bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stabilization of the integrase‐DNA complex by Mg2+ ions and prediction of key residues for binding HIV‐1 integrase inhibitors
Authors: Miri Lamia , Bouvier Guillaume , Kettani Anass , Mikou Afaf , Wakrim Lahcen , Nilges Michael , Malliavin Thérèse E. 
Published: September 2013

ABSTRACTThe HIV‐1 integrase is an attractive target for the therapeutics development against AIDS, as no host homologue of this protein has been identified. The integrase strand transfer inhibitors (INSTIs), including raltegravir, specifically target the second catalytic step of the integration process by binding to the DDE motif of the catalytic site and coordinating Mg2+ ions. Recent X‐ray crystallographic structures of the integrase/DNA complex from prototype foamy virus allowed to investigate the role of the different partners (integrase, DNA, Mg2+ ions, raltegravir) in the complex stability using molecular dynamics (MD) simulations. The presence of Mg2+ ions is found to be essential for the stability, whereas the simultaneous presence of raltegravir and Mg2+ ions has a destabilizing influence. A homology model of HIV‐1 integrase was built on the basis of the X‐ray crystallographic information, and protein marker residues for the ligand binding were detected by clustering the docking poses of known HIV‐1 integrase inhibitors on the model. Interestingly, we had already identified some of these residues to be involved in HIV‐1 resistance mutations and in the stabilization of the catalytic site during the MD simulations. Classification of protein conformations along MD simulations, as well as of ligand docking poses, was performed by using an original learning method, based on self‐organizing maps. This allows us to perform a more in‐depth investigation of the free‐energy basins populated by the complex in MD simulations on the one hand, and a straightforward classification of ligands according to their binding residues on the other hand. Proteins 2014; 82:466–478. © 2013 Wiley Periodicals, Inc.
Large anisotropic magnetoresistance in graphene‐based junctions
Authors: Rataj Marek , Barna´ Józef 
Published: September 2013

AbstractElectronic transport properties of graphene‐based junctions are considered theoretically in the linear response regime and in terms of the effective continuous electronic model. The junctions under consideration consist of two parts; one part is magnetic, while the other one is non‐magnetic but exhibits strong Rashba spin–orbit coupling. Transport properties of such junctions depend on relative orientation of the magnetization, graphene plane, and direction of charge current. A relatively large anisotropic magnetoresistance, associated with a change in the relative orientation of the magnetization and electric current has been found. This magnetoresistance can be either positive or negative. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimized invertase expression and secretion cassette for improving Yarrowia lipolytica growth on sucrose for industrial applications
Authors: Lazar Zbigniew , Rossignol Tristan , Verbeke Jonathan , Crutz-Le Coq Anne-Marie , Nicaud Jean-Marc , Robak Małgorzata 
Published: September 2013

Abstract
Yarrowia lipolytica requires the expression of a heterologous invertase to grow on a sucrose-based substrate. This work reports the construction of an optimized invertase expression cassette composed of Saccharomyces cerevisiae Suc2p secretion signal sequence followed by the SUC2 sequence and under the control of the strong Y. lipolytica pTEF promoter. This new construction allows a fast and optimal cleavage of sucrose into glucose and fructose and allows cells to reach the maximum growth rate. Contrary to pre-existing constructions, the expression of SUC2 is not sensitive to medium composition in this context. The strain JMY2593, expressing this new cassette with an optimized secretion signal sequence and a strong promoter, produces 4,519 U/l of extracellular invertase in bioreactor experiments compared to 597 U/l in a strain expressing the former invertase construction. The expression of this cassette strongly improved production of invertase and is suitable for simultaneously high production level of citric acid from sucrose-based media.
Responses of a rice–wheat rotation agroecosystem to experimental warming
Authors: Cheng Hao , Ren Wenwei , Ding Lele , Liu Zengfu , Fang Changming 
Published: September 2013

