bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ion exclusion mechanism in aquaporin at an atomistic level
Authors: Ko Youn Jo , Huh June , Jo Won Ho 
Published: September 2007

AbstractAlthough the mechanism of proton exclusion in aquaporin is investigated by many researchers, the detailed molecular mechanism for ion exclusion in aquaporin is still not completely understood. In the present work, a detailed mechanism for ion exclusion in aquaporin‐1 (AQP1) at an atomistic level is investigated by calculating the free energy for transport of ions in AQP1 using an atomistic molecular dynamics simulation. For this purpose, sodium and chloride ions are chosen as representatives for nonprotonic ions. The simulation shows that the free energy barrier showing its maximum is located at the NPA region for sodium ion while it is located at both the front and the rear for chloride ion and that the barrier height is 18 and 9 kcal/mol, respectively, indicating that the ions are not able to pass through aquaporin. Analysis of the pair interaction energy between the permeating ion and its environment reveals that sodium ion is excluded by the positive charge generated by two α‐helical macro‐dipoles, while chloride ion is expelled by carbonyl oxygen atoms protruding from pore‐making residues before it reaches the NPA motif. It is also found that the number of water molecules hydrating the ions is reduced as the ions enter the pore, implying that the energetic cost for detaching water molecules from a permeating ion also contributes to the free energy barriers of ion transport in AQP1. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12
Authors: Chaudhury Sidhartha , Sircar Aroop , Sivasubramanian Arvind , Berrondo Monica , Gray Jeffrey J. 
Published: September 2007

AbstractIn CAPRI rounds 6–12, RosettaDock successfully predicted 2 of 5 unbound–unbound targets to medium accuracy. Improvement over the previous method was achieved with computational mutagenesis to select decoys that match the energetics of experimentally determined hot spots. In the case of Target 21, Orc1/Sir1, this resulted in a successful docking prediction where RosettaDock alone or with simple site constraints failed. Experimental information also helped limit the interacting region of TolB/Pal, producing a successful prediction of Target 26. In addition, we docked multiple loop conformations for Target 20, and we developed a novel flexible docking algorithm to simultaneously optimize backbone conformation and rigid‐body orientation to generate a wide diversity of conformations for Target 24. Continued challenges included docking of homology targets that differ substantially from their template (sequence identity <50%) and accounting for large conformational changes upon binding. Despite a larger number of unbound–unbound and homology model binding targets, Rounds 6–12 reinforced that RosettaDock is a powerful algorithm for predicting bound complex structures, especially when combined with experimental data Proteins 2007. © 2007 Wiley‐Liss, Inc.
Analyzing hazards of sour water spills
Authors: Woodward J.L. 
Published: September 2007

AbstractThis article illustrates evaluating the consequence of a large spill of sour water by modeling the plume of hydrogen sulfide and ammonia to toxic limits. This modeling uses chemical equilibrium constants and rigorous thermodynamic formulas, coupled with dispersion modeling to show how the plume contours of H2S and of NH3 vary with initial concentrations and pH. The results show that a pH adjustment is an effective mitigation measure. © 2007 American Institute of Chemical Engineers Process Saf Prog 27, 2007
Near band‐edge 3.357 eV emission of Ga‐face (0001) GaN grown by ammonothermal method
Authors: Fujii Katsushi , Fujimoto Gakuyo , Goto Takenari , Yao Takafumi , Kagamitani Yuji , Hoshino Naruhiro , Ehrentraut Dirk , Fukuda Tsuguo 
Published: September 2007

AbstractExcitonic emission was observed at 3.357 eV by photoluminescence only from the (0001) Ga‐face of GaN grown by an ammonothermal method. The emission intensity varied over the crystal surface. The temperature dependence of the emission intensity is similar to that of excitons bound to neutral donors for hexagonal (2H) GaN. The origin of the emission is discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of microcrystallization on noise in boron‐doped silicon film
Authors: Li Shibin , Wu Zhiming , Li Wei , Liao Naiman , Yu Junsheng , Jiang Yadong 
Published: September 2007

