julilili42/papers huggingface dataset:
Measurement of Medial Olivocochlear Efferent Activity in Humans
2011-10-01

The suppression effects on DPOAE demonstrated in this study reflect MOC activity. However, the new conclusion from our data is that CS of DPOAE measurements, as they were used in this study, may not allow for a consistent quantitative classification of human subjects according to their MOCR strength. This finding concerns interpretation of previous studies using CS of DPOAE and analogous future studies. One future approach may lie in the separation of the DPOAE components to distinguish interference phenomena, which complicate interpretation of CS values.
TIALA &#x2014; Time series alignment analysis
2011-10-01

The analysis of time series expression data is widely employed for investigating biological mechanisms. Microarrays are often used to generate time series for several different experimental conditions. These time series then need to be compared to each other. For a successful comparison it is necessary to perform a time series alignment because the experiments can differ in the number of time points, as well as in the time points themselves. In this work we propose a novel visual analytics approach for the analysis of multiple time series experiments in parallel. Our time series alignment analysis tool Tiala allows one to align multiple time series experiments and to visually explore the aligned expression profiles. A two- and three-dimensional visualization strategy was implemented that is especially designed to enhance the display of multiple aligned time series expression profiles. Tiala is available as a part of the microarray data analysis software Mayday. Mayday itself is open source software distributed under the terms of the GNU General Public License. It is available from http://www.microarray-analysis.org. We apply our approach to time series showing abiotic stress responses of Arabidopsis thaliana and to data sets from two replicates of the antibiotics producing bacterium Streptomyces coelicolor.
Detection and clinical outcome of urinary bladder cancer with 5-aminolevulinic acid-induced fluorescence cystoscopy: a multicenter randomized, double-blind, placebo-controlled trial
2011-10-01

BACKGROUND: The medical community lacks results from prospective controlled multicenter studies of the diagnostic efficacy of 5-aminolevulinic acid (5-ALA) cystoscopy on tumor recurrence in patients with superficial bladder tumors. METHODS: A prospective randomized, double-blind, placebo-controlled study was conducted in 370 patients with nonmuscle-invasive urinary bladder carcinoma who received either 5-ALA (n = 187) or a placebo (n = 183) intravesically before cystoscopy. Each group underwent cystoscopy under visible white light and under fluorescent light followed by transurethral tumor resection. The primary study objective was to evaluate the 12-month recurrence-free survival. RESULTS: Slightly more patients with tumors were detected by using 5-ALA than by using the placebo (88.5% vs 84.7%). The mean numbers of tumor specimens per patient were 1.8 (5-ALA) and 1.6 (placebo). Intrapatient comparison of fluorescent light versus white light cystoscopy in patients randomized to receive 5-ALA showed a higher tumor detection rate with fluorescent light than with white light cystoscopy. In patients receiving 5-ALA cystoscopy, the percentage of lesions that would not have been detected in these patients by white light cystoscopy ranged between 10.9% (pT1) and 55.9% (atypia). Progression-free survival was 89.4% (5-ALA) and 89.0% (placebo) (P = .9101), and recurrence-free survival 12 months after tumor resection was 64.0% (5-ALA) and 72.8% (placebo) (P = .2216). CONCLUSIONS: In comparison to the placebo, 5-ALA cystoscopy did not increase the rates of recurrence-free or progression-free survival 12 months after tumor resection. Although more tumors per patient were detected in the 5-ALA group, the higher detection rate did not translate into differences in long-term outcome. Cancer 2011. © 2010 American Cancer Society.
Loop-free convergence using ordered FIB updates: Analysis and routing optimization
2011-10-01

