bluuebunny/crossref_metadata_2025_split huggingface dataset:
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology
Authors: Grossetête Sandrine , Labedan Bernard , Lespinet Olivier 
Published: February 2010

Abstract

Background
More and more completely sequenced fungal genomes are becoming available and many more sequencing projects are in progress. This deluge of data should improve our knowledge of the various primary and secondary metabolisms of Fungi, including their synthesis of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional annotation of many fungal genomes is imperfect, especially of genes encoding enzymes, so we need dedicated tools to analyze their metabolic pathways in depth.

Description
FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances. It is freely accessible at http://www.fungipath.u-psud.fr.

Conclusions
As more and more fungal genomes are expected to be sequenced during the coming years, FUNGIpath should help progressively to reconstruct the ancestral primary and secondary metabolisms of the main branches of the fungal tree of life and to elucidate the evolution of these ancestral fungal metabolisms to various specific derived metabolisms.
Gene prioritization in Type 2 Diabetes using domain interactions and network analysis
Authors: Sharma Amitabh , Chavali Sreenivas , Tabassum Rubina , Tandon Nikhil , Bharadwaj Dwaipayan 
Published: February 2010

Abstract

Background
Identification of disease genes for Type 2 Diabetes (T2D) by traditional methods has yielded limited success. Based on our previous observation that T2D may result from disturbed protein-protein interactions affected through disrupting modular domain interactions, here we have designed an approach to rank the candidates in the T2D linked genomic regions as plausible disease genes.

Results
Our approach integrates Weight value (Wv) method followed by prioritization using clustering coefficients derived from domain interaction network. Wv for each candidate is calculated based on the assumption that disease genes might be functionally related, mainly facilitated by interactions among domains of the interacting proteins. The benchmarking using a test dataset comprising of both known T2D genes and non-T2D genes revealed that Wv method had a sensitivity and specificity of 0.74 and 0.96 respectively with 9 fold enrichment. The candidate genes having a Wv > 0.5 were called High Weight Elements (HWEs). Further, we ranked HWEs by using the network property-the clustering coefficient (Ci). Each HWE with a Ci < 0.015 was prioritized as plausible disease candidates (HWEc) as previous studies indicate that disease genes tend to avoid dense clustering (with an average Ci of 0.015). This method further prioritized the identified disease genes with a sensitivity of 0.32 and a specificity of 0.98 and enriched the candidate list by 6.8 fold. Thus, from the dataset of 4052 positional candidates the method ranked 435 to be most likely disease candidates. The gene ontology sharing for the candidates showed higher representation of metabolic and signaling processes. The approach also captured genes with unknown functions which were characterized by network motif analysis.

Conclusions
Prioritization of positional candidates is essential for cost-effective and an expedited discovery of disease genes. Here, we demonstrate a novel approach for disease candidate prioritization from numerous loci linked to T2D.
Reduced blood brain barrier breakdown in P-selectin deficient mice following transient ischemic stroke: a future therapeutic target for treatment of stroke
Authors: Jin Albert Y , Tuor Ursula I , Rushforth David , Kaur Jaspreet , Muller Robert N , Petterson Jodie Lee , Boutry Sébastien , Barber Philip A 
Published: February 2010

Abstract

Background
The link between early blood- brain barrier (BBB) breakdown and endothelial cell activation in acute stroke remain poorly defined. We hypothesized that P-selectin, a mediator of the early phase of leukocyte recruitment in acute ischemia is also a major contributor to early BBB dysfunction following stroke. This was investigated by examining the relationship between BBB alterations following transient ischemic stroke and expression of cellular adhesion molecule P-selectin using a combination of magnetic resonance molecular imaging (MRMI), intravital microscopy and immunohistochemistry. MRMI was performed using the contrast, gadolinium diethylenetriaminepentaacetic acid (Gd-DTPA) conjugated to Sialyl Lewis X (Slex) where the latter is known to bind to activated endothelium via E- or P selectins. Middle cerebral artery occlusion was induced in male C57/BL 6 wild-type (WT) mice and P-selectin-knockout (KO) mice. At 24 hours following middle cerebral artery occlusion, T1 maps were acquired prior to and following contrast injection. In addition to measuring P- and E-selectin expression in brain homogenates, alterations in BBB function were determined immunohistochemically by assessing the extravasation of immunoglobulin G (IgG) or staining for polymorphonuclear (PMN) leukocytes. In vivo assessment of BBB dysfunction was also investigated optically using intravital microscopy of the pial circulation following the injection of Fluorescein Isothiocyanate (FITC)-dextran (MW 2000 kDa).

