gebhart/patrepeval huggingface dataset:
Inhibitors of cruzipain and cathepsin L (2006)

Cysteine proteases represent important molecular targets for the development of antiparasitic chemotherapy. Cruzipain (cruzain), a cathepsin L‐like member of the C1 (papain) family of endopeptidases, is the major cysteine protease of Trypanosoma cruzi, the protozoan etiologic agent of Chagas’ disease. Chagas’ is the leading cause of heart disease in Latin America. Here we report the biochemical evaluation of a series of new compounds designed to inhibit cruzipain. More than twenty thiosemicarbazones containing α, and β‐tetralones, chroman‐4‐ones, thiochroman‐4‐ones, 3‐bromophenylcyclopentanones and 3‐bromophenylcyclohexanones were synthesized. Several of these compounds inhibited recombinant cruzain with IC 50 values in the low n M range using the fluorogenic substrate, Cbz‐Phe‐Arg‐7‐amino‐4‐methylcoumarin. This series of compounds was also tested against cathepsin L, one of the major cysteine proteases found in and secreted from animal tissues. Cathepsin L is of particular interest because of reports of its involvement in the development of rheumatoid arthritis and the suggested role of the enzyme in tumor invasion and metastasis. A number of the semithiocarbazone compounds were very effective inhibitors of cathepsin L. The authors thank Elizabeth Hansell and Dr. James McKerrow for the gift of cruzipain and the Vice‐Provost for Research of Baylor University, the Welch Foundation and Oxigene, Inc. for support.
Estimation of Body Hydration in Dialysis Patients Using a Calf Bioimpedance Method (2010)

Accurate estimation of normal hydration (dry weight) in hemodialysis (HD) patients is an important factor affecting patient mortality. Bioimpedance spectroscopy (BIS) has been used to measure extracellular (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> ) and intracellular resistance (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> ) with a calf method (cBIS). An algorithm based on a fluid dynamic (FD) model has been developed to estimate change in intradialytic fluid volume in the calf during HD. We hypothesize that the flattening curve of change in R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> and reaching the normal range of resistivity are the criteria to determine normal hydration state. The aim of this study was to evaluate whether the model and algorithm can be used in the clinic. 32 stable HD patients (19m/13f, age 55.8±15 yrs, height (H) 1.68±0.99 m and post-HD weight 71.9±15.3 kg) were studied with cBIS during HD treatments. To achieve dry weight, post HD weight were gradually reduced according to the criteria. Pre- and post-HD weight were reduced by mean of 1.36 kg and 1.15 kg respectively. The systolic blood pressure (SBP) decreased significantly (122.5± 22, vs. 114.3±21 mmHg, p<0.05). In conclusion, the FD model and algorithm has been applied successfully in dialysis patients.
Universal Marker and Detection Tool for Human Sarcoma Circulating Tumor Cells (2014)

To date, no specific marker exists for the detection of circulating tumor cells (CTC) from different types of sarcomas, though tools are available for detection of CTCs in peripheral blood of patients with cancer for epithelial cancers. Here, we report cell-surface vimentin (CSV) as an exclusive marker on sarcoma CTC regardless of the tissue origin of the sarcoma as detected by a novel monoclonal antibody. Utilizing CSV as a probe, we isolated and enumerated sarcoma CTCs with high sensitivity and specificity from the blood of patients bearing different types of sarcoma, validating their phenotype by single cell genomic amplification, mutation detection, and FISH. Our results establish the first universal and specific CTC marker described for enumerating CTCs from different types of sarcoma, thereby providing a key prognosis tool to monitor cancer metastasis and relapse.
Evaluation of Influenza A/Hong Kong/123/77 (H1N1) <i>ts</i> -1A2 and Cold-Adapted Recombinant Viruses in Seronegative Adult Volunteers (1980)

Two attenuated influenza A donor viruses, the A/Udorn/72 ts-1A2 and the A/Ann Arbor/6/60 cold-adapted (ca) viruses, are being evaluated for their ability to reproducibly attenuate each new variant of influenza A virus to a specific and desired level by the transfer of one or more attenuating genes. Each of these donor viruses has been able to attenuate influenza A viruses belonging to the H3N2 subtype by the transfer of one or more attenuating genes. To determine whether these two donor viruses could attenuate a wild-type virus that belonged to a different influenza A subtype, ts-1A2 and ca recombinants of a wild-type virus representative of the A/USSR/77 (H1N1) Russian influenza strain were prepared and evaluated in adult doubly seronegative volunteers at several doses. The recombinants derived from both donor viruses were attenuated for the doubly seronegative adults. Less than 5% of infected vaccinees developed a febrile or systemic reaction, whereas five of six recipients of wild-type virus developed such a response. The 50% human infectious dose (HID(50)) for each recombinant was approximately 10(5.0) 50% tissue culture infective doses. The virus shed by the ts-1A2 and ca vaccinees retained the ts or ca phenotype, or both. This occurred despite replication of the recombinant viruses for up to 9 days. No evidence for transmission of the ca or ts-1A2 recombinant virus to controls was observed. A serum hemagglutination inhibition response was detected in less than 50% of the infected vaccinees. However, with the more sensitive enzyme-linked immunosorbent assay, a serological response was detected in 100% of the ca vaccinees given 300 HID(50) and approximately 70% of ca or ts vaccinees who received 10 to 32 HID(50) of virus. These results indicate that the recombinants derived from both donor viruses were satisfactorily attenuated and were stable genetically after replication in doubly seronegative adults although they induced a lower serum hemagglutination inhibition response than that found previously for H3N2 ts and ca recombinants.
Dynamic Zero-Parallax-Setting Techniques for Multi-View Autostereoscopic Display (2020)

