bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatch: Target‐binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds
Authors: Zhang Changsheng , Lai Luhua 
Published: December 2011

AbstractProteins perform their functions mainly via active sites, whereas other parts of the proteins comprise the scaffolds, which support the active sites. One strategy for protein functional design is transplanting active sites, such as catalytic sites for enzyme or binding hot spots for protein–protein interactions, onto a new scaffold. AutoMatch is a new program designed for efficiently elucidating suitable scaffolds and potential sites on the scaffolds. Backrub motions are used to treat backbone flexibility during the design process. A step‐by‐step checking strategy and cluster‐representation examination strategy were developed to solve the large combinatorial problem for the matching of active‐site conformations. In addition, a grid‐based binding energy scoring method was used to filter the solutions. An enzyme design benchmark and a protein–protein interaction design benchmark were built to test the algorithm. AutoMatch could identify the hot spots in the nonbinding protein and rank them within the top five results for 8 of 10 target‐binding protein design cases. In addition, among the 15 enzymes tested, AutoMatch can identify the catalytic active sites in the apoprotein and rank them within the top five results for 13 cases. AutoMatch was also tested for screening scaffold library in designing binding proteins targeting influenza hemagglutinin, HIV gp120, and epidermal growth factor receptor kinase, respectively. AutoMatch, and the two test sets, ActApo and ActFree, are available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi‐bin/down.cgi. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Predictive event modelling in multicenter clinical trials with waiting time to response
Authors: Anisimov Vladimir V. 
Published: December 2011

A new analytic statistical technique for predictive event modeling in ongoing multicenter clinical trials with waiting time to response is developed. It allows for the predictive mean and predictive bounds for the number of events to be constructed over time, accounting for the newly recruited patients and patients already at risk in the trial, and for different recruitment scenarios.For modeling patient recruitment, an advanced Poisson‐gamma model is used, which accounts for the variation in recruitment over time, the variation in recruitment rates between different centers and the opening or closing of some centers in the future. A few models for event appearance allowing for ‘recurrence’, ‘death’ and ‘lost‐to‐follow‐up’ events and using finite Markov chains in continuous time are considered.To predict the number of future events over time for an ongoing trial at some interim time, the parameters of the recruitment and event models are estimated using current data and then the predictive recruitment rates in each center are adjusted using individual data and Bayesian re‐estimation. For a typical scenario (continue to recruit during some time interval, then stop recruitment and wait until a particular number of events happens), the closed‐form expressions for the predictive mean and predictive bounds of the number of events at any future time point are derived under the assumptions of Markovian behavior of the event progression. The technique is efficiently applied to modeling different scenarios for some ongoing oncology trials. Case studies are considered. Copyright © 2011 John Wiley & Sons, Ltd.
The effect of vertical shear orientation on tropical cyclogenesis
Authors: Rappin Eric D. , Nolan David S. 
Published: December 2011

AbstractThe effect of the relative orientation of the vertical wind shear to the surface wind on tropical cyclogenesis is explored in environments of radiative‐convective equilibrium (RCE) through numerical simulation. This study serves as a companion paper to an earlier study on the thermodynamics of genesis in RCE.It is found, when the mean surface wind and shear are aligned, a negative surface wind anomaly arises from the superposition of the mean and vortex surface flows left of the shear vector. The resulting weak surface enthalpy fluxes and up‐shear quasi‐balanced subsidence leads to dry air being located cyclonically down‐wind of the down‐shear convective anomaly. Thus convection is inhibited from propagating cyclonically around the core leading to a large down‐shear vortex tilt. Conversely, in a counter‐aligned orientation, the negative surface wind anomaly and driest air is found right of the shear vector. Hence the driest air rotates into the down‐shear flank where it moistened by shear‐organized convection. Furthermore, the boundary layer is relatively moist left of shear due to the positive surface wind anomaly, therefore promoting the cyclonic propagation from down‐shear and constraining the magnitude of the vortex tilt.Genesis is intimately tied to the magnitude of the tilt and is found to occur once the mid‐level vortex has precessed into the up‐shear flank. For smaller values of maximum tilt, vortex precession is comparatively rapid, aided by “showerhead” moistening provided by the up‐shear advection of frozen condensate aloft. With the up‐shear flank pre‐moistened, rapid precession of the mid‐level vortex, at smaller radii, leads to near saturation on the mesoscale and the onset of rapid intensification. When the magnitude of the tilt is quite large, precession is much slower and the showerhead effect is significantly reduced until just prior to the emergence of the mid‐level vortex in the up‐shear flank. Copyright © 2011 Royal Meteorological Society
Hydrostatic Hamiltonian particle‐mesh (HPM) methods for atmospheric modelling
Authors: Shin Seoleun , Reich Sebastian , Frank Jason 
Published: December 2011

