julilili42/papers huggingface dataset:
Quantification of tumor cell burden by analysis of single cell lymph node disaggregates in metastatic prostate cancer
2010-04-28

Abstract BACKGROUND The size of lymph node (LN) metastases in prostate cancer patients represents an important prognosticator, but histological work‐up may not reflect the true extent of tumor invasion. We present a novel technique (1) to detect early tumor cell dissemination and (2) to quantify the true tumor burden. METHODS Prospectively 232 LN of 20 consecutive patients with prostate cancer after lymph node dissection were longitudinally bisected, one half was subjected to single cell immunocytochemistry for pancytokeratine (CK), the other half underwent routine histopathological work‐up and step section analysis. In immunocytochemistry, tumor cell density (TCD) was quantified by calculating the number of CK‐positive cells/million leucocytes and compared to routine histopathology and step section analysis. RESULTS Eight of 20 patients were positive in histopathology and step sectioning, but 14 of 20 patients were positive in single cell analysis. Twenty‐five of 232 LN were positive in routine histopathology, whereas 52 of 232 LN were positive in single cell analysis. Median TCD in histopathologically positive LN was 3060.0 × 10 −6 and 9.9 × 10 −6 in histopathologically negative LN ( P &lt; 0.0001). Mean TCD of histopathologically negative LN of pN1 patients was significantly higher than the mean TCD of pN0 patients ( P &lt; 0.003). Mean TCD per patient correlated with serum‐PSA (r 2 = 0.48, P &lt; 0.006). CONCLUSIONS Single cell analysis has an increased detection rate compared to routine histopathology and even to serial step section analysis. The method can detect early tumor dissemination and enables quantification of the tumor burden. The subgroup of histopathologically negative LN with CK‐positive cells represents tumor cell dissemination not depicted histologically. Prostate 70: 1110–1118, 2010. © 2010 Wiley‐Liss, Inc.
Formation of the resonant system HD 60532
2010-04-28

Among multi-planet planetary systems there are a large fraction of resonant systems. Studying the dynamics and formation of these systems can provide valuable informations on processes taking place in protoplanetary disks where the planets are thought have been formed. The recently discovered resonant system HD 60532 is the only confirmed case, in which the central star hosts a pair of giant planets in 3:1 mean motion resonance. We intend to provide a physical scenario for the formation of HD 60532, which is consistent with the orbital solutions derived from the radial velocity measurements. Observations indicate that the system is in an antisymmetric configuration, while previous theoretical investigations indicate an asymmetric equilibrium state. The paper aims at answering this discrepancy as well. We performed two-dimensional hydrodynamical simulations of thin disks with an embedded pair of massive planets. Additionally, migration and resonant capture are studied by gravitational N-body simulations that apply properly parametrized non-conservative forces. Our simulations suggest that the capture into the 3:1 mean motion resonance takes place only for higher planetary masses, thus favouring orbital solutions having relatively smaller inclination i=20 degrees. The system formed by numerical simulations qualitatively show the same behaviour as HD 60532. We also find that the presence of an inner disk (between the inner planet and the star) plays a very important role in determining the final configurations of resonant planetary systems. Its damping effect on the inner planet's eccentricity is responsible for the observed antisymmetric state of HD 60532.
High‐resolution animal PET imaging of prostate cancer xenografts with three different 64Cu‐labeled antibodies against native cell‐adherent PSMA
2010-04-29

Abstract BACKGROUND The prostate specific membrane antigen (PSMA) is expressed by virtually all prostate cancers and represents an ideal target for diagnostic and therapeutic strategies. This article compares the in vivo behavior and tumor uptake of three different radiolabeled anti‐PSMA monoclonal antibodies (mAbs) and corresponding F(ab) 2 and Fab fragments thereof. METHODS The mAbs 3/A12, 3/F11, and 3/E7 and fragments of 3/A12 were conjugated with the chelating agent DOTA and radiolabeled with 64 Cu. For the microPET imaging studies, SCID mice bearing PSMA‐positive C4‐2 and PSMA‐negative DU 145 prostate cancer xenografts were used. Each animal received 20–30 μg radiolabeled mAb or fragment corresponding to an activity of 8–14 MBq. Imaging was performed 3, 24, and 48 hr post‐injection. After the last scan, mice were sacrificed and tracer in vivo biodistribution was measured by gamma‐counting. RESULTS Static microPET images of mice with PSMA‐positive tumors revealed a high uptake of the mAbs in the C4‐2 tumors at 24 and 48 hr after tracer injection and only a minimal distribution in the DU 145 tumors and other organs. In contrast, the F(ab) 2 and Fab fragments of 3/A12 were detected at a high extend in the kidney but not in the C4‐2 tumors. These results were confirmed by gamma counting of dissected organs after the final imaging. CONCLUSIONS Due to the high and specific uptake of the 64 Cu‐labeled mAbs in PSMA‐positive tumors, these antibodies represent excellent tools for prostate cancer imaging. Prostate 70: 1413–1421, 2010. © 2010 Wiley‐Liss, Inc.
Temperature sensitivity of suicidal erythrocyte death
2010-04-29

