gebhart/patrepeval huggingface dataset:
Defective expression of p56lck in an infant with severe combined immunodeficiency. (1998)

Severe combined immune deficiency (SCID) is a heterogeneous disorder characterized by profound defects in cellular and humoral immunity. We report here an infant with clinical and laboratory features of SCID and selective CD4 lymphopenia and lack of CD28 expression on CD8(+) T cells. T cells from this patient showed poor blastogenic responses to various mitogens and IL-2. Other T cell antigen receptor- induced responses, including upregulation of CD69, were similarly inhibited. However, more proximal T cell antigen receptor signaling events, such as anti-CD3 induced protein tyrosine phosphorylation, phosphorylation of mitogen-associated protein kinase, and calcium mobilization were intact. Although p59fyn and ZAP-70 protein tyrosine kinases were expressed at normal levels, a marked decrease in the level of p56lck was noted. Furthermore, this decrease was associated with the presence of an alternatively spliced lck transcript lacking the exon 7 kinase encoding domain. These data suggest that a deficiency in p56lck expression can produce a SCID phenotype in humans.
Gamma dosimetry with Al2O3 thermoluminescent phosphor (1976)

Preparation of thermoluminscence (TL) dosimetric grade A12O3 powder and pellets five times more sensitive than TLD-100 is described. Glow peaks at 50, 125, 250, 325, 475 and 625 degrees C with emission in the blue region have been observed; Si and Ti have been identified as the impurities responsible for TL in this phosphor. Studies of the TL growth rate with exposure showed that the 250 degrees c peak grew linearly up to 400 R and then at a supralinear rate of (exposure). The growth of the 475 degrees c peak was almost linear at a rate of (exposure) 1-05, while that for the 625 degrees C peak was sublinear at (exposure) 0-85. The 250 and 475 degrees peaks together show a linear response up to 40 000 R. The phosphor had no light sensitivity and is very well suited for gamma dosimetry as pellets or powder. Studies of sensitization and supralinearity, with sensitizing exposure, sensitizing anneal temperature and test gamma and alpha exposures are reported. Initially filled 625 degrees C TL related traps were found to be essential for sensitizaiton. Supralinearity and sensitization in Al2O3 phosphor could be consistently explained by the deep trap model.
Phase I Multidose-Escalation Study of the Anti-CD19 Maytansinoid Immunoconjugate SAR3419 Administered by Intravenous Infusion Every 3 Weeks to Patients With Relapsed/Refractory B-Cell Lymphoma (2012)

Using an every 3-week-schedule of SAR3419 for six cycles, the MTD is 160 mg/m(2). SAR3419 can be safely administered to patients with relapsed B-cell lymphoma and demonstrates promising clinical activity, including patients who were refractory to rituximab.
Nitrogen Removal from Wastewaters by Microalgae Without Consuming Organic Carbon Sources (2002)

The possibility of microalgal nitrogen treatment was tested in wastewaters with a low carbon/nitrogen (C/N) ratio. Chlorella kessleri was cultured in the two different artificial wastewaters with nitrate as a nitrogen source: one contained glucose for an organic carbon source and the other without organic carbon sources. The growth rates of the two cultures were almost identical when the aeration rate was over 1 vvm. These results suggest that microalgae could successfully remove nitrogen from wastewater, as far as the mass transfer of CO 2 was not limited. Nitrate was successfully reduced to below 2 mg NO 3 -N/ml from the initial nitrate concentration of 140 mg NO 3 -N/ml in 10 days, even in the wastewater with no organic carbon source. Similar results were obtained when ammonium was used as the sole nitrogen source instead of nitrate. Higher concentrations of nitrogen of 140, 280, 560 and 1,400 mg/ml were also tested and similar amounts of nitrogen were removed by algal cultures without showing any substrate inhibition.
Phylogenetic relationships of aquatic birnaviruses based on deduced amino acid sequences of genome segment A cDNA (2001)

