bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Modeling of Vasopressin V2 Receptor Tetramer in Hydrated Lipid Membrane
Authors: Witt Magdalena , Ślusarz Magdalena J. , Ciarkowski Jerzy 
Published: December 2007

AbstractBased on accessible experimental data we have constructed a model of Vasopressin V2 Receptor (V2R) tetramer in fully hydrated lipid membrane. To the best of our knowledge, this is the first Molecular Dynamics (MD) simulation of the tetramer model of a GPCR other than rhodopsin. The model consists of three inactive and one active V2R monomers. The activated unit is stabilized by Gsα (Ile382‐Leu394) fragment and includes its natural ligand – vasopressin (AVP) docked. The pairs of neighboring protomers form contact dimers with the interface created by transmembrane helices TM3, TM4 of one partner and TM7, TM6 of the other. The between‐dimers interface is composed by TM5 and TM4 of all monomers. Since experimental studies of GPCR oligomerization are not generally possible, there is a strong interest in using theoretical methods to predict their structure. Herein the NAnoscale Molecular Dynamics (NAMD) 2.6 package and CHARMm force field were used to conduct unconstrained MD calculations in periodic conditions. The optimal adjusting of monomers in lipid membrane surrounding was the purpose of simulation. Residues responsible for the oligomer stabilization were suggested and a compatibility of the whole model with available experimental data was discussed.
Signaling through the high affinity IgE receptor and conditions able to modify IgE‐antigen responsiveness of mast cells
Authors: Gonzalez‐Espinosa Claudia , Medina‐Tamayo Jaciel , Sanchez‐Miranda Elizabeth , Benitez‐Garrido Juan Pablo , Avila‐Hernandez Alejandro Martin , Padilla Alejandro , Garcia‐Roman Jonathan 
Published: December 2007

AbstractSignaling through the high affinity receptor for IgE (FcεRI) on mast cells comprises an intricate network of protein‐protein modifications and interactions leading to mast cell degranulation, lipid‐derived mediator production and cytokine release. Depending on the tissue where mast cells are activated, mediator release can induce distinct allergy symptoms. FcεRI receptor mainly couples to at least two Src family kinases (Lyn and Fyn), which are responsible for the initiation of the signaling cascade. Distinct membrane bound adapters couple the initial signal to the formation of particular multi‐molecular complexes that, in turn, will mediate a specific final response. In this review we summarize the molecular mechanisms initiated by the FcεRI receptor on mast cells that have been involved in cytokine expression. At the same time, some conditions where the main signal transduction mechanism is modified will be analyzed in order to understand how locally produced mediators could alter IgE‐antigen‐induced allergic responses.
Microfluidic Pump Powered by Self‐Organizing Bacteria
Authors: Kim Min Jun , Breuer Kenneth S. 
Published: December 2007

AbstractResults are presented that demonstrate the successful use of live bacteria as mechanical actuators in microfabricated fluid systems. The flow deposition of bacteria is used to create a motile bacterial carpet that can generate local fluid motion inside a microfabricated system. By tracking the motion of tracer particles, we demonstrate that the bacterial cells that comprise the carpet self‐organize, generating a collective fluid motion that can pump fluid autonomously through a microfabricated channel at speeds as high as 25 µm s−1. The pumping performance of the system can also be augmented by changing the chemical environment. The addition of glucose to the working buffer raises the metabolic activity of the bacterial carpet, resulting in increased pumping performance. The performance of the bacterial pump is also shown to be strongly influenced by the global geometry of the pump, with narrower channels achieving a higher pumping velocity with a faster rise time.
Stress‐induced synaptic changes in the rat anterior cingulate cortex are dependent on endocrine developmental time windows
Authors: Gos Tomasz , Bock Jörg , Poeggel Gerd , Braun Katharina 
Published: December 2007

