gebhart/patrepeval huggingface dataset:
Synthesis of a Phosphonic Acid Analogue of <i>N</i>‐Acetyl‐2,3‐didehydro‐2‐deoxyneuraminic Acid, an Inhibitor of <i>Vibrio cholerae</i> Sialidase (1991)

Abstract The synthesis of the phospha analogue 10 of DANA ( 2 ) is described. Bromo‐hydroxylation of the known 11 (→ 12 and 13 ) followed by treatment of the major bromohydrin 13 with 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) gave the oxirane 14 ( Scheme 1 ). Depending on the solvent, TiBr 4 transformed 14 into 16 or into a 15 / 16 mixture. Reductive debromination of 16 (→ 17 ), followed by benzylation provided 18 . Oxidattve decarboxylation (Pb(OAc) 4 ) of the acid, obtained by saponification of 18 , yielded the anomeric acetates 19 and 20 . While 19 was inert under the conditions of phosphonoylation, the more reactive imidate 22 , obtained together with 23 from 19 / 20 via 21 ( Scheme 2 ), gave a mixture of the phosphonates 24 / 25 and the bicyclic acetal 26 . Debenzylation of 24 / 25 and acetylation led to the acetoxyphosphonates 27 / 28 . Since β‐elimination of AcOH from 27 / 28 proved difficult, the bromide 34 was prepared from 27 / 28 by photobromination and subjected to reductive elimination with Zn/Cu (→ 35 ; Scheme 3 ). This two‐step sequence was first investigated using the model compounds 30 and 31 . Transesterification of 35 , followed by deacetylation gave 10 , which is a strong inhibitor of the Vibrio Cholerae sialidase.
Activities of Temporin Family Peptides against the Chytrid Fungus (<i>Batrachochytrium dendrobatidis</i>) Associated with Global Amphibian Declines (2003)

Temporin A and structurally related peptides produced in amphibian dermal granular glands and in wasp venom were tested for growth inhibition of Batrachochytrium dendrobatidis, a pathogen associated with global amphibian declines. Two natural amphibian temporins, a wasp temporin, and six synthetic analogs effectively inhibited growth. Differences in potency due to amino acid substitution suggest that ability to penetrate membranes and form an alpha-helical structure is important for their effectiveness against this pathogen.
Theory of Focusing Radiators (1949)

An approximate theory has been derived describing part of the sound field due to a concave spherical radiator, vibrating with uniform normal velocity; the radius a of the circular boundary is assumed to be large relative to the wave-length and large relative to the depth of the concave surface. The theory describes the distribution of pressure, particle velocity, and intensity along the axis of symmetry and in the vicinity of the focal plane, perpendicular to the axis at the center of curvature. It is shown that the ratio of the intensity at the center of curvature to the average intensity at the radiating surface is nearly equal to (2πh/λ)2 where h is the depth of the concave surface and λ is the wave-length. This ratio can be made very large by suitable choice of dimensions, and the focusing is then very sharp. The point of greatest intensity is not at the center of curvature but approaches it with increasing kh = 2πh/λ, and the greatest intensity is not much greater than the intensity at the center of curvature except when kh is small. In the central part of the focal plane, at angle θ from the axis, the pressure is approximately proportional to (2/ka sinθ)J1(ka sinθ), which is equivalent to the directivity function of a flat circular piston of radius a, for the region at large distance from the piston. The calculations are in reasonable agreement with G. W. Willard's experimental data for a 5-mc concave quartz crystal, when allowance is made for the non-uniform normal velocity of the crystal.
Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway (2012)

A functional 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway is required for isoprenoid biosynthesis and hence survival in Escherichia coli and most other bacteria. In the first two steps of the pathway, MEP is produced from the central metabolic intermediates pyruvate and glyceraldehyde 3-phosphate via 1-deoxy-D-xylulose 5-phosphate (DXP) by the activity of the enzymes DXP synthase (DXS) and DXP reductoisomerase (DXR). Because the MEP pathway is absent from humans, it was proposed as a promising new target to develop new antibiotics. However, the lethal phenotype caused by the deletion of DXS or DXR was found to be suppressed with a relatively high efficiency by unidentified mutations. Here we report that several mutations in the unrelated genes aceE and ribB rescue growth of DXS-defective mutants because the encoded enzymes allowed the production of sufficient DXP in vivo. Together, this work unveils the diversity of mechanisms that can evolve in bacteria to circumvent a blockage of the first step of the MEP pathway.
Spatially Selective Filter Design for High-Resolution EMG Arrays (2007)

