gebhart/patrepeval huggingface dataset:
Fok I dimerization is required for DNA cleavage (1998)

FokI is a type IIs restriction endonuclease comprised of a DNA recognition domain and a catalytic domain. The structural similarity of the FokI catalytic domain to the type II restriction endonuclease BamHI monomer suggested that the FokI catalytic domains may dimerize. In addition, the FokI structure, presented in an accompanying paper in this issue of Proceedings, reveals a dimerization interface between catalytic domains. We provide evidence here that FokI catalytic domain must dimerize for DNA cleavage to occur. First, we show that the rate of DNA cleavage catalyzed by various concentrations of FokI are not directly proportional to the protein concentration, suggesting a cooperative effect for DNA cleavage. Second, we constructed a FokI variant, FokN13Y, which is unable to bind the FokI recognition sequence but when mixed with wild-type FokI increases the rate of DNA cleavage. Additionally, the FokI catalytic domain that lacks the DNA binding domain was shown to increase the rate of wild-type FokI cleavage of DNA. We also constructed an FokI variant, FokD483A, R487A, which should be defective for dimerization because the altered residues reside at the putative dimerization interface. Consistent with the FokI dimerization model, the variant FokD483A, R487A revealed greatly impaired DNA cleavage. Based on our work and previous reports, we discuss a pathway of DNA binding, dimerization, and cleavage by FokI endonuclease.
Purified human factor VIII procoagulant protein: comparative hemostatic response after infusions into hemophilic and von Willebrand disease dogs. (1985)

The procoagulant protein F.VIII:C is noncovalently bound to von Willebrand factor (vWF) to give the factor VIII macromolecular complex. New highly purified preparations of isolated human F.VIII:C, devoid of vWF and about 500,000-fold purified, were administered to hemophilia A and von Willebrand disease (vWD) dogs to determine their hemostatic effectiveness and survival in the circulation. Two preparations of F.VIII:C were used: peak 1, with active components of Mr 185,000-280,000, and peak 2, with a single component of Mr 170,000. In hemophilic dogs, with no plasma F.VIII:C but normal vWF, both preparations immediately elevated plasma F.VIII:C to expected levels, promptly stopped induced and spontaneous hemorrhages, and gave sustained plasma levels of F.VIII:C. The isolated F.VIII:C immediately complexed with endogenous vWF in hemophilic plasma and was eliminated exponentially, with a half-life (t1/2) of about 9 hr. Survival of peak 2 F.VIII:C was longer than that of peak 1 material. In contrast, F.VIII:C complexed to vWF in a therapeutic concentrate administered to hemophilic dogs was eliminated biexponentially with first-phase t1/2 of 3.2 hr and second-phase t1/2 of 9 hr. In vWD dogs with no vWF and reduced F.VIII:C levels, the isolated F.VIII:C produced supernormal levels of F.VIII:C without effect on induced bleeding. It was rapidly eliminated from plasma with a t1/2 of about 1 hr, as was the complexed F.VIII:C in the concentrate. These data indicate that isolated F.VIII:C promptly complexes with vWF and in this form is highly effective in controlling hemophilic hemorrhages with good survival in plasma. Without endogenous vWF with which to complex, the F.VIII:C is promptly eliminated.
Antifouling Block Copolymer Surfaces that Resist Settlement of Barnacle Larvae (2007)

Stature, total arm length, and subischial length were studied in a cross-sectional sample of 387 working (career women) and 460 nonworking women (housewives), 20-75 years of age, from one endogamous group, the Khatris. Statural decrease due to aging was separated from secular effects by using total arm length, which was least affected by aging. The rate of loss in stature due to aging was 0.142 cm/year in the working women and 0.140 cm/year in the nonworking women. Both estimates are significantly different from zero. After adjusting stature for estimated aging effects, the resulting secular estimates were 0.004 cm/year in working women and 0.01 cm/year for nonworking women, both of which do not significantly differ from zero. © 1995 Wiley-Liss, Inc.
An ATP-dependent inhibitor of TBP binding to DNA. (1993)

