bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is Asp‐His‐Ser/Thr‐Trp tetrad hydrogen‐bond network important to WD40‐repeat proteins: A statistical and theoretical study
Authors: Wu Xian‐Hui , Zhang Hui , Wu Yun‐Dong 
Published: October 2009

AbstractWD40‐repeat proteins are abundant and play important roles in forming protein complexes. The domain usually has seven WD40 repeats, which folds into a seven β‐sheet propeller with each β‐sheet in a four‐strand structure. An analysis of 20 available WD40‐repeat proteins in Protein Data Bank reveals that each protein has at least one Asp‐His‐Ser/Thr‐Trp (D‐H‐S/T‐W) hydrogen‐bonded tetrad, and some proteins have up to six or seven such tetrads. The relative positions of the four residues in the tetrads are also found to be conserved. A sequence alignment analysis of 560 WD40‐repeat protein sequences in human reveals very similar features, indicating that such tetrad may be a general feature of WD40‐repeat proteins. We carried out density functional theory and found that these tetrads can lead to significant stabilization including hydrogen‐bonding cooperativity. The hydrogen bond involving Trp is significant. These results lead us to propose that the tetrads may be critical to the stability and the mechanism of folding of these proteins. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Detection of multiscale pockets on protein surfaces using mathematical morphology
Authors: Kawabata Takeshi 
Published: October 2009

AbstractDetection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid‐based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocket‐finding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, Rinaccess (minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server (http://biunit.naist.jp/ghecom). Proteins 2010. © 2009 Wiley‐Liss, Inc.
Symmetry‐based analysis of the electron–phonon interaction in graphene
Authors: Milošević I. , Kepčija N. , Dobardžić E. , Mohr M. , Maultzsch J. , Thomsen C. , Damnjanović M. 
Published: October 2009

AbstractSymmetry‐based analysis of the electron–phonon interaction in graphene is performed. Some nontrivial physical properties of graphene are shown to be direct consequence of symmetry, independent on the applied dynamical model. Namely, it is found that there are vibronically uncoupled non symmetric modes which thus might be responsible for the stability of the honeycomb lattice. Symmetry also predicts vanishing of the electron–phonon interaction for quite a number of the normal displacements. Consequently, lattice dynamics along these degrees of freedom is governed by the ion repulsion which leads to the anharmonic terms, being linear in absolute elongation. In particular, this effect is attributed to the K and Γ points of the Brillouin zone, giving insight into origin of the Kohn anomaly. The results are further numerically confirmed within full and tight‐binding density functional calculations and force constants model.
AFM induced electrostatic charging of nanocrystalline diamond on silicon
Authors: Verveniotis E. , Čermák J. , Kromka A. , Rezek B. 
Published: October 2009

AbstractA nanocrystalline diamond (NCD) thin film (80 nm) is deposited on a p‐type Si substrate and oxygen terminated by r.f. oxygen plasma. An atomic force microscope (AFM) is used to induce electrostatically charged micrometer‐sized areas on the diamond film by applying a bias voltage on the AFM tip during contact mode scan. Trapped charge is detected by Kelvin force microscopy showing a potential difference of up to 1.4 V. The potential amplitude and spatial distribution are controlled by the bias voltage applied on the tip (±30 V) and scan speed (2–20 µm/s). Contribution of diamond bulk and grain boundaries to the charging effects shows no significant variations. We compare the results with the charging of bare Si substrate.
Donor–acceptor nanocomposite structures for organic photovoltaic applications
Authors: Fostiropoulos Konstantinos , Schindler Wolfram 
Published: October 2009

