointestinal-effects-on-the-biokinetics-and-cellular-toxicity-of-ingested-engineered-nanomaterials
#4
Glen M DeLoid, Yanli Wang, Klara Kapronezai, Laura Rubio Lorente, Roujie Zhang, Georgios Pyrgiotakis, Nagarjun V Konduru, Maria Ericsson, Jason C White, Roberto De La Torre-Roche, Hang Xiao, David Julian McClements, Philip Demokritou
BACKGROUND: Engineered nanomaterials (ENMs) are increasingly added to foods to improve their quality, sensory appeal, safety and shelf-life. Human exposure to these ingested ENMs (iENMS) is inevitable, yet little is known of their hazards. To assess potential hazards, efficient in vitro methodologies are needed to evaluate particle biokinetics and toxicity. These methodologies must account for interactions and transformations of iENMs in foods (food matrix effect) and in the gastrointestinal tract (GIT) that are likely to determine nano-biointeractions...
October 13, 2017: Particle and Fibre Toxicology
https://www.readbyqxmd.com/read/29027419/-optimization-of-lime-milk-precipitation-process-of-lonicera-japonica-aqueous-extract-based-on-quality-by-design-concept
#5
Jin-Jing Shen, Xing-Chu Gong, Jian-Yang Pan, Hai-Bin Qu
Design space approach was applied in this study to optimize the lime milk precipitation process of Lonicera Japonica (Jinyinhua) aqueous extract. The evaluation indices for this process were total organic acid purity and amounts of 6 organic acids obtained from per unit mass of medicinal materials. Four critical process parameters (CPPs) including drop speed of lime milk, pH value after adding lime milk, settling time and settling temperature were identified by using the weighted standardized partial regression coefficient method...
March 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29027415/-application-of-quality-by-design-in-granulation-process-for-ginkgo-leaf-tablet-%C3%A2-%C3%AF-process-control-strategy-based-on-design-space
#6
Xiang-Long Cui, Bing Xu, Fei Sun, Sheng-Yun Dai, Xin-Yuan Shi, Yan-Jiang Qiao
In this paper, under the guidance of quality by design (QbD) concept, the control strategy of the high shear wet granulation process of the ginkgo leaf tablet based on the design space was established to improve the process controllability and product quality consistency. The median granule size (D50) and bulk density (Da) of granules were identified as critical quality attributes (CQAs) and potential critical process parameters (pCPPs) were determined by the failure modes and effect analysis (FMEA). The Plackeet-Burmann experimental design was used to screen pCPPs and the results demonstrated that the binder amount, the wet massing time and the wet mixing impeller speed were critical process parameters (CPPs)...
March 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29027027/decoupling-of-behavioural-and-physiological-thermal-performance-curves-in-ectothermic-animals-a-critical-adaptive-trait
#7
Cristián J Monaco, Christopher D McQuaid, David J Marshall
Thermal performance curves (TPCs) represent an increasingly popular tool in ecology for anticipating species responses to climate change. TPC theory has been developed using species that experience similar temperatures during activity and at rest and consequently exhibit thermal ranges for activity that closely coincide with their physiological thermal tolerances. Many species, however, experience other stressors, such as desiccation, that limit active behaviour at temperatures below the maximum values experienced...
October 12, 2017: Oecologia
https://www.readbyqxmd.com/read/29023094/high-speed-atomic-force-microscopy-visualization-of-the-dynamics-of-the-multienzyme-fatty-acid-synthase
#8
Friederike M C Benning, Yusuke Sakiyama, Adam Mazur, Habib S T Bukhari, Roderick Y H Lim, Timm Maier
Multienzymes, such as the protein metazoan fatty acid synthase (FAS), are giant and highly dynamic molecular machines for critical biosynthetic processes. The molecular architecture of FAS was elucidated by static high-resolution crystallographic analysis, while electron microscopy revealed large-scale conformational variability in FAS with some correlation to functional states in catalysis. However, little is known about time scales of conformational dynamics, the trajectory of motions in individual FAS molecules and the extent of coupling between catalysis and structural changes...
October 12, 2017: ACS Nano
https://www.readbyqxmd.com/read/29021095/the-role-of-wind-field-induced-flow-velocities-in-destratification-and-hypoxia-reduction-at-meiling-bay-of-large-shallow-lake-taihu-china
#9
Abdul Jalil, Yiping Li, Wei Du, Wencai Wang, Jianwei Wang, Xiaomeng Gao, Hafiz Osama Sarwar Khan, Baozhu Pan, Kumud Acharya
Wind induced flow velocity patterns and associated thermal destratification can drive to hypoxia reduction in large shallow lakes. The effects of wind induced hydrodynamic changes on destratification and hypoxia reduction were investigated at the Meiling bay (N 31° 22' 56.4″, E 120° 9' 38.3″) of Lake Taihu, China. Vertical flow velocity profile analysis showed surface flow velocities consistency with the wind field and lower flow velocity profiles were also consistent (but with delay response time) when the wind speed was higher than 6...
