bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using comparative genomics to uncover new kinds of protein‐based metabolic organelles in bacteria
Authors: Jorda Julien , Lopez David , Wheatley Nicole M. , Yeates Todd O. 
Published: November 2012

AbstractBacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B12‐independent, glycyl radical‐based degradation of 1,2‐propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical‐based microcompartment binds an iron‐sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical‐based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.
Broad‐substrate screen as a tool to identify substrates for bacterial Gcn5‐related N‐acetyltransferases with unknown substrate specificity
Authors: Kuhn Misty L. , Majorek Karolina A. , Minor Wladek , Anderson Wayne F. 
Published: November 2012

AbstractDue to a combination of efforts from individual laboratories and structural genomics centers, there has been a surge in the number of members of the Gcn5‐related acetyltransferasesuperfamily that have been structurally determined within the past decade. Although the number of three‐dimensional structures is increasing steadily, we know little about the individual functions of these enzymes. Part of the difficulty in assigning functions for members of this superfamily is the lack of information regarding how substrates bind to the active site of the protein. The majority of the structures do not show ligand bound in the active site, and since the substrate‐binding domain is not strictly conserved, it is difficult to predict the function based on structure alone. Additionally, the enzymes are capable of acetylating a wide variety of metabolites and many may exhibit promiscuity regarding their ability to acetylate multiple classes of substrates, possibly having multiple functions for the same enzyme. Herein, we present an approach to identify potential substrates for previously uncharacterized members of the Gcn5‐related acetyltransferase superfamily using a variety of metabolites including polyamines, amino acids, antibiotics, peptides, vitamins, catecholamines, and other metabolites. We have identified potential substrates for eight bacterial enzymes of this superfamily. This information will be used to further structurally and functionally characterize them.
Human C3a and C3a desArg anaphylatoxins have conserved structures, in contrast to C5a and C5a desArg
Authors: Bajic Goran , Yatime Laure , Klos Andreas , Andersen Gregers Rom 
Published: November 2012

AbstractComplement is a part of innate immunity that has a critical role in the protection against microbial infections, bridges the innate with the adaptive immunity and initiates inflammation. Activation of the complement, by specific recognition of molecular patterns presented by an activator, for example, a pathogen cell, in the classical and lectin pathways or spontaneously in the alternative pathway, leads to the opsonization of the activator and the production of pro‐inflammatory molecules such as the C3a anaphylatoxin. The biological function of this anaphylatoxin is regulated by carboxypeptidase B, a plasma protease that cleaves off the C‐terminal arginine yielding C3a desArg, an inactive form. While functional assays demonstrate strikingly different physiological effects between C3a and C3a desArg, no structural information is available on the possible conformational differences between the two proteins. Here, we report a novel and simple expression and purification protocol for recombinant human C3a and C3a desArg anaphylatoxins, as well as their crystal structures at 2.3 and 2.6 Å, respectively. Structural analysis revealed no significant conformational differences between the two anaphylatoxins in contrast to what has been reported for C5a and C5a desArg. We compare the structures of different anaphylatoxins and discuss the relevance of their observed conformations to complement activation and binding of the anaphylatoxins to their cognate receptors.
The effect of top contact on ZnO write‐once–read‐many‐times memory
Authors: Qi Jing , Zhang Qing , Liu Jianlin 
Published: November 2012

AbstractWrite‐once–read‐many‐times memory (WORM) devices were fabricated using Ti/Au and Au as top contacts on ZnO thin films on Si. Electrical characterization shows that both types of WORM devices have large resistance OFF/ON ratio (R ratio), small resistance distribution range, long retention and good endurance. WORM devices with Au top contact have better performance of higher R ratio because of a larger work function of Au compared to Ti.magnified image(© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
FACTORS CONTRIBUTING TO BANK STABILITY IN CHANNELIZED, ALLUVIAL STREAMS
Authors: Davis L. , Harden C. P. 
Published: November 2012

