gebhart/patrepeval huggingface dataset:
The Sequence of Amino Acids in the Vicinity of the Active Serine Residue of Porcine Trypsin (1965)

Porcine trypsin has been shown to be very similar to bovine trypsin with respect to gross physical and chemical properties despite the fact that they differ significantly in composition (I-3).These two proteins thus afford a unique opportunity for making a detailed comparison of those structural features that are directly involved in the catalytic function of these enzymes.The inhibition of trypsin and other animal proteases or esterases by diisopropyl phosphofluoridate is accompanied by the phosphorylation of a single serine residue which is believed to be an important component of the active site of these enzymes (4).We wish to report here the sequence of amino acids in the vicinity of the active serine residue of porcine trypsin for the purpose of comparing it with the known sequence of bovine trypsin.The finding that an identical sequence of 13 amino acids is present in this region of the molecule of both enzymes suggests that this particular sequence may be of functional importance in the catalytic mechanism of trypsin.EXPERIMENTAL PROCEDURE Preparation of Enzyme Digests Preparation of Oxidized DP*Pl-trypsins-Twice crystallized porcine trypsin was prepared as described in a previous paper (3).Twice crystallized bovine trypsin was a commercial product purchased from Worthington Biochemical Corporation.The oxidized D13*P-derivatives of these enzymes were prepared by following the procedure described by Dixon, Kauffman, and Neurath (5).The DF3*P was a product of New England Nuclear Corporation with a specific activity of 200 MC per mg when prepared by the manufacturer.Digestion of Oxidized DP*P-trypsinsoxidized preparations of pork and beef DP*P-trypsin were digested with bovine trypsin in essentially the same manner as described by Dixon et al. (5).Digests were also prepared in which 10 mg of crystalline (Ychymotrypsin (Worthington) were added to 500 mg of oxidized * Paper No.
A 190-210GHz Power Amplifier with 17.7-18.5dBm Output Power and 6.9-8.5% PAE (2021)

We report a high-efficiency G-band power amplifier in 250nm InP HBT technology. The amplifier has four capacitively linearized common base stages. Four power cells are combined by a low loss 4:1 corporate combiner. The drivers are scaled to sustain high power-added efficiency (PAE). At 202GHz operation, the amplifier has 18.3dBm saturated output power with 7.9% PAE. Over 190-210GHz, the amplifier's output power at 1dB gain compression (OP <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</inf> ) is 16-17.4dBm with an associated 4.7-6.4%PAE and 17.9-23.1dB gain. The peak small signal gain is 23.5dB at 204GHz with more than 20.5GHz 3dB bandwidth. The amplifier has a low DC power consumption of 814mW and a compact area of 1.2mm×0.95mm. To the authors' knowledge, this result demonstrates a record PAE at OP <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</inf> .
Using Aurora Road Network Modeler for Active Traffic Management (2010)

Active Traffic Management (ATM) is the ability to dynamically manage recurrent and nonrecurrent congestion based on prevailing traffic conditions. Focusing on trip reliability, it maximizes the effectiveness and efficiency of freeway corridors. ATM relies on fast and trustworthy traffic simulation software that can assess a large number of control strategies for a given road network, given various scenarios, in a matter of minutes. Effective traffic density estimation is crucial for the successful deployment of feedback algorithms for congestion control. Aurora Road Network Modeler (RNM) is an open-source macrosimulation tool set for operational planning and management of freeway corridors. Aurora RNM employs Cell Transmission Model (CTM) for road networks extended to support multiple vehicle classes. It allows dynamic filtering of measurement data coming from traffic sensors for the estimation of traffic density. In this capacity, it can be used for detection of faulty sensors. The virtual sensor infrastructure of Aurora RNM serves as an interface to the real world measurement devices, as well as a simulation of such measurement devices.
Characteristics of Ruthenium Films Prepared by Chemical Vapor Deposition Using Bis(ethylcyclopentadienyl)ruthenium Precursor (2002)