Aquatic birnaviruses, such as infectious pancreatic necrosis virus (IPNV), cause serious diseases in a variety of fish species used worldwide in aquaculture and have also been isolated from a variety of healthy fish and shellfish species. These viruses exhibit a high degree of antigenic heterogeneity and variation in biological properties such as pathogenicity, host range, and temperature of replication. To better understand genetic and biological diversity among these viruses, the nucleotide and deduced amino acid sequences were determined from cDNA of the large open reading frame (ORF) of genome segment A of the 9 type strains of Serogroup A and 4 other representative strains of Serotype A1, the predominant serotype in the United States. In addition, nucleotide and deduced amino acid sequences were determined for the VP2 coding region of a variety of isolates representing 5 of the 9 serotypes. VP2 is the major outer capsid protein of aquatic birnaviruses. RT-PCR was used to amplify a 2904 bp cDNA fragment including all but a few bp of the large ORF of genome segment A or a 1611 bp fragment representing the entire VP2 coding region. Nucleotide and deduced amino acid sequences were determined from the PCR products. Pairwise comparisons were made among our data and 2 other aquatic birnavirus sequences previously published. Several hypervariable regions were identified within the large ORF. The most divergent pair of viruses exhibited a similarity of 80.1% in the deduced amino acid sequence encoded by the large ORF. Genomic relationships revealed in a phylogenetic tree constructed from comparison of the deduced amino acid sequences of the large ORF demonstrated that these viruses were clustered into several genogroups. Phylogenetic comparison of the deduced amino acid sequences of the VP2 coding region of 28 aquatic birnavirus isolates, including the type strains of all 9 serotypes, demonstrated 6 genogroups, some of which were comprised of several genotypes. The most divergent pair of viruses exhibited a similarity of 81.2% in the deduced amino acid sequence from the VP2 coding region. In contrast to previous studies of much shorter genomic sequences within the C-terminus-pVP2/NS junction coding region, these genogroups based on the entire large ORF or the VP2 coding region generally correlated with geographical origin and serological classification. Isolates from the major Canadian serotypes were more closely related to the European isolates than to isolates from the United States.
Full spectrum filterless fluorescence microscopy (2009)

In conventional microscopes, fluorescence emission is separated from the backscattered illumination using the Stokes shift, whereby the emission occurs at a longer wavelength to the excitation. Such separation is usually achieved through a combination of wavelength filters that divide the spectrum into mutually exclusive excitation and emission bands. It is therefore impossible in these microscopes to access the full excitation/emission spectrum of the specimen in a single image. We report on a microscope that acquired fluorescence images using illumination across the spectral range 450-680 nm; the full emission spectrum was detected simultaneously across the same range. The microscope was also combined with structured illumination optical sectioning to give three-dimensionally resolved images with improved background rejection. Full spectrum fluorescence images of biological specimens are demonstrated. As this system is more versatile than the standard fluorescence microscope, it could be of benefit in many fluorescence imaging applications.
Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA. (1995)

Positions 2-6 of the substrate-binding internal guide sequence (IGS) of the L-21 Sca I form of the Tetrahymena thermophila intron were mutagenized to produce a GN5 IGS library. Ribozymes within the GN5 library capable of efficient cleavage of an 818-nt human immunodeficiency virus type 1 vif-vpr RNA, at 37 degrees C, were identified by ribozyme-catalyzed guanosine addition to the 3' cleavage product. Three ribozymes (IGS = GGGGCU, GGCUCC, and GUGGCU) within the GN5 library that actively cleaved the long substrate were characterized kinetically and compared to the wild-type ribozyme (GGAGGG) and two control ribozymes (GGAGUC and GGAGAU). The two control ribozymes have specific sites within the long substrate, but were not identified during screening of the library. Under single-turnover conditions, ribozymes GGGGCU, GGCUCC, and GUGGCU cleaved the 818-nt substrate 4- to 200-fold faster than control ribozymes. Short cognate substrates, which should be structureless and therefore accessible to ribozyme binding, were cleaved at similar rates by all ribozymes except GGGGCU, which showed a fourfold rate enhancement. The rate of cleavage of long relative to short substrate under single-turnover conditions suggests that GGCUCC and GUGGCU were identified because of accessibility to their specific cleavage sites within the long substrate (substrate-specific effects), whereas GGGGCU was identified because of an enhanced rate of substrate binding despite a less accessible site in the long substrate. Even though screening was performed with 100-fold excess substrate (relative to total ribozyme), the rate of multiple-turnover catalysis did not contribute to identification of trans-cleaving ribozymes in the GN5 library.
Toward Reservoir-on-a-Chip: Rapid Performance Evaluation of Enhanced Oil Recovery Surfactants for Carbonate Reservoirs Using a Calcite-Coated Micromodel (2020)