ABSTRACTBank failure is a common fluvial process and can be a pervasive fluvial response to natural and anthropogenic disturbances. Previous research has identified causes and types of bank failure, but the conditions that lead to the cessation of bank failure remain poorly explained. This research examines differences between banks with active bank failure and banks that exhibit evidence of past bank failure that ceased (dormant) throughout three West Tennessee (USA) rivers to provide insight into the processes that cause bank failure to end. Bank characteristics were observed at 68 sites, and data from 55 banks were used to create a logistic regression model. Bank characteristics entered into the model included: vegetative cover, failure location, bar association, bank material, channel width‐to‐depth (w/d) ratio, and average bank angle. Results of the logistic regression suggest that bank angle best explains (p = 0.31 and odds ratio = 8.2) the difference between banks with active and dormant bank failure. Interestingly, vegetative cover and bank material composition, which have been found to be important in bank stabilization by previous researchers, were not significant predictors of bank stability according to the logistic regression model. These results suggest that in absence of drastic differences in bank material resistance (bedrock vs sediment): (1) spatial patterns of bank failure at the system‐scale will be diffuse, (2) bank stability can require a multiple decades, and (3) the potential for vegetation to stabilize banks may be limited in some alluvial systems because of positive feedbacks created by repeated human disturbance. Copyright © 2012 John Wiley & Sons, Ltd.
A survey of architectures and scenarios in satellite‐based wireless sensor networks: system design aspects
Authors: Celandroni N. , Ferro E. , Gotta A. , Oligeri G. , Roseti C. , Luglio M. , Bisio I. , Cello M. , Davoli F. , Panagopoulos A. D. , Poulakis M. , Vassaki S. , De Cola T. , Marchitti M. A. , Hu Y. F. , Pillai P. , Verma S. , Xu K. , Acar G. 
Published: November 2012

ABSTRACTThis paper is not a survey related to generic wireless sensor networks (WSNs), which have been largely treated in a number of survey papers addressing more focused issues; rather, it specifically addresses architectural aspects related to WSNs in some way connected with a satellite link, a topic that presents challenging interworking aspects. The main objective is to provide an overview of the potential role of a satellite segment in future WSNs. In this perspective, requirements of the most meaningful WSN applications have been drawn and matched to characteristics of various satellite/space systems in order to identify suitable integrated configurations. Copyright © 2012 John Wiley & Sons, Ltd.
Process improvement dynamics under constrained resources: managing the work harder versus work smarter balance
Authors: Bradley Morrison J. 
Published: November 2012

AbstractThis paper considers the problem of managing process improvement when resources are constrained. The paper develops a system dynamics model that formalizes the critical interaction between first‐ and second‐order improvements as options for governing production. Both first‐ and second‐order improvement are effective in boosting short‐term organizational performance, whereas only second‐order improvement builds sustainable capability. Analytical results characterize the optimal trade‐off between these options (working harder and working smarter). Simulation results show how pressuring the workforce to work harder can set off a vicious cycle of deteriorating process capability that squeezes out improvement activity. Results also highlight the key role of process capability as a form of organizational slack and demonstrate tipping points in the dynamics of process improvement. By moving from causal loops to a simulating model, this paper provides an example of how formal quantitative modeling can lead to important insights not discovered with causal loop diagramming alone. Copyright © 2012 System Dynamics Society.
Striatal development involves a switch in gene expression networks, followed by a myelination event: Implications for neuropsychiatric disease
Authors: Novak Gabriela , Fan Theresa , O'dowd Brian F. , George Susan R. 
Published: November 2012

AbstractBecause abnormal development of striatal neurons is thought to be the part of pathology underlying major psychiatric illnesses, we studied the expression pattern of genes involved in striatal development and of genes comprising key striatal‐specific pathways, during an active striatal maturation period, the first two postnatal weeks in rat. This period parallels human striatal development during the second trimester, when prenatal stress is though to lead to increased risk for neuropsychiatric disorders. To identify genes involved in this developmental process, we used subtractive hybridization, followed by quantitative real‐time PCR, which allowed us to characterize the developmental expression of over 60 genes, many not previously known to play a role in neuromaturation. Of these 12 were novel transcripts, which did not match known genes, but which showed strict developmental expression and may play a role in striatal neurodevelopment. An additional 89 genes were identified as strong candidates for involvement in this neurodevelopmetnal process. We show that during the first two postnatal weeks in rat, an early gene expression network, still lacking key striatal‐specific signaling pathways, is downregulated and replaced by a mature gene expression network, containing key striatal‐specific genes including the dopamine D1 and D2 receptors, conferring to these neurons their functional identity. Therefore, before this developmental switch, striatal neurons lack many of their key phenotypic characteristics. This maturation process is followed by a striking rise in expression of myelination genes, indicating a striatal‐specific myelination event. Such strictly controlled developmental program has the potential to be a point of susceptibility to disruption by external factors. Indeed, this period is known to be a susceptibility period in both humans and rats. Synapse, 2013. © 2012 Wiley Periodicals, Inc.
Emotional arousal of beginning physics teachers during extended experimental investigations
Authors: Ritchie Stephen M. , Tobin Kenneth , Sandhu Maryam , Sandhu Satwant , Henderson Senka , Roth Wolff‐Michael 
Published: November 2012