AbstractA series of hydrogenated silicon (Si:H) thin films of about 350 nm in thickness were fabricated on K9 glass substrate by plasma enhanced chemical vapor deposition. The transition between hydrogenated amorphous silicon (a‐Si:H) and microcrystalline hydrogenated silicon (μc‐Si:H) was characterized by atomic force microscopy and X‐ray diffraction microstructure analysis. The low‐frequency noise (1/f noise) and random telegraph switching (RTS) noise of Si:H films were measured using a designed semiconductor system. The results show that the 1/f noise of μc‐Si:H is 4 orders of magnitude lower than that of a‐Si:H and no RTS noise of Si:H films was found. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
QSAR of Novel Hydroxyphenylureas as Antioxidant Agents
Authors: Deeb Omar , Youssef Khairia M. , Hemmateenejad Bahram 
Published: September 2007

AbstractA set of descriptors consisting of quantum, chemical, and topological descriptors has been used for modeling the activity of novel hydroxyphenylureas to scavenge Free Radicals (FRs) produced by Peripheral Multinuclear Neutrophil Cells (PMNs) expressed as the rate of change per unit added volume of FR (Kapp min−1). Simple as well as multiple regressions have indicated that PW2 (Path\Walk‐2‐Randic Shape Index) is the most dominating parameter to be used in modeling Kapp. Excellent results are obtained in multiparametric regressions. The results are critically discussed using a variety of statistical parameters. The models are validated using Leave‐One‐Out (LOO) and Leave‐Group‐Out (LGO) crossvalidation, external test set, and chance correlation.
Application of the statistical test of equivalent pathways (STEP) method to the triple quadrupole mass spectrometer
Authors: Dalpathado Dilusha S. , Chang Qing , Burkett Colleen M. , Bandu Mary L. , Desaire Heather 
Published: September 2007

AbstractRecently, we demonstrated a new method, STEP (Statistical Test of Equivalent Pathways) analysis, which differentiates first‐generation product ions (primary product ions) from second‐generation product ions (secondary product ions) obtained in tandem mass spectrometric (MS/MS) experiments on a quadrupole ion trap mass spectrometer. The study presented here defines how to adapt the STEP method to a more routinely used mass analyzer, the triple quadrupole. New ion activation conditions were developed to adapt the STEP method to the triple quadrupole mass spectrometer using peptides and carbohydrates. The application of this method to the triple quadrupole is useful because it provides an efficient approach to differentiate primary and secondary ions on this instrument. Out of the total number of ions that were subjected to the STEP analysis, this method correctly identified 96% of ions as primary or secondary, indicating that this analysis is effective for carbohydrates and peptides undergoing collision‐induced dissociation (CID) on a triple quadrupole mass spectrometer. Copyright © 2007 John Wiley & Sons, Ltd.
Ethics of Surgical Training in Developing Countries
Authors: Ramsey Kevin M. , Weijer Charles 
Published: September 2007

AbstractThe practice of surgical trainees operating in developing countries is gaining interest in the medical community. Although there has been little analysis about the ethical impact of these electives, there has been some concerns raised over the possible exploitation of trainees and their patients. An ethical review of this practice shows that care needs to be taken to prevent harm. Inexperienced surgeons learning surgical skills in developing countries engender greater risk of violating basic ethical principles. Advanced surgical trainees who have already achieved surgical competence are best qualified to satisfy these ethical issues. All training programs need to develop a structured ethical review for international electives to protect their trainees and their patients from harm.
Can minimum convex polygon home ranges be used to draw biologically meaningful conclusions?
Authors: Nilsen Erlend B. , Pedersen Simen , Linnell John D. C. 
Published: September 2007

AbstractMany conclusions about mammalian ranging behaviour have been drawn based on minimum convex polygon (MCP) estimates of home range size, although several studies have revealed its unpredictable nature compared to that of the kernel density estimator. We investigated to what extent the choice of home range estimator affected the biological interpretation in comparative studies. We found no discrepancy when the question asked covered a wide range of taxa, as real and very large differences in range size were likely to have masked smaller differences due to the choice of home range estimator. However, when the question asked concerned within‐species characteristics, the choice of home range estimator explained as much of the variation in range size as did the ecological variable in question. The implications for macro‐ecological and intraspecific studies are discussed.
Impacts of Bleaching and Packed Column Steam Refining on Cocoa Butter Properties
Authors: Vila Ayala José , Calliauw Gijs , Foubert Imogen , Dewettinck Koen , Dyer Bill , De Greyt Wim 
Published: September 2007