We prepared ruthenium thin films by chemical vapor deposition using a liquid bis(ethylcyclopentadienyl)ruthenium precursor in an oxidizing atmosphere, and then investigated the electrical resistivity, thermal stability, and conformality of these films. As a result of amorphous partly forming in the ruthenium film, the electrical resistivity increased with increasing growth temperature and ratio, However, the partial oxides did not affect the intrinsic transport mechanism of electrical conduction. In addition, no change in the morphology of the ruthenium film was observed after heat-treatment at 700°C, even when the partial oxides remained in the as-deposited ruthenium films. Precise control of the growth conditions enabled fabrication of conformal ruthenium electrodes. For example, using a low ratio of 1.3% and a low growth temperature of 230°C or less resulted in excellent step coverage of almost 100%. © 2001 The Electrochemical Society. All rights reserved.
The performance of silver modified tungsten oxide for the removal of 2-CP and 2-NP in sunlight exposure: Optical, electrochemical and photocatalytic properties (2015)

The optical and electrochemical characterization of the synthesized Ag+ modified WO3 photocatalysts was performed and its photocatalytic activity was estimated in the visible region (420–800 nm) of sunlight for the degradation of 2-chloro and 2-nitrophenol. The catalysts with the varying loading of Ag+ ranging from 0.5% to 10%, exhibited significantly higher activity as compared to pure WO3. Attempts were made to correlate the enhanced activity of Ag+ loaded catalysts with the optical and electrochemical properties. At lower loading (up to 1% Ag+), the enhanced degradation was attributed to the excited electron trap and transfer ability of surface mounted Ag+ species, while the synergic effect between the WO3 support and surface Ag2O resulted the same at higher loadings. The electrochemical properties of the synthesized powders, in comparison with pure WO3, also supported the same findings. The identification of the intermediates and the estimation of the released anions evidenced the contribution of both hydroxyl radicals (HO) and superoxide anion (O2−) radicals in the degradation process. The identification of aliphatic oxygenates as majority intermediates and release of respective ions verified the replacement of Cl− and NO2 groups, insertion of oxygen and aromatic ring cleavage.
Automated Detection of Toxigenic Clostridium difficile in Clinical Samples: Isothermal tcdB Amplification Coupled to Array-Based Detection (2012)

Clostridium difficile can carry a genetically variable pathogenicity locus (PaLoc), which encodes clostridial toxins A and B. In hospitals and in the community at large, this organism is increasingly identified as a pathogen. To develop a diagnostic test that combines the strengths of immunoassays (cost) and DNA amplification assays (sensitivity/specificity), we targeted a genetically stable PaLoc region, amplifying tcdB sequences and detecting them by hybridization capture. The assay employs a hot-start isothermal method coupled to a multiplexed chip-based readout, creating a manual assay that detects toxigenic C. difficile with high sensitivity and specificity within 1 h. Assay automation on an electromechanical instrument produced an analytical sensitivity of 10 CFU (95% probability of detection) of C. difficile in fecal samples, along with discrimination against other enteric bacteria. To verify automated assay function, 130 patient samples were tested: 31/32 positive samples (97% sensitive; 95% confidence interval [CI], 82 to 99%) and 98/98 negative samples (100% specific; 95% CI, 95 to 100%) were scored correctly. Large-scale clinical studies are now planned to determine clinical sensitivity and specificity.
Application of Metabolite-Responsive Biosensors for Plant Natural Products Biosynthesis (2023)

Plant natural products (PNPs) have shown various pharmaceutical activities, possessing great potential in global markets. Microbial cell factories (MCFs) provide an economical and sustainable alternative for the synthesis of valuable PNPs compared with traditional approaches. However, the heterologous synthetic pathways always lack native regulatory systems, bringing extra burden to PNPs production. To overcome the challenges, biosensors have been exploited and engineered as powerful tools for establishing artificial regulatory networks to control enzyme expression in response to environments. Here, we reviewed the recent progress involved in the application of biosensors that are responsive to PNPs and their precursors. Specifically, the key roles these biosensors played in PNP synthesis pathways, including isoprenoids, flavonoids, stilbenoids and alkaloids, were discussed in detail.
Endometrial Cancer in Reproductive Age: Fertility-Sparing Approach and Reproductive Outcomes (2022)