AbstractTeachers often have difficulty implementing inquiry‐based activities, leading to the arousal of negative emotions. In this multicase study of beginning physics teachers in Australia, we were interested in the extent to which their expectations were realized and how their classroom experiences while implementing extended experimental investigations (EEIs) produced emotional states that mediated their teaching practices. Against rhetoric of fear expressed by their senior colleagues, three of the four teachers were surprised by the positive outcomes from their supervision of EEIs for the first time. Two of these teachers experienced high intensity positive emotions in response to their students' success. When student actions/outcomes did not meet their teachers' expectations, frustration, anger, and disappointment were experienced by the teachers, as predicted by a sociological theory of human emotions (Turner, J. H. (2007). Human emotions: A sociological theory. London, England: Routledge). Over the course of the EEI projects, the teachers' practices changed along with their emotional states and their students' achievements. We account for similarities and differences in the teachers' emotional experiences in terms of context, prior experience, and expectations. The findings from this study provide insights into effective supervision practices that can be used to inform new and experienced teachers alike. © 2012 Wiley Periodicals, Inc. J Res Sci Teach 50:137–161, 2013
Using mutants, knockdowns, and transgenesis to investigate gene function in Drosophila
Authors: St Johnston Daniel 
Published: November 2012

AbstractThe sophisticated genetic techniques available in Drosophila are largely responsible for its success as a model organism. One of the most important of these is the ability to disrupt gene function in vivo and observe the resulting phenotypes. This review considers the ever‐increasing repertoire of approaches for perturbing the functions of specific genes in flies, ranging from classical and transposon‐mediated mutageneses to newer techniques, such as homologous recombination and RNA interference. Since most genes are used over and over again in different contexts during development, many important advances have depended on being able to interfere with gene function at specific times or places in the developing animal, and a variety of approaches are now available to do this. Most of these techniques rely on being able to create genetically modified strains of Drosophila and the different methods for generating lines carrying single copy transgenic constructs will be described, along with the advantages and disadvantages of each approach. WIREs Dev Biol 2013, 2:587–613. doi: 10.1002/wdev.101This article is categorized under:

Technologies > Perturbing Genes and Generating Modified Animals
Technologies > Generating Chimeras and Lineage Analysis
Technologies > Analysis of Cell, Tissue, and Animal Phenotypes
Accelerating cancer systems biology research through Semantic Web technology
Authors: Wang Zhihui , Sagotsky Jonathan , Taylor Thomas , Shironoshita Patrick , Deisboeck Thomas S. 
Published: November 2012

AbstractCancer systems biology is an interdisciplinary, rapidly expanding research field in which collaborations are a critical means to advance the field. Yet the prevalent database technologies often isolate data rather than making it easily accessible. The Semantic Web has the potential to help facilitate web‐based collaborative cancer research by presenting data in a manner that is self‐descriptive, human and machine readable, and easily sharable. We have created a semantically linked online Digital Model Repository (DMR) for storing, managing, executing, annotating, and sharing computational cancer models. Within the DMR, distributed, multidisciplinary, and inter‐organizational teams can collaborate on projects, without forfeiting intellectual property. This is achieved by the introduction of a new stakeholder to the collaboration workflow, the institutional licensing officer, part of the Technology Transfer Office. Furthermore, the DMR has achieved silver level compatibility with the National Cancer Institute's caBIG, so users can interact with the DMR not only through a web browser but also through a semantically annotated and secure web service. We also discuss the technology behind the DMR leveraging the Semantic Web, ontologies, and grid computing to provide secure inter‐institutional collaboration on cancer modeling projects, online grid‐based execution of shared models, and the collaboration workflow protecting researchers' intellectual property. WIREs Syst Biol Med 2013, 5:135–151. doi: 10.1002/wsbm.1200This article is categorized under:

Analytical and Computational Methods > Computational Methods
Models of Systems Properties and Processes > Mechanistic Models
The New Alkali Cyclotrisilicate Cs8[Si6O16]
Authors: Hlukhyy Viktor , Fässler Thomas F. 
Published: November 2012

AbstractTransparent single crystals of Cs8[Si6O16] have been obtained by a high‐temperature reaction at 900 °C in an arc‐welded niobium crucible. The structure of Cs8[Si6O16] was solved and refined from single crystal X‐ray diffraction data: new structure type, P$\bar{1}$, Z = 2, a = 9.3544(3) Å, b = 11.1152(4) Å, c = 13.5035(5) Å, α = 101.311(3)°, β = 100.958(3)°, γ = 114.121(3)°, R1 = 0.032. The structure of Cs8[Si6O16] contains isolated dimeric cyclotrisilicate anions [Si6O16]8– that are separated by cesium atoms.The anion consists of six vertex‐sharing [SiO4] tetrahedra which form three interconnected rings: two rings consisting of three tetrahedra share edges with the opposite sides of a square of four [SiO4] thetrahedra. With respect to the plane of the four‐membered rings the triangles strike a trans‐type arrangement. [Si6O16]8– is the first example of the third possible structural arrangement in the class of unbranched dimeric cyclotrisilicate anions.
The New Carbodiimide Li2Gd2Sr(CN2)5 Having a Crystal Structure Related to That of Gd2(CN2)3
Authors: Unverfehrt Leonid , Ströbele Markus , Meyer H.‐Jürgen 
Published: November 2012

