gebhart/patrepeval huggingface dataset:
A simple, high sensitivity mutation screening using Ampligase mediated T7 endonuclease I and Surveyor nuclease with microfluidic capillary electrophoresis (2012)

Mutation and polymorphism detection is of increasing importance for a variety of medical applications, including identification of cancer biomarkers and genotyping for inherited genetic disorders. Among various mutation‐screening technologies, enzyme mismatch cleavage (EMC) represents a great potential as an ideal scanning method for its simplicity and high efficiency, where the heteroduplex DNAs are recognized and cleaved into DNA fragments by mismatch‐recognizing nucleases. Thereby, the enzymatic cleavage activities of the resolving nucleases play a critical role for the EMC sensitivity. In this study, we utilized the unique features of microfluidic capillary electrophoresis and de novo gene synthesis to explore the enzymatic properties of T7 endonuclease I and Surveyor nuclease for EMC. Homoduplex and HE DNAs with specific mismatches at desired positions were synthesized using PCR (polymerase chain reaction) gene synthesis. The effects of nonspecific cleavage, preference of mismatches, exonuclease activity, incubation time, and DNA loading capability were systematically examined. In addition, the utilization of a thermostable DNA ligase for real‐time ligase mediation was investigated. Analysis of the experimental results has led to new insights into the enzymatic cleavage activities of T7 endonuclease I and Surveyor nuclease, and aided in optimizing EMC conditions, which enhance the sensitivity and efficiency in screening of unknown DNA variations.
Action of phosphorylated mannanoligosaccharides on immune and hematological responses and fecal consistency of dogs experimentally infected with enteropathogenic Escherichia coli strains (2013)

The therapeutic action of phosphorylated mannanoligosaccharides (MOS) was investigated regarding its prebiotic activity on enteropathogenic Escherichia coli (EPEC). Diarrhea was induced in dogs by experimental infection with EPEC strains. Then MOS was supplied once a day, in water for 20 days. Immunological (IgA and IgG), hematological (lymphocytes, neutrophils and monocytes) and bacteriological variables (PCR detection of the eae gene of EPEC recovered from stool culture), as well as occurrence of diarrhea were evaluated. All strains caused diarrhea at 24, 48 and 72 h after infection. PCR results indicated that E. coli isolated from stool culture of all infected animals had the eae gene. There was no significant difference among groups as to number of blood cells in the hemogram and IgA and IgG production. MOS was effective in recovering of EPEC-infected dogs since prebiotic-treated animals recovered more rapidly from infection than untreated ones (p < 0.05). This is an important finding since diarrhea causes intense dehydration and nutrient loss. The use of prebiotics for humans and other animals with diarrhea can be an alternative for the treatment and prophylaxis of EPEC infections.
Slender PUF Protocol: A Lightweight, Robust, and Secure Authentication by Substring Matching (2012)

We introduce Slender PUF protocol, an efficient and secure method to authenticate the responses generated from a Strong Physical Unclonable Function (PUF). The new method is lightweight, and suitable for energy constrained platforms such as ultra-low power embedded systems for use in identification and authentication applications. The proposed protocol does not follow the classic paradigm of exposing the full PUF responses (or a transformation of the full string of responses) on the communication channel. Instead, random subsets of the responses are revealed and sent for authentication. The response patterns are used for authenticating the prover device with a very high probability. We perform a thorough analysis of the method's resiliency to various attacks which guides adjustment of our protocol parameters for an efficient and secure implementation. We demonstrate that Slender PUF protocol, if carefully designed, will be resilient against all known machine learning attacks. In addition, it has the great advantage of an inbuilt PUF error tolerance. Thus, Slender PUF protocol is lightweight and does not require costly additional error correction, fuzzy extractors, and hash modules suggested in most previously known PUF-based robust authentication techniques. The low overhead and practicality of the protocol are confirmed by a set of hardware implementation and evaluations.
Molecular Cloning and Sequence Analysis of the Gene Encoding the H2O2-forming NADH Oxidase fromStreptococcus mutans (1994)

