bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagen-bound low density lipoprotein modifies endothelial cell adhesion to type V collagen: Implications for atherosclerosis
Authors: Lorkowski Stefan , Rauterberg Jürgen , Harrach-Ruprecht Bärbel , Troyer David 
Published: October 2007

AbstractLow density lipoprotein (LDL) is retained in the extracellular matrix of the arterial wall where it is considered to be atherogenic, but little is known about how cell adhesion to the matrix is affected by collagen-bound LDL. We tested the effect of native, oxidized and acetylated LDL reacted with adsorbed monomeric type I, III and V collagen on endothelial cell adhesion to collagen using a colorimetric adhesion assay. We found that none of the LDL species affected adhesion to type I and III collagen, but that collagen-bound native and acetylated LDL enhanced attachment to type V collagen, whereas bound oxidized LDL inhibited adhesion to this collagen. We suggest that oxidized LDL associated with type V collagen in the arterial wall would favor de-endothelialization and contribute to atherogenesis and thrombosis.
Proteasome function is required to maintain muscle cellular architecture
Authors: Haas Kevin F. , Woodruff Elvin , Broadie Kendal 
Published: October 2007

Background information. Protein degradation via the UPS (ubiquitin—proteasome system) plays critical roles in muscle metabolism and signalling pathways. The present study investigates temporal requirements of the UPS in muscle using conditional expression of mutant proteasome β subunits to cause targeted inhibition of proteasome function.Results and conclusions. The Drosophila GeneSwitch system was used, with analyses of the well‐characterized larval somatic body wall muscles. This method acutely disrupts proteasome function and causes rapid accumulation of polyubiquitinated proteins, specifically within the muscle. Within 12 h of transgenic proteasome inhibition, there was a gross disorganization of muscle architecture and prominent muscle atrophy, progressing to the arrest of all co‐ordinated movement by 24 h. Progressive muscle architecture changes include rapid loss of sarcomere organization, loss of nuclei spacing/patterning, vacuole formation and the accumulation of nuclear and cytoplasmic aggregates at the ultrastructural level. At the neuromuscular junction, the highly specialized muscle membrane folds of the subsynaptic reticulum were rapidly lost. Within 24 h after transgenic proteasome inhibition, muscles contained numerous autophagosomes and displayed highly elevated expression of the endoplasmic reticulum chaperone GRP78 (glucose‐regulated protein of 78 kDa), indicating that the loss of muscle maintenance correlates with induction of the unfolded protein response. Taken together, these results demonstrate that the UPS is acutely required for maintenance of muscle and neuromuscular junction architecture, and provides a Drosophila genetic model to mechanistically evaluate this requirement.
Is Written Language Production More Difficult Than Oral Language Production? A Working Memory Approach
Authors: Bourdin Béatrice , Fayol Michel 
Published: October 2007

Is written language production more difficult than oral language production? Probably, yes. But why?Several experiments were conducted in order to test the impact of low‐level activities involved in writing on the performance of higher‐level activities also involved in writing. Three assumptions were made: (1) the capacity of working‐memory is limited, (2) every component of writing has a cognitive load, and (3) every increase in the load devoted to the activity of one component would lead to a decrease in the remaining resources available for the other components. These low‐level activities are more resource‐consuming in children than in adults because children have not yet automated these activities. So, it was hypothezised that the difficulties encountered by children in dealing with the low‐level activities would have a negative impact on the performance of higher activities.To test that hypothesis, a serial recall paradigm was used. Adults and children were asked to recall series of words, either orally or in writing. The results showed that: (1) serial recall of children, but not of adults, was weaker with writing as compared to speaking; (2) the slowness of writing relative to speaking did not explain these results; and (3) the difficulties of graphic and of orthographic transcription were partially responsible for these results.These results are discussed in the general framework of production models.
Typicality of Interpersonal Situations: The Role of Affect in Determining Contextual Variations in Typicality Norms
Authors: Mallet Pascal , Cordier Françoise 
Published: October 2007