AbstractWe develop a hydrostatic Hamiltonian particle‐mesh (HPM) method for efficient long‐term numerical integration of the atmosphere. In the HPM method, the hydrostatic approximation is interpreted as a holonomic constraint for the vertical position of particles. This can be viewed as defining a set of vertically buoyant horizontal meshes, with the altitude of each mesh point determined so as to satisfy the hydrostatic balance condition and with particles modelling horizontal advection between the moving meshes. We implement the method in a vertical‐slice model and evaluate its performance for the simulation of idealized linear and nonlinear orographic flow in both dry and moist environments. The HPM method is able to capture the basic features of the gravity wave to a degree of accuracy comparable with that reported in the literature. The numerical solution in the moist experiment indicates that the influence of moisture on wave characteristics is represented reasonably well and the reduction of momentum flux is in good agreement with theoretical analysis. Copyright © 2011 Royal Meteorological Society
Abcg2 Expression Marks Tissue-Specific Stem Cells in Multiple Organs in a Mouse Progeny Tracking Model
Authors: Fatima Soghra , Zhou Sheng , Sorrentino Brian P. 
Published: December 2011

Abstract
The side population phenotype is associated with the Hoechst dye efflux activity of the Abcg2 transporter and identifies hematopoietic stem cells (HSCs) in the bone marrow. This association suggests the direct use of Abcg2 expression to identify adult stem cells in various other organs. We have generated a lineage tracing mouse model based on an allele that coexpresses both Abcg2 and a CreERT2 expression cassette. By crossing these mice with lox-STOP-lox reporter lines (LacZ or YFP), cells that express Abcg2 and their progeny were identified following treatment with tamoxifen (Tam). In the liver and kidney, in which mature cells express Abcg2, reporter gene expression verified the expected physiologic expression pattern of the recombinant allele. Long-term marking of HSCs was seen in multiple peripheral blood lineages from adult mice, demonstrating that Abcg2+ bone marrow HSCs contribute to steady-state hematopoiesis. Stem cell tracing patterns were seen in the small intestine and in seminiferous tubules in the testis 20 months after Tam treatment, proving that stem cells from these organs express Abcg2. Interstitial cells from skeletal and cardiac muscle were labeled, and some cells were costained with endothelial markers, raising the possibility that these cells may function in the repair response to muscle injury. Altogether, these studies prove that Abcg2 is a stem cell marker for blood, small intestine, testicular germ cells, and possibly for injured skeletal and/or cardiac muscle and provide a new model for studying stem cell activity that does not require transplant-based assays.
Disclosure of potential conflicts of interest is found at the end of this article.
Wind‐induced torsion vibration of the super high‐rise building of Shenzhen Energy Center
Authors: Ruo‐qiang Feng , Jihong Ye , Yan Guirong , Qing‐xiang Li , Bin Yao 
Published: December 2011

SUMMARYThe synchronous multipoint scanning system technique in wind tunnel tests and random vibration theory method were used to analyze the wind‐induced torsion vibration of some irregularly shaped super high‐rise buildings in downtowns. The torsion vibration modes and the spectra of torsion wind load were studied, and the proportions of mean wind torsion, inertia torsion and the mass eccentricity torsion caused by horizontal inertia forces are discussed. The following conclusions can be drawn. First, the third and fourth modes have torsion vibration shapes, and their frequencies are in the high‐energy area of the spectra of the torsion wind load; the third and fourth modes are included in the resonant component of the spectra of the top torsion angle of the building, and the third mode is dominant. Second, the torsion stiffness is weak in the high stories of the building, so the inertia torsion is dominant, whereas the torsion stiffness is strong in the low stories; the mean wind torsion is dominant. The proportion of the mass eccentricity torsion moment caused by horizontal inertia forces is small. Finally, the wind‐induced torsion moment at a 90° wind angle is the largest, whereas the torsion eccentricity is 46% of the radius of gyration and is much greater than the mass eccentricity; thus, the wind‐induced torsion should be considered. The wind‐induced torsion vibration of the building is sensitive to wind directions. Copyright © 2011 John Wiley & Sons, Ltd.
Virtual Cell: computational tools for modeling in cell biology
Authors: Resasco Diana C. , Gao Fei , Morgan Frank , Novak Igor L. , Schaff James C. , Slepchenko Boris M. 
Published: December 2011