Eur J Clin Invest 2010; 40 (6): 534–540 Abstract Background Fever and hyperthermia are frequently associated with anaemia. Under most clinical conditions, they are considered to be two mutually independent clinical consequences of a common cause. The present study explored the possibility that anaemia results from temperature‐sensitive suicidal erythrocyte death or eryptosis. Eryptosis is characterised by cell shrinkage and cell membrane scrambling with phosphatidylserine (PS) exposure at the erythrocyte surface. It is triggered by increase in the cytosolic Ca 2+ activity on the one hand and by ceramide formation on the other. Material and methods Annexin V‐binding was utilised to disclose PS exposure, forward scatter to analyse cell volume, Fluo 3 fluorescence to estimate cytosolic Ca 2+ activity, binding of fluorescent antibodies to determine ceramide abundance and a luciferin/luciferase‐based assay to measure the cytosolic ATP concentration. Results Graded increases in temperature from 37 to 41 °C decreased the forward scatter and stimulated annexin V‐binding of human erythrocytes. The effect was accompanied by increased cytosolic Ca 2+ activity, decrease of the cellular ATP content and a moderate rise in ceramide formation. The effect of hyperthermia on annexin V‐binding was significantly blunted by the leukotriene receptor CysLT1 antagonist cinalukast (1 μM). Conclusions Hyperthermia stimulates Ca 2+ entry into erythrocytes leading to cell shrinkage and PS exposure. As PS‐exposing erythrocytes are rapidly cleared from circulating blood, the eryptosis during hyperthermia may cause anaemia.
Frequency band of thef-mode Chandrasekhar-Friedman-Schutz instability
2010-04-29

Rapidly rotating neutron stars can be unstable to the gravitational-wave-driven CFS mechanism if they have a neutral point in the spectrum of nonaxisymmetric f-modes. We investigate the frequencies of these modes in two sequences of uniformly rotating polytropes using nonlinear simulations in full general relativity, determine the approximate locations of the neutral points, and derive limits on the observable frequency band available to the instability in these sequences. We find that general relativity enhances the detectability of a CFS-unstable neutron star substantially, both by widening the instability window and enlarging the band into the optimal range for interferometric detectors like LIGO, VIRGO, and GEO-600.
Photogeneration of Octacene and Nonacene
2010-04-30

Take it to the limit: Parent acenes larger than heptacene have eluded synthesis for decades. When 1,2-diketone bridges in suitably designed tetraketone precursors were removed by irradiation under matrix-isolation conditions (see scheme), the parent systems of the two next higher acenes were accessible experimentally.
Optimization of high‐reliability‐based hydrological design problems by robust automatic sampling of critical model realizations
2010-04-30

This study demonstrates the high efficiency of the so‐called stack‐ordering technique for optimizing a groundwater management problem under uncertain conditions. The uncertainty is expressed by multiple equally probable model representations, such as realizations of hydraulic conductivity. During optimization of a well‐layout problem for contaminant control, a ranking mechanism is applied that extracts those realizations that appear most critical for the optimization problem. It is shown that this procedure works well for evolutionary optimization algorithms, which are to some extent robust against noisy objective functions. More precisely, differential evolution (DE) and the Covariance Matrix Adaptation Evolution Strategy (CMA‐ES) are applied. Stack ordering is comprehensively investigated for a plume management problem at a hypothetical template site based on parameter values measured at and on a geostatistical model developed for the Lauswiesen study site near Tübingen, Germany. The straightforward procedure yields computational savings above 90% in comparison to always evaluating the full set of realizations. This is confirmed by cross testing with four additional validation cases. The results show that both evolutionary algorithms obtain highly reliable near‐optimal solutions. DE appears to be the better choice for cases with significant noise caused by small stack sizes. On the other hand, there seems to be a problem‐specific threshold for the evaluation stack size above which the CMA‐ES achieves solutions with both better fitness and higher reliability.
Dual Induction of TREM2 and Tolerance-Related Transcript, Tmem176b, in Amyloid Transgenic Mice: Implications for Vaccine-Based Therapies for Alzheimer’s Disease
2010-05-01