Intradomain IP routing protocols like OSPF or IS-IS are robust against failures. New fast reroute mechanisms can minimize packet loss directly after an outage by temporarily detouring packets around the failed network element. This buys time for a loop-free convergence, which brings the topology to a new stable path layout without causing temporary micro-loops. We analyze the link utilizations during this loop-free convergence phase using the ordered FIB updates (OFIB) mechanism. We show that depending on the router update order, OFIB can temporarily increase the utilization on certain links in the network. To minimize the temporary load increase, we present a heuristic link cost optimization that minimizes the link utilizations both during failure-free routing and all phases of a failure recovery process. As OFIB does not define a unique global update order but provides only local constraints, it is difficult to calculate the highest possible link utilizations. We introduce a tight upper bound to the maximum link utilization, independent of the actual update order. It can quickly be calculated and allows us to perform link cost optimization including the loop-free convergence phase. We show that this results in a routing configuration that avoids additional overload during the OFIB phase without impairing normal routing performance.
Simulation studies of optical photons in monolithic block scintillators
2011-10-01

The interest in PET detectors with monolithic block scintillators is growing. In order to obtain high spatial resolutions dedicated positioning algorithms are required. But even an ideal algorithm can only deliver information which is provided by the detector. In this simulation study we investigated the light distribution on one surface of cuboid LSO scintillators of different size. Scintillators with a large aspect ratio (small footprint and large height) showed significant position information only for a minimum interaction depth of the gamma particle. The results allow a quantitative estimate for a useful aspect ratio.
Cor triatriatum in an 86-year-old woman: initial presentation with pulmonary hypertension discovered during preoperative evaluation.
2011-10-01

Cor triatriatum is a congenital heart malformation that is characterised by the division of the left or right atrium into two separate chambers by a membrane or diaphragm. Reports among adults are scarce, as most cases are diagnosed during childhood. The risk of mortality is increased when cor triatriatum is complicated by pulmonary hypertension. This is a report of an 86-year-old woman with World Health Organization Group 2 pulmonary hypertension secondary to cor triatriatum, discovered during preoperative workup. Echocardiography showed a membrane dividing the left atrium into two. Doppler studies revealed a reversal of normal flow, similar to mitral stenosis. The right ventricle was dilated, with reduced long axis function.
MoBiFlow
2011-10-01

Web-based problem solving environments provide sharing, execution and monitoring of scientific workflows. Where they depend on general purpose workflow development systems, the workflow notations are likely far too powerful and complex, especially in the area of biology, where programming skills are rare. On the other hand, application specific workflow systems may use special purpose languages and execution engines, suffering from a lack of standards, portability, documentation, stability of investment etc. In both cases, the need to support yet another application on the desk-top places a burden on the system administration of a research lab. In previous research the authors have developed the web based workflow systems Calvin and Hobbes, which enable biologists and computer scientists to approach these problems in collaboration. Both systems use a server-centric Web 2.0 based approach. Calvin is tailored to molecular biology applications, with a simple graphical workflow-language and easy access to existing BioMoby web services. Calvin workflows are compiled to industry standard BPEL workflows, which can be edited and refined in collaboration between researchers and computer scientists using the Hobbes tool. Together, Calvin and Hobbes form our workflow platform MoBiFlow, whose principles, design, and use cases are described in this paper.
Activity and Surface Expression of the Intestinal Anion Exchanger Down-Regulated in Adenoma (DRA)
2011-10-01