AbstractClimate change is likely to affect agroecosystems in many ways. This study was performed to investigate how a rice–winter wheat rotation agroecosystem in southeast China would respond to global warming. By using an infrared heater system, the soil surface temperature was maintained about 1.5 °C above ambient milieu over 3 years. In the third growing season (2009–2010), the evapotranspiration (ET) rate, crop production, soil respiration, and soil carbon pool were monitored. The ET rate was 23 % higher in the warmed plot as compared to the control plot during the rice paddy growing season, and the rice grain yield was 16.3 % lower, but there was no significant difference in these parameters between the plots during the winter wheat‐growing season. The phenology of the winter wheat shifted under experimental warming, and ET may decrease late in the winter wheat‐growing season. Experimental warming significantly enhanced soil respiration, with mean annual soil respiration rates of 2.57 ± 0.17 and 1.96 ± 0.06 μmol CO2 m−2 s−1 observed in the warmed and control plots, respectively. After 3 years of warming, a significant decrease in the total organic carbon was observed, but only in the surface soil (0–5 cm). Warming also stimulated the belowground biomass, which may have compensated for any heat‐induced loss of soil organic carbon. Paddy rice seemed to be more vulnerable to warming than winter wheat in terms of water‐use efficiency and grain production.
Isotopic decay of urinary or plasma 3‐methylhistidine as a potential biomarker of pathologic skeletal muscle loss
Authors: Sheffield-Moore M. , Dillon E. L. , Randolph K. M. , Casperson S. L. , White G. R. , Jennings K. , Rathmacher J. , Schuette S. , Janghorbani M. , Urban R. J. , Hoang V. , Willis M. , Durham W. J. 
Published: September 2013

BackgroundSkeletal muscle loss accompanying aging or cancer is associated with reduced physical function and predicts morbidity and mortality. 3‐Methylhistidine (3MH) has been proposed as a biomarker of myofibrillar proteolysis, which may contribute to skeletal muscle loss.MethodsWe hypothesized that the terminal portion of the isotope decay curve following an oral dose of isotopically labeled 3MH can be measured non‐invasively from timed spot urine samples. We investigated the feasibility of this approach by determining isotope enrichment in spot urine samples and corresponding plasma samples and whether meat intake up to the time of dosing influences the isotope decay.ResultsIsotope decay constants (k) were similar in plasma and urine, regardless of diet. Post hoc comparison of hourly sampling over 10 h with three samples distributed over 10 or fewer hours suggests that three distributed samples over 5–6 h of plasma or urine sampling yield decay constants similar to those obtained over 10 h of hourly sampling.ConclusionThe findings from this study suggest that an index of 3MH production can be obtained from an easily administered test involving oral administration of a stable isotope tracer of 3MH followed by three plasma or urine samples collected over 5–6 h the next day.
Factors that Influence Functional Mobility Outcomes of Patients after Traumatic Brain Injury
Authors: Haffejee Sameera , Ntsiea Veronica , Mudzi Witness 
Published: September 2013

Objective/Background The consequences of traumatic brain injury (TBI) include physical, cognitive, psychological, behavioural, and emotional deficits. Prognostic factors such as age, mechanism of injury, and severity of injury assist in determining the outcome of the patient. It is believed that predictors of recovery assist both the patient as well as family members in determining the potential outcomes for the patient. The objective of this study was to identify factors that influence functional mobility outcome of patients after TBI. Methods This was a cross-sectional study. Participants were assessed predischarge. The Glasgow Coma Scale on admission was noted to establish the severity of the TBI. The Rivermead Mobility Index was used to establish the functional mobility outcome. Results The sample consisted of 60 participants of which 56 (93%) were males. The average age of the participants in the study was 28 ± 8.5 years. More than 50% of the participants were unable to walk outside and 37% were able to climb a flight of stairs without help at the time of discharge from the hospital. Younger age (p < .001), male gender (p = .001), Grade 12 education (p = .001), being self employed (p < .001), having bowel and bladder continence (p < .001), not smoking and drinking (p < .001), and having occupational therapy sessions (p = .002) had a positive impact on function after TBI. Conclusion Previous studies have identified a multitude of factors and this study has served to confirm factors that have a positive impact on physical function after TBI within this study group.
Assessment of female sexual function among women with pelvic organ prolapse or urinary incontinence via an Arabic validated short‐form sexual questionnaire
Authors: Shaaban Mohamed M. , Abdelwahab Hassan A. , Ahmed Magdy R. , Shalaby Essam 
Published: September 2013