October 8, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29020440/influence-of-dna-lesions-on-polymerase-mediated-dna-replication-at-single-molecule-resolution
#10
Hailey Gahlon, Louis J Romano, David Rueda
Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high fidelity polymerases do this rapidly and at low error rates. For example, the holoenzyme of DNA polymerase III in E. coli can replicate at speeds of 600-1,000 bases per second and an error rate of 1 mistake per million nucleotides inserted.1-2 Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase...
October 11, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28993700/vegetation-morphologic-and-aerodynamic-characteristics%C3%A2-reduce%C3%A2-aeolian-erosion
#11
Abbas Miri, Deirdre Dragovich, Zhibao Dong
Vegetation cover is crucial to controlling aeolian erosion but highly efficient vegetation is critical. How this efficiency is influenced by vegetation response to airflow is not clear. Here we evaluate the responses of Cosmos bipinnatus and Ligustrum lucidum Ait to a range of wind speeds in a wind tunnel. For both species, we calculate shelter effect and sand flux. We show that plant effectiveness in reducing wind speed and sediment transport is linked to their aerodynamic response to airflow which results from their morphology...
October 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28991149/decisional-informatics-for-psychosocial-rehabilitation-a-feasibility-pilot-on-tailored-and-fluid-treatment-algorithms-for-serious-mental-illness
#12
Jimmy Choi, Paul H Lysaker, Morris D Bell, Lisa Dixon, Paul Margolies, Matthew Gold, Elizabeth Golden-Roose, Warren Thime, Lawrence C Haber, Michael J Dewberry, Michael Stevens, Godfrey D Pearlson, Joanna M Fiszdon
This study introduces a computerized clinical decision-support tool, the Fluid Outpatient Rehabilitation Treatment (FORT), that incorporates individual and ever-evolving patient needs to guide clinicians in developing and updating treatment decisions in real-time. In this proof-of-concept feasibility pilot, FORT was compared against traditional treatment planning using similar behavioral therapies in 52 adults with severe mental illness attending community-based day treatment. At posttreatment and follow-up, group differences and moderate-to-large effect sizes favoring FORT were detected in social function, work readiness, self-esteem, working memory, processing speed, and mental flexibility...
October 4, 2017: Journal of Nervous and Mental Disease
https://www.readbyqxmd.com/read/28990754/the-effect-of-an-interfacial-layer-on-electron-tunneling-through-atomically-thin-al2o3-tunnel-barriers
#13
Jamie Samantha Wilt, Ridwan Sakidja, Ryan Goul, Judy Z Wu
Electron tunneling through high-quality, atomically thin dielectric films can provide a critical enabling technology for future microelectronics, bringing enhanced quantum coherent transport, fast speed, small size, and high energy-efficiency. A fundamental challenge is in controlling the interface between the dielectric and device electrodes. An interfacial layer (IL) will contain defects and introduce defects in the dielectric film grown atop, preventing electron tunneling through the formation of shorts...
October 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28985072/crystallization-induced-fouling-during-boiling-formation-mechanisms-to-mitigation-approaches
#14
Susmita Dash, Leonid Rapoport, Kripa K Varanasi
Boiling is significantly altered by the presence of dissolved salts. In particular, salts whose solubility decreases with temperature have the tendency to crystallize and adhere to the heat transfer surface and adversely affect the thermal performance. Scaling due to the precipitation of such salts poses serious operational and safety challenges in several practical applications including heat exchangers, pipelines, and desalination. Here, we study the effect of dissolved salts on the dynamics of pool boiling and its impact on the heat transfer coefficient and critical heat flux (CHF)...
October 6, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28981683/altering-the-speed-of-a-dna-packaging-motor-from-bacteriophage-t4
#15
Siying Lin, Tanfis I Alam, Vishal I Kottadiel, Carl J VanGessel, Wei-Chun Tang, Yann R Chemla, Venigalla B Rao
The speed at which a molecular motor operates is critically important for the survival of a virus or an organism but very little is known about the underlying mechanisms. Tailed bacteriophage T4 employs one of the fastest and most powerful packaging motors, a pentamer of gp17 that translocates DNA at a rate of up to ∼2000-bp/s. We hypothesize, guided by structural and genetic analyses, that a unique hydrophobic environment in the catalytic space of gp17-adenosine triphosphatase (ATPase) determines the rate at which the 'lytic water' molecule is activated and OH- nucleophile is generated, in turn determining the speed of the motor...
