gebhart/patrepeval huggingface dataset:
Protection of mice against yellow fever virus encephalitis by immunization with a vaccinia virus recombinant encoding the yellow fever virus non-structural proteins, NS1, NS2a and NS2b (1990)

Recent evidence of a protective immune response to the flavivirus non-structural protein, NS1, has suggested its incorporation into possible recombinant vaccines. The region of the 17D yellow fever virus (YFV) genome encoding the C terminus of envelope glycoprotein and extending to the N terminus of non-structural protein NS3 (NS1-NS2a-NS2b; nucleotides 2030 to 4940) was expressed in vaccinia virus and physical and immunogenic properties of the NS1 moiety were studied. Recombinant NS1 protein, and native YFV NS1, was detected at the surface of infected cells by immunofluorescence and by immune cytolysis after treatment with anti-NS1 antibody and complement. NS1 was also detected in the extracellular medium as a secreted form. Recombinant NS1 was immunoprecipitated as a single protein of approximately the same size as native 17D YFV NS1. Unboiled, both recombinant and native NS1 formed polymers of high Mr. Immunization of mice with this recombinant vaccinia virus stimulated production of non-neutralizing, complement-fixing cytolytic antibody and conferred partial protection against lethal intracerebral inoculation of mice with live 17D YFV.
Application of Multielement Stable Isotope Ratio Analysis to the Characterization of French, Italian, and Spanish Cheeses (2004)

The stable isotope ratios (delta13C, delta15N, and delta34S of casein and delta13C and delta18O of glycerol) measured by IRMS of French, Italian, and Spanish cheeses are presented and discussed. Variability factors such as animal-feeding regimen, geographical origin, and climatic and seasonal conditions were studied to check the possibilities of cheese characterization offered by each isotopic parameter. Delta13C values of both casein and glycerol appeared to be strongly correlated to the amount of maize in the animal diet. Delta15N and delta34S of casein proved to be mostly influenced by the geoclimatic conditions of the area (aridity, closeness to the sea, altitude). Delta18O of glycerol was more dependent on the geographical origin of the cheeses and on climatic/seasonal parameters. By applying a multivariate stepwise canonical discriminant analysis, good discrimination possibilities for the different European cheeses were obtained, confirmed by the classification analysis, when >90% of the samples were correctly reclassified.
Requirement for distinct Janus kinases and STAT proteins in T cell proliferation versus IFN-gamma production following IL-12 stimulation. (1998)

While IL-12 is known to activate JAK2 and TYK2 and induce the phosphorylation of STAT4 and STAT3, little is known regarding how the activation of these signaling molecules is related to the biologic effects of IL-12. Using an IL-12-responsive T cell clone (2D6), we investigated their requirements for proliferation and IFN-gamma production of 2D6 cells. 2D6 cells could be maintained with either IL-12 or IL-2. 2D6 lines maintained with IL-12 (2D6(IL-12)) or IL-2 (2D6(IL-2)) exhibited comparable levels of proliferation, but produced large or only small amounts of IFN-gamma, respectively, when restimulated with IL-12 after starvation of either cytokine. 2D6(IL-12) induced TYK2 and STAT4 phosphorylation. In contrast, their phosphorylation was marginally induced in 2D6(IL-2). The reduced STAT4 phosphorylation was due to a progressive decrease in the amount of STAT4 protein along with the passages in IL-2-containing medium. 2D6(IL-12) and 2D6(IL-2) similarly proliferating in response to IL-12 induced comparable levels of JAK2 activation and STAT5 phosphorylation. JAK2 was associated with STAT5, and IL-12-induced STAT5 phosphorylation was elicited in the absence of JAK3 activation. These results indicate that IL-12 has the capacity to induce/maintain STAT4 and STAT5 proteins, and that TYK2 and JAK2 activation correlate with STAT4 phosphorylation/IFN-gamma induction and STAT5 phosphorylation/cellular proliferation, respectively.
Effect of blood bonding on bursting strength of laser‐assisted microvascular anastomoses (1988)