A new technique for designing EMG spatial filters with optimized spatial selectivity is described. Simulations were used to model an action potential (AP) as a tripole source within the muscle, and to calculate the voltage induced at an array of surface monopolar electrodes. Next, a map of desired spatial filter output voltages was created as a function of the location of an AP beneath the array. Linear least squares was used to solve for the filter weights which optimally matched the desired filter outputs to those resulting from the tripole model. The optimized filters were found to be consistently superior to the conventional normal double differentiating filter. Selectivity was a function of the simulated inter-electrode spacing and the number of electrodes in the array.
Pepstatin analogs as novel renin inhibitors (1986)

Pepstatin analogues corresponding to the general formula A-X-Y-Sta-Ala-Sta-R were synthesized in solution phase. Various changes in the nature of the A, X, and Y groups were made to improve the inhibitory potency against human plasma renin activity. The results were interpreted by use of the active-site model based on the sequence of human angiotensinogen. The tert-butyloxycarbonyl group and the isovaleryl group were found to be the most effective acyl groups (A). The analogues having a Phe residue in place of Val1 (X) and His or amino acid with an aliphatic side chain such as norleucine or norvaline in the Y position showed the highest inhibition of human plasma renin activity with IC50 values of about 10(-8)M. Esterification or amidification of the carboxyl group of the C-terminal statine did not change the inhibitory potency. The selectivity for rat, dog, pig, and monkey plasma renin of the most interesting compounds was studied.
Applications of a miniature pin-array tactile module for a mobile device (2008)

Tactile sensation in the mobile device has been generated by vibration motors because of the size and the power consumption of a tactile module. However, the vibration motor is not enough to provide detail texture or small-scale shape. Therefore, we developed a miniature pin-array tactile module which can be embedded into a mobile device using the elastic and the electromagnetic force. In this paper, the various applications of the pin-array tactile module in the mobile device are presented. The pin-array tactile stimulating system plays important roles such as a braille display, a various alarming system, walking aid.
A Fast Flowgraph Based Classification System for Packed and Polymorphic Malware on the Endhost (2010)

Identifying malicious software provides great benefit for distributed and networked systems. Traditional real-time malware detection has relied on using signatures and string matching. However, string signatures ineffectively deal with polymorphic malware variants. Control flow has been proposed as an alternative signature that can be identified across such variants. This paper proposes a novel classification system to detect polymorphic variants using flowgraphs. We propose using an existing heuristic flowgraph matching algorithm to estimate graph isomorphisms. Moreover, we can determine similarity between programs by identifying the underlying isomorphic flowgraphs. A high similarity between the query program and known malware identifies a variant. To demonstrate the effectiveness and efficiency of our flowgraph based classification, we compare it to alternate algorithms, and evaluate the system using real and synthetic malware. The evaluation shows our system accurately detects real malware, performs efficiently, and is scalable. These performance characteristics enable real-time use on an intermediary node such as an Email gateway, or on the endhost.
Mucin 13: Structure, Function, and Potential Roles in Cancer Pathogenesis (2011)

Mucin 13 (MUC13) is a high-molecular-weight transmembrane glycoprotein that is frequently and aberrantly expressed in a variety of epithelial carcinomas, including gastric, colorectal, and ovarian cancers. On the basis of the high expression of MUC13 in cancer cells as well as recent laboratory findings suggesting a malignant phenotype of MUC13-transfected cell lines, the oncogenic potential of MUC13 has emerged. The various functional domains of MUC13 may confer oncogenic potential to MUC13. For example, the bulky extracellular domain with extensive modification with glycan chains may prevent cell-cell and cell-extracellular matrix binding whereas the cytoplasmic tail containing serine and tyrosine residues for potential phosphorylation may participate in cell signaling. MUC13 exhibits the characteristics suitable as an early marker for cancer screening and presents a promising target for antibody-guided targeted therapy.
Disruption of MDA5-Mediated Innate Immune Responses by the 3C Proteins of Coxsackievirus A16, Coxsackievirus A6, and Enterovirus D68 (2017)