This study deals with the relationship between affect and cognition. This relationship is conceptualized in the terms of Bower's (Bower & Cohen, 1982) theory. Subjects (early adolescents aged 12 or 14, boy or girl) were asked to imagine themselves as the actor in an interpersonal situation. The situation was either intimate or non‐intimate, and the hypothetical partner was either a boy or a girl. The subject's task was to produce a series of sentences expressing the behaviours considered representative of each situation.The results indicated (1) the existence of a typicality hierarchy (whose characteristics are examined here) and (2) variations in this hierarchy according to the affective tone of the situation (intimate or non‐intimate). We explain how the cultural, interpersonal situation norms acquired by adolescents can account for these variations. Thus, contrary to what some authors contend, variations in typicality are not random.
Clostridium difficile-Associated Disease in Patients in a Small Rural Hospital
Authors: Kuntz Jennifer L. , Cavanaugh Joseph E. , Becker Laura K. , Ward Melissa A. , Appelgate Dianna M. , Herwaldt Loreen A. , Polgreen Philip M. 
Published: October 2007

Objective.To determine the risk factors for Clostridium difficile–associated disease (CDAD) in a 25-bed rural hospital and to compare antimicrobial use ratios at the study hospital with those at a large academic medical center.Design.Case-control study.Setting.A 25-bed rural hospital in Iowa during the period from August 2002 through January 2005.Patients.A total of 17 case patients with CDAD and 34 control patients matched for age (ie, within 10 years of the case patient's age), sex, and admission date (ie, within 2 weeks of the case patient's admission date).Methods.Retrospective medical record review was performed to obtain data on antimicrobial exposures during the 6 weeks before hospital admission for both case and control patients. Exact conditional logistic regression was used for univariable and multivariable analyses. Antimicrobial use ratios were calculated to compare the rates of antimicrobial use for case and control patients at the study hospital with the rates for patients evaluated in a study of CDAD at a nearly 700-bed teaching hospital.Results.Case patients had a larger cumulative number of days of antimicrobial use (P = .004), and they received a larger total number of antimicrobial agents during hospitalization (P = .001). Antimicrobial use ratios were higher for both case and control patients at the smaller hospital, compared with the larger hospital.Conclusions.CDAD at a small rural hospital was not associated with exposure to the antimicrobial classes that are typically associated with CDAD, but was instead related to the total number of antimicrobials used to treat patients. The rate of antimicrobial use for case and control patients was about 40% higher at the small rural hospital, compared with the corresponding rates at a large academic medical center.
Increasing Prevalence of Gastrointestinal Colonization With Ceftazidime-Resistant Gram-Negative Bacteria Among Intensive Care Unit Patients
Authors: Thom Kerri A. , Johnson Judith A. , Strauss Sandra M. , Furuno Jon P. , Perencevich Eli N. , Harris Anthony D. 
Published: October 2007

Background.The occurrence of nosocomial infections due to third-generation cephalosporin–resistant gram-negative bacteria is increasing. Gastrointestinal colonization is an important reservoir for antibiotic-resistant bacteria, and it often precedes clinical infection.Objective.To estimate the prevalence of gastrointestinal colonization with ceftazidime-resistant gram-negative bacteria among intensive care unit (ICU) patients at a university-affiliated tertiary-care hospital during 2 distinct periods and to assess whether, at any time during the index hospitalization, colonized patients had a clinical culture positive for the same organism that was recovered from surveillance culture.Setting.Two ICUs at the University of Maryland Medical Center, a 656-bed tertiary-care hospital located in Baltimore, Maryland. Both ICUs provide care to adult patients.Methods.We performed a cross-sectional study of adult patients admitted to the medical ICU or the surgical ICU from June 14 to July 14, 2003, and from June 14 to July 14, 2006. Perirectal swab samples were obtained for surveillance culture on admission to the intensive care unit, weekly thereafter, and at discharge. Each culture sample was plated onto MacConkey agar supplemented with ceftazidime.Results.In 2003, a total of 33 (18.8%) of 176 patients were colonized with ceftazidime-resistant gram-negative bacilli; in 2006, 60 (31.4%) of 191 patients were (P<.01). This increase was largely driven by an increase in ceftazidime-resistantKlebsiellaisolates (which accounted for 6.4% of isolates in 2003 and for 22.8% in 2006;P<.01). In 2003, a total of 16 (48.5%) of 33 colonized patients had a clinical culture positive for the same organism that was recovered from the perirectal surveillance culture, compared with 22 (36.6%) of 60 colonized patients in 2006 (P= .28).Conclusion.Our data suggest that gastrointestinal colonization with ceftazidime-resistant gram-negative bacilli is common, that its prevalence is increasing, and that colonization may result in clinical cultures positive for these bacilli.
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
Authors: Song Jiangning , Yuan Zheng , Tan Hao , Huber Thomas , Burrage Kevin 
Published: October 2007

