gebhart/patrepeval huggingface dataset:
A strategy for single site PCR amplification of dsDNA: priming digested cloned or genomic DNA from an anchor-modified restriction site and a short internal sequence. (1990)

Amplification of dsDNA by polymerase chain reaction (PCR) has been limited to those instances in which segments of known sequence flank the fragment to be amplified. A strategy for the PCR amplification of cloned or genomic dsDNA that necessitates sequence information from only a single short segment (single site PCR) has been devised. The region of known sequence may be located at any position within or adjacent to the segment to be amplified. The basic procedure for amplification consists of 1) digestion of dsDNA with one or more restriction enzymes, 2) ligation with a universal anchor adaptor and 3) PCR amplification using an anchor primer and the primer for the single site of known sequence. The anchor adaptor is designed in such a way as to facilitate the amplification of only those fragments containing the sequence of interest. We have demonstrated the utility of this technique by specifically amplifying and directly sequencing antibody variable region genes from cloned dsDNA and from genomic DNA.
Facile and convenient synthesis of B‐amino‐9‐borabicyclo[3.3.1]nonanes. Aminoboration of lsocyanates (1992)

Abstract The reaction of 9‐borabicyclo[3.3.1]nonane (9‐BBN) with aliphatic and aromatic primary and secondary amines in tetrahydrofuran (THF) at 65°C proceeds rapidly and quantitatively with evolution of hydrogen and the formation of the corresponding B‐amino‐9‐borabicyclo[3.3.1] nonane (B‐amino‐9‐BBN). Simple evaporation of THF from the reaction mixture gives the B‐amino‐9‐BBN derivatives in high yield and purity. These B‐amino‐9‐BBN derivatives are reactive towards alkyl and aryl isocyanates. Consequently, the aminoboration of various isocyanates has been studied using B‐phenylamino‐9‐BBN. Thus, two equivalents of isocyanates react with one equivalent of B‐phenylamino‐9‐BBN to afford, following the hydrolysis of the intermediate with ethanolamine, N, N'‐disubstituted‐N ‐(phenylamido)‐ureas in excellent yields. A plausible mechanism for this aminoboration reaction of isocyanates is also presented.
Caveolin mRNA levels are up-regulated by free cholesterol and down-regulated by oxysterols in fibroblast monolayers (1997)

In confluent fibroblast monolayers, an increase in the selective uptake of free cholesterol (FC) from plasma low density lipoprotein (LDL) was accompanied by an increase in FC efflux. The rate of FC efflux was proportional to the FC content of the cell surface caveolae and to mRNA levels of caveolin, an FC-binding protein of caveolae. Inhibitors of LDL-FC internalization reduced the increase in caveolin mRNA levels and FC efflux. Oxysterols reduced caveolin mRNA levels, as well as transport of FC to the cell surface and FC efflux. DNA antisense to caveolin reduced caveolin mRNA and inhibited FC efflux. These data suggest that regulation of FC efflux can contribute to cellular FC homeostasis when LDL levels are modified over the physiological range, and they link this regulation to caveolin.
Time to put the CAR-T before the horse (2011)

In this issue of Blood , Brentjens and colleagues report on the feasibility, tolerability, and persistence of autologous CD19-directed chimeric antigen receptor (CAR) T cells in patients with relapsed chronic lymphocytic leukemia (CLL) and B-cell acute lymphocytic leukemia (B-ALL).[1][1] These
Screening and Treatment to Prevent Sequelae in Women withChlamydia trachomatisGenital Infection: How Much Do We Know? (2010)

Additional studies of the effectiveness of chlamydia screening would be valuable; feasible study designs may depend on the degree to which screening programs are already established. In addition, better natural history data on the timing of tubal inflammation and damage after C. trachomatis infection and development of more accurate, noninvasive tools to assess chlamydial sequelae are essential to informing chlamydia control efforts.
Lewis X Biosynthesis in Helicobacter pylori (1997)

