gebhart/patrepeval huggingface dataset:
Cover Picture: Structure–Activity Relationship Studies of the Cyclic Depsipeptide Natural Product YM‐254890, Targeting the Gq Protein (ChemMedChem 11/2017) (2017)

The front cover picture shows the X-ray crystal structure of the natural product, cyclic depsipeptide YM-254890 bound to the Gαi/q protein (PDB: 3AH8). YM-254890, together with its structural analogue FR900359, is the only known inhibitor of Gq proteins. The inhibition of Gq by YM-254890 is achieved by stabilizing an inactive GDP-bound form of Gq, which then blocks the fundamental GDP/GTP exchange of the G protein. By performing structure–activity relationship studies of YM-254890 focusing NMe-Ala and Ala, we discovered three new selective Gq signaling inhibitors (YM-13, YM-14, and YM-18) which show potencies equivalent with that of the natural compound YM-254890, while YM-14 was the most potent analogue. These results provide pertinent information for understanding the Gq inhibitory mechanism. Importantly, they also provide a pathway for the development of labeled YM-254890 analogues. More information can be found in the Communication by Kristian Strømgaard et al. on page 830 in Issue 11, 2017 (DOI: 10.1002/cmdc.201700155).
ChemInform Abstract: 25th Anniversary Article: MXenes: A New Family of Two‐Dimensional Materials (2014)

Abstract Review: MXenes: early transition metal carbides or carbonitrides resulting from the selective removal of the A element from ternary carbides called MAX phases like Ti 2 AlC, Ti 3 AlC 2 , or Ta 4 AlC 3 ; 70 refs.
Toward a Statistical Framework for Source Anonymity in Sensor Networks (2011)

In certain applications, the locations of events reported by a sensor network need to remain anonymous. That is, unauthorized observers must be unable to detect the origin of such events by analyzing the network traffic. Known as the source anonymity problem, this problem has emerged as an important topic in the security of wireless sensor networks, with variety of techniques based on different adversarial assumptions being proposed. In this work, we present a new framework for modeling, analyzing, and evaluating anonymity in sensor networks. The novelty of the proposed framework is twofold: first, it introduces the notion of "interval indistinguishability” and provides a quantitative measure to model anonymity in wireless sensor networks; second, it maps source anonymity to the statistical problem of binary hypothesis testing with nuisance parameters. We then analyze existing solutions for designing anonymous sensor networks using the proposed model. We show how mapping source anonymity to binary hypothesis testing with nuisance parameters leads to converting the problem of exposing private source information into searching for an appropriate data transformation that removes or minimize the effect of the nuisance information. By doing so, we transform the problem from analyzing real-valued sample points to binary codes, which opens the door for coding theory to be incorporated into the study of anonymous sensor networks. Finally, we discuss how existing solutions can be modified to improve their anonymity.
Classical vs. crowdsourcing surveys for eliciting geographic relevance criteria (2012)

Geographic relevance aims to assess the relevance of physical entities (e.g., shops and museums) in geographic space for a mobile user in a given context, thereby shifting the focus from the digital world (the realm of classical information retrieval) to the physical world. We study the elicitation of geographic relevance criteria by means of both a classical survey and an Amazon Mechanical Turk (a crowdsourcing platform) survey. This allows us to obtain three results: first, we gather a set of criteria and their relative importance; second, we gain a first insight on the differences between geographic relevance and classical relevance as commonly understoon in the IR field; and third we draw some considerations on the agreement, on the importance of specific criteria, among the participants to the classical and the crowdsourcing surveys.
Supplementary Figure S1 from Identification of Novel Target Genes by an Epigenetic Reactivation Screen of Renal Cancer (2023)

Supplementary Figure S1 from Identification of Novel Target Genes by an Epigenetic Reactivation Screen of Renal Cancer
APOE genotype regulates pathology and disease progression in synucleinopathy (2020)