AbstractWe investigated the effect of substrate temperature TS on the growth of 80 nm donor–acceptor nanocomposite (DAN) layers consisting of co‐evaporated Zn‐phthalocyanine (ZnPc) and C60 as absorber materials in organic solar cells. High temperature devices show lower series resistances RS but also reduced VOC. Both effects are diminished when the upper 20 nm of the blend are deposited at room temperature (RT). Moreover, the temperature profile improves the photocurrent density JSC. Best efficiencies (up to 2.1%) were achieved applying a 90 °C/RT profile. Transmission electron microscopy studies on the corresponding DAN revealed the temperature‐dependent formation of crystalline C60 phases (already at low TS) and crystalline ZnPc phases (at highest TS). The strong phase separation at 90 °C results in less compact and mechanical unstable films. Such devices exhibit low parallel resistance RP. When the cold cover layer is applied RP doubles.
Mass separation of metallic and semiconducting single‐wall carbon nanotubes using agarose gel
Authors: Tanaka Takeshi , Jin Hehua , Miyata Yasumitsu , Fujii Shunjiro , Nishide Daisuke , Kataura Hiromichi 
Published: October 2009

AbstractMetallic and semiconducting single‐wall carbon nanotubes (SWCNTs) were separated using agarose gel. When the SWCNTs isolated with sodium dodecyl sulfate (SDS) were embedded in agarose gel, the metallic SWCNTs were eluted from the gel by applying electronic field or mechanical stress, for example, centrifugation etc., and semiconducting SWCNTs remained in the gel. The purities for metallic and semiconducting SWCNTs were ∼70% and ∼95%, respectively. One of the simplest methods was freeze, thaw and squeeze the SWCNTs containing gel. These methods can separate various kinds of SWCNTs. By using centrifugation method, we could separate about 10 mg of SWCNTs with a 500 ml bottle.
Atoms, elements, molecules, and matter: An investigation into the congenitally blind adolescents' conceptual frameworks on the nature of matter
Authors: Smothers Sinikka M. , Goldston M. Jenice 
Published: October 2009

AbstractThis qualitative multiple case study explored the conceptual frameworks of two congenitally blind male adolescents on the nature of matter. We examined participants' responses on four tactile investigations focused on concepts and processes associated with matter changes. The matter changes investigated were dissolution, chemical change, expansion, and condensation. Individual interview and model‐making sessions comprised the primary data collection, whereas journal writing and focus group interviews provided additional, secondary data. Participants' responses during matter activities were analyzed by using three data frames: structural views of matter, types of understanding of matter changes, and conceptual consistency of students' explanatory schemes. Coding of the responses identified macro‐ (physically observable) and microparticulate (invisible) views of matter and both scientifically accurate and alternate understandings of matter changes coexisting within one response set. Data analysis led to the development of individual meandering mind maps as an analytical tool that illustrates the shifting of each participant's thinking between the macro‐ and microparticulate views of matter. A meandering mind map utilized in the study consists of a macroparticulate outer layer, microparticulate inner layer, and an interface layer that includes lynchpin concepts compound, molecule, atom, and element. The lynchpin concepts are perceived to mediate and scaffold cognitive shifts between the macroparticulate and the microparticulate views of matter. During individual interviews, each participant's responses were coded to one of the three categories, plotted in clockwise sequence and connected with a line. The findings include that congenitally blind participants hold (a) both macro‐ and microparticulate views of the nature of matter, (b) scientifically accepted and scientifically alternative understandings about matter concepts, and (c) conceptually inconsistent explanatory schemes of matter across the four data collection activities. © 2009 Wiley Periodicals, Inc. Sci Ed 94:448–477, 2010
Generation of Human-Induced Pluripotent Stem Cells in the Absence of Exogenous Sox2
Authors: Li Wenlin , Zhou HongYan , Abujarour Ramzey , Zhu Saiyong , Young Joo Jin , Lin Tongxiang , Hao Ergeng , Schöler Hans R. , Hayek Alberto , Ding Sheng 
Published: October 2009