Results
MRI confirmed similar infarct sizes and T1 values at 24 hours following stroke for both WT and KO animals. However, the blood to brain transfer constant for Gd DTPA (Kgd) demonstrated greater tissue extravasation of Gd DTPA in WT animals than KO mice (P < 0.03). In the P selectin KO mice, Δ T1 stroke -Δ T1 contralateral control cortex, decreased significantly in the Gd-DTPA(sLeX) group compared to Gd-DTPA, indicative of sLeX mediated accumulation of the targeted contrast agent. Regarding BBB function, in the P-selectin KO mice compared to WT control mice, there was an attenuation in the extravasation of IgG (P < 0.001), a trend for decreased FITC extravasation and less infiltration of PMN leukocytes (P < 0.001) thereby supporting the observed increase in Kgd permeability in stroke brain of WT compared to KO mice.

Conclusion
P-selectin expression contributes to enhanced BBB dysfunction at 24 hours after transient focal cerebral ischemia.
A novel germline PALB2 deletion in Polish breast and ovarian cancer patients
Authors: Dansonka-Mieszkowska Agnieszka , Kluska Anna , Moes Joanna , Dabrowska Michalina , Nowakowska Dorota , Niwinska Anna , Derlatka Pawel , Cendrowski Krzysztof , Kupryjanczyk Jolanta 
Published: February 2010

Abstract

Background
PALB2 protein was recently identified as a partner of BRCA1 and BRCA2 which determines their proper function in DNA repair.

Methods
Initially, the entire coding sequence of the PALB2 gene with exon/intron boundaries was evaluated by the PCR-SSCP and direct sequencing methods on 70 ovarian carcinomas. Sequence variants of interest were further studied on enlarged groups of ovarian carcinomas (total 339 non-consecutive ovarian carcinomas), blood samples from 334 consecutive sporadic and 648 consecutive familial breast cancer patients, and 1310 healthy controls from central Poland.

Results
Ten types of sequence variants were detected, and among them four novel polymorphisms: c.2996+58T>C in intron 9; c.505C>A (p.L169I), c.618T>G (p.L206L), both in exon 4; and c.2135C>T (A712V) in exon 5 of the PALB2 gene. Another two polymorphisms, c.212-58A>C and c.2014G>C (E672Q) were always detected together, both in cancer (7.5% of patients) and control samples (4.9% of controls, p = 0.2). A novel germline truncating mutation, c.509_510delGA (p.R170fs) was found in exon 4: in 2 of 339 (0.6%) unrelated ovarian cancer patients, in 4 of 648 (0.6%) unrelated familial breast cancer patients, and in 1 of 1310 controls (0.08%, p = 0.1, p = 0.044, respectively). One ovarian cancer patient with the PALB2 mutation had also a germline nonsense mutation of the BRCA2 gene.

Conclusions
The c.509_510delGA is a novel PALB2 mutation that increases the risk of familial breast cancer. Occurrence of the same PALB2 alteration in seven unrelated women suggests that c.509_510delGA (p.R170fs) is a recurrent mutation for Polish population.
Should we use closed or open infusion containers for prevention of bloodstream infections?
Authors: Rangel-Frausto Manuel S , Higuera-Ramirez Francisco , Martinez-Soto Jose , Rosenthal Victor D 
Published: February 2010

Abstract

Background
Hospitalized patients in critical care settings are at risk for bloodstream infections (BSI). Most BSIs originate from a central line (CL), and they increase length of stay, cost, and mortality. Open infusion containers may increase the risk of contamination and administration-related (CLAB) because they allow the entry of air into the system, thereby also providing an opportunity for microbial entry. Closed infusion containers were designed to overcome this flaw. However, open infusion containers are still widely used throughout the world.
The objective of the study was to determine the effect of switching from open (glass, burettes, and semi-rigid) infusion containers to closed, fully collapsible, plastic infusion containers (Viaflex®) on the rate and time to onset of central line-associated bloodstream infections CLABs.