Apolipoprotein E (<i>APOE</i>) ε4 genotype is associated with increased risk of dementia in Parkinson's disease (PD), but the mechanism is not clear, because patients often have a mixture of α-synuclein (αSyn), amyloid-β (Aβ), and tau pathologies. <i>APOE</i> ε4 exacerbates brain Aβ pathology, as well as tau pathology, but it is not clear whether <i>APOE</i> genotype independently regulates αSyn pathology. In this study, we generated A53T αSyn transgenic mice (A53T) on <i>Apoe</i> knockout (A53T/EKO) or human <i>APOE</i> knockin backgrounds (A53T/E2, E3, and E4). At 12 months of age, A53T/E4 mice accumulated higher amounts of brainstem detergent-insoluble phosphorylated αSyn compared to A53T/EKO and A53T/E3; detergent-insoluble αSyn in A53T/E2 mice was undetectable. By immunohistochemistry, A53T/E4 mice displayed a higher burden of phosphorylated αSyn and reactive gliosis compared to A53T/E2 mice. A53T/E2 mice exhibited increased survival and improved motor performance compared to other <i>APOE</i> genotypes. In a complementary model of αSyn spreading, striatal injection of αSyn preformed fibrils induced greater accumulation of αSyn pathology in the substantia nigra of A53T/E4 mice compared to A53T/E2 and A53T/EKO mice. In two separate cohorts of human patients with PD, <i>APOE</i> ε4/ε4 individuals showed the fastest rate of cognitive decline over time. Our results demonstrate that <i>APOE</i> genotype directly regulates αSyn pathology independent of its established effects on Aβ and tau, corroborate the finding that <i>APOE</i> ε4 exacerbates pathology, and suggest that <i>APOE</i> ε2 may protect against αSyn aggregation and neurodegeneration in synucleinopathies.
Pulse Radiolysis of Hexameric Nitrite Reductase Containing Two Type 1 Cu Sites in a Monomer (2008)

Abstract Pulse radiolysis of hexameric nitrite reductase containing the two type 1 Cu sites in a monomer has been carried out. Reduction of the enzyme with N-methylnicotinamide radical follows biphasic kinetics, and the fast and slow phases were assigned to reductions of type 1 CuN and type 1 CuC, respectively.
Spectral Narrowing and Stabilization for Broad-Area Lasers via Modified Delivery Fiber (2015)

A proof-of-concept experiment for fiber-based broad-area laser stabilization is experimentally demonstrated using coupling optics and a 1-nm wide, 98% reflectivity fiber Bragg grating. The output spectrum of a 3-W, 100-μm wide, 2-mm long commercial broad-area laser was narrowed by more than 10× to 0.26-nm full-width half-max. In addition, the system showed 7%-13% enhanced output power. The system also shows potential for slow-axis beam quality improvement in the desired operating regime. A pump delivery fiber scheme is proposed for integration of the diode feedback into a pump system package for enhanced-brightness fiber pumping.
Infrared Ellipsometry - a Novel Tool for Characterization of Group-III Nitride Heterostructures for Optoelectronic Device Applications (2001)

We demonstrate the application of spectroscopic infrared ellipsometry to determine nondestructively the free-carrier distribution in group-III nitride heterostructures, such as for optoelectronic and electronic device applications. Results are shown for a blue-light emitting diode structure based on wurtzite III–N materials grown on (0001) sapphire by metal-organic vapor phase epitaxy.
ChemInform Abstract: New Basic Esters of 2‐Phenyl‐3‐methyl‐4‐oxo‐4H‐1‐benzopyran‐8‐ carboxylic Acid Endowed with Spasmolytic Properties. Synthesis and Pharmacological‐Pharmacokinetic Evaluation. (1993)

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.
Single Perivascular Delivery of Mitomycin C Stimulates p21 Expression and Inhibits Neointima Formation in Rat Arteries (2005)

These studies demonstrate that MMc exerts a potent inhibitory effect on VSMC proliferation and neointima formation after arterial injury. MMc represents a potentially new therapeutic agent in treating and preventing vasculoproliferative disease.
Online Nonlinear System Identification With Parameter Constraints: Application to Automotive Engine Systems (2019)