Coxsackievirus A16 (CV-A16), CV-A6, and enterovirus D68 (EV-D68) belong to the <i>Picornaviridae</i> family and are major causes of hand, foot, and mouth disease (HFMD) and pediatric respiratory disease worldwide. The biological characteristics of these viruses, especially their interplay with the host innate immune system, have not been well investigated. In this study, we discovered that the 3C<sup>pro</sup> proteins from CV-A16, CV-A6, and EV-D68 bind melanoma differentiation-associated gene 5 (MDA5) and inhibit its interaction with MAVS. Consequently, MDA5-triggered type I interferon (IFN) signaling in the retinoic acid-inducible gene I-like receptor (RLR) pathway was blocked by the CV-A16, CV-A6, and EV-D68 3C<sup>pro</sup> proteins. Furthermore, the CV-A16, CV-A6, and EV-D68 3C<sup>pro</sup> proteins all cleave transforming growth factor β-activated kinase 1 (TAK1), resulting in the inhibition of NF-κB activation, a host response also critical for Toll-like receptor (TLR)-mediated signaling. Thus, our data demonstrate that circulating HFMD-associated CV-A16 and CV-A6, as well as severe respiratory disease-associated EV-D68, have developed novel mechanisms to subvert host innate immune responses by targeting key factors in the RLR and TLR pathways. Blocking the ability of 3C<sup>pro</sup> proteins from diverse enteroviruses and coxsackieviruses to interfere with type I IFN induction should restore IFN antiviral function, offering a potential novel antiviral strategy.<b>IMPORTANCE</b> CV-A16, CV-A6, and EV-D68 are emerging pathogens associated with hand, foot, and mouth disease and pediatric respiratory disease worldwide. The pathogenic mechanisms of these viruses are largely unknown. Here we demonstrate that the CV-A16, CV-A6, and EV-D68 3C<sup>pro</sup> proteins block MDA5-triggered type I IFN induction. The 3C<sup>pro</sup> proteins of these viruses bind MDA5 and inhibit its interaction with MAVS. In addition, the CV-A16, CV-A6, and EV-D68 3C<sup>pro</sup> proteins cleave TAK1 to inhibit the NF-κB response. Thus, our data demonstrate that circulating HFMD-associated CV-A16 and CV-A6, as well as severe respiratory disease-associated EV-D68, have developed a mechanism to subvert host innate immune responses by simultaneously targeting key factors in the RLR and TLR pathways. These findings indicate the potential merit of targeting the CV-A16, CV-A6, and EV-D68 3C<sup>pro</sup> proteins as an antiviral strategy.
Alkaline phosphatase and an acid arylamidase as marker enzymes for normal and transformed WI-38 cells. (1980)

A survey of eleven enzyme activity levels in normal and SV40 transformed (VA-13) WI-38 cells revealed that the transformed cell enzymes differed by a quantitative and qualitative change of alkaline phosphatase and a quantitative loss of an arylamidase. Alkaline phosphatase activity was found to be elevated in the transformed cells at confluency but not in log phase cultures. This elevated activity was heat stable, L-homoarginine resistant and L-phenylalanine sensitive and is probably the term placental isoenzyme. In nontransformed WI-38 cells, the alkaline phosphatase was heat labile, L-homoarginine sensitive and L-phenylalanine resistant and so is probably the liver isoenzyme. While the arylamidase activity from both normal and transformed WI-38 cells had identical pH optima and Km values, the activity was approximately 20 times higher in confluent WI-38 cells than in confluent VA-13 cells. Cytochemical staining techniques for both activities are described that permit identification of fluorescent product within the cells, analysis of activity levels, and separation of cells with high and low activities. Mixtures of WI-38 cells and VA-13 cells separated by flow cytometry on the basis of arylamidase activity were subsequently evaluated for alkaline phosphatase isoenzyme and found to have been simultaneously separated into heat labile and heat stable samples.
Natural Language Processing Based Instrument for Classification of Free Text Medical Records (2016)