Streptococcus mutans induces both H2O2-forming and H2O-forming NADH oxidases in the presence of O2 [M. Higuchi, J. Gen. Microbiol., 130, 1819-1826 (1984)]. In this paper, a nox-1 gene encoding H2O2-forming NADH oxidase (NOX-1) from Streptococcus mutans was cloned, and the nucleotides sequenced. The structural gene of nox-1 consisted of 1530 base pairs, which encode a polypeptide consisting of 510 amino acids with a predicted molecular mass of 55,196 Da. The deduced N-terminal amino acid sequence was consistent with that previously found for the purified NOX-1 protein. The nox-1 gene was expressed in Escherichia coli using its own promoter. Alignment of the amino acid sequence of NOX-1 with those of NADH oxidases from other microorganisms showed identities of 55.6%, 20.8%, 20.3%, and 7.3% for those of Amphibacillus xylanus Ep01, Streptococcus faecalis 10C1, Thermoanaerobium brockii Rt8.G4, and Thermus thermophilus HB8, respectively.
In Vitro Effects of Recombinant TNF-α Binding Protein (rTBP-1) on Hematopoiesis of HIV-Infected Patients (2001)

Summary: Tumor necrosis factor-alpha (TNF-α) is believed to contribute to the hematopoietic failure often observed in patients with AIDS. Soluble TNF receptors (sTNFR) compete for TNF-α with cell surface receptors and thus may block its activity. The effect of the p55 sTNFR (recombinant TNF-binding protein-1 [rTBP-1]) on the clonogenic growth of hematopoietic progenitor cells from 27 HIV-infected patients was evaluated in comparison with 11 normal study subjects. Peripheral bloodderived, myelopoietic (i.e., granulomonocytic colony-forming cells [GM-CFC]) and erythropoietic (i.e, burst-forming unit, erythroid [BFU-E]) colonies were grown in 10-day semisolid cultures with increasing concentrations of rTBP-1. Significantly, dose-dependent increases occurred in GM-CFC from 17 of 21 AIDS patients and 12 of 21 in BFU-E at rTBP-1 concentrations of 1μ/ml to 25 μ/ml. In contrast, rTBP-1 failed to induce any appreciably increased colony formation in normal cell cultures. In 6 patients treated with highly active antiretroviral treatment (HAART), TBP-1 alone did not demonstrate the in vitro hematopoiesis-enhancing effect. This study may provide an initial step in development of therapeutic use of TBP as a TNF-α antagonist in HIV-infected patients who do not benefit sufficiently from antiretroviral treatment, and in other conditions in which increased levels of TNF-α may contribute to hematopoietic deficiencies.
Surface organometallic chemistry: synthesis and characterization of a tris(neopentyl)zirconium(IV) complex grafted to the surface of a partially dehydroxylated silica (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSurface organometallic chemistry: synthesis and characterization of a tris(neopentyl)zirconium(IV) complex grafted to the surface of a partially dehydroxylated silicaFrancoise Quignard, Christine Lecuyer, Catherine Bougault, Frederic Lefebvre, Agnes Choplin, Daniele Olivier, and Jean Marie BassetCite this: Inorg. Chem. 1992, 31, 5, 928–930Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://pubs.acs.org/doi/10.1021/ic00031a042https://doi.org/10.1021/ic00031a042research-articleACS PublicationsRequest reuse permissionsArticle Views600Altmetric-Citations94LEARN 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
Immune enhancement of the tumorigenicity of hamster brain tumor cells persistently infected with measles virus (1975)

Studies were conducted on the tumorigenicity of a hamster brain tumor (HBT) cell line persistently infected with measles virus (MV). This cell population, termed HBT-M, exhibited decreased tumorigenicity in weanling hamsters when implanted intracutaneously. The lowered tumorigenicity of the HBT-M cells could be counteracted by concurrent hydrocortisone treatment restoring the tumor-producing capacity to levels comparable to those of the highly tumorigenic HBT cells. It was also determined that prior immunization of hamsters with MV resulted in enhancement of tumor formation from usually subtumorigenic doses of HBT-M cells. This increase in tumorigenicity appeared to correlate with high titers of MV antibody. Treatment of hamsters with cyclophosphamide resulted in a reduction of MV antibody titers and effected a decrease of HBT-M cell tumorigenicity to control levels. Preliminary studies with passive immunizations indicated that the enhancing factor could be transferred in the sera from hamsters hyperimmunized with MV. These data suggested that MV antibody may potentiate the development of neoplasia of cells persistently infected with MV in a manner similar to the enhancement of tumor growth by blocking antibody.
The application of a cytochrome P450 enzyme eluted from encapsulated biomaterials for the catalysis of enantioselective oxidation (2014)