An activity in yeast nuclear extracts (termed ADI) is described that inhibits the binding of the TATA-binding protein (TBP) to DNA in an ATP-dependent manner. The effect is reversible, ATP specific, rapid, and is not promoter specific. ADI is specific for TBP because three other protein-DNA complexes are not affected by ADI. The action of ADI is blocked by association of TFIIA with the TBP-DNA complex. ADI activity at the adenovirus major late promoter requires a segment of DNA upstream from the TATA sequence, suggesting that ADI recognizes aspects of both TBP and DNA. The evolutionarily conserved carboxy-terminal domain of TBP is sufficient for ADI recognition, and amino acids in the basic region of TBP are required for ADI action. ADI can repress transcription in vitro in an ATP-dependent manner. In the presence of ADI, both TFIIA and TBP are required to commit a template to transcription. A model of ADI action is proposed, and possible roles of ADI in the regulation of the transcription complex assembly are discussed.
Molecular and immunologic approaches (1994)

Oncogenes and tumor suppressor genes Antisense and triple helix therapy Immunotherapy Photodynamic therapy Boron neutron capture therapy Hyperthermia Gene therapy The hypoxic tumor cell Agents that effect multidrug resistance, angiogenesis, and metastises Drug targeting Oncogenic viruses Advances in cancer prediction, diagnosis and prognosis Cancer prevention
Salvage of a free flap after late total thrombosis of the flap and revascularisation (2004)

We report a case of successful salvage of a free flap after a late total venous thrombosis. A free forearm flap was used to cover an exposed plate over the ankle. After a normal postoperative course, the patient suddenly developed a total venous thrombosis on day 11. Nevertheless the flap was salvaged completely. This event raises further questions about the revascularisation process, which is commonly thought to occur in 7-8 days.
Halftone Image Generation and a Coding Method Based on Optimum Pixel Assignment. (1994)

This paper proposes a high quality halftone method and a highly efficient coding method for halftone images by the method In the proposed halftone method, a M x M threshold-matrix of m x m ( m <M) gray tones is adopted as the basic structure of image generation and is suitable for high quality image generation and highly efficient coding For high quality halftone image generation, the matrix is optimized on the basis of the optimal pixel assignment model which has been proposed by us For highly efficient coding of the halftone images, the structure is utilized as a priori knowledge in the coding model of arithmetic coding employed in the proposed coding method Simulation results show that the proposed method is a highly efficient loss less coding method for high quality halftone images 1.
Production of a Monoclonal Antibody Reacted Broadly with Feline Calicivirus Field Isolates. (1998)

A monoclonal antibody (MAb) reactive with 36 field isolates and 2 laboratory strains of feline calicivirus (FCV) was produced by immunizing mice with the mixture of FCVs. The MAb (4D7) reacted with FCVs in an enzyme-linked immunosorbent assay (ELISA), but had no neutralizing activity against the F4 strain of FCV. MAb 8G1, previously produced against the FCV F4 strain, also reacted in ELISA with all FCVs used in the present study. However, the epitopes recognized by 4D7 and 8G1 were different. Using these two MAbs and a polyclonal rabbit antibody, we attempted to develop a sandwich ELISA for detection of FCV antigen. The combination of 4D7 and the polyclonal rabbit IgG was most sensitive. Using this system, all the field isolates of FCV cultured in vitro were detected. However, among the 36 swab samples, from which FCV was isolated, 4 were negative.
Search for Naturally Occurring Substances to Prevent the Complications of Diabetes. II. Inhibitory Effect of Coumarin and Flavonoid Derivatives on Bovine Lens Aldose Reductase and Rabbit Platelet Aggregation. (1995)