AbstractThe Virtual Cell (VCell) is a general computational framework for modeling physicochemical and electrophysiological processes in living cells. Developed by the National Resource for Cell Analysis and Modeling at the University of Connecticut Health Center, it provides automated tools for simulating a wide range of cellular phenomena in space and time, both deterministically and stochastically. These computational tools allow one to couple electrophysiology and reaction kinetics with transport mechanisms, such as diffusion and directed transport, and map them onto spatial domains of various shapes, including irregular three‐dimensional geometries derived from experimental images. In this article, we review new robust computational tools recently deployed in VCell for treating spatially resolved models. WIREs Syst Biol Med 2012, 4:129–140. doi: 10.1002/wsbm.165This article is categorized under:

Models of Systems Properties and Processes > Cellular Models
Analytical and Computational Methods > Computational Methods
Models of Systems Properties and Processes > Mechanistic Models
Structural and Solution Studies of two Mercury(II) Complexes with [1,3‐Bis(2‐ethoxy)benzene]triazene
Authors: Rofouei Mohammad Kazem , Attar Gharamaleki Jafar , Fereyduni Ehsan , Aghaei Abolfazl , Bruno Giuseppe , Rudbari Hadi Amiri 
Published: December 2011

AbstractThe reaction of [1,3‐bis(2‐ethoxy)benzene]triazene, [HL], with Hg(SCN)2 and Hg(CH3COO)2, resulted in the formation of the complexes [HgL(SCN)] (1) and [HgL2]·CH3OH (2). They were characterized by means of X‐ray crystallography, CHN analysis, FT‐IR, 1H NMR, and 13C NMR spectroscopy. The structure of compound 1 consists of two independent complexes in which the HgII atoms are stacked along the crystallographic a axis to form infinite chains. Each HgII atom is chelated by one L ligand and one SCN ligand, whereas in compound 2, the HgII atom is surrounded by two L ligands. In addition, 1D chains formed by metal–π interactions are connected to each other by C–H···π stacking interactions in the structure of 1, which results in a 2D architecture. An interesting feature of compound 2 is the presence of C–H···π edge‐to‐face interactions.
Synthesis and Structural Characterization of a Novel Heterodinuclear Vanadium(IV)‐Nickel(II) Complex
Authors: Du Shi‐Zhen , Feng Jun , Cheng Yi‐Feng , An Lan , Lu Xiao‐Ming 
Published: December 2011

AbstractA novel VIV‐NiII heterodinuclear complex [VO(cat)2][Ni(1, 2‐PDA)2H2O] (1) (cat = catechol; 1, 2‐PDA = 1, 2‐propane diamine) was synthesized at low temperature (10 °C) and characterized by IR spectroscopy and X‐ray diffraction. A novel Ni–O=V structure exists in the complex, the vanadyl–catechol moiety and the nickel–diamine moiety are connected by an oxygen bridge; all molecules are further assembled into crystallites by O–H···O hydrogen bonds.
Changing Pattern of Intestinal Obstruction in Northern Jordan
Authors: Omari Abdulkareem H. , Alkhatib Loiy L. , Khammash Muhammad R. 
Published: December 2011