Vaccine-based autoimmune (anti-amyloid) treatments are currently being examined for their therapeutic potential in Alzheimer's disease. In the present study we examined, in a transgenic model of amyloid pathology, the expression of two molecules previously implicated in decreasing the severity of autoimmune responses: TREM2 (triggering receptor expressed on myeloid cells 2) and the intracellular tolerance-associated transcript, Tmem176b (transmembrane domain protein 176b). In situ hybridization analysis revealed that both molecules were highly expressed in plaque-associated microglia, but their expression defined two different zones of plaque-associated activation. Tmem176b expression was highest in the inner zone of amyloid plaques, whereas TREM2 expression was highest in the outer zone. Induced expression of TREM2 occurred co-incident with detection of thioflavine-S-positive amyloid deposits. Transfection studies revealed that expression of TREM2 correlated negatively with motility, but correlated positively with the ability of microglia to stimulate CD4(+) T-cell proliferation, TNF (tumour necrosis factor) and CCL2 (chemokine ligand 2) production, but not IFNgamma (interferon gamma) production. TREM2 expression also showed a positive correlation with amyloid phagocytosis in unactivated cells. However, activating cells with LPS (lipopolysaccharide), but not IFNgamma, reduced the correlation between TREM2 expression and phagocytosis. Transfection of Tmem176b into both microglial and macrophage cell lines increased apoptosis. Taken together, these data suggest that, in vivo, Tmem176b(+) cells in closest apposition to amyloid may be the least able to clear amyloid. Conversely, the phagocytic TREM2(+) microglia on the plaque outer zones are positioned to capture and present self-antigens to CNS (central nervous system)-infiltrating lymphocytes without promoting pro-inflammatory lymphocyte responses. Instead, plaque-associated TREM2(+) microglia have the potential to evoke neuroprotective immune responses that may serve to support CNS function during pro-inflammatory anti-amyloid immune therapies.
High-mobility copper-phthalocyanine field-effect transistors with tetratetracontane passivation layer and organic metal contacts
2010-05-01

We investigate ambipolar charge transport in organic field-effect transistors (OFETs) with copper-phthalocyanine (CuPc) as active material. It is shown that charge carrier mobilities can be increased by at least one order of magnitude using the long-chain alkane tetratetracontane (TTC) as a passivation layer on top of silicon dioxide. TTC and CuPc films are characterized by atomic force microscopy and x-ray diffraction. TTC forms a highly crystalline layer that passivates electron traps on the SiO2 surface very efficiently and serves as a template for the growth of CuPc films with significantly improved crystallinity. High electron mobilities comparable to the values reported on single crystals are reached. We show that the contact resistance for hole transport as determined by the transmission line method can be reduced considerably by using organic charge-transfer complexes as top contacts in OFETs based on CuPc.
WikiNet: A Very Large Scale Multi-Lingual Concept Network
2010-05-01

This paper describes a multi-lingual concept network obtained automatically by mining for concepts and relations and exploiting a variety of sources of knowledge from Wikipedia. Concepts and their lexicalizations are extracted from Wikipedia pages. Relations are extracted from the category and page network, infoboxes and the body of the articles. The network consists of a central, language independent list of concepts (keeping track of their lexicalizations in various languages), interconnected with a variety of relations to form a very large scale multi-lingual concept network. 1.
GernEdiT - The GermaNet Editing Tool
2010-05-01

