gebhart/patrepeval huggingface dataset:
Rabies Virus Ocular Disease: T-Cell-Dependent Protection Is under the Control of Signaling by the p55 Tumor Necrosis Factor Alpha Receptor, p55TNFR (2001)

Following brain infection, the Challenge Virus Standard strain of rabies virus infects the retina. Rabies virus ocular infection induces the infiltration of neutrophils and predominantly T cells into the eye. The role of tumor necrosis factor alpha (TNF-alpha)-lymphotoxin signaling in the control of rabies virus ocular infection and inflammatory cell infiltration was assessed using mice lacking the p55 TNF-alpha receptor (p55TNFR(-/-) mice). The incidence of ocular disease and the intensity of retinal infection were greater in p55TNFR(-/-) mice than in C57BL/6 mice: the aggravation correlated with less neutrophil and T-cell infiltration. This indicates that cellular infiltration is under the control of the p55 TNF-alpha receptor and suggests that inflammatory cells may protect the eye against rabies virus ocular infection. The role of T cells following rabies virus ocular disease was assessed by comparison of rabies virus infection in nude mice with their normal counterparts. Indeed, the incidence and severity of the rabies virus ocular disease were higher in athymic nude mice than in BALB/c mice, indicating that T lymphocytes are protective during rabies virus ocular infection. Moreover, few T cells and neutrophils underwent apoptosis in rabies virus-infected retina. Altogether, these data suggest that T lymphocytes and neutrophils are able to enter the eye, escape the immune privilege status, and limit rabies virus ocular disease. In conclusion, rabies virus-mediated eye disease provides a new model for studying mechanisms regulating immune privilege during viral infection.
Genome Sequence of the Cellulosome-Producing Mesophilic Organism <i>Clostridium cellulovorans</i> 743B (2009)

Clostridium cellulovorans 743B was isolated from a wood chip pile and is an anaerobic and mesophilic spore-forming bacterium. This organism degrades native substrates in soft biomass such as corn fiber and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Here we report the genome sequence of C. cellulovorans 743B.
Formation of intermediate phases, Ni3Si2 and Pt6Si5: Nucleation, identification, and resistivity (1986)

The formation of Ni3Si2 from the reaction of Ni2Si with NiSi, and that of Pt6Si5 from the reaction of Pt2Si with PtSi have been investigated by Rutherford backscattering, x-ray diffraction, resistance measurements, and optical and electronic microscopy. Standard x-ray diffraction patterns were calculated for Pt6Si5 and for the high-temperature form (hexagonal) of Pt2Si. These are shown to match experimental diffraction patterns. Both Ni3Si2 and Pt6Si5 form quite suddenly (at 470 and 535 °C, respectively) according to the pattern of nucleation-controlled reactions which are anticipated when the free energies of formation of the new phases are sufficiently small. These observations are discussed with respect to the absence of both Ni3Si2 and Pt6Si5 from the sequence of phases which form when Ni and Pt thin films react with Si. Resistivity measurements are reported for Ni3Si2, Pt6Si5, and for the two forms (low and high temperature) of Pt2Si.
Improved Strains and Plasmid Vectors for Conditional Overexpression of His-Tagged Proteins in <i>Haloferax volcanii</i> (2010)

Research into archaea will not achieve its full potential until systems are in place to carry out genetics and biochemistry in the same species. Haloferax volcanii is widely regarded as the best-equipped organism for archaeal genetics, but the development of tools for the expression and purification of H. volcanii proteins has been neglected. We have developed a series of plasmid vectors and host strains for conditional overexpression of halophilic proteins in H. volcanii. The plasmids feature the tryptophan-inducible p.tnaA promoter and a 6xHis tag for protein purification by metal affinity chromatography. Purification is facilitated by host strains, where pitA is replaced by the ortholog from Natronomonas pharaonis. The latter lacks the histidine-rich linker region found in H. volcanii PitA and does not copurify with His-tagged recombinant proteins. We also deleted the mrr restriction endonuclease gene, thereby allowing direct transformation without the need to passage DNA through an Escherichia coli dam mutant.
Hepatitis B and C virus infections and anti‐tumor necrosis factor‐α therapy: Guidelines for clinical approach (2006)

