gebhart/patrepeval huggingface dataset:
Synthesis of the carbocyclic analogs of uracil nucleosides (1976)

Abstract Treatment of the required hydroxyl derivatives of cis ‐3‐aminocyclopentanemethanol with 3‐ethoxyacryloyl isocyanate gave N ‐(3‐ethoxyacryloyl)‐ N ′‐[hydroxy‐ or dihydroxy(hydroxy‐methyl)cyclopentyl]ureas. Cyclization of the ureas in dilute sulfuric acid afforded high yields of the carbocyclic analogs of uridine, 2′‐deoxyuridine, and 3′‐deoxyuridine. The uridine and 3′‐deoxyuridine analogs were also obtained in good yields by cyclizing the ureas in concentrated aqueous ammonia. None of the three analogs showed activity in tests versus KB cells in culture or L1210 leukemia in vivo.
The Delivery of Biologically Active (Therapeutic) Peptides and Proteins into Cells (2011)

Biologically active peptides and proteins have a great potential to act as targeted drug therapies in the treatment of a variety of diseases, including cancer. However, their use in vivo is limited by their low stability and cell permeability. Thus, it is necessary to develop efficient and safe peptide/protein delivery systems that can overcome these problems and increase a therapy's bioavailability. The search for promising vectors has led to the use of compounds called cell-penetrating peptides or protein transduction domains. The cell-penetrating peptides, as effective transporter, are utilized to enhance uptake of various biologically active peptide/protein cargos upon fusion or attachment to its sequences. Cell-penetrating peptides have been the subject of investigation of many researchers, however this review only focuses on the arginine-rich and amphipathic carriers and their potential therapeutic use.
Ancylostoma caninum anticoagulant peptide: cloning by PCR and expression of soluble, active protein in E. coli (1996)

Ancylostoma caninum Anticoagulant Peptide (AcAP) is the major anticoagulant activity present in extracts of adult Ancylostoma caninum hookworms. This 8.7 kDa protein is a potent and specific inhibitor of human coagulation factor Xa. Using PCR, we have isolated a cDNA encoding for AcAP from an adult A. caninum cDNA library. The 5' end of the AcAP cDNA was identified by reverse transcription PCR (RT-PCR) using A. caninum cDNA and a 5' primer corresponding to a nematode spliced leader sequence. The AcAP cDNA was expressed in E. coli using a prokaryotic expression vector, and the recombinant fusion protein (rAcAP) was purified to homogeneity using nickel resin affinity chromatography and reverse phase HPLC. Purified rAcAP is comparable to the native protein in inhibitor activity, with an apparent equilibrium inhibitory dissociation constant (Ki*) for the inhibition of factor Xa of 265 +/- 71 pM. The purified protein also prolongs the prothrombin and partial thromboplastic times of human plasma in a dose dependent manner.
The Glycoprotein Ib-IX-V Complex in Platelet Adhesion and Signaling (1999)

Introduction Thrombosis can result in unstable angina, acute myocardial infarction, or stroke, all major causes of death in the Western world. Circulating platelets become adherent and form an occlusive thrombus, either by exposure to sclerotic lesions following plaque rupture or in response to pathological shear stress in obstructed coronary arteries. This process parallels normal haemostasis, where platelets adhere to the subendothelium at sites of vascular injury, become activated, and recruit additional platelets to the developing thrombus. At high shear, thrombus formation is initiated by a specific platelet membrane adhesion receptor, the glycoprotein (GP) Ib-IX-V complex, which binds the adhesive glycoprotein, von Willebrand factor (vWF), in the vessel wall or plasma. Recent evidence also suggests that platelet adhesion to endothelial cells and leukocytes may be involved in atherogenesis, thrombosis, and inflammation. Preliminary findings indicate that GP Ib-IX-V specifically recognizes P-selectin, a member of the selectin superfamily, an interaction that may, at least partially, regulate platelet-endothelial cell adhesion. This review focuses on recent advances in understanding structure-activity relationships of GP Ib-IX-V.
Identification of a PA-Binding Peptide with Inhibitory Activity against Influenza A and B Virus Replication (2009)

