keyword
MENU ▼
Read by QxMD icon Read
search

Prediction

keyword
https://www.readbyqxmd.com/read/27936518/computational-investigation-of-proton-transfer-pka-shifts-and-ph-optimum-of-protein-dna-and-protein-rna-complexes
#1
Yunhui Peng, Emil Alexov
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936513/probing-the-structural-dynamics-of-the-crispr-cas9-rna-guided-dna-cleavage-system-by-coarse-grained-modeling
#2
Wenjun Zheng
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936510/systematic-evaluation-of-cs-rosetta-for-membrane-protein-structure-prediction-with-sparse-noe-restraints
#3
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/27936500/sodium-co-limits-and-catalyzes-macronutrients-in-a-prairie-food-web
#4
Michael Kaspari, Karl A Roeder, Brittany Benson, Michael D Weiser, Nathan Sanders
Nitrogen and phosphorus frequently limit terrestrial plant production, but have a mixed record in regulating the abundance of terrestrial invertebrates. We contrasted four ways that Na could interact with an NP fertilizer to shape the plants and invertebrates of an inland prairie. We applied NP and Na to m(2) plots in a factorial design. Aboveground invertebrate abundance was independently co-limited by NaCl and NP, but with +NP plots supporting more individuals. We suggest the disparity arises because NP enhanced plant height by 35% (1SD) over controls, providing both food and habitat while NaCl provides only food...
December 9, 2016: Ecology
https://www.readbyqxmd.com/read/27936498/invasive-exotic-shrub-modifies-a-classic-animal-habitat-relationship-and-alters-patterns-of-vertebrate-seed-predation
#5
Peter W Guiden, John L Orrock
Recent evidence suggests that invasive exotic plants can provide novel habitats that alter animal behavior. However, it remains unclear whether classic animal-habitat associations that influence the spatial distribution of plant-animal interactions, such as small mammal use of downed woody debris, persist in invaded habitats. We removed an invasive exotic shrub (buckthorn, Rhamnus cathartica) from 7 of 15 plots in Wisconsin. In each plot, we deployed 200 tagged Quercus rubra seeds in November 2014. After five months, tags were recovered to track spatial patterns of small mammal seed predation...
December 9, 2016: Ecology
https://www.readbyqxmd.com/read/27936491/intrinsic-%C3%AE-helix-propensities-compact-hydrodynamic-radii-in-intrinsically-disordered-proteins
#6
Lance R English, Erin C Tilton, Benjamin J Ricard, Steven T Whitten
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936467/clinical-relevance-of-cell-free-dna-in-gastrointestinal-tract-malignancy
#7
Yuan-Tzu Lan, Ming-Huang Chen, Wen-Liang Fang, Chih-Cheng Hsieh, Chien-Hsing Lin, Fang-Yu Jhang, Shung-Haur Yang, Jen-Kou Lin, Wei-Shone Chen, Jeng-Kai Jiang, Pei-Ching Lin, Shih-Ching Chang
BACKGROUND: Cell-free DNA (cfDNA) extracted from blood has become a clinically feasible biomarker in various types of cancer. However, the clinical significance of cfDNA in gastrointestinal (GI) tract cancer among Asian populations requires further investigation. RESULTS: The median cfDNA copy number was highest in esophageal cancer, followed by colorectal cancer and gastric cancer, which were all significantly higher than those of healthy individuals. The cfDNA levels were higher in GI tract cancer, followed by those in carcinoma in situ and then healthy individuals (P = 0...
December 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27936458/predictors-of-functional-disability-with-focus-on-activities-of-daily-living-a-community-based-follow-up-study-in-older-adults-in-india
#8
Aarti Nagarkar, Yashoda Kashikar
BACKGROUND: Disability in activities of daily living is a growing concern among older populations all over the world. India has one of the rapidly ageing populations and predicted burden of functional disability is higher for Indian older adults as compared to other ageing Asian countries. METHODS: Total 1140 aged 60 years and over participated in a baseline study. 560 of them participated in the prospective cohort study conducted in the city of Pune, India. An interview and functional assessment using a questionnaire and Pune-FAAT tool was carried out in 2013-14...