Abstract In this paper, we treat the problem of online nonlinear system identification with parameter constraints. This approach is based upon our prior work on nonlinear system identification that exploits evolving Spatial-Temporal Filters (STF) to dynamically decompose system’s input/output space into a nonlinear combination of weighted local models. We extend the nonlinear system identification framework with the capability of dealing with linear equality and inequality parameter constraints. We leverage the gradient projection method in the local model parameter estimation process to inherently enforce the parameter constraints while retaining optimality. We apply the proposed algorithm to a turbo-charged gasoline engine system and promising results are demonstrated by experimental data.
Pressure-Pressure Deconvolution Analysis of Multiwell-Interference and Interval-Pressure-Transient Tests (2011)

Summary This paper investigates the use of pressure-pressure (p-p) deconvolution for interpretation of conventional multiwall-interference and wireline-formation-tester (WFT) interval pressure-transient tests (IPTTs). The investigation is limited to interference tests for which only a single source/sink well exists in a single-layer system. It is shown that the recent deconvolution algorithms developed for pressure-rate (p-r) deconvolution based on the same assumptions (i.e., a single source/ sink well) can also be used for performing p-p deconvolution by simply replacing the rate data in p-r deconvolution algorithms by the pressure data recorded at a source/sink location or at one of the observation locations. We apply p-p deconvolution to both synthetic and field-transient test data sets from IPTTs and multiwall-interference tests. Specifically, we investigate the applicability of p-p deconvolution for inconsistent data sets, where wellbore storage and skin may change from one flow period to another one. The results show that the impulse functions deconvolved from p-p deconvolution have signatures for various flow regimes (e.g., radial, spherical, linear) that are similar to from p-r deconvolution except from the pseudosteady-state (pss)-flow regime. Therefore, p-p deconvolution can also be used for model identification in the similar way based on p-r deconvolution algorithms, without requiring the flow-rate information.
An integrated IP/optical approach for efficient access router failure recovery (2004)

We propose and experimentally demonstrate a novel IP/optical integrated architecture to cost effectively recover from access router failures in large ISP networks.
Guaranteed Performance Region in Fading Orthogonal Space-Time Coded Broadcast Channels (2008)

Recently, the capacity region of the MIMO broadcast channel (BC) was completely characterized and duality between MIMO multiple access channel (MAC) and MIMO BC with perfect channel state information (CSI) at transmitter and receiver was established. In this work, we propose a MIMO BC approach in which only information about the channel norm is available at the base and hence no joint beamforming and dirty paper precoding (DPC) can be applied. However, a certain set of individual performances in terms of MSE or zero-outage rates can be guaranteed at any time by applying an orthogonal space-time block code (OSTBC). The guaranteed MSE region without superposition coding is characterized in closed form and the impact of diversity, fading statistics, and number of transmit antennas and receive antennas is analyzed. Finally, six CSI and precoding scenarios with different levels of CSI and precoding are compared numerically in terms of their guaranteed MSE region. Depending on the long-term SNR, superposition coding as well as successive interference cancellation (SIC) with norm feedback performs better than linear precoding with perfect CSI.
Development of Uncertainty Quantification Capability for NESTLE (2017)

This work aims to develop an uncertainty analysis methodology for the propagation and quantification of the effects of nuclear cross-section uncertainties on important core-wide attributes, such as power distribution and core critical eigenvalue. Given the computationally taxing nature of this endeavor, our goal is to develop a methodology capable of preserving the accuracy of brute force sampling techniques for uncertainty quantification while realizing the efficiency of deterministic techniques. To achieve that, a reduced order modeling (ROM) approach is proposed to deal with the enormous size of the uncertainty space, comprising all the cross-section few-group parameters required in core-wide simulation. The idea is to generate a compressed representation of the uncertainty space, as represented by a covariance matrix, that renders sampling techniques computationally a feasible option for quantifying and prioritizing the various sources of uncertainties. While the proposed developments are general to any reactor physics computational sequence, we customize our approach to the NESTLE [1]-TRITON [2] computational sequence, which will serve as a demonstrative tool for the implementation of our approach. NESTLE is a software used for core wide simulation, which relies on the few-group cross-sections to calculate core wide attributes over multiple cycles of depletion. Its input cross-sections are generated using a matrix of conditions evaluated using a lattice physics code, which in our implementation is done using the TRITON software of the ORNL’ SCALE suit. This manuscript presents one of the early steps towards this goal. Specifically, we focus here on the development of the algorithms for determining the reduced dimension of covariance matrix. Numerical experiment using the TRITON software is employed to demonstrate how the reduction is achieved.
Visual Crypto Displays Enabling Secure Communications. (2003)

