bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces
Authors: Aliste Marcela P , Tieleman D Peter 
Published: December 2005

Abstract

Background
Peptide-membrane interactions play a key role in the binding, partitioning and folding of membrane proteins, the activity of antimicrobial and fusion peptides, and a number of other processes. To gain a better understanding of the thermodynamics of such interactions, White and Wimley created an interfacial hydrophobicity scale based of the transfer free energy from water to octanol or lipid bilayers of a series of synthetic peptapeptides (Ace-WLXLL, with X being any of the twenty natural amino acids) (White and Wimley (1996) Nat. Struct. Biol. 3, 842–848). In this study, we performed molecular dynamics simulations of a representative set of ten of these peptides (X = D, K, R, N, A, T, S, I, F and W) in two membrane mimetic interfaces: water-cyclohexane (10 ns) and a fully solvated dioleoylphosphatidylcholine (DOPC) bilayer (50 ns) using both constant pressure and constant area ensembles. We focus on partitioning of the ten peptides at the cyclohexane/water and lipid/water interfaces.

Results
The peptides rapidly equilibrate (< 2 ns) and partition at the cyclohexane/water interface. The X3 guest residue assumes average orientations that depend on the nature of the side chain. At the DOPC/water interface, dynamics is much slower and convergence is difficult to achieve on a 50 ns timescale. Nonetheless, all peptides partition to the lipid/water interface with distributions with widths of 1–2 nm. The peptides assume a broad range of side chain and backbone orientations and have only a small effect on the area of the unit cell. On average, hydrophobic guest residues partition deeper into the hydrophobic core than hydrophilic residues. In some cases the peptides penetrate sufficiently deep to somewhat affect the distribution of the C=C double bond in DOPC. The relative distribution of the X3 guest residue compared to W1 and L5 is similar in the water/cyclohexane and water/lipid simulations. Snapshots show mostly extended backbone conformations in both environments. There is little difference between simulations at a constant area of 0.66 nm2 and simulations at constant pressure that approximately yield the same average area of 0.66 nm2.

Conclusion
These peptides were designed to assume extended conformations, which is confirmed by the simulations. The distribution of the X3 side chain depends on its nature, and can be determined from molecular dynamics simulations. The time scale of peptide motion at a phospholipids-water interface is too long to directly calculate the experimentally measured hydrophobicity scale to test and improve the simulation parameters. This should be possible at the water/cyclohexane interface and likely will become feasible in the future for the phospholipids/water case.
Internet-based profiler system as integrative framework to support translational research
Authors: Kim Robert , Demichelis Francesca , Tang Jeffery , Riva Alberto , Shen Ronglai , Gibbs Doug F , Mahavishno Vasudeva , Chinnaiyan Arul M , Rubin Mark A 
Published: December 2005

Abstract
Background
Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions.

Results
The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems.

Conclusion
We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing.
Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources
Authors: Smith Jeramiah J , Putta Srikrishna , Walker John A , Kump D Kevin , Samuels Amy K , Monaghan James R , Weisrock David W , Staben Chuck , Voss S Randal 
Published: December 2005

Abstract
Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1) Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2) Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3) Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4) Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5) Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6) Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at http://www.ambystoma.org.
Comparison of gene expression signatures of diamide, H2O2 and menadione exposed Aspergillus nidulans cultures – linking genome-wide transcriptional changes to cellular physiology
Authors: Pócsi István , Miskei Márton , Karányi Zsolt , Emri Tamás , Ayoubi Patricia , Pusztahelyi Tünde , Balla György , Prade Rolf A 
Published: December 2005

Abstract

Background
In addition to their cytotoxic nature, reactive oxygen species (ROS) are also signal molecules in diverse cellular processes in eukaryotic organisms. Linking genome-wide transcriptional changes to cellular physiology in oxidative stress-exposed Aspergillus nidulans cultures provides the opportunity to estimate the sizes of peroxide (O2
2-), superoxide (O2
•-) and glutathione/glutathione disulphide (GSH/GSSG) redox imbalance responses.

