gebhart/patrepeval huggingface dataset:
Noisy Bayesian active learning (2012)

Consider the problem of noisy Bayesian active learning given a sample space, a finite label set, and a finite set of label generating functions from the sample space to the label set, also known as the function class. The objective is to identify the function in the function class that generates the labels using as few label queries as possible and with low probability of error despite possible corruption by independent noise. The key to achieving this objective relies on the selection of queries in a strategic and adaptive manner. The problem generalizes the problem of noisy generalized binary search [1]. This paper explores the connection between the above Bayesian active learning problem and the problem of information acquisition in which a Bayesian decision maker is responsible for dynamically collecting noisy observations so as to enhance her/his information in a speedy manner about an underlying phenomena of interest with a constraint on the probability of error. This view of the problem allows for developing a general lower bound on the expected number of queries to identify the function that generates the labels in terms of the observation noise statistics, the desired probability of error, and the cardinality of the function class. Furthermore, viewing the problem as an information acquisition problem enables a deterministic and Markov heuristic policy based on greedy maximization of Extrinsic Jensen-Shannon divergence [2]. The performance of this heuristic is compared with the state of the art strategies for noisy generalized binary search. In the case where the function class is sample-rich, it is shown that this heuristic is better than previous results and, in particular, matches the earlier proposed lower bound asymptotically.
Calcium Channel Structural Determinants of Synaptic Transmission between Identified Invertebrate Neurons (2003)

We report here that unlike what was suggested for many vertebrate neurons, synaptic transmission in Lymnaea stagnalis occurs independent of a physical interaction between presynaptic calcium channels and a functional complement of SNARE proteins. Instead, synaptic transmission in Lymnaea requires the expression of a C-terminal splice variant of the Lymnaea homolog to mammalian N- and P/Q-type calcium channels. We show that the alternately spliced region physically interacts with the scaffolding proteins Mint1 and CASK, and that synaptic transmission is abolished following RNA interference knockdown of CASK or after the injection of peptide sequences designed to disrupt the calcium channel-Mint1 interactions. Our data suggest that Mint1 and CASK may serve to localize the non-L-type channels at the active zone and that synaptic transmission in invertebrate neurons utilizes a mechanism for optimizing calcium entry, which occurs independently of a physical association between calcium channels and SNARE proteins.
Synthesis of dihydrophenanthridines by a sequence of Ugi-4CR and palladium-catalyzed intramolecular C-H functionalization (2008)

Highly functionalized dihydrophenanthridines are synthesized in only two steps from readily accessible starting materials in good to excellent overall yields.
Two-layer anti-reflection strategies for implant applications (2006)

A two-layer bottom anti-reflective coating (BARC) concept in which a layer that develops slowly is coated on top of a bottom layer that develops more rapidly was demonstrated. Development rate control was achieved by selection of crosslinker amount and BARC curing conditions. A single-layer BARC was compared with the two-layer BARC concept. The single-layer BARC does not clear out of 200-nm deep vias. When the slower developing single-layer BARC was coated on top of the faster developing layer, the vias were cleared. Lithographic evaluation of the two-layer BARC concept shows the same resolution advantages as the single-layer system. Planarization properties of a two-layer BARC system are better than for a single-layer system, when comparing the same total nominal thicknesses.
Stereologic, histopathologic, flow cytometric, and clinical parameters in the prognostic evaluation of 74 patients with intraoral squamous cell carcinomas (1992)

These findings may contribute to optimal and individualized therapy.
Well Test Interpretation in Geologically Complex Channelized Reservoirs (1993)

Abstract The interpretation of pressure transients by the use of analytical models generally leads to a simplified description of the geological heterogeneities around the well. Although this approach works when the geology is simple, clearly, more complex geological environments will prove difficult to analyse. In channelized systems, such as alluvial and deep sea fans, the reservoir geometry may be poorly represented by simplistic geometrical arrangements that exist in the current analytical models. For example, the calculation of the distance to the no-flow boundaries is disturbed by the presence of levees. This aspect of the problem is clearly important as such calculations lead to an estimation of channel width, which may later be used as an input parameter for stochastic modelling. Results of flow simulations of well tests from such complex geometries are presented in this paper. Using finely-gridded models generated from outcrop description and stochastic modelling, the influence of different geological parameters on pressure response is evaluated. The study is performed in four steps. Firstly, a field example is used to define the problem: a pressure transient test is interpreted in terms of complex geology by the use of a combination of analytical solutions. Secondly, a known reservoir geometry (from outcrop study) is input into a well-test flow simulation model. Thirdly, a more complex reservoir is generated by stochastic (Boolean) techniques which is also simulated as in step 2. Fourthly, a new analytical solution allows for the correct interpretation of the original field example. When reservoirs are characterized by channel type features, and particularly stacked channels, the no-flow boundaries identified on the derivative curve represent the limits of the system, rather than the limits of individual features. When channels are connected by levees, the levees influence the calculation of the distance to no-flow boundaries. The presence of levees increases the apparent channel width. All well-test interpretation results must be checked by comparison with the best available geological description of the sedimentary environment before quantitative data are supplied for geostatistical modelling.
GPU-accelerated digitally reconstructed radiographs (2008)