Anti-tumor necrosis factor-alpha (TNF) therapy has recently been recognized to be associated with activation of hepatitis B virus (HBV) infection, with a potentially fatal outcome, mirroring experience in the setting of immune suppression and subsequent reconstitution in cancer chemotherapy and transplantation. Although there is no current evidence that anti-TNF therapy influences the natural history of hepatitis C virus (HCV) infection, the involvement of TNF in the pathogenesis of hepatic injury and extrapolation from other clinical situations heighten awareness of a potential conflict. Preventive strategies should be mandatory. These include screening of all patients for HBV and HCV infection prior to commencement of anti-TNF therapy, and active monitoring of aminotransferases and, for HBV, viral load during and for 3 months after therapy has terminated. Prophylactic or early intervention strategies with nucleoside analogs are recommended for patients with evidence of HBV infection.
Compatibility of caspofungin acetate injection with other drugs simulated y-site coadministration. (2015)

The physical compatibility of caspofungin acetate injection with selected other drugs during simulated Y-site coadministration was evaluated by visual observation and turbidity measurement. Five-milliliter samples of caspofungin acetate 0.7 mg/mL in 0.9% sodium chloride injection were combined with 5 mL of 67 other drugs including antineoplastics,analgesics, anti-infectives, and supportive care drugs, undiluted or diluted in 0.9% sodium chloride injection or 5% dextrose injection, and with a parenteral nutrition admixture. Visual examinations were performed with the unaided eye in normal laboratory fluorescent light and with a Tyndall beam (high-intensity monodirectional light beam) to enhance visualization of small particles and low-level turbidity. The turbidity of each sample was measured as well. The sample mixtures were evaluated immediately and at 1 and 4 hours after preparation. Nineteen of the drugs tested and the parenteral nutrition admixture were incompatible with caspofungin acetate 0.7 mg/mL during the 4-hour observation period. The remaining drugs were compatible for at least 4 hours. Gross precipitation or turbidity changes visible in normal diffuse room light with the unaided eye occurred with 18 drugs and with the parenteral nutrition admixture. Microprecipitation of particulates not visible with the unaided eye occurred with cytarabine. The measured turbidity of the caspofungin acetate control solutions and the compatible test samples remained essentially unchanged throughout the observation period. In combination with caspofungin acetate, 48 drugs and a parenteral nutrition admixture were considered to be physically compatible. In contrast, 19 drugs with the parenteral nutrition admixture exhibited frank precipitation or microparticulate formation within 4 hours and should not be simultaneously administered via Y-site with caspofungin acetate.
A broadband optoelectronic packet switching system (1989)

A novel architecture is presented for a optoelectronic hybrid packet-switching system (HYPASS) for the distribution of multiple-bit-rate broadband services. HYPASS is based on an input-buffered/output-controlled arbitration protocol. This packet switch uses novel multiwave-length optical networks to accomplish routing and transmission of the packets. This system is specifically adapted to utilize the strengths of both optical and electronic technologies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Possible mechanisms of immune modulation in chronic dermatophytoses: an in vitro study (1992)

