bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of new autoantibody specificities directed at proteins involved in the transforming growth factor β pathway in patients with systemic sclerosis
Authors: Bussone Guillaume , Dib Hanadi , Tamby Mathieu C , Broussard Cedric , Federici Christian , Woimant Geneviève , Camoin Luc , Guillevin Loïc , Mouthon Luc 
Published: May 2011

Abstract
Introduction
Antinuclear antibodies (ANAs), usually detected by indirect immunofluorescence on HEp-2 cells, are identified in 90% of patients with systemic sclerosis (SSc). Thus, approximately 10% of SSc patients have no routinely detectable autoantibodies, and for 20% to 40% of those with detectable ANAs, the ANAs do not have identified specificity (unidentified ANAs). In this work, we aimed to identify new target autoantigens in SSc patients.

Methods
Using a proteomic approach combining two-dimensional electrophoresis and immunoblotting with HEp-2 cell total and enriched nuclear protein extracts as sources of autoantigens, we systematically analysed autoantibodies in SSc patients. Sera from 45 SSc patients were tested in 15 pools from groups of three patients with the same phenotype. A sera pool from 12 healthy individuals was used as a control. Proteins of interest were identified by mass spectrometry and analysed using Pathway Studio software.

Results
We identified 974 and 832 protein spots in HEp-2 cell total and enriched nuclear protein extracts, respectively. Interestingly, α-enolase was recognised by immunoglobulin G (IgG) from all pools of patients in both extracts. Fourteen and four proteins were recognised by IgG from at least 75% of the 15 pools in total and enriched nuclear protein extracts, respectively, whereas 15 protein spots were specifically recognised by IgG from at least four of the ten pools from patients with unidentified ANAs. The IgG intensity for a number of antigens was higher in sera from patients than in sera from healthy controls. These antigens included triosephosphate isomerase, superoxide dismutase mitochondrial precursor, heterogeneous nuclear ribonucleoprotein L and lamin A/C. In addition, peroxiredoxin 2, cofilin 1 and calreticulin were specifically recognised by sera from phenotypic subsets of patients with unidentified ANAs. Interestingly, several identified target antigens were involved in the transforming growth factor β pathway.

Conclusions
We identified several new target antigens shared among patients with SSc or specific to a given phenotype. The specification of new autoantibodies could help in understanding the pathophysiology of SSc. Moreover, these autoantibodies could represent new diagnostic and/or prognostic markers for SSc.
In silico tandem affinity purification refines an Oct4 interaction list
Authors: Cheong Clara Yujing , Lon Ng Patricia Miang , Ponnampalam Rhonda , Tsai Heng-Hang , Bourque Guillaume , Lufkin Thomas 
Published: May 2011

Abstract
Introduction
Octamer-binding transcription factor 4 (Oct4) is a master regulator of early mammalian development. Its expression begins from the oocyte stage, becomes restricted to the inner cell mass of the blastocyst and eventually remains only in primordial germ cells. Unearthing the interactions of Oct4 would provide insight into how this transcription factor is central to cell fate and stem cell pluripotency.

Methods
In the present study, affinity-tagged endogenous Oct4 cell lines were established via homologous recombination gene targeting in embryonic stem (ES) cells to express tagged Oct4. This allows tagged Oct4 to be expressed without altering the total Oct4 levels from their physiological levels.

Results
Modified ES cells remained pluripotent. However, when modified ES cells were tested for their functionality, cells with a large tag failed to produce viable homozygous mice. Use of a smaller tag resulted in mice with normal development, viability and fertility. This indicated that the choice of tags can affect the performance of Oct4. Also, different tags produce a different repertoire of Oct4 interactors.

Conclusions
Using a total of four different tags, we found 33 potential Oct4 interactors, of which 30 are novel. In addition to transcriptional regulation, the molecular function associated with these Oct4-associated proteins includes various other catalytic activities, suggesting that, aside from chromosome remodeling and transcriptional regulation, Oct4 function extends more widely to other essential cellular mechanisms. Our findings show that multiple purification approaches are needed to uncover a comprehensive Oct4 protein interaction network.
Mammographic characteristics and vacuum-assisted breast biopsy (VABB) of non-palpable breast lesions
Authors: Ventrella Vincenzo , Tufaro Antonio , Zito Francesco A , Addante Maria , Stea Baldassarre , Dentamaro Rosalba , D'Amico Cosimo , Paradiso Angelo 
Published: May 2011

