gebhart/patrepeval huggingface dataset:
ABHD2 Inhibitor Identified by Activity-Based Protein Profiling Reduces Acrosome Reaction (2019)

ABHD2\nis a serine hydrolase that belongs to the subgroup of the\nα,β-hydrolase fold-containing proteins, which is involved\nin virus propagation, immune response, and fertilization. Chemical\ntools to selectively modulate the activity of ABHD2 in an acute setting\nare highly desired to investigate its biological role, but are currently\nlacking. Here, we report a library-versus-library screening using\nactivity-based protein profiling (ABPP) to evaluate in parallel the\nselectivity and activity of a focused lipase inhibitor library against\nABHD2 and a panel of closely related ABHD proteins. This screen resulted\nin the rapid identification of novel inhibitors for ABHD2. The selectivity\nof the inhibitor was further investigated in native mouse testis proteome\nby competitive ABPP, revealing a highly restricted off-target profile.\nThe progesterone-induced acrosome reaction was reduced in a dose-dependent\nmanner by the newly identified inhibitor, which provides further support\nfor the key-role of ABHD2 in the P4-stimulated acrosome reaction.\nOn this basis, the ABHD2 inhibitor is an excellent starting point\nfor further optimization of ABHD2 inhibitors that can modulate sperm\nfertility and may lead to novel contraceptives.
Elevated plasma tissue inhibitor of metalloproteinase‐1 levels predict decreased survival in castration‐resistant prostate cancer patients (2010)

Elevated plasma TIMP-1 levels predicted decreased survival in metastatic castration-resistant PC patients, independent of known prognostic markers.
Modified N-Heterocyclic Carbene Ligand for the Recovery of Olefin Metathesis Catalysts via Noncovalent Host–Guest Interactions (2017)

A general method, focusing upon olefin metathesis, was developed for the recovery of homogeneous olefin metathesis catalysts from crude reaction solutions. This method utilizes the supramolecular host-guest interaction between an azobenzene-modified N-heterocyclic carbene ligand and a silica-grafted β-cyclodextrin to remove homogeneous catalyst in a heterogeneous manner, allowing for the recovery of more than 97% of ruthenium in solution. The robust and simple nature of the guest molecule allows for the application of this method to a wide range of homogeneous catalysts. This study reports the synthesis and characterization of the said precatalyst and host compound as well as proof-of-concept recovery trials for a number of common substrates, with the residual ruthenium content of reaction mixtures evaluated by inductively coupled plasma mass spectrometry.
Development of a neutron capture gamma-ray facility at the University of Missouri Research Reactor (1980)

Congenital left ventricular aneurysm (CLVA) associated with multiple aneurysms with rupture into the left atrium (LA) is rare. We report a 17-year-old male with two CLVAs, one of which ruptured into the LA, and discuss the surgical management and review the literature of this rare disease.
Plutonium Immobilization Task 5.6 Metal Conversion: Milestone Report - Perform Feasibility Demonstrations on Pu-Al Alloys (2001)

The Plutonium Conversion Task within the Plutonium Immobilization Program (PIP) transforms incoming plutonium (Pu) feed materials into an oxide acceptable for blending with ceramic precursors. One of the feed materials originally planned for PIP was unirradiated fuel, which consisted mainly of the Zero Power Plutonium Reactor (ZPPR) fuel. Approximately 3.5 metric tons of Pu is in ZPPR fuel. The ZPPR fuel is currently stored at the Argonne National Laboratory-West as stainless steel clad metal plates and oxide pellets, with the vast majority of the Pu in the metal plates. The metal plates consist of a Pu-U-Mo alloy (containing 90% of the ZPPR plutonium metal) and a Pu-Al alloy (containing 10% of the ZPPR plutonium metal). The Department of Energy (DOE) decided that ZPPR fuel is a national asset and, therefore, not subject to disposition. This report documents work done prior to that decision. The Hydnde-Oxidation (HYDOX) Process was selected as the method for Metal Conversion in PIP because it provides a universal means for preparing oxide from all feed materials. HYDOX incorporates both the hydride process, originally developed to separate Pu from other pit materials, as well as the oxide formation step. Plutonium hydride is very reactive and is readily converted to either the nitride or the oxide. A previous feasibility study demonstrated that the Pu-U-Mo alloy could be successfully converted to oxide via the HYDOX Process. Another Metal Conversion milestone was to demonstrate the feasibility of the HYDOX Process for converting plutonium-aluminum (Pu-Al) alloy in ZPPR fuel plates to an acceptable oxide. This report documents the results of the latter feasibility study which was performed before the DOE decision to retain ZPPR fuel rather than immobilize it.
A “hotspot” for autoimmune T cells in type 1 diabetes (2016)