It has been suggested that patients with chronic superficial Trichophyton rubrum infection have defective cellular immunity to dermatophyte antigens. This may be due to a selective anergy to dermatophyte antigens or reflect the activity of dermatophyte-derived lymphocyte inhibitory factors. To explore these possibilities, we assessed lymphocyte transformation to a variety of recall antigens, including a cytoplasmic and exoantigen preparation of Trichophyton rubrum in 15 patients with chronic dermatophyte infection and 15 age- and sex-matched positive controls. In a duplicate set of experiments, autologous serum was replaced by heat-inactivated fetal calf serum. In addition, the direct effect of Trichophyton rubrum extracts on lymphoproliferation was assessed in vitro. Comparable lymphocyte transformation to each recall antigen was observed in patients and controls. Moreover, we found no evidence for a circulating dermatophyte-derived lymphocyte inhibitory factor in sera from patients with chronic superficial infection. A direct inhibitory effect of Trichophyton rubrum on lymphocyte proliferation to recall antigens was observed, however, at protein concentrations of > 10 micrograms/ml (exoantigen preparation) and > 25 micrograms/ml (cytoplasmic preparation). This inhibitory effect was rapidly reversible, not associated with loss of cell viability and maximal when added within 24 h of antigen to cultured lymphocytes. Class II MHC antigen HLA-DR, a surface marker of T-cell activation, was observed on inhibited lymphocytes co-cultured with antigen, suggesting the primary target for the inhibitory effect in vitro is the lymphocyte rather than the antigen-presenting cell.(ABSTRACT TRUNCATED AT 250 WORDS)
Accurate and efficient expression evaluation and linear algebra (2008)

We survey and unify recent results on the existence of accurate algorithms for evaluating multivariate polynomials, and more generally for accurate numerical linear algebra with structured matrices. By ‘accurate’ we mean that the computed answer has relative error less than 1, i.e. , has some correct leading digits. We also address efficiency, by which we mean algorithms that run in polynomial time in the size of the input. Our results will depend strongly on the model of arithmetic: most of our results will use the so-called traditional model (TM), where the computed result of op( a , b ), a binary operation like a + b , is given by op( a , b ) * (1+δ) where all we know is that |δ| ≤ ε ≪ 1. Here ε is a constant also known as machine epsilon. We will see a common reason for the following disparate problems to permit accurate and efficient algorithms using only the four basic arithmetic operations: finding the eigenvalues of a suitably discretized scalar elliptic PDE, finding eigenvalues of arbitrary products, inverses, or Schur complements of totally non-negative matrices (such as Cauchy and Vandermonde), and evaluating the Motzkin polynomial. Furthermore, in all these cases the high accuracy is ‘deserved’, i.e. , the answer is determined much more accurately by the data than the conventional condition number would suggest. In contrast, we will see that evaluating even the simple polynomial x + y + z accurately is impossible in the TM, using only the basic arithmetic operations. We give a set of necessary and sufficient conditions to decide whether a high accuracy algorithm exists in the TM, and describe progress toward a decision procedure that will take any problem and provide either a high-accuracy algorithm or a proof that none exists. When no accurate algorithm exists in the TM, it is natural to extend the set of available accurate operations by a library of additional operations, such as x + y + z , dot products, or indeed any enumerable set which could then be used to build further accurate algorithms. We show how our accurate algorithms and decision procedure for finding them extend to this case. Finally, we address other models of arithmetic, and the relationship between (im)possibility in the TM and (in)efficient algorithms operating on numbers represented as bit strings.
Optical frequency division using an optical parametric oscillator (1990)

A novel method of frequency division based on optical parametric oscillation is proposed. This scheme converts with high efficiency an input signal into two intense, coherent subharmonic outputs whose frequencies are tunable and whose linewidths are essentially limited by the input pump linewidth. By locking their difference frequency to a microwave, a millimeter-wave, or an infrared reference source, the output frequencies are precisely determined. The proposed frequency dividers can be operated in series or in parallel to measure, compare, and synthesize frequencies from optical to microwave. A line-narrowing effect for the generation of ultrastable radiation is discussed.
Systematic review and network meta-analysis of combination and monotherapy treatments in disease-modifying antirheumatic drug-experienced patients with rheumatoid arthritis: analysis of American College of Rheumatology criteria scores 20, 50, and 70 (2012)

Licensed bDMARDs are efficacious in patients with an inadequate response to conventional therapy, but tumor necrosis factor-α inhibitor combination therapies are not equally effective.
Comparisons of the Hbv and HIV Polymerase, and Antiviral Resistance Mutations (2004)