Background The new imaging technology made available today allows for an early detection of small subclinical breast lesions which frequently call for guided presurgical micro-histology. Purpose To evaluate the relationship between vacuum-assisted breast biopsy (VABB) histopathological diagnoses and mammographic findings in non-palpable breast lesions. Material and Methods The breast lesions of 1393 women who had received consecutive screening mammograms between 2001 and 2007 were assessed by VABB. The mammographic breast lesions, classified according to the Breast Imaging Reporting and Data System (BI-RADS), were subjected to VABB only if rated as highly suspicious (2%), suspicious (64.5%) for malignancy, or probably benign (33.5%). Results VABB findings included 981 (70.5%) probably benign lesions, 407 (29.2%) suspicious/malignant lesions, and five (0.3%) cases which were considered as inappropriate for diagnostic purposes. At histology, 10.2% of the suspicious/malignant lesions were classified as proliferative lesions, 11.1% as ductal carcinoma in situ (DCIS), and 8% as invasive ductal carcinoma (IDC). The positive predictive value (PPV) of BI-RADS assessment categories 3, 4 and 5 was 4.1%, 25.3% and 75%, respectively. The occurrence of obscured or spiculated masses was found to exhibit the highest PPV for malignancy (12.5% in BI-RADS 3 and 63% in BI-RADS 4), followed by microcalcifications which showed a malignancy rate of 6.4% in BI-RADS 3, and 20% in BI-RADS 4. Conclusion VABB turns out to be effective in the assessment of many malignant and benign preclinical tumour lesions thus allowing for a significant reduction of the number of surgical biopsies.
Detection of hypoplasia of bony cochlear nerve canal by virtual endoscopy: a pilot study
Authors: Quan Yong , Wu Lebin , Xu Zushan , Gong Wuxian , Gong Ruozhen 
Published: May 2011

Background Dimensions of the bony cochlear nerve canal (BCNC) have been proposed as a potential diagnostic standard for hypoplasia of BCNC, but the standard remains inconsistent. We have previously found that a helix-like shape appears in normal BCNCs at VE images, whereas, the sign does not appear in some hypoplastic BCNCs. Purpose To retrospectively examine the feasibility of computed tomographic (CT) virtual endoscopy (VE) in the evaluation of hypoplasia of BCNC on the basis of absence of a helix-like shape. Material and Methods Twenty ears in 14 consecutive patients (mean age 5.5 years, range 1–15 years, 6 boys, 8 girls) diagnosed with hypoplasia of BCNC were included in this work. One hundred ears in 50 gender- and age-matched individuals (mean age 6.6 years, range 1–15 years, 29 boys, 21 girls) without inner ear disease and internal auditory canal (IAC) malformations served as controls. The presence or absence of a helix-like shape was evaluated by two independent reviewers. The value of VE for the diagnosis of hypoplasia of BCNC was assessed with clinical results and routine radiologic evaluation as the reference standard. Inter-observer agreement was calculated. Sensitivity, specificity, and accuracy were selected to test the diagnostic ability of the VE. Results Absence of a helix-like shape was found in the cochlear area of 17 of 20 ears in patients with hypoplasia of BCNC but in none of the control subjects. Inter-observer agreement was substantial (к = 0.773). The diagnostic rates of absence of a helix-like shape for hypoplasia of BCNC in terms of sensitivity, specificity, and accuracy were 85%, 100%, and 98%, respectively. There were significant differences between the two groups with respect to VE findings for absence of a helix-like shape ( P < 0.001). Conclusion The absence of a helix-like shape at VE images may be used as a potentially useful sign in the diagnosis of hypoplasia of BCNC.
A Comparison of Equivocal Immunohistochemical Results With Anti-HER2/neu Antibodies A0485 and SP3 With Corresponding FISH Results in Routine Clinical Practice
Authors: Manion Elizabeth , Hornick Jason L. , Lester Susan C. , Brock Jane E. 
Published: May 2011

