gebhart/patrepeval huggingface dataset:
Clathrate hydrates are poor models of biomolecule hydration (1998)

Clathrate hydrates form the basis of a general model of biomolecule hydration. In clathrate hydrate crystal structures, the size of hydrogen-bonded water rings is highly constrained to five members. The clathrate hydrate model predicts that the size of water rings near biomolecule surfaces is similarly constrained to five members. This report describes a test of this model of biomolecule hydration. We have demonstrated that five-membered water rings are not a general feature of protein or nucleic acid hydration. The clathrate hydrate model appears to be inappropriate for soluble biomolecules.
Pharmacological evaluation of pioglitazone and candesartan cilexetil in a novel mouse model of non‐alcoholic steatohepatitis, modified choline‐deficient, amino acid‐defined diet fed low‐density lipoprotein receptor knockout mice (2016)

Pioglitazone showed anti-fibrotic effects accompanied by improving hepatic transaminase activity and hepatic lipid accumulation, but the effect of candesartan cilexetil was only limited, unlike previous reports for angiotensin II type 1 receptor blockers. As the pharmacological effects of pioglitazone in the current animal model are similar to those reported in patients with NASH, this model may represent some aspects of the pathophysiology of NASH. Further profiling using other agents or mechanisms that have been tested in the clinic will better clarify the utility of the animal model.
Optimal design and experimental verification of a magnetically actuated optical image stabilization system for cameras in mobile phones (2008)

A novel miniaturized optical image stabilizer (OIS) is proposed, which is installed inside the limited inner space of a mobile phone. The relation between the VCM electromagnetic force inside the OIS and the applied voltage is first established via an equivalent circuit and further validated by a finite element model. Various dimensions of the VCMs are optimized by a genetic algorithm (GA) to maximize sensitivities and also achieving high uniformity of the magnetic flux intensity.
Wavelength-tunable optical ring resonators (2017)

Optical ring resonator devices are disclosed that can be used for optical filtering, modulation or switching, or for use as photodetectors or sensors. These devices can be formed as microdisk ring resonators, or as open-ring resonators with an optical waveguide having a width that varies adiabatically. Electrical and mechanical connections to the open-ring resonators are made near a maximum width of the optical waveguide to minimize losses and thereby provide a high resonator Q. The ring resonators can be tuned using an integral electrical heater, or an integral semiconductor junction.
Effects of Cu Addition on Hydrogen Absorption and Diffusion Properties of 1470 MPa Grade Thin-walled Steel in a Solution of HCl (2011)

Hydrogen embrittlement is caused by the introduction of hydrogen into steel and is critical for high strength steels. To clarify the effects of the addition of Cu on the suppression of hydrogen embrittlement in a solution of HCl, hydrogen permeation tests and dynamic polarization measurements were conducted on TS 1470 MPa grade, low-carbon martensite steels. To this end, steels containing 0.19% C, 0.2% Si, 1.3% Mn, Cr, Ti, Nb and B were prepared with and without 0.16% Cu. For comparison, ferrite and pearlite steels were also examined. The results of hydrogen permeation tests indicated that the steady-state hydrogen permeation current (JH) of steel containing 0.16% Cu was considerably lower than that of basic steel in 0.1 N HCl at the corrosion potential. Moreover, the JH of martensite steel was suppressed by the addition of Cu, and the cathode current, (iC) and the JH/iC were reduced. The results obtained in this study corroborated the hypothesis that the 1 or 2-μm metallic Cu particles precipitated on the surface of the steel in a solution of HCl suppressed the cathodic reaction and the introduction of hydrogen. The hydrogen diffusion constant (Deff) was obtained from hydrogen permeation tests under a potential gradient. Cu addition has only small effect on Deff regardless of microstructure. The occupancy of trap site (nX) was estimated to be greater than 99% independent of Cu content and microstructure.
<title>Realization and accuracy of a phase-shifting speckle interferometer for full 3D shape measurement</title> (1996)