In this paper we describe a low-tech and user friendly solution for secure twoway communication between two parties over a network of untrusted devices. We present a solution in which displays play a central role. Our approach guarantees privacy and allows to check the authenticity of information presented on displays. Furthermore, we provide the user with a secure return channel. To this end we propose to provide every user with a small decryption display which is, for example, integrated in a credit card and requires very limited computing power. The authentication and security are based on visual cryptography which was first introduced by Naor and Shamir in 1994. We solve some practical shortcomings of traditional visual cryptography and develop protocols for two-way authentication and privacy in untrusted environments.
Supplementary Figure S1 from Induction of Telomere Dysfunction Mediated by the Telomerase Substrate Precursor 6-Thio-2′-Deoxyguanosine (2023)

&lt;p&gt;In vitro cell viability.&lt;/p&gt;
Optical Fiber Delay-Line Signal Processing (1985)

Single-mode optical fiber is an attractive delay medium for processing microwave frequency signals due to its extremely low loss (<0.1 dB/µs) and large available time-bandwidth product (in excess of 10/sup 5/). Recent progress in the efficient tapping of light from single-mode fibers has made it possible to construct recirculating and nonrecirculating (tapped) delay-line structures that can perform a variety of important signal processing functions. These functions include coded sequence generation, convolution, correlation, matrix-vector multiplication, and frequency filtering. This paper presents the fundamental properties of single-mode fiber delay lines and reviews recent experimental results that demonstrate the feasibility of fiber delay-line devices for broad-band signal-processing applications.
A green and black tea extract benefits urological health in men with lower urinary tract symptoms (2014)

Oral administration of AMH improved LUTS and quality of life in as little as 6 weeks.
TY032, a potent opioid agonist/neurokinin 1 antagonist produces analgesia without motor impairment or sedation (2013)

The use of opioids for the treatment of pain has been restricted by their side effects including constipation, somnolence, antinociceptive tolerance, addiction, and respiratory depression. Here, we use an in vivo model of neuropathic pain to characterize TY032, a bifunctional pharmacophore containing both opioid agonist and Neurokinin 1(NK1) antagonist activity. Following spinal nerve ligation (SNL) to induce neuropathic pain in rats, intrathecal ( i.t. ) administration of TY032 produced statistically significant dose dependent antiallodynia to innocuous mechanical stimulation with a peak effect 80 min post‐injection. Similarly, dose dependent antihyperalgesia and analgesia to thermal stimuli were achieved in rats following i.t. administration of TY032, with the peak effect 20 min after injection. Naloxone attenuated the analgesic effect of TY032 in a tail‐flick model of thermal pain. With naloxone on board, i.t. administration of TY032 in mice significantly reduced the average number of flinches during a 5 min period immediately following Substance P administration. Finally, TY032 had no effect on motor impairment or sedation using rotarod. Studies here put forth the idea that a non‐addictive, non‐constipating opioid can and should be made available for both patients suffering from chronic pain and physicians’ uneasiness in prescribing narcotics.
Detection of inflammation/infection with human polyclonal immunoglobulin G labelled with 99Tcm (1994)

Radiolabelled human polyclonal immunoglobulin G (IgG) has been successful in identifying inflammatory/infectious processes in human and animal models. We studied 71 patients with suspicion of inflammation of varied origin and location (44 of musculoskeletal location and 27 other) using 99Tcm. IgG images correctly identified 21/22 inflammatory sites of musculoskeletal origin and only 4/14 sites of soft-tissue location. Five false negative studies corresponded to granulomatous processes, three of them tuberculosis. Four false positive studies were obtained in the musculoskeletal group corresponding to three synovial tumours and a Charcot joint. No false positive results were seen in the soft tissue group. 99Tcm-IgG performs well in the identification of bone-joint lesions and rules out non-inflammatory conditions (with the important exception of tumours). The role of 99Tcm-IgG in soft-tissue inflammatory sites, especially in highly vascular organs is inferior, with a high yield of false negative studies. Granulomatous lesions probably represent situations of low or absent IgG uptake.
Estimation of the Effective Medium for Planar Microstrip Antennas on a Dielectric and Magnetic Truncated Substrate (2012)