Abstract
HER2/neu status in breast cancer is determined by immunohistochemical analysis and/or fluorescence in situ hybridization (FISH). Previous studies have found widely varying sensitivities and specificities for anti-HER2/neu antibodies, including recently developed rabbit monoclonal antibodies. The current prospective study compared rabbit monoclonal antibody SP3 and rabbit polyclonal antibody A0485 immunostaining on routinely processed consecutive cases of breast carcinoma.
Of 1,610 cases tested, 261 (16.2%) equivocal (2+) cases were evaluated by FISH. Of 253 cases equivocal with A0485 results, 125 (49.4%) were negative with SP3. In 22 (8.7%) of 253 cases equivocal with A0485, there was amplification by FISH, and 3 of these cases were SP3– (0/1+). Of the 20 (14.8%) of 135 SP3-equivocal cases amplified by FISH, 1 case was A0485–.
The reported false-negative rate with A0485 is 2.8%, and the American Society of Clinical Oncology/College of American Pathologists guidelines recommend a rate of less than 5%. Compared with A0485, the false-negative rate with SP3 is only 0.3% (3/1,156) higher, but it shows about a 50% reduction in equivocal scores, reducing the need for reflex FISH testing.
Diversity Counts
Authors: Langeveld Danielle , Jansen Marnix , Brosens Lodewijk , Morsink Folkert , Offerhaus G. Johan , de Leng Wendy 
Published: May 2011

Abstract
Tumor progression is critically dependent on the selection of genetic alterations. This clonal evolution can be traced to the stage preceding visible tumor formation called pretumor progression, in which genetic change occurs without visible change. Recently, the identification of intestinal stem cell markers in animal models has made visualization of stem cells possible in vivo. Translating this work to the clinical setting by visualizing stem cells in patient material may allow us to understand differences in patients’ vulnerability to cancer development and target preventive measures to high-risk groups. In this review article, we examine some of the analytic methods currently used in research settings tracing stem cell dynamics.
Flow Cytometric Immunophenotypic Assessment of T-Cell Clonality by Vβ Repertoire Analysis
Authors: Tembhare Prashant , Yuan Constance M. , Xi Liqiang , Morris John C. , Liewehr David , Venzon David , Janik John E. , Raffeld Mark , Stetler-Stevenson Maryalice 
Published: May 2011

AbstractFlow cytometric T-cell receptor (TCR)-Vβ repertoire analysis (TCR-Vβ-R) is a sensitive method for detection of T-cell clonality; however, no uniform approach exists to define clonality in neoplastic T cells. TCR-Vβ-R was evaluated in patients with a diagnosis of T-cell neoplasia in initial diagnostic specimens from 41 patients and for minimal residual disease (MRD) monitoring in 61 sequential samples from 14 patients with mature T-cell neoplasia. Gating strategies and criteria for detection of T-cell clonality were determined. In all 41 initial specimens, T-cell clonality was demonstrated via TCR-Vβ-R. The frequency of Vβ usage was consistent with random neoplastic transformation of TCR-Vβ subsets. MRD was successfully detected in follow-up samples from all 14 patients evaluated, Furthermore, MRD after therapy was quantitated in 48 peripheral blood specimens. TCR-Vβ-R analysis is a sensitive method for detection of T-cell clonality and is useful for diagnosis and MRD detection in multiple specimen types.
Ein Routing-Atlas für die strukturelle und visuelle Exposition des deutschen Internets
Authors: Schmidt Thomas C. , Wählisch Matthias , de Brün Markus , Häberlen Thomas 
Published: May 2011

Zusammenfassung
Ursprünglich wurde das Internets von der Idee geprägt, Übertragungsdienste für alle anzubieten, die eine wechselseitige Kopplung eingehen wollten. Seine skalierbare Architektur zielte auf eine globale Informationsinfrastruktur, in welcher nationale Ebenen oder staatengebundene Strukturen bedeutungslos waren. Das heutige Internet bildet jedoch in vielen Ländern eine potentiell kritische Infrastruktur, deren transparentes Funktionieren für die öffentliche Verwaltung und das private Geschäftshandeln, für Erziehung und Wissenschaft sowie die Information und Unterhaltung großer Bevölkerungskreise maßgeblich ist. Folgerichtig haben die Funktionsweise und die Funktionsqualität der Internet-Infrastruktur eine vielbeachtete politische Dimension angenommen.
In diesem Beitrag stellen wir Verfahren, methodische Auswertungen und deren Ergebnisse vor, welche das ‚deutsche Internet‘ identifizieren, inhaltlich und strukturell charakterisieren sowie seine verschiedenen Aspekte visualisieren. Ausgehend von der Fragestellung, welche Akteure an üblichen Kommunikationsprozessen mitwirken und diese folglich beeinflussen können, rekonstruieren und visualisieren wir Routing-Graphen auf der Ebene Autonomer Systeme, welche die zum Messzeitpunkt gültige Vermittlungsstruktur wiedergeben. Diese Messungen und Charakterisierungen werden aus einer vollständig automatisierten Kette von Abfrage- und Verfeinerungswerkzeugen gewonnen. Das Vorgehen ist insofern geeignet, ein online Monitoring-System für die Fehler- und Leistungsüberwachung des deutschen Internet-Routings zu errichten.
Experimentalumgebungen für das Internet der Dinge: Überblick, Taxonomie und praktische Nutzung
Authors: Pfisterer Dennis , Bimschas Daniel , Fischer Stefan 
Published: May 2011

