gebhart/patrepeval huggingface dataset:
Fig S3 from <i>Frizzled-7</i> Is Required for Wnt Signaling in Gastric Tumors with and Without <i>Apc</i> Mutations (2023)

&lt;p&gt;Figure S3 depicts experimental design, body weight and tissue histology of gp130F/F animals following treatment with vehicle or OMP-18R5.&lt;/p&gt;
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations (2021)

Recently, molecular generation models based on deep learning have attracted significant attention in drug discovery. However, most existing molecular generation models have serious limitations in the context of drug design wherein they do not sufficiently consider the effect of the three-dimensional (3D) structure of the target protein in the generation process. In this study, we developed a new deep learning-based molecular generator, SBMolGen, that integrates a recurrent neural network, a Monte Carlo tree search, and docking simulations. The results of an evaluation using four target proteins (two kinases and two G protein-coupled receptors) showed that the generated molecules had a better binding affinity score (docking score) than the known active compounds, and the generated molecules possessed a broader chemical space distribution. SBMolGen not only generates novel binding active molecules but also presents 3D docking poses with target proteins, which will be useful in subsequent drug design. The code is available at https://github.com/clinfo/SBMolGen.
The development and validation of a GC-MS method for the quantification of glycolaldehyde formed from carbohydrate fragmentation processes (2020)

Glycolaldehyde is a small sugar-like molecule that is readily formed by the thermochemical fragmentation of carbohydrates and it has similar physico-chemical properties to sugars.
Homogeneous and heterogeneous chemistry of atmospheric species: Progress report covering the period 1 March 1984 through 31 December 1984 (1985)

Our overall plan is (1) to continue our investigation of the homogeneous and heterogeneous interactions among water vapor, nitrogen dioxide, and sulfur dioxide by the methods developed previously with DOE support and (2) to attack the difficult measurement of the reaction rate constant for the reaction of methoxy radicals with oxygen. Experimental investigation of radical-radical disproportionation reactions will begin when the first two studies have been concluded.
The charge order transition and elastic/anelastic properties of LiMn2O4 (2003)

We studied the charge ordering transition of LiMn2O4 by means of anelastic spectroscopy, measuring the Young’s modulus, E′, and the elastic energy loss function, Q−1. Our measurements confirm the occurrence of a phase transition at 296 K on cooling, showing a large hysteresis on heating. The anelastic spectroscopy results also indicate that the transformation is characterized by the coexistence of two phases. The shape of the real part of the Young’s modulus seems to indicate that the elastic constant which is more strongly affected by the transition is c44, like in the case of Fe3O4. The time evolution of E′ in the coexistence region was measured. The characteristic time, τ, of this evolution rapidly decreases from 296 to 290 K and then increases on further cooling. This behaviour of τ can possibly be related to the temperature dependence of E′. The absolute value of the Young’s modulus of LiMn2O4 obtained considering the effect of the porosity of the sample was estimated to be of the order of 10 GPa. Finally a new thermally activated peak, centred around 100 K at a measurement frequency of ∼1 kHz, has been observed, which cannot be described by the Debye or Fuoss–Kirkwood model. This relaxation may be ascribed to the stress-induced jumps of charges from Mn3+ to Mn4+ sites, similarly to an analogous process found in Fe3O4, or to possible small movements of the octahedra and tetrahedra composing the crystal structure.
Two regions of homozygous deletion clusters at chromosome band 9p21 in human lung cancer (2000)

We examined 149 lung cancer cell lines for homozygous deletions using 24 DNA markers, which were mapped and ordered in chromosome band 9p21, to define the target regions for 9p21 deletions in human lung cancer. Homozygous deletions were detected in 39 (26%) cell lines and clustered at 2 independent regions. One was the region containing the p16/CDKN2A tumor suppressor gene, and this region was deleted in 32 (21%) cell lines. The other was the region containing D9S171, which is the locus approximately 3 Mb proximal to the CDKN2A locus. This region, designated as the D9S171 region, was deleted in 18 (12%) cell lines. Seven of the 18 cell lines had identical minimum deletions of a 17,036 bp sequence located 20 kb distal to the D9S171 locus. However, such a deletion was also observed in the corresponding B-lymphoblastoid cell line from 1 of the 7 cell lines and in 5 (16%) of 32 noncancerous tissues, suggesting that the deletion was a genetic polymorphism. By considering this polymorphism, 11 (7%) cell lines still had deletions at the D9S171 region. Two NSCLC cell lines showed deletions at the D9S171 region and retentions of the CDKN2A locus. Furthermore, an NSCLC cell line showed discontinuous deletions including either the CDKN2A or D9S171 locus. Therefore, the region surrounding the D9S171 locus was defined as another target region for the 9p21 deletions. It is possible that unknown tumor suppressor gene(s) are present in this chromosomal region. Genes Chromosomes Cancer 27:308–318, 2000. © 2000 Wiley-Liss, Inc.
Diphenyl Furans and Aza Analogs: Effects of Structural Modification on In Vitro Activity, DNA Binding, and Accumulation and Distribution in Trypanosomes (2007)