AbstractNatural and alkalized cocoa butters were bleached and subsequently steam refined in a continuous packed column at temperatures ranging between 160 and 220 °C. None of the processes evaluated gave rise to any detectable formation of trans fatty acids, interesterification or polymerization. For the pressures and steam injection rates used, packed‐column steam refining required a minimum temperature of 170 °C to achieve acceptable taste. Bleaching was highly effective in preventing darkening at high steam‐refining temperatures, as well as in removing alkaloids, such as theobromine and caffeine, before steam refining. The impacts on the crystallization properties of cocoa butter were studied using DSC and P‐NMR. The more significant changes in crystallization kinetics and equilibrium values can be reliably predicted on the basis of FFA removal from the butter.
Patients Reported Health-Related Quality of Life Five Years Post Coronary Artery Bypass Graft Surgery – A Methodological Study
Authors: Lee Geraldine A. 
Published: September 2007

Background: The number of individuals undergoing Coronary Artery Bypass Graft Surgery (CABGS) to treat coronary artery disease is steadily increasing. Aim: The purpose of the study was to describe the cohort's characteristics, their angina and breathless symptoms and report health-related quality of life (HRQoL) five years after CABGS. Methods: One hundred and twenty-eight patients participated in the follow-up study using the quality of life Short-Form 36 (SF-36) questionnaire. Angina and breathless symptoms were also recorded. Results: One hundred and nine patients were interviewed (face-to-face) and 19 completed postal questionnaires. The SF-36 component summaries of the face-to-face patients indicated that their physical (PCS) and mental (MCS) health was relatively good (45.8 and 53.6, respectively, with 0 = worst health and 100 = best health and 50 being the mean score), compared to the postal patients' mean PCS of 30.8 ( p < .001). The postal MCS was also lower but not statistically significant (49.6, p = .081). At follow-up, the majority of patients were asymptomatic in terms of angina and breathlessness compared to their pre-operative status. Conclusion: The findings demonstrate that patient perceived HRQoL five years after CABGS is generally good and patients remain relatively asymptomatic although data collection methods highlight differences in physical HRQoL.
Dysmenorrhea among Japanese women
Authors: Ohde S. , Tokuda Y. , Takahashi O. , Yanai H. , Hinohara S. , Fukui T. 
Published: September 2007

AbstractObjective: To investigate the epidemiology of dysmenorrhea in Japanese women of menstrual age. Methods: A prospective cohort study was conducted using a health diary in a sample representative of Japanese women. Information on health care use was also collected. Results: Among 823 enrolled participants (age range, 18–51 years), dysmenorrhea (mean duration 1.75 days; range 1–5 days) was reported in 15.8% (95% CI, 13.3–18.3) during the 1‐month study period. Common associated symptoms included headache (10.77%), back pain (6.92%), and fatigue (5.38%). No participant with dysmenorrhea visited a physician, while 51.5% of the women used self‐medication, and 7.7% used complementary/alternative medicine. Conclusion: Dysmenorrhea is common in Japanese women. In our study, about half used self‐medication, while some preferred complementary/alternative medicine. Dysmenorrhea is significantly associated with younger age and employment status.
Bringing Human Rights Home: An Examination of the Domestication of Human Rights Treaties in Nigeria
Authors: Egede Edwin 
Published: September 2007

AbstractThis article analyses the domestication of human rights treaties in Nigeria. It points out the shortcomings of the present dualist model under the 1999 constitution of the Federal Republic of Nigeria and makes suggestions for reform. It also examines the effect of beliefs and cultural values on the effective application of human rights treaties in Nigeria.
Genetic and environmental contributions to retrospectively reported DSM-IV childhood attention deficit hyperactivity disorder
Authors: Haberstick B. C. , Timberlake D. , Hopfer C. J. , Lessem J. M. , Ehringer M. A. , Hewitt J. K 
Published: September 2007