There is an urgent need for new drugs against influenza type A and B viruses due to incomplete protection by vaccines and the emergence of resistance to current antivirals. The influenza virus polymerase complex, consisting of the PB1, PB2 and PA subunits, represents a promising target for the development of new drugs. We have previously demonstrated the feasibility of targeting the protein-protein interaction domain between the PB1 and PA subunits of the polymerase complex of influenza A virus using a small peptide derived from the PA-binding domain of PB1. However, this influenza A virus-derived peptide did not affect influenza B virus polymerase activity. Here we report that the PA-binding domain of the polymerase subunit PB1 of influenza A and B viruses is highly conserved and that mutual amino acid exchange shows that they cannot be functionally exchanged with each other. Based on phylogenetic analysis and a novel biochemical ELISA-based screening approach, we were able to identify an influenza A-derived peptide with a single influenza B-specific amino acid substitution which efficiently binds to PA of both virus types. This dual-binding peptide blocked the viral polymerase activity and growth of both virus types. Our findings provide proof of principle that protein-protein interaction inhibitors can be generated against influenza A and B viruses. Furthermore, this dual-binding peptide, combined with our novel screening method, is a promising platform to identify new antiviral lead compounds.
On Visual Similarity Based 3D Model Retrieval (2003)

Abstract A large number of 3D models are created and available on the Web, since more and more 3D modelling anddigitizing tools are developed for ever increasing applications. The techniques for content‐based 3D model retrievalthen become necessary. In this paper, a visual similarity‐based 3D model retrieval system is proposed.This approach measures the similarity among 3D models by visual similarity, and the main idea is that if two 3Dmodels are similar, they also look similar from all viewing angles. Therefore, one hundred orthogonal projectionsof an object, excluding symmetry, are encoded both by Zernike moments and Fourier descriptors as features forlater retrieval. The visual similarity‐based approach is robust against similarity transformation, noise, model degeneracyetc., and provides 42%, 94% and 25% better performance (precision‐recall evaluation diagram) thanthree other competing approaches: (1) the spherical harmonics approach developed by Funkhouser et al., (2) theMPEG‐7 Shape 3D descriptors, and (3) the MPEG‐7 Multiple View Descriptor. The proposed system is on the Webfor practical trial use ( http://3d.csie.ntu.edu.tw ), and the database contains more than 10,000 publicly available3D models collected from WWW pages. Furthermore, a user friendly interface is provided to retrieve 3D modelsby drawing 2D shapes. The retrieval is fast enough on a server with Pentium IV 2.4 GHz CPU, and it takes about2 seconds and 0.1 seconds for querying directly by a 3D model and by hand drawn 2D shapes, respectively. Categories and Subject Descriptors (according to ACM CCS): H.3.1 [Information Storage and Retrieval]: Indexing Methods
Unique Properties of Selectively Formed Zirconia Nanostructures (2006)

Hollow ZrO2 nanoshells are formed over a precise range of temperature and pressure from the oxidation of ZrCl2. The greatly enhanced photoluminescence (∼ 110×) that the nanoshells exhibit compared to that of either nanospheres or irregularly shaped nanoparticles is attributed to the nanoshell geometry (see Figure). Potential future applications include information-storage devices.
Compartment switching of WNT-2 expression in human breast tumors. (1996)

WNT-2 is a secreted polypeptide with mitogenic effects in murine mammary epithelial cells, but its role in human cancer is unknown. Using RNase protection analysis of primary cell preparations and in situ hybridization analysis, we report that WNT-2 is expressed at low levels in normal human breast fibroblasts but not in epithelial cells. WNT-2 was found to be expressed at high levels in both the epithelium and stroma of 5 of 11 infiltrating carcinomas and 2 of 6 fibroadenomas. The high level of WNT-2 expression in tumor epithelium suggests that tumorigenesis may involve the ectopic expression of WNT-2 and the creation of an autocrine Wnt signaling loop.
The S228P Mutation Prevents in Vivo and in Vitro IgG4 Fab-arm Exchange as Demonstrated using a Combination of Novel Quantitative Immunoassays and Physiological Matrix Preparation (2015)