Zusammenfassung
Die experimentelle Validierung neuartiger Ansätze hat, besonders im Kontext des Internet der Dinge, stark an Bedeutung gewonnen. Dieser Beitrag identifiziert Anforderungen an Experimentaleinrichtungen für das Internet der Dinge, gibt einen Überblick über aktive und öffentlich zugängliche Experimentaleinrichtungen und stellt verschiedene Plattformen auf Basis dieser Anforderungen qualitativ gegenüber. Es wird beispielhaft auf eine der Plattformen (WISEBED) näher eingegangen, um den Lesern einen Eindruck zu vermitteln, welche Möglichkeiten der experimentellen Forschung heute bereits zur Verfügung stehen. Des Weiteren wird besprochen, wie eigene Testbeds auf Basis der WISEBED Software betrieben und – falls gewünscht – mit anderen föderiert werden können.
A Mobility Model for the Realistic Simulation of Social Context
Authors: Fischer Daniel 
Published: May 2011

Abstract
Simulation is a fundamental means for evaluating mobile applications based on ad-hoc networks. In recent years, the new breed of social mobility models (SMMs) has risen. Contrary to most classical mobility models, SMMs model the social aspects of human mobility, i.e. which users meet, when and how often. Such information is indispensable for the simulation of a wide range of socially-aware communication protocols mostly based on delay-tolerant networks, including opportunistic ad-hoc routing and data dissemination systems. Each SMM needs a model of the relations between a set of relevant people (called social network model – SNM) in order to simulate their mobility. Existing SMMs lack flexibility since each of them is implicitly restricted to a specific, simplifying SNM.
We present GeSoMo (General Social Mobility Model), a new SMM that separates the core mobility model from the structural description of the social network underlying the simulation. This simple and elegant design principle gives GeSoMo generalizing power: Arbitrary existing and future SNMs can be used without changing GeSoMo itself. Our evaluation results show that GeSoMo produces simulations that are coherent with a broad range of empirical data describing real-world human social behavior and mobility.
Building a Distributed Trust Anchor in P2P Systems – Creating Trustworthy System Signatures without a Trusted Third Party
Authors: Liebau Nicolas C. , Mauthe Andreas U. , Steinmetz Ralf 
Published: May 2011

Abstract
Trustworthy applications in fully decentralized systems require a trust anchor. However, in p2p systems there does not exist a central trust anchor. This paper describes how a distributed anchor can be implemented efficiently in such and environment. Different alternatives have been proposed in the literature; most of them suggesting distributing the trust anchor by using a quorum decision, assuming that a random quorum would ensure trustworthiness. However, there are major issues, e.g., can it be assumed that a quorum was actually randomly chosen? how can it be verified, that a signature was created by a truly random quorum? In this paper a solution for this is presented through the token-based accounting scheme using specific mechanisms that ensure a distributed trust anchor in p2p systems and its evaluation.
A Novel Algorithm for Distributed Dynamic Interference Coordination in Cellular Networks
Authors: Necker Marc C. 
Published: May 2011

Abstract
Wireless systems based on Orthogonal Frequency Division Multiple Access (OFDMA) multiplex different users in time and frequency. One of the main problems in OFDMA-systems is the inter-cell interference. A promising approach to solve this problem is interference coordination (IFCO). In this paper, we present a novel distributed IFCO scheme, where a central coordinator communicates coordination information in regular time intervals. This information is the basis for a local inner optimization in every basestation. The proposed scheme achieves an increase of more than 100% with respect to the cell edge throughput, and a gain of about 30% in the aggregate spectral efficiency compared to a reuse 3 system.
ÖPNV-optimiertes Routing in unterbrechungstoleranten Netzen
Authors: Pögel Tobias 
Published: May 2011

