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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/27936500/sodium-co-limits-and-catalyzes-macronutrients-in-a-prairie-food-web
#2
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/27936479/the-galad-scoring-algorithm-based-on-afp-afp-l3-and-dcp-significantly-improves-detection-of-bclc-early-stage-hepatocellular-carcinoma
#3
J Best, H Bilgi, D Heider, C Schotten, P Manka, S Bedreli, M Gorray, J Ertle, L A van Grunsven, A Dechêne
Background: Hepatocellular carcinoma (HCC) is one of the leading causes of death in cirrhotic patients worldwide. The detection rate for early stage HCC remains low despite screening programs. Thus, the majority of HCC cases are detected at advanced tumor stages with limited treatment options. To facilitate earlier diagnosis, this study aims to validate the added benefit of the combination of AFP, the novel biomarkers AFP-L3, DCP, and an associated novel diagnostic algorithm called GALAD. Material and methods: Between 2007 and 2008 and from 2010 to 2012, 285 patients newly diagnosed with HCC and 402 control patients suffering from chronic liver disease were enrolled...
December 2016: Zeitschrift Für Gastroenterologie
https://www.readbyqxmd.com/read/27936423/optimising-the-community-based-approach-to-healthcare-improvement-comparative-case-studies-of-the-clinical-community-model-in-practice
#4
Emma-Louise Aveling, Graham Martin, Georgia Herbert, Natalie Armstrong
Community-based approaches to healthcare improvement are receiving increasing attention. Such approaches could offer an infrastructure for efficient knowledge-sharing and a potent means of influencing behaviours, but their potential is yet to be optimised. After briefly reviewing challenges to community-based approaches, we describe in detail the clinical community model. Through exploring clinical communities in practice, we seek to identify practical lessons for optimising this community-based approach to healthcare improvement...
November 22, 2016: Social Science & Medicine
https://www.readbyqxmd.com/read/27936419/unexplained-gastrointestinal-bleed-due-to-arteriobiliary-fistula-after-percutaneous-liver-biopsy
#5
John Smirniotopoulos, Paul Barone, Marc Schiffman
We represent a case of a 54-year-old male who presented to the emergency department with right upper quadrant abdominal pain and melena three weeks after percutaneous liver biopsy. He was found to have anemia secondary to an upper gastrointestinal hemorrhage, unresponsive to multiple blood transfusions. Angiography later revealed an arteriobiliary fistula with contrast extravasation entering the duodenum. The fistula was successfully embolized and the patient was discharged without complication. This report demonstrates the importance in considering a vascular intrahepatic fistula in patients with right upper quadrant abdominal pain after remote liver biopsy...
December 5, 2016: Clinical Imaging
https://www.readbyqxmd.com/read/27936379/clinical-and-epidemiological-characteristics-associated-with-unfavorable-tuberculosis-treatment-outcomes-in-tb-hiv-co-infected-patients-in-brazil-a-hierarchical-polytomous-analysis
#6
Thiago Nascimento do Prado, Jayant V Rajan, Angélica Espinosa Miranda, Elias Dos Santos Dias, Lorrayne Beliqui Cosme, Lia Gonçalves Possuelo, Mauro N Sanchez, Jonathan E Golub, Lee W Riley, Ethel Leonor Maciel
BACKGROUND: TB patients co-infected with HIV have worse treatment outcomes than non-coinfected patients. How clinical characteristics of TB and socioeconomic characteristics influence these outcomes is poorly understood. Here, we use polytomous regression analysis to identify clinical and epidemiological characteristics associated with unfavorable treatment outcomes among TB-HIV co-infected patients in Brazil. METHODS: TB-HIV cases reported in the Brazilian information system (SINAN) between January 1, 2001 and December 31, 2011 were identified and categorized by TB treatment outcome (cure, default, death, and development of MDR TB)...
December 6, 2016: Brazilian Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27936350/adaptation-of-reactive-saccades-is-influenced-by-unconscious-priming-of-the-attention-focus
#7
Otmar Bock, Valentina Grigorova, Milena Ilieva-Staneva
The authors investigated whether the size of the attention focus can influence saccadic adaptation, and whether this influence changes in older age. Using the scrambled sentence task, young and older participants were either primed for a wide attention focus, or primed of a narrow attention focus, or were not primed for any specific attention focus. Subsequently, all participants underwent a double-step saccadic adaptation paradigm aimed at changing the direction of reflexive saccades. The authors found that compared to the nonprimed control group, priming for a wide attention focus enhanced saccadic adaptation in both age groups by a similar amount; the benefit persisted throughout the adaptation phase, but was absent during the deadaptation phase...