Enhanced oil recovery (EOR) plays a significant role in improving oil production. Tertiary EOR, including surfactant flooding, can potentially mobilize residual oil after water flooding. Prior to the field deployment, the surfactant performance must be evaluated using site-specific crude oil at reservoir conditions. Core flood experiments are common practice to evaluate surfactants for oil displacement efficiency using core samples. Core flood experiments, however, are expensive and time-consuming and do not allow for pore scale observations of fluid-fluid interactions. This work introduces the framework to evaluate the performance of EOR surfactants via a Reservoir-on-a-Chip approach, which uses microfluidic devices to mimic the oil reservoir. A unique feature of this study is the use of chemically modified micromodels such that the pore surfaces are representative of carbonate reservoir rock. To represent calcium carbonate reservoir pores, the inner channels of glass microfluidic devices were coated with thin layers of calcium carbonate nanocrystals and the surface was modified to exhibit oil-wet conditions through a crude oil aging process. During surfactant screening, oil and water phases were imaged by fluorescence microscopy to reveal the micro to macro scale mechanisms controlling surfactant-assisted oil recovery. The role of the interfacial tension (IFT) and wettability in the microfluidic device was simulated using a phase-field model and compared to laboratory results. We demonstrated the effect of low IFT at the oil-water interface and wettability alteration on surfactant-enhanced oil displacement efficiency; thus providing a time-efficient and low-cost strategy for quantitative and qualitative assessment. In addition, this framework is an effective method for pre-screening EOR surfactants for use in carbonate reservoirs prior to further core and field scale testing.
Windows on the world (1993)

We describe the design and implementation of a prototype heads-up window system intended for use in a 3D environment. Our system includes a see-through head-mounted display that runs a full X server whose image is overlaid on the user's view of the physical world. The user's head is tracked so that the display indexes into a large X bitmap, effectively placing the user inside a display space that is mapped onto part of a surrounding virtual sphere. By tracking the user's body, and interpreting head motion relative to it, we create a portable information surround that envelopes the user as they move about.
Differential effects of myocarditic variants of Coxsackievirus B3 in inbred mice. A pathologic characterization of heart tissue damage. (1991)

The histopathologic features reflecting the influence of virus genotype and host differences on myocarditis were evaluated in six inbred mouse strains (C57BL/6, B10.D2, BALB/c, DBA/2, A/J, and C3H/HeJ) inoculated with four respective variants of coxsackievirus B3 (CVB3-CG, -SH, -ST, or -NR). The most severe and most prevalent histologic lesions occurred after infection with CVB3-SH or -CG variants, regardless of mouse strain. In general, C57BL/6 mice showed the lowest susceptibility to myocarditis while A/J or C3H/HeJ animals had the highest susceptibility, whether early (7 days) or late (21 days) after CVB3 inoculation. Lesion size and calcification depended to an extent on disease severity, but calcification in the C3H/HeJ myocardium was notably sparse. Lesions clustered distinctly in the midthird of the ventricular wall in some animals, particularly in DBA/2 mice. Extensive pericarditis occurred exclusively in BALB/c and DBA/2 animals and predominated over the right ventricle anterolaterally. Virus titer in the heart did not account for disease susceptibility among mouse strains. These characteristics reflect differences in pathogenicity and are important considerations in the study of mechanisms in CVB3-induced myocarditis in mice.
Blackleg disease of canola in Australia (2016)

Blackleg disease caused by the fungus Leptosphaeria maculans is the most important disease of canola worldwide. The impact of this disease on the development of the Australian canola industry, particularly over the last 20 years, is discussed. Deployment of a range of disease control measures has resulted in a thriving canola industry with production now approaching 4 million tonnes annually. Discoveries about disease mechanisms and key plant and fungal genes are described. Analysis of the L. maculans genome sequence has enabled an understanding of how fungal populations can evolve rapidly to overcome disease resistance bred into canola cultivars.
Adsorption of viruses to charge-modified silica (1985)