Down-regulated in adenoma (DRA; SLC26A3) is an intestinal chloride/bicarbonate exchanger that is functionally coupled to NHE3 (Na/H exchanger-isoform 3) in the ileum and proximal colon to mediate electroneutral NaCl absorption. This NaCl absorption is a major regulator of total body volume and electrolyte homeostasis. Knock out of either transporter (DRA or NHE3) causes chronic diarrhea [10,11]. Furthermore, a nonfunctional DRA leads to life-threatening diarrhea (human genetic disorder congenital chloride diarrhea) [2]. NHE3 and several other transport proteins are associated with lipid rafts. These microdomains contain a special subset of lipids, mainly sphingolipids and cholesterol [8]. They are involved in cellular processes that include membrane sorting and recycling, protein trafficking [3] and cell signaling [12]. In case of NHE3 the raft association is necessary for its normal activity as well as for its basal and stimulated trafficking [5]. Lipid rafts are involved in phosphatidylinositol-3-(PI3)-kinase-dependent exocytosis of NHE3 as well as in its basal endocytosis [7]. Since the function of NHE3 and DRA appears to be regulated in parallel [4] DRA may be associated with lipid rafts as well. Both transporters posses PDZ binding motifs that facilitate binding to PDZ adaptor proteins of the NHERF family [4]. The four members of the NHERF family (NHERF, E3KARP, PDZK1 and IKEPP) appear to play important roles for the regulation of intestinal ion transport [4]. However, the potential interplay of raft association and PDZ interaction of both transporters has not been studied. To this end, we have generated HEK293 cells stably expressing DRA (EGFP-DRA) or a DRA mutant that lacks the PDZ binding motif (EGFP-DRA-ETKFminus). We have studied whether DRA associates with lipid rafts – independent or dependent of its PDZ interaction and whether the activity of DRA depends on the raft association. Furthermore, we examined the possibility that DRA is inserted into the plasma membrane in a lipid raft and PI3-kinase dependent manner.
Bone Marrow Suppression by c-Kit Blockade Enhances Tumor Growth of Colorectal Metastases through the Action of Stromal Cell-Derived Factor-1
2011-10-02

Background . Mobilization of c-Kit + hematopoietic cells (HCs) contributes to tumor vascularization. Whereas survival and proliferation of HCs are regulated by binding of the stem cell factor to its receptor c-Kit, migration of HCs is directed by stromal cell-derived factor (SDF)-1. Therefore, targeting migration of HCs provides a promising new strategy of anti-tumor therapy. Methods . BALB/c mice () were pretreated with an anti-c-Kit antibody followed by implantation of CT26.WT-GFP colorectal cancer cells into dorsal skinfold chambers. Animals () additionally received a neutralizing anti-SDF-1 antibody. Animals () treated with a control antibody served as controls. Investigations were performed using intravital fluorescence microscopy, immunohistochemistry, flow cytometry and western blot analysis. Results . Blockade of c-Kit significantly enhanced tumor cell engraftment compared to controls due to stimulation of tumor cell proliferation and invasion without markedly affecting tumor vascularization. C-Kit blockade significantly increased VEGF and CXCR4 expression within the growing tumors. Neutralization of SDF-1 completely antagonized this anti-c-Kit-associated tumor growth by suppression of tumor neovascularization, inhibition of tumor cell proliferation and reduction of muscular infiltration. Conclusion . Our study indicates that bone marrow suppression via anti-c-Kit pretreatment enhances tumor cell engraftment of colorectal metastases due to interaction with the SDF-1/CXCR4 pathway which is involved in HC-mediated tumor angiogenesis.
Fundamentals of tracer kinetics for dynamic contrast‐enhanced MRI
2011-10-03

Abstract Tracer kinetic methods employed for quantitative analysis of dynamic contrast‐enhanced (DCE) magnetic resonance imaging (MRI) share common roots with earlier tracer studies involving arterial‐venous sampling and other dynamic imaging modalities. This article reviews the essential foundation concepts and principles in tracer kinetics that are relevant to DCE MRI, including the notions of impulse response and convolution, which are central to the analysis of DCE MRI data. We further examine the formulation and solutions of various compartmental models frequently used in the literature. Topics of recent interest in the processing of DCE MRI data, such as the account of water exchange and the use of reference tissue methods to obviate the measurement of an arterial input, are also discussed. Although the primary focus of this review is on the tracer models and methods for T 1 ‐weighted DCE MRI, some of these concepts and methods are also applicable for analysis of dynamic susceptibility contrast‐enhanced MRI data. J. Magn. Reson. Imaging 2011;. © 2011 Wiley Periodicals, Inc.
Analytical Model of Surface Flow on Hillslopes Based on the Zero Inertia Equations
2011-10-03