The antiviral treatment of chronic hepatitis B is limited by the selection of antiviral resistance mutations. Primary resistance to lamivudine occurs at rtM2041/V in the C Domain of the polymerase. Recently, resistance to adefovir has also been described in the D Domain at rtN236T. The treatment of patients with resistant virus without complete suppression can lead to the further selection of compensatory mutations. Thus, to gain an understanding of the hepatitis B virus (HBV) polymerase and also mutations associated with resistance, a three-dimensional model of the HBV reverse transcriptase core region based on homology with human immunodeficiency virus (HIV) was created. A comparative analysis of the HIV polymerase and the model of HBV polymerase was performed. In addition, the antiviral resistance mutations including potential compensatory mutations were mapped to determine their effect on the HBV polymerase model, especially in the nucleotide binding site.
Optimal transmission scheme for a distributed antenna in CDMA system (2004)

Distributed antenna diversity employs separately installed, but cooperating, antennas within a single base-station; it has been proved that the uplink capacity (per cell) in terms of maximum achievable SIR (signal-to-interference ratio) is linear with the number of deployed antenna units. While in the downlink, because of the multiple-to-one propagation topology, equal power (transmission power at each antenna) allocation (providing equal SIR) in the base-station results in fixed SIR at the mobile terminal, irrespective of the number of base-station antennas used. A transmission scheme, using optimal power allocation and SIR-balanced power control, is proposed to increase the SIR by exploiting multiple base-station antennas. The downlink diversity (called antenna-multipath diversity) transfers the antenna diversity to multipath diversity by utilizing the spread-spectrum signal property. If optimal, rather than equal, power allocation is employed with antenna-multipath diversity, the SDMA advantage can be exploited. The optimisation result shows that, for a particular user, transmitting a signal from one antenna, instead of all base-station antennas, gives better SIR performance. The SIR CDF has been examined by simulation to verify this scheme. Compared to sending from all antennas, the result shows, that for 8 users, this scheme yields improved SIR by 3 dB with 5 antennas. The SIR advantage increases with increasing numbers of antennas and decreases, however, with increasing numbers of users in the cell.
Symbolic/numeric algorithms for partial differential equations (1976)

Symbolic computation has been used to generate classes of numeric algorithms for solving linear partial differential equations A two-phase procedure is described for automatically producing multiparameter families of difference approximations to the heat operator. In the first phase, a truncated series expansion is used to form the appropriate difference operator. The coefficients of the operator, functions of free parameters, are determined in the second phase. When the region is rectilinear, Vandermonde matrices are constructed which permit this phase to be computed numerically. When the region is irregular, a symbolic approach appears to be more efficient
Modeling Polymer Systems Using the Perturbed-Chain Statistical Associating Fluid Theory Equation of State (2001)

The perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state is applied to binary and ternary mixtures of polymers, solvents, and gases. The three pure-component parameters required for nonassociating molecules were identified for six polymer compounds. The phase equilibrium of polymer systems, which often involves high-pressure liquid−liquid mixtures as well as vapor−liquid mixtures at lower pressures, was investigated. Using a constant binary interaction parameter (kij), the PC-SAFT equation of state gives good correlations of the appropriate phase behavior over wide ranges of conditions. Comparisons to an earlier version of SAFT reveal an improvement of the proposed model.
Staphylococcus aureus and Atopic Dermatitis (1983)

Atopic dermatitis is a genetically determined skin disease that is strongly influenced by environmental factors. The skin of affected patients is usually colonized by large numbers of Staphylococcus aureus bacteria. These bacteria may aggravate atopic dermatitis or prevent resolution of the disease. The deleterious effects of S aureus on atopic dermatitis may be due to direct biologic action or may be due to indirect damage mediated by the immune and inflammatory systems.
Small farm improvement strategies‐the implications of a computer simulation study of indigenous farming in South East Ghana (1975)