Results
Genome-wide transcriptional changes triggered by diamide, H2O2 and menadione in A. nidulans vegetative tissues were recorded using DNA microarrays containing 3533 unique PCR-amplified probes. Evaluation of LOESS-normalized data indicated that 2499 gene probes were affected by at least one stress-inducing agent. The stress induced by diamide and H2O2 were pulse-like, with recovery after 1 h exposure time while no recovery was observed with menadione. The distribution of stress-responsive gene probes among major physiological functional categories was approximately the same for each agent. The gene group sizes solely responsive to changes in intracellular O2
2-, O2
•- concentrations or to GSH/GSSG redox imbalance were estimated at 7.7, 32.6 and 13.0 %, respectively. Gene groups responsive to diamide, H2O2 and menadione treatments and gene groups influenced by GSH/GSSG, O2
2- and O2
•- were only partly overlapping with distinct enrichment profiles within functional categories. Changes in the GSH/GSSG redox state influenced expression of genes coding for PBS2 like MAPK kinase homologue, PSK2 kinase homologue, AtfA transcription factor, and many elements of ubiquitin tagging, cell division cycle regulators, translation machinery proteins, defense and stress proteins, transport proteins as well as many enzymes of the primary and secondary metabolisms. Meanwhile, a separate set of genes encoding transport proteins, CpcA and JlbA amino acid starvation-responsive transcription factors, and some elements of sexual development and sporulation was ROS responsive.

Conclusion
The existence of separate O2
2-, O2
•- and GSH/GSSG responsive gene groups in a eukaryotic genome has been demonstrated. Oxidant-triggered, genome-wide transcriptional changes should be analyzed considering changes in oxidative stress-responsive physiological conditions and not correlating them directly to the chemistry and concentrations of the oxidative stress-inducing agent.
Balance of IL-10 and Interferon-γ plasma levels in human visceral leishmaniasis: Implications in the pathogenesis
Authors: Caldas Arlene , Favali Cecília , Aquino Dorlene , Vinhas Vera , van Weyenbergh Johan , Brodskyn Cláudia , Costa Jackson , Barral-Netto Manoel , Barral Aldina 
Published: December 2005

AbstractBackgroundLeishmaniasis remains a serious public health problem in several parts of the developing world. Effective prophylactic measurements are hampered by imprecise comprehension of different aspects of the disease, including its immunoregulation. A better comprehension of immunoregulation in human VL may be useful both for designing and evaluating immunoprophylaxis.MethodsTo explore immunoregulatory mechanisms, 20 visceral leishmaniasis (VL) patients were evaluated during active disease and at different periods up to one year after treatment determining their plasma cytokine levels, clinical parameters (palpable spleen and liver) and antibody levels.ResultsElevated plasma levels of IFN-γ and of IL-12 p40 were observed during active disease, significantly decreasing after treatment whereas in vitro Leishmania antigen-stimulated IFN-γ production by PBMC exhibited an inverse pattern being low during disease and increasing steadily thereafter. Absence of IFN-γ activity is a hallmark of VL. The main candidate for blunting IFN-γ activity is IL-10, a cytokine highly elevated in plasma with sharp decrease after treatment. Activity of IL-10 is inferred by high levels of anti-Leishmania specific IgG1 and IgG3. TGF-β had elevated total, but not of active, levels lessening the likelihood of being the IFN-γ counterpart. Spleen or liver size presented a steady decrease but return to normal values at only 120 days after treatment. Anti-Leishmania IgG (total and subclasses) levels and DTH or Leishmania-stimulated lymphocyte proliferation conversion to positive also present a slow decrease after treatment. IL-6 plasma levels were elevated in only a few patients.ConclusionTaken together our results suggest that IFN-γ and IL-10 are the molecules most likely involved in determining fate of disease. After treatment, there is a long delay before the immune profile returns to normal what precludes using plasma cytokine levels as criteria of cure as simpler clinical evaluations, as a palpable spleen or liver, can be used.
Takifugu obscurus is a euryhaline fugu species very close to Takifugu rubripes and suitable for studying osmoregulation
Authors: Kato Akira , Doi Hiroyuki , Nakada Tsutomu , Sakai Harumi , Hirose Shigehisa 
Published: December 2005

