bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational approach to the free radical polymerization kinetics of alkyl α‐hydroxymethacrylate monomers: A structure–reactivity relationship
Authors: Işık Mehtap , Karahan Özlem , Avci Duygu , Aviyente Viktorya 
Published: March 2013

ABSTRACTDensity functional theory calculations at the B3LYP/6–31+G(d) level were carried out for 16 alkyl α‐hydroxymethacrylate (RHMA) monomers, and the calculated quantum chemical descriptors were used to construct a quantitative structure–activity relationship model of the reactivity parameters of those monomers. A multiple regression analysis was adopted to predict the polymerization kinetics. The molecular descriptors used in this study are the Mulliken and APT charges of the backbone C atoms in proximity of the reactive center, the total dipole moment (µ), the energy of the highest occupied molecular orbital (EHOMO), the energy of the lowest unoccupied molecular orbital (ELUMO), the isotropic polarizability (α), the Mulliken atomic spin density (ρs), the ionization energy (IE), the electron affinity (EA), the resonance parameter (Res), the natural atomic orbital occupancies, and the bond distances of the bonds in the proximity to the reactive center of the RHMA monomers and their corresponding radicals. Among the various descriptors considered, the IE and EA of the monomers, the bond order of carbonyl double bond of monomer (BOCO), the resonance stabilization parameter of the monomeric radical, and the Mulliken atomic spin density (ρs) of C5 of the radical were found to be correlated (R2 = 0.9416) with the experimental rates of photopolymerization. The correlation with experiment is also satisfactory when additional monomers are included in the data set; a new correlation is thus generated (R2 = 0.9186). This study is expected to shed light on predicting the reactivities of RHMA monomers prior to their synthesis and to rank their photopolymerization rates based on their quantitative structural properties. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2375–2384
Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences
Authors: Chen Peng , Li Jinyan , Wong Limsoon , Kuwahara Hiroyuki , Huang Jianhua Z. , Gao Xin 
Published: March 2013

ABSTRACTHot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time‐consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K‐nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state‐of‐the‐art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. Proteins 2013; 81:1351–1362 © 2013 Wiley Periodicals, Inc.
Inositol phosphates compete with nucleic acids for binding to bovine leukemia virus matrix protein: Implications for deltaretroviral assembly
Authors: Qualley Dominic F. , Lackey Crystal M. , Paterson Justin P. 
Published: March 2013

ABSTRACTThe matrix (MA) domain of retroviral Gag proteins plays a crucial role in virion assembly. In human immunodeficiency virus type 1 (HIV‐1), a lentivirus, the presence of phosphatidylinositol‐(4,5)‐bisphosphate triggers a conformational change allowing the MA domain to bind the plasma membrane (PM). In this study, the MA protein from bovine leukemia virus (BLV) was used to investigate the mechanism of viral Gag binding to the membrane during replication of a deltaretrovirus. Fluorescence spectroscopy was used to measure the binding affinity of MA for two RNA constructs derived from the BLV genome as well as for single‐stranded DNA (ssDNA). The importance of electrostatic interactions and the ability of inositol hexakisphosphate (IP6) to compete with nucleic acids for binding to MA were also investigated. Our data show that IP6 effectively competes with RNA and DNA for BLV MA binding, while [NaCl] of greater than 100 mM is required to produce any observable effect on DNA‐MA binding. These results suggest that BLV assembly may be highly dependent on the specific interaction of the MA domain with components of the PM, as observed previously with HIV‐1. The mode of MA binding to nucleic acids and the implications for BLV assembly are discussed. Proteins 2013; 81:1377–1385. © 2013 Wiley Periodicals, Inc.
The role of latent heating in warm frontogenesis
Authors: Igel Adele L. , van den Heever Susan C. 
Published: March 2013

AbstractThe role of latent heating from individual cloud processes associated with one part of a springtime extratropical cyclone, the warm front, is assessed using high‐resolution modelling. Condensation and cloud droplet nucleation are the largest sources of latent heat along the frontal surface and together produce rates of horizontal frontogenesis that are of the same order of magnitude as the deformation and tilting terms at mid levels; however, near the surface latent heating does not cause strong frontogenesis. In the vertical, stabilization caused by condensation and cloud nucleation is nearly everywhere higher than stabilization caused by dry dynamics, and is the primary process through which high static stability is found along the frontal surface. The frontogenesis and static stability tendency equations are combined to form an expression for the frontal slope tendency. While dynamic processes lead to increases in frontal slope, latent heating often counteracts this tendency. This indicates that the direct effect of latent heating on the thermal structure of the front is to decrease the slope and in that sense weaken the warm front.
General resonance mediation
Authors: McGarrie Moritz 
Published: March 2013