AbstractFetal and neonatal brain development is characterized by developmental time windows during which brain regions or neuron types are specifically sensitive to environmental influences. Previous studies on cortical development have revealed evidence for the hypothesis that the extent and the direction of experience‐induced neuronal and synaptic changes correlate with time windows of endocrine development. To further test this hypothesis we exposed rats to neonatal separation stress during different phases of endocrine maturation, i.e. prior, during and after the stress hyporesponsive period (SHRP) of the hypothalamic‐pituitary‐adrenal (HPA) axis. We show here that only stress during the SHRP resulted in significantly decreased (−29%) spines densities on the basal dendrites of pyramidal cells in layer V of the anterior cingulate cortex (ACd), whereas stress during the other two tested time windows had no effect on these parameters. Dendritic length remained unaffected by stress exposure at any of the tested time windows. These results reveal specific developmental time window for synaptic wiring within the deeper layers of the anterior cingulate cortex, which seem not to be mediated by hormonally induced mechanisms. Synapse 62:229–232, 2008. © 2007 Wiley‐Liss, Inc.
Structured Estolides: Control of Length and Sequence
Authors: Zerkowski Jonathan A. , Nuñez Alberto , Solaiman Daniel K. Y. 
Published: December 2007

AbstractUsing ester‐forming reactions such as carbodiimide coupling and a modified Yamaguchi symmetrical anhydride method, a variety of estolides based on 17‐hydroxy oleic and 17‐hydroxy stearic acid have been prepared. These hydroxy fatty acids are produced in good yields from hydrolysis of sophorolipids, which are in turn derived from fermentation of fats and oils. Since the estolides are formed one unit, or ester bond, at a time, their length and sequence can be precisely controlled. The key to this control is the use of protecting groups at either the carboxylic or hydroxy end of the starting hydroxy fatty acids. Two mono‐protected dimers, for example, when combined in a fragment‐condensation approach, give a tetramer with no “contamination” from estolides of other lengths. This methodology opens the way to functionalized estolides, and several variants were prepared: hybrid estolides, containing non‐fatty acid moieties such as amino acids; polymerizable estolides, containing a norbornene unit; and non‐linear estolides that extend from a branched core such as glycerol or pentaerythritol. With the benzoyl chloride‐mediated symmetrical anhydride method, yields for individual coupling steps ranged from 75 to 93%.
Teaching Research Skills Outside the Curriculum: Lessons Learnt at Oxford University
Authors: Carritt Angela 
Published: December 2007

AbstractAngela Carritt of the Bodleian Law Library gave a paper at the 38th Annual BIALL Study Conference in Sheffield in June 2007. She discusses Oxford University's Legal Research Skills Programme (LRSP), looking at its content, methodology and effectiveness. She also looks at the programme as an example of a stand-alone skills course and asks whether such courses can be effective. Additionally, she discusses students' use of online resources and suggests that they have developed computer based study strategies which make the use of print resources inconvenient. The paper draws on research by Sandra Meredith into students' expectations and experiences of the LRSP and how they use their learning after the classes.
A New Partnership in Law at Sheffield: Collaboration in the Design of a New Module
Authors: Mawson Maria , Semmens Natasha , Taylor Mark 
Published: December 2007

AbstractThis article by Maria Mawson, Natasha Semmens and Mark Taylor, is based on a paper given at the 38th BIALL Annual Study Conference held in Sheffield in June 2007 and describes a new partnership between colleagues from the Library and the School of Law at the University of Sheffield, which has led to the development of an innovative new undergraduate foundation module in law. It begins by describing the situation which existed before the project. Next, two key changes which provided the impetus for the new collaboration are described. Finally, key elements of the new foundation module are discussed.
Collection Development for Knowledge Management
Authors: Bailey Penny 
Published: December 2007

AbstractThis paper was presented by Penny Bailey at the 38th BIALL Annual Study Conference held in Sheffield in June 2007 and covers the challenges involved in introducing a knowledge management strategy to a law firm. It suggests methods to be adopted in trying to implement such a service including identification with the firm's business objectives; persuasive communication; identification of the benefits accruing and strategies for collecting knowledge.
A
Salmonella enterica
Serovar Typhimurium Succinate Dehydrogenase/Fumarate Reductase Double Mutant Is Avirulent and Immunogenic in BALB/c Mice
Authors: Mercado-Lubo Regino , Gauger Eric J. , Leatham Mary P. , Conway Tyrrell , Cohen Paul S. 
Published: December 2007