AbstractObjectiveTo assess female sexual function among women with pelvic organ prolapse or urinary incontinence via an Arabic, validated, short‐form sexual questionnaire (PISQ‐12).MethodsThe present study was conducted among women attending Suez Canal University Hospital, Ismailia, Egypt, between September 2009 and August 2011. In the pilot study, 42 women completed the final version of the Arabic PISQ‐12 at recruitment and then 2 weeks later, and the data were compared to evaluate reliability and internal consistency. The formal comparative study included 154 premenopausal sexually active women: 80 control women, and 74 women with some degree of pelvic prolapse with or without stress incontinence. All participants had a vaginal examination and completed the questionnaire. The main outcome measures were the mean questionnaire scores within its 3 domains (behavioral, physical, and partner‐related).ResultsThe test–retest reliability and internal consistency of the Arabic PISQ‐12 were excellent. Validity was approved by an expert panel. The case group had a significantly lower mean total questionnaire score (31.07 ± 4.2 vs 34.7 ± 6.2; P < 0.05) but a higher partner‐related score (9.0 ± 2.4 vs 8.4 ± 2.5; P < 0.05).ConclusionThe Arabic version of PISQ‐12 was shown to be an effective and objective method of evaluating sexual function among patients with pelvic organ prolapse.
Infertility today: The management of female medical causes
Authors: Tinneberg Hans‐Rudolf , Gasbarrini Antonio 
Published: September 2013

AbstractIt has to be suspected that some environmentally hazardous substances have genotoxic properties, revealing their reproductive toxicity at a later stage only. Cancer, including childhood cancer, is more common than usually expected. Undesirable side effects of surgery, chemotherapy, and/or radiation can be premature ovarian failure or even premature menopause. In cases of autoimmune disease, autoantibodies can directly affect maturation of oocytes in the follicle, fertilization, and implantation. Spontaneous abortions are more common in patients with autoimmune disease. Thrombophilia is known to display a higher rate of spontaneous abortions as well as pre‐eclampsia and intrauterine growth retardation. Infections are a common threat to pregnancy. Metabolic syndrome is increasingly frequent in western countries and often associated with hyperandrogenemia and polycystic disease. Women with inflammatory bowel disease such as Crohn disease or ulcerative colitis usually have no problems conceiving. In conclusion, even though infertility is a multifactorial disease, various medical and non‐medical conditions can be attributed to it.
Sodium thiosulfate protects human aortic smooth muscle cells from osteoblastic transdifferentiation via high‐level phosphate
Authors: Zhong Hui , Liu Fang , Dai Xiaoyu , Zhou Li , Fu Ping 
Published: September 2013

AbstractVascular calcification is recognized as a common complication in some patients, such as chronic renal failure. The purpose of this study was to investigate the role of sodium thiosulfate (STS) for the transdifferentiation of human aortic vascular smooth muscle cells into osteoblast‐like cells induced by high‐level phosphate. All human aortic vascular smooth muscle cells were divided into STS group 1 (treatment with STS) and STS group 2 (culture in a medium containing a high level of phosphate). STS group 1 included a normal group, a high‐level phosphate group, and other subgroups based on treatment with different concentrations of STS. Cells of STS group 2 were cultured in a medium containing a high level of phosphate for 72 hours, and then divided into a high‐phosphate control group and other subgroups based on treatment with different concentrations of STS. The mRNA and protein expressions of bone morphogenetic protein‐2 (BMP‐2), core binding factor α‐1 (Cbfα‐1), and matrix Gla protein (MGP) were detected. Meanwhile, calcium concentration and alkaline phosphatase (ALP) activation were measured. In STS group 1, the mRNA levels of BMP‐2 and Cbfα‐1 were elevated significantly in the high‐level phosphate group compared with the normal group (p < 0.05). However, both gene expressions were attenuated in the STS‐treated groups (vs. normal group, p < 0.05). MGP mRNA levels were reduced in the high‐level phosphate group (vs. normal group, p < 0.05). In the STS‐treated groups, mRNA expression of MGP was elevated compared to the high‐level phosphate group (p < 0.05). In STS group 2, expression of MGP was enhanced significantly (vs. high‐phosphate control group, p < 0.05) with both BMP‐2 and Cbfα‐1 reducing in the STS‐treated groups (vs. high‐phosphate‐control group, p < 0.05). STS attenuates calcium concentration and ALP activation. It can reverse osteoblast differentiation of vascular smooth muscle cells and modulate the expressions of calcification‐related factors.
Skp2‐mediated degradation of p27 regulates cell cycle progression in compressed human bladder smooth muscle cells
Authors: Chen Lin , Wu Tao , Wei Tang‐Qiang , Wei Xin , Li Sheng‐Fu , Wang Kun‐Jie , Li Hong 
Published: September 2013