The ability of a single T cell antigen receptor (TCR) to cross-react with multiple antigens allows the finite number of T cells within an organism to respond to the compendium of pathogen challenges faced during a lifetime. Effective immune surveillance, however, comes at a price. TCR cross-reactivity can allow molecular mimics to spuriously activate autoimmune T cells; it also underlies T cell rejection of organ transplants and drives graft-versus-host disease. In this issue of the JCI, Cole and colleagues provide insight into how an insulin-reactive T cell cross-reacts with pathogen-derived antigens by focusing on a limited portion of the peptides to provide a hotspot for binding. These findings dovetail with recent studies of alloreactive and autoimmune TCRs and suggest that the biochemical principles that govern conventional protein-protein interactions may allow the specificity and cross-reactivity profiles of T cells to be predicted.
Discourse annotation in the Monroe corpus (2004)

We describe a method for annotating spoken dialog corpora using both automatic and manual annotation. Our semi-automated method for corpus development results in a corpus combining rich semantics, discourse information and reference annotation, and allows us to explore issues relating these.
An Elementary Treatise on Electricity (2011)

James Clerk Maxwell (1831–1879), first Cavendish Professor of Physics at Cambridge, made major contributions to many areas of theoretical physics and mathematics, not least his discoveries in the fields of electromagnetism and of the kinetic theory of gases, which have been regarded as laying the foundations of all modern physics. This work of 1881 was edited from Maxwell's notes by a colleague, William Garnett, and had formed the basis of his lectures. Several of the articles included in the present work were also included in his two-volume Treatise on Electricity and Magnetism (1873), also reissued in this series. The preface indicates that the two works were aimed at somewhat different audiences, the larger work assuming a greater knowledge of higher mathematics. Maxwell had also modified some of his methodology, and hoped to encourage the reader to develop an understanding of concepts relating to electricity.
Channelopathy-related SCN10A gene variants predict cerebellar dysfunction in multiple sclerosis (2016)

Our data suggest that SCN10A variation substantially influences functional status, including prominent effects on motor coordination in patients with MS. These findings were supported by the effects of this variant on a neural system important for motor coordination, namely cerebello-thalamic circuitry. Overall, our findings add to the emerging evidence that suggests that sodium channel NaV1.8 could serve as a target for future drug-based interventions to treat cerebellar dysfunction in MS.
Oil-absorbent cellulosic derivatives. [Cellulose-containing substance having cationic exchange properties and a quaternary ammonium salt] (1986)

A composition is described for absorbing oil from oil-in-water emulsions comprising the reaction product of a cellulose-containing substance having cationic exchange properties and a fatty quaternary ammonium salt.
Quality of Service Abstractions for Software-defined Networks (2015)

Software-defined networking (SDN) provides a means of configuring the packet-forwarding behavior of a network from a logically-centralized controller. Expressive, high-level languages have emerged for expressing data-plane configurations, and new tools allow for verifying packet reachability properties in real time. But SDN largely ignores quality of service (QoS) primitives, such as queues, queuing disciplines, and rate limiters, leaving configuration of these elements to be performed out of band in an ad-hoc manner. Not only does this make QoS elements difficult to configure, it also leads to a “try it and see” approach to analysis and verification of QoS properties. We propose a new language for configuring SDNs with quality of service primitives. Our language comes equipped with a well-defined semantics drawn from the network calculus, which we believe will yield an equational theory for reasoning about network quality of service as well as decision procedures for verifying QoS properties.
Spectral decomposition and matrix element effects in scanning tunneling spectroscopy ofBi2Sr2CaCu2O8+δ (2009)