This experiment evaluated the influence of blood on the weld strength of laser-assisted microvascular anastomoses (LAMA). Rat femoral arteries were anastomosed end-to-end by either direct laser welding (group I) or by a blood-bonded technique (group II) whereby fresh blood was applied to the vessel edges before laser exposure. Bursting strength was measured at 0, 1, and 24 hours and at 3 and 7 days by infusing methylene blue into the vessel while pressure was monitored. The results showed significantly increased bursting strength in group II compared with group I at 0 hour and 7 days (P less than 0.05). There was a significant increase in bursting strength in group I from 0 hour to 1 hour (P less than 0.05). It is concluded that blood-bonding enhances the early bursting strength of LAMAs and may facilitate arterial wall healing.
Dirhodium(II) Tetrakis[methyl 2-oxaazetidine-4-carboxylate]:  A Chiral Dirhodium(II) Carboxamidate of Exceptional Reactivity and Selectivity (2000)

[formula: see text] A new chiral azetidinone-carboxylate ligand for dirhodium(II) catalysis enhances reactivity toward diazo decomposition and selectivity toward cyclopropanation enabling diazomalonates, vinyldiazoacetates, and aryldiazoacetates to be effectively used with a dirhodium(II) carboxamidate catalyst.
Low V_π Silicon photonics modulators with highly linear epitaxially grown phase shifters (2015)

We report on the design of Silicon Mach-Zehnder carrier depletion modulators relying on epitaxially grown vertical junction diodes. Unprecedented spatial control over doping profiles resulting from combining local ion implantation with epitaxial overgrowth enables highly linear phase shifters with high modulation efficiency and comparatively low insertion losses. A high average phase shifter efficiency of VπL = 0.74 V⋅cm is reached between 0 V and 2 V reverse bias, while maintaining optical losses at 4.2 dB/mm and the intrinsic RC cutoff frequency at 48 GHz (both at 1 V reverse bias). The fabrication process, the sensitivity to fabrication tolerances, the phase shifter performance and examples of lumped element and travelling wave modulators are modeled in detail. Device linearity is shown to be sufficient to support complex modulation formats such as 16-QAM.
Active site labeling of HIV-1 reverse transcriptase (1993)

The human immunodeficiency virus-1 reverse transcriptase (HIV-1 RT) heterodimer (M(r) = 66,000 and M(r) = 51,000) has been photoaffinity labeled using 4-thiodeoxyuridine triphosphate (S4-dUTP) as a probe. A nascent polymerization complex was assembled from a single-stranded DNA template, a 12-mer DNA primer, and the necessary dNTPs (one of which was alpha-32P-labeled) to extend the primer to produce the n-1 product. The photoaffinity probe was then uniquely added at the 3'-terminal position of the extended primer bound at the catalytic site and photolyzed. The larger subunit (p66) was exclusively derivatized. The unique radioactive peptide resulting from proteolysis was isolated and identified by amino acid sequencing.
Walter and Miller's Textbook of radiotherapy : radiation physics, therapy, and oncology (2003)

PART 1: RADIATION PHYSICS Some basic physics. Section 1: Physics of radiation: The atom and the production of X-rays. The nucleus and radioactivity. Radiation interactions with matter. Measurement and detection of X- and gamma rays. Radiation protection. Section 2: Imaging with Radiation: X-ray imaging. Nuclear medicine. Section 3: Physics of Radiotherapy: Kilovoltage beam generators. Megavoltage beam generators. Radiation treatment planning - immobilisation and contouring. Principles of radiation treatment planning. Practice of radiation treatment planning. Brachytherapy. Therapy with unsealed radionuclides. PART 2: RADIOTHERAPY AND ONCOLOGY Cancer: epidemiology, prevention, early diagnosis and education. Biological and pathological introduction. Principles of radiobiology. Effects of radiation on normal tissues. Principles of management and dosage. Skin and lip. Interstitial implantation. Mouth, secondary node of neck, tonsil, nasopharynx, paranasal sinuses, ear, salivary glands. Larynx, lower pharynx, postcricoid, thyroid. Oesophagus, stomach, gastrointestinal tract, lung, thymus, pancreas, liver. Breast. Cervix, body of uterus, ovary, vagina, vulva, gestational trophoblastic tumours. Kidney, bladder, prostate, testis, urethra, penis. Lymphoreticular tissues and bone marrow. Central nervous system, eye and orbit. Sarcomas. Paediatric oncology. Non-malignant disorders. Cancer chemotherapy. Hormones and oncology. Palliative and continuing care. Quality of life. Medical complications of malignant disease. Bibliography. Index.
Local cooling reduces skin ischemia under surface pressure in rats: an assessment by wavelet analysis of laser Doppler blood flow oscillations (2012)