According to the Ministry of Labor, Health and Social Affairs of Georgia a new health management system has to be introduced in the nearest future. In this context arises the problem of structuring and classifying documents containing all the history of medical services provided. The present work introduces the instrument for classification of medical records based on the Georgian language. It is the first attempt of such classification of the Georgian language based medical records. On the whole 24.855 examination records have been studied. The documents were classified into three main groups (ultrasonography, endoscopy, and X-ray) and 13 subgroups using two well-known methods: Support Vector Machine (SVM) and <i>K</i>-Nearest Neighbor (KNN). The results obtained demonstrated that both machine learning methods performed successfully, with a little supremacy of SVM. In the process of classification a "shrink" method, based on features selection, was introduced and applied. At the first stage of classification the results of the "shrink" case were better; however, on the second stage of classification into subclasses 23% of all documents could not be linked to only one definite individual subclass (liver or binary system) due to common features characterizing these subclasses. The overall results of the study were successful.
A Fingerprint Matching Algorithm Using Phase-Only Correlation (2004)

This paper presents an algorithm for fingerprint matching using the Phase-Only Correlation (POC) function. One of the most difficult problems in human identification by fingerprints has been that the matching performance is significantly influenced by fingertip surface condition, which may vary depending on environmental or personal causes. This paper proposes a new fingerprint matching algorithm using phase spectra of fingerprint images. The proposed algorithm is highly robust against fingerprint image degradation due to inadequate fingertip conditions. A set of experiments is carried out using fingerprint images captured by a pressure sensitive fingerprint sensor. The proposed algorithm exhibits efficient identification performance even for difficult fingerprint images that could not be identified by the conventional matching algorithms. key words: phase-only correlation, phase-only matched filtering, phase correlation, biometrics, fingerprint verification, fingerprint identification
Molecular Structure and Expression of Anthropic, Ovine, and Murine Forms of Complement Receptor Type 2 (2008)

Complement receptor type 2 (CR2), also called CD21, is a cell surface glycoprotein expressed on the surfaces of mature human B lymphocytes, follicular dendritic cells (FDCs), a few T cells, and some striated epithelia (1).Two splice variants of CR2 have been detected in human B cells.The extracellular region of the prototype "short" form (145 kDa) contains 15 tandem short consensus repeat (SCR) domains (1), while the "long" form of CR2, containing 16 SCR domains, has been detected at the transcript level (58).Human CR2 associates with other molecules on the B-cell surface to form two distinct complexes.The most commonly expressed form of CR2 consists of a noncovalently associated complex formed between CR2 and CD19/CD81/Leu13 (104), although CR2 can also form complexes with CR1 (CD35) (110).The two complement receptors that are expressed by B lymphocytes both bind fragments of C3 that become covalently attached to activators of complement, providing the B cell with a nonclonal means for interacting with antigen that has been identified by this innate immune system.Therefore, CR2 rather than CR1 was the more likely candidate for the receptor that communicated innate recognition of antigen to the B lymphocyte (29).
Receptors for human plasminogen on gram-negative bacteria (1990)

A total of 188 strains representing 11 species of gram-negative bacteria were examined for the ability to interact with human plasminogen. Highly purified human plasminogen was labeled with 125I, and its uptake by different bacterial strains was measured. All 14 strains of Haemophilus influenzae and all 13 strains of Branhamella catarrhalis tested were positive with respect to plasminogen uptake. Also, eight species belonging to the family Enterobacteriaceae were tested, and of those, Proteus mirabilis demonstrated the most substantial uptake, with 28 of 39 strains taking up more than 10% of the plasminogen. Ten strains of Pseudomonas aeruginosa were also tested, of which seven showed uptake values higher than 10%. With H. influenzae and B. catarrhalis strains, Scatchard analysis indicated a two-phase receptor interaction, one more-avid receptor with a Kd of 6 to 8 nM and 2,000 to 2,500 sites per bacterium and a second receptor with a Kd of 50 to 80 nM and 9,000 sites per bacterium. With Pseudomonas aeruginosa strains, a single receptor interaction was detected with a Kd of 60 nM and the number of sites was estimated as 8,000 per bacterium. Scatchard analysis with strains of P. mirabilis indicated binding of a less-specific nature. However, plasminogen uptake by this species could be reduced by 50% by the addition of 2 mM unlabeled plasminogen. This estimate of Kd, as well as uptake studies with plasminogen fragments, suggests different properties of this receptor. With all receptor types, the addition of plasmin-aprotinin complex inhibited plasminogen uptake, which demonstrates that both forms of the molecule react with the same receptors. Plasminogen uptake could be eliminated by the addition of lysine or epsilon-aminocaproic acid, which suggests that the lysine-binding sites of the plasminogen molecule are involved in the receptor-ligand interaction.
Low-Dose Metronomic Oral Dosing of a Prodrug of Gemcitabine (LY2334737) Causes Antitumor Effects in the Absence of Inhibition of Systemic Vasculogenesis (2011)