An EtOAc extract of Artemisiae Capillari Spica inhibited both bovine lens aldose reductase (bovine-LAR) and rabbit platelet aggregation. Two simple coumarins, scoparone (1) and scopoletin (2), and three flavonoids, capillarisin (21), cirsimaritin (22) and rhamnocitrin (23), were isolated from this extract. Scoparone (1) and scopoletin (2) exhibit a potent inhibitory effect on rabbit platelet aggregation induced by four types of agent, ADP, PAF, sodium arachidonate and/or collagen. Capillarisin (21) exhibits a potent inhibitory effect on bovine-LAR. In addition, thirteen simple coumarins, five coumarin glycosides and two flavonoids were tested for their inhibitory effect against bovine-LAR and rabbit platelet aggregation.
Selective metalations of methylated pyridines and quinolines. Condensation reactions (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective metalations of methylated pyridines and quinolines. Condensation reactionsEdwin M. Kaiser, Gregory J. Bartling, William R. Thomas, Susan B. Nichols, and Diane R. NashCite this: J. Org. Chem. 1973, 38, 1, 71–75Publication Date (Print):January 1, 1973Publication History Published online1 May 2002Published inissue 1 January 1973https://pubs.acs.org/doi/10.1021/jo00941a013https://doi.org/10.1021/jo00941a013research-articleACS PublicationsRequest reuse permissionsArticle Views316Altmetric-Citations43LEARN 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
Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants (2004)

Anti-AIDS drug candidate and non-nucleoside reverse transcriptase inhibitor (NNRTI) TMC125-R165335 (etravirine) caused an initial drop in viral load similar to that observed with a five-drug combination in naïve patients and retains potency in patients infected with NNRTI-resistant HIV-1 variants. TMC125-R165335 and related anti-AIDS drug candidates can bind the enzyme RT in multiple conformations and thereby escape the effects of drug-resistance mutations. Structural studies showed that this inhibitor and other diarylpyrimidine (DAPY) analogues can adapt to changes in the NNRTI-binding pocket in several ways: (1). DAPY analogues can bind in at least two conformationally distinct modes; (2). within a given binding mode, torsional flexibility ("wiggling") of DAPY analogues permits access to numerous conformational variants; and (3). the compact design of the DAPY analogues permits significant repositioning and reorientation (translation and rotation) within the pocket ("jiggling"). Such adaptations appear to be critical for potency against wild-type and a wide range of drug-resistant mutant HIV-1 RTs. Exploitation of favorable components of inhibitor conformational flexibility (such as torsional flexibility about strategically located chemical bonds) can be a powerful drug design concept, especially for designing drugs that will be effective against rapidly mutating targets.
Adenovirus E1B proteins are required for accumulation of late viral mRNA and for effects on cellular mRNA translation and transport. (1985)

Late in adenovirus infection, large amounts of viral mRNA accumulate while cell mRNA transport and translation decrease. Viruses deleted in the E1B region of type 5 adenovirus do not produce the same outcome: (i) viral mRNA synthesis by the mutants is normal, delivery to the cytoplasm is 50 to 75% of normal, but steady-state levels of viral mRNA are decreased 10-fold; (ii) cell mRNA synthesis and transport continue normally in the mutant virus-infected cell; and (iii) translation of preexisting cell mRNA which is disrupted in wild-type infection remains normal in mutant-virus-infected cells. Thus E1B proteins are required for accumulation of virus mRNA and for induction of the failure of host cell mRNA transport and translation. If a single function is involved, by inference the transport and some aspect of translation of mRNAs could be linked.
Surface tension of poly[(3,3,4,4,5,5,6,6,6-nonafluorohexyl)methylsiloxane] (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSurface tension of poly[(3,3,4,4,5,5,6,6,6-nonafluorohexyl)methylsiloxane]Hideki Kobayashi and Michael J. OwenCite this: Macromolecules 1990, 23, 23, 4929–4933Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/ma00225a008https://doi.org/10.1021/ma00225a008research-articleACS PublicationsRequest reuse permissionsArticle Views767Altmetric-Citations75LEARN 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
Potentially Amyloidogenic, Carboxyl-Terminal Derivatives of the Amyloid Protein Precursor (1992)