The purpose of this study was to provide a clearer understanding of virus adsorption, focusing specifically on the role of electrostatic interactions between virus particles and adsorbent surfaces. The adsorption of poliovirus 1, reovirus types 1 and 3, and coliphages MS-2 and T2 to colloidal silica synthetically modified to carry either positive or negative surface charge was evaluated. Adsorption experiments were performed by combining virus and silica in 0.1-ionic-strength buffers of pH 4.0, 6.4, and 8.5. Samples agitated for specified adsorption periods were centrifuged to pellet adsorbent particles plus adsorbed virus, and the supernatants were assayed for unadsorbed virus. All viruses adsorbed exclusively to negatively charged silica at pH values below their isoelectric points, i.e., under conditions favoring a positive surface charge on the virions. Conversely, all viruses adsorbed exclusively to positively charged silica at pH values above their isoelectric points, i.e., where virus surface charge is negative. Viruses in near-isoelectric state adsorbed to all types of silica, albeit to a lesser degree.
Novel gold‐dithiol nano‐networks with non‐metallic electronic properties (1995)

Stable nanostructured networks of quantum‐sized particles have been prepared “see Figure” using self‐assembly techniques. Here, two new techniques are reported for the preparation of non‐metallic composite materials comprising nanometersized gold particles self assembled into a 3‐D network by means of organic dithiols magnified image .
Fuzzy set based initial placement for IC layout (1990)

Three novel fuzzy algorithms for constructing initial placement of integrated circuits are introduced. These algorithms are based on the use of fuzzy set theory and show superior performance to conventional placement algorithms. One of these algorithms, namely the fuzzy clustering method, has inherent potential for placement of large and very large scale integrated circuits due to its comparative efficiency, flexibility and hierarchical structure. Placement examples for all three algorithms are presented and compared with conventional approaches. >
An Interferon α2 Mutant Optimized by Phage Display for IFNAR1 Binding Confers Specifically Enhanced Antitumor Activities (2007)

All alpha-interferons (IFNalpha) bind the IFNAR1 receptor subunit with low affinity. Increasing the binding affinity was shown to specifically increase the antiproliferative potency of IFNalpha2. Here, we constructed a phage display library by randomizing three positions on IFNalpha2 previously shown to confer weak binding to IFNAR1. The tightest binding variant selected, comprised of mutations H57Y, E58N, and Q61S (YNS), was shown to bind IFNAR1 60-fold tighter compared with wild-type IFNalpha2, and 3-fold tighter compared with IFNbeta. Binding of YNS to IFNAR2 was comparable with wild-type IFNalpha2. The YNS mutant conferred a 150-fold higher antiproliferative potency in WISH cells compared with wild-type IFNalpha2, whereas its antiviral activity was increased by only 3.5-fold. The high antiproliferative activity was related to an induction of apoptosis, as demonstrated by annexin V binding assays, and to specific gene induction, particularly TRAIL. To determine the potency of the YNS mutant in a xenograft cancer model, we injected it twice a week to nude mice carrying transplanted MDA231 human breast cancer cells. After 5 weeks, no tumors remained in mice treated with YNS, whereas most mice treated with wild-type IFNalpha2 showed visible tumors. Histological analysis of these tumors showed a significant anti-angiogenic effect of YNS, compared with wild-type IFNalpha2. This work demonstrates the application of detailed biophysical understanding in the process of protein engineering, yielding an interferon variant with highly increased biological potency.
Integrin-EGF-3 domain of bovine CD18 is critical forMannheimia haemolyticaleukotoxin species-specific susceptibility (2007)

Mannheimia haemolytica leukotoxin (LktA) is the primary virulence factor contributing to the pathogenesis of lung injury in bovine pneumonic pasteurellosis. Results from the authors' previous studies demonstrated that the site required for LktA binding leading to susceptibility to its biological effects resides within amino acid residues 500-600 of the extracellular region of bovine CD18. Experiments were designed to identify a much smaller functional domain within this 100 amino acid region of bovine CD18 that is critically required for species-specific susceptibility to LktA effects. Chimeric bovine X human CD18 with different integrin epidermal growth factor(I-EGF) like domains switched between bovine and human CD18 were generated and coexpressed with bovine CD11a in the human K562 cell line. The resulting chimeric transductants were tested for susceptibility to LktA-induced effects. The results demonstrate unequivocally that the I-EGF-3 domain of bovine CD18 (amino acid residues 541-581) is critical for conferring species-specific susceptibility to M. haemolytica leukotoxin.
Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70 (2010)