This paper introduces GernEdiT (short for: GermaNet Editing Tool), a new graphical user interface for the lexicographers and developers of GermaNet, the German version of the Princeton WordNet. GermaNet is a lexical-semantic net that relates German nouns, verbs, and adjectives. Traditionally, lexicographic work for extending the coverage of GermaNet utilized the Princeton WordNet development environment of lexicographer files. Due to a complex data format and no opportunity of automatic consistency checks, this process was very error prone and time consuming. The GermaNet Editing Tool GernEdiT was developed to overcome these shortcomings. The main purposes of the GernEdiT tool are, besides supporting lexicographers to access, modify, and extend GermaNet data in an easy and adaptive way, as follows: Replace the standard editing tools by a more user-friendly tool, use a relational database as data storage, support export formats in the form of XML, and facilitate internal consistency and correctness of the linguistic resource. All these core functionalities of GernEdiT along with the main aspects of the underlying lexical resource GermaNet and its current database format are presented in this paper.
Pushing the Envelope
2010-05-01

Multidetector row computed tomography (MDCT) has been used for cardiothoracic imaging since the advent of 4-slice computed tomography (CT) in 1999. Available since 2004, 64-slice CT systems are currently considered a prerequisite for successfully integrating cardiothoracic CT into routine clinical algorithms. Developments are ongoing that aim to solve the remaining challenges of cardiothoracic CT. In this review article, we focus on 3 aspects that have significantly influenced the design of newer CT scanners. (1) A faster scan speed enables coverage of the cardiothoracic anatomy in shorter scan times, which is beneficial for patients with limited ability to cooperate and opens new clinical possibilities. A coveted goal for cardiac CT is a "snapshot image" of the entire heart in 1 cardiac cycle, which can be obtained by using MDCT systems with area detectors or dual-source CT systems with electrocardiogram (ECG)-triggered high-pitch spiral. (2) Techniques to reduce the radiation dose to the patient, such as ECG-controlled dose modulation, ECG-triggered sequential CT, low kV scanning, and iterative reconstruction, have gained considerable attention as a consequence of the ongoing discussion of radiation exposure by CT. (3) New developments aim to establish a role for CT in the functional imaging of the lung and of the heart beyond the mere visualization of anatomy. Evaluation of the first-pass enhancement of the myocardium, with single-energy or with dual-energy data acquisition, and cardiac perfusion examinations may have the potential to enhance the application spectrum of cardiac CT by providing the means to determine the hemodynamic relevance of coronary artery stenosis.
A Corpus Representation Format for Linguistic Web Services: The D-SPIN Text Corpus Format and its Relationship with ISO Standards
2010-05-01

In the framework of the preparation of linguistic web services for corpus processing, the need for a representation format was felt, which supports interoperability between different web services in a corpus processing pipeline, but also provides a well-defined interface to both, legacy tools and their data formats and upcoming international standards. We present the D-SPIN text corpus format, TCF, which was designed for this purpose. It is a stand-off XML format, inspired by the philosophy of the emerging standards LAF (Linguistic Annotation Framework) and its “instances ” MAF for morpho-syntactic annotation and SynAF for syntactic annotation. Tools for the exchange with existing (best practice) formats are available, and a converter from MAF to TCF is being tested in spring 2010. We describe the usage scenario where TCF is embedded and the properties and architecture of TCF. We also give examples of TCF encoded data and describe the aspects of syntactic and semantic interoperability already addressed. 1. Layers of corpus formats for linguistic web services 1.1. Scenario – Requirements Part of the work of the D-SPIN project1 is devoted to the creation of web services for the linguistic annotation and exploration of corpus data. Several standard tools, pro-
Anaphoric Annotation of Wikipedia and Blogs in the Live Memories Corpus
2010-05-01

The Live Memories corpus is an Italian corpus annotated for anaphoric relations. The corpus includes manual annotated information about morphosyntactic agreement, anaphoricity, and semantic class of the NPs. For the annotation of the anaphoric links the corpus takes into account specific phenomena of the Italian language like incorporated clitics and phonetically non realized pronouns. The Live Memories Corpus contains texts from the Italian Wikipedia about the region Trentino/Süd Tirol and from blog sites with users’ comments. It is planned to add a set of articles of local news papers. 1.
Activation of the AMP-activated protein kinase enhances glucose-stimulated insulin secretion in mouse β-cells
2010-05-01