September 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28972197/coherent-averaging-of-pseudorandom-binary-stimuli-is-the-dynamic-cerebral-autoregulatory-response-symmetrical
#16
Emmanuel Katsogridakis, David M Simpson, Glen Bush, Lingke Fan, Anthony A Birch, Robert Allen, John F Potter, Ronney B Panerai
Previous studies on cerebral autoregulation have shown the existence of hemispheric symmetry, which may be altered in stroke and traumatic brain injury. There is a paucity of data however on whether the response is symmetrical between those disturbances that cause cerebral hyperperfusion, to those that cause hypoperfusion. Our aim was to investigate whether the responses of cerebral autoregulation to haemodynamic stimuli of different directions are symmetrical. Approach: Using a previously described assessment method, we employed coherent averaging of the cerebral blood flow velocity (CBFV) responses to thigh cuff inflation and deflation, as driven by pseudorandom binary sequences, whilst simultaneously altering the inspired CO2...
October 3, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28969171/eye-donation-awareness-and-conversion-rate-in-hospital-cornea-retrieval-programme-in-a-tertiary-hospital-of-central-india
#17
Bhavana Sharma, Ulka Shrivastava, Kavita Kumar, Rajendra Baghel, Farhana Khan, Shridhar Kulkarni
INTRODUCTION: Corneal blindness accounts for 6-8 million blinds in the world. In India, it is estimated that there are approximately 6.8 million people who have vision less than 6/60 in at least one eye due to corneal diseases. AIM: This study was done to assess the awareness about eye donation amongst attendants of critically ill and deceased patients, their willingness to donate eyes, the efficacy of grief counselling by Eye Donation Counsellors (EDC), its impact on the conversion rate and the reasons for poor donation rate...
August 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28961443/eye-tracking-to-evaluate-evidence-recognition-in-crime-scene-investigations
#18
Renuka Devi Watalingam, Nicole Richetelli, Jeff B Pelz, Jacqueline A Speir
Crime scene analysts are the core of criminal investigations; decisions made at the scene greatly affect the speed of analysis and the quality of conclusions, thereby directly impacting the successful resolution of a case. If an examiner fails to recognize the pertinence of an item on scene, the analyst's theory regarding the crime will be limited. Conversely, unselective evidence collection will most likely include irrelevant material, thus increasing a forensic laboratory's backlog and potentially sending the investigation into an unproductive and costly direction...
August 23, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28960286/standardization-procedure-for-plasma-biomarker-analysis-in-rat-models-of-epileptogenesis-focus-on-circulating-micrornas
#19
REVIEW
Erwin A van Vliet, Noora Puhakka, James D Mills, Prashant K Srivastava, Michael R Johnson, Paolo Roncon, Shalini Das Gupta, Jenni Karttunen, Michele Simonato, Katarzyna Lukasiuk, Jan A Gorter, Eleonora Aronica, Asla Pitkänen
The World Health Organization estimates that globally 2.4 million people are diagnosed with epilepsy each year. In nearly 30% of these cases, epilepsy cannot be properly controlled by antiepileptic drugs. More importantly, treatments to prevent or modify epileptogenesis do not exist. Therefore, novel therapies are urgently needed. In this respect, it is important to identify which patients will develop epilepsy and which individually tailored treatment is needed. However, currently, we have no tools to identify the patients at risk, and diagnosis of epileptogenesis remains as a major unmet medical need, which relates to lack of diagnostic biomarkers for epileptogenesis...
September 27, 2017: Epilepsia
https://www.readbyqxmd.com/read/28958430/limitations-of-oxygen-uptake-and-leg-muscle-activity-during-ascending-evacuation-in-stairways
#20
Amitava Halder, Kalev Kuklane, Chuansi Gao, Michael Miller, Mattias Delin, Johan Norén, Karl Fridolf
Stair ascending performance is critical during evacuation from buildings and underground infrastructures. Healthy subjects performed self-paced ascent in three settings: 13 floor building, 31 floor building, 33 m stationary subway escalator. To investigate leg muscle and cardiorespiratory capacities and how they constrain performance, oxygen uptake (VO2), heart rate (HR) and ascending speed were measured in all three; electromyography (EMG) in the first two. The VO2 and HR ranged from 89 to 96% of the maximum capacity reported in the literature...
January 2018: Applied Ergonomics
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