Abstract
Induced pluripotent stem cell technology has attracted enormous interest for potential application in regenerative medicine. Here, we report that a specific glycogen synthase kinase 3 (GSK-3) inhibitor, CHIR99021, can induce the reprogramming of mouse embryonic fibroblasts transduced by only two factors, Oct4 and Klf4. When combined with Parnate (also named tranylcypromine), an inhibitor of lysine-specific demethylase 1, CHIR99021 can cause the reprogramming of human primary keratinocyte transduced with the two factors, Oct4 and Klf4. To our knowledge, this is the first time that human iPS cells have been generated from somatic cells without exogenous Sox2 expression. Our studies suggest that the GSK-3 inhibitor might have a general application to replace transcription factors in both mouse and human reprogramming.
Disclosure of potential conflicts of interest is found at the end of this article.
Requirement of α4β1 and α5β1 Integrin Expression in Bone-Marrow-Derived Progenitor Cells in Preventing Endotoxin-Induced Lung Vascular Injury and Edema in Mice
Authors: Wary Kishore K. , Vogel Stephen M. , Garrean Sean , Zhao Yidan D. , Malik Asrar B. 
Published: October 2009

Abstract
The goal of this study was to determine the role of integrin-mediated adhesion of bone-marrow-derived progenitor cells (BMPCs) as a requirement for the endothelial barrier protection in a lung injury model. C57BL mice were used as the source for BMPCs, which were characterized as CD34+ and fetal liver kinase-1 (Flk1)+ and also an expression of a repertoire of integrins. We used a mouse model of bacterial lipopolysaccharide (LPS)-induced lung vascular injury and edema formation to test the effects of BMPC integrin expression in preventing endothelial barrier injury. Adhesion of BMPCs to purified extracellular matrix proteins induced focal adhesion kinase (Fak) phosphorylation and formation of branching point structures in a α4 and α5 integrin-dependent manner. BMPCs expressing red fluorescent protein (RFP) were administered via the retro-orbital venous route in mice treated intraperitonially with LPS (7.5 mg/kg body weight). We observed increased retention of RFP-labeled Flk1+ and CD34+ BMPCs for up to 8 weeks in mice injured with LPS. BMPC transplantation increased survival by 50% (at 72–96 hours after LPS) and reduced lung vascular injury and extravascular water content induced by LPS. However, blocking with anti-α4 or anti-α5 integrin antibody or shRNA-mediated silencing of α4 or α5 integrins in donor BMPCs failed to prevent the vascular injury or edema formation and mortality. Thus, α4 and α5 integrin-dependent adhesion of BMPCs in lung tissue plays a critical role in preventing lung vascular injury and increasing survival in a mouse model of LPS-induced acute lung injury.
Disclosure of potential conflicts of interest is found at the end of this article.
Performance‐based plastic design (PBPD) method for earthquake‐resistant structures: an overview
Authors: Goel Subhash C. , Liao Wen‐Cheng , Reza Bayat M. , Chao Shih‐Ho 
Published: October 2009

AbstractThis paper presents a brief overview of performance‐based plastic design method as applied to the seismic design of building structures. The method uses pre‐selected target drift and yield mechanisms as key performance criteria. The design base shear for a selected hazard level is calculated by equating the work needed to push the structure monotonically up to the target drift to that required by an equivalent single degree of freedom to achieve the same state. Plastic design is performed to detail the frame members and connections in order to achieve the targeted yield mechanism and behaviour. The method has been successfully applied to a variety of common steel framing systems and, more recently, to Reinforced Concrete (RC) moment frames. Results of extensive inelastic static and dynamic analyses showed that the frames developed desired strong column‐sway mechanisms, and the storey drifts and ductility demands were well within the target values, thus meeting the desired performance objectives. The examples of 20‐storey steel and RC moment frames, as presented in the paper, showed that the method is especially advantageous for tall frames, where cumbersome and lengthy iterative design work in current practice can be completely eliminated, while leading to excellent performance as targeted. The basic work‐energy equation can also be used for seismic evaluation of existing structures. The results, as presented in this paper, showed excellent agreement with those obtained from more elaborate inelastic time‐history analyses. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis and Characterization of Diorganotin(IV) Complexes Bearing Binary Schiff‐Bases and Crystal Structure of nBu2SnL1
Authors: Wang Qibao , Ding Ruifang , Wang Ning , Zhang Daodong , Li Jikun 
Published: October 2009