December 9, 2016: Journal of Motor Behavior
https://www.readbyqxmd.com/read/27936328/segmental-deuteration-of-%C3%AE-synuclein-for-neutron-reflectometry-on-tethered-bilayers
#8
Zhiping Jiang, Frank Heinrich, Ryan P McGlinchey, James M Gruschus, Jennifer C Lee
Neutron reflectometry (NR) is uniquely suited for studying protein interaction with phospholipid bilayers along the bilayer normal on an angstrom scale. However, NR on its own cannot discern specific membrane-bound regions due to a lack of scattering contrast within a protein. Here we report the successful coupling of native chemical ligation (NCL) and NR to study α-synuclein (α-syn), a membrane-binding neuronal protein central in Parkinson's disease. Two α-syn variants were generated where either the first 86 or last 54 residues are deuterated, allowing for region-specific contrast within the protein and the identification of membrane interacting residues by NR...
December 9, 2016: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27936287/combining-item-response-theory-with-multiple-imputation-to-equate-health-assessment-questionnaires
#9
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
https://www.readbyqxmd.com/read/27936284/utility-of-preclinical-drug-versus-food-choice-procedures-to-evaluate-candidate-medications-for-methamphetamine-use-disorder
#10
Matthew L Banks
Substance use disorders are diagnosed as a manifestation of inappropriate behavioral allocation toward abused drugs and away from other behaviors maintained by more adaptive nondrug reinforcers (e.g., money and social relationships). Substance use disorder treatment goals include not only decreasing drug-maintained behavior but also promoting behavioral reallocation toward these socially adaptive alternative reinforcers. Preclinical drug self-administration procedures that offer concurrent access to both drug and nondrug reinforcers provide a translationally relevant dependent measure of behavioral allocation that may be useful for candidate medication evaluation...
December 9, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27936282/metabolomic-data-suggest-regulation-of-black-howler-monkey-alouatta-pigra-diet-composition-at-the-molecular-level
#11
Katherine R Amato, Alexander Ulanov, Kou-San Ju, Paul A Garber
In addition to macronutrients, foods consist of a complex set of chemical compounds that can influence dietary selectivity and consumer physiology. Metabolomics allow us to describe this complexity by quantifying all small molecules, or metabolites, in a food item. In this study we use GC-MS based metabolomics to describe the metabolite profiles of foods consumed by one population of Mexican black howler monkeys (Alouatta pigra) over a 10-month period. Our data indicate that each food exhibited a distinct metabolite profile, and the average weekly intake of metabolites such as neochlorogenic acid and serotonin (5-hydroxytryptamine) was correlated with the consumption of certain plant parts...
December 9, 2016: American Journal of Primatology
https://www.readbyqxmd.com/read/27936270/the-relative-contribution-of-noise-and-adaptation-to-competition-during-tri-stable-motion-perception
#12
Andrew Isaac Meso, James Rankin, Olivier Faugeras, Pierre Kornprobst, Guillaume S Masson
Animals exploit antagonistic interactions for sensory processing and these can cause oscillations between competing states. Ambiguous sensory inputs yield such perceptual multistability. Despite numerous empirical studies using binocular rivalry or plaid pattern motion, the driving mechanisms behind the spontaneous transitions between alternatives remain unclear. In the current work, we used a tristable barber pole motion stimulus combining empirical and modeling approaches to elucidate the contributions of noise and adaptation to underlying competition...
December 1, 2016: Journal of Vision
https://www.readbyqxmd.com/read/27936245/in-vitro-selective-growth-inhibitory-effect-of-8-hydroxyquinoline-on-clostridium-perfringens-versus-bifidobacteria-in-a-medium-containing-chicken-ileal-digesta
#13
Eva Skrivanova, Filip Van Immerseel, Petra Hovorkova, Ladislav Kokoska
Clostridium perfringens-induced necrotic enteritis is generally controlled by antibiotics. However, because of increasing antibiotic resistance, other antibacterial agents are required, preferably ones that do not affect the beneficial intestinal microbiota of the host. This study evaluated the in vitro selective growth-inhibitory effect of 8-hydroxyquinoline (8HQ) on C. perfringens vs. bifidobacteria in a medium containing chicken ileal digesta. Prior to the experiments, the minimum inhibitory concentrations of 8HQ and penicillin G were determined by broth microdilution assay...
2016: PloS One
https://www.readbyqxmd.com/read/27936238/trehalose-6-phosphate-mediated-toxicity-determines-essentiality-of-otsb2-in-mycobacterium-tuberculosis-in-vitro-and-in-mice
#14
Jan Korte, Marina Alber, Carolina M Trujillo, Karl Syson, Hendrik Koliwer-Brandl, René Deenen, Karl Köhrer, Michael A DeJesus, Travis Hartman, William R Jacobs, Stephen Bornemann, Thomas R Ioerger, Sabine Ehrt, Rainer Kalscheuer
Trehalose biosynthesis is considered an attractive target for the development of antimicrobials against fungal, helminthic and bacterial pathogens including Mycobacterium tuberculosis. The most common biosynthetic route involves trehalose-6-phosphate (T6P) synthase OtsA and T6P phosphatase OtsB that generate trehalose from ADP/UDP-glucose and glucose-6-phosphate. In order to assess the drug target potential of T6P phosphatase, we generated a conditional mutant of M. tuberculosis allowing the regulated gene silencing of the T6P phosphatase gene otsB2...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27936198/tree-diversity-enhances-stand-carbon-storage-but-not-leaf-area-in-a-subtropical-forest
#15
Nadia Castro-Izaguirre, Xiulian Chi, Martin Baruffol, Zhiyao Tang, Keping Ma, Bernhard Schmid, Pascal A Niklaus
Research about biodiversity-productivity relationships has focused on herbaceous ecosystems, with results from tree field studies only recently beginning to emerge. Also, the latter are concentrated largely in the temperate zone. Tree species diversity generally is much higher in subtropical and tropical than in temperate or boreal forests, with reasons not fully understood. Niche overlap and thus complementarity in the use of resources that support productivity may be lower in forests than in herbaceous ecosystems, suggesting weaker productivity responses to diversity change in forests...
