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https://www.readbyqxmd.com/read/29351266/from-extraction-of-local-structures-of-protein-energy-landscapes-to-improved-decoy-selection-in-template-free-protein-structure-prediction
#1
Nasrin Akhter, Amarda Shehu
Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging...
January 19, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29351023/does-talking-on-a-cell-phone-with-a-passenger-or-dialing-affect-driving-performance-an-updated-systematic-review-and-meta-analysis-of-experimental-studies
#2
Jeff K Caird, Sarah M Simmons, Katelyn Wiley, Kate A Johnston, William J Horrey
Objective An up-to-date meta-analysis of experimental research on talking and driving is needed to provide a comprehensive, empirical, and credible basis for policy, legislation, countermeasures, and future research. Background The effects of cell, mobile, and smart phone use on driving safety continues to be a contentious societal issue. Method All available studies that measured the effects of cell phone use on driving were identified through a variety of search methods and databases. A total of 93 studies containing 106 experiments met the inclusion criteria...
February 2018: Human Factors
https://www.readbyqxmd.com/read/29345600/an-open-source-storage-solution-for-cryo-electron-microscopy-samples
#3
Eveline Ultee, Fred Schenkel, Wen Yang, Susanne Brenzinger, Jamie S Depelteau, Ariane Briegel
Cryo-electron microscopy (cryo-EM) enables the study of biological structures in situ in great detail and to solve protein structures at Ångstrom level resolution. Due to recent advances in instrumentation and data processing, the field of cryo-EM is a rapidly growing. Access to facilities and national centers that house the state-of-the-art microscopes is limited due to the ever-rising demand, resulting in long wait times between sample preparation and data acquisition. To improve sample storage, we have developed a cryo-storage system with an efficient, high storage capacity that enables sample storage in a highly organized manner...
January 18, 2018: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/29345131/photolithography-based-nanopatterning-using-re-entrant-photoresist-profile
#4
Tong Kim, Yei Hwan Jung, Huilong Zhang, Kwangeun Kim, Juhwan Lee, Zhenqiang Ma
Photolithography based on optical mask is widely used in academic research laboratories due to its low-cost, simple mechanism, and ability to pattern in micron sized features on a wafer scale area. Since the resolution is bound by diffraction limits of the light source, nano-scale patterning using photolithography requires short wavelength light source combined with sophisticated optical elements, adding complexity and cost. In this paper, a novel method of sub-wavelength patterning process using conventional i-line mercury lamp is introduced, without the use of such advanced optical tools...
January 18, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29344968/a-novel-nested-polymerase-chain-reaction-assay-targeting-plasmodium-mitochondrial-dna-in-field-collected-anopheles-mosquitoes
#5
M Calzetta, E Perugini, G Seixas, C A Sousa, W M Guelbeogo, N Sagnon, A Della Torre, J Pinto, M Pombi, E Mancini
Sensitive techniques for the detection of Plasmodium (Aconoidasida: Plasmodiidae) sporozoites in field-collected malaria vectors are essential for the correct assessment of risk for malaria transmission. A real-time polymerase chain reaction (RT-PCR) protocol targeting Plasmodium mtDNA proved to be much more sensitive in detecting sporozoites in mosquitoes than the widely used enzyme-linked immunosorbent assay targeting Plasmodium circumsporozoite protein (CSP-ELISA). However, because of the relatively high costs associated with equipment and reagents, RT-PCRs are mostly used to assess the outcomes of experimental infections in the frame of research experiments, rather than in routine monitoring of mosquito infection in the field...
January 18, 2018: Medical and Veterinary Entomology
https://www.readbyqxmd.com/read/29344749/diagnosis-of-sleep-apnea-in-patients-with-stable-chronic-heart-failure-using-a-portable-sleep-test-diagnostic-device
#6
Inês Araújo, Filipa Marques, Sandra André, Manuel Araújo, Sara Marques, Rita Ferreira, Patrícia Moniz, Margarida Proença, Pedro Borrego, Cândida Fonseca
PURPOSE: ApneaLink is a portable device for the screening of sleep apnea, a prevalent and underdiagnosed comorbidity in heart failure patients. A prospective cross-sectional study in patients with chronic heart failure was carried out to assess the sensitivity and specificity of apnea-hypopnea index (AHI) measurements using ApneaLink against the standard polysomnography test. METHODS: Adult patients with a prior hospitalization in an acute heart failure hospital unit were recruited for the study...