ABSTRACT

Previously we showed that the tricarboxylic acid (TCA) cycle operates as a full cycle during
Salmonella enterica
serovar Typhimurium SR-11 peroral infection of BALB/c mice (M. Tchawa Yimga et al., Infect. Immun. 74:1130-1140, 2006). The evidence was that a Δ
sucCD
mutant (succinyl coenzyme A [succinyl-CoA] synthetase), which prevents the conversion of succinyl-CoA to succinate, and a Δ
sdhCDA
mutant (succinate dehydrogenase), which blocks the conversion of succinate to fumarate, were both attenuated, whereas an SR-11 Δ
aspA
mutant (aspartase) and an SR-11 Δ
frdABCD
mutant (fumarate reductase), deficient in the ability to run the reductive branch of the TCA cycle, were fully virulent. In the present study, evidence is presented that a serovar Typhimurium SR-11 Δ
frdABCD
Δ
sdhCDA
double mutant is avirulent in BALB/c mice and protective against subsequent infection with the virulent serovar Typhimurium SR-11 wild-type strain via the peroral route and is highly attenuated via the intraperitoneal route. These results suggest that fumarate reductase, which normally runs in the reductive pathway in the opposite direction of succinate dehydrogenase, can replace it during infection by running in the same direction as succinate dehydrogenase in order to run a full TCA cycle in an SR-11 Δ
sdhCDA
mutant. The data also suggest that the conversion of succinate to fumarate plays a key role in serovar Typhimurium virulence. Moreover, the data raise the possibility that
S. enterica
Δ
frdABCD
Δ
sdhCDA
double mutants and Δ
frdABCD
Δ
sdhCDA
double mutants of other intracellular bacterial pathogens with complete TCA cycles may prove to be effective live vaccine strains for animals and humans.
p38 Mitogen-Activated Protein Kinase Mediates Lipopolysaccharide and Tumor Necrosis Factor Alpha Induction of Shiga Toxin 2 Sensitivity in Human Umbilical Vein Endothelial Cells
Authors: Stone Matthew K. , Kolling Glynis L. , Lindner Matthew H. , Obrig Tom G. 
Published: December 2007

ABSTRACTEscherichia coliO157:H7 Shiga toxin 2 (Stx2), one of the causative agents of hemolytic-uremic syndrome, is toxic to endothelial cells, including primary cultured human umbilical vein endothelial cells (HUVEC). This sensitivity of cells to Stx2 can be increased with either lipopolysaccharide (LPS) or tumor necrosis factor alpha (TNF-α). The goal of the present study was to identify the intracellular signaling pathway(s) by which LPS and TNF-α sensitize HUVEC to the cytotoxic effects of Stx2. To identify these pathways, specific pharmacological inhibitors and small interfering RNAs were tested with cell viability endpoints. A time course and dose response experiment for HUVEC exposure to LPS and TNF-α showed that a relatively short exposure to either agonist was sufficient to sensitize the cells to Stx2 and that both agonists stimulated intracellular signaling pathways within a short time. Cell viability assays indicated that the p38 mitogen-activated protein kinase (MAPK) inhibitors SB202190 and SB203580 and the general protein synthesis inhibitor cycloheximide inhibited both the LPS and TNF-α sensitization of HUVEC to Stx2, while all other inhibitors tested did not inhibit this sensitization. Additionally, SB202190 reduced the cellular globotriaosylceramide content under LPS- and TNF-α-induced conditions. In conclusion, our results show that LPS and TNF-α induction of Stx2 sensitivity in HUVEC is mediated through a pathway that includes p38 MAPK. These results indicate that inhibition of p38 MAPK in endothelial cells may protect a host from the deleterious effects of Stx2.
Occupational exposure levels to wood dust in Italy, 1996–2006
Authors: Scarselli A , Binazzi A , Ferrante P , Marinaccio A 
Published: December 2007

