bluuebunny/crossref_metadata_2025_split huggingface dataset:
CytochromecBiogenesis: Mechanisms for Covalent Modifications and Trafficking of Heme and for Heme-Iron Redox Control
Authors: Kranz Robert G. , Richard-Fogal Cynthia , Taylor John-Stephen , Frawley Elaine R. 
Published: August 2009

SUMMARYHeme is the prosthetic group for cytochromes, which are directly involved in oxidation/reduction reactions inside and outside the cell. Many cytochromes contain heme with covalent additions at one or both vinyl groups. These include farnesylation at one vinyl in hemesoandaand thioether linkages to each vinyl in cytochromec(at CXXCH of the protein). Here we review the mechanisms for these covalent attachments, with emphasis on the three unique cytochromecassembly pathways called systems I, II, and III. All proteins in system I (called Ccm proteins) and system II (Ccs proteins) are integral membrane proteins. Recent biochemical analyses suggest mechanisms for heme channeling to the outside, heme-iron redox control, and attachment to the CXXCH. For system II, the CcsB and CcsA proteins form a cytochromecsynthetase complex which specifically channels heme to an external heme binding domain; in this conserved tryptophan-rich “WWD domain” (in CcsA), the heme is maintained in the reduced state by two external histidines and then ligated to the CXXCH motif. In system I, a two-step process is described. Step 1 is the CcmABCD-mediated synthesis and release of oxidized holoCcmE (heme in the Fe+3state). We describe how external histidines in CcmC are involved in heme attachment to CcmE, and the chemical mechanism to form oxidized holoCcmE is discussed. Step 2 includes the CcmFH-mediated reduction (to Fe+2) of holoCcmE and ligation of the heme to CXXCH. The evolutionary and ecological advantages for each system are discussed with respect to iron limitation and oxidizing environments.
Molecular Aspects ofMoraxella catarrhalisPathogenesis
Authors: de Vries Stefan P. W. , Bootsma Hester J. , Hays John P. , Hermans Peter W. M. 
Published: August 2009

SUMMARYIn recent years,Moraxella catarrhalishas established its position as an important human mucosal pathogen, no longer being regarded as just a commensal bacterium. Further, current research in the field has led to a better understanding of the molecular mechanisms involved inM. catarrhalispathogenesis, including mechanisms associated with cellular adherence, target cell invasion, modulation of the host's immune response, and metabolism. Additionally, in order to be successful in the host,M. catarrhalishas to be able to interact and compete with the commensal flora and overcome stressful environmental conditions, such as nutrient limitation. In this review, we provide a timely overview of the current understanding of the molecular mechanisms associated withM. catarrhalisvirulence and pathogenesis.
Lessons in Signaling and Tumorigenesis from Polyomavirus Middle T Antigen
Authors: Fluck Michele M. , Schaffhausen Brian S. 
Published: August 2009

SUMMARYThe small DNA tumor viruses have provided a very long-lived source of insights into many aspects of the life cycle of eukaryotic cells. In recent years, the emphasis has been on cancer-related signaling. Here we review murine polyomavirus middle T antigen, its mechanisms, and its downstream pathways of transformation. We concentrate on the MMTV-PyMT transgenic mouse, one of the most studied models of breast cancer, which permits the examination of in situ tumor progression from hyperplasia to metastasis.
StreptococcusAdherence and Colonization
Authors: Nobbs Angela H. , Lamont Richard J. , Jenkinson Howard F. 
Published: August 2009