The objective of this paper is to research a dynamic computation of Zero-Parallax-Setting (ZPS) for multi-view autostereoscopic displays in order to effectively alleviate blurry 3D vision for images with large disparity. Saliency detection techniques can yield saliency map which is a topographic representation of saliency which refers to visually dominant locations. By using saliency map, we can predict what attracts the attention, or region of interest, to viewers. Recently, deep learning techniques have been applied in saliency detection. Deep learning-based salient object detection methods have the advantage of highlighting most of the salient objects. With the help of depth map, the spatial distribution of salient objects can be computed. In this paper, we will compare two dynamic ZPS techniques based on visual attention. They are 1) maximum saliency computation by Graphic-Based Visual Saliency (GBVS) algorithm and 2) spatial distribution of salient objects by a convolutional neural networks (CNN)-based model. Experiments prove that both methods can help improve the 3D effect of autostereoscopic displays. Moreover, the spatial distribution of salient objects-based dynamic ZPS technique can achieve better 3D performance than maximum saliency-based method.
Synthesis of Substituted Imidazo[1,2-<i>h</i>][1,7]naphthyridines as H<sup>+</sup>/K<sup>+</sup>-ATPase Inhibiting Drug Precursors via Directed<i>ortho</i>-Metalation of Imidazo[1,2-<i>a</i>]pyridines (2008)

Selective directed ortho-metalation (DOM) of 2,3-di­methyl-8-(pivaloylamino)imidazo[1,2-a]pyridine in the 7-position was achieved with tert-butyllithium. Subsequent reaction of the lithiated derivative with tributylchlorostannane to the corresponding 7-trialkylstannyl analogue and palladium-catalyzed Stille acylation with 3-arylpropenoic acid chlorides in the presence of lithium chloride gave the corresponding 7-acylated imidazopyridines in good yields. Cyclization to the target imidazonaphthyridines, which are precursors in the synthesis of gastric H+/K+-ATPase inhibiting drugs, was achieved by treatment with strong acid. For scaled-up production of 2,3-dimethyl-9-phenyl-9,10-dihydroimidazo[1,2-h][1,7]naphthyridin-7(8H)-one, a tin-free process has been developed. Accordingly, the 7-lithiated 2,3-dimethyl-8-(pivaloyl­amino)imidazo[1,2-a]pyridine was reacted directly with cinnamaldehyde and the resultant alcohol oxidized with manganese dioxide to give the unsaturated 7-acylated imidazopyridine.
Optoelectronic integration of silicon photonic wire biosensors (2009)

We review our work developing label-free molecular sensors using silicon nanophotonic waveguides. We show that the high index contrast of these waveguides provides high surface sensitivity and enables compact sensor designs to be realized. We also describe new waveguide circuit geometries that allow photonic wire waveguide sensors to be conveniently arrayed in two dimensions for compatibility with commercial spotting tools, while simultaneously providing long interaction length and improved molecular capture efficiency. These sensor designs are shown to provide a practical route to the development of label-free, microarrayed biochips for multiparameter analysis.
Extended para-hydrogenation monitored by NMR spectroscopy (2010)

A system that provides a sustained hyperpolarized (1)H NMR signal in an aqueous medium is reported. The enhanced signal lasts much longer than typical (1)H T(1) values, uncovering new possibilities for implementing hyperpolarized (1)H NMR/MRI experiments or performing kinetics studies that would not otherwise be detectable.
Basic Properties of Magnetorheological Fluids for Optical Finishing (1994)

Magnetorheological (MR) fluids are multicomponent systems consisting of a non-colloidal magnetic-dispersed phase in a carrier liquid, which undergo rapid, sharp and reversible changes of their internal structure in an external magnetic field. As a consequence, their rheological properties, such as viscosity, plasticity and elasticity are controllably changed (for example, see Figure 1).
The PB2 co‐adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice (2021)