We present a Green's function-based framework for modeling the scanning tunneling spectrum from the normal as well as the superconducting state of complex materials where the nature of the tunneling process---i.e., the effect of the tunneling ``matrix element,'' is properly taken into account. The formalism is applied to the case of optimally doped ${\text{Bi}}_{2}{\text{Sr}}_{2}{\text{CaCu}}_{2}{\text{O}}_{8+\ensuremath{\delta}}$ (Bi2212) high-${T}_{\text{c}}$ superconductor using a large tight-binding basis set of electron and hole orbitals. The results show clearly that the spectrum is modified strongly by the effects of the tunneling matrix element and that it is not a simple replica of the local density of states of the $\text{Cu}\text{ }{d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ orbitals with other orbitals playing a key role in shaping the spectra. We show how the spectrum can be decomposed usefully in terms of tunneling ``channels'' or paths through which the current flows from various orbitals in the system to the scanning tip. Such an analysis reveals symmetry-forbidden and symmetry-enhanced paths between the tip and the cuprate layers. Significant contributions arise from not only the ${\text{CuO}}_{2}$ layer closest to the tip but also from the second ${\text{CuO}}_{2}$ layer. The spectrum also contains a longer range background reflecting the nonlocal nature of the underlying Bloch states. In the superconducting state, coherence peaks are found to be dominated by the anomalous components of Green's function.
Structure and rifting evolution of the northern Newfoundland Basin from Erable multichannel seismic reflection profiles across the southeastern margin of Flemish Cap (2010)

We present the results from processing and interpreting five lines from the 1992 Erable multichannel seismic reflection experiment extending from the southeastern margin of Flemish Cap into the northern Newfoundland Basin. These profiles reveal significant along strike variations in the rifting styles experienced by Flemish Cap. In the southwest, a 100-km-wide transition zone is identified between thinned continental crust and thin oceanic crust. Similar to the conjugate Galicia Bank and Iberian margins, this transition zone contains a section of deep basement adjacent to a series of shallower ridges and is interpreted as exhumed serpentinized mantle. Along strike towards the northeast, this transition zone pinches out completely within 100 km and is replaced by thin oceanic crust directly adjacent to thinned continental crust. By interpreting nearby seismic profiles and profiles on the conjugate margins using the same classification criteria, we construct regional maps of the distribution of crustal domains on both sides of the North Atlantic. These maps reveal significant variations in rifting style on the conjugate margins and along strike of each margin and also highlight the role of ancient transfer zones in compartmentalizing these rifting variations into four distinct regions. We propose that the limited localization of shallow topographically high serpentinized peridotite ridges on the Newfoundland-Iberia and Flemish Cap-Galicia Bank conjugate margins, was directly related to an increase in the rate of extension following the separation of Flemish Cap and Galicia Bank which exhumed deeper, less serpentinized mantle.
Supporting software evolution through dynamically retrieving traces to UML artifacts (2004)

The ability to trace new and changed requirements to their impacted components provides critical support for managing change in an evolving software system. Unfortunately numerous studies have shown the difficulties of maintaining links using traditional traceability methods. Information retrieval techniques can be used to dynamically generate traces and alleviate the need to maintain explicit links, however prior work in this area has focused primarily on establishing intra-requirement links or links between requirements and code. We compare several retrieval techniques for generating links between requirements, code, and UML models. Tracing to UML elements provides a higher perspective on the proposed change than would be possible if links were generated directly to the code and supports the growing trend towards model driven development. Our experiment returned better results for establishing links to UML artifacts than to code, suggesting the usefulness of establishing links to code via UML artifacts. We conclude the paper by discussing the implications of this approach for managing the evolution of a software system.
Silicon microdisplay with photo-alignment (2004)