December 2, 2016: Archives of Gerontology and Geriatrics
https://www.readbyqxmd.com/read/27936450/clinical-outcome-following-medical-treatment-of-cavernous-malformation-related-epilepsy
#9
Yoonju Lee, Kyoo Ho Cho, Hye Ihn Kim, Seung-Koo Lee, Yang-Je Cho, Kyoung Heo, Byung In Lee
PURPOSE: The study was conducted to assess the long-term outcome of antiepileptic drug (AED) treatment in drug-naïve patients with cavernous malformation (CM) related epilepsy (CRE). METHOD: This is a retrospective, single-center, long-term observational study of 34 patients with previously untreated seizures related to CM. All patients were followed-up for at least two years. Drug resistant epilepsy (DRE) was defined as two or more seizures per year after trial of two appropriate AEDs...
November 18, 2016: Seizure: the Journal of the British Epilepsy Association
https://www.readbyqxmd.com/read/27936449/methotrexate-treated-ectopic-pregnancy-beta-human-chorionic-gonadotropin-serum-changes-as-a-success-predictor-using-a-mathematical-model-validation
#10
Aleksandra Kovaleva, Natalia Irishina, Augusto Pereira, Tatiana Cuesta-Guardiola, Luis Ortiz-Quintana
BACKGROUND: Surgical rescue of methotrexate-treated ectopic pregnancy is necessary when tubal rupture or medical therapy failure is detected during post-therapeutic monitoring. It is known that an increased beta human chorionic gonadotropin (β-hCG) concentration is the most important factor associated with treatment failure. Therefore, we suggested that relative changes in serum β-hCG could predict a successful result of medical treatment, leading to facilitation of the decision to forgo the prospect of possible surgical rescue...
October 27, 2016: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/27936446/design-synthesis-and-evaluation-of-4-aminoquinoline-purine-hybrids-as-potential-antiplasmodial-agents
#11
P Linga Reddy, Shabana I Khan, Prija Ponnan, Mohit Tripathi, Diwan S Rawat
A novel series of 4-aminoquinoline-purine hybrids were synthesized and assessed for their antiplasmodial activity against CQ-sensitive and CQ-resistant strains of P. falciparum. It was envisaged that linking of the 4-aminoquinoline pharmacophore (targeting heme-detoxification pathway of malarial parasite) with the purine functionality (targeting plasmodial HG(X)PRT enzyme) will produce a hybrid antiplasmodial agent with increased potency. The synthesized hybrids displayed good antiplasmodial activities against both the sensitive and resistant strains of P...
December 1, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27936439/symptoms-of-prolonged-grief-post-traumatic-stress-and-depression-after-loss-in-a-dutch-community-sample-a-latent-class-analysis
#12
A A A Manik J Djelantik, Geert E Smid, Rolf J Kleber, Paul A Boelen
Mental health problems following loss can manifest as heterogeneous symptomatology that may include symptoms of Prolonged Grief Disorder (PGD), Post-Traumatic Stress Disorder (PTSD), and Major Depressive Disorder (MDD). However, the co-occurrence of symptoms of these three disorders is still only partially explored. The aims of this study were to identify subgroups (i.e., classes) in a Dutch sample of bereaved individuals, based on severity and/or co-occurrence of symptoms and to identify predictors for these subgroups, taking into account all three disorders...
November 22, 2016: Psychiatry Research
https://www.readbyqxmd.com/read/27936438/stressful-life-transitions-and-wellbeing-a-comparison-of-the-stress-buffering-hypothesis-and-the-social-identity-model-of-identity-change
#13
Nurul F Praharso, Morgan J Tear, Tegan Cruwys
The relationship between stressful life transitions and wellbeing is well established, however, the protective role of social connectedness has received mixed support. We test two theoretical models, the Stress Buffering Hypothesis and the Social Identity Model of Identity Change, to determine which best explains the relationship between social connectedness, stress, and wellbeing. Study 1 (N=165) was an experiment in which participants considered the impact of moving cities versus receiving a serious health diagnosis...
November 29, 2016: Psychiatry Research
https://www.readbyqxmd.com/read/27936412/contribution-of-cellular-autolysis-to-tissular-functions-during-plant-development
#14
REVIEW
Sacha Escamez, Hannele Tuominen
Plant development requires specific cells to be eliminated in a predictable and genetically regulated manner referred to as programmed cell death (PCD). However, the target cells do not merely die but they also undergo autolysis to degrade their cellular corpses. Recent progress in understanding developmental cell elimination suggests that distinct proteins execute PCD sensu stricto and autolysis. In addition, cell death alone and cell dismantlement can fulfill different functions. Hence, it appears biologically meaningful to distinguish between the modules of PCD and autolysis during plant development...