SUMMARYStreptococci readily colonize mucosal tissues in the nasopharynx; the respiratory, gastrointestinal, and genitourinary tracts; and the skin. Each ecological niche presents a series of challenges to successful colonization with which streptococci have to contend. Some species exist in equilibrium with their host, neither stimulating nor submitting to immune defenses mounted against them. Most are either opportunistic or true pathogens responsible for diseases such as pharyngitis, tooth decay, necrotizing fasciitis, infective endocarditis, and meningitis. Part of the success of streptococci as colonizers is attributable to the spectrum of proteins expressed on their surfaces. Adhesins enable interactions with salivary, serum, and extracellular matrix components; host cells; and other microbes. This is the essential first step to colonization, the development of complex communities, and possible invasion of host tissues. The majority of streptococcal adhesins are anchored to the cell wall via a C-terminal LPxTz motif. Other proteins may be surface anchored through N-terminal lipid modifications, while the mechanism of cell wall associations for others remains unclear. Collectively, these surface-bound proteins provideStreptococcusspecies with a “coat of many colors,” enabling multiple intimate contacts and interplays between the bacterial cell and the host. In vitro and in vivo studies have demonstrated direct roles for many streptococcal adhesins as colonization or virulence factors, making them attractive targets for therapeutic and preventive strategies against streptococcal infections. There is, therefore, much focus on applying increasingly advanced molecular techniques to determine the precise structures and functions of these proteins, and their regulatory pathways, so that more targeted approaches can be developed.
Microbial NAD Metabolism: Lessons from Comparative Genomics
Authors: Gazzaniga Francesca , Stebbins Rebecca , Chang Sheila Z. , McPeek Mark A. , Brenner Charles 
Published: August 2009

SUMMARY

NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes
nadV
and
pncA
, found in distinct bacteria, appear to have spread throughout the tree of life via horizontal gene transfer. Biochemical, genetic, and genomic analyses have advanced to the point at which the precursors and pathways utilized by a microorganism can be predicted. Challenges remain in dissecting regulation of pathways.
(ℓ, k)-ROUTING ON PLANE GRIDS
Authors: HUC FLORIAN , SAU IGNASI , ŽEROVNIK JANEZ 
Published: September 2009

The packet routing problem plays an essential role in communication networks. It involves how to transfer data from some origins to some destinations within a reasonable amount of time. In the (ℓ, k)-routing problem, each node can send at most ℓ packets and receive at most k packets. Permutation routing is the particular case ℓ = k = 1. In the r-central routing problem, all nodes at distance at most r from a fixed node v want to send a packet to v.In this article we study the permutation routing, the r-central routing and the general (ℓ, k)-routing problems on plane grids, that is square grids, triangular grids and hexagonal grids. We use the store-and-forward Δ-port model, and we consider both full and half-duplex networks. We first survey the existing results in the literature about packet routing, with special emphasis on (ℓ, k)-routing on plane grids. Our main contributions are the following:1. Tight permutation routing algorithms on full-duplex hexagonal grids, and half duplex triangular and hexagonal grids.2. Tight r-central routing algorithms on triangular and hexagonal grids.3. Tight (k, k)-routing algorithms on square, triangular and hexagonal grids.4. Good approximation algorithms (in terms of running time) for (ℓ, k)-routing on square, triangular and hexagonal grids, together with new lower bounds on the running time of any algorithm using shortest path routing.These algorithms are all completely distributed, i.e., can be implemented independently at each node. Finally, we also formulate the (ℓ, k)-routing problem as a WEIGHTED EDGE COLORING problem on bipartite graphs.
A data type to exploit online data sources
Authors: Thornton Matthew , Edwards Stephen H. 
Published: September 2009

Recent work in developing student assignments has involved making use of online data resources to make them more interesting and to give students real world information to interact with in some manner. While definitely a practical approach, the work that has been done so far is either for "CS0" courses targeted at non-majors, often using tools like Microsoft Excel, or courses that require a level of skill at programming from the students. Additionally, existing tools are specific to a particular structure of the data (CSV, XML, and others). As a result, these constraints make on-line real-world data sets difficult to use in typical introductory programming courses for majors.
Objects-first approaches to teaching introductory programming advocate the use of objects early on. Consequently, students are able to take advantage of using data types early on. We have created an interface that allows students to access real-world data sets from online (or local) sources in a uniform fashion. This abstraction allows students with minimal programming experience to load, process, and manipulate external data sets in a variety of formats. We also developed a lab assignment where students accessed an online CSV data source to demonstrate feasibility and to gain experience with classroom use of this approach.
Group work support for the BlueJ IDE
Authors: Fisker Kasper , McCall Davin , Kölling Michael , Quig Bruce 
Published: September 2009