AbstractFour novel diorganotin(IV) complexes with general formula R2SnL (R = nBu, PhCH2) were synthesized from diorganotin dichlorides and binary Schiff‐bases (H2L) containing N2O2 donor atoms in the presence of sodium ethoxide. The Schiff bases were prepared by reactions of o‐phenylenediamine with 3‐tert‐butyl‐2‐hydroxy‐5‐methylbenzaldehyde (H2L1) and salicylaldehyde (H2L2) respectively. The compounds were characterized by elemental analyses, IR, and NMR spectroscopy. The solid‐state crystal structure of the compound nBu2SnL1 was determined by single‐crystal structural analysis.
Impact of Preoperative Bevacizumab on Complications After Resection of Colorectal Liver Metastases: Case‐Matched Control Study
Authors: Mahfud Mahfud , Breitenstein Stefan , El‐Badry Ashraf Mohammad , Puhan Milo , Rickenbacher Andreas , Samaras Panagiotis , Pessaux Patrick , Lopez‐Ben Santiago , Jaeck Daniel , Figueras Joan , Alain‐Clavien Pierre 
Published: October 2009

AbstractBackground
Chemotherapy may increase postoperative morbidity and mortality after liver surgery. Especially bevacizumab, a monoclonal antibody against vascular endothelial growth factor (VEGF), could have a detrimental effect. To assess the impact of neoadjuvant bevacizumab on clinical outcome after hepatectomy for colorectal liver metastases (CRLMs) this case‐matched control study was initiated.MethodsThe multicentric data collection was performed in the Swiss HPB Center of the University Hospital Zurich (CH), the Department of Digestive Surgery and Transplantation Strasbourg (F), and the Division of Hepato‐biliary‐pancreatic surgery of “Josep Tureta” Hospital Girona (E). Consecutive patients operated onbetween July 2005 and December 2007 due to CRLMs who received neoadjuvant chemotherapy were assessed. Patients were divided in two groups: group A had neoadjuvant chemotherapy with bevacicumab, and group B had it without bevacizumab.ResultsNo differences in overall morbidity (56 vs. 40% in the bevacizumab and control groups, respectively, p = 0.23) or mortality could be documented. Similarly, the incidence of severe postoperative complications was not statistically different between the bevacizumab and control groups (31 and 18%, respectively, p = 0.31). Wound complications were comparable (11% in the bevacizumab group compared and 9% in the control group, p = 1.00). However, bevacizumab was associated with a significantly decreased incidence of postoperative hepatic insufficiency (7 vs. 20%, p = 0.03).ConclusionsNo impact on the incidence or severity of complications by bevacizumab could be shown. Bevacizumab may even reduce the incidence of liver failure after liver surgery.
Eight‐Year Experience with Minimally Invasive Cardiothoracic Surgery
Authors: Iribarne Alexander , Karpenko Anna , Russo Mark J. , Cheema Faisal , Umann Tianna , Oz Mehmet C. , Smith Craig R. , Argenziano Michael 
Published: October 2009