The 39- to 43-amino acid amyloid beta protein (beta AP), which is deposited as amyloid in Alzheimer's disease, is encoded as an internal peptide that begins 99 residues from the carboxyl terminus of a 695- to 770-amino acid glycoprotein referred to as the amyloid beta protein precursor (beta APP). To clarify the processing that produces amyloid, carboxyl-terminal derivatives of the beta APP were analyzed. This analysis showed that the beta APP is normally processed into a complex set of 8- to 12-kilodalton carboxyl-terminal derivatives. The two largest derivatives in human brain have the entire beta AP at or near their amino terminus and are likely to be intermediates in the pathway leading to amyloid deposition.
Role of Flagella in Pathogenesis ofPseudomonas aeruginosaPulmonary Infection (1998)

Pseudomonas aeruginosa strains are opportunistic pathogens associated with infections in immunocompromised hosts and patients with cystic fibrosis. Like many other mucosal pathogens, P. aeruginosa cells express flagella which provide motility and chemotaxis toward preferred substrates but also provide a ligand for clearance by phagocytic cells. We tested the role of flagella in the initial stages of respiratory tract infection by comparing the virulence of fliC mutants in a neonatal mouse model of pneumonia. In the absence of fliC, there was no mortality, compared with 30% mortality attributed to the parental strain PAK or 15% mortality associated with infection due to a pilA mutant PAK/NP (P < 0.0001). The fliC mutants caused pneumonia in only 25% of the mice inoculated, regardless of whether there was expression of the pilus, whereas the parental strain was associated with an 80% rate of pneumonia. Histopathological studies demonstrated that the fliC mutants caused very focal inflammation and that the organisms did not spread through the lungs as seen in infection due to either PAK or PAK/NP. Purified flagellin elicited an intense inflammatory response in the mouse lung. 125I-labeled flagellin bound to the glycolipids GM1 and GD1a and to asialoGM1 in an in vitro binding assay. However, flagellin-mediated binding to epithelial gangliosides was a relatively unusual event, as quantified by binding assays of wild-type or fliC mutant organisms to CHO Lec-2 cells with membrane-incorporated GM1. Fla+ organisms but not fliC mutants were efficiently taken up by murine macrophages. P. aeruginosa flagella are important in the establishment of respiratory tract infection and may act as a tether in initial interactions with epithelial membranes. This function is offset by the contribution of flagella to host clearance mechanisms facilitating phagocytic clearance and the role of flagellar genes in mucin binding and clearance.
An Indoor-Location Sensing System using WLAN and Ultrasonic/Radio Technologies (2008)

A recently described splice variant of CD44 has been shown to confer metastatic potential to non-metastasizing rat pancreatic carcinoma and sarcoma cell lines. Using antibodies raised against a bacterial fusion protein encoded by variant CD44 sequences, we have explored the expression of variant CD44 glycoproteins in human lymphoid cells and tissues, in non-Hodgkin's lymphomas, and in colorectal neoplasia. Normal lymphohematopoietic cells express barely detectable low levels of variant CD44 glycoproteins, while T lymphocytes, upon activation by mitogen or antigen, transiently upregulate expression of specific CD44 variant glycoproteins. The reaction pattern of various antibodies indicates that these CD44 variants contain the domain encoded by exon v6, which is part of the variant that in the rat confers metastatic capability. Interestingly, overexpression of v6 was also found in several aggressive, but not in low-grade, non-Hodgkin's lymphomas (NHL). In human colorectal neoplasia we also observed strong overexpression of CD44 splice variants in all invasive carcinomas and carcinoma metastasis. Interestingly, focal expression was already observed in adenomatous polyps, expression being related to areas of dysplasia. The findings establish CD44 variants as tumor progression markers in colorectal cancer.
Principles of immunology and its nuances in the central nervous system: Fig. 1. (2015)