The lipopolysaccharide of certain strains of Helicobacter pylori was recently shown to contain the Lewis X (Lex) trisaccharide (Galbeta-1, 4-(Fucalpha(1,3))-GlcNAc). Lex is an oncofetal antigen which appears on human gastric epithelium, and its mimicry by carbohydrate structures on the surface of H. pylori may play an important part in the interaction of this pathogen with its host. Potential roles for bacterial Lex in mucosal adhesion, immune evasion, and autoantibody induction have been proposed (Moran, A. P., Prendergast, M. M., and Appelmelk, B. J. (1996) FEMS Immunol. Med. Microbiol. 16, 105-115). In mammals, the final step of Lex biosynthesis is the alpha(1,3)-fucosylation of GlcNAc in a terminal Galbeta(1-->4)GlcNAc unit, and a corresponding GDP-fucose:N-acetylglucosaminyl alpha(1,3) fucosyltransferase (alpha(1,3)-Fuc-T) activity was recently discovered in H. pylori extracts. We used part of a human alpha(1, 3)-Fuc-T amino acid sequence to search an H. pylori genomic data base for related sequences. Using a probe based upon weakly matching data base sequences, we retrieved clones from a plasmid library of H. pylori DNA. DNA sequence analysis of the library clones revealed a gene which we have named fucT, encoding a protein with localized homology to the human alpha(1,3)-Fuc-Ts. We have demonstrated that fucT encodes an active Fuc-T enzyme by expressing the gene in Escherichia coli. The recombinant enzyme shows a strong preference for type 2 (e.g. LacNAc) over type 1 (e.g. lacto-N-biose) acceptors in vitro. Certain residues in a short segment of the H. pylori protein are completely conserved throughout the alpha(1,3)-Fuc-T family, defining an alpha(1,3)-Fuc-T motif which may be of use in identifying new fucosyltransferase genes.
Reflectance spectroscopy can quantify cutaneous haemoglobin oxygenation by oxygen uptake from the atmosphere after epidermal barrier disruption (2003)

Significant changes in skin haemoglobin oxygenation were observed for skin areas with reduced lipid concentration and a reduced stratum corneum layer, as determined from the quantitative evaluation of the diffuse reflectance skin spectra. The result can be interpreted as an increase of oxygen diffusion after the removal of the upper horny layer.
HIF1-alpha functions as a tumor promoter in cancer-associated fibroblasts, and as a tumor suppressor in breast cancer cells (2010)

Our recent studies have mechanistically implicated a loss of stromal Cav-1 expression and HIF1-alpha-activation in driving the cancer-associated fibroblast phenotype, through the paracrine production of nutrients via autophagy and aerobic glycolysis. However, it remains unknown if HIF1a-activation is sufficient to confer the cancer-associated fibroblast phenotype. To test this hypothesis directly, we stably-expressed activated HIF1a in fibroblasts and then examined their ability to promote tumor growth using a xenograft model employing human breast cancer cells (MDA-MB-231). Fibroblasts harboring activated HIF1a showed a dramatic reduction in Cav-1 levels and a shift towards aerobic glycolysis, as evidenced by a loss of mitochondrial activity, and an increase in lactate production. Activated HIF1a also induced BNIP3 and BNIP3L expression, markers for the autophagic destruction of mitochondria. Most importantly, fibroblasts expressing activated HIF1a increased tumor mass by ∼2-fold and tumor volume by ∼3-fold, without a significant increase in tumor angiogenesis. In this context, HIF1a also induced an increase in the lymph node metastasis of cancer cells. Similar results were obtained by driving NFκB activation in fibroblasts, another inducer of autophagy. Thus, activated HIF1a is sufficient to functionally confer the cancer-associated fibroblast phenotype. It is also known that HIF1a expression is required for the induction of autophagy in cancer cells. As such, we next directly expressed activated HIF1a in MDA-MB-231 cells and assessed its effect on tumor growth via xenograft analysis. Surprisingly, activated HIF1a in cancer cells dramatically suppressed tumor growth, resulting in a 2-fold reduction in tumor mass and a 3-fold reduction in tumor volume. We conclude that HIF1a activation in different cell types can either promote or repress tumorigenesis. Based on these studies, we suggest that autophagy in cancer-associated fibroblasts promotes tumor growth via the paracrine production of recycled nutrients, which can directly "feed" cancer cells. Conversely, autophagy in cancer cells represses tumor growth via their "self-digestion". Thus, we should consider that the activities of various known oncogenes and tumor-suppressors may be compartment and cell-type specific, and are not necessarily an intrinsic property of the molecule itself. As such, other "classic" oncogenes and tumor suppressors will have to be re-evaluated to determine their compartment specific effects on tumor growth and metastasis. Lastly, our results provide direct experimental support for the recently proposed "Autophagic Tumor Stroma Model of Cancer".
Evolution of the selenoproteome inHelicobacter pyloriand Epsilonproteobacteria (2015)

By competing for the acquisition of essential nutrients, Helicobacter pylori has the unique ability to persist in the human stomach, also causing nutritional insufficiencies in the host. Although the H. pylori genome apparently encodes selenocysteine synthase (SelA, HP1513), a key pyridoxal phosphate (PLP)-dependent enzyme for the incorporation of selenium into bacterial proteins, nothing is known about the use of this essential element in protein synthesis by this pathogen. We analyzed the evolution of the complete machinery for incorporation of selenium into proteins and the selenoproteome of several H. pylori strains and related Epsilonproteobacteria. Our searches identified the presence of selenoproteins-including the previously unknown DUF466 family-in various Epsilonproteobacteria, but not in H. pylori. We found that a complete system for selenocysteine incorporation was present in the Helicobacteriaceae ancestor and has been recently lost before the split of Helicobacter acinonychis and H. pylori. Our results indicate that H. pylori, at variance with other gastric and enterohepatic Helicobacter, does not use selenocysteine in protein synthesis and does not use selenium for tRNA wobble base modification. However, selA has survived as a functional gene, having lost the domain for the binding of selenocysteine tRNA, but maintaining the ability to bind the PLP cofactor. The evolutionary modifications described for the SelA protein of H. pylori find parallels in other bacterial and archaeal species, suggesting that an alternative enzymatic function is hidden in many proteins annotated as selenocysteinyl-tRNA synthase.
QPM-GaAs for Mid-Infrared Applications (2008)