AbstractBackgroundObstructed abdominal wall hernias have been reported to be the leading cause of mechanical intestinal obstruction (MIO) among adults in developing countries. In the developed countries, postoperative adhesions are the commonest cause. With the worldwide improvements in health services and education, especially in developing countries, we aimed to determine the effects of these improvements on the patterns and outcomes of management of MIO in JordanMethodsThe records of all patients who were treated for MIO between the years 2005 and 2010 were reviewed retrospectively. Causes of MIO, presenting symptoms, the main imaging study performed, and the results of management are described. The pattern was compared with that in a previous 1993 report from Jordan.ResultsA total of 88 patients were treated for MIO. Postoperative adhesions in 52.5%, gastrointestinal tumors in 21.0%, and obstructed abdominal wall hernias in 9.5% were the three major causes of MIO. Three patients developed surgical‐site infections (3.3%), and one developed a minor anastomotic leak that was treated accordingly (1.1%). There were no mortalities. In 1993, obstructed hernias accounted for 30% of the MIOs followed by postoperative adhesions and tumors (27 and 14%, respectively). There was a 7% mortality rate.ConclusionsOur data confirmed that improved health education programs and services changed the pattern of causes improved the outcomes of management of MIO in Jordan.
Engineered glucose isomerase from Streptomyces sp. SK is resistant to Ca2+ inhibition and Co2+ independent
Authors: Ben Hlima Hajer , Aghajari Nushin , Ben Ali Mamdouh , Haser Richard , Bejar Samir 
Published: December 2011

Abstract
The role of two amino acid residues linked to the two catalytic histidines His54 and His220 in kinetics and physicochemical properties of the Streptomyces sp. SK glucose isomerase (SKGI) was investigated by site-directed mutagenesis and molecular modeling. Two single mutations, F53L and G219D, and a double mutation F53L/G219D was introduced into the xylA SKGI gene. The F53L mutation increases the thermostability and the catalytic efficiency and also slightly shifts the optimum pH from 6.5 to 7, but displays a profile being similar to that of the wild-type enzyme concerning the effect of various metal ions. The G219D mutant is resistant to calcium inhibition retaining about 80% of its residual activity in 10 mM Ca2+ instead of 10% for the wild-type. This variant is activated by Mn2+ ions, but not Co2+, as seen for the wild-type enzyme. It does not require the latter for its thermostability, but has its half-life time displaced from 50 to 20 min at 85°C. The double mutation F53L/G219D restores the thermostability as seen for the wild-type enzyme while maintaining the resistance to the calcium inhibition. Molecular modeling suggests that the increase in thermostability is due to new hydrophobic interactions stabilizing α2 helix and that the resistance to calcium inhibition is a result of narrowing the binding site of catalytic ion.
Recurrent Aspergillus contamination in a biomedical research facility: a case study
Authors: Cornelison Christopher T , Stubblefield Bryan , Gilbert Eric , Crow Sidney A 
Published: December 2011

Abstract
Fungal contamination of biomedical processes and facilities can result in major revenue loss and product delay. A biomedical research facility (BRF) culturing human cell lines experienced recurring fungal contamination of clean room incubators over a 3-year period. In 2010, as part of the plan to mitigate contamination, 20 fungal specimens were isolated by air and swab samples at various locations within the BRF. Aspergillus niger and Aspergillus fumigatus were isolated from several clean-room incubators. A. niger and A. fumigatus were identified using sequence comparison of the 18S rRNA gene. To determine whether the contaminant strains isolated in 2010 were the same as or different from strains isolated between 2007 and 2009, a novel forensic approach to random amplified polymorphic DNA (RAPD) PCR was used. The phylogenetic relationship among isolates showed two main genotypic clusters, and indicated the continual presence of the same A. fumigatus strain in the clean room since 2007. Biofilms can serve as chronic sources of contamination; visual inspection of plugs within the incubators revealed fungal biofilms. Moreover, confocal microscopy imaging of flow cell-grown biofilms demonstrated that the strains isolated from the incubators formed dense biofilms relative to other environmental isolates from the BRF. Lastly, the efficacies of various disinfectants employed at the BRF were examined for their ability to prevent spore germination. Overall, the investigation found that the use of rubber plugs around thermometers in the tissue culture incubators provided a microenvironment where A. fumigatus could survive regular surface disinfection. A general lesson from this case study is that the presence of microenvironments harboring contaminants can undermine decontamination procedures and serve as a source of recurrent contamination.
Decreased serum antioxidant capacity in patients with Wilson disease is associated with neurological symptoms
Authors: Bruha Radan , Vitek Libor , Marecek Zdenek , Pospisilova Lenka , Nevsimalova Sona , Martasek Pavel , Petrtyl Jaromir , Urbanek Petr , Jiraskova Alena , Malikova Ivana , Haluzik Martin , Ferenci Peter 
Published: December 2011