The objectives of this study were to investigate the effects of local cooling on skin blood flow response to prolonged surface pressure and to identify associated physiological controls mediating these responses using the wavelet analysis of blood flow oscillations in rats. Twelve Sprague-Dawley rats were randomly assigned to three protocols, including pressure with local cooling (Δt = -10 °C), pressure with local heating (Δt = 10 °C) and pressure without temperature changes. Pressure of 700 mmHg was applied to the right trochanter area of rats for 3 h. Skin blood flow was measured using laser Doppler flowmetry. The 3 h loading period was divided into non-overlapping 30 min epochs for the analysis of the changes of skin blood flow oscillations using wavelet spectral analysis. The wavelet amplitudes and powers of three frequencies (metabolic, neurogenic and myogenic) of skin blood flow oscillations were calculated. The results showed that after an initial loading period of 30 min, skin blood flow continually decreased under the conditions of pressure with heating and of pressure without temperature changes, but maintained stable under the condition of pressure with cooling. Wavelet analysis revealed that stable skin blood flow under pressure with cooling was attributed to changes in the metabolic and myogenic frequencies. This study demonstrates that local cooling may be useful for reducing ischemia of weight-bearing soft tissues that prevents pressure ulcers.
The alveolar rhabdomyosarcoma PAX3/FKHR fusion protein is a transcriptional activator. (1995)

Chimeric transcription factors, created by gene fusions as the result of chromosomal translocations, have been implicated in the pathogenesis of several pathologically disparate solid tumors. The PAX3/FKHR fusion gene, formed by a t(2;13)(q35;q14) in alveolar rhabdomyosarcoma, encodes a hybrid protein that contains both PAX3 DNA binding domains, the paired box and homeodomain, linked to the bisected DNA binding domain of FKHR, a member of the forkhead family of transcription factors. Here we report that PAX3 and PAX3/FKHR display similar, but not identical transactivation activities when tested with model Pax recognition sequences. No functional role could be ascribed solely to the residual FKHR binding domain present in the fusion protein, but FKHR was found to contribute a strong carboxyl terminal activation domain replacing the one located in the unrearranged PAX3 gene. We show that the native PAX3/FKHR protein present in tumor cells with this translocation has transcriptional characteristics similar to the in vitro expressed protein. The ability of the PAX3/FKHR hybrid protein to bind DNA in a sequence specific manner and to transactivate the expression of artificial reporter genes suggests that its aberrant expression could subvert the transcriptional programs that normally control the growth, differentiation, and survival of primitive myogenic precursors in vivo.
Delayed Borate Crosslinked Fluids Minimize Pipe Friction Pressure (1992)

ABSTRACT Borate-crosslinked fluids have increased in usage for fracturing treatments in recent years because of their low cost and low damage potential to formations. Until recently, most applications have been in shallow wells below 200°F because of high friction pressures and relatively low thermal stability. Recent advances in borate fluid chemistry have resulted in new techniques to minimize pumping pressure through the use of chemically delayed borate crosslinking agent. Ability to minimize friction pressure with delayed borate crosslinker has reduced treatment cost and extended the application of borate-crosslinked fluids in deeper wells with higher bottomhole temperature (to 300°F). Laboratory and field data have been gathered to investigate the effects of fluid parameters on the friction behavior of the delayed borate-crosslinked fluid. The laboratory experiments were performed with a recirculation flow loop to simulate field conditions. The field test was performed in a vertical wellbore. Measurements were made with three bottomhole memory gauges installed at various depths. This paper presents friction pressure correlations derived from laboratory and field data for calculating realtime bottomhole treating pressure on-site to enhance the fracturing treatment analysis. Case histories are used to demonstrate the accuracy in friction pressure prediction for delayed borate-crosslinked fluids using the correlations presented in this paper. A method is also presented for field application of the friction pressure correlations provided in this paper.
Cloning and Expression of an α-1,3-Glucanase Gene fromBacillus circulansKA-304: The Enzyme Participates in Protoplast Formation ofSchizophyllum commune (2006)