Endometrial cancer is the most common gynecologic malignancy in developed countries and approximately 7% of the women with endometrial cancer are below the age of 45. Management of endometrial cancer in young women who desire to maintain fertility presents a unique set of challenges since the standard surgical treatment based on hysterectomy and salpingo-oophorectomy is often not compatible with the patient's goals. A fertility-preserving approach can be considered in selected patients with early stage and low-grade endometrial cancer. An increasing amount of data suggest that oncologic outcomes are not compromised if a conservative approach is utilized with close monitoring until childbearing is completed. If a fertility-preserving approach is not possible, assisted reproductive technologies can assist patients in achieving their fertility goals.
Synthesis and 12-Helical Secondary Structure of β-Peptides Containing (2R,3R)-Aminoproline (2002)

[structure: see text] (2R,3R)-Aminoproline, a pyrrolidine-based beta-amino acid, was synthesized and incorporated into hexa-beta-peptide 4. This residue confers water solubility when the ring nitrogen is protonated and allows for 12-helix formation in aqueous solution. Circular dichroism spectra display the 12-helical signature, and 12-helical structure was confirmed by 2D NMR analysis.
Antagonistic Analogs of Oxytocin with Substituted Phenylalanine or Tyrosine in Position 2 (1994)

Solid phase method on p-methylbenzhydrylamine resin was used for the synthesis of seven analogs of oxytocin with non-coded amino acids in position 2. [L-Phe(4-Me) 2 ]oxytocin ( I ), [D-Phe(4-Me) 2 ]oxytocin ( II ), [L-Phe(2-Me,4-Et) 2 ]oxytocin ( III ), [D-Phe(2-Me,4-Et) 2 ]oxytocin ( IV ), [D-Tyr(Me) 2 ]oxytocin ( V ), [D-Tyr(Et) 2 ]oxytocin ( VI ) and [L-Tyr(2-Me) 2 ]oxytocin ( VII ) were synthesized. All analogs with D-stereoisomer of alkyl or alkoxy substituted phenylalanine possess uterus in vitro inhibiting activity. In the case of L-stereoisomers the structure activity relationship is more complicated. As far as the pressor activity is concerned, the analogs have either very low agonistic activity or low degree of antagonism.
1,3,8-Triazaspiro[4.5]decane-2,4-diones as Efficacious Pan-Inhibitors of Hypoxia-Inducible Factor Prolyl Hydroxylase 1–3 (HIF PHD1–3) for the Treatment of Anemia (2012)

The discovery of 1,3,8-triazaspiro[4.5]decane-2,4-diones (spirohydantoins) as a structural class of pan-inhibitors of the prolyl hydroxylase (PHD) family of enzymes for the treatment of anemia is described. The initial hit class, spirooxindoles, was identified through affinity selection mass spectrometry (AS-MS) and optimized for PHD2 inhibition and optimal PK/PD profile (short-acting PHDi inhibitors). 1,3,8-Triazaspiro[4.5]decane-2,4-diones (spirohydantoins) were optimized as an advanced lead class derived from the original spiroindole hit. A new set of general conditions for C-N coupling, developed using a high-throughput experimentation (HTE) technique, enabled a full SAR analysis of the spirohydantoins. This rapid and directed SAR exploration has resulted in the first reported examples of hydantoin derivatives with good PK in preclinical species. Potassium channel off-target activity (hERG) was successfully eliminated through the systematic introduction of acidic functionality to the molecular structure. Undesired upregulation of alanine aminotransferese (ALT) liver enzymes was mitigated and a robust on-/off-target margin was achieved. Spirohydantoins represent a class of highly efficacious, short-acting PHD1-3 inhibitors causing a robust erythropoietin (EPO) upregulation in vivo in multiple preclinical species. This profile deems spirohydantoins as attractive short-acting PHDi inhibitors with the potential for treatment of anemia.
A fiber-optic nanoplasmonic hydrogen sensor via pattern-transfer of nanofabricated PdAu alloy nanostructures (2018)

We demonstrate the transfer of arrays of nanofabricated noble metal and alloy nanostructures obtained by high-temperature annealing on a flat parent support onto optical fibers, to create a hysteresis-free fiber optic nanoplasmonic hydrogen sensor. This work enables the integration of complex nanofabricated structures and their arrangements in tailored arrays with fiber optics to realize optical sensors, which will find application in a wide range of disciplines.
A Benchmark for 3D Mesh Watermarking (2010)