Methods
An open label, prospective cohort, active healthcare-associated infection surveillance, sequential study was conducted in four ICUs in Mexico. Centers for Disease Control National Nosocomial Infections Surveillance Systems definitions were used to define device-associated infections.

Results
A total of 1,096 adult patients who had a central line in place for >24 hours were enrolled. The CLAB rate was significantly higher during the open versus the closed container period (16.1 versus 3.2 CLAB/1000 central line days; RR = 0.20, 95% CI = 0.11-0.36, P < 0.0001). The probability of developing CLAB remained relatively constant in the closed container period (1.4% Days 2-4 to 0.5% Days 8-10), but increased in the open container period (4.9% Days 2-4 to 5.4% Days 8-10). The chance of acquiring a CLAB was significantly decreased (81%) in the closed container period (Cox proportional hazard ratio 0.19, P < 0.0001). Mortality was statistically significantly lower during the closed versus the open container period (23.4% versus 16.1%; RR = 0.69, 95% CI = 0.54-0.88, P < 0.01).

Conclusions
Closed infusion containers significantly reduced CLAB rate, the probability of acquiring CLAB, and mortality.
Role of platelets in neuroinflammation: a wide-angle perspective
Authors: Horstman Lawrence L , Jy Wenche , Ahn Yeon S , Zivadinov Robert , Maghzi Amir H , Etemadifar Masoud , Steven Alexander J , Minagar Alireza 
Published: February 2010

AbstractObjectivesThis review summarizes recent developments in platelet biology relevant to neuroinflammatory disorders. Multiple sclerosis (MS) is taken as the "Poster Child" of these disorders but the implications are wide. The role of platelets in inflammation is well appreciated in the cardiovascular and cancer research communities but appears to be relatively neglected in neurological research.OrganizationAfter a brief introduction to platelets, topics covered include the matrix metalloproteinases, platelet chemokines, cytokines and growth factors, the recent finding of platelet PPAR receptors and Toll-like receptors, complement, bioactive lipids, and other agents/functions likely to be relevant in neuroinflammatory diseases. Each section cites literature linking the topic to areas of active research in MS or other disorders, including especially Alzheimer's disease.ConclusionThe final section summarizes evidence of platelet involvement in MS. The general conclusion is that platelets may be key players in MS and related disorders, and warrant more attention in neurological research.
Jane: a new tool for the cophylogeny reconstruction problem
Authors: Conow Chris , Fielder Daniel , Ovadia Yaniv , Libeskind-Hadas Ran 
Published: February 2010

Abstract

Background
This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.

Results
The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program.

Conclusions

Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.
Temporal Trends in Cause-Specific Late Mortality Among 5-Year Survivors of Childhood Cancer
Authors: Armstrong Gregory T. , Pan Zhenyu , Ness Kirsten K. , Srivastava Deokumar , Robison Leslie L. 
Published: February 2010

Purpose Five-year survival rates for childhood cancer have improved over the past four decades. However, it is unknown whether changes in primary cancer therapy have improved rates of long-term (> 5 years from diagnosis) durable remissions and reduced treatment-related deaths. We investigated changes in patterns of late mortality over time and cause-specific attribution of late-mortality among 5-year survivors. Patients and Methods Using data from the Surveillance, Epidemiology and End Results (SEER) population-based registry, we assessed all-cause and cause-specific (recurrence/progression of primary disease, external cause, and nonrecurrence/nonexternal cause) late mortality during four consecutive time periods from 1974 through 2000 among 26,643 5-year survivors of childhood cancer. Results All-cause late mortality improved during more recent eras, dropping from 7.1% (95% CI, 6.4% to 7.8%) among children diagnosed during 1974 to 1980 to 3.9% (95% CI, 3.3% to 4.4%) among children diagnosed during 1995 to 2000 (P < .001), largely because of reduced mortality from recurrence or progression. While there was no significant reduction in mortality attributable to other health conditions (including treatment-related health conditions), analysis controlling for demographic characteristics identified a trend toward reduced risk during more recent eras (P = .007). Disparity by race/ethnicity was identified, with higher mortality among non-Hispanic blacks than among non-Hispanic whites for all-cause and nonrecurrence/nonexternal -cause late mortality. Conclusion While overall patterns of mortality from other health conditions do not differ over time, adjustment for demographic characteristics provides evidence that risk of treatment-related mortality may be lower in more recent eras. Disparities in health care utilization among survivors should be explored.
Functional intersection of the kallikrein-related peptidases (KLKs) and thrombostasis axis
Authors: Blaber Michael , Yoon Hyesook , Juliano Maria A. , Scarisbrick Isobel A. , Blaber Sachiko I. 
Published: February 2010