This letter proposes a simple formula to estimate the effective medium of planar microstrip antennas printed on a magneto-dielectric truncated substrate. The proposed empirical formulas shown in this letter yield a good accuracy with a maximum error of less than 7% for a permittivity between 1-10, a permeability between 1-10, and a ratio 0.01 <; h/W <; 0.25. These proposed empirical models are validated by electromagnetic simulations and measurements.
Immunomodulatory Therapy of Visceral Leishmaniasis in Human Immunodeficiency Virus-Coinfected Patients (2018)

Patients with visceral leishmaniasis (VL)-human immunodeficiency virus (HIV) coinfection experience increased drug toxicity and treatment failure rates compared to VL patients, with more frequent VL relapse and death. In the era of VL elimination strategies, HIV coinfection is progressively becoming a key challenge, because HIV-coinfected patients respond poorly to conventional VL treatment and play an important role in parasite transmission. With limited chemotherapeutic options and a paucity of novel anti-parasitic drugs, new interventions that target host immunity may offer an effective alternative. In this review, we first summarize current views on how VL immunopathology is significantly affected by HIV coinfection. We then review current clinical and promising preclinical immunomodulatory interventions in the field of VL and discuss how these may operate in the context of a concurrent HIV infection. Caveats are formulated as these interventions may unpredictably impact the delicate balance between boosting of beneficial VL-specific responses and deleterious immune activation/hyperinflammation, activation of latent provirus or increased HIV-susceptibility of target cells. Evidence is lacking to prioritize a target molecule and a more detailed account of the immunological status induced by the coinfection as well as surrogate markers of cure and protection are still required. We do, however, argue that virologically suppressed VL patients with a recovered immune system, in whom effective antiretroviral therapy alone is not able to restore protective immunity, can be considered a relevant target group for an immunomodulatory intervention. Finally, we provide perspectives on the translation of novel theories on synergistic immune cell cross-talk into an effective treatment strategy for VL-HIV-coinfected patients.
Self-alignment structures for heterogeneous 3D integration (2013)

A novel self-alignment technology, called positive self-alignment structures (PSAS), for heterogeneous 3D integration is described. Using a set of precisely reflowed photoresist structures in conjunction with the corresponding inverse pyramid pits, we demonstrate that submicron alignment can be achieved without an advanced placement tool. The positive self-alignment structure technology is fabricated on top of electronics or devices, and as a result, it does not take up additional electronic real estate, and it can be fabricated on any surface, including glass. This enables heterogeneous integration that involves non-silicon substrates, and at the same time simplifies the stacking of three or more chips. This paper describes the self-alignment mechanism, the fabrication of positive self-alignment structures (PSAS), and the test structures to measure the accuracy of alignment; the resulting misalignment on various substrates including glass and unpolished silicon surfaces are reported. In addition, the stacking of five chips is demonstrated and the resulting misalignment at each of the chip-to-chip interfaces is measured and reported.
EUV process establishment through litho and etch for N7 node (2016)

Extreme ultraviolet lithography (EUVL) technology is steadily reaching high volume manufacturing for 16nm half pitch node and beyond. However, some challenges, for example scanner availability and resist performance (resolution, CD uniformity (CDU), LWR, etch behavior and so on) are remaining. Advance EUV patterning on the ASML NXE:3300/ CLEAN TRACK LITHIUS Pro Z- EUV litho cluster is launched at imec, allowing for finer pitch patterns for L/S and CH. Tokyo Electron Ltd. and imec are continuously collabo rating to develop manufacturing quality POR processes for NXE:3300. TEL’s technologies to enhance CDU, defectivity and LWR/LER can improve patterning performance. The patterning is characterized and optimized in both litho and etch for a more complete understanding of the final patterning performance. This paper reports on post-litho CDU improvement by litho process optimization and also post-etch LWR reduction by litho and etch process optimization.