BackgroundA variety of methodologies and techniques converge on the notion that adults and children with attention deficit hyperactivity disorder (ADHD) have similar deficits, but there is limited knowledge about whether adult retrospective reports reflect similar genetic and environmental influences implicated in childhood ADHD.MethodDSM-IV ADHD symptoms were collected retrospectively from 3896 young adults participating in the National Longitudinal Study of Adolescent Health. Responses from this genetically informative sample of same- and opposite-sex twins and siblings were used to determine the magnitude of genetic and environmental influences. Possible gender differences in these effects were also examined. The degree of familial specificity of the genetic and environmental influences on the Inattentive and Hyperactive-Impulsive symptom dimensions was also determined.ResultsAdditive genetic effects contributed moderately to DSM-IV Inattentive, Hyperactive-Impulsive and Combined ADHD subtypes (heritability estimates of 0.30–0.38). Individual-specific influences accounted for the remaining proportion of the variance. Both genetic and individual-specific environmental effects contributed to the covariation of Inattentive and Hyperactive-Impulsive symptomologies.ConclusionsResults from our genetic analyses agree with previous findings based on self-assessment of current and retrospectively reported ADHD symptoms in adolescents and adults. Large individual-specific environmental influences as identified here suggest that current questionnaires used for retrospective diagnoses may not provide the most accurate reconstruction of the etiological influences on childhood ADHD in general population samples.
Social domain dysfunction and disorganization in borderline personality disorder
Authors: Hill J. , Pilkonis P. , Morse J. , Feske U. , Reynolds S. , Hope H. , Charest C. , Broyden N. 
Published: September 2007

BackgroundSocial dysfunction in personality disorder is commonly ascribed to abnormal temperamental traits but may also reflect deficits in social processing. In this study, we examined whether borderline and avoidant personality disorders (BPD, APD) may be differentiated by deficits in different social domains and whether disorganization of social domain functioning uniquely characterizes BPD.MethodPatients were recruited from psychiatric clinics in Pittsburgh, USA, to provide a sample with BPD, APD and a no-personality disorder (no-PD) comparison group. Standardized assessments of Axis I and Axis II disorders and social domain dysfunction were conducted, including a new scale of ‘domain disorganization’ (DD).ResultsPervasive social dysfunction was associated with a 16-fold increase in the odds of an Axis II disorder. Both APD and BPD were associated with elevated social dysfunction. Romantic relationship dysfunction was associated specifically with BPD symptoms and diagnosis. DD was associated specifically with a categorical BPD diagnosis and with a dimensional BPD symptom count.ConclusionsA focus on the inherently interpersonal properties of personality disorders suggests specific mechanisms (within and across interpersonal domains) that may help to account for the origins and maintenance of some disorders. In particular, BPD reflects disturbances in romantic relationships, consistent with a role for attachment processes, and in the organization of functioning across social domains.
Long‐Term Maintenance of a Transgenic Catharanthus roseus Hairy Root Line
Authors: Peebles Christie A. M. , Gibson Susan I. , Shanks Jacqueline V. , San Ka‐Yiu 
Published: September 2007

AbstractStably transformed transgenic hairy root cultures have the potential to be a valuable production platform for a variety of secondary metabolites. This study reports that a transgenic hairy root culture of Catharanthus roseus has been stably maintained for over 4.5 years. This culture carries a transgene that expresses the green fluorescent protein under the control of the glucocorticoid‐inducible promoter. Genomic PCR confirmed the presence of the GFP insert within the hairy roots, and induction with dexamethasone caused a significant (p < 0.02) increase in GFP levels.
Basic helix–loop–helix protein E47-mediated p21Waf1/Cip1 gene expression regulates apoptosis of intestinal epithelial cells
Authors: Bhattacharya Sujoy , Guo Huazhang , Ray Ramesh M. , Johnson Leonard R. 
Published: September 2007

Inhibition of ornithine decarboxylase by DFMO (α-difluromethylornithine) and subsequent polyamine depletion increases p21Cip1 protein, induces cell cycle arrest and confers resistance to apoptosis on intestinal epithelial cells. However, the mechanism by which polyamines regulate p21Cip1 expression and apoptosis is unknown. On the basis of the involvement of p21Cip1 as an anti-apoptotic protein, we tested the role of p21Cip1 in providing protection from apoptosis. Simultaneously, we investigated the role of E47, a basic helix–loop–helix protein, in the regulation of p21Cip1 gene transcription. Gene-specific siRNA (small interfering RNA) decreased E47 protein levels, increased p21Cip1 promoter activity and protein levels and protected cells from TNFα (tumour necrosis factor α)-induced apoptosis. Knockdown of p21Cip1 protein by siRNA resulted in cells becoming more susceptible to apoptosis. In contrast, incubation with EGF (epidermal growth factor) stimulated p21Cip1 mRNA and protein levels and rescued cells from apoptosis. During apoptosis, the level of E47 mRNA increased, causing a concomitant decrease in p21Cip1 mRNA and protein levels. Polyamine depletion decreased E47 mRNA levels and cell survival. Caspase 3-mediated cleavage of p130Cas has been implicated in p21Cip1 transcription. The progression of apoptosis led to a caspase 3-dependent cleavage of p130Cas and generated a 31 kDa fragment, which translocated to the nucleus, associated with nuclear E47 and inhibited p21Cip1 transcription. Polyamine depletion inhibited all these effects. Transient expression of the 31 kDa fragment prevented the expression of p21Cip1 protein and increased apoptosis. These results implicate p21Cip1 as an anti-apoptotic protein and suggest a role for polyamines in the regulation of p21Cip1 via the transcription repressor E47. Caspase-mediated cleavage of p130Cas generates a 31 kDa fragment, inhibits p21Cip1 transcription and acts as an amplifier of apoptotic signalling.
The control of phosphatidylinositol 3,4-bisphosphate concentrations by activation of the Src homology 2 domain containing inositol polyphosphate 5-phosphatase 2, SHIP2
Authors: Batty Ian H. , van der Kaay Jeroen , Gray Alex , Telfer Joan F. , Dixon Miles J. , Downes C. Peter 
Published: September 2007