Avian influenza (AI) is an important zoonotic disease, which can be transmitted across species barriers to other hosts, especially humans, posing a serious threat to the poultry industry and public health. In recent years, human cases infected with the H10N8, H9N2, and H7N9 of avian influenza viruses (AIVs) have been identified frequently as have the internal genes of H7N9 and H10N8, which are derived from H9N2 viruses. The adaptive mutation of the PB2 gene is an important way for the H10N8, H9N2, and H7N9 AIVs to spread across species to adapt to new hosts. Several well-known adaptive mutations in the PB2 gene, such as E627K, D701N, and A588V, significantly enhanced the virulence of the AIVs in mammals. However, the co-adaptation of AIVs to avian and mammalian hosts is rarely studied. In this study, we found that the mutations of PB2-I292V, PB2-R389K, PB2-A588V, PB2-T598M/V, PB2-L648V, and PB2-T676M substitutions significantly increased after 2012. In addition, in our previous studies, we found that the human-origin and avian-origin of H10N8 AIVs with very high homology also have these six mutation differences in PB2 gene, and the avian-origin H10N8 strain known as JX102 with all the key amino acids on the PB2 protein in the pre-evolutionary stage, so JX102 was chosen as a model strain. Among them, PB2-A588V significantly enhanced the activity of polymerase in avian and mammalian cells. Notably, animal experiments showed that PB2-A588V substitution increased the pathogenicity and transmissibility in chickens and the virulence of mice. The combined mutations of PB2-F6 (including PB2-I292V, PB2-R389K, PB2-A588V, PB2-T598M, PB2-L648V, and PB2-T676M) obtained higher adaptability of AIVs in avians and mammals than that of the single mutation of PB2-A588V, which suggested that the PB2 588 site is a key co-adaptation site and that synergies with other mutation sites can further enhance this co-adaptability. The results of this study show that the emergence of co-adaptation not only increases the threat to avians and mammals but may also contribute to a pandemic among avians and cross the interspecies barrier to mammals.
Role of microRNA-30c in lipid metabolism, adipogenesis, cardiac remodeling and cancer (2015)

These studies highlight the important role miR-30c plays in lipid metabolism, adipogenesis, and cell proliferation and differentiation. Further, they point to pathologic outcomes associated with reduced expression in cancer and cardiac hypertrophy. Additionally, they suggest that increasing miR-30c expression in the liver and cancerous tissue might reduce hyperlipidemia and atherosclerosis, and cancer progression and metastasis, respectively. Studies are needed to evaluate the efficacy of miR-30c mimic in the treatment of these disorders.
Effect of superhydrophobicity/superhydrophilicity of titanium surface on hemocompatibility (2016)

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Multiscale Modeling of Skin Electroporation (2020)

Human skin, the largest external organ of the body, provides a selective barrier to therapeutics applied topically. The molecules having specific chemical and physical properties can only penetrate the deeper layer of the skin. However, the lag time for reaching a steady state in the deeper layer is generally of the order of hours. In order to deliver higher-molecular-weight, charged, and hydrophilic therapeutics in the deeper layer, the skin barrier must be breached. Electroporation is one of the methods used to breach the skin barrier for enhancement of drug permeation and reduction of lag time. However, the underlying mechanism responsible for the enhancement of drug permeation is not well understood. In this study, a multiscale model of skin electroporation is developed by connecting molecular phenomena to a macroscopic model. At the atomic scale, molecular dynamics simulations of the lipid matrix of the human stratum corneum (SC) were performed under the influence of an external electric field. The pores get formed during the electroporation process and the transport properties (diffusivity) of drug molecules are computed. The diffusion coefficient obtained during electroporation was found to be higher than passive diffusion. However, this alone could not explain the multifold increase in the drug flux on application of an electric field as observed in the experiments. Hence, a finite element method (FEM) model of the skin SC is also developed. The release of fentanyl through this model is compared with the available experimental results. Both experimental and simulated results of pore formation on application of an electric field and many folds' increase in drug flux are comparable. Once validated, the framework was used for the design of skin electroporation experiments (in silico) by changing the electric pulse parameters such as voltage, pulse duration, and number of pulses. This multiscale modeling framework provides valuable insight at the molecular and macroscopic levels to design the electroporation experiments. The framework can be utilized as a design tool for skin electroporation applications.
Recovery from control plane failures in GMPLS‐controlled optical networks (2002)