Intensity based two-dimensional to three-dimensional (2D- 3D) registration algorithms usually rely on the generation of a Digitally Reconstructed Radiograph (DRR) in each iteration of the registration algorithm. The vast majority of the computation time of such registration algorithms can be contributed to the calculations needed to produce DRRs. Since 2D-3D registration often is applied during clinical interventions, it is of great importance to obtain the result of the registration within limited time. We present an approach that is both very fast and accurate, harvesting the parallel processing power of today's mainstream graphics hardware. Especially we use the high precision z-buffer as intermediate buffer, in order to produce accurate results.
Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (MetAP-2) Inhibitors (2019)

Co- and post-translational processing are crucial maturation steps to generate functional proteins. MetAP-2 plays an important role in this process, and inhibition of its proteolytic activity has been shown to be important for angiogenesis and tumor growth, suggesting that small-molecule inhibitors of MetAP-2 may be promising options for the treatment of cancer. This work describes the discovery and structure-based hit optimization of a novel MetAP-2 inhibitory scaffold. Of critical importance, a cyclic tartronic diamide coordinates the MetAP-2 metal ion in the active site while additional side chains of the molecule were designed to occupy the lipophilic methionine side chain recognition pocket as well as the shallow cavity at the opening of the active site. The racemic screening hit from HTS campaign 11a was discovered with an enzymatic IC50 of 150 nM. The resynthesized eutomer confirmed this activity and inhibited HUVEC proliferation with an IC50 of 1.9 μM. Its structural analysis revealed a sophisticated interaction pattern of polar and lipophilic contacts that were used to improve cellular potency to an IC50 of 15 nM. In parallel, the molecular properties were optimized on plasma exposure and antitumor efficacy which led to the identification of advanced lead 21.
Enhancements of the Range Consensus Algorithm (RANCO) (2008)

In anticipation of the future GNSS constellations&#13;\nbecoming operational, it will no longer be possible to&#13;\nassume that the probability of failure for more than one&#13;\nsatellite within a certain timeframe is negligible. Further,&#13;\nit is questionable whether it is always reasonable to&#13;\ncompute a position estimate based on all satellites in&#13;\nview, rather than selecting the “best” subset.&#13;\nThe Range Consensus (RANCO) algorithm is not only&#13;\ncapable of detecting multiple satellite failures at a time,&#13;\nbut it also allows the determination of good estimates of&#13;\nthe current ranging biases. RANCO calculates position&#13;\nsolutions based on subsets of four satellites and compares&#13;\nthis estimate with the pseudoranges of all the satellites not&#13;\ncontributing to this solution. The residuals of this estimate&#13;\nare then used as a measure of statistical consensus.&#13;\nThe scope of this work is the optimization of the&#13;\nperformance of RANCO by restricting it to the detection&#13;\nof a certain number of failed satellites at a time and by&#13;\nfinding an optimal subset selection process for this&#13;\nconstraint. Furthermore, the computation of the subset&#13;\nquality was reconsidered and significantly improved by&#13;\nthe use of the Weighted Dilution of Precision (WDOP).&#13;\nIn this paper, the physical model for determining the&#13;\nthreshold for the separation between correct and faulty&#13;\nsatellite signals has been extended. The RANCO&#13;\nalgorithm was also verified with respect to its capability&#13;\nof detecting and identifying satellites with a bias higher&#13;\nthan a given threshold. Throughout the paper those&#13;\nsatellites are defined to fail.&#13;\nThe abilities of RANCO, to exclude multiple&#13;\nsimultaneous ranging faults and low biases, paves the way&#13;\nfor safety critical applications by combining receiver&#13;\nautonomous algorithms with the integrity channel&#13;\ninformation from future GNSS systems.
Mining text and social streams (2014)

The large amount of text data which are continuously produced over time in a variety of large scale applications such as social networks results in massive streams of data. Typically massive text streams are created by very large scale interactions of individuals, or by structured creations of particular kinds of content by dedicated organizations. An example in the latter category would be the massive text streams created by news-wire services. Such text streams provide unprecedented challenges to data mining algorithms from an efficiency perspective. In this paper, we review text stream mining algorithms for a wide variety of problems in data mining such as clustering, classification and topic modeling. A recent challenge arises in the context of social streams , which are generated by large social networks such as Twitter . We also discuss a number of future challenges in this area of research.
Role of 67 kDa Cell Surface Laminin Binding Protein of Leishmania donovani in Pathogenesis (2001)