A culture filtrate of Bacillus circulans KA-304 grown on a cell-wall preparation of Schizophyllum commune has an activity to form protoplasts from S. commune mycelia, and a combination of alpha-1,3-glucanase and chitinase I, which were isolated from the filtrate, brings about the protoplast-forming activity. The gene of alpha-1,3-glucanase was cloned from B. circulans KA-304. It consists of 3,879 nucleotides, which encodes 1,293 amino acids including a putative signal peptide (31 amino acid residues), and the molecular weight of alpha-1,3-glucanase without the putative signal peptide was calculated to be 132,184. The deduced amino acid sequence of alpha-1,3-glucanase of B. circulans KA-304 showed approximately 80% similarity to that of mutanase (alpha-1,3-glucanase) of Bacillus sp. RM1, but no significant similarity to those of fungal mutanases. The recombinant alpha-1,3-glucanase was expressed in Escherichia coli Rosetta-gami B (DE 3), and significant alpha-1,3-glucanase activity was detected in the cell-free extract of the organism treated with isopropyl-beta-D-thiogalactopyranoside. The recombinant alpha-1,3-glucanase showed protoplast-forming activity when the enzyme was combined with chitinase I.
Rapid-scanning forward-imaging miniature endoscope for real-time optical coherence tomography (2004)

We developed a miniature endoscope that is capable of rapid lateral scanning and is suitable for real-time forward-imaging optical coherence tomography (OCT). The endoscope has an outer diameter of 2.4 mm, consisting of a miniature tubular lead zirconate titanate (PZT) actuator, a single-mode fiber-optic cantilever, and a graded-index lens. Rapid lateral scanning at 2.8 kHz is achieved when the fiber-optic cantilever is resonated with the PZT actuator. This allows OCT imaging to be performed by fast lateral beam scanning followed by slow depth scanning, which is different from the conventional OCT imaging sequence. Real-time OCT imaging with the endoscope operated in the new image acquisition sequence at 6 frames/s is demonstrated.
Sensitive and Visual Detection of Sequence-Specific DNA-Binding Protein via a Gold Nanoparticle-Based Colorimetric Biosensor (2010)

A novel exonuclease III (Exo III) protection-based colorimetric biosensing strategy was developed for rapid, sensitive, and visual detection of sequence-specific DNA-binding proteins. This strategy relied on the protection of DNA-cross-linked gold nanoparticle (AuNP) aggregates from Exo III-mediated digestion by specific interactions of target proteins with their binding sequences. Interestingly, we disclosed a new finding that binding of target proteins to their binding sequences in the aggregated AuNP network rendered a stable and long-period protection of DNA. Unlike conventional fluorescence assays merely based on temporal protection of DNA from Exo III digestion, the stable protection afforded a static color transition indicator for DNA-protein interactions with no time-dependent monitoring required in the assay. Therefore, it furnished the developed strategy with improved technical robustness and operational convenience. Furthermore, we introduced thioctic acid as a stable anchor for tethering DNA on AuNPs. This DNA-tethering protocol circumvented the interferences from thiol compounds in common enzymatic systems. The Exo III protection-based colorimetric biosensor was demonstrated using a model target of TATA binding protein, a key transcriptional factor involving in various transcriptional regulatory networks. The results revealed that the method allowed a specific, simple, and quantitative assay of the target protein with a linear response range from 0 to 120 nM and a detection limit of 10 nM.
Breaking the DNA‐binding code of Ralstonia solanacearum TAL effectors provides new possibilities to generate plant resistance genes against bacterial wilt disease (2013)

Ralstonia solanacearum is a devastating bacterial phytopathogen with a broad host range. Ralstonia solanacearum injected effector proteins (Rips) are key to the successful invasion of host plants. We have characterized Brg11(hrpB-regulated 11), the first identified member of a class of Rips with high sequence similarity to the transcription activator-like (TAL) effectors of Xanthomonas spp., collectively termed RipTALs. Fluorescence microscopy of in planta expressed RipTALs showed nuclear localization. Domain swaps between Brg11 and Xanthomonas TAL effector (TALE) AvrBs3 (avirulence protein triggering Bs3 resistance) showed the functional interchangeability of DNA-binding and transcriptional activation domains. PCR was used to determine the sequence of brg11 homologs from strains infecting phylogenetically diverse host plants. Brg11 localizes to the nucleus and activates promoters containing a matching effector-binding element (EBE). Brg11 and homologs preferentially activate promoters containing EBEs with a 5' terminal guanine, contrasting with the TALE preference for a 5' thymine. Brg11 and other RipTALs probably promote disease through the transcriptional activation of host genes. Brg11 and the majority of homologs identified in this study were shown to activate similar or identical target sequences, in contrast to TALEs, which generally show highly diverse target preferences. This information provides new options for the engineering of plants resistant to R. solanacearum.
Control of lymphatic and hematogenous metastasis of a rat mammary carcinoma by the matrix metalloproteinase inhibitor batimastat (BB-94). (1996)