In a two-wavelength phase-shifting speckle interferometer for object contouring one usually obtains only the height coordinate of the object surface, which is parallel to the direction of observation. In order to measure the lateral surface coordinates x and y by the same technique the light source is shifted in two directions perpendicular to the optical axis. Two additional phase maps of parallel fringes are generated, which are then used to assign the lateral coordinates x and y to the corresponding pixels of the camera. Nevertheless the intensity distribution of speckle fields seems unfavorable in terms of precision metrology, as interferometers have to rely on a saturable photodetector and an analog-to-digital converter with finite resolution. We calculate the optimum beam ratio, modulation of the camera and lens aperture for a speckle interferometer with maximum phase-measurement accuracy. To obtain the minimum error of 10.6 mrad it is found that the mean speckle intensity ought to be adjusted to be 1/11 times the saturation intensity of the camera, the beam ratio is to be 4 and that the space-bandwidth product must be chosen 0.31. The latter is of particular practical interest, because stopping down the lens increases the need for a high-power laser. The results are valid for all kinds of speckle interferometers and are not restricted to the above- mentioned arrangement. They are confirmed by computer simulation of a two-wavelength speckle interferometer.
Improved pH-Metry and Symptom Scores 3 mo Post-ENTERYX® (2005)

Purpose: To compare pH-metry and GERD-HRQL scores in ENTERYX treated (EG) vs control (CG) groups. Methods: PPI-dependent and responsive pts were randomized to either EG or CG. CG pts underwent endoscopy; DMSO was sprayed on distal esophagus. 3 mo post initial procedure, EG pts w/ GERD-HRQL score >11 (off PPIs) were eligible for retreatment; CG pts who were off PPIs with GERD-HRQL ≥20 and pH<4.0 for >5% of total time were eligible for crossover to ENTERYX. pH-metry success was defined as either total time pH ≤4.0 for ≤5% or total time pH ≤4.0 reduced ≥50% from baseline. GERD-HRQL score success was defined as either a score of ≤11 or an improvement from baseline ≥9 points. Results: Interim 3-mo data were available for 62 pts (31/group). To date, 61% (19/31) of CG pts crossed over and 13% (4/31) of EG pts were retreated. These initial results reflect outcomes from one ENTERYX treatment. Mean change from baseline (CFB) in pH-metry (% total time pH ≤ 4.0) was −4.3% in EG, vs −0.5% in CG (p < 0.05). pH-metry success was achieved by 50% of EG vs 23% of CG (p < 0.05). EG had more patients achieve GERD-HRQL heartburn score success (83% vs 54%, p < 0.05) and had larger mean CFB for GERD-HRQL heartburn (−14.9 vs −9.2, p < 0.05) than the CG. Conclusions: At 3 mo, ENTERYX Procedure significantly improves pH-metry and GERD-HRQL measures vs control. Furthermore, the proportion of pts eligible for retreatment/crossover was lower in the ENTERYX group than in controls, despite similar eligibility criteria. These results confirm the true effect of ENTERYX in the treatment of GERD.
Performance evaluation and trade-offs of optimal back-off misbehavior detection schemes in wireless networks in the presence of interference (2008)

In this work we evaluate the impact of interference caused by concurrent transmissions of neighboring stations on the performance of quickest detection schemes for detection of back-off misbehavior in the IEEE 802.11 MAC. We evaluate the trade-offs that both the adversary and the detector face under
Coupled chromatography-atomic spectrometry for arsenic speciation—a comparative study (1988)

Several methods for the quantitative determination of different forms of arsenic (AsIII, AsV, monomethyl and dimethyl) in a variety of samples are described and compared. In each instance separation is achieved by chromatographic means, using either gas (GC) or high-performance liquid chromatography (HPLC), with detection by atomic spectrometry, namely flame atomic absorption spectrometry (FAAS), flame atomic fluorescence spectrometry (FAFS) and inductively coupled plasma atomic emission spectrometry (ICP-AES). For the GC separation it is necessary to derivatise the As compounds either as the hydrides or as the methylthioglycolates. As the arsenic hydrides can be pre-concentrated using cryogenic trapping, this yields the lowest detection limits. The As species studied can be separated without derivatisation by HPLC but after HPLC separation hydride generation can be used to increase the sensitivity for FAAS, FAFS and ICP-AES. While each technique is best suited to certain applications, the hydride generation-cryogenic trapping-GC-FAAS system is capable of detection at the sub-p.p.b. level (0.22–0.55 ng absolute for different species) and is preferred for low-level As samples. When levels permit, HPLC-hydride generation-FAAS is probably the simplest routine method and HPLC-hydride generation-ICP-AES will probably be preferred for multi-element analysis.
Surface Growth of Soot Particles in Premixed Ethylene/Air Flames (1983)