Background:Wood dust has been classified as carcinogenic to humans and the association with nasal cancer risk has been observed in a large number of epidemiological studies.Objectives:The aim of this study is to summarise data about occupational exposure levels to wood dust in Italy and to examine some exposure determinants.Methods:Exposure measurements on wood dust were extracted from the SIREP (Italian Information System on Occupational Exposure to Carcinogens) database between 1996–2006. Descriptive statistics were calculated for exposure-related variables using univariate analyses. The prevalence of elevated exposure levels was estimated overall and for some industrial sectors. A multifactorial analysis of variance was performed to determine which factors influenced exposure levels to wood dust.Results:The total number of exposure measurements (n) reported is 10 837, which refer to 10 528 workers and 1181 companies. The overall arithmetic mean is 1.44 mg/m3and the geometric mean is 0.97 mg/m3. Industrial sectors at high risk are “manufacture of wood and wood products” (n = 5539) as well as “manufacture of furniture” (n = 4347). About 74% of exposure measurements report a value <2 mg/m3. In the multifactorial analysis, it has been found that job category, industrial sector, company size and geographical location of the company influence the exposure levels.Conclusions:This study confirms the previous findings about occupational exposure to wood dust (mainly in wood industry and among woodworking machine operators) and suggests further investigations on other risk sectors (building and repairing of ships and boats). The potential of the occupational exposure database as a source of data for exposure assessment and surveillance is also confirmed.
Preliminary landslide hazard assessment in remote areas
Authors: Charman J. H. 
Published: December 2007

Rationale

In remote areas decisions on the need for remedial and maintenance works on linear projects such as roads and canals may involve the evaluation of risk based on
the identification and distribution of definable hazards
. A terrain model provides the basis for a classification scheme to enable this to be done cost effectively. In addition it facilitates the identification of problem areas that may require more detailed subsequent design investigation. In the absence of more detailed investigation it provides the basis for a conceptual construction approach.

The site

This example relates to hill irrigation schemes in the Himalaya of Nepal and Bhutan and involved the upgrading of existing village canals irrigating between 50 and 200 hectares of agricultural land for rice production. Each canal ran across steep slopes and was experiencing difficulties with slope instability. In the feasibility stage a limited number of projects had to be selected from a large initial listing.

Area model

The Himalaya form part of an active fold mountain belt characterized by moderate to high rates of uplift, regular seismic events and extreme relief. They are also subject to a tropical monsoon climate, at least at lower elevations, which causes significant weathering and erosion.
Mountain-building activity is not uniform but comprises episodes of uplift interposed between quieter periods. In active times rivers rapidly downcut and form steep incised valleys. In quieter periods weathering and slope evolution and more mature rivers result in a less severe landscape. The model in Figure 1 uses this concept to classify the landscape.
Sediment budget analysis for coastal management, west Dorset
Authors: Lee E. M. , Brunsden D. 
Published: December 2007

Background

The identification and characterization of geomorphological units or systems is particularly important in the coastal zone. Indeed, the consequences of failure to appreciate the physical environment can be more acute on the coast, as rapid, major changes are a reality for land use planning and development. On the coast, it is often more useful to map the landscape in terms of sediment ‘cells’ (i.e. process units) rather than terrain units (i.e. landform units) as an understanding of the supply and transport of sediment (e.g. sand and shingle) is fundamental to dealing with many shoreline problems. Sediment is circulated in what often can be regarded, for practical purposes, as almost closed cells that are separated by boundaries across which little beach material is transferred. Each cell can be characterized in terms of the inputs, outputs, stores and sinks of sediment.
For example, to understand the development of a beach it is useful to consider it as a store of shingle or sand supplied from source areas on the adjacent coastline or offshore (Fig. 1). Beach building material might be supplied from the seabed, moved onshore by wave energy, or from rivers and eroding cliffs. This material is then redistributed along the shoreline by waves (‘longshore drift’), unless prevented by barriers such as headlands or breakwaters. Although longshore drift might be prevented by these barriers, some of the material can still be ‘lost’ to the system around the seaward end of the barriers or offshore, particularly during large storms.
Sediment inputs
Hazard assessment in Eastern Taiwan
Authors: Petley D. N. 
Published: December 2007

Introduction

The topography of Taiwan is dominated by the Central Mountain Range, which has steep, densely vegetated slopes, deeply incised valleys and fractured, unstable rock masses. Although most of the population is located on the low-lying coastal plains, there is a need in this rapidly developing island to construct transportation links through the mountains. Unfortunately, the steep topography makes development difficult and there have been many instances in which poor terrain evaluation has led to inappropriate engineering solutions.
This paper outlines how landslide hazard assessment is being used as part of the planning process for the development of infrastructure along one such road through the mountains.

