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https://www.readbyqxmd.com/read/28045384/q-r-quantum-based-refinement
#1
Min Zheng, Jeffrey R Reimers, Mark P Waller, Pavel V Afonine
Quantum-based refinement utilizes chemical restraints derived from quantum-chemical methods instead of the standard parameterized library-based restraints used in refinement packages. The motivation is twofold: firstly, the restraints have the potential to be more accurate, and secondly, the restraints can be more easily applied to new molecules such as drugs or novel cofactors. Here, a new project called Q|R aimed at developing quantum-based refinement of biomacromolecules is under active development by researchers at Shanghai University together with PHENIX developers...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28006723/synthesis-of-scalable-and-tunable-slightly-oxidized-graphene-via-chemical-vapor-deposition
#2
Rizwan Ur Rehman Sagar, Mina Namvari, Sachin T Navale, Florian J Stadler
Semiconducting, large sheets of carbon as an active material in optoelectronic research are missing and reduced graphene oxide (rGO) can be a good candidate. However, chemical synthesis cannot produce large sheets of rGO (i.e. maximum: 20-30μm) as well as high quality rGO due to the restraints of fabrication method. Thus, a novel strategy for the synthesis of large sheets of semiconducting rGO is urgently required. Large area slightly oxidized graphene (SOG) is fabricated at the interface of silicon dioxide (SiO2) and silicon via Chemical Vapor Deposition (CVD) method, herein for the first time...
March 15, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27939290/the-disvis-and-powerfit-web-servers-explorative-and-integrative-modeling-of-biomolecular-complexes
#3
G C P van Zundert, M Trellet, J Schaarschmidt, Z Kurkcuoglu, M David, M Verlato, A Rosato, A M J J Bonvin
Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-resolution structures of atomic subunits with density maps from cryo-electron microscopy or distance restraints, typically acquired by chemical cross-linking coupled with mass spectrometry, respectively...
December 7, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27936510/systematic-evaluation-of-cs-rosetta-for-membrane-protein-structure-prediction-with-sparse-noe-restraints
#4
Katrin Reichel, Olivier Fisette, Tatjana Braun, Olivier F Lange, Gerhard Hummer, Lars V Schäfer
We critically test and validate the CS-Rosetta methodology for de novo structure prediction of α-helical membrane proteins (MPs) from NMR data, such as chemical shifts and NOE distance restraints. By systematically reducing the number and type of NOE restraints, we focus on determining the regime in which MP structures can be reliably predicted and pinpoint the boundaries of the approach. Five MPs of known structure were used as test systems, phototaxis sensory rhodopsin II (pSRII), a subdomain of pSRII, disul_de binding protein B (DsbB), microsomal prostaglandin E2 synthase-1 (mPGES-1), and translocator protein (TSPO)...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27910948/improved-in-cell-structure-determination-of-proteins-at-near-physiological-concentration
#5
Teppei Ikeya, Tomomi Hanashima, Saori Hosoya, Manato Shimazaki, Shiro Ikeda, Masaki Mishima, Peter Güntert, Yutaka Ito
Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27891593/remote-chemical-immobilisation-method-for-free-ranging-australian-cattle
#6
J O Hampton, A Skroblin, A L Perry, T R De Ridder
BACKGROUND: Many situations are encountered in Australia where the capture and restraint of free-ranging cattle (Bos taurus/Bos indicus) is required. Chemical immobilisation via darting is a potentially useful tool for managing and researching large wild herbivores; however, there is no reliable method for its application to Australian cattle. The aim of this study was to develop an efficacious, humane, cost-effective ground darting method for free-ranging cattle. METHODS: The 30 female cattle were darted and captured on a pastoral station in north-west Australia from a vehicle...
December 2016: Australian Veterinary Journal
https://www.readbyqxmd.com/read/27881185/melatonin-and-melatonin-agonists-to-prevent-and-treat-delirium-in-critical-illness-a-systematic-review-protocol
#7
Jennifer Foster, Lisa D Burry, Lehana Thabane, Karen Choong, Kusum Menon, Mark Duffett, Alexandra Cheung, Melanie Guenette, Timothy Chimunda, Louise Rose
BACKGROUND: Delirium is a syndrome characterized by acute fluctuations and alterations in attention and arousal. Critically ill patients are at particularly high risk, and those that develop delirium are more likely to experience poor clinical outcomes such as prolonged duration of ICU and hospital length of stay, and increased mortality. Melatonin and melatonin agonists (MMA) have the potential to decrease the incidence and severity of delirium through their hypnotic and sedative-sparing effects, thus improving health-related outcomes...
November 24, 2016: Systematic Reviews
https://www.readbyqxmd.com/read/27871314/a-mixed-methods-systematic-review-protocol-to-examine-the-use-of-physical-restraint-with-critically-ill-adults-and-strategies-for-minimizing-their-use
#8
Louise Rose, Craig Dale, Orla M Smith, Lisa Burry, Glenn Enright, Dean Fergusson, Samir Sinha, Lesley Wiesenfeld, Tasnim Sinuff, Sangeeta Mehta
BACKGROUND: Critically ill patients frequently experience severe agitation placing them at risk of harm. Physical restraint is common in intensive care units (ICUs) for clinician concerns about safety. However, physical restraint may not prevent medical device removal and has been associated with negative physical and psychological consequences. While professional society guidelines, legislation, and accreditation standards recommend physical restraint minimization, guidelines for critically ill patients are over a decade old, with recommendations that are non-specific...