Abstract The surface growth rate of soot increases steeply with increasing equivalence ratio. We have found that the increased growth rate is accounted for primarily by the increased surface area available for growth rather than by increased concentrations of surface growth species. We have shown that the surface growth species are not depleted by the process of surface growth. Our data suggest that the surface growth seen in our flames can be accounted for primarily by reaction of acetylene with the soot particles.
Outcomes of patients (pts) with de novo metastatic hormone-sensitive prostate cancer (mHSPC) who progressed to metastatic castration-resistant prostate cancer (mCRPC): A post-hoc analysis of the TRUMPET registry. (2023)

e17085 Background: Significant lack of treatment (Tx) intensification is seen in clinical practice for pts with mHSPC until progression to mCRPC. The TRUMPET registry enabled a post-hoc analysis of clinical outcomes in pts with mCRPC, initially diagnosed with de novo mHSPC vs nmHSPC. Methods: TRUMPET, a prospective, observational study of US pts with CRPC, enrolled male adults (03/2015-09/2018) who began first or second-line Tx for M0/M1 CRPC. For this post hoc, pts with M1 CRPC at enrollment initially diagnosed with de novo mHSPC (clinical TNM1 stage) were compared to M1 CRPC pts initially diagnosed with nmHSPC (clinical TNM0 stage). Clinical outcomes (radiographic progression-free survival [rPFS], prostate specific antigen [PSA] progression, time to opiate initiation [OI], mortality) were analysed with Kaplan–Meier and Cox proportional hazards models. An exploratory subanalysis investigated outcomes in de novo mHSPC pts who received Tx intensification (docetaxel or abiraterone) with androgen-deprivation therapy (ADT) as primary Tx prior to mCRPC vs pts who did not. Results: M1 CRPC pts initially diagnosed with de novo mHSPC (n = 199) or nmHSPC (n = 254) were included; median age: 70.0 vs 73.0 years, duration from initial PC diagnosis to baseline mCRPC visit: 1.62 vs 6.72 years, PSA at PC diagnosis: 113.1 vs 10.1 ng/mL, Gleason score: 9.0 vs 8.0, respectively. In the de novo mHSPC and nmHSPC groups, initial CRPC Tx was chemotherapy in 9.0% vs 5.9% of pts, novel hormonal therapy (enzalutamide or abiraterone) in 55.3% vs 59.1%, immunotherapy in 35.2% vs 42.9%, respectively. No differences were seen in rPFS or PSA progression (table). The de novo mHSPC group showed a trend toward shorter time to OI and significantly increased risk of mortality (37%) with 6.6 months shorter median survival vs nmHSPC. The subanalysis included 44 (22.1%) de novo mHSPC pts who received Tx intensification with ADT at initial diagnosis. A trend towards improved survival was seen in the Tx-intensified vs nonintensified subgroup (median time to death [95%CI]; 47.7 months [22.18, NE] vs 37.3 months [28.35, 43.01]). Conclusions: At mCRPC diagnosis, pts with de novo mHSPC have significantly higher mortality risk than pts with nmHSPC, indicating a need to delay progression of de novo mHSPC to mCRPC. The trend for improved survival benefit in pts with Tx-intensified de novo mHSPC further underlines the need for early Tx intensification. [Table: see text]
Comprehensive Peptide Cyclization Examination Yields Optimized APP Scaffolds with Improved Affinity toward Mint2 (2023)

Peptides targeting disease-relevant protein-protein interactions are an attractive class of therapeutics covering the otherwise undruggable space between small molecules and therapeutic proteins. However, peptides generally suffer from poor metabolic stability and low membrane permeability. Hence, peptide cyclization has become a valuable approach to develop linear peptide motifs into metabolically stable and potentially cell-permeable cyclic leads. Furthermore, cyclization of side chains, also known as "stapling", can stabilize particular secondary peptide structures. Here, we demonstrate that a comprehensive examination of cyclization strategies in terms of position, chemistry, and length is a prerequisite for the selection of optimal cyclic peptide scaffolds. Our systematic approach identifies cyclic APP dodecamer peptides targeting the phosphotyrosine binding domain of Mint2 with substantially improved affinity. We show that especially all-hydrocarbon stapling provides improved metabolic stability, a significantly stabilized secondary structure and membrane permeability.
Low Temperature Direct Bonding of InP and Si3N4-Coated Silicon Wafers for Photonic Device Integration (2012)