January 17, 2018: Sleep & Breathing, Schlaf & Atmung
https://www.readbyqxmd.com/read/29343758/electronic-properties-of-synthetic-shrimp-pathogens-derived-dna-schottky-diodes
#7
Nastaran Rizan, Chan Yen Yew, Maryam Rajabpour Niknam, Jegenathan Krishnasamy, Subha Bhassu, Goh Zee Hong, Sridevi Devadas, Mohamed Shariff Mohd Din, Hairul Anuar Tajuddin, Rofina Yasmin Othman, Siew Moi Phang, Mitsumasa Iwamoto, Vengadesh Periasamy
The exciting discovery of the semiconducting-like properties of deoxyribonucleic acid (DNA) and its potential applications in molecular genetics and diagnostics in recent times has resulted in a paradigm shift in biophysics research. Recent studies in our laboratory provide a platform towards detecting charge transfer mechanism and understanding the electronic properties of DNA based on the sequence-specific electronic response, which can be applied as an alternative to identify or detect DNA. In this study, we demonstrate a novel method for identification of DNA from different shrimp viruses and bacteria using electronic properties of DNA obtained from both negative and positive bias regions in current-voltage (I-V) profiles...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343265/rnase-if-treated-quantitative-pcr-for-dsrna-quantitation-of-rnai-trait-in-genetically-modified-crops
#8
Po-Hao Wang, Greg Schulenberg, Shannon Whitlock, Andrew Worden, Ning Zhou, Stephen Novak, Wei Chen
BACKGROUND: RNA interference (RNAi) technology has been widely used to knockdown target genes via post-transcriptional silencing. In plants, RNAi is used as an effective tool with diverse applications being developed such as resistance against insects, fungi, viruses, and metabolism manipulation. To develop genetically modified (GM) RNAi traits for insect control, a transgene is created and composed of an inversely-repeated sequence of the target gene with a spacer region inserted between the repeats...
January 17, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29341498/review-article-sepsis-in-the-emergency-department-part-2-investigations-and-monitoring
#9
REVIEW
Amith Shetty, Stephen Pj Macdonald, Gerben Keijzers, Julian M Williams, Benjamin Tang, Bas de Groot, Kelly Thompson, John F Fraser, Simon Finfer, Rinaldo Bellomo, Jonathan Iredell
Sepsis is characterised by organ dysfunction resulting from infection, with no reliable single objective test and current diagnosis based on clinical features and results of investigations. In the ED, investigations may be conducted to diagnose infection as the cause of the presenting illness, identify the source, distinguish sepsis from uncomplicated infection (i.e. without organ dysfunction) and/ or risk stratification. Appropriate sample collection for microbiological testing remains key for subsequent confirmation of diagnosis and rationalisation of antimicrobials...
January 16, 2018: Emergency Medicine Australasia: EMA
https://www.readbyqxmd.com/read/29340299/prospective-study-of-the-feasibility-of-point-of-care-testing-strategy-for-carbapenem-resistant-organism-detection
#10
Rahul Pannala, Bruce Baldwin, Vijay Aluru, Thomas E Grys, Jordan Holmes, Laurence J Miller, M Edwyn Harrison, Cuong C Nguyen, Fred C Tenover, David Persing, Douglas O Faigel
Background/aims:  In an investigator-initiated, prospective study, we evaluated the feasibility of a five-gene sequence point-of-care (POC) testing strategy (Xpert CARBA-R Assay, Cepheid Inc., Sunnyvale, CA, USA), compared to reference laboratory PCR (48 - 72 hours turnaround time, two gene sequences), in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and in a hospital outbreak investigation. Methods:  After informed consent, patients undergoing ERCP (September 2015 - April 2016, n = 191) at Mayo Clinic and potential hospital contacts (n = 9) of an index carbapenem-resistant organism (CRO)-positive inpatient were included...