Human African trypanosomiasis is a devastating disease with only a few treatment options, including pentamidine. Diamidine compounds such as pentamidine, DB75, and DB820 are potent antitrypanosomal compounds. Previous investigations have shown that diamidines accumulate to high concentrations in trypanosomes. However, the mechanism of action of this class of compounds remains unknown. A long-hypothesized mechanism of action has been binding to DNA and interference with DNA-associated enzymes. The fluorescent diamidines, DB75 and DB820, have been shown to localize not only in the DNA-containing nucleus and kinetoplast of trypanosomes but also to the acidocalcisomes. Here we investigate two series of analogs of DB75 and DB820 with various levels of in vitro antitrypanosomal activity to determine whether any correlation exists between trypanosome accumulation, distribution, and in vitro activity. Despite wide ranges of in vitro antitrypanosomal activity, all of the compounds investigated accumulated to millimolar concentrations in trypanosomes over a period of 8 h. Interestingly, some of the less potent compounds accumulated to concentrations much higher than those of more potent compounds. All of the compounds were localized to the DNA-containing nucleus and/or kinetoplast, and many were also found in the acidocalcisomes. Accumulation in the nucleus and kinetoplast should be important to the mechanism of action of these compounds. The acidocalcisomes may also play a role in the mechanism of action of these compounds. This investigation suggests that the extent of accumulation alone is not responsible for killing trypanosomes and that organelle-specific accumulation may not predict in vitro activity.
Ciudad y Música (1996)

Recent studies have shown that various tumor cells accumulate ubiquitin (Ub)-conjugated proteins, the profiles of which differ from those of normal cells. To identify the Ub-conjugated proteins accumulated specifically by human carcinoma cells, a two-dimensional immunoblot analysis of 31 surgically resected human primary colorectal carcinoma tissues was performed using an anti-Ub monoclonal antibody, KM691. Two distinct Mr 42,000 and 45,000 proteins in the Triton X-insoluble fractions of carcinoma tissues reacted with this antibody, whereas only one Mr 45,000 protein reacted in normal tissues. The Mr 42,000 Ub-conjugated proteins were specific to carcinoma tissues from 25 patients (80.6%). One of the purified Mr 42,000 proteins was digested with Achromobacter protease I. This protein was identified as a cytokeratin 8 (CK 8) fragment based on both molecular mass determination and molecular mass searching of Achromobacter protease I-digested fragments of proteins registered in a protein sequence data base. Two-dimensional immunoblot analysis with an anti-CK 8 antibody confirmed that all of the Mr 42,000 proteins were CK 8 degradation products. These results demonstrate that human colorectal carcinomas specifically accumulate Mr 42,000 Ub-conjugated CK 8 fragments. This accumulation was observed frequently not only in advanced (18/22, 81.8%), but also in early stage cases (7/9, 77.8%), suggesting that it occurs even in the early stages of colorectal carcinoma progression.
Validity of the Alarm Point in Intraoperative Neurophysiological Monitoring of the Spinal Cord by the Monitoring Working Group of the Japanese Society for Spine Surgery and Related Research (2021)

The alarm point of IONM by the Monitoring WG of the JSSR appeared to be valid for each disease in Group HR. Meanwhile, applying the JSSR alarm point for Group C potentially needed attention.Level of Evidence: 3.
Functional Dendritic Macromolecules: Preparation and Optical Properties (1997)

Abstract Repetitive coupling reactions of branched azobenzene derivatives resulted in dendritic macromolecules, or “wedges” and “dendrimers”. These molecules were designed to incorporate aliphatic and polar units in order to prepare Langmuir-Blodgett (LB) films. Atomic force microscopy (AFM), absorption spectroscopy, and second harmonic generation (SHG) measurements revealed structural properties of the LB films in terms of size, aggregation, and orientation. AFM measurements revealed that growth of the branches increased as a function of the generation. In absorption spectroscopy and SHG measurements, results showed that wedges had an unsymmetric orientation in the LB films, while dendrimers had a symmetrically functionalized structure.
Motion analysis during piano playing using inertial sensors (2022)