AbstractBackground & AimsWilson disease (WD) is an inherited disorder of copper disposition caused by an ATP7B transporter gene mutation, leading to copper accumulation in predisposed tissues. In addition to a genetic predisposition, other factors are likely to contribute to its clinical manifestation. The aim of the study was to assess whether oxidative stress affects the phenotypic manifestation of WD.MethodsIn 56 patients with WD (29 men; 26 with the hepatic form, 22 with the neurologic form, and eight asymptomatic; mean age 38.5 ± 12 years), total serum antioxidant capacity (TAC) and inflammatory parameters (hs‐CRP, IL‐1β, IL‐2, IL‐6, IL‐10, and TNF‐α) were analyzed and related to the clinical manifestation, and mutations of the ATP7B gene. The control group for the TAC and inflammatory parameters consisted of 50 age‐ and gender‐matched healthy individuals.ResultsWD patients had a significantly lower TAC (p < 0.00001), lower IL‐10 levels (p = 0.039), as well as both higher IL‐1β (p = 0.019) and IL‐6 (p = 0.005) levels compared to the control subjects. TNF‐α, hs‐CRP, and IL‐2 did not differ from the controls. Patients with the neurological form of WD had a significantly lower TAC than those with the hepatic form (p < 0.001). In addition, the lower TAC was associated with the severity of the neurological symptoms (p = 0.02). No relationship between the inflammatory parameters and clinical symptoms was found.ConclusionsData from our study suggest that the increased oxidative stress contributes significantly to the clinical manifestation of WD; as a lower TAC is associated with the neurological symptoms in WD patients.
Essential Elements of Genetic Cancer Risk Assessment, Counseling, and Testing: Updated Recommendations of the National Society of Genetic Counselors
Authors: Riley Bronson D. , Culver Julie O. , Skrzynia Cécile , Senter Leigha A. , Peters June A. , Costalas Josephine W. , Callif‐Daley Faith , Grumet Sherry C. , Hunt Katherine S. , Nagy Rebecca S. , McKinnon Wendy C. , Petrucelli Nancie M. , Bennett Robin L. , Trepanier Angela M. 
Published: December 2011

AbstractUpdated from their original publication in 2004, these cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of counseling at‐risk individuals through genetic cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Familial Cancer Risk Counseling Special Interest Group. The information contained in this document is derived from extensive review of the current literature on cancer genetic risk assessment and counseling as well as the personal expertise of genetic counselors specializing in cancer genetics. The recommendations are intended to provide information about the process of genetic counseling and risk assessment for hereditary cancer disorders rather than specific information about individual syndromes. Essential components include the intake, cancer risk assessment, genetic testing for an inherited cancer syndrome, informed consent, disclosure of genetic test results, and psychosocial assessment. These recommendations should not be construed as dictating an exclusive course of management, nor does use of such recommendations guarantee a particular outcome. These recommendations do not displace a health care provider's professional judgment based on the clinical circumstances of a client.
Glutaraldehyde‐induced colitis: Case reports and literature review
Authors: Shih Hsiang‐Yao , Wu Deng‐Chyang , Huang Wan‐Ting , Chang Yong‐Yu , Yu Fang‐Jung 
Published: December 2011

AbstractGlutaraldehyde‐induced colitis is an uncommon colitis in clinical practice. Because the involvement of colonic segment is determined by the endoscopic part where glutaraldehyde remains, a recent history of endoscopy and a demarcated involvement of colonic segment are the most characteristic signs of glutaraldehyde‐induced colitis. The typical clinical scenario is acute onset of lower abdominal pain, fever, and bloody stool. Laboratory data usually show leukocytosis and elevated C‐reactive protein. The endoscopic pictures of involved segments are compatible with acute colitis, including hyperemic, edematous, with or without multiple erosions. Acute ischemic colitis and infectious colitis should be differentiated at the outset of the disease. Stool pathogen tests are usually negative. Parenteral empiric antibiotic may be considered if severe transmural edema of the involved segment is observed in computed tomography. Conservative treatment, including bowel rest and parenteral hydration, is able to stabilize the condition in a week. Herein, we present two cases of acute proctocolitis caused by glutaraldehyde after uneventful colonoscopy.