A reflective mode liquid crystal microdisplay is presented using photo-alignment technology. The alignment layer, SD1, was aligned by three-step UV exposure process and MTN 90/spl deg/ mode is chosen to evaluate the performance. The comparison shows that the photo-alignment is comparable with and even better than the rubbing method in some aspect, such as sharper RVC curve and higher contrast ratio.
A Hardware Architecture for Color Image Enhancement Using a Machine Learning Approach with Adaptive Parameterization (2006)

A novel architecture for performing color image enhancement using a machine learning algorithm called Ratio Rule is proposed in this paper. The threshold width of the activation function is automatically determined from the image characteristics. The approach promotes log-domain computation to eliminate all multiplications and divisions, utilizing approximation techniques for efficient estimation of the log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and inverse-log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> . The design incorporates the dynamic thresholds of the activation functions and update rate. The improved quadrant symmetric architecture is also presented to provide very high throughput rate for homomorphic filters which is part of the pixel intensity enhancement across RGB components in the system. The pipelined design of the filter features the flexibility in reloading a wide range of kernels for different frequency responses. A new approach for the design of the uniform filters is also presented to reduce the processing element arrays (PEAs) from W PEAs to 2 PEAs for W × W window. This new concept is applied to assist in training the synaptic weights of the neural network for color balancing to restore the intensity enhanced image to its natural color existed in the original image. The concept of uniform filter is further extended to design max/min filters. It is observed that the performance of the system with parallel and pipelined architectures is able to achieve 139.3 million outputs per second (MOPS), or equivalently 54.7 billion operations per second on Xilinx's Virtex II XC2V2000-4ff896 FPGA at a clock frequency of 139.3 MHz.
OPTIMIZATION OF THE SYNTHESIS OF SOME NEW THIAZOLIDINE-4-ONE DERIVATIVES WITH XANTHINE SCAFFOLD (2017)

In the last time many researchers were focused on synthesis of new compounds with thiazolidine-4-one scaffold based on the important biological effects of this heterocycle. Aim: The aim of this study was to optimize the synthesis of some new thiazolidine-4-one derivatives with xanthine scaffold in order to obtain high yields and advanced purity. Material and methods: The synthesis was based on a cyclization reaction between various hydrazones and thioglycolic acid. The optimization was performed for 2-(4-methylphenyl)-3-[(1,3-dimethylxanthin-7-yl)acetamido]thiazolidine-4-one (b) by varying different parameters such as molar ratio between reagents, solvent, catalyst, temperature, time of reaction and type of method. There were used ten chemistry procedures for detecting the desired compound and other ones for establishing the optimal conditions. The optimized method was also applied for other thiazolidine-4-one derivatives with xanthine structure. Results: The most favorable parameters for optimal synthesis were established as follow: an excess of 20 equivalents of thioglycolic acid to 1 equivalent of hydrazone, freshly distilled toluene as solvent, temperature of 120 °C and reflux for 18 hours. The time and temperature of reaction proved to have a key role for increased yield. Conclusions: The optimal conditions of reaction were established in order to obtain new thiazolidine-4-one derivatives in high yields and increased purity.
Does the Online Card Payment Landscape Unwittingly Facilitate Fraud? (2017)

An extensive study of the current practice of online payment using credit and debit cards reveals the intrinsic security challenges caused by differences in how payment sites operate.In this article, we present the online payment landscape in detail. In particular, we aim to highlight the different manners in which online payment is performed and the varying security measures put in place by online merchants-from checking only the card number and the expiry date to fully fledged centralized bank security mechanisms such as 3D Secure.
CD40L/IL-4–stimulated CLL demonstrates variation in translational regulation of DNA damage response genes including ATM (2018)