Abstract The health status of the control plane and the data plane of a GMPLS‐controlled optical network is independent in the physically separated control network implementation. In most control plane designs, besides the topology information, the entities of the routing protocol only record the number of available wavelengths on each link. However, the status of each wavelength is maintained by the entities of the signalling protocol. Without recovery ability of the signalling protocol CR‐LDP, a failure in the control plane will result in the permanent loss of the status information of wavelengths. A mechanism to recover the status information of the wavelengths is proposed. A downstream node maintains a label information database (LID) about assignable (free) labels in each incoming link. A copy of LID is redundantly stored in the upstream node as a label information mirror (LIM). A systematic procedure is proposed to synchronize the contents of a LIM and the corresponding LID. The initialization of a new LDP session with the enhanced recovery mechanism will guarantee the revival of the status information of wavelengths. It can recover multiple control channel failures, but it only applies to single node failure among any pair of adjacent nodes. © Crown copyright 2002. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.
Performance Extrapolation of IO Intensive Workloads (2016)

Performance prediction of an application before migrating from a source system and deploying on the target system is a challenging but important task. In this paper, we present a method for predicting the performance of an IO intensive multithreaded enterprise application workload on target systems connected to advanced storage devices. Our approach is an extension of well-known trace and replay method. We extract traces of IO intensive enterprise workloads representing temporal and spatial characteristics (e.g. read and write requests) on the source system where application is currently deployed. These traces are replayed on the system of interest called target system. The experimental results presented demonstrate the effectiveness and accuracy of this method.
Performance of eccentric-cycloid engagement with change in the interaxial distance: Modification of tooth configuration (2011)

The influence of the interaxial distance of the gears on the performance of an eccentric-cycloid engagement is studied by computer simulation. With wide variation in the interaxial distance, there is little shift in the contact point of the profiles, which remains at the front of the cycloid curves describing the tooth shape. This greatly simplifies gear manufacture for such engagements, since the surface area to be finished is considerably reduced.
Novel S1P<sub>1</sub> Receptor Agonists - Part 2: From Bicyclo[3.1.0]hexane-Fused Thiophenes to Isobutyl Substituted Thiophenes (2013)

Previously, we reported on the discovery of a novel series of bicyclo[3.1.0]hexane fused thiophene derivatives that serve as potent and selective S1P1 receptor agonists. Here, we discuss our efforts to simplify the bicyclohexane fused thiophene head. In a first step the bicyclohexane moiety could be replaced by a simpler, less rigid cyclohexane ring without compromising the S1P receptor affinity profile of these novel compounds. In a second step, the thiophene head was simplified even further by replacing the cyclohexane ring with an isobutyl group attached either to position 4 or position 5 of the thiophene. These structurally much simpler headgroups again furnished potent and selective S1P1 agonists (e.g., 87), which efficiently and dose dependently reduced the number of circulating lymphocytes upon oral administration to male Wistar rats. For several compounds discussed in this report lymphatic transport is an important route of absorption that may offer opportunities for a tissue targeted approach with minimal plasma exposure.
Strategies in the development of vaccines to prevent infections with group A streptococcus (2013)

There has long been interest and demand for the development of a vaccine to prevent infections caused by the Gram-positive organism group A streptococcus. Despite numerous efforts utilizing advanced approaches such as genomics, proteomics and bio-informatics, there is currently no vaccine. Here we review various strategies employed to achieve this goal. We also discuss the approach that we have pursued, a non-host reactive, conformationally constrained minimal B cell epitope from within the C-repeat region of M-protein, and the potential limitations in moving forward.
A miniaturized nebulization catheter for improved gene delivery to the mouse lung (2005)

The use of the nebulization catheter device provides a promising alternative for aerosol gene delivery to the mouse lung.
PLC symbol naming rule for auto generation of Plant model in PLC simulation (2008)

Proposed in the paper is an automated procedure to construct a plant model for PLC simulation. Since PLC programs only contain the control logic without the information on the plant model, it is necessary to build the corresponding plant model to perform simulation. Conventionally, a plant model for PLC simulation has been constructed manually, and it requires much efforts as well as the in-depth knowledge of simulation. As a remedy for the problem, we propose an automated procedure to generate a plant model from the symbol table of a PLC program. To do so, we propose a naming rule for PLC symbols so that the symbol names include enough information on the plant model. By analyzing such symbol names, we extract a plant model automatically. The proposed methodology has been implemented, and test runs were made.
<sup>13</sup>C and 2D NMR Analysis of Propylene Polymers Made with α-Diimine Late Metal Catalysts (2000)

Late transition metal catalysts bearing α-diimine ligands allow ethylene and α-olefin homo- and copolymerizations to polyolefins with unprecedented structures. The polypropylenes made with these new late metal catalysts have very complex microstructures that include combinations of features not seen in any known polypropylenes. These unusual structures include long branches, branches on branches including isobutyl branches, and moderate highly variable levels of 1,3-enchainment leading to runs of methylenes in the backbone of many different well-defined lengths. These features vary with the nature of the catalyst used for polymerization and with the polymerization conditions. Many of the polypropylenes are made primarily by 1,2-insertions to give syndiotactic placements via chain end control. A mechanistic description of catalyst behavior has been developed to explain these observed microstructures.