AbstractBackgroundOver the past decade, minimally invasive cardiac surgery (MICS) has emerged as an accepted approach for the management of cardiac disease that requires a surgical solution. We report the results of an 8‐year, single‐institution experience with MICS.MethodsBetween January 1, 2000 and December 31, 2007, a total of 910 patients underwent MICS. Major cases included aortic valve procedures (71, 7.8%), coronary artery bypass grafting (96, 10.5%), atrioseptal defect repair (103, 11.3%), and mitral valve procedures (507, 55.7%). Major outcomes of interest included the complication and mortality rates.ResultsThe mean age of the patients was 57 ± 15 years; the mean ejection fraction was 55% ± 11%; and the mean body mass index was 26.1 ± 4.9. Overall, 782 cases (85.9%) were performed through a mini‐thoracotomy. Most of the cases were accomplished through central cannulation (765, 84.0%), and venous drainage was most commonly performed in a bicaval fashion (percutaneous superior vena cava and percutaneous inferior vena cava). The mean aortic cross‐clamp and cardiopulmonary bypass (CPB) times were 58.1 ± 44.9 and 101.9 ± 66.8 min, respectively. Conversion to full sternotomy occurred in 10 patients, and the median length of stay in hospital was 6 days. The overall complication rate was 8.8%, and the 30‐day mortality rate was 2.9%. In the multivariate logistic regression analysis, risk factors associated with in‐hospital complications included age, CPB time, arterial cannulation location, conversion from off‐CPB to on‐CPB, hepatic insufficiency, and diabetes. In the multivariate hazards regression analysis, risk factors associated with mortality included postoperative stroke, renal failure, and sternal wound infection; CPB time; and previous surgery.ConclusionsIn our experience, minimally invasive approaches are effective and reproducible for a variety of cardiac operations, with acceptable operating time durations, morbidity, and mortality.
The Importance of the Community Context in the Epidemiology of Early Adolescent Substance Use and Delinquency in a Rural Sample
Authors: Chilenski Sarah M. , Greenberg Mark T. 
Published: October 2009

AbstractConsiderable research has demonstrated that substance use and delinquency during early adolescence can have long‐term negative health consequences. As the correlates of these behaviors cross levels and contexts, it is likely that a social ecological approach will provide insight to inform community prevention. This approach informs the present study, which focuses on developing a multiple‐method measurement strategy to examine associations among community risks, resources, and rates of early adolescent substance use and delinquency in 28 rural and small town communities. Measures include five domains of community risk, four domains of community resources, and population rates of early adolescent substance use and delinquency. Results demonstrated that several measures of context were significantly associated with community rates of adolescent substance use and delinquency, and different risks and resources appear important for different outcomes. Multiple associations were curvilinear, and interactions may also be important. Findings suggest that it may be worthwhile to create and test new intervention strategies that target community factors in the pursuit of prevention.
African‐American Women's Conceptualizations of Health Disparities: A Community‐Based Participatory Research Approach
Authors: Baffour Tiffany D. , Chonody Jill M. 
Published: October 2009

AbstractHealth disparities among African‐American families represent a significant social problem. Nationally, African‐American infants have dramatically worse birth outcomes than other racial and ethnic groups. A Community‐Based Participatory Research approach was utilized to engage community residents. This study examined participants' definitions of infant mortality, views on the community impact of infant mortality, and strengths and vulnerabilities in the health care service delivery system. Qualitative data were gathered in a rural North Florida community where health education groups are conducted. Eight focus groups were arranged with African‐American women (n = 46), ranging in age from 14 to 35, who were pregnant, parenting children under the age of two. Respondents poignantly described personal experiences of loss associated with infant mortality. They indicated awareness of problems related to lack of accessibility and availability of medical and social services. The use of social‐ecological theory and implications for policy and social justice are discussed.
Area‐Based Socioeconomic Characteristics of Industries at High Risk for Violence in the Workplace
Authors: Ta Myduc L. , Marshall Stephen W. , Kaufman Jay S. , Loomis Dana , Casteel Carri , Land Kenneth C. 
Published: October 2009

AbstractThis study examined socioeconomic factors associated with the presence of workplaces belonging to industries reported to be at high risk for worker homicide. The proportion of 2004 North Carolina workplaces in high‐risk industries was computed following spatial linkage of individual workplaces to 2000 United States Census Block Groups (n = 3,925). Thirty census‐derived socioeconomic variables (selected a priori as potentially predictive of violence) were summarized using exploratory factor analysis into poverty/deprivation, human/economic capital, and transience/instability. Multinomial logistic regression models indicate associations between higher proportion of workplaces belonging to high‐risk industries and Block Groups with more poverty/deprivation or transience/instability and less human/economic capital. The relationship between human/economic capital and Block Groups proportion of high‐risk industry workplaces was modified by levels of transience/instability. Community characteristics therefore contribute to the potential for workplace violence, and future research should continue to understand the relationship between social context and workplace violence risk.