November 21, 2016: Systematic Reviews
https://www.readbyqxmd.com/read/27859597/quality-of-care-for-people-with-dementia-and-professional-caregivers-perspectives-regarding-palliative-care-in-japanese-community-care-settings
#9
Miharu Nakanishi, Kayo Hirooka, Yuko Morimoto, Atsushi Nishida
OBJECTIVE: Palliative care for dementia includes psychosocial interventions as first-line treatment for challenging behaviour. However, the national dementia plan in Japan contradicts recommendations for palliative care for dementia. This study aimed to examine the association between care quality for patients with dementia and professional caregivers' perspectives regarding palliative care for dementia in Japanese community care settings. METHODS: In total, 2116 professional caregivers from 329 agencies (217 in-home long-term care support providers; 29 small-scale, multiple home-care providers; and 83 group homes) in Tokyo prefecture, Japan, completed cross-sectional, paper-based questionnaires about 3603 people diagnosed with dementia, in May 2016...
November 17, 2016: International Journal of Geriatric Psychiatry
https://www.readbyqxmd.com/read/27855720/pharmacological-interventions-for-agitation-in-patients-with-traumatic-brain-injury-protocol-for-a-systematic-review-and-meta-analysis
#10
David R Williamson, Anne Julie Frenette, Lisa Burry, Marc M Perreault, Emmanuel Charbonney, François Lamontagne, Marie-Julie Potvin, Jean-François Giguère, Sangeeta Mehta, Francis Bernard
BACKGROUND: Traumatic brain injury (TBI) is a worldwide leading cause of mortality and disability. Among TBI complications, agitation is a frequent behavioural problem. Agitation causes potential harm to patients and caregivers, interferes with treatments, leads to unnecessary chemical and physical restraints, increases hospital length of stay, delays rehabilitation, and impedes functional independence. Pharmacological treatments are often considered for agitation management following TBI...
November 17, 2016: Systematic Reviews
https://www.readbyqxmd.com/read/27842924/dexmedetomidine-use-in-the-emergency-department-for-control-of-methamphetamine-induced-agitation-a-report-of-two-cases
#11
Rex Pui Kin Lam, Wai Lam Yip, Chi Keung Wan, Matthew Sik Hon Tsui
BACKGROUND: Chemical restraint is often required to control agitation induced by methamphetamine. Dexmedetomidine is an α-2 adrenergic receptor agonist with sedative, analgesic, and sympatholytic properties. Its use in the emergency department (ED) to control methamphetamine-induced agitation has not been reported. OBJECTIVE: To report two cases of methamphetamine-induced agitation successfully sedated with dexmedetomidine in the ED. CASE REPORT: The first case was a 42-year-old man with unstable emotion and violent behaviours after smoking methamphetamine...
November 3, 2016: American Journal of Emergency Medicine
https://www.readbyqxmd.com/read/27803998/accelerating-proton-spin-diffusion-in-perdeuterated-proteins-at-100%C3%A2-khz-mas
#12
Johannes J Wittmann, Vipin Agarwal, Johannes Hellwagner, Alons Lends, Riccardo Cadalbert, Beat H Meier, Matthias Ernst
Fast magic-angle spinning (>60 kHz) has many advantages but makes spin-diffusion-type proton-proton long-range polarization transfer inefficient and highly dependent on chemical-shift offset. Using 100%-HN-[(2)H,(13)C,(15)N]-ubiquitin as a model substance, we quantify the influence of the chemical-shift difference on the spin diffusion between proton spins and compare two experiments which lead to an improved chemical-shift compensation of the transfer: rotating-frame spin diffusion and a new experiment, reverse amplitude-modulated MIRROR...
November 1, 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27781358/pseudo-contact-nmr-shifts-over-the-paramagnetic-metalloprotein-commp-12-from-first-principles
#13
Ladislav Benda, Jiří Mareš, Enrico Ravera, Giacomo Parigi, Claudio Luchinat, Martin Kaupp, Juha Vaara
Long-range pseudo-contact NMR shifts (PCSs) provide important restraints for the structure refinement of proteins when a paramagnetic metal center is present, either naturally or introduced artificially. Here we show that ab initio quantum-chemical methods and a modern version of the Kurland-McGarvey approach for paramagnetic NMR (pNMR) shifts in the presence of zero-field splitting (ZFS) together provide accurate predictions of all PCSs in a metalloprotein (high-spin cobalt-substituted MMP-12 as a test case)...