Learning to work in teams is essential for every software professional. Developing software as a team project is the standard practice in industry, and should be practiced in university courses. Starting effective group work practices early can lead to better acceptance of group work as a standard development mode.
Nonetheless, group work is often not included in introductory programming courses. The reason is often the necessary overhead associated with developing software in groups. We present a design and implementation of group work support tools integrated into the educational BlueJ IDE, which remove much of the tool overhead and make it easier to include group work in introductory courses.
Practical tips for creating podcasts in higher education
Authors: Sheridan-Ross Jakki , Gorra Andrea , Finlay Janet 
Published: September 2009

Podcasts are of particular interest in order to promote flexibility in teaching and learning. In this note, we provide tips for creating podcasts with a particular relevance for computing students, based on our experience at Leeds Metropolitan University.
A number of trials have taken place within Innovation North Faculty of Information and Technology including the development of learning materials and support mechanisms for academic staff wishing to develop new (or adapt existing) resources to this new format. To date, podcasts have been created to support the teaching of motion capture, advanced video technologies, and project-based work for computing students. CETL ALiC (Active Learning in Computing) is supporting the trials through the development of a Podcast Solutions Pilot which has allowed us to observe, support, develop and explore some of the issues around using this type of technology in a teaching and learning environment.
Targeting Sphingosine Kinase 1 Inhibits Akt Signaling, Induces Apoptosis, and Suppresses Growth of Human Glioblastoma Cells and Xenografts
Authors: Kapitonov Dmitri , Allegood Jeremy C. , Mitchell Clint , Hait Nitai C. , Almenara Jorge A. , Adams Jeffrey K. , Zipkin Robert E. , Dent Paul , Kordula Tomasz , Milstien Sheldon , Spiegel Sarah 
Published: September 2009

Abstract
Sphingosine-1-phosphate is a potent sphingolipid mediator of diverse processes important for brain tumors, including cell growth, survival, migration, invasion, and angiogenesis. Sphingosine kinase 1 (SphK1), one of the two isoenzymes that produce sphingosine-1-phosphate, is up-regulated in glioblastoma and has been linked to poor prognosis in patients with glioblastoma multiforme (GBM). In the present study, we found that a potent isotype-specific SphK1 inhibitor, SK1-I, suppressed growth of LN229 and U373 glioblastoma cell lines and nonestablished human GBM6 cells. SK1-I also enhanced GBM cell death and inhibited their migration and invasion. SK1-I rapidly reduced phosphorylation of Akt but had no significant effect on activation of extracellular signal-regulated kinase 1/2, another important survival pathway for GBM. Inhibition of the concomitant activation of the c-Jun-NH2-kinase pathway induced by SK1-I attenuated death of GBM cells. Importantly, SK1-I markedly reduced the tumor growth rate of glioblastoma xenografts, inducing apoptosis and reducing tumor vascularization, and enhanced the survival of mice harboring LN229 intracranial tumors. Our results support the notion that SphK1 may be an important factor in GBM and suggest that an isozyme-specific inhibitor of SphK1 deserves consideration as a new therapeutic agent for this disease. [Cancer Res 2009;69(17):6915–23]
CCAAT Enhancer Binding Protein-β Regulates Matrix Metalloproteinase-1 Expression in Interleukin-1β–Stimulated A549 Lung Carcinoma Cells
Authors: Armstrong David A. , Phelps Lauren N. , Vincenti Matthew P. 
Published: September 2009