Coming from the zero inertia (ZI) equations, an analytical model to describe sheet flow phenomena with a special focus on rainfall runoff processes is developed. A slight modification of the ZI equations, which draws upon the concept of a momentum-representative cross-section of the moving water body, leads—after comprehensive mathematical calculus—to an analytical solution describing essentially one-dimensional, shallow overland flow. In a test series, the analytical ZI model is applied together with three numerical models, one based on the Saint-Venant equations, one on the kinematic wave equations, and another one on diffusion wave equations. The test application refers to a typical rainfall runoff situation, i.e., rather shallow overland flow on a hillslope as a consequence of excess rainfall. Contrary to the analytical model, the comparative analysis clearly shows the difficulties of the numerical solutions in terms of exactness and robustness when approaching typical shallow water depths. This problem of numerical models is tackled by applying small time and space discretization, which, however, comes along with higher CPU execution times. Besides the good computational efficiency and freedom of any numerical inconvenience, the new analytical model outperforms the numerical models for typical overland flow simulations. This particularly refers to a highly satisfactory fulfillment of the mass balance and a nearly perfect match of peak flow rates.
Mucosal melanomas of the head and neck
2011-10-04

Approximately 50% of mucosal melanomas affect the head and neck region representing approximately 9% of all malignant head and neck tumors. The pathogenesis of this disease is unknown. Mucosal melanomas are characterized by an aggressive biological behavior, leading to a 5-year survival rate of less than 25%. Data for this review were identified by searches of Medline, Current Contents, PubMed, and references from relevant articles using the terms 'mucosal melanoma,' 'head and neck melanoma,' 'c-kit mutation in melanoma,' and 'c-kit inhibitors'. Therapy aims for the complete surgical excision of the primary tumor, whereas sentinel node biopsy is not established and present data do not support the addition of radiotherapy. Mutilating operations of larger tumors should be avoided, as they do not inhibit the frequent development of distant metastasis. C-kit mutations and amplifications are found in approximately 15-30% of mucosal and acral-lentiginous melanomas. Therefore, the use of so-called targeted therapies addressing molecular structures in mucosal melanomas seem to represent new promising treatment tools. In this study, we review the literature regarding epidemiology, molecular pathology, and therapy of mucosal melanomas of the head and neck emphasizing c-kit protein inhibiting treatment modalities for tumors carrying c-kit mutations.
Toward functioning and usable brain–computer interfaces (BCIs): A literature review
2011-10-04

In most of the examined works, the focus was on the development of systems and algorithms able to recognise and classify brain events. Although this kind of research is fundamental, a user-centred point of view was rarely adopted. [Box: see text].
Prospective evaluation of supportive care with or without CVD chemotherapy as a second-line treatment in advanced melanoma by patient’s choice
2011-10-04

This prospective, nonrandomized multicentre, phase III study compared best supportive care (BSC) alone with cisplatin, vindesine and dacabazine-based (CVD) chemotherapy and BSC in patients with advanced melanoma. A total of 117 pretreated patients with metastatic melanoma were evaluated, 34 patients in arm A (BSC) and 83 in arm B (BSC and CVD). Primary endpoint was overall survival and secondary endpoints were disease control rate and quality of life (European Organisation for Research and Treatment of Cancer QLQ-C30). Owing to sparse recruitment of patients for randomization, the protocol has been changed based on patients' choice. Baseline characteristics were imbalanced with respect to the Karnofsky Performance Index (P=0.001), the existence of brain metastases (P=0.035) and earlier application of chemoimmunotherapy (P=0.038). Disease control was observed in 8.8% of patients in arm A and in 28.9% of patients in arm B (P=0.028). Median overall survival time was 137 days in arm A and 229 days in arm B (P=0.014). Multivariate analyses could not ascribe this prognostic benefit to CVD treatment. No significant difference in the quality of life could be found. This study could not detect clear survival benefits for polychemotherapy with CVD compared with BSC alone in patients with advanced metastatic melanoma. Interestingly, having the choice of chemotherapy or BSC alone in a second-line situation, more than 70% of patients chose polychemotherapy.
Inheritance of moyamoya disease in a Caucasian family
2011-10-04