2016: PloS One
https://www.readbyqxmd.com/read/27936197/vascular-tone-regulation-induced-by-c-type-natriuretic-peptide-differences-in-endothelium-dependent-and-independent-mechanisms-involved-in-normotensive-and-spontaneously-hypertensive-rats
#16
Carolina Caniffi, Flavia M Cerniello, María N Gobetto, María L Sueiro, María A Costa, Cristina Arranz
Given that the role of C-type natriuretic peptide (CNP) in the regulation of vascular tone in hypertensive states is unclear, we hypothesized that impaired response of the nitric oxide system to CNP in spontaneously hypertensive rats (SHR) could affect vascular relaxation induced by the peptide in this model of hypertension, and that other endothelial systems or potassium channels opening could also be involved. We examined the effect of CNP on isolated SHR aortas, and the hindlimb vascular resistance (HVR) in response to CNP administration compared to normotensive rats...
2016: PloS One
https://www.readbyqxmd.com/read/27936182/structural-changes-in-molluscan-community-over-a-15-year-period-before-and-after-the-2011-great-east-japan-earthquake-and-subsequent-tsunami-around-matsushima-bay-miyagi-prefecture-northeastern-japan
#17
Shin'ichi Sato, Tomoki Chiba
We examined structural changes in the molluscan community for ten years (2001-2010) before and five years (2011-2015) after the 2011 Great East Japan Earthquake and subsequent tsunami around Matsushima Bay, Miyagi Prefecture, northeastern Japan. Before the earthquake and tsunami, Ruditapes philippinarum, Macoma incongrua, Pillucina pisidium, and Batillaria cumingii were dominant, and an alien predator Laguncula pulchella appeared in 2002 and increased in number. After the tsunami, R. philippinarum and M. incongrua populations quickly recovered in 2012, but P...
2016: PloS One
https://www.readbyqxmd.com/read/27936175/effects-of-neonatal-dexamethasone-exposure-on-adult-neuropsychiatric-traits-in-rats
#18
Nathanael J Yates, Donald Robertson, Jennifer Rodger, Mathew T Martin-Iverson
The effects of early life stress in utero or in neonates has long-term consequences on hypothalamic-pituitary-adrenal (HPA) stress axis function and neurodevelopment. These effects extend into adulthood and may underpin a variety of mental illnesses and be related to various developmental and cognitive changes. We examined the potential role of neonatal HPA axis activation on adult psychopathology and dopamine sensitivity in the mature rat using neonatal exposure to the synthetic glucocorticoid receptor agonist and stress hormone, dexamethasone...
2016: PloS One
https://www.readbyqxmd.com/read/27936166/increased-age-but-not-parity-predisposes-to-higher-bacteriuria-burdens-due-to-streptococcus-urinary-tract-infection-and-influences-bladder-cytokine-responses-which-develop-independent-of-tissue-bacterial-loads
#19
Matthew J Sullivan, Alison J Carey, Sophie Y Leclercq, Chee K Tan, Glen C Ulett
Streptococcus agalactiae causes urinary tract infection (UTI) in pregnant adults, non-pregnant adults, immune-compromised individuals and the elderly. The pathogenesis of S. agalactiae UTI in distinct patient populations is poorly understood. In this study, we used murine models of UTI incorporating young mice, aged and dam mice to show that uropathogenic S. agalactiae causes bacteriuria at significantly higher levels in aged mice compared to young mice and this occurs coincident with equivalent levels of bladder tissue colonisation at 24 h post-infection (p...
2016: PloS One
https://www.readbyqxmd.com/read/27936153/impact-of-transient-and-persistent-acute-kidney-injury-on-chronic-kidney-disease-progression-and-mortality-after-gastric-surgery-for-gastric-cancer
#20
Chang Seong Kim, Eun Hui Bae, Seong Kwon Ma, Sun-Seog Kweon, Soo Wan Kim
Acute kidney injury (AKI) is common after gastric surgery for gastric cancer and associated with adverse outcomes. However, the impact of transient or persistent AKI on clinical outcomes after gastric surgery for gastric cancer has not been described. We performed a retrospective study of 4,886 patients with normal renal function who underwent partial or total gastrectomy for gastric cancer between June 2002 and December 2012. AKI patients were classified as transient and persistent AKI based on the return of serum creatinine to the level indicating no AKI within 7 days...
2016: PloS One
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