A membrane-bound enzyme (ME) eluted from encapsulated pea protein (PP) under aeration is applicable for the kinetic resolutions of turnover: each enantiomer of rac-1-(6-methoxynaphthalen-2-yl)ethanol (rac-1) can be selectively synthesized (>99% ee; ∼50% chemical yield), utilizing two types of biomaterials: (1) a PEG (1000/4000 = 2/1)-aggregated ME (AGME: synthesizing highly enantiopure R-(−)-1) and (2) a glutaraldehyde (GA)/a PEG (4000)-coated ME (a CMME: synthesizing S-(+)-1 (S-naproxen precursor)). Both reactions occur in the absence of an added cofactor (e.g., NAD(P)) in aqueous media. The specific activities of AGME and CMME were determined to be 0.8 ± 0.03 mU (mean ± SD) mg−1 min−1 and 0.6 ± 0.02 mU (mean ± SD) mg−1 min−1, respectively, and the species exact nature engaged in the key reaction was consistent with that of a heme-binding protein (HBP) based on an N-terminal sequence comparison, which showed 93% similarity with a 20.853 kDa hemophore HasA gene product [Pseudomonas fluorescens Pf-5, a plant commensal bacterium]. The PP-HBP can be regenerated via a successive asymmetric catalytic event using an incorporated iron electron-transfer system in the presence of oxygen—a process seemingly similar to that utilized by the oxygen-driven cytochrome P450 enzyme (Cyt-P450: cysteine – Fe2+ + O2 → Fe3+–O–O− → Fe4+O (oxidizing rac-1 or rac-2) → Fe2+ + H2O). The use of a raw biomaterial as an ME-catalytic system with an incorporated redox cofactor for asymmetric oxidation overcomes the apparent difficulties in working with pure dehydrogenase enzyme/redox cofactor systems for biotransformation.
Copper-Catalyzed Oxidative Cross-Coupling of H-Phosphonates and Amides to N-Acylphosphoramidates (2013)

A simple combination of copper(II) acetate (Cu(OAc)(2)) and an appropriate base could promote oxidative cross-coupling of H-phosphonates and amides using air as a terminal oxidant. The substrate scope was broad with respect to both dialkyl H-phosphonates and nitrogen nucleophiles (including oxazolidinone, lactam, pyrrolidinone, urea, indole, and sulfonamide derivatives), giving the corresponding P-N coupling products in moderate to high yields.
Characterization of the fliE genes of Escherichia coli and Salmonella typhimurium and identification of the FliE protein as a component of the flagellar hook-basal body complex (1992)

Within flagellar region III of Escherichia coli and Salmonella typhimurium, the genomic organization has been largely established. An exception is fliE, a gene whose exact location and product function are not well understood. We cloned the fliE gene, obtained its DNA sequence, and identified its product.fliE was found to be a monocistronic transcriptional unit, adjacent to and divergent from the large fliF operon. It is several kilobases distant from the nearest flagellar operon in the other direction, the fliD operon, and constitutes the first operon within the newly defined region IIIb, which contains the genes fliE through fliR.fliE encodes a small, moderately hydrophilic protein with a deduced molecular mass of 11,114 Da (E. coli) or 11,065 Da (S. typhimurium). We identified a protein within the isolated hook-basal body complex as the fliE gene product on the basis of its size and comparison of its N-terminal amino acid sequence with that deduced from the gene sequence. From gel electrophoresis and autoradiography of 35S-labeled S. typhimurium hook-basal body complexes (C.J. Jones, R.M. Macnab, H. Okino, and S.-I. Aizawa, J. Mol. Biol. 212:377-387, 1990) and the deduced number of sulfur-containing residues in FliE, we estimated the stoichiometry of the protein in the hook-basal body complex to be about nine subunits. FliE does not undergo cleavage of a signal peptide, nor does it show any sequence similarity to the axial components like the rod or hook proteins, which are believed to be exported by the flagellum-specific export pathway. On the basis of this and other evidence, we suggest that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between the ring and rod substructures.
Defects in limb, craniofacial, and thymic development in Jagged2 mutant mice (1998)