Abstract
A large body of emerging evidence indicates a functional interaction between the kallikrein-related peptidases (KLKs) and proteases of the thrombostasis axis. These interactions appear relevant for both normal health as well as pathologies associated with inflammation, tissue injury, and remodeling. Regulatory interactions between the KLKs and thrombostasis proteases could impact several serious human diseases, including neurodegeneration and cancer. The emerging network of specific interactions between these two protease families appears to be complex, and much work remains to elucidate it. Complete understanding how this functional network resolves over time, given specific initial conditions, and how it might be controllably manipulated, will probably contribute to the emergence of novel diagnostics and therapeutic agents for major diseases.
KLK5 gene expression is severely upregulated in androgen-independent prostate cancer cells after treatment with the chemotherapeutic agents docetaxel and mitoxantrone
Authors: Mavridis Konstantinos , Talieri Maroulio , Scorilas Andreas 
Published: February 2010

AbstractKallikrein-related peptidases (KLKs), includingKLK5, have been proposed as promising biomarkers for prostate cancer diagnosis and prognosis. In the present study, we report that distinct augmentations (up to 6.4-fold) ofKLK5mRNA expressional levels, calculated via quantitative real-time PCR, occur after treatment of DU145 cells with appropriate concentrations, determined by the MTT method, of docetaxel and mitoxantrone. Our data reveal the endogenous need of prostate cancer cells for modifiedKLK5expression to cope with the administration of chemotherapeutic drugs. Furthermore, it is proposed that the expression profile ofKLK5could serve as a putative biomarker for monitoring the treatment response in hormone refractory prostate cancer patients.
Using Cartesian Space in Motion Planning for 7 DoF ManipulatorNutzung des kartesischen Raums in der Bewegungsplannung für Manipulatoren mit 7 Freiheitsgraden
Authors: Ojdanic Darko , Gräser Axel 
Published: February 2010

Abstract
This paper introduces motion planning algorithms that are suitable for real-time applications with dexterous manipulators. Developed motion planner obtains needed efficiency by using the Cartesian space information, and therefore avoids the dimensionality problem of the configuration space. In this work, a skillful planner is developed together with a post-processing path-smoothing technique, which is independent from the planner. A comparison with the state-of-the-art planners emphasises the advantages of this approach. Described algorithms successfully operate on a rehabilitation robotic system FRIEND.
Bahnplanung und Regelung unteraktuierter Manipulatoren mittels nichtlinearer zeitdiskreter AnsätzePath-planning and Control of Underactuated Manipulators by Nonlinear Discrete-time Approaches
Authors: Weidemann Dirk , Scherm Norbert , Heimann Bodo 
Published: February 2010

Zusammenfassung
In der Klasse der unteraktuierten Systeme stellen horizontal bewegte Manipulatoren mit passiven Gelenken eine besondere Herausforderung dar, weil die Linearisierung in einer Ruhelage zu einem nicht vollständig steuerbaren Modell führt. Für Bewegungen, die in Ruhelagen beginnen und enden, sind lineare Ansätze zum Reglerentwurf ungeeignet. Auch bei Wahl eines nichtlinearen Modells liegt in der Umgebung einer Ruhelage ein schlecht konditioniertes Regelungsproblem vor. Zeitkontinuierliche Ansätze, die ein asymptotisches Annähern an die Ruhelage fordern, führen daher selten auf ein zufriedenstellendes Systemverhalten. Die vorgestellten zeitdiskreten Ansätze ermöglichen dieses Problem mittels Bahnplanung auf endlichem Zeitintervall und Dead-Beat-Regelung zu umgehen. Neben Bahnplanungsansätzen, die schnelle Konvergenz und systematische Berechnung der Bewegungsdauer gewährleisten, werden zwei Regler präsentiert und verifiziert.
Vollständige Modale Synthese regulärer DeskriptorsystemeParametric Feedback Design of Regular Descriptor Systems
Authors: Manderla Maximilian , Konigorski Ulrich 
Published: February 2010