AbstractBackgroundThe genome sequence of the pufferfishTakifugu rubripesis an enormously useful tool in the molecular physiology of fish. Euryhaline fish that can survive both in freshwater (FW) and seawater (SW) are also very useful for studying fish physiology, especially osmoregulation. Recently we learned that there is a pufferfish,Takifugu obscurus, common name "mefugu" that migrates into FW to spawn. IfT. obscurusis indeed a euryhaline fish and shares a high sequence homology withT. rubripes, it will become a superior animal model for studying the mechanism of osmoregulation. We have therefore determined its euryhalinity and phylogenetic relationship to the members of theTakifugufamily.ResultsThe following sixTakifuguspecies were used for the analyses:T. obscurus,T. rubripes,T. niphobles,T. pardalis,T. poecilonotus, andT. porphyreus. When transferred to FW, onlyT. obscuruscould survive while the others could not survive more than ten days in FW. During this course of FW adaptation, serum Na+concentration ofT. obscurusdecreased only slightly, but a rapid and large decrease occurred even in the case ofT. niphobles, a peripheral fresh water species that is often seen in brackish river mouths. Phylogenetic analysis using nucleotide sequences of the mitochondrial 16S ribosomal RNA gene of each species indicated that the sixTakifuguspecies are very closely related with each other.ConclusionT. obscurusis capable of adapting to both FW and SW. Its genomic sequence shares a very high homology with those of the otherTakifuguspecies such that the existingTakifugugenomic information resources can be utilized. These properties make "mefugu", which has drawn little attention from animal physiologists until this study, a useful model animal for studying the molecular mechanism of maintaining body fluid homeostasis.
The influence of objectives, learning experiences and examination blueprint on medical students' examination preparation
Authors: McLaughlin K , Coderre S , Woloschuk W , Lim T , Muruve D , Mandin H 
Published: December 2005

Abstract

Background
The influence of intended and informal curricula on examination preparation has not been extensively studied. This study aims to firstly describe how students utilized components of intended and informal curricula to guide examination preparation, and secondly to study the relationship between examination preparation and performance.

Methods
Students received a pre-examination questionnaire to identify components from the intended curriculum (objectives and examination blueprint), and informal curriculum (content emphasised during lectures and small groups), used during examination preparation. Multiple logistic regression was used to study the relationship between these variables and student performance (above versus at or below average).

Results
Eighty-one students participated. There was no difference in the proportions using the examination blueprint, content emphasised during lectures, and content emphasised during small groups (87 – 93%) but fewer students used objectives (35%, p < 0.001). Objectives use was associated with reduced odds of above average examination performance (adjusted odds ratio 0.27 [0.07, 0.97], p = 0.04).

Conclusion
When preparing for the renal course examination, students were influenced at least as much by the informal as the intended curriculum. Of the two intended curriculum components, the examination blueprint appeared to be more widely used than the course objectives. This decreased use of objectives on examination preparation did not appear to have a detrimental effect on student performance.
Providing education on evidence-based practice improved knowledge but did not change behaviour: a before and after study
Authors: McCluskey Annie , Lovarini Meryl 
Published: December 2005

Abstract

Background
Many health professionals lack the skills to find and appraise published research. This lack of skills and associated knowledge needs to be addressed, and practice habits need to change, for evidence-based practice to occur. The aim of this before and after study was to evaluate the effect of a multifaceted intervention on the knowledge, skills, attitudes and behaviour of allied health professionals.

Methods
114 self-selected occupational therapists were recruited. The intervention included a 2-day workshop combined with outreach support for eight months. Support involved email and telephone contact and a workplace visit. Measures were collected at baseline, post-workshop, and eight months later. The primary outcome was knowledge, measured using the Adapted Fresno Test of Evidence-Based Practice (total score 0 to 156). Secondary outcomes were attitude to evidence-based practice (% reporting improved skills and confidence; % reporting barriers), and behaviour measured using an activity diary (% engaging/not engaging in search and appraisal activities), and assignment completion.

Results
Post-workshop, there were significant gains in knowledge which were maintained at follow-up. The mean difference in the Adapted Fresno Test total score was 20.6 points (95% CI, 15.6 to 25.5). The change from post-workshop to follow-up was small and non-significant (mean difference 1.2 points, 95% CI, -6.0 to 8.5). Fewer participants reported lack of searching and appraisal skills as barriers to evidence-based practice over time (searching = 61%, 53%, 24%; appraisal 60%, 65%, 41%). These differences were statistically significant (p = 0.0001 and 0.010 respectively). Behaviour changed little. Pre-workshop, 6% engaged in critical appraisal increasing to 18% post-workshop and 18% at follow-up. Nearly two thirds (60%) were not reading any research literature at follow-up. Twenty-three participants (20.2%) completed their assignment.