Low temperature (200°C) direct bonding of InP and Si3N4 coated silicon wafers using oxygen plasma surface treatment has been demonstrated, which transfers InP-based thin films onto Si substrates for heterogeneous photonic integration. Pulling test shows a high bonding energy comparable to the InP fracture energy. The high crystalline quality of the bonded thin film is preserved, as evident from photoluminescence and high resolution X-ray diffraction measurements. Cross-sectional transmission electron microscopy shows an intimately bonded interface with no observable defects generated near the bonded interface. A thin layer of amorphous oxide about 6 nm thick has been detected at the bonded interface. The hydrophilic interface obtained by oxygen plasma activation helps to achieve high quality bonding. Due to the high thermal conductivity of Si3N4, these high quality bonded structures of InP/Si with Si3N4 sandwiched in-between have potential applications in enhancing performance of high power Si photonic integrated devices.
Powerformer/sup TM/-the prototype and beyond (2002)

The general concept of Powerformer/sup TM/, a high voltage generator connected directly to the grid, is described. By using high-voltage cable technology it is possible to confine the electrical field to inside the winding and reach high voltage levels on the generator terminals. The prototype high-voltage generator rated at 45 kV, 11 MVA has been operating since spring 1998. The accumulated operating time is now 3700 hours. Some test results are presented. Contracts for two Powerformer generators have been granted, one turbogenerator rated at 136 kV, 42 MVA and a hydropower generator rated at 155 kV. 75 MVA. Some data and background information for these two units is presented.
The identification and treatment of poor durability Karoo dolerite base course aggregate - evidence from case studies (comment and response) (2016)

Table 1 (referencing COLTO 1998) of the above-mentioned technical paper incorrectly states that the PI shall be < 12 when the PI is determined on the -0.075 mm fraction because -0.425 mm fraction is non-plastic. COLTO requires that the PI of the -0.075 mm fraction shall not exceed 12 without any qualification. If the PI exceeds 12, the material shall be chemically modified. After chemical modification the PI of the -0.075 mm fraction shall not exceed 8. The Technical Committee involved in the COLTO 1998 edition based these criteria.
Investigations of BLER requirements of associated control channels for IP packet transmission in forward link for VSF-OFCDM broadband packet wireless access (2005)

We have investigated experimentally the influence of decoding errors of associated control channels (CCHs) on the achievable packet loss rate (PLR), and the throughput performance of IP packet transmission using a shared forward packet data channel (FPDCH) employing hybrid automatic repeat request (ARQ) with soft combining in the medium access control (MAC) layer for orthogonal frequency and code division multiplexing (OFCDM) broadband wireless access in the forward link. Using broadband base station (BS) and mobile station (MS) transceivers with forward and reverse link channel bandwidths of 100 MHz and 40 MHz, respectively, we applied turbo and convolutional coding to a shared FPDCH and the associated CCHs along with a very short transmission time interval (TTI) of 0.5 msec. Laboratory experiments using hardware fading simulators show that the average block error rate (BLER) of the forward link CCH (FCCH) should be identical to the required PLR of the shared FPDCH for real-time traffic data and be less than approximately 10/sup -2/ for non-real-time traffic data to avoid decreasing the throughput, and that of the reverse link CCH (RCCH) should be less than approximately 10/sup -2/ to avoid an increase in the code channel utilization rate. Furthermore, we validate the laboratory results by field experiments in a real propagation channel, which are conducted in a cellular environment with a cell distance of approximately 1 km at an average speed of 30 km/h.
A Low Molecular Weight Allergen of White Birch <i>(Betula verrucosa</i><i>)</i> Is Highly Homologous to Human Profilin (1991)