In recent years, MIDI data has been used mainly in piano education. However, MIDI data does not contain information on the player's hand movements. Therefore, the purpose of this study was to clarify the movements required for more skillful performance by using a measurement system with inertial sensors that have fewer spatial constraints. In this study, tremolo, a piano playing technique in which two notes separated by the little finger and thumb are quickly repeated alternately, was taken up as a measurement movement, and the movements of three subjects were measured and their skills were evaluated. As a result of breaking down the tremolo into cycles, the number of cycles per second tended to be larger for subjects with longer piano experience. It was found that in order to perform the tremolo required to play a piece of music, it is important to minimize finger movements and use mainly the elbow and shoulder joints, and that synchronized internal and external rotation of the shoulders and flexion and extension of the elbows enable faster tremolo performance.
High quality interpoly dielectrics deposited on the nitrided-polysilicon for nonvolatile memory devices (2002)

In this study, a NH/sub 3/ with RTA N/sub 2/O process to incorporate nitrogen at dielectric/polysilicon interface has demonstrated an improvement in the integrity of the polyoxide. The polyoxide deposited on these nitrided polysilicon films with the additional N/sub 2/O densification on TEOS exhibits a lower leakage current, higher electric breakdown field, higher electron barrier height, lower electron trapping rate, and much higher charge-to-breakdown than the as-deposited polyoxide. SIMS result shows the incorporation of nitrogen at the polyoxide/poly-1 interface, which improves electrical properties in return. Polyoxides formed by this method can achieve a high breakdown field up to 19 MV/cm and charge-to-breakdown more than 20 C/cm/sup 2/. This process appears to be a very attractive alternative for conventional polyoxides.
A novel molecular approach to modeling phase change in micro-fluidic systems (2004)

The dimensions and time-scales of operation encountered in micro-fluidic systems often require that the fluid behavior is considered and analyzed over a wide range of pressures and temperatures. Such wide ranges of conditions are often inherent in systems where the fluid changes phase. The accurate prediction of phase change and its impact on the thermal and mechanical behavior of a system is critical for many engineering applications. This study demonstrates that fluid behavior can be modeled, including phase change prediction, over wide ranges of conditions using compact expressions that are consistent with molecular behavior analyses. The proposed approach is applied to model the phase change and the fluid ejection in a thermally-driven fluid micro-ejector. The operation of the ejector is analyzed through several phases, starting with a simple heating pulse model, followed by fluid superheating and bubble formation, and finally through droplet ejection and bubble collapse.
An application of a constrained adaptive lattice-structure allpass-based notch filter for advanced control of surface-mounted permanent-magnet synchronous drives (1999)

A constrained adaptive lattice-structure allpass-based notch filter provides minimal phase delay and complete attenuation of the notch frequency. The allpass sections of the filter are realized as structurally lossless bounded real functions, with a minimum number of delay elements and multipliers. The filter structure admits orthogonal tuning of the notch frequency and notch bandwidth. An improved control scheme for surface-mounted permanent-magnet synchronous (SMPMS) drives ensures stable high-performance operation in the Bur weakening region, utilizing the over-modulation and six-step modes of the space vector modulation (SVM). An automatic transition into the flux weakening region is achieved by controlling the reference voltage magnitude. The fifth and seventh stator current harmonics of the fundamental frequency, generated in the over-modulation and six-step modes, propagate through the current control loops, resulting in the sixth harmonic in the reference voltage for the flux weakening loop and deteriorating drive performance. To properly filter the sixth harmonic over the extended speed range of the drive, the constrained adaptive lattice-structure allpass-based notch filter is employed.
Chiral salen manganese complex encapsulated within zeolite Y: a heterogeneous enantioselective catalyst for the epoxidation of alkenes (1997)

A chiral (salen)Mn III complex [salen: trans-(R,R)-1,2-bis(salicylideneamino)cyclohexane] analogous to Jacobsen’s catalyst is prepared inside the supercages of zeolite Y, showing catalytic activity very similar to that of the chloride complex in the homogeneous phase.
Distinct Structural Requirements for Interleukin-4 (IL-4) and IL-13 Binding to the Shared IL-13 Receptor Facilitate Cellular Tuning of Cytokine Responsiveness (2009)

Both interleukin-4 (IL-4) and IL-13 can bind to the shared receptor composed of the IL-4 receptor alpha chain and the IL-13 receptor alpha1 chain (IL-13Ralpha1); however, the mechanisms by which these ligands bind to the receptor chains are different, enabling the principal functions of these ligands to be different. We have previously shown that the N-terminal Ig-like domain in IL-13Ralpha1, called the D1 domain, is the specific and critical binding unit for IL-13. However, it has still remained obscure which amino acid has specific binding capacity to IL-13 and why the D1 domain acts as the binding site for IL-13, but not IL-4. To address these questions, in this study we performed mutational analyses for the D1 domain, combining the structural data to identify the amino acids critical for binding to IL-13. Mutations of Lys-76, Lys-77, or Ile-78 in c' strand in which the crystal structure showed interaction with IL-13, and those of Trp-65 and Ala-79 adjacent to the interacting site, resulted in significant impairment of IL-13 binding, demonstrating that these amino acids generate the binding site. Furthermore, mutations of Val-35, Leu-38, or Val-42 at the N-terminal beta-strand also resulted in loss of IL-13 binding, probably from decreased structural stability. None of the mutations employed here affected IL-4 binding. These results demonstrate that the D1 domain of IL-13Ralpha1 acts as an affinity converter, through direct cytokine interactions, that allows the shared receptor to respond differentially to IL-4 and IL-13.
Partitioning and Assignment Exploration for Multiple Modes of IEEE 802.11n Modem on Heterogeneous MPSoC Platforms (2012)