Click to increase image sizeClick to decrease image size Notes This study was undertaken with support from the Ministry of Overseas Development, as a dissertation in part fulfilment of the degree of Master of Agricultural Science from the University of Reading.
The effect of knot geometry on the strength of laparoscopic slip knots (1996)

The 4S and fisherman's knots are the strongest laparoscopic slip knots and are the only slip knots similar in strength to multiple-throw square knots.
Quantitative liquid-chromatographic estimation of bilirubin species in pathological serum. (1983)

Earlier we described a "high-performance" liquid-chromatographic procedure for separating the four distinct fractions of bilirubin (unconjugated, monoconjugated, diconjugated, and protein-bound) in pathological human serum (J. Chromatogr. 226: 391-402, 1981). We have modified the prechromatography precipitation of the serum globulins required in that method and have measured the bilirubin content of the precipitate spectrophotometrically. On average, the precipitate contained less than 10% of the total bilirubin in the serum samples. Adding the value obtained for the precipitate to that obtained by chromatography for the individual bilirubin fractions gave an estimate of the concentration of the total bilirubin in the sample. For 357 samples from 132 patients, this total value correlated well with that obtained by the Jendrassik-Gróf diazo procedure (slope = 1.00; r = 0.995, linear least-squares fit). The CV for the total and fractional bilirubin measurements was, on average, less than or equal to 5% for pathological sera. Serum sampled at different times from the same patient showed significant changes in the distribution of bilirubin among the four fractions.
RAPD Markers Linked to Three Major Anthracnose Resistance Genes in Common Bean (1997)

Durability of the resistance to anthracnose, caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lambs.‐Scrib., could be increased if more than one resistance gene were incorporated into current bean ( Phaseolus vulgaris L.) cultivars. The objective of this study was to identify random amplified polymorphic DNA (RAPD) markers linked to three independent resistance loci to facilitate gene pyramiding in common bean. Markers were identified by means of bulked segregant analysis and heterogeneous inbred populations. RAPD marker OF10 530 cosegregated in repulsion‐phase (1.9 ± 1.4 cM) with the Co‐1 (A) allele. A survey of diverse bean genotypes showed that the OF10 530 RAPD band could facilitate introgression of the Co‐1 gene across the Andean and Middle American Phaseolus gene pools. RAPD marker OAB3 450 was linked in coupling‐phase (5.9 ± 1.7 cM) to the Co‐5 ( Mexique 3 ) allele. A coupling‐phase (OAH1 780 ) and repulsion‐phase (OAK20 890 ) RAPD marker were linked to the Co‐6 locus. These markers flanked the Co‐6 locus and mapped at 12.3 ± 1.9 from the Co‐6 allele and at 7.3 ± 1.5 cM from the co‐6 allele, respectively. Coupling and repulsion‐phase RAPD markers used as a codominant pair showed a higher selection efficiency (95%), for the identification of homozygous ( Co‐6 Co‐6 ) F 2 individuals, than individual selection either for a coupling‐phase (33%) or against a repulsion‐phase (92%) RAPD phenotype. Durability of resistance to anthracnose could be improved if (i) two major resistance genes were pyramided by marker assisted selection, (ii) different genes were deployed in different regions, and (iii) resistance genes from different gene pools were combined.
The knowledge of coordination for supply chain integration (2002)

Abstract Increasing competition due to market globalisation, product diversity and technological breakthroughs stimulates independent firms to collaborate in a supply chain that allows them to gain mutual benefits. This requires the collective know‐how of the coordination mode, including the ability to synchronise interdependent processes, to integrate information systems and to cope with distributed learning. However, research into coordination has paid little attention to acknowledging different modes of coordination. This study promotes the notion of mutuality and the focus of coordination in order to establish a comprehensive taxonomy of coordination modes. Four different modes of coordination have been identified: logistics synchronisation, information sharing, incentive alignment, and collective learning. The knowledge of coordination is then proposed as an explicit understanding about key drivers of coordination modes that have positive impacts on supply chain performance. This paper also presents a research agenda.