AbstractBladder outlet obstruction (BOO) results in smooth muscle cell hyperplasia, decreased bladder wall compliance, and lower and upper urinary tract pathology. Mechanical stimulus on detrusor tissue is critical to BOO disease progression. Our previous studies confirm that mechanical stimulus triggers human bladder smooth muscle cell (HBSMC) proliferation. To better understand the signal transduction mechanisms for this process we detected cell cycle machinery of HBSMC (Bose ® Biodynamic, Minnetonka, MN, USA). HBSMCs cultured in scaffolds were subjected to four different pressures (0 cmH2O, 100 cmH2O, 200 cmH2O, and 300 cmH2O) for 24 hours, which were controlled by a BOSE BioDynamic bioreactor. Then we used flow cytometry to examine cell cycle distribution, polymerase chain reaction, and immunoblotting to quantify Skp2, p27, and p21 expression in each group. Additionally, Skp2 was silenced in HBSMCs using small interfering RNA to validate the role of Skp2 in mediating pressure‐induced cell cycle progression. Compared with the 0 cmH2O control, HBSMCs in the 200 cmH2O and 300 cmH2O groups exhibited high‐level expression of Skp2 gene and low‐level expression of p27 protein. However, p21, another downstream signal of Skp2, showed no significant change between groups. In addition, Skp2 silencing abolished increases in cell proliferation induced by pressure. To the best of our knowledge, this is the first report on the functional importance of Skp2 in cyclic hydrodynamic pressure stimulated HBSMC proliferation. The signal transduction mechanism for this process involves p27 as well as p21 signaling pathway.
V‐ATPase inhibition overcomes trastuzumab resistance in breast cancer
Authors: von Schwarzenberg Karin , Lajtos Tamás , Simon Làszló , Müller Rolf , Vereb György , Vollmar Angelika M. 
Published: September 2013

The HER2 oncogene targeting drug trastuzumab shows remarkable efficacy in patients overexpressing HER2. However acquired or primary resistance develops in most of the treated patients why alternative treatment strategies are strongly needed. As endosomal sorting and recycling are crucial steps for HER2 activity and the vacuolar H+‐ATPase (V‐ATPase) is an important regulator of endocytotic trafficking, we proposed that targeting V‐ATPase opens a new therapeutic strategy against trastuzumab‐resistant tumor cells in vitro and in vivo. V‐ATPase inhibition with archazolid, a novel inhibitor of myxobacterial origin, results in growth inhibition, apoptosis and impaired HER2 pro‐survival signaling of the trastuzumab‐resistant cell line JIMT‐1. This is accompanied by a decreased expression on the plasma membrane and accumulation of HER2 in the cytosol, where it colocalizes with endosomes, lysosomes and autophagosomes. Importantly, microscopic analysis of JIMT‐1 xenograft tumor tissue of archazolid treated mice confirms the defect in HER2‐recycling which leads to reduced tumor growth. These results suggest that V‐ATPase inhibition by archazolid induces apoptosis and inhibits growth of trastuzumab‐resistant tumor cells by retaining HER2 in dysfunctional vesicles of the recycling pathway and consequently abrogates HER2‐signaling in vitro as well as in vivo. V‐ATPase inhibition is thus suggested as a promising strategy for treatment of trastuzumab‐resistant tumors.
Effect of orange peel and black tea extracts on markers of performance and cytokine markers of inflammation in horses
Authors: Streltsova Jennifer M , McKeever Kenneth H , Liburt Nettie R , Gordon Mary E , Filho Helio Manso , Horohov David W , Rosen Robert T , Franke William 
Published: September 2013