Cloning of allergens has contributed substantially to the understanding of mechanisms in allergic diseases by providing information about the sequence and hence biological functions of allergens. The major birch pollen allergen, Bet v I [Breiteneder H, et al: EMBO J 1989;8:1935-1938] and the white-faced hornet venom allergen (antigen 5) [Si Yun Fang K, et al: Proc. Natl. Acad. Sc. USA 1988;85:895-899] were shown to be highly homologous to pathogenesis-related proteins of plants. In the case of the major allergen of house dust mite, Der p I, homology to proteases was demonstrated. Therefore, the proposed biological function of these IgE-binding proteins might be related to their allergenic potential. In this paper we tentatively identify a ubiquitous family of low molecular weight allergens as profilins. The identification is based on a sequence homology, (b) binding to poly(L-proline), and (c) immunological cross-reactivity. Recombinant birch profilin was purified to homogeneity and showed the same properties as natural profilins.
Pseudo Value Network Distillation for High-Performance Exploration (2023)

Solving hard exploration tasks with sparse rewards is notoriously challenging in reinforcement learning (RL), which needs to address two key issues simultaneously: exploiting past successful experiences and exploring the unknown environment. Many prior works take expert demonstrations as successful experiences and learn to imitate them directly. However, these demonstrations are often not available in practice. Recently, curiosity-driven RL methods provide intrinsic rewards, encouraging the agent to explore states with high novelty. Nonetheless, they lack a mechanism for leveraging past good experiences effectively. This work presents a Pseudo Value Network Distillation (PVND) framework to balance the RL agent's exploitative and exploratory behaviors effectively and automatically. In particular, PVND learns to set high exploitation bonuses to the critical states in rewarded trajectories from past experiences and high exploration bonuses to the novel states that agents rarely visit during exploration. We theoretically demonstrate that PVND gives larger positive intrinsic rewards to more critical states. Furthermore, PVND automatically finds meaningful and critical hierarchical sub-tasks for agents to accomplish the final goal progressively. Competitive results in several hard exploration sparse reward problems have verified its effectiveness and efficiency.
Autoimmunity in HLA-DQ8 transgenic mice expressing granulocyte/macrophage-colony stimulating factor in the beta cells of islets of langerhans (2007)

Type 1 diabetes (T1D) is a polygenic autoimmune disease with a strong HLA association particularly, HLA-DQ8. We investigated whether islet-specific expression of granulocyte/macrophage colony-stimulating factor (Ins.GM-CSF) in A Beta degrees.NOD.DQ8 mice (HLA-DQ8 transgenic mice on a NOD background lacking endogenous mouse MHC class II molecules) would predispose to development of spontaneous autoimmune diabetes. A Beta degrees.NOD.DQ8 mice expressing GM-CSF in the pancreatic ss cells (8+ G+) as well as litter mates lacking either HLA-DQ8 (8 - G+) or GM-CSF (8+ G -) or both (8 - G -) exhibited insulitis and sialadenitis of varying degrees. But none of the mice progressed to develop T1D. Other than the marked mononuclear cell infiltration in livers of mice expressing GM-CSF irrespective of HLA-DQ8 expression (8+ G+ or 8 - G+), no other changes were observed in the animals. Thus, we have shown for the first time that expression of HLA-DQ8 in the diabetes-predisposing mileu of NOD genetic background is not sufficient to predispose to development of autoimmune diabetes even when the potent immunostimulatory cytokine, GM-CSF is expressed in the pancreatic islets.
ChemInform Abstract: Syntheses and Structure—Activity Relationships of 5,6,7,8‐Tetrahydro‐5,5,8,8‐tetramethyl‐2‐quinoxaline Derivatives with Retinoic Acid Receptor α Agonistic Activity. (2000)

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.
Visual Auditor: Interactive Visualization for Detection and Summarization of Model Biases (2022)

As machine learning (ML) systems become increasingly widespread, it is necessary to audit these systems for biases prior to their deployment. Recent research has developed algorithms for effectively identifying intersectional bias in the form of interpretable, underperforming subsets (or slices) of the data. However, these solutions and their insights are limited without a tool for visually understanding and interacting with the results of these algorithms. We propose Visual Auditor, an interactive visualization tool for auditing and summarizing model biases. Visual Auditor assists model validation by providing an interpretable overview of intersectional bias (bias that is present when examining populations defined by multiple features), details about relationships between problematic data slices, and a comparison between underperforming and overperforming data slices in a model. Our open-source tool runs directly in both computational notebooks and web browsers, making model auditing accessible and easily integrated into current ML development workflows. An observational user study in collaboration with domain experts at Fiddler AI highlights that our tool can help ML practitioners identify and understand model biases.