November 14, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27777418/the-phf21b-gene-is-associated-with-major-depression-and-modulates-the-stress-response
#14
M-L Wong, M Arcos-Burgos, S Liu, J I Vélez, C Yu, B T Baune, M C Jawahar, V Arolt, U Dannlowski, A Chuah, G A Huttley, R Fogarty, M D Lewis, S R Bornstein, J Licinio
Major depressive disorder (MDD) affects around 350 million people worldwide; however, the underlying genetic basis remains largely unknown. In this study, we took into account that MDD is a gene-environment disorder, in which stress is a critical component, and used whole-genome screening of functional variants to investigate the 'missing heritability' in MDD. Genome-wide association studies (GWAS) using single- and multi-locus linear mixed-effect models were performed in a Los Angeles Mexican-American cohort (196 controls, 203 MDD) and in a replication European-ancestry cohort (499 controls, 473 MDD)...
October 25, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27736233/evaluation-of-the-sedative-effects-of-diazepam-midazolam-and-xylazine-after-intranasal-administration-in-juvenile-ostriches-struthio-camelus
#15
Mostafa Araghi, Saeed Azizi, Nasser Vesal, Bahram Dalir-Naghade
The sedative effects of diazepam, midazolam, and xylazine after intranasal administration were evaluated in 72 (36 male and 36 female) juvenile healthy ostriches ( Struthio camelus ), weighing 50-61 kg and aged 4-5 months. The birds were randomly divided into 3 groups (n = 24), then each group was further subdivided to 4 subgroups (n = 6). For each drug, 4 different doses were chosen and the total calculated dose was equally administered into either naris of the individual bird. The appropriate dose of each drug to produce standing chemical restraint or sternal recumbency was evaluated based on the onset time, the duration of maximum effect, and the duration of sedation...
September 2016: Journal of Avian Medicine and Surgery
https://www.readbyqxmd.com/read/27721047/nmr-characterization-of-weak-interactions-between-rhogdi2-and-fragment-screening-hits
#16
Jiuyang Liu, Jia Gao, Fudong Li, Rongsheng Ma, Qingtao Wei, Aidong Wang, Jihui Wu, Ke Ruan
BACKGROUND: The delineation of intrinsically weak interactions between novel targets and fragment screening hits has long limited the pace of hit-to-lead evolution. Rho guanine-nucleotide dissociation inhibitor 2 (RhoGDI2) is a novel target that lacks any chemical probes for the treatment of tumor metastasis. METHODS: Protein-observed and ligand-observed NMR spectroscopy was used to characterize the weak interactions between RhoGDI2 and fragment screening hits. RESULTS: We identified three hits of RhoGDI2 using streamlined NMR fragment-based screening...
January 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27705101/chemical-restraint-of-free-ranging-south-american-coatis-nasua-nasua-with-a-combination-of-tiletamine-and-zolazepam
#17
Valéria Amorim Conforti, Fernando Cesar Cascelli de Azevedo, Otávio Luís de Oliveira Henriques Paulo, Wanderlei de Moraes, James Albert Deddens
We describe the use of a combination of tiletamine and zolazepam (Zoletil®) for chemical restraint of South American coatis ( Nasua nasua ) under field conditions. We immobilized 53 coatis from a free-ranging population at Iguaçu National Park, Brazil, with Zoletil. Males and females (1.0-8.7 kg) of different age groups participated in the study. Four dosage (milligram per kilogram body weight) groups were created based on quartiles as follows: 1) 4.76-6.68 mg/kg (n=13), 2) 6.83-7.71 mg/kg (n=13), 3) 7.72-8...
January 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/27665599/rna-secondary-structure-determination-by-nmr
#18
Jonathan L Chen, Stanislav Bellaousov, Douglas H Turner
Dynamic programming methods for predicting RNA secondary structure often use thermodynamics and experimental restraints and/or constraints to limit folding space. Chemical mapping results typically restrain certain nucleotides not to be in AU or GC pairs. Two-dimensional nuclear magnetic resonance (NMR) spectra can reveal the order of AU, GC, and GU pairs in double helixes. This chapter describes a program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS), that constrains possible secondary structures on the basis of the NMR determined order and 5'-3' direction of AU, GC, and GU pairs in helixes...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27665550/unconventional-protein-secretion-in-plants
#19
Destiny J Davis, Byung-Ho Kang, Angelo S Heringer, Thomas E Wilkop, Georgia Drakakaki
Unconventional protein secretion (UPS) describes secretion pathways that bypass one or several of the canonical secretion pit-stops on the way to the plasma membrane, and/or involve the secretion of leaderless proteins. So far, alternatives to conventional secretion were primarily observed and studied in yeast and animal cells. The sessile lifestyle of plants brings with it unique restraints on how they adapt to adverse conditions and environmental challenges. Recently, attention towards unconventional secretion pathways in plant cells has substantially increased, with the large number of leaderless proteins identified through proteomic studies...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27649470/determinants-of-the-rigor-of-state-protection-policies-for-persons-with-dementia-in-assisted-living
#20
Matthew C Nattinger, Brian Kaskie
Continued growth in the number of individuals with dementia residing in assisted living (AL) facilities raises concerns about their safety and protection. However, unlike federally regulated nursing facilities, AL facilities are state-regulated and there is a high degree of variation among policies designed to protect persons with dementia. Despite the important role these protection policies have in shaping the quality of life of persons with dementia residing in AL facilities, little is known about their formation...
September 20, 2016: Journal of Aging & Social Policy
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