AbstractMotivation: Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space. Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications.Results: We have developed a novel method to predict disulfide connectivity patterns from protein primary sequence, using a support vector regression (SVR) approach based on multiple sequence feature vectors and predicted secondary structure by the PSIPRED program. The results indicate that our method could achieve a prediction accuracy of 74.4% and 77.9%, respectively, when averaged on proteins with two to five disulfide bridges using 4-fold cross-validation, measured on the protein and cysteine pair on a well-defined non-homologous dataset. We assessed the effects of different sequence encoding schemes on the prediction performance of disulfide connectivity. It has been shown that the sequence encoding scheme based on multiple sequence feature vectors coupled with predicted secondary structure can significantly improve the prediction accuracy, thus enabling our method to outperform most of other currently available predictors. Our work provides a complementary approach to the current algorithms that should be useful in computationally assigning disulfide connectivity patterns and helps in the annotation of protein sequences generated by large-scale whole-genome projects.Availability: The prediction web server and Supplementary Material are accessible at http://foo.maths.uq.edu.au/~huber/disulfideContact: kb@maths.uq.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
The ArabidopsisDESPERADO/AtWBC11Transporter Is Required for Cutin and Wax Secretion
Authors: Panikashvili David , Savaldi-Goldstein Sigal , Mandel Tali , Yifhar Tamar , Franke Rochus B. , Höfer René , Schreiber Lukas , Chory Joanne , Aharoni Asaph 
Published: October 2007

AbstractThe cuticle fulfills multiple roles in the plant life cycle, including protection from environmental stresses and the regulation of organ fusion. It is largely composed of cutin, which consists of C16-18 fatty acids. While cutin composition and biosynthesis have been studied, the export of cutin monomers out of the epidermis has remained elusive. Here, we show that DESPERADO (AtWBC11) (abbreviated DSO), encoding a plasma membrane-localized ATP-binding cassette transporter, is required for cutin transport to the extracellular matrix. The dso mutant exhibits an array of surface defects suggesting an abnormally functioning cuticle. This was accompanied by dramatic alterations in the levels of cutin monomers. Moreover, electron microscopy revealed unusual lipidic cytoplasmatic inclusions in epidermal cells, disappearance of the cuticle in postgenital fusion areas, and altered morphology of trichomes and pavement cells. We also found that DSO is induced by salt, abscisic acid, and wounding stresses and its loss of function results in plants that are highly susceptible to salt and display reduced root branching. Thus, DSO is not only essential for developmental plasticity but also plays a vital role in stress responses.
The F-Box Protein MAX2 Functions as a Positive Regulator of Photomorphogenesis in Arabidopsis
Authors: Shen Hui , Luong Phi , Huq Enamul 
Published: October 2007