Zusammenfassung
Für die Realisierung vieler neuer Dienste ist eine Kommunikation zwischen Fahrzeugen im ÖPNV notwendig. Die Bereitstellung geeigneter Infrastruktur oder die Nutzung bestehender kommerzieller Systeme verursacht aber hohe Kosten. Ein anderer Ansatz ist die Nutzung von DTN-Netzen, welche eine direkte Kommunikation der Fahrzeuge untereinander ermöglicht. Für den hierbei verfolgten ‚Store-and-Forward‘- Ansatz wird ein geeignetes Routing benötigt, welches möglichst effizient und ressourcenschonend arbeitet. Ein auf dieses Anwendungsszenario optimiertes Routing soll vorgestellt und analysiert werden. Dabei müssen die besonderen Eigenschaften des ÖPNV in dem Routing berücksichtigt werden. Mittels zusätzlich bereitgestellter Kontextinformationen werden dabei die potenziellen Kontakte zwischen den Fahrzeugen berechnet und für das Routing ausgenutzt.
Zur DIN SPEC 1041
Authors: Bauer Hans-Jörg 
Published: May 2011

Zusammenfassung
DIN SPEC 1041 beschreibt ein Phasenmodell für das „Outsourcing technologieorientierter wissensintensiver Dienstleistungen“. Das Modell deckt viele Aspekte von IT-Outsourcing- Verfahren ab. Für Rechenzentren von Hochschulen erscheint von das Dokument gerade angesichts zahlreicher Cloud-Angebote von hoher praktischer Relevanz.
Role of the basolateral amygdala and NMDA receptors in higher-order conditioned fear
Authors: Parkes Shauna L. , Westbrook R. Frederick 
Published: May 2011

Abstract
Laboratory rats learn to fear relatively innocuous stimuli which signal the imminent arrival of an innate source of danger, typically brief but aversive foot shock. Much is now known about the neural substrates underling the acquisition, consolidation and subsequent expression of this fear. Rats also learn to fear stimuli which signal learned sources of danger but relatively little is known about the neural substrates underlying this form of fear. Two Pavlovian conditioning paradigms used to study this form of fear are second-order conditioning and sensory preconditioning. In second-order conditioning, rats are first exposed to a signaling relationship between one stimulus, such as a tone, and aversive foot shock, and then to a signaling relationship between a second stimulus, such as a light, and the now dangerous tone. In sensory preconditioning, these phases are reversed: rats are first exposed to a signaling relationship between the light and the tone and then to a signaling relationship between the tone and the foot shock. In both paradigms, rats exhibit fear when tested with the light. In this review paper, we describe the evidence for higher-order forms of conditioning, the conditions which promote this learning and its contents. We compare and contrast the substrates of the learning underlying second-order and sensory preconditioning fear with those known to underlie the better studied first-order conditioned fear. We conclude with some comments as to the role of higher-order processes in anxiety disorders.
Process Capability Evaluation for Square Bumps with Mean Shift
Authors: Pearn W. L. , Hung H. N. , Tai Y. T. , Hou H. H. 
Published: May 2011

Abstract
Process capability indices have been widely used in manufacturing industries to provide numerical measures of process potential and performance. In in-plant applications, some inevitable process mean shift may be undetected when the statistical process control charts are applied, particularly, in the bumping process for square bumps. Bothe in 2002 provided a statistical reason for considering such a shift in the process mean to accommodate the undetected mean shifts for normally distributed processes when evaluating process capability. In this paper, we consider a bumping process for square bumps in which the data can be formulated as a non-central chi-square distribution, a class of non-normal distributions. To evaluate the popular yield-based process capability Cpk more accurately, we accommodate the magnitudes of undetected mean shifts using the modified capability evaluation formula and tabulate the detection powers under various subgroup sizes and non-central chi-square parameters. Based on the modified process capability evaluation, we can provide a more reliable process capability evaluation of capability index Cpk for square bumps and make more correct decisions. For illustration purpose, a real application in a bumping factory which is located on the Science-based Industrial Park in Hsinchu, Taiwan, is presented.
Use of Electronic Technologies to Promote Community and Personal Health for Individuals Unconnected to Health Care Systems
Authors: Crilly John F. , Keefe Robert H. , Volpe Fred 
Published: May 2011

Ensuring health care services for populations outside the mainstream health care system is challenging for all providers. But developing the health care infrastructure to better serve such unconnected individuals is critical to their health care status, to third-party payers, to overall cost savings in public health, and to reducing health disparities. Our increasingly sophisticated electronic technologies offer promising ways to more effectively engage this difficult to reach group and increase its access to health care resources. This process requires developing not only newer technologies but also collaboration between community leaders and health care providers to bring unconnected individuals into formal health care systems. We present three strategies to reach vulnerable groups, outline benefits and challenges, and provide examples of successful programs.