AbstractWe extend the framework of general gauge mediation to cases where the mediating fields have a nontrivial spectral function, as might arise from strong dynamics. Demonstrating through examples, this setup describes a broad class of possible models of gauge mediated supersymmetry breaking. A main emphasis is to give general formulas for cross sections forσ(visible→hidden) in these resonance models. We will also give formulas for soft masses, A-terms and demonstrate the framework with a holographic setup.
Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB)
Authors: Diminic Janko , Zucko Jurica , Ruzic Ida Trninic , Gacesa Ranko , Hranueli Daslav , Long Paul F , Cullum John , Starcevic Antonio 
Published: March 2013

Abstract
Modular biosynthetic clusters are responsible for the synthesis of many important pharmaceutical products. They include polyketide synthases (PKS clusters), non-ribosomal synthetases (NRPS clusters), and mixed clusters (containing both PKS and NRPS modules). The ClustScan database (CSDB) contains highly annotated descriptions of 170 clusters. The database has a hierarchical organization, which allows easy extraction of DNA and protein sequences of polypeptides, modules, and domains as well as an organization of the annotation so as to be able to predict the product chemistry to view it or export it in a standard SMILES format. The recombinant ClustScan database contains information about predicted recombinants between PKS clusters. The recombinants are generated by modeling homologous recombination and are associated with annotation and prediction of product chemistry automatically generated by the model. The database contains over 20,000 recombinants and is a resource for in silico approaches to detecting promising new compounds. Methods are available to construct the corresponding recombinants in the laboratory.
Sesamol Treatment Reduces Plasma Cholesterol and Triacylglycerol Levels in Mouse Models of Acute and Chronic Hyperlipidemia
Authors: Kumar Nitesh , Mudgal Jayesh , Parihar Vipan K. , Nayak Pawan G. , Kutty N. Gopalan , Rao C. Mallikarjuna 
Published: March 2013

AbstractThe active constituents of Sesamum indicum, sesamin and sesamolin, have already been explored for hypolipidemic action. In this study we have explored the anti‐dyslipidemic activity of another active component and metabolite of sesamolin (sesamol), by using acute models of hyperlipidemia viz., a fat tolerance test, a tyloxapol‐induced hyperlipidemia model and a chronic model of hyperlipidemia viz., a high‐fat diet‐induced hyperlipidemia model in Swiss albino mice. Sesamol (100 and 200 mg/kg) significantly (P < 0.05) decreased triacylglycerol absorption in the fat tolerance test by showing a dose‐dependent decrease in triacylglycerol levels. The hypolipidemic effect of sesamol at 200 mg/kg was equivalent to 10 mg/kg of orlistat. In the tyloxapol‐induced hyperlipidemia model, Sesamol at 200 mg/kg reversed the elevated levels of cholesterol and triacylglycerol compared with the tyloxapol group at 12 and 24 h, which indicates its probable effect on cholesterol synthesis. Chronic hyperlipidemia in mice was produced by feeding a high‐diet, a mixture of cholesterol (2 % w/w), cholic acid (1 % w/w) and coconut oil 30 % (v/w) with standard powdered standard animal chow (up to 100 g). Niacin (100 mg/kg) and sesamol (100 mg/kg) significantly (P < 0.05) reduced the elevated body weight compared with the high fat diet control group. Elevated levels of cholesterol and triacylglycerol were significantly (P < 0.05) reversed by the sesamol (50 and 100 mg/kg), implying that it might reduce the absorption and increase the excretion of cholesterol as well.
Effect of Liquid Oil on the Distribution and Reactivity of a Hydrophobic Solute in Solid Lipid Nanoparticles
Authors: Yucel Umut , Elias Ryan J. , Coupland John N. 
Published: March 2013