Abstract
Matrix metalloproteinase-1 (MMP-1) is an inflammation-inducible neutral protease that mediates extracellular matrix remodeling and promotes tumor invasion. In this study, we examined the activation of MMP-1 gene expression in A549 lung carcinoma cells stimulated with the inflammatory cytokine interleukin-1β (IL-1β). We found that MMP-1 mRNA levels were maximal following 16 hours of IL-1β stimulation and that this correlated with the expression of the transcription factor CCAAT enhancer-binding protein-β (CEBPB). Knockdown of CEBPB expression with short hairpin RNA abrogated the expression of MMP-1, MMP-3, and MMP-10 in IL-1β–stimulated A549 cells. An established CEBP element in the MMP-1 promoter was found to be required for basal and IL-1β–induced transcription. Electrophoresis mobility shift assays showed that CEBPB binds to this promoter element maximally 16 hours after IL-1β stimulation. DNA affinity chromatography studies showed that the LAP1, LAP2, and LIP isoforms of CEBPB bind to the IL-1β–responsive CEBPB site in the MMP-1 promoter. Exogenous expression of the LAP1 and LAP2 isoforms stimulated the MMP-1 promoter, whereas LIP had no effect. Phosphorylation of CEBPB at Thr235 peaked at 16 hours in IL-1β–stimulated cells. The MEK inhibitor U0126 inhibited this phosphorylation and reduced MMP-1 gene induction. These studies establish CEBPB as an important mediator of metalloproteinase gene activation during inflammatory responses in lung cancer cells and highlight the different regulatory roles of CEBPB isoforms. (Mol Cancer Res 2009;7(9):1517–24)
The Word Processing Deficit in Semantic Dementia: All Categories Are Equal, but Some Categories Are More Equal than Others
Authors: Pulvermüller Friedemann , Cooper-Pye Elisa , Dine Clare , Hauk Olaf , Nestor Peter J. , Patterson Karalyn 
Published: September 2009

Abstract
It has been claimed that semantic dementia (SD), the temporal variant of fronto-temporal dementia, is characterized by an across-the-board deficit affecting all types of conceptual knowledge. We here confirm this generalized deficit but also report differential degrees of impairment in processing specific semantic word categories in a case series of SD patients (N = 11). Within the domain of words with strong visually grounded meaning, the patients' lexical decision accuracy was more impaired for color-related than for form-related words. Likewise, within the domain of action verbs, the patients' performance was worse for words referring to face movements and speech acts than for words semantically linked to actions performed with the hand and arm. Psycholinguistic properties were matched between the stimulus groups entering these contrasts; an explanation for the differential degrees of impairment must therefore involve semantic features of the words in the different conditions. Furthermore, this specific pattern of deficits cannot be captured by classic category distinctions such as nouns versus verbs or living versus nonliving things. Evidence from previous neuroimaging research indicates that color- and face/speech-related words, respectively, draw most heavily on anterior-temporal and inferior-frontal areas, the structures most affected in SD. Our account combines (a) the notion of an anterior-temporal amodal semantic “hub” to explain the profound across-the-board deficit in SD word processing, with (b) a semantic topography model of category-specific circuits whose cortical distributions reflect semantic features of the words and concepts represented.
An Extremum Solution of the Monin–Obukhov Similarity Equations
Authors: Wang Jingfeng , Bras Rafael L. 
Published: August 2009

Abstract
An extremum hypothesis of turbulent transport in the atmospheric surface layer is postulated. The hypothesis has led to a unique solution of Monin–Obukhov similarity equations in terms of simple expressions linking shear stress (momentum flux) and heat flux to mean wind shear and temperature gradient. The extremum solution is consistent with the well-known asymptotic properties of the surface layer. Validation of the extremum solution has been made by comparison to field measurements of momentum and heat fluxes. Furthermore, a modeling test of predicting surface heat fluxes using the results of this work is presented. A critical reexamination of the interpretation of the Obukhov length is given.
Mixed Layer Temperature Response to the Southern Annular Mode: Mechanisms and Model Representation
Authors: Screen James A. , Gillett Nathan P. , Karpechko Alexey Yu , Stevens David P. 
Published: August 2009