We examined the effects of the synthetic matrix metalloproteinase inhibitor batimastat (BB-94) on lung colonization and spontaneous metastasis of a rat mammary carcinoma, HOSP.1P. This tumor expresses both latent and active forms of the matrix metalloproteinases MMP-2 and MMP-9, although the former, as in human breast cancer, is the most prominent. Administration of batimastat (6 x 30 mg/kg i.p.) inhibited by up to 80% both the number and median weights of HOSP.1P lung colonies following i.v. inoculation of cells. This implies an effect both on seeding efficiency and subsequent tumor development. In spontaneous metastasis assays, limited treatment with batimastat (commencing when s.c. tumors were established and continuing until 5 or 14 days after their surgical removal) significantly inhibited lung metastasis but had little effect on lymphatic metastasis. However, when treatment was initiated 2 days prior to surgery and continued until day 70, 100% of animals survived to day 120 when there was no evidence of metastatic disease. All control animals (n = 25) in two separate experiments died before day 100 with lymphatic, lung, and extrapulmonary metastases. Taken together, these data suggest that lymphatic dissemination by HOSP.1P tumor cells is less susceptible to inhibition by batimastat than vascular invasion, but that long-term treatment can effectively prevent the outgrowth of putative micrometastases in both lymph nodes and lungs, allowing sustained tumor-free survival.
Use of prescribed fire to reduce wildfire potential (1989)

Fires were a part of our wildlands prehistorically. Prescribed burning reduces fire hazard and potential fire behavior primarily by reducing fuel quantity and continuity. Fuel continuity should be considered on the micro scale within stands, the mid-scale among, and the macro-scale among watersheds or entire forests. Prescribed fire is only one of the tools which can be used to reduce fire hazard, but it can be effective at all scales.
Retrovirus Vectors Displaying the IgG-Binding Domain of Protein A (1997)

We have designed and constructed retrovirus particles displaying the IgG-binding domain of protein A. We fused the gene for the synthetic antibody-binding portion of protein A with the envelope gene of ecotropic Moloney murine leukemia virus. The fusion gene was coexpressed in ecotropic retroviral packaging cells, and retrovirus particles with IgG-binding activities were recovered. In principle, the protein A–envelope chimeric retrovirus complexed with specific monoclonal antibody could be used for cell-targeted gene delivery.
Collagenase Increases the Transcapillary Pressure Gradient and Improves the Uptake and Distribution of Monoclonal Antibodies in Human Osteosarcoma Xenografts (2004)

Cancer therapy based on tumor-selective macromolecules may fail due to the elevated interstitial fluid pressure (IFP) that reduces the transvascular and interstitial convection in solid tumors. Modulation of the tumor extracellular matrix (ECM) may reduce IFP and enhance transvascular filtration and interstitial transport of macromolecules. We therefore measured the effect of the ECM-degrading enzyme collagenase on IFP and microvascular pressure (MVP) in human osteosarcoma xenografts using the wick-in-needle and micropipette methods, respectively. The tumor uptake and distribution of a systemically administered osteosarcoma-associated monoclonal antibody (TP-3) after i.v. injection of collagenase were analyzed using confocal laser scanning microscopy. Collagenase (0.1%) reduced both IFP (45%) and MVP (60%), but the kinetics of the recoveries differed, because MVP had recovered by the time IFP reached its minimum level. Thus, collagenase increased the transcapillary pressure gradient, inducing a 2-fold increase in the tumor uptake and improving the distribution of the monoclonal antibody, which was localized further into the tumor. To study the mechanism of the reduction in MVP, mean arterial blood pressure was measured and found not to be affected by the collagenase treatment. The reduction in MVP was rather due to reduced vascular resistance because microvascular-associated collagen was totally or partially disintegrated. Although collagenase may favor metastasis and thus not be clinically relevant, this study shows proof of principle that degradation of the ECM leads to a favorable change in the transvascular pressure gradient, thereby increasing antibody penetration and binding to tumor cells.