AbstractLight is vital for plant growth and development. To respond to ambient light signals, plants are equipped with an array of photoreceptors, including phytochromes that sense red (R)/far-R (FR) regions and cryptochromes and phototropins that respond to the ultraviolet-A/blue (B) region of the light spectrum, respectively. Several positively and negatively acting components in light-signaling pathways have been identified using genetic approaches; however, the pathways are not saturated. Here, we characterize a new mutant named pleiotropic photosignaling (pps), isolated from a genetic screen under continuous R light. pps has longer hypocotyls and slightly smaller cotyledons under continuous R, FR, and B light compared to that of the wild type. pps is also hyposensitive to both R and FR light-induced seed germination. Although photosynthetic marker genes are constitutively expressed in pps in the dark at high levels, the expression of early light-regulated genes is reduced in the pps seedlings compared to wild-type seedlings under R light. PPS encodes MAX2/ORE9 (for MORE AXILLARY BRANCHES2/ORESARA9), an F-box protein involved in inflorescence architecture and senescence. MAX2 is expressed ubiquitously in the seedling stage. However, its expression is restricted to vascular tissues and meristems at adult stages. MAX2 is also localized to the nucleus. As an F-box protein, MAX2 is predicted to be a component of the SCF (for SKP, Cullin, and F-box protein) complex involved in regulated proteolysis. These results suggest that SCFMAX2 plays critical roles in R, FR, and B light-signaling pathways. In addition, MAX2 might regulate multiple targets at different developmental stages to optimize plant growth and development.
Cell Wall Proteome in the Maize Primary Root Elongation Zone. II. Region-Specific Changes in Water Soluble and Lightly Ionically Bound Proteins under Water Deficit
Authors: Zhu Jinming , Alvarez Sophie , Marsh Ellen L. , LeNoble Mary E. , Cho In-Jeong , Sivaguru Mayandi , Chen Sixue , Nguyen Henry T. , Wu Yajun , Schachtman Daniel P. , Sharp Robert E. 
Published: October 2007

Abstract
Previous work on the adaptation of maize (Zea mays) primary roots to water deficit showed that cell elongation is maintained preferentially toward the apex, and that this response involves modification of cell wall extension properties. To gain a comprehensive understanding of how cell wall protein (CWP) composition changes in association with the differential growth responses to water deficit in different regions of the elongation zone, a proteomics approach was used to examine water soluble and loosely ionically bound CWPs. The results revealed major and predominantly region-specific changes in protein profiles between well-watered and water-stressed roots. In total, 152 water deficit-responsive proteins were identified and categorized into five groups based on their potential function in the cell wall: reactive oxygen species (ROS) metabolism, defense and detoxification, hydrolases, carbohydrate metabolism, and other/unknown. The results indicate that stress-induced changes in CWPs involve multiple processes that are likely to regulate the response of cell elongation. In particular, the changes in protein abundance related to ROS metabolism predicted an increase in apoplastic ROS production in the apical region of the elongation zone of water-stressed roots. This was verified by quantification of hydrogen peroxide content in extracted apoplastic fluid and by in situ imaging of apoplastic ROS levels. This response could contribute directly to the enhancement of wall loosening in this region. This large-scale proteomic analysis provides novel insights into the complexity of mechanisms that regulate root growth under water deficit conditions and highlights the spatial differences in CWP composition in the root elongation zone.
Proteome Analysis ofArabidopsisLeaf Peroxisomes Reveals Novel Targeting Peptides, Metabolic Pathways, and Defense Mechanisms
Authors: Reumann Sigrun , Babujee Lavanya , Ma Changle , Wienkoop Stephanie , Siemsen Tanja , Antonicelli Gerardo E. , Rasche Nicolas , Lüder Franziska , Weckwerth Wolfram , Jahn Olaf 
Published: October 2007