Human immunoglobulin G isotype 4 (IgG4) antibodies (Abs) are potential candidates for immunotherapy when reduced effector functions are desirable. IgG4 Abs are dynamic molecules able to undergo a process known as Fab arm exchange (FAE). This results in functionally monovalent, bispecific antibodies (bsAbs) with unknown specificity and hence, potentially, reduced therapeutic efficacy. IgG4 FAE is suggested to be an important biological mechanism that provides the basis for the anti-inflammatory activity attributed to IgG4 Abs. To date, the mechanism of FAE is not entirely understood and studies measuring FAE in ex vivo matrices have been hampered by the presence and abundance of endogenous IgG4 wild-type (WT) Abs. Using representative humanized WT IgG4 monoclonal Abs, namely, anti-IL-6 and anti-TNF, and a core-hinge stabilized serine 228 to proline (S228P) anti-IL-6 IgG4 mutant, it is demonstrated for the first time how anti-IgG4 affinity chromatography can be used to prepare physiologically relevant matrices for assessing and quantifying FAE. A novel method for quantifying FAE using a single MSD immunoassay is also reported and confirms previous findings that, dependent on the redox conditions, the S228P mutation can prevent IgG4 FAE to undetectable levels both in vitro and in vivo. Together, the findings and novel methodologies will allow researchers to monitor and quantify FAE of their own IgG4 molecules in physiologically relevant matrices.
Plexin-A4 Mediates Axon-Repulsive Activities of Both Secreted and Transmembrane Semaphorins and Plays Roles in Nerve Fiber Guidance (2005)

It has been proposed that four members of the plexin A subfamily (plexin-As; plexin-A1, -A2, -A3, and -A4) and two neuropilins (neuropilin-1 and neuropilin-2) form complexes and serve as receptors for class 3 secreted semaphorins (Semas), potent neural chemorepellents. The roles of given plexin-As in semaphorin signaling and axon guidance, however, are mostly unknown. Here, to elucidate functions of plexin-A4 in semaphorin signaling and axon guidance events in vivo, we generated plexin-A4 null mutant mice by targeted disruption of the plexin-A4 gene. Plexin-A4 mutant mice were defective in the trajectory and projection of peripheral sensory axons and sympathetic ganglion (SG) axons and the formation of the anterior commissure and the barrels. The defects in peripheral sensory and SG axons were fundamentally related to those of neuropilin-1 or Sema3A mutant embryos reported but were more moderate than the phenotype in these mutants. The growth cone collapse assay showed that dorsal root ganglion axons and SG axons of plexin-A4 mutant embryos partially lost their responsiveness to Sema3A. These results suggest that plexin-A4 plays roles in the propagation of Sema3A activities and regulation of axon guidance and that other members of the plexin-A subfamily are also involved in the propagation of Sema3A activities. Plexin-A4-deficient SG axons did not lose their responsiveness to Sema3F, suggesting that plexin-A4 serves as a Sema3A-specific receptor, at least in SG axons. In addition, the present study showed that plexin-A4 bound class 6 transmembrane semaphorins, Sema6A and Sema6B, and mediated their axon-repulsive activities, independently of neuropilin-1. Our results imply that plexin-A4 mediates multiple semaphorin signals and regulates axon guidance in vivo.
Implications of the User's Information Processing Strategy on the Design of Decision Aids for Complex Systems (1993)

Performance was evaluated in a single and dual task environment which simulated basic tasks carried out by sonar operators, using processed, visual representations of acoustic data. Two general classes of performance functions were obtained. One group of subjects performed at high levels in both single and dual task conditions and responded to increasing demand with increased throughput. The second group showed performance levelling or decrement once information load reached a critical level. The strategies used by the two groups (heuristics/pattern recognition for the former, and serial analysis for the latter) have clear importance for the type of decision aids which need to be provided in future generation sonar systems.
RNAi for Treating Hepatitis B Viral Infection (2007)