December 6, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27936407/sentence-context-influences-the-subjective-perception-of-foreign-accents
#15
Sara Incera, Amee P Shah, Conor T McLennan, Matthew T Wetzel
We examined whether sentence context (the predictability of the final word) influences listeners' ratings of foreign-accented words. Previous work has demonstrated that accent manipulations affect listeners' processing of spoken language. We examined the converse of this relationship; whether context manipulations affect listeners' perceptions of accents. If there is a bidirectional relationship, listeners should be more likely to rate an accent as strong when the accented word is not predicted by the sentence...
December 6, 2016: Acta Psychologica
https://www.readbyqxmd.com/read/27936372/strategic-self-presentation-or-authentic-communication-predicting-adolescents-alcohol-references-on-social-media
#16
Femke Geusens, Kathleen Beullens
OBJECTIVE: The current study is one of the first to examine how self-reported alcohol consumption, friends' perceived alcohol consumption, and the perceived number of friends sharing alcohol references on social networking sites (SNS) is associated with adolescents' sharing of alcohol references on SNS. METHOD: A cross-sectional paper-and-pencil survey was administered among 3,172 adolescents (n = 3,133 used for analyses, mean age = 17.16 years, SD = 0.93; 50.7% male)...
January 2017: Journal of Studies on Alcohol and Drugs
https://www.readbyqxmd.com/read/27936332/an-association-of-serum-alt-with-elevated-blood-pressure-in-senior-adults-a-case-control-study
#17
Xiuqin Hong, Nualnong Wongtongkam, Paul Russell Ward, Shuiyuan Xiao, Shuling Wang, Qian Peng, Qi Zuo, Dan Zeng, Jia Wang, Chenxu Wang, Jian Chen, Na Zhang
Hypertension is a major risk factor for cardiovascular diseases in China; hence, identifying good serum markers might provide cost benefits in terms of reducing morbidity rates. In this population-based case-control study, participants were recruited from five districts in Hunan province, and 416 cases were matched with an equal number of controls. Markers related to elevated blood pressure were assessed: Body Mass Index, total cholesterol, triglycerides, fasting blood glucose, and creatinine. Three potential serum markers homocysteine (HCY), C-reactive protein (CRP), and alanine aminotransferase (ALT) were dichotomized as normal or high level...
December 9, 2016: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/27936325/effect-of-heteroatom-substitution-on-transport-in-alkane-dithiol-based-molecular-tunnel-junctions-evidence-for-universal-behavior
#18
Zuoti Xie, Ioan Baldea, Stuart Oram, Christopher E Smith, C Daniel Frisbie
The transport properties of molecular junctions based on alkane dithiols with three different methylene chain lengths were compared with junctions based on similar chains wherein every third -CH2- was replaced with O or S, i.e., following the general formula: HS(CH2CH2X)nCH2CH2SH, where X = CH2, O or S, and n = 1, 2, or 3. Conducting probe atomic force microscopy (CP-AFM) revealed that the low bias resistance of the chains increased upon substitution in the order CH2 < O < S. This change in resistance is ascribed to the observed identical trend in contact resistance, R_c, whereas the exponential prefactor β (length sensitivity) was essentially the same for all chains...
December 9, 2016: ACS Nano
https://www.readbyqxmd.com/read/27936323/decyltrimethylammonium-bromide-micelles-in-acidic-solutions-counterion-binding-water-structuring-and-micelle-shape
#19
Daniel Timothy Bowron, Karen J Edler
Wide-angle neutron scattering experiments combined with Empirical Potential Structural Refinement modelling have been used to study the detailed structure of decyltrimethylammonium bromide micelles in the presence of acid solutions of HCl or HBr. These experiments demonstrate considerable variation in micelle structure and water structuring between micelles in the two acid solutions and in comparison with the same micelles in pure water. In the presence of the acids, the micelles are smaller, however in the presence of HCl the micelles are more loosely structured and disordered while in the presence of HBr the micelles are more compact and closer to spherical...
December 9, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/27936287/combining-item-response-theory-with-multiple-imputation-to-equate-health-assessment-questionnaires
#20
Chenyang Gu, Roee Gutman
The assessment of patients' functional status across the continuum of care requires a common patient assessment tool. However, assessment tools that are used in various health care settings differ and cannot be easily contrasted. For example, the Functional Independence Measure (FIM) is used to evaluate the functional status of patients who stay in inpatient rehabilitation facilities, the Minimum Data Set (MDS) is collected for all patients who stay in skilled nursing facilities, and the Outcome and Assessment Information Set (OASIS) is collected if they choose home health care provided by home health agencies...
December 9, 2016: Biometrics
keyword
keyword
15428
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"