CD40L/interleukin-4 (IL-4) stimulation occurs in vivo in the tumor microenvironment and induces global translation to varying degrees in individuals with chronic lymphocytic leukemia (CLL) in vitro. However, the implications of CD40L/IL-4 for the translation of specific genes is not known. To determine the most highly translationally regulated genes in response to CD40L/IL-4, we carried out ribosome profiling, a next-generation sequencing method. Significant differences in the translational efficiency of DNA damage response genes, specifically ataxia-telangiectasia-mutated kinase (ATM) and the MRE11/RAD50/NBN (MRN) complex, were observed between patients, suggesting different patterns of translational regulation. We confirmed associations between CD40L/IL-4 response and baseline ATM levels, induction of ATM, and phosphorylation of the ATM targets, p53 and H2AX. X-irradiation was used to demonstrate that CD40L/IL-4 stimulation tended to improve DNA damage repair. Baseline ATM levels, independent of the presence of 11q deletion, correlated with overall survival (OS). Overall, we suggest that there are individual differences in translation of specific genes, including ATM, in response to CD40L/IL-4 and that these interpatient differences might be clinically important.
2P1-D35 A Consideration on Accuracy of Tracking Task and Arm Position/Posture (2006)

It is thought that the operators explore position and posture during the operation in which they can maneuver a tool more easily and more accurately. If we know such position and posture in advance, it is expected to reduce the time to be skillful and to improve the performance. In this paper, we analyze manipulability on planar 3 DOF tracking task in consideration of arm position and posture, and compare simulation results and experimental results.
BscF as a vaccine candidate for Bordetella pertussis infection (“Whooping Cough”) (VAC9P.1064) (2015)

Abstract Bordetella pertussis, a Gram- bacterium, causes pertussis (“Whopping Cough”). Despite widespread vaccination, 48 million cases of pertussis occur annually worldwide. The resurgence of pertussis is linked to antigenic divergence of circulating pertussis and waning and/or ineffective immunity induced by the current acellular vaccine. YscF, a Yersiniaprotein that, in multimeric form, makes up the Type III Secretion System (T3SS) needle, has been shown to be both an excellent protective antigen for Y. pestis,as well as a strong adjuvant via TLR signaling. We characterized here immune responses induced by BscF, the Bordetella homolog of YscF. BscF activated NF-κB through both TLR-2 and TLR-4 in vitro. Moreover, BscF induced IL-1β and IL-12 secretion in human THP-1 cells and bone marrow-derived macrophages. In vivo,BscF immunization in alum induced both a Th1 and Th17 response, with stimulated CD4+T cell secreting both IFN-γ and IL-17A. Interestingly, in vivoBscF (in alum) also induced significant titers of BscF-specific antibody of all IgG isotypes (1, 2a, 2b, 3), suggesting the induction of both Th1 and Th2 responses. In toto we demonstrated that BscF induces a strong humoral and cell-mediated protein-specific immune response. This, along with the adjuvant characteristic and external structural location of BscF, suggests that BscF may provide an excellent addition to the current acellular vaccine to yield a stronger and/or more persisted protection against pertussis.
Dynamical encoding of cursive handwriting (2002)

Online cursive handwriting is considered as a slow modulation of an underlying cycloidal motion. Two dimensional oscillation, with a constant linear drift, describes the general pen motion. The dynamical equations describing the oscillations are coupled through fixed ratios of the angular velocities and phase lags. The entire process is viewed as an almost constant vertical oscillatory movement with changing horizontal velocity phase lag. An estimation scheme of the cycloidal motion parameters is presented. In the estimation process, the instantaneous amplitude and phase lag of the horizontal velocity are calculated and quantized. The result is a many-to-one mapping from the continuous pen movements to discrete motor control symbols. Using this motor control representation, word spotting and matching are performed successfully.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Search-and-replace editing for personal photo collections (2010)

We propose a new system for editing personal photo collections, inspired by search-and-replace editing for text. In our system, local edits specified by the user in a single photo (e.g., using the “clone brush” tool) can be propagated automatically to other photos in the same collection, by matching the edited region across photos. To achieve this, we build on tools from computer vision for image matching. Our experimental results on real photo collections demonstrate the feasibility and potential benefits of our approach.