Cancer immunotherapy represents the biggest change in the cancer treatment landscape in the last several years. Indeed, the clinical successes in several cancer types have generated widespread enthusiasm that immune-based treatments may influence the management of patients with malignant brain tumors as well. A number of promising clinical trials in this area are currently ongoing in neuro-oncology, and a wave of additional efforts are sure to follow. However, the basic immunology underlying immunotherapy-and the nuances unique to the immunobiology in the central nervous system-is often not in the daily lexicon of the practicing neuro-oncologist and neurosurgeon. To this end, here we provide a timely and working overview of key principles of fundamental immunology as a pragmatic context for understanding where therapeutic efforts may act in the cellular dynamics of the immune response. Moreover, we review the issues of lymphatic drainage, antigen presentation, and the blood-brain barrier as considerations that are germane to thinking about immunity to tumors arising in the brain. Together, these topics will provide a foundation for the exciting efforts in immune-based treatments that will hopefully provide real benefit to brain tumor patients.
Promising vanadium oxide and hydroxide nanostructures: from energy storage to energy saving (2010)

The great energy demand for fossil fuels impacts air pollution and water pollution, which significantly influences human life today, and thus efficient utilization of energy has directed a global trend towards a diversified energy portfolio, particularly focusing on energy storage and saving applications. Owing to their special structural characteristics, vanadium oxides have received particular interest for efficient energy utilization, and the search for new kinds of vanadium oxides in the applications of the energy issues has been highlighted in recent years. This review surveys recent advances in tackling energy utilization issues, such as organic electrolyte or aqueous electrolyte lithium-ion batteries (LIB), by the development of vanadium oxide nanostructures, as well as energy-saving applications, via regulating the desired structure and morphology characteristics of vanadium oxides. The nanoarchitectured vanadium oxides with valence state from +3 to +5 all seem ripe for further development for the organic-electrolyte LIB application with improved energy density and cycling performance. In addition, solution-based synthesis gives a facile and inexpensive route to grow and assemble their nanoarchitectures for organic-electrolyte LIB applications. Moreover, although the application of vanadium oxides in aqueous LIB is still in its infant stage, controlling the morphology and structure of vanadium oxides also plays a vital role in the improvement of the aqueous LIB performance. Furthermore, the energy-saving application of vanadium oxides, which arises from the smart switching properties, bring us drastic changes in electrical conductivity and near-IR optical properties for the energy-saving application as the “smart window” coatings. The challenges and ongoing research strategies of the application of vanadium oxides for efficient energy utilization are also discussed in this review article.
Detection of Deep-Vein Thrombosis by Real-Time B-Mode Ultrasonography (1989)

In 220 consecutive outpatients with clinically suspected deep-vein thrombosis of the leg, we compared contrast venography with real-time B-mode ultrasonography, using the single criterion of vein compressibility with the ultrasound transducer probe. The common femoral and popliteal veins were evaluated for full compressibility (no thrombosis) and noncompressibility (thrombosis). Both veins were fully compressible in 142 of the 143 patients with normal venograms (specificity, 99 percent; 95 percent confidence interval, 97 to 100). All 66 patients with proximal-vein thrombosis had noncompressible femoral veins, popliteal veins, or both (sensitivity, 100 percent; 95 percent confidence interval, 95 to 100). For all patients (including 11 with calf-vein thrombi), sensitivity and specificity were 91 (95 percent confidence interval, 82 to 96) and 99 percent, respectively. The sensitivity for isolated calf-vein thrombosis was only 36 percent. The compression ultrasound test was repeated in a subset of 45 consecutive patients by a second examiner, unaware of the results of the first test, whose results agreed in all patients with those of the first examiner (kappa = 1). We conclude that ultrasonography with the single criterion of vein compressibility is a highly accurate, simple, objective, and reproducible noninvasive method for detecting proximal-vein thrombosis in outpatients with clinically suspected deep-venous thrombosis.