AbstractThe performance of solid lipid nanoparticles is often modified by the addition of small amounts of liquid oil. The effects of added liquid lipid (tetradecane, C14) on the distribution and reactivity of the spin probe 4‐phenyl‐2,2,5,5‐tetramethyl‐3‐imidazoline‐1‐oxyl nitroxide (PTMIO) in solid lipid nanoparticles (eicosane, C20) were investigated as a function of storage time and temperature. Emulsions prepared with blends of C14:C20 (100 % C14, 90 % C20, 99 % C20, and 100 % C20) and stabilized by sodium caseinate (1 wt%) were stored at 21.5 °C or 5 °C for 5 or 24 h prior to EPR analyses. In the liquid C14 droplets the PTMIO partitioned between the droplet and aqueous phases (70 and 30 %, respectively) independent of storage conditions. However, the proportion of probe in droplets decreased with increasing crystalline C20 concentration. The fraction of PTMIO in droplets containing C20 decreased in the following sequence: 5 h at room temperature >24 h at room temperature >24 h at refrigerated temperature and was lower in droplets with a higher proportion of C20. The residual PTMIO in semicrystalline droplets has higher polarity and lower mobility than PTMIO in liquid oil droplets suggesting it is in a layer surrounding the crystalline lipid core, and partly immobilized by interaction with the surface layer. The model of PTMIO distribution was consistent with the kinetics of PTMIO reduction by aqueous ascorbate ions.
pepgrep: A Tool for Peptide MS/MS Pattern Matching
Authors: Chernukhin Igor 
Published: March 2013

Abstract
Typically, detection of protein sequences in collision-induced dissociation (CID) tandem MS (MS2) dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search (PDS) engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a compact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 fingerprint for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to-MS2 scoring algorithm. pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications (PTMs) into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface (API) or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity purification techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http://bsproteomics.essex.ac.uk:8080/data/download/pepgrep-1.4.tgz.
Emerging concepts on the epigenetic and transcriptional regulation of the Kiss1 gene
Authors: Semaan Sheila J. , Kauffman Alexander S. 
Published: March 2013

AbstractKisspeptin and its receptor have been implicated as critical regulators of reproductive physiology, with humans and mice without functioning kisspeptin systems displaying severe pubertal and reproductive defects. Alterations in the expression of Kiss1 (the gene encoding kisspeptin) over development, along with differences in Kiss1 expression between the sexes in adulthood, may be critical for the maturation and functioning of the neuroendocrine reproductive system and could possibly contribute to pubertal progression, sex differences in luteinizing hormone secretion, and other facets of reproductive physiology. It is therefore essential to understand how Kiss1 gene expression develops and what possible regulatory mechanisms govern the modulation of its expression. A number of recent studies, primarily in rodent or cell line models, have focused on the contributions of epigenetic mechanisms to the regulation of Kiss1 gene expression; thus far, mechanisms such as DNA methylation, histone acetylation, and histone methylation have been investigated. This review discusses the most recent findings on the epigenetic control of Kiss1 expression in adulthood, the evidence for epigenetic factors affecting Kiss1 expression during puberty and development, and findings regarding the contribution of epigenetics to the sexually dimorphic expression of Kiss1 in the hypothalamus.
Predictors of emergency cesarean delivery among international migrant women in Canada
Authors: Gagnon Anita J. , Merry Lisa , Haase Kristen 
Published: March 2013

AbstractObjectiveTo determine the predictors of emergency cesarean delivery among international migrant women.MethodsBetween February 2006 and May 2009, 1025 postpartum migrant women were recruited from 12 hospitals in Toronto, Montreal, and Vancouver. Logistic regression was used to model migration, social, health service, and biomedical factors predictive of emergency cesarean.ResultsOverall, 14% percent of participants underwent emergency cesarean. The greatest risk was for women having their first delivery (odds ratio [OR], 5.9; 95% confidence interval [CI], 3.1–11.3); newborns weighing 4000 g or more (OR, 3.5; 95% CI, 1.9–6.5); no health insurance (OR, 2.8; 95% CI, 1.2–6.4); delivery on a Friday (OR, 2.2; 95% CI, 1.2–3.9); incomes of less than 30 000 Canadian dollars (OR, 1.9; 1.2–3.0); and induced labor (OR, 1.8; 95% CI, 1.1–3.0). Compared with immigrants, asylum seekers (OR, 0.3; 95% CI, 0.2–0.6) and refugees (OR, 0.5; 95% CI, 0.2–1.0) were protected against emergency cesarean.ConclusionIndicators specific to, or more common among, migrants were informative in assessing the likelihood of emergency cesarean. The risk associated with being uninsured, day of delivery, income, and immigration class suggests the importance of considering non‐biomedical factors in reducing the need for emergency cesarean among migrants.
Association of maternal sleep practices with pre‐eclampsia, low birth weight, and stillbirth among Ghanaian women
Authors: Owusu Jocelynn T. , Anderson Frank J. , Coleman Jerry , Oppong Samuel , Seffah Joseph D. , Aikins Alfred , O'Brien Louise M. 
Published: March 2013