The role that interaction with laminin may play in Leishmania donovani infection was investigated. Binding of (125)I-radiolabeled laminin, in a liquid-phase assay, by the parasite was rapid, saturable, specific, reversible, and of high affinity. Using a Western blotting procedure, a 67 kDa laminin-binding protein (LBP) was identified from the membrane of both the promastigote and amastigote forms of L. donovani. Subsequently, the protein was purified by affinity chromatography. Immunofluorescence with a polyclonal antibody against LBP as well as flow cytometric analysis demonstrated its presence at the parasite surface. After stimulation with phorbol-12-myristate-13-acetate (PMA), U937 cells exhibited the ability to adhere to laminin and LBP specifically inhibited this adhesion. The reduced parasite adhesion after tunicamycin treatment suggested the importance of sugar residues in cell adhesion. Although co-administration of either laminin or LBP or anti LBP antibody reduced parasite virulence, resulting in a lower level of infection in the BALB/c mouse model, an in vitro macrophage culture-enhanced level of infection was observed in the case of laminin-coated parasites. The results collectively suggest a role for LBP in the interaction of the parasite with extracellular matrix elements, which may constitute a basis for the homing of the parasite to its physiological address.
Tumor necrosis factor induces the production of urokinase-type plasminogen activator by human endothelial cells (1990)

Endothelial cells play an important role in the regulation of fibrinolysis by the production of several key regulatory proteins. The cytokines tumor necrosis factor (TNF), lymphotoxin, and interleukin-1 (IL-1), but not interleukin-6, increase the production of plasminogen activator inhibitor-1 (PAI-1) by endothelial cells, whereas they have no stimulatory effect on the production of tissue-type plasminogen activator (t-PA). Primary cultures of human endothelial cells release very little urokinase-type plasminogen activator (u-PA). We report here that TNF and lymphotoxin induce, in a concentration-dependent way, the production of both cellular and secreted u-PA antigen in primary and subcultured human endothelial cells. The TNF-induced increase was accompanied by a more than 10-fold increase in u-PA mRNA. Upon stimulation of early passage umbilical vein endothelial cells by TNF, u-PA was predominantly secreted at the basolateral side, whereas PAI activity and t-PA were found in more equal amounts at the apical and basolateral sides of the cell monolayers. TNF-stimulated u-PA secretion by subcultured human aorta endothelial cells showed only a marginal polarity. The u-PA antigen was present in a plasmin-activatable form (single chain u-PA) and in a nonactivatable form (probably u-PA: PAI-1 complex). During the induction of u-PA by TNF, the ratio between plasmin-activatable u-PA and total u-PA decreased markedly. This may indicate that TNF also increases the degree of u-PA activation. The parallel induction of the synthesis and secretion of both u-PA and PAI-1 by endothelial cells adds a new aspect to the alterations of the fibrinolytic system caused by inflammatory mediators. This aspect may be significant for the regulation of cell-associated and interstitial plasminogen activator activity.
Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism (2017)

Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated metabolic flux states for the NCI60 cell line collection and correlated the variance between metabolic states of these lines with their other properties. The analysis revealed a remarkably consistent structure underlying high flux metabolism. The three primary uptake pathways, glucose, glutamine and serine, are each characterized by three features: (1) metabolite uptake sufficient for the stoichiometric requirement to sustain observed growth, (2) overflow metabolism, which scales with excess nutrient uptake over the basal growth requirement, and (3) redox production, which also scales with nutrient uptake but greatly exceeds the requirement for growth. We discovered that resistance to chemotherapeutic drugs in these lines broadly correlates with the amount of glucose uptake. These results support an interpretation of the Warburg effect and glutamine addiction as features of a growth state that provides resistance to metabolic stress through excess redox and energy production. Furthermore, overflow metabolism observed may indicate that mitochondrial catabolic capacity is a key constraint setting an upper limit on the rate of cofactor production possible. These results provide a greater context within which the metabolic alterations in cancer can be understood.
Vanadium oxide thin film with improved sheet resistance uniformity (2014)

This paper reports on the deposition of vanadium oxide thin films with sheet resistance uniformity better than 2.5% over a 150 mm wafer. The resistance uniformity within the array is estimated to be less than 1%, which is comparable with the value reported for amorphous silicon-based microbolometer arrays. In addition, this paper also shows that the resistivity of vanadium oxide, like amorphous silicon, can be modeled by Arrhenius' equation. This result is expected to significantly ease the computation of the correction table required for TEC-less operation of VO<sub>x-</sub>based microbolometer arrays.
Experimental evaluation of space vector oriented active DC-side current balancing of two parallel connected three-phase three-switch buck-type unity power factor rectifier systems (2003)