January 2018: Endoscopy International Open
https://www.readbyqxmd.com/read/29339667/improving-laboratory-assessment-in-disorders-of-sex-development-through-a-multidisciplinary-network
#11
Sabine E Hannema, Yolanda B de Rijke
The aim of the European Reference Network for Rare Endocrine Disorders (Endo-ERN) is to ensure equal access to high-quality care for all those affected by a rare endocrine condition across Europe, such as a disorder/difference of sex development (DSD), both for children and adults. Although differences in resources, health care systems, and health insurances between the European countries are challenging and require political action, a European laboratory network within Endo-ERN could improve the diagnostic process in individuals with DSD, building on the work done by previous European collaborations such as the COST action DSDnet...
January 17, 2018: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/29339425/secondary-metabolism-and-interspecific-competition-affect-accumulation-of-spontaneous-mutants-in-the-gacs-gaca-regulatory-system-in-pseudomonas-protegens
#12
Qing Yan, Lucas D Lopes, Brenda T Shaffer, Teresa A Kidarsa, Oliver Vining, Benjamin Philmus, Chunxu Song, Virginia O Stockwell, Jos M Raaijmakers, Kerry L McPhail, Fernando D Andreote, Jeff H Chang, Joyce E Loper
Secondary metabolites are synthesized by many microorganisms and provide a fitness benefit in the presence of competitors and predators. Secondary metabolism also can be costly, as it shunts energy and intermediates from primary metabolism. In Pseudomonas spp., secondary metabolism is controlled by the GacS-GacA global regulatory system. Intriguingly, spontaneous mutations in gacS or gacA (Gac- mutants) are commonly observed in laboratory cultures. Here we investigated the role of secondary metabolism in the accumulation of Gac- mutants in Pseudomonas protegens strain Pf-5...
January 16, 2018: MBio
https://www.readbyqxmd.com/read/29339275/biochar-based-functional-materials-in-the-purification-of-agricultural-wastewater-fabrication-application-and-future-research-needs
#13
REVIEW
Dongning Wei, Bingyu Li, Hongli Huang, Lin Luo, Jiachao Zhang, Yuan Yang, Jiajun Guo, Lin Tang, Guangming Zeng, Yaoyu Zhou
Nowadays, agricultural contamination is becoming more and more serious due to the rapid growth of agricultural industry, which discharged antibiotics, pesticides or toxic metals into farmlands. A large number of researchers have applied biochar-based functional materials to the treatment of agricultural wastewater contamination. Meanwhile, biochar has also proved to be a very promising and effective technology in water purification field due to its various beneficial properties (e.g., cost effective, high specific surface area, and surface reactive groups)...
January 2, 2018: Chemosphere
https://www.readbyqxmd.com/read/29339205/agreement-of-musculoskeletal-ultrasound-and-clinical-assessment-of-shoulder-impairment-in-manual-wheelchair-users-with-various-duration-of-spinal-cord-injury
#14
Margaret Finley, David Ebaugh, Thomas Trojian
OBJECTIVE: To determine agreement of musculoskeletal ultrasound (MSK-US) findings of shoulder pathology and related shoulder special test results in individuals with varied duration of manual wheelchair (MWC) use following spinal cord injury (SCI) and determine if shoulder musculoskeletal impairments, per MSK-US and clinical examination, differed in individuals with SCI and varying duration of MWC use. DESIGN: Cross-sectional cohort study SETTING: Laboratory setting PARTICIPANTS: Twenty-three adult volunteers with SCI who used a MWC for community mobility...
January 12, 2018: Archives of Physical Medicine and Rehabilitation
https://www.readbyqxmd.com/read/29339059/moving-toward-rapid-and-low-cost-point-of-care-molecular-diagnostics-with-a-repurposed-3d-printer-and-rpa
#15
Kamfai Chan, Pui-Yan Wong, Chaitanya Parikh, Season Wong
Traditionally, the majority of nucleic acid amplification-based molecular diagnostic tests are done in centralized settings. In recent years, point-of-care tests have been developed for use in low-resource settings away from central laboratories. While most experts agree that point-of-care molecular tests are greatly needed, their availability as cost-effective and easy-to-operate tests remains an unmet goal. In this article, we discuss our efforts to develop a recombinase polymerase amplification reaction-based test that will meet these criteria...