The AMP-activated protein kinase (AMPK) is one of the key players in cellular energy regulation adapting cellular demands to nutritional and metabolic variations. Oral antidiabetic drugs like metformin and glitazones (thiazolidinediones) are known to stimulate this enzyme. Besides their established action on peripheral organs including liver and muscles, it has been claimed that these drugs may affect β-cell function. However, it is still a matter of debate whether pharmacological AMPK stimulation increases or decreases insulin secretion. To study this point and to reveal mechanisms underlying changes in insulin secretion we used the specific AMPK activator AICAR and investigated its effects on stimulus-secretion coupling. Membrane potential and currents were measured by the patch-clamp technique, [Ca (2+)]c, mitochondrial membrane potential, and NAD(P)H by fluorescence techniques and insulin secretion by a radioimmunoassay. AICAR enhanced glucose-stimulated insulin release, an effect that can be attributed to the augmentation of electrical activity and [Ca (2+)]c resulting from an AICAR-evoked inhibition of the KATP current. This latter effect was not due to a direct interaction of AICAR with the K[ATP] channels but was dependent on cell metabolism. AICAR did not affect mitochondrial membrane potential or NAD(P)H autofluorescence. Metformin mimicked the action of AICAR on electrical activity, [Ca (2+) ]c, and K[ATP] current. However, compared to AICAR the effects were less pronounced and not sufficient to stimulate insulin secretion. In conclusion, activation of AMPK augments nutrient-induced insulin secretion. Thus, targeting AMPK of β-cells may be an appropriate strategy for the treatment of disturbed glucose homeostasis..
THE EFFECT OF 40 HOURS OF CONSTANT WAKEFULNESS ON NUMBER COMPARISON PERFORMANCE
2010-05-01

We investigated the effects of sleep loss and circadian rhythm on number comparison performance. Magnitude comparison of single-digits is robustly characterized by a distance effect: Close numbers (e.g., 5 versus 6) produce longer reaction times than numbers further apart (e.g., 2 versus 8). This distance effect is assumed to reflect the difficulty of a comparison process based on an analogous representation of general magnitude. Twelve male participants were required to stay awake for 40 h in a quasi-constant-routine protocol. Response speed and accuracy deteriorated between 00:00 and 06:00 h but recovered afterwards during the next day, indicating a circadian rhythm of elementary cognitive function (i.e., attention and speed of mental processing). The symbolic distance effect, however, did not increase during the nighttime, indicating that neither cumulative sleep loss nor the circadian clock prolongs numerical comparison processes. The present findings provide first evidence for a relative insensitivity of symbolic magnitude processing against the temporal variation in energy state.
Compliance profiles derived from a three-dimensional finite-element model of the basilar membrane
2010-05-01

A finite-element analysis is used to explore the impact of elastic material properties, boundary conditions, and geometry, including coiling, on the spatial characteristics of the compliance of the unloaded basilar membrane (BM). It is assumed that the arcuate zone is isotropic and the pectinate zone orthotropic, and that the radial component of the effective Young’s modulus in the pectinate zone decreases exponentially with distance from base to apex. The results concur with tonotopic characteristics of compliance and neural data. Moreover, whereas the maximum compliance in a radial profile is located close to the boundary between the two zones in the basal region, it shifts to the midpoint of the pectinate zone for the apical BM; the width of the profile also expands. This shift begins near the 1 kHz characteristic place for guinea pig and the 2.4 kHz place for gerbil. Shift and expansion are not observed for linear rather than exponential decrease of the radial component of Young’s modulus. This spatial change of the compliance profile leads to the prediction that mechanical excitation in the apical region of the organ of Corti is different to that in the basal region.
Fully autonomous trajectory estimation with long-range passive RFID
2010-05-01

Abstract — We present a novel approach which enables a mobile robot to estimate its trajectory in an unknown environment with long-range passive radio-frequency identification (RFID). The estimation is based only on odometry and RFID measurements. The technique requires no prior observation model and makes no assumptions on the RFID setup. In particular, it is adaptive to the power level, the way the RFID antennas are mounted on the robot, and environmental characteristics, which have major impact on long-range RFID measurements. Tag positions need not be known in advance, and only the arbitrary, given infrastructure of RFID tags in the environment is utilized. By a series of experiments with a mobile robot, we show that trajectory estimation is achieved accurately and robustly. I.