The physical setting of Taiwan

Taiwan is located on the eastern margin of the Eurasian continental plate (Fig. 1). The island, which is approximately 385 km in length and 143 km in width, has formed as a result of the ongoing collision of the Philippine Sea (oceanic) and Eurasian (continental) plates. Damaging, shallow seismic activity is frequent. The most seismically active region is in the central portion of the east coast of the island. However, the recent ‘Chi-Chi’ earthquake of 21 September 1999 occurred in the centre of Taiwan and caused the loss of over 2100 lives and induced damage island-wide.

Terrain evaluation in Taroko National Park

Taroko National Park is located on the eastern margin of Taiwan 121°40′ E and 24°0′ N (Fig. 1). It is centred upon the drainage basin of the Li-Wu River, with terrain that varies from lowland plains
Ground models for the design and construction of a high-speed rail link
Authors: Phipps P. J. 
Published: December 2007

Purpose of survey

Engineering geomorphological, geological and geotechnical information, pertinent to a long linear engineering project, was required to provide support to a Parliamentary Bill and assist the future design and construction of the Channel Tunnel Rail Link. A wide variety of reports, maps and borehole logs had been collated for locations in the vicinity of the route alignment. These were to be supplemented with Phase I ground investigations for limited locations along the route during the winter of 1993/94. Phase I information was to be incorporated with the desk study information to provide an initial classification of the route geomorphology and ground conditions, and provide a sensible basis from which to design subsequent Phase II ground investigations.

The site

The Channel Tunnel Rail Link (CTRL) is to be constructed between St Pancras and the Channel Tunnel Railway Terminal at Cheriton, near Folkestone. The CTRL is a high-speed railway, 108 km in length, and its construction will incorporate a variety of engineered structures. The route traverses a wide range of topography, and solid and drift geology, which produce a wide variety of ground conditions to be considered for design and construction purposes.
At a macroscale the CTRL is located in three distinct geomorphological areas: the London Basin, the North Downs and the northern limb of the Weald. A wide variety of solid and drift geologies were evident from available British Geological Survey mapping: these included Lower London Tertiary deposits. Pleistocene Terrace deposits and recent alluvium in
The structural evolution of dilational stepovers in regional transtensional zones
Authors: De Paola N. , Holdsworth R. E. , Collettini C. , Mccaffrey K. J. W. , Barchi M. R. 
Published: December 2007

Abstract
We propose a theoretical model, supported by a field study, to describe the patterns of fault/fracture meshes formed within dilational stepovers developed along faults accommodating regional scale wrench-dominated transtension. The geometry and kinematics of the faulting in the dilational stepovers is related to the angle of divergence (α), and differs from the patterns traditionally predicted in dilation zones associated with boundary faults accommodating strike-slip displacements (where α = 0°). For low values of oblique divergence (α<30°) and low strain, the fault–fracture mesh comprises interlinked tensile fractures and shear-extensional planes, consistent with wrench-dominated transtension. At higher values of strain, a switch occurs from wrench- to extension-dominated transtension, leading to the reactivation and/or disruption of the early-formed structures. These structural processes lead to the development of a geometrically complex and kinematically heterogeneous fault pattern, which may affect and/or perturb the development of a through-going fault linking and facilitating the slip transfer between the two overlapping fault segments. As a result, dilational stepover zones will tend to form long-lived sites of localized extension and subsidence in regional transtensional tectonic settings. Cyclic increases/decreases of structural permeability will be related to slip on the major boundary faults that control the distribution of fluid-flow paths and, consequently, the long- and short-term structural evolution of these sites. Our model also predicts complex and more realistic subsurface fluid migration pathways relevant to our current understanding of hydrothermal ore deposits and hydrocarbon migration and storage.