AbstractObjectiveTo assess sleep practices, and investigate their relationship with maternal and fetal outcomes, among pregnant Ghanaian women.MethodsIn a cross‐sectional study conducted at Korle Bu Teaching Hospital, Accra, Ghana, between June and July 2011, postpartum women were interviewed within 48 hours of delivery about sleep quality and practices during pregnancy. Interviews were coupled with a systematic review of participants' medical charts for key outcomes including maternal hypertension, pre‐eclampsia, premature delivery, low birth weight, and stillbirth.ResultsMost women reported poor sleep quality during pregnancy. Snoring during pregnancy was independently associated with pre‐eclampsia (odds ratio [OR], 3.5; 95% confidence interval [CI], 1.4–8.5; P = 0.007). The newborns of women who reported supine sleep during pregnancy were at increased risk of low birth weight (OR, 5.0; 95% CI, 1.2–20.2; P = 0.025) and stillbirth (OR, 8.0; 95% CI, 1.5–43.2; P = 0.016). Low birth weight was found to mediate the relationship between supine sleep and stillbirth.ConclusionThe present findings in an African population demonstrate that maternal sleep, a modifiable risk factor, has a significant role in pre‐eclampsia, low birth weight, and subsequently stillbirth.
Myomectomy during cesarean delivery
Authors: Song Dianrong , Zhang Wei , Chames Mark C. , Guo Jie 
Published: March 2013

AbstractBackgroundThe optimal management of leiomyomas during cesarean delivery is unclear.ObjectivesTo assess the safety of myomectomy performed during cesarean delivery.Search strategyPubMed, MEDLINE, EMBASE, and Cochrane Library were searched to identify potentially relevant studies published prior to June 30, 2012.Selection criteriaCase‐control study comparing myomectomy with no myomectomy in patients undergoing cesarean delivery.Data collection and analysisThe quality of the studies was assessed and data were extracted independently by 2 authors.Main resultsNine studies, including 1 082 women with leiomyomas, met the inclusion criteria; 443 (41.0%) women underwent cesarean myomectomy and 639 (59.1%) underwent cesarean delivery alone. The drop in hemoglobin after surgery was 0.30 g/dL greater in the cesarean myomectomy group than in the control group, but the difference was not significant. The operative time was 4.94 minutes longer in the cesarean myomectomy group, but again the difference was not significant. The overall incidence of fever was comparable in the 2 groups. No hysterectomies were performed in any of the included studies.ConclusionsCesarean myomectomy may be a reasonable option for some women with leiomyoma. However, no definite conclusion can be drawn because the data included in the meta‐analysis were of low quality.
Putting provider abortion skills into practice
Authors: Healy Joan 
Published: March 2013

AbstractGlobal progress to reduce maternal deaths from unsafe abortion is inadequate. Clarifying abortion values and attitudes, using updated WHO safe abortion technical guidance, networking with other providers, and securing adequate abortion and contraceptive supplies can support providers to put induced abortion, postabortion care, and contraceptive skills into practice. Revised national guidelines based on updated WHO guidance can support women's healthcare providers to offer safe abortion for all legal indications and other measures to protect women's life and health. Recommendations of the United Nations and partner agencies can be used to support integration of abortion into other health programs, to expand provision of abortion care by midlevel providers, such as midwives, and to advocate for resources and results based on an expanded reproductive, maternal, newborn, and child health Continuum of Care. Together, these efforts can generate concerted progress toward eliminating unsafe abortion, which is an entirely preventable cause of maternal mortality.
The role of AV and VV optimization for CRT
Authors: Brabham William W. , Gold Michael R. 
Published: March 2013

AbstractCardiac resynchronization therapy is an effective therapy for patients with left ventricular systolic dysfunction and a ventricular conduction delay; however, approximately 30% of patients do not experience significant clinical improvement with this treatment. Modern devices allow individualized programming of the AV delay and VV offset, which offer the possibility of improving clinical response rates with optimized programming. AV and VV delay optimization techniques have included echocardiography, device‐based algorithms, and several other novel noninvasive techniques. While an acute improvement in hemodynamic function has been clearly demonstrated with optimized device settings, long‐term clinical benefit is limited. In the majority of cases, an empiric AV delay with simultaneous biventricular or left ventricular pacing is adequate. The value of optimization of these intervals in “non‐responders” still requires further investigation.