Metronomic chemotherapy refers to the close, regular administration of conventional chemotherapy drugs at relatively low, minimally toxic doses, with no prolonged break periods; it is now showing encouraging results in various phase II clinical trials and is currently undergoing phase III trial evaluation. It is thought to cause antitumor effects primarily by antiangiogenic mechanisms, both locally by targeting endothelial cells of the tumor neovasculature and systemically by effects on bone marrow-derived cells, including circulating endothelial progenitor cells (CEP). Previous studies have shown reduction of CEPs by metronomic administration of a number of different chemotherapeutic drugs, including vinblastine, cyclophosphamide, paclitaxel, topotecan, and tegafur plus uracil (UFT). However in addition to, or even instead of, antiangiogenic effects, metronomic chemotherapy may cause suppression of tumor growth by other mechanisms such as stimulating cytotoxic T-cell responses or by direct antitumor effects. Here we report results evaluating the properties of metronomic administration of an oral prodrug of gemcitabine LY2334737 in nontumor-bearing mice and in preclinical models of human ovarian (SKOV3-13) and breast cancer (LM2-4) xenografts. Through daily gavage (at 6 mg/kg/d), the schedules tested were devoid of toxicity and caused antitumor effects; however, a suppressive effect on CEPs was not detected. Unexpectedly, metronomic LY2334737 administration caused increased blood flow in luciferase-tagged LM2-4 tumor xenografts, and this effect, readily measured using contrast micro-ultrasound, coincided with a relative increase in tumor bioluminescence. These results highlight the possibility of significant antitumor effects mediated by metronomic administration of some chemotherapy drugs without a concomitant inhibition of systemic angiogenesis.
Global motion estimation for mpeg-encoded streams (2005)

This paper explains a method for global motion characterization using a Hough-transform-like technique to estimate the motion parameters. Motion information provided by each picture sample is gathered in an accumulator corresponding to a parameter space, which is derived from our simple motion model. The document then focuses on the use of MPEG stream as input data, dealing with the available motion compensation information as input vectors for our system. Pros, cons and improvements are discussed.
2L-RBACG: A new framework for resource access control in grid environments (2010)

With the increasing complexity of dynamic and collaborative computing environments in Grid, access control has become a critical factor. Several approaches have been proposed in grid environment for scalable and efficient authorizations that are either VO-centric or Resource-centric. Reviewing different kinds of proposed authorization systems, we find out that VO-level and Resource-level authorization systems look at two different aspects of the grid authorization. Indeed, they complement each other, and can be implemented together to provide a holistic authorization solution. For this purpose, we propose a new access control framework which uses an extended two level RBAC model in Grid computing environments. By separating the administrations of users by VO level policies and mapping these policies to resources by resource or service providers, our scheme provides decentralized, autonomous, and fine-grained security management. The art of this approach is support of high flexibility in policy configuration, dynamically modifying authorization policies and reducing the cost of policy management.
Effect of Manganese (II), Cobalt (II), and Copper (I) Hydroxides on the Kinetics of the Oxidation of Cellulose by Hypochlorite (1986)

The catalytic effect of Mn (II), Co(II), and Cu(I) hydroxides on the oxidation of cellulose by hypochlorite has been examined, particularly the very early stages of the reaction where the primary process may be presumed to predominate. The rate of oxidation in the absence of any catalyst and in the presence of manganese and cobalt is greatest at pH 7.0, and in the presence of copper, the rate is greatest at pH 7.5. The catalytic activity of the three hydroxides is in the order Co ⪢ Cu > Mn. Copper numbers and acid contents of some of the oxycelluloses have been measured before and after treatment with chlorous acid. The results show that the faster the reaction the greater the ratio of aldehyde to other reducing groups in the product and that, with copper, initially formed aldehyde groups are more readily oxidized further by hypochlorite than with the other catalysts.