In this paper the parallel connection of two three phase buck-type unity power factor rectifier systems is investigated experimentally for a 10 kW DSP-controlled prototype. There, a space vector modulation scheme is employed which shows all advantages of interleaved operation of the two systems. Three control schemes for active DC-side current balancing are described. The control schemes do differ concerning their control action and concerning additional switching losses. All control structures discussed in this paper are based on employing an additional free-wheeling states which do allow influence of the rate of change of the DC-side currents and can therefore be used for DC-side current balancing.
Progress in RAFT/MADIX Polymerization: Synthesis, Use, and Recovery of Chain Transfer Agents (2006)

We report the synthesis of novel chain transfer agents for RAFT/MADIX polymerization, and their use to mediate the polymerization of a variety of monomers, in order to produce a range of functional materials. After polymerization, the chain transfer agent is recovered in a one pot reaction, which also permits to introduce functional groups at the chain-end of the polymers.
ChemInform Abstract: Recent Developments in the Biology and Medicinal Chemistry of Potassium Channel Modulators: Update from a Decade of Progress (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Improvement of Luminescence Degradation of PDP Blue Phosphor with New UV Phosphor (2003)

phosphor is a useful blue phosphor for plasma display panel (PDP) and fluorescent lamps, but is liable to be degraded by vacuum ultraviolet (VUV) irradiation. We found that phosphor has a high efficiency of emission at 313 nm under VUV excitation and strong resistance to luminescence degradation caused by heat and VUV irradiation. To prevent this degradation, is mixed with In this mixed phosphor, the VUV energy absorbed by the former is efficiently transformed to the blue emission of the latter. Consequently, the luminescence degradation inherent in the blue phosphor is decreased with a small sacrifice of the emission intensity. © 2003 The Electrochemical Society. All rights reserved.
Multi-Modal Attack Detection for Cyber-Physical Additive Manufacturing (2021)

Cyber-Physical Additive Manufacturing (AM) constructs a physical 3D object layer-by-layer according to its digital representation and has been vastly applied to fast prototyping and the manufacturing of functional end-products across fields. The computerization of traditional production processes propels these technological advancements; however, this also introduces new vulnerabilities, necessitating the study of cyberattacks on these systems. The AM Sabotage Attack is one kind of kinetic cyberattack that originates from the cyber domain and can eventually lead to physical damage, injury, or even death. By introducing inconspicuous yet damaging alterations in any specific process of the AM digital process chain, the attackers can compromise the structural integrity of a manufactured component in a manner that is invisible to a human observer. If the manufactured objects are critical for their system, those attacks can even compromise the whole system's structural integrity and pose a severe safety risk to its users. For example, an inconspicuous void (less than 1 mm in dimension) placed in the 3D design of a tensile test specimen can reduce its yield load by 14%. However, security studies primarily focus on securing digital assets, overlooking the fact that AM systems are CPSs.
Syntenin-1 and Ezrin Proteins Link Activated Leukocyte Cell Adhesion Molecule to the Actin Cytoskeleton (2014)

Activated leukocyte cell adhesion molecule (ALCAM) is a type I transmembrane protein member of the immunoglobulin superfamily of cell adhesion molecules. Involved in important pathophysiological processes such as the immune response, cancer metastasis, and neuronal development, ALCAM undergoes both homotypic interactions with other ALCAM molecules and heterotypic interactions with the surface receptor CD6 expressed at the T cell surface. Despite biochemical and biophysical evidence of a dynamic association between ALCAM and the actin cytoskeleton, no detailed information is available about how this association occurs at the molecular level. Here, we exploit a combination of complementary microscopy techniques, including FRET detected by fluorescence lifetime imaging microscopy and single-cell force spectroscopy, and we demonstrate the existence of a preformed ligand-independent supramolecular complex where ALCAM stably interacts with actin by binding to syntenin-1 and ezrin. Interaction with the ligand CD6 further enhances these multiple interactions. Altogether, our results propose a novel biophysical framework to understand the stabilizing role of the ALCAM supramolecular complex engaged to CD6 during dendritic cell-T cell interactions and provide novel information on the molecular players involved in the formation and signaling of the immunological synapse at the dendritic cell side.
Single-Carrier Frequency-Domain Equalizer with Multi-Antenna Transmit Diversity (2012)

Single-carrier (SC) block transmission with cyclic prefix (CP) is a method with several advantages that has been incorporated into standards. This paper investigates the performance of multi-antenna SC-FDE under cyclic-delay diversity (CDD) and Alamouti signaling. Our analysis fully characterizes the diversity, showing that it depends not only on the antenna configuration and channel memory, but also on data block length and data transmission rate. Below a certain rate threshold, full diversity is available to both CDD and Alamouti signaling, while at higher rates their diversity diminishes, albeit not quite in the same way. Our analysis shows that at high rates the CDD diversity degenerates to the diversity of the SISO SC-FDE, while Alamouti signaling provides twice the diversity of SISO SC-FDE.