AbstractThe new carbodiimide compounds Li2RE2Sr(CN2)5 (RE = Sm, Gd, Eu, Tb) were prepared by a straight forward solid state metathesis reaction of REF3, SrF2, and Li2(CN2) at around 600 °C. The crystal structure of Li2Gd2Sr(CN2)5 was solved based on X‐ray single‐crystal diffraction data. Corresponding Li2RE2Sr(CN2)5 compounds were analyzed by isotypic indexing of their powder patterns. The crystal structure of Li2Gd2Sr(CN2)5 can be well related to that of Gd2(CN2)3, because both structures are based on layered structures composed of close packed layers of [N=C=N]2– sticks, alternating with layers of metal ions. The crystal structure of Li2Gd2Sr(CN2)5 can be considered to contain an ABC layer sequence of [N = C=N]2– layers with the interlayer voids being occupied by (three) distinct types of cations.
Zur Elektronenstruktur metallorganischer Komplexe der f‐Elemente. 80[1] Gelingt die Identifizierung der Streck‐ und Kippschwingungen des pseudo‐trigonal‐planaren La(η5‐C5H5)3‐Fragments in den Schwingungsspektren von [La(η5‐C5H5)3­(NCCH3)2] ohne die Hilfe von Modellrechnungen auf der Basis der Dichtefunktionaltheorie?
Authors: Amberger Hanns‐Dieter , Reddmann Hauke 
Published: November 2012

AbstractIn order to reliably assign the four previously observed coincidences in the range 210–260 cm–1 in the low temperature vibrational spectra of [LaCp3(NCCH3)2] (Cp = η5‐C5H5–) (1) to the expected stretching and tilting modes of the pseudo trigonal planar LaCp3 moiety, additionally the “polarized“ Raman spectra of an oriented single crystal of 1 were recorded. By this means, the signal of the tilting vibration of the irreducible representation (irrep) E′' could be separated from the remaining skeletal vibrations consisting of the irreps A1′, E' and E′. The bands of the two latter could be identified by applying the less common method of the “symmetry allowed vibronic couplings of electronic zero point transitions“ to the vibronic sidebands of the purely electronic transition 1Γ1(3H4)→8Γ1(3P0) of [LaCp3(NCCH3)2]:Pr3+ (2). Hence, the remaining band corresponds to the symmetric stretching of A1′ symmetry.
NSGC Practice Guideline: Risk Assessment and Genetic Counseling for Hereditary Breast and Ovarian Cancer
Authors: Berliner Janice L. , Fay Angela Musial , Cummings Shelly A. , Burnett Brittany , Tillmanns Todd 
Published: November 2012

PurposeThe purpose of this document is to present a current and comprehensive set of practice recommendations for effective genetic cancer risk assessment, counseling and testing for hereditary breast and ovarian cancer. The intended audience is genetic counselors and other health professionals who care for individuals with, or at increased risk of, hereditary breast and/or ovarian cancer.
A population‐based survey on the influence of the menstrual cycle and the use of hormonal contraceptives on sleep patterns in São Paulo, Brazil
Authors: Hachul Helena , Andersen Monica L. , Bittencourt Lia , Santos‐Silva Rogério , Tufik Sergio 
Published: November 2012

AbstractObjectiveTo investigate the effects of the phases of the menstrual cycle and the use of hormonal contraception on sleep patterns in a population‐based study.MethodsIn a prospective study carried out among premenopausal women between July and December 2007, a 3‐stage cluster sampling was used to ensure accurate representation of the general population of São Paulo, Brazil. Questionnaires were administered, hormonal assays were performed, and full‐night polysomnography was recorded.ResultsThe study sample included 297 premenopausal women. Women in the follicular phase complained of fatigue more than those in the luteal phase and those using hormonal contraceptive treatment. Premenopausal women using hormonal contraceptives had a significantly lower apnea–hypopnea index (1.1 ± 2.0) compared with women in both the follicular (2.2 ± 4.5) and the luteal (2.9 ± 5.4) phases (P = 0.01). Women taking hormonal contraceptives tended to have increased sleep efficiency compared with women in either the follicular or luteal phases.ConclusionThe use of hormonal contraceptives was associated with a lower apnea–hypopnea index and a trend toward improved sleep efficiency. The current findings suggest that the use of hormonal contraceptives has a stronger association with sleep duration compared with menstrual cycle phase.