Chronic hepatitis B virus (HBV) infection is one of the leading causes of liver cirrhosis and hepatocellular carcinoma (HCC). Current treatment strategies of HBV infection including the use of interferon (IFN)-alpha and nucleotide analogues such as lamivudine and adefovir have met with only partial success. Therefore, it is necessary to develop more effective antiviral therapies that can clear HBV infection with fewer side effects. RNA interference (RNAi), by which a small interfering RNA (siRNA) induces the gene silence at a post-transcriptional level, has the potential of treating HBV infection. The successful use of chemically synthesized siRNA, endogenous expression of small hairpin RNA (shRNA) or microRNA (miRNA) to silence the target gene make this technology towards a potentially rational therapeutics for HBV infection. However, several challenges including poor siRNA stability, inefficient cellular uptake, widespread biodistribution and non-specific effects need to be overcome. In this review, we discuss several strategies for improving the anti-HBV therapeutic efficacy of siRNAs, while avoiding their off-target effects and immunostimulation. There is an in-depth discussion on the (1) mechanisms of RNAi, (2) methods for siRNA/shRNA production, (3) barriers to RNAi-based therapies, and (4) delivery strategies of siRNA for treating HBV infection.
EEG patterns from acute to chronic stroke phases in focal cerebral ischemic rats: correlations with functional recovery (2013)

Monitoring the neural activities from the ischemic penumbra provides critical information on neurological recovery after stroke. The purpose of this study is to evaluate the temporal alterations of neural activities using electroencephalography (EEG) from the acute phase to the chronic phase, and to compare EEG with the degree of post-stroke motor function recovery in a rat model of focal ischemic stroke. Male Sprague-Dawley rats were subjected to 90 min transient middle cerebral artery occlusion surgery followed by reperfusion for seven days (n = 58). The EEG signals were recorded at the pre-stroke phase (0 h), acute phase (3, 6 h), subacute phase (12, 24, 48, 72 h) and chronic phase (96, 120, 144, 168 h) (n = 8). This study analyzed post-stroke seizures and polymorphic delta activities (PDAs) and calculated quantitative EEG parameters such as the alpha-to-delta ratio (ADR). The ADR represented the ratio between alpha power and delta power, which indicated how fast the EEG activities were. Forelimb and hindlimb motor functions were measured by De Ryck's test and the beam walking test, respectively. In the acute phase, delta power increased fourfold with the occurrence of PDAs, and the histological staining showed that the infarct was limited to the striatum and secondary sensory cortex. In the subacute phase, the alpha power reduced to 50% of the baseline, and the infarct progressed to the forelimb cortical region. ADRs reduced from 0.23 ± 0.09 to 0.04 ± 0.01 at 3 h in the acute phase and gradually recovered to 0.22 ± 0.08 at 168 h in the chronic phase. In the comparison of correlations between the EEG parameters and the limb motor function from the acute phase to the chronic phase, ADRs were found to have the highest correlation coefficients with the beam walking test (r = 0.9524, p < 0.05) and De Ryck's test (r = 0.8077, p < 0.05). This study measured EEG activities after focal cerebral ischemia and showed that functional recovery was closely correlated with the neural activities in the penumbra. Longitudinal EEG monitoring at different phases after a stroke can provide information on the neural activities, which are well correlated with the motor function recovery.
A Novel Bocavirus Associated with Acute Gastroenteritis in Australian Children (2009)

Acute gastroenteritis (AGE) is a common illness affecting all age groups worldwide, causing an estimated three million deaths annually. Viruses such as rotavirus, adenovirus, and caliciviruses are a major cause of AGE, but in many patients a causal agent cannot be found despite extensive diagnostic testing. Proposing that novel viruses are the reason for this diagnostic gap, we used molecular screening to investigate a cluster of undiagnosed cases that were part of a larger case control study into the etiology of pediatric AGE. Degenerate oligonucleotide primed (DOP) PCR was used to non-specifically amplify viral DNA from fecal specimens. The amplified DNA was then cloned and sequenced for analysis. A novel virus was detected. Elucidation and analysis of the genome indicates it is a member of the Bocavirus genus of the Parvovirinae, 23% variant at the nucleotide level from its closest formally recognized relative, the Human Bocavirus (HBoV), and similar to the very recently proposed second species of Bocavirus (HBoV2). Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%). In this same group of children, HBoV2 prevalence was exceeded only by rotavirus (39.2%) and astrovirus (21.5%) and was more prevalent than norovirus genogroup 2 (13.4%) and adenovirus (4.8%). In a univariate analysis of the matched pairs (McNemar's Test), the odds ratio for the association of AGE with HBoV2 infection was 2.6 (95% confidence interval 1.2-5.7); P = 0.007. During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3). The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE. HBoV2 and HBoV3 are newly discovered bocaviruses, of which HBoV2 is the thirdmost-prevalent virus, after rotavirus and astrovirus, associated with pediatric AGE in this study.
Catalytic antibodies. Circular dichroism and UV-vis studies of antibody-metalloporphyrin interactions (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic antibodies. Circular dichroism and UV-vis studies of antibody-metalloporphyrin interactionsE. Keinan, E. Benory, S. C. Sinha, A. Sinha-Bagchi, D. Eren, Z. Eshhar, and B. S. GreenCite this: Inorg. Chem. 1992, 31, 26, 5433–5438Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://pubs.acs.org/doi/10.1021/ic00052a019https://doi.org/10.1021/ic00052a019research-articleACS PublicationsRequest reuse permissionsArticle Views389Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fade counter-measures applied to transmissions at 20/30 GHz (1991)