The Notch signaling pathway is a conserved intercellular signaling mechanism that is essential for proper embryonic development in numerous metazoan organisms. We have examined the in vivo role of the Jagged2 (Jag2) gene, which encodes a ligand for the Notch family of transmembrane receptors, by making a targeted mutation that removes a domain of the Jagged2 protein required for receptor interaction. Mice homozygous for this deletion die perinatally because of defects in craniofacial morphogenesis. The mutant homozygotes exhibit cleft palate and fusion of the tongue with the palatal shelves. The mutant mice also exhibit syndactyly (digit fusions) of the fore- and hindlimbs. The apical ectodermal ridge (AER) of the limb buds of the mutant homozygotes is hyperplastic, and we observe an expanded domain of Fgf8 expression in the AER. In the foot plates of the mutant homozygotes, both Bmp2 and Bmp7 expression and apoptotic interdigital cell death are reduced. Mutant homozygotes also display defects in thymic development, exhibiting altered thymic morphology and impaired differentiation of gamma delta lineage T cells. These results demonstrate that Notch signaling mediated by Jag2 plays an essential role during limb, craniofacial, and thymic development in mice.
4‐substituted‐1,2,3,4‐tetrahydro‐3,3‐dimethylisoquinolines. II. (1982)

Abstract A practical synthesis (Scheme I) is described for the preparation of a series of 4‐substituted‐3,3‐dimethyl‐1,2,3,4‐tetrahydroisoquinolines ( 3 ). Treatment of α‐(1‐amino‐1‐methylethyl)arylmethanols or α‐(1‐amino‐1‐methylethyl)heteroarylmethanols ( 5 ) with aromatic aldehydes gave imines 7 from which amino alcohols 8 were derived by reduction with potassium borohydride. Acid catalyzed cyclization of 8 yielded 3 . An acyl substituent was installed by Friedel‐Crafts acylation as a final step. The biological activities of 3a (1) are briefly described.
Phase I/II Study of Galiximab, an Anti-CD80 Antibody, for Relapsed or Refractory Follicular Lymphoma (2005)

The favorable safety profile of galiximab and evidence of single-agent biologic activity and dose-dependent pharmacokinetics support further evaluation of galiximab as a treatment for follicular lymphoma, possibly in combination with other lymphoma therapies.
Tilted fiber phase gratings (1996)

A detailed theoretical treatment is presented of bound-mode to bound-mode Bragg reflection and bound-mode to radiation-mode coupling loss in a tilted optical-fiber phase grating. Numerical predictions of the effects of grating tilt on the spectral characteristics of such a grating are calculated. These predictions are compared with experimentally measured spectra of strong gratings written by ultraviolet irradiation of deuterium-sensitized fiber with grating tilt angles ranging from 0° to 15°. Good agreement is obtained between the theoretical predictions and the experimental results.
Management of Heat and Cold stress (2013)

Educate the Soldiers on the steps needed to minimize the risk of heat/cold casualties and optimize performance. 5) Develop heat
Ligand interactions with the kringle 5 domain of plasminogen. A study by 1H NMR spectroscopy. (1990)