Abstract
Previous studies have shown that simulated sea surface temperature (SST) responses to the southern annular mode (SAM) in phase 3 of the Coupled Model Intercomparison Project (CMIP3) climate models compare poorly to the observed response. The reasons behind these model inaccuracies are explored. The ocean mixed layer heat budget is examined in four of the CMIP3 models and by using observations–reanalyses. The SST response to the SAM is predominantly driven by sensible and latent heat flux and Ekman heat transport anomalies. The radiative heat fluxes play a lesser but nonnegligible role. Errors in the simulated SST responses are traced back to deficiencies in the atmospheric response to the SAM. The models exaggerate the surface wind response to the SAM leading to large unrealistic Ekman transport anomalies. During the positive phase of the SAM, this results in excessive simulated cooling in the 40°–65°S latitudes. Problems with the simulated wind stress responses, which relate partly to errors in the simulated winds themselves and partly to the transfer coefficients used in the models, are a key cause of the errors in the SST response. In the central Pacific sector (90°–150°W), errors arise because the simulated SAM is too zonally symmetric. Substantial errors in the net shortwave radiation are also found, resulting from a poor representation of the changes in cloud cover associated with the SAM. The problems in the simulated SST responses shown by this study are comparable to deficiencies previously identified in the CMIP3 multimodel mean. Therefore, it is likely that the deficiencies identified here are common to other climate models.
Mechanisms of Climate Change in the Semiarid African Sahel: The Local View
Authors: Giannini Alessandra 
Published: September 2009

Abstract
Application of the moist static energy framework to analyses of vertical stability and net energy in the Sahel sheds light on the divergence of projections of climate change. Two distinct mechanisms are sketched. In one, anthropogenic warming changes continental climate indirectly: warming of the oceans increases moist static energy at upper levels, affecting vertical stability globally, from the top down, and driving drying over the Sahel, in a way analogous to the impact of El Niño–Southern Oscillation on the global tropical atmosphere. In the other, the increase in anthropogenic greenhouse gases drives a direct continental change: the increase in net terrestrial radiation at the surface increases evaporation, favoring vertical instability and near-surface convergence from the bottom up.
In both cases the surface warms, but in the first precipitation and evaporation decrease, while in the second they increase. In the first case, land surface warming is brought about by the remotely forced decrease in precipitation and consequent decrease in evaporation and increase in net solar radiation at the surface. In the second, it is brought about by the increase in net terrestrial radiation at the surface, amplified by the water vapor feedback associated with an increase in near-surface humidity.
Simulating the Effects of Irrigation over the United States in a Land Surface Model Based on Satellite-Derived Agricultural Data
Authors: Ozdogan Mutlu , Rodell Matthew , Beaudoing Hiroko Kato , Toll David L. 
Published: August 2009

Abstract
A novel method is introduced for integrating satellite-derived irrigation data and high-resolution crop-type information into a land surface model (LSM). The objective is to improve the simulation of land surface states and fluxes through better representation of agricultural land use. Ultimately, this scheme could enable numerical weather prediction (NWP) models to capture land–atmosphere feedbacks in managed lands more accurately and thus improve forecast skill. Here, it is shown that the application of the new irrigation scheme over the continental United States significantly influences the surface water and energy balances by modulating the partitioning of water between the surface and the atmosphere. In this experiment, irrigation caused a 12% increase in evapotranspiration (QLE) and an equivalent reduction in the sensible heat flux (QH) averaged over all irrigated areas in the continental United States during the 2003 growing season. Local effects were more extreme: irrigation shifted more than 100 W m−2 from QH to QLE in many locations in California, eastern Idaho, southern Washington, and southern Colorado during peak crop growth. In these cases, the changes in ground heat flux (QG), net radiation (RNET), evapotranspiration (ET), runoff (R), and soil moisture (SM) were more than 3 W m−2, 20 W m−2, 5 mm day−1, 0.3 mm day−1, and 100 mm, respectively. These results are highly relevant to continental-to-global-scale water and energy cycle studies that, to date, have struggled to quantify the effects of agricultural management practices such as irrigation. On the basis of the results presented here, it is expected that better representation of managed lands will lead to improved weather and climate forecasting skill when the new irrigation scheme is incorporated into NWP models such as NOAA’s Global Forecast System (GFS).