The paper deals with the future use of the 20/30 GHz satellite communications band, especially with regard to small earth terminals. The 20/30 GHz bands are attractive for private link applications, but are subject to large signal attenuations in the presence of rainfall. Methods to overcome the rain attenuation, known as fade counter-measures, are investigated.
Development and Evaluation of Real-Time PCR-Based Fluorescence Assays for Detection of Chlamydia pneumoniae (2002)

Chlamydia pneumoniae is an important respiratory pathogen recently associated with atherosclerosis and several other chronic diseases. Detection of C. pneumoniae is inconsistent, and standardized PCR assays are needed. Two real-time PCR assays specific for C. pneumoniae were developed by using the fluorescent dye-labeled TaqMan probe-based system. Oligonucleotide primers and probes were designed to target two variable domains of the ompA gene, VD2 and VD4. The limit of detection for each of the two PCR assays was 0.001 inclusion-forming unit. Thirty-nine C. pneumoniae isolates obtained from widely distributed geographical areas were amplified by the VD2 and VD4 assays, producing the expected 108- and 125-bp amplification products, respectively. None of the C. trachomatis serovars, C. psittaci strains, other organisms, or human DNAs tested were amplified. The amplification results of the newly developed assays were compared to the results of culturing and two nested PCR assays, targeting the 16S rRNA and ompA genes. The assays were compared by testing C. pneumoniae purified elementary bodies, animal tissues, 228 peripheral blood mononuclear cell (PBMC) specimens, and 179 oropharyngeal (OP) swab specimens obtained from ischemic stroke patients or matched controls. The real-time VD4 assay and one nested PCR each detected C. pneumoniae in a single, but different, PBMC specimen. Eleven of 179 OP specimens (6.1%) showed evidence of the presence of C. pneumoniae in one or more tests. The real-time VD4 assay detected the most positive results of the five assays. We believe that this real-time PCR assay offers advantages over nested PCR assays and may improve the detection of C. pneumoniae in clinical specimens.
Palladium-Catalysed Reactions of Organotin Compounds (1992)

Palladium-catalysed reactions involving organotin compounds are of rapidly increasing importance in organic synthesis. Carbon-carbon bond formation via cross-coupling reactions is of primary interest in view of the variety of functionalities which can be used. A variety of applications in natural product synthesis have been described, and intramolecular reactions can be used for the formation of small, medium and large rings. Reactions involving additions of tin-element bonds to multiply bonded systems are also of increasing significance. Although "general-purpose" catalysts are available, specific catalysts are often required for certain applications. 1. Introduction 2. Palladium-Catalysed Substitution Reactions Involving Residues R′ 2.1. R′ = Various 2.2. R′ = Vinyl 2.3. R′ = Aryl 2.4. R′ = Heteroaryl 2..5. R′ = Allyl 2.6. R′ = Alkynyl 2.7. R′= Other Organic Residues 2.8. R′ = Residue Containing Elements other than Carbon 2.8.1. Group 13 Elements 2.8.2. Other Group 14 Elements 2.8.3. Group 15 Elements 2.8.4. Group 16 Elements 2.8.5. R′ = Cl 3. Palladium-Catalysed Addition Reactions Involving Sn-E Bonds 3.1. E=H 3.2. E = SnR′3 3.3. E = SiR′3, GeR′3 3.4. E = Other Elements 4. The Choice of Tin Reagent and Catalyst 5. Conclusion