AbstractThis study tested the hypothesis that orange peel (O) and decaffeinated black tea (T) extracts would alter markers of exercise performance as well as exercise-induced mRNA expression for the inflammatory cytokines IL-6, TNF-alpha and IFN-gamma. Nine healthy, unfit Standardbred mares (age: 10±4years, ∼450kg) were assigned to three treatment groups in a randomized crossover design where each horse was administered one of the following; placebo (O; 21 water), black tea extract in water (T; 21) or orange peel extract in water (W; 21), via a nasogastric tube. One hour later the horses completed an incremental graded exercise test (GXT) on a treadmill at a fixed 6% grade with measurements and blood samples obtained at rest, at the end of each 1min step of the GXT and at 2 and 5min post-GXT. An additional set of blood samples for Polymerase Chain Reaction (PCR) measurements of mRNA was obtained before exercise and at 5 and 30min and 1, 2, 4 and 24h post-GXT. The GXTs were conducted between 0700 and 1200h not less than 7days apart. There were no differences (P>0.05) in VO2max, respiratory exchange ratio, run time, velocity at VO2max, core body temperature, haematocrit, creatine kinase (CK), plasma lactate concentrations, HR, right ventricular pressure (RVP) or pulmonary artery pressure (PAP) across treatments. A major finding was that orange peel extract significantly reduced post-exercise VO2recovery time (W = 112±7, O = 86±6, and T = 120±11s). There was a significant difference in plasma total protein concentration (TP) in the O runs compared with water and T. TNF-alpha mRNA expression was lower in the T runs compared with water and O trials. IFN-gamma mRNA expression levels appeared to be lower in both the T and O extract runs compared with the water trials. The mRNA expression of IL-6 was unaltered across treatment groups. These data suggest that orange peel and black tea extracts may modulate the cytokine responses to intense exercise. Orange peel extract reduced post-exercise recovery time and may potentially enhance the ability of horses to perform subsequent bouts of high-intensity exercise.
The Age of Revolution in the Indian Ocean, Bay of Bengal, and South China Sea: A Maritime Perspective
Authors: Anderson Clare 
Published: September 2013

AbstractThis essay explores the history of empire and rebellion from a seaborne perspective, through a focus on convict-ship mutiny in the Indian Ocean. It will show that the age of revolution did not necessarily spread outward from Europe and North America into colonies and empires, but rather complex sets of interconnected phenomena circulated regionally and globally in all directions. Convict transportation and mutiny formed a circuit that connected together imperial expansion and native resistance. As unfree labour, convicts might be positioned in global histories of the Industrial Revolution. And, as mutinous or insurgent colonial subjects, they bring together the history of peasant unrest and rebellion in south Asia with piracy in south-east Asia and the Pearl River delta. A subaltern history of convict transportation in the Indian Ocean thus has much to offer for an understanding of the maritime dimensions of the age of revolution.
“All We Have Done, We Have Done for Freedom”: TheCreoleSlave-Ship Revolt (1841) and the Revolutionary Atlantic
Authors: Rupprecht Anita 
Published: September 2013

AbstractThe revolt aboard the American slaving ship theCreole(1841) was an unprecedented success. A minority of the 135 captive African Americans aboard seized the vessel as it sailed from Norfolk, Virginia, to the New Orleans slave markets. They forced the crew to sail to the Bahamas, where they claimed their freedom. Building on previous studies of theCreole, this article argues that the revolt succeeded due to the circulation of radical struggle. Condensed in collective memory, political solidarity, and active protest and resistance, this circulation breached the boundaries between land and ocean, and gave shape to the revolutionary Atlantic. These mutineers achieved their ultimate aim of freedom due to their own prior experiences of resistance, their preparedness to risk death in violent insurrection, and because they sailed into a Bahamian context in which black Atlantic cooperation from below forced the British to serve the letter of their own law.