AbstractWe have established a protocol for the isolation of highly purified peroxisomes from mature Arabidopsis thaliana leaves and analyzed the proteome by complementary gel-based and gel-free approaches. Seventy-eight nonredundant proteins were identified, of which 42 novel proteins had previously not been associated with plant peroxisomes. Seventeen novel proteins carried predicted peroxisomal targeting signals (PTS) type 1 or type 2; 11 proteins contained PTS-related peptides. Peroxisome targeting was supported for many novel proteins by in silico analyses and confirmed for 11 representative full-length fusion proteins by fluorescence microscopy. The targeting function of predicted and unpredicted signals was investigated and SSL&gt;, SSI&gt;, and ASL&gt; were established as novel functional PTS1 peptides. In contrast with the generally accepted confinement of PTS2 peptides to the N-terminal domain, the bifunctional transthyretin-like protein was demonstrated to carry internally a functional PTS2. The novel enzymes include numerous enoyl-CoA hydratases, short-chain dehydrogenases, and several enzymes involved in NADP and glutathione metabolism. Seven proteins, including β-glucosidases and myrosinases, support the currently emerging evidence for an important role of leaf peroxisomes in defense against pathogens and herbivores. The data provide new insights into the biology of plant peroxisomes and improve the prediction accuracy of peroxisome-targeted proteins from genome sequences.
User‐Centered Design in a Large‐Scale Naval Ship Design Program: Usability Testing of Complex Military Systems—DDG 1000
Authors: QUINTANA VINCE , HOWELLS ROBERT A. , HETTINGER LAWRENCE 
Published: October 2007

AbstractThe US Navy is currently developing a new class of surface combatant ships referred to as DDG 1000. Unlike past ship designs, DDG 1000 is explicitly focused on the execution of a user‐centered approach—one that captures the requirements, capabilities, and limitations of sailors expected to operate the ship. Additionally, DDG 1000 presents a number of significant human factors and challenges related to its greatly reduced crew size (compared with similar legacy ships) and high reliance on automated systems. Usability testing and usability assessments (UT and UAs) for the purpose of validation of human systems integration (HSI) principles, and the validation of the DDG 1000 Sailor Systems Specification (S3), play a key role in the DDG 1000 Human‐Centered Design (HCD). Through the use of summative and formative design analysis and design verification events, UT/UA is critical in identifying and rectifying issues early in the design process, and verifying system functionality later in the design process. For the DDG 1000 program, the Human Systems Integration—Design Verification Integrated Product Team (HSI‐DV‐IPT) has also combined its efforts with both the DDG 1000 Safety and Training Cross Product Teams to realize the economies of scale associated with conducting these tests to obtain data for the needs of all three HCD disciplines. Through the course of the DDG 1000 detailed design phase, UTs and UAs have become a defined procedural process, which is governed by both the DDG 1000 Human Systems Integration Plan and as an extension of the total testing plan for the DDG 1000 ship. Almost all DDG 1000 HSI‐DV‐IPT evolutions combine the efforts of system engineering and design teams with HSI engineers and fleet users to ensure that the combined test output product has received a “cut” from the entire chain of influence from concept to end user. To date, over 30 user interaction and test events employing 1,100 users have been conducted to verify the utility of aspects of the DDG 1000 design, from the most sophisticated to the most mundane systems and processes. In addition, a series of tools that includes 3D visualization aids for modeling and simulation, and weighted assessment systems like NASA‐TLX have been included in the DDG 1000 HSI test engineers' tool bag to provide the best of breed solutions to HCD‐oriented testing. The test results obtained to date provided valuable insight into the validity of the DDG 1000 HCD and provided feedback that led to optimization of both crew and ship as its HCD objectives intended, in addition to providing cost‐effective and timely feedback into the DDG 1000 design.
The High‐Speed Navy: Vessel Motion Influences on Human Performance
Authors: McCAULEY MICHAEL E. , PIERCE ERIC C. , MATSAGAS PANAYIOTIS 
Published: October 2007

AbstractThis paper presents the recent results from an ongoing analysis of the effects of high‐speed naval operations on the performance, comfort, and safety of crew and passengers. A 127‐m trimaran, the Benchijigua Express, which is similar in hull design to the General Dynamics Littoral Combat Ship (LCS) vessel, was investigated for motion‐induced interruptions, motion sickness, and biodynamic feed‐through to manual tasks. Data were obtained on two 2‐hour transits per day for a total of 86 transits during February and March 2006. Survey questionnaires were obtained from nearly 2,000 passengers. The motion effects on manual dexterity were negligible, but motion sickness symptoms were reported by a majority of the passengers. The capability to manage the motion sickness issue for unadapted passengers may be important for the effective use of LCS to transport ground combatants and for Sea Basing concepts.