This paper presents a benchmarking system for the evaluation of robust mesh watermarking methods. The proposed benchmark has three different components: a ''standard'' mesh model collection, a software tool and two application-oriented evaluation protocols. The software tool integrates both geometric and perceptual measurements of the distortion induced by watermark embedding, and also the implementation of a variety of attacks on watermarked meshes. The two evaluation protocols define the main steps to follow when conducting the evaluation experiments. The efficiency of the benchmark is demonstrated through the evaluation and comparison of two recent robust algorithms.
Exploiting the frame coherence in visibility for walk/fly-through (1996)

The paper is concerned with the efficient generation of graphic images by exploiting the frame coherence in visibility to minimize polygon flow. The basic idea is to manage the visible polygon set (VPS) somewhat loosely, thereby reducing the computation effort considerably, while maintaining the quality of the rendered image reasonably high. Our method executes the culling-prediction-interpolation-rendering loop repeatedly, in an intelligent fashion. It calculates the exact visible polygons for two frames; one for the current view and the other for the predicted view after some frames. The in-between frames can be rendered from those polygons that belong to the two extreme frames. Furthermore, our algorithm regulates the frame rate to the desired target frame rate by controlling the number of the in-between frames. As our algorithm needs to calculate the visible polygons for the key frames, any other culling algorithms can be easily used with our algorithm in this part.
Application Layer Forward Error Correction for Mobile Multimedia Broadcasting (2008)

Application Layer Forward Error Correction (AL-FEC) is an innovative way to provide reliability in mobile broadcast systems. Conventional data such as multimedia files or multimedia streams are extended with repair information that can be used to recover lost data at the receiver. AL-FEC is integrated into content delivery protocols (CDPs) to support reliable delivery. Several standardization committees such as 3GPP and DVB have recognized the importance of AL-FEC and have standardized Raptor codes as the most powerful AL-FEC codes to be used for such applications. The major characteristics of Raptor codes are channel efficiency, low complexity, and flexibility. An important consideration when using AL-FEC is system integration. With the right system design including AL-FEC, the efficiency or quality of delivery services can be significantly enhanced. This work shows these benefits in selected use cases, specifically focusing on 3G-based multimedia broadcasting within the MBMS standard.
A Comparison of Structural and Mechanical Properties of Tubularized and Native Semitendinosus Graft (2010)

Background: The semitendinosus tendon has a broad and thin length of aponeurosis. Tubularizing this portion of the graft converts it into a cylindrical structure, which may have implications for graft fixation. Hypothesis: A tubularized semitendinosus tendon will demonstrate a higher tensile load to failure and increased stiffness compared with its native form. Study Design: Controlled laboratory study. Methods: Twenty cadaveric paired semitendinosus specimens were used. Ten served as the control group; the other 10 underwent tubularization along the length of the aponeurosis. All testing was performed on the MTS 858 Mini Bionix II. Outcome measures included cross-sectional area, stress, stiffness, and peak load to failure. Results: The nontubularized tendons had a higher peak tensile load to failure (mean 1112.6 ± 345.0 N) than the tubularized tendons (mean 711.4 ± 228.7 N, P = .007). The nontubularized specimens also had a higher stiffness (213.0 ± 37.2 N) than the tabularized group (144.9 ± 44.8 N, P = .002). Conclusion: Tubularization of the semitendinosus graft weakens its structural and mechanical properties. Clinical Relevance: On the basis of the results of this study, we do not tubularize the semitendinosus graft in ACL reconstruction because of weakened structural and mechanical properties.
A conserved eEF2 coding variant in SCA26 leads to loss of translational fidelity and increased susceptibility to proteostatic insult (2012)

The autosomal dominant spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of disorders exhibiting cerebellar atrophy and Purkinje cell degeneration whose subtypes arise from 31 distinct genetic loci. Our group previously published the locus for SCA26 on chromosome 19p13.3. In this study, we performed targeted deep sequencing of the critical interval in order to identify candidate causative variants in individuals from the SCA26 family. We identified a single variant that co-segregates with the disease phenotype that produces a single amino acid substitution in eukaryotic elongation factor 2. This substitution, P596H, sits in a domain critical for maintaining reading frame during translation. The yeast equivalent, P580H EF2, demonstrated impaired translocation, detected as an increased rate of -1 programmed ribosomal frameshift read-through in a dual-luciferase assay for observing translational recoding. This substitution also results in a greater susceptibility to proteostatic disruption, as evidenced by a more robust activation of a reporter gene driven by unfolded protein response activation upon challenge with dithiothreitol or heat shock in our yeast model system. Our results present a compelling candidate mutation and mechanism for the pathogenesis of SCA26 and further support the role of proteostatic disruption in neurodegenerative diseases.
Lateral Electromagnetic Waves for Ocean Floor Telemetry (1991)