With the advent of heterogeneous MPSoC platform architecture based implementations for the IEEE 802.11n PHY processing, system partitioning and assignment (P&A) have become a key challenge. In this paper we have analyzed the area and energy trade-offs across different P&A schemes for the 4×4 and the 2×2 MIMO 40MHz modes of 802.11n. We have considered the payload processing part of the inner-modem processing for 802.11n PHY. We also present a framework for systematically carrying out the P&A exploration. We show that by exploiting parallelism at different levels, the energy can be reduced with negligible area overheads, by about 40% and 15% for the 4×4 and 2×2 modes, respectively. We also show that the P&A schemes with fine-grained partitioning are more energy efficient for mapping both the modes together on the same platform.
Mediating effect of soluble B-cell activation immune markers on the association between anthropometric and lifestyle factors and lymphoma development (2020)

Sustained B-cell activation is an important mechanism contributing to B-cell lymphoma (BCL). We aimed to validate four previously reported B-cell activation markers predictive of BCL risk (sCD23, sCD27, sCD30, and CXCL13) and to examine their possible mediating effects on the association between anthropometric and lifestyle factors and major BCL subtypes. Pre-diagnostic serum levels were measured for 517 BCL cases and 525 controls in a nested case-control study. The odds ratios of BCL were 6.2 in the highest versus lowest quartile for sCD23, 2.6 for sCD30, 4.2 for sCD27, and 2.6 for CXCL13. Higher levels of all markers were associated with increased risk of chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and diffuse large B-cell lymphoma (DLBCL). Following mutual adjustment for the other immune markers, sCD23 remained associated with all subtypes and CXCL13 with FL and DLBCL. The associations of sCD23 with CLL and DLBCL and CXCL13 with DLBCL persisted among cases sampled > 9 years before diagnosis. sCD23 showed a good predictive ability (area under the curve = 0.80) for CLL, in particular among older, male participants. sCD23 and CXCL13 showed a mediating effect between body mass index (positive) and DLBCL risk, while CXCL13 contributed to the association between physical activity (inverse) and DLBCL. Our data suggest a role of B-cell activation in BCL development and a mediating role of the immune system for lifestyle factors.
Suppression of Dimpling in Sheet Metal Parts Formed on Discrete Tooling (2006)

Discrete-element reconfigurable tools are attractive for some low-volume metal forming processes. However, the use of these “pin” dies, where the ends of the pins are hemispherically shaped, can cause unacceptable dimpling of the finished parts. Thus, polymeric interpolators are used between the die and the part to suppress dimpling. This paper presents the results of experiments performed to characterize the dimpling process and to establish the requirements for useful interpolator materials.
Reducing RFID Reader Load with the Meet-in-the-Middle Strategy. (2009)

In almost any RFID system, a reader needs to identify, and optionally authenticate, a multitude of tags. If each tag has a unique secret, identification and authentication are trivial, however, the reader (or a back-end server) needs to perform a brute-force search for each tagreader interaction. In this paper, we suggest a simple, efficient and secure technique that reduces reader computation to O ( √ N · log N). Our technique is based on the well-known “meet-in-themiddle” strategy used in the past to attack certain symmetric ciphers. Keywords: RFID Identification, Authentication, Meet-in-the-Middle Strategy, PRF. 1
The effects of fluorine passivation on polysilicon thin-film transistors (1994)

The fluorine implantation on polysilicon was found to improve the characteristics of polysilicon thin-film transistors (TFT's). The fluorine passivates the trap states within the polysilicon channel, as compared with the H/sub 2/-plasma passivation. The fluorine implantation passivates more uniformly both the band tail-states and midgap deep-state, while the H/sub 2/-plasma treatment is more effective to passivate deep states than tail states. A fluorine-implanted device can be further improved its performance if an H/sub 2/-plasma treatment is applied. In contrast to the H/sub 2/-plasma passivation, the fluorine passivation improves the device hot-carrier immunity. Combining the fluorine passivation and H/sub 2/-plasma passivation, a high performance TFT with a high hot-carrier immunity can be obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>