The binding of small molecules to the kringle 5 domain fragment of human plasminogen has been investigated by 1H NMR spectroscopy at 300 MHz. The compounds tested as potential ligands include L-arginine, L-lysine, and a number of aliphatic and aromatic analogs of similar size but different ionic charge configurations. Ligand/kringle 5 association constant (Ka) values were obtained from ligand titration experiments at 22 degrees C, pH 7.2. Neither L-arginine nor N alpha-acetyl-L-arginine and N alpha-acetyl-L-arginine methyl ester bind measurably to kringle 5 (Ka approximately less than 0.05 mM-1). In contrast, binding of hexylamine or epsilon-aminocaproic acid (epsilon ACA) is favored (Ka approximately 2.9 and 10.5 mM-1, respectively). Benzamidine and p-benzylaminesulfonic acid associate with kringle 5 with similar affinities (Ka approximately 3.4 and 2.2 mM-1, respectively) while benzylamine binds about twice as tightly (Ka approximately 6.3 mM-1). The higher affinities toward both benzylamine and epsilon ACA indicate that a free carboxylate group is not, by itself, a main determinant of ligand-binding to kringle 5. The experiments also reveal a definite affinity for L-arginine methyl ester, L-lysine, and N alpha-acetyl-L-lysine methyl ester. It is suggested that, although weak (0.1 approximately less than Ka approximately less than 0.6 mM-1), these interactions could be of physiological relevance in the context of plasminogen binding to the fibrin clot. Ligand-induced shifts of kringle 5 proton resonances indicate that the Trp25, His33, Tyr50, Trp62, and Tyr72 (kringle numbering convention) side chains form or neighbor the kringle 5-binding site. Benzamidine-kringle 5 magnetization transfer (Overhauser) experiments verify a close proximity of the bound ligand to these aromatic groups. A model of the binding site is proposed in which the above residues interact closely with each other and define a lipophilic surface which is accessible to the free ligand.
The Diagnosis of Cytomegalovirus Retinitis (1988)

Immunosuppressed patients are at risk for developing cytomegalovirus retinitis. This disorder is the most common cause of vision loss in patients with the acquired immunodeficiency syndrome (AIDS). Cytomegalovirus retinitis is probably the result of hematogenous spread of the virus to the retina after systemic reactivation of a latent cytomegalovirus infection. Although the ophthalmic infection may initially be asymptomatic, the retinal necrosis it produces may result in both loss of visual field and decreased visual acuity. Routine screening of these patients is required for early diagnosis. The retinitis is detected with ophthalmoscopy as either a perivascular yellow-white retinal lesion frequently associated with retinal hemorrhage or as a focal white granular infiltrate, often without hemorrhage. Both lesions enlarge in a progressively expanding "brushfire" pattern. The diagnosis of cytomegalovirus retinitis, as well as the evaluation of its response to therapy, is determined primarily by clinical criteria. Serial retinal photography is an objective method to assess the changing appearance of these lesions. Ganciclovir and foscarnet are investigational antiviral drugs that appear to be effective in treating cytomegalovirus retinitis. However, maintenance therapy with these medications is required after initial treatment because the disease often relapses. The combined expertise of the internist and the ophthalmologist is needed to diagnose and treat these patients.
Expansion of the sortase-mediated labeling method for site-specific N-terminal labeling of cell surface proteins on living cells (2009)

The sortase-mediated labeling method, whose applications have been limited to C-terminal labeling of cell surface proteins, has been expanded for site-specific N-terminal labeling of cell surface proteins.
Interleukin-2 and STAT5 in regulatory T cell development and function (2013)

Interleukin-2 and its downstream target STAT5 have effects on many aspects of immune function. This has been perhaps best documented in regulatory T cells. In this review we summarize the initial findings supporting a role for IL2 and STAT5 in regulatory T cell development and outline more recent studies describing how this critical signaling pathway entrains regulatory T cell differentiation and affects regulatory T cell function.
Role of Protein C in Renal Dysfunction after Polymicrobial Sepsis (2007)

Protein C (PC) plays an important role in vascular function, and acquired deficiency during sepsis is associated with increased mortality in both animal models and in clinical studies. This study explored the consequences of PC suppression on the kidney in a cecal ligation and puncture model of polymicrobial sepsis. This study shows that a rapid drop in PC after sepsis is strongly associated with an increase in blood urea nitrogen, renal pathology, and expression of known markers of renal injury, including neutrophil gelatinase-associated lipocalin, CXCL1, and CXCL2. The endothelial PC receptor, which is required for the anti-inflammatory and antiapoptotic activity of activated PC (APC), was significantly increased after cecal ligation and puncture as well as in the microvasculature of human kidneys after injury. Treatment of septic animals with APC reduced blood urea nitrogen, renal pathology, and chemokine expression and dramatically reduced the induction of inducible nitric oxide synthase and caspase-3 activation in the kidney. The data demonstrate a clear link between acquired PC deficiency and renal dysfunction in sepsis and suggest a compensatory upregulation of the signaling receptor. Moreover, these data suggest that APC treatment may be effective in reducing inflammatory and apoptotic insult during sepsis-induced acute renal failure.