January 12, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29337661/maintaining-quality-of-candidate-strains-of-transgenic-mosquitoes-for-studies-in-containment-facilities-in-disease-endemic-countries
#16
John D Mumford, Adrian W Leach, Mark Q Benedict, Luca Facchinelli, M Megan Quinlan
Transgenic mosquitoes are being developed as novel components of area-wide approaches to vector-borne disease control. Best practice is to develop these in phases, beginning with laboratory studies, before moving to field testing and inclusion in control programs, to ensure safety and prevent costly field testing of unsuitable strains. The process of identifying and developing good candidate strains requires maintenance of transgenic colonies over many generations in containment facilities. By working in disease endemic countries with target vector populations, laboratory strains may be developed and selected for properties that will enhance intended control efficacy in the next phase, while avoiding traits that introduce unnecessary risks...
January 2018: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/29337022/reaction-time-and-joint-kinematics-during-functional-movement-in-recently-concussed-individuals
#17
Robert C Lynall, J Troy Blackburn, Kevin M Guskiewicz, Stephen W Marshall, Prudence Plummer, Jason P Mihalik
OBJECTIVE: To compare movement reaction time and joint kinematics between recently concussed and matched control recreational athletes during 3 functional tasks. DESIGN: Cross-sectional. SETTING: Laboratory. PARTICIPANTS: Thirty college-aged recreational athletes comprising two groups (15 participants each): 1) Recent concussion group (median time since concussion 126 days, range 28-432 days), and 2) Age- and sex-matched control group with no recent concussions...
January 11, 2018: Archives of Physical Medicine and Rehabilitation
https://www.readbyqxmd.com/read/29336954/high-voltage-fragmentation-of-composites-from-secondary-raw-materials-potential-and-limitations
#18
T Leißner, D Hamann, L Wuschke, H-G Jäckel, U A Peuker
The comminution of composites for liberation of valuable components is a costly and energy-intensive process within the recycling of spent products. It therefore is continuously studied and optimized. In addition to conventional mechanical comminution innovative new principles for size reduction have been developed. One is the use of high voltage (HV) pulses, which is known to be a technology selectively liberating along phase boundaries. This technology offers the advantage of targeted liberation, preventing overgrinding of the material and thus improving the overall processing as well as product quality...
January 11, 2018: Waste Management
https://www.readbyqxmd.com/read/29336679/arcobacter-butzleri-ciprofloxacin-resistance-point-mutations-in-dna-gyrase-a-and-role-on-fitness-cost
#19
Susana Ferreira, Daniela R Correia, Mónica Oleastro, Fernanda C Domingues
Arcobacter butzleri is a widely distributed emerging pathogen resistant to various classes of antimicrobial agents, namely fluoroquinolones. A. butzleri resistance to fluoroquinolones is conferred by point mutations at the antibiotic target. The aim of this study was to evaluate mutations at gyrA associated with ciprofloxacin resistance and evaluate whether acquisition of resistance impacts on fitness and stress tolerance of A. butzleri. A. butzleri ciprofloxacin mutants were generated by laboratory induction...
January 16, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29334955/the-inverted-cup-device-for-blood-transfer-on-malaria-rdts-ease-of-use-acceptability-and-safety-in-routine-use-by-health-workers-in-nigeria
#20
Sandra Incardona, Magoma Mwancha-Kwasa, Roxanne R Rees-Channer, Audrey Albertini, Joshua Havumaki, Peter Chiodini, Wellington Oyibo, Iveth J Gonzalez
BACKGROUND: Malaria rapid diagnostic tests (RDTs) are becoming widely adopted for case management at community level. However, reports and anecdotal observations indicate that the blood transfer step poses a significant challenge to many users. This study sought to evaluate the inverted cup device in the hands of health workers in everyday clinical practice, in comparison with the plastic pipette, and to determine the volume accuracy of the device made of a lower-cost plastic. METHODS: The volume accuracy of inverted cup devices made of two plastics, PMMA and SBC, was compared by transferring blood 150 times onto filter paper and comparing the blood spot areas with those produced by 20 reference transfers with a calibrated micropipette...
January 15, 2018: Malaria Journal
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