Conclusion
Evidence-based practice skills and knowledge improved markedly with a targetted education intervention and outreach support. However, changes in behaviour were small, based on the frequency of searching and appraisal activities. Allied health educators should focus more on post-workshop skill development, particularly appraisal, and help learners to establish new routines and priorities around evidence-based practice. Learners also need to know that behaviour change of this nature may take months, even years.
Mechanomyographic amplitude and frequency responses during dynamic muscle actions: a comprehensive review
Authors: Beck Travis W , Housh Terry J , Cramer Joel T , Weir Joseph P , Johnson Glen O , Coburn Jared W , Malek Moh H , Mielke Michelle 
Published: December 2005

AbstractThe purpose of this review is to examine the literature that has investigated mechanomyographic (MMG) amplitude and frequency responses during dynamic muscle actions. To date, the majority of MMG research has focused on isometric muscle actions. Recent studies, however, have examined the MMG time and/or frequency domain responses during various types of dynamic activities, including dynamic constant external resistance (DCER) and isokinetic muscle actions, as well as cycle ergometry. Despite the potential influences of factors such as changes in muscle length and the thickness of the tissue between the muscle and the MMG sensor, there is convincing evidence that during dynamic muscle actions, the MMG signal provides valid information regarding muscle function. This argument is supported by consistencies in the MMG literature, such as the close relationship between MMG amplitude and power output and a linear increase in MMG amplitude with concentric torque production. There are still many issues, however, that have yet to be resolved, and the literature base for MMG during both dynamic and isometric muscle actions is far from complete. Thus, it is important to investigate the unique applications of MMG amplitude and frequency responses with different experimental designs/methodologies to continually reassess the uses/limitations of MMG.
Hemangiopericytoma of the spleen: Unusual presentation as multiple abscess
Authors: Kumar Mukesh , Tripathi Kamlakar , Khanna Rahul , Kumar Mohan , Khanna Ajay K 
Published: December 2005

Abstract

Background
Hemangiopericytoma is a soft tissue vascular neoplasm arising from capillary pericytes and is found throughout the body in soft tissues and bone. It was first described in 1942. Primary vascular neoplasm of the spleen constitutes the majority of nonhaematolymphoid splenic tumors like haemangioma, lymphangioma, hemangioendothelioma, hemangiopericytoma etc. Splenic hemangiopericytoma is a rare tumor and probably first case was described in 1989. Uptill now only eight cases are reported in the English literature.

Case presentation
A-35-year old male presented with fever and dull aching pain in left hypochondriac region. Radiological evaluation showed presence of multiple abscesses in spleen. Investigations were done to rule out common causes of abscess in spleen. After failure of medical management, he was subjected to elective splenectomy. There were dense adhesions between the spleen and the adjacent structures and the diaphragm. The histopathology of the resected specimen showed hemangiopericytoma of spleen.

Conclusion
The present case illustrate that the hemangiopericytoma of spleen can mimic as multiple abscess. Splenectomy is the treatment of choice.
Involvement of claudin-7 in HIV infection of CD4(-) cells
Authors: Zheng Junying , Xie Yiming , Campbell Richard , Song Jun , Massachi Samira , Razi Miriam , Chiu Robert , Berenson James , Yang Otto O , Chen Irvin SY , Pang Shen 
Published: December 2005

Abstract

Background
Human immunodeficiency virus (HIV) infection of CD4(-) cells has been demonstrated, and this may be an important mechanism for HIV transmission.

Results
We demonstrated that a membrane protein, claudin-7 (CLDN-7), is involved in HIV infection of CD4(-) cells. A significant increase in HIV susceptibility (2- to 100-fold) was demonstrated when CLDN-7 was transfected into a CD4(-) cell line, 293T. In addition, antibodies against CLDN-7 significantly decreased HIV infection of CD4(-) cells. Furthermore, HIV virions expressing CLDN-7 on their envelopes had a much higher infectivity for 293T CD4(-) cells than the parental HIV with no CLDN-7. RT-PCR results demonstrated that CLDN-7 is expressed in both macrophages and stimulated peripheral blood leukocytes, suggesting that most HIV virions generated in infected individuals have CLDN-7 on their envelopes. We also found that CLDN-7 is highly expressed in urogenital and gastrointestinal tissues.

Conclusion
Together these results suggest that CLDN-7 may play an important role in HIV infection of CD4(-) cells.