Although it uses the endogenous E. coli transcription machinery, this cell-free system can produce active proteins in quantities comparable to bacteriophage systems. The E. coli transcription provides much more possibilities to engineer informational processes in vitro. Many E. coli promoters/operators specific to sigma factor 70 are available that form a broad library of regulatory parts. In this work, cell-free expression is developed as a toolbox to design and to study synthetic gene circuits in vitro.
Democratic Group Signatures with Threshold Traceability. (2008)

Recently, democratic group signatures(DGSs) particularly catch our attention due to their great flexibilities, i.e., no group manager, anonymity, and individual traceability. In existing DGS schemes, individual traceability says that any member in the group can reveal the actual signer’s identity from a given signature. In this paper, we formally describe the definition of DGS, revisit its security notions by strengthening the requirement for the property of traceability, and present a concrete DGS construction with (t, n)-threshold traceability which combines the concepts of group signatures and of threshold cryptography. The idea behind the (t, n)-threshold traceability is to distribute between n group members the capability of tracing the actual signer such that any subset of not less than t members can jointly reconstruct a secret and reveal the identity of the signer while preserving security even in the presence of an active adversary which can corrupt up to t− 1 group members.
A Practical and Efficient Synthesis of Thalidomide via Na/Liquid NH3 Methodology1 (2005)

A facile, efficient, concise, cost-effective, and scalable synthesis of thalidomide in high overall yield (55%) is presented. Treatment of Boc-protected l-glutamic acid diester via Na/liquid (liq.) NH3 (−33 °C) mediated cyclization methodology produces a corresponding glutarimide ring which was subsequently condensed with phthalic anhydride in the presence of glacial acetic acid to afford thalidomide.
Genes of succinyl‐CoA ligase from Saccharomyces cerevisiae (1998)

Succinyl-CoA ligase (succinyl-CoA synthetase) catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate. This enzyme functions in the tricarboxylic acid (TCA) cycle and is also involved in ketone-body breakdown in animals. The enzyme is composed of alpha and beta subunits that are required for catalytic activity. Two genes, LSC1 (YOR142W) and LSC2 (YGR244C), with high similarity to succinyl-CoA ligase subunits from other species were isolated from Saccharomyces cerevisiae. The expression of these genes was repressed by growth on glucose and was induced threefold to sixfold during growth on nonfermentable carbon sources. The LSC genes were deleted singly and in combination. Unlike other yeast strains with defects in TCA cycle genes, strains lacking either or both LSC genes were able to grow with acetate as a carbon source. However, growth on glycerol or pyruvate was impaired. An antiserum against both subunits of the Escherichia coli enzyme was capable of recognizing the yeast succinyl-CoA ligase alpha subunit, and this band was absent in delta lsc1 deletion strains. Succinyl-CoA ligase activity was absent in mitochondria isolated from strains deleted for one or both LSC genes, but activity was restored by the presence of the appropriate LSC gene on a plasmid. The yeast succinyl-CoA ligase was shown to utilize ATP but not GTP for succinyl-CoA synthesis.
The Production of Organic Acids (1992)

The production of organic acids covers two aspects: first, the metabolic pathways involved in the biosynthesis, and, second, the industrial process strategy adopted. The review seeks to show the underlying biochemical similarities in the biosynthesis of organic acids and the resulting similarities in the commercial processes. Two groups of acids are defined, those with a "long" biosynthetic path from glucose, involving much of the glycolytic pathway and the tricarboxylic acid cycle, and those acids with a "short pathway", essentially a biotransformation of glucose. The regulation of the pathways and the future developments in metabolic control theory and genetic manipulations relating to them are considered. The organisms used industrially are also limited, Aspergillus sp. and Candida yeasts; again the underlying metabolic similarities lead to similar strategies for all the acids discussed.