ABSTRACT In this paper, an ocean floor telemetry system is proposed that employs the lateral electromagnetic wave. The lateral electromagnetic wave's advantage is that it travels along the low conductivity rock sea boundary instead of through the high conductivity seawater. Existing theory, laboratory scale model experimental data, and at-sea measurements form the basis of the design of such a system. INTRODUCTION The problem of obtaining telemetry in the ocean environment will be addressed through the use of a novel communications system that employs the lateral electromagnetic wave. The lateral wave's unique advantage is that it propagates along the low conductivity ocean bottom making long distance reception of telemetric data possible. In the past rf systems for this purpose have not been feasible due to the high conductivity of seawater which causes a signal propagating through it to be rapidly attenuated and therefore useless for long distance communication. The ocean bottom communications system design presented is introduced by building a foundation based upon a detailed explanation of the theory of the lateral electromagnetic wave, and by verifying this theory with data acquired from laboratory and at-sea measurements. This approach establishes confidence in the subsequent design. THEORY OF LATERAL WAVE PROPAGATION Lateral wave propagation has been investigated quite thoroughly in the electromagnetic literature over the past several decades starting with the work of Sommerfeld in 1909. Surprisingly, its use so far for communications has been limited and its application to the ocean floor environment is unknown. The simplest way to visualize lateral wave propagation is through ray optics (see Figure 1). When an electromagnetic wave impinges on the interface between regions 1 and 2 (seawater and rock respectively) three possible propagation paths may take place. The wave may be reflected back in to region 1 if the incident angle is greater than the critical angle; it may propagate into region 2 if the incident angle is less than the critical angle; or it may propagate along the boundary (in region 2) if the incident angle is equal to the critical angle. As the wave propagates along the interface the amplitude decreases continuously due to a diffusion process into the electrically more dense Region 1. This complicated phenomenon had been analyzed by Sommerfeld and his final expression for the radial E-field in Region 1 generated by a short unit current dipole (also in region 1) is expressed in terms of a very complicated integral1. Mathematical equation (Available in full paper) His expression gives the radial electric field at the receiver point Rx generated by the dipole at the transmitter Tx. Unfortunately, this expression appears to be too involved to be useful. The following years witnessed a series of numerical approaches to the Sommerfeld integral. In 1966, Banes approximated Sommerfeld's integral by means of the near field, intermediate field, and far field2. His approximations are:Mathematical equation (Available in full paper)
Identification of Novel GPR55 Modulators Using Cell-Impedance-Based Label-Free Technology (2016)

The orphan G protein-coupled receptor GPR55 has been proposed as a novel receptor of the endocannabinoid system. However, the validity of this categorization is still under debate mainly because of the lack of potent and selective agonists and antagonists of GPR55. Binding assays are not yet available for GPR55 screening, and discrepancies in GPR55 mediated signaling pathways have been reported. In this context, we have designed and synthesized novel GPR55 ligands based on a chromenopyrazole scaffold. Appraisal of GPR55 activity was accomplished using a label-free cell-impedance-based assay in hGPR55-HEK293 cells. The real-time impedance responses provided an integrative assessment of the cellular consequence to GPR55 stimulation taking into account the different possible signaling pathways. Potent GPR55 partial agonists (14b, 18b, 19b, 20b, and 21-24) have been identified; one of them (14b) being selective versus classical cannabinoid receptors. Upon antagonist treatment, chromenopyrazoles 21-24 inhibited lysophosphatidylinositol (LPI) effect. One of these GPR55 antagonists (21) is fully selective versus classic cannabinoid receptors. Compared to LPI, the predicted physicochemical parameters of the new compounds suggest a clear pharmacokinetic improvement.
Intramolecular Cyclization Reactions of 5‐Halo‐ and 5‐Nitro‐Substituted Furans. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.