Zusammenfassung
Der Beitrag beschreibt ein neues Verfahren zur Synthese konstanter Zustandsrückführungen für lineare, zeitinvariante Deskriptorsysteme. Ausgehend von bekannten parametrischen Entwurfsmethoden für gewöhnliche Zustandsraumbeschreibungen wird eine Synthesevorschrift angegeben, welche sämtliche Freiheitsgrade beim Entwurf regulärer Deskriptorsysteme und deren Auswirkungen auf die Dynamik des geschlossenen Regelkreises sichtbar macht. Insbesondere lassen sich alle steuerbaren endlichen sowie unendlichen Eigenwerte explizit vorgeben.
Die Bedeutung der Materialentwicklung für elektrochemische SensorenMaterials Research and Development for Electrochemical Sensors
Authors: Vonau Winfried , Oelßner Wolfram , Zosel Jens , Kohler Heinz 
Published: February 2010

Zusammenfassung
Elektrochemische Sensoren werden in verschiedenen Ausführungsformen in einem weiten Temperaturbereich von ca. -30°C bis über 1500°C in festen, flüssigen und gasförmigen Medien eingesetzt. Die Erschließung neuer Anwendungsgebiete sowie die Erweiterung des Temperatureinsatzbereiches, die Erhöhung von Sensitivität, Selektivität und Stabilität und die Optimierung von Fertigungstechnologien der Sensoren beruhen fast immer auf Neu- und Weiter-entwicklungen von Sensormaterialien und Verfahren zu deren Herstellung. Der Übersichtsartikel zeigt die Vielfalt dieser Bemühungen anhand von Beispielen zu Materialentwicklungen für elektrochemische Referenzelektroden, Metalloxidelektroden, Metalloxid-Gassensoren sowie YSZ-basierten Festelektrolytsensoren.
Die kombinierte Standardunsicherheit als Variationsproblem am Beispiel eines TurbinenradzählersThe Combined Standard Uncertainty as Variation Problem Using the Example of a Turbine Meter
Authors: Riedel Jörg 
Published: February 2010

Zusammenfassung
Die Verifizierung der Unsicherheit, die einem ermittelten Wert einer Messgröße anhaftet, ist mit Hilfe der kombinierten Standardunsicherheit möglich. Ebenfalls ist eine Unsicherheitsanalyse zur Planung einer Messaufgabe nützlich, um die richtige Auswahl der Messgeräte und eines geeigneten Messverfahrens treffen zu können. Dazu wird in diesem Beitrag die relative kombinierte Standardunsicherheit als Variationsproblem beteiligter Unsicherheitskomponenten aufgefasst und am Beispiel eines Turbinenradzählers für Flüssigkeitsmessungen behandelt.
Thermoelektrische Dünnschicht-Generatoren. Energieautarke Versorgung für KleinleistungsverbraucherThin Film Thermoelectric Generators. Autonomous Power Supply for Low-Power Devices
Authors: Nurnus Joachim , Habbe Burkhard 
Published: February 2010

Zusammenfassung
Thermoelektrische Bauteile zur Erzeugung von elektrischer Energie aus Verlustwärme lassen sich mittels Halbleitertechnologien extrem miniaturiesieren. Mithilfe eines waferbasierten, MEMS-ähnlichen Herstellungsprozesses können Bauteile mit Gesamtdicken zwischen 0,5 mm und 1 mm sowie Grundflächen von weniger als 1 mm2 bis zu 25 mm2 hergestellt werden. Die Herstellung der Bauteile erfolgt auf Standard-Halbleiterequipment. Daher sind von anderen chipbasierten Produkten bekannte Expansionsszenarien und die daraus resultierenden Skaleneffekte bei großen Stückzahlen (“economy-of-scale”) auch auf diese Bauteile anwendbar. Dass aufgrund der verwendeten Dünnschicht-Technologie zusätzlich ca. 1000 Mal weniger thermoelektrisches Material als bei konventionellen Modulen benötigt wird, ist ein weiterer Garant für langfristig kostengünstige Bauteile. In diesem Artikel wird neben dem Herstellverfahren für Micropelt-Thermogeneratoren auch deren Einsatz in thermischen Harvesting-Modulen anhand des Evaluationsmoduls TE-Power NODE beschrieben.