Background and purpose: Moyamoya disease is a very rare occlusive cerebrovascular disorder characterized by progressive stenosis or occlusion of the intracranial portion of the internal carotid artery and proximal cerebral arteries with an extensive network of fine collaterals. The aetiology and genetic susceptibility of moyamoya disease, especially in Caucasians, still remains unclear. Methods and results: We describe the cases of affected German father, daughter and son with juvenile stroke because of idiopathic moyamoya disease. The rare existing literature is reviewed and discussed. Conclusions: This is the first report on a father‐to‐child inheritance pattern in Caucasian patients with idiopathic Moyamoya disease (MMD). Our cases indicate possible genetic risk factors for the genesis of Caucasian Moyamoya disease.
Listening to factually incorrect sentences activates classical language areas and thalamus
2011-10-04

Neurophysiological underpinnings of the integration of information during sentence comprehension have been studied since 1980. However, little is known about integrative processes in sentences containing a word that is semantically congruent, but factually incompatible with the context. In this study, we aimed at investigating the differences between the brain regions involved in responses to factually correct and incorrect sentences. Eighteen healthy volunteers underwent functional MRI while listening passively to 40 correct and 40 incorrect sentences. The contrast between factually correct and incorrect sentence endings revealed large activation areas in the left inferior frontal gyrus, the left middle/superior temporal gyrus, and smaller activations of these areas' homologs in the right hemisphere, in the thalamus, and Brodmann area 6.
Large-Scale Co-Phylogenetic Analysis on the Grid
2011-10-04

Phylogenetic data analysis represents an extremely compute-intensive area of Bioinformatics and thus requires high-performance technologies. Another compute- and memory-intensive problem is that of host-parasite co-phylogenetic analysis: given two phylogenetic trees, one for the hosts (e.g., mammals) and one for their respective parasites (e.g., lice) the question arises whether host and parasite trees are more similar to each other than expected by chance alone. CopyCat is an easy-to-use tool that allows biologists to conduct such co-phylogenetic studies within an elaborate statistical framework based on the highly optimized sequential and parallel AxParafit program. We have developed enhanced versions of these tools that efficiently exploit a Grid environment and therefore facilitate large-scale data analyses. Furthermore, we developed a freely accessible client tool that provides co-phylogenetic analysis capabilities. Since the computational bulk of the problem is embarrassingly parallel, it fits well to a computational Grid and reduces the response time of large scale analyses.
General Growth Mixture Analysis of Adolescents' Developmental Trajectories of Anxiety: The Impact of Untested Invariance Assumptions on Substantive Interpretations
2011-10-05

Substantively, this study investigates potential heterogeneity in the developmental trajectories of anxiety in adolescence. Methodologically, this study demonstrates the usefulness of general growth mixture analysis (GGMA) in addressing these issues and illustrates the impact of untested invariance assumptions on substantive interpretations. This study relied on data from the Montreal Adolescent Depression Development Project (MADDP), a 4-year follow-up of more than 1,000 adolescents who completed the Beck Anxiety Inventory each year. GGMA models relying on different invariance assumptions were empirically compared. Each of these models converged on a 5-class solution, but yielded different substantive results. The model with class-varying variance–covariance matrices was retained as providing a better fit to the data. These results showed that although elevated levels of anxiety might fluctuate over time, they clearly do not represent a transient phenomenon. This model was then validated in relation to multiple predictors (mostly related to school violence) and outcomes (grade-point average, school dropout, depression, loneliness, and drug-related problems).
Chameleon-like Appearance of Immunotactoid Keratopathy
2011-10-05

ITK of MGUS can mimic cystinosis, Schnyder corneal dystrophy (CD), pre-Descemet CD, lattice CD, granular CD, arcus lipoides, lecithin-cholesterol acyltransferase deficiency, gelatinous drop-like CD, and Salzmann nodular degeneration. ITK can be the first symptom of MGUS. An annual internal check of MGUS is recommended because of occurrence of a systemic monoclonal gammopathy in 20% of cases.