Activation of class Ia PI3K (phosphoinositide 3-kinase) produces PtdInsP3, a vital intracellular mediator whose degradation generates additional lipid signals. In the present study vanadate analogues that inhibit PTPs (protein tyrosine phosphatases) were used to probe the mechanisms which regulate the concentrations of these molecules allowing their independent or integrated function. In 1321N1 cells, which lack PtdInsP3 3-phosphatase activity, sodium vanadate or a cell permeable derivative, bpV(phen) [potassium bisperoxo(1,10-phenanthroline)oxovanadate (V)], increased the recruitment into anti-phosphotyrosine immunoprecipitates of PI3K activity and of the p85 and p110α subunits of class Ia PI3K and enhanced the recruitment of PI3K activity stimulated by PDGF (platelet-derived growth factor). However, neither inhibitor much increased cellular PtdInsP3 concentrations, but both diminished dramatically the accumulation of PtdInsP3 stimulated by PDGF or insulin and markedly increased the control and stimulated concentrations of PtdIns(3,4)P2. These actions were accounted for by the ability of PTP inhibitors to stimulate the activity of endogenous PtdInsP3 5-phosphatase(s), particularly SHIP2 (Src homology 2 domain containing inositol polyphosphate 5-phosphatase 2) and to inhibit types I and II PtdIns(3,4)P2 4-phosphatases. Thus bpV(phen) promoted the translocation of SHIP2 from the cytosol to a Triton X-100-insoluble fraction and induced a marked (5–10-fold) increase in SHIP2 specific activity mediated by enhanced tyrosine phosphorylation. The net effect of these inhibitors was, therefore, to switch the signal output of class I PI3K from PtdInsP3 to PtdIns(3,4)P2. A key component controlling this shift in the balance of lipid signals is the activation of SHIP2 by increased tyrosine phosphorylation, an effect observed in HeLa cells in response to both PTP inhibitors and epidermal growth factor.
The acquisition of inflectional prefixes in Nairobi Swahili
Authors: Deen Kamil 
Published: September 2007

This study investigates the acquisition of inflectional prefixes in Swahili, an eastern Bantu language. The order of morphemes in adult Swahili is: Subject Agreement – Tense – (Object Agreement) –Verb Root – (derivational suffixes) –Mood Vowel. I present data from an original corpus of 4 Swahili-speaking children (ages 1;8-3;0) who were recorded in Nairobi, Kenya. An analysis of the children’s verbal utterances reveals that four clause types occur in the speech of all four children:
a. Agr–T–Verb StemFull Clause
b. Ø–T–Verb Stem[-SA] Clause
c. Agr–Ø–Verb Stem[-T] Clause
d. Ø–Ø–Verb StemBare Verb Stem
Of these four, only full clauses and [-SA] clauses are permitted by adults in this non-standard dialect of Swahili. A review of five influential theories on the acquisition of morphosyntax (the Metrical Omission Model, Gerken, 1991; the Truncation Hypothesis, Rizzi, 1994; the Underspecification of T, Wexler, 1994; the underspecification of Agr, Clahsen et al. , 1996; and the underspecification of Agr and T, Schütze & Wexler, 1996) shows that the data support the Agr-Tense Omission Model (Schütze & Wexler, 1996) in showing that agreement and tense may be optionally and independently underspecified.