Powerful coherent laser sources are needed throughout the mid-infrared region for a number of civilian or defense applications, exploiting either the atmospheric transmission windows, or the fingerprint of common molecules. Nonlinear optical materials play a key role as they permit the frequency down-conversion of mature near-infrared solid-state lasers into the mid-IR, where few direct laser solutions exist. Gallium arsenide (GaAs) has excellent characteristics for parametric frequency conversion and is potentially one of the most attractive mid-IR nonlinear-optical materials. It has an extremely large second-order nonlinear optical coefficient d14 ≈ 100 pm/V, wide transparency range 1-16 µm, excellent mechanical properties and high thermal conductivity [1]. The crystal is optically isotropic precluding birefringent phasematching, however with appropriate quasi-phasematching (QPM) means, it can be used for numerous nonlinear optical applications. The drawbacks of previous QPM GaAs devices based on diffusion bonding of thin GaAs wafers with periodic orientations [2], have been eliminated by the use of wafer-scale processing techniques for fabricating periodically-inverted (orientation-patterned) structures in GaAs and Hydride Vapour Phase Epitaxy (HVPE) thick-film regrowth [3,4]. HVPE allows growth rates of about 30 µm/h resulting in low doped layers with excellent optical properties. Careful growth parameters selection can preserve the periodic orientation of the template substrate to thicknesses in excess of 500 µm, thus enabling free space propagation of pump and signal
Interleukin 1 Gene Cluster, Myocardial Infarction at Young Age and Inflammatory Response of Human Mononuclear Cells (2009)

The objective was to investigate whether genotypes, haplotypes and haplotype-pairs of interleukin (IL) gene cluster are associated with risk of Myocardial Infarction (MI) at young age and with the release of IL-1B and expression of tissue factor pro-coagulant activity (TFPCA), after stimulation in vitro with lipopolysaccharide (LPS) of human peripheral blood mononuclear cells (PBMCs). Patients with MI at young age, frequency-matched for age, sex and recruitment centre, with healthy population-based controls and PBMCs from healthy volunteers were studied. Five single nucleotide polymorphisms (SNPs), identifying two haplotype-blocks, in IL-1B gene and one SNP in IL-1A and IL-RA genes were genotyped. In multivariate analyses, haplotype A2 (122) and A4 (112) were associated with decreased risk of MI [OR = 0.62 (95% CI = 0.40-0.95), p = 0.01; OR = 0.69 (95% CI = 0.51-0.92), p = 0.03, respectively]. Haplotype-pair A2/A2 showed significant reduction in the risk of MI [OR = 0.38 (95% CI = 0.18-0.81); p = 0.01]. Haplotype A2 and A4 were associated with lower levels of IL-1B (respectively p = 0.01; p = 0.04, multivariate analysis) and haplotype-pair A2/A4 showed decreased levels of IL-1beta (p = 0.02). No association was found between block "B" IL-1B haplotypes or IL-1A and IL-RA polymorphisms and risk of MI. IL-1B haplotypes influence the inflammatory response of human mononuclear cells to LPS and affect the risk of MI at young age.
Single-Phase Inverter Control Techniques for Interfacing Renewable Energy Sources With Microgrid—Part I: Parallel-Connected Inverter Topology With Active and Reactive Power Flow Control Along With Grid Current Shaping (2010)

In this paper, a novel current control technique is proposed to control both active and reactive power flow from a renewable energy source feeding a microgrid system through a single-phase parallel-connected inverter. The parallel-connected inverter ensures active and reactive power flow from the grid with low-current total harmonic distortion even in the presence of nonlinear load. A p–q theory-based approach is used to find the reference current of the parallel-connected converter to ensure desired operating conditions at the grid terminal. The proposed current controller is simple to implement and gives superior performance over the conventional current controllers, such as rotating frame proportional–integral controller or stationary frame proportional resonant controller. The stability of the proposed controller is ensured by direct Lyapunov method. A new technique based on the spatial repetitive controller is also proposed to improve the performance of the current controller by estimating the grid and other periodic disturbances. Detailed experimental results are presented to show the efficacy of the proposed current control scheme along with the proposed nonlinear controller to control the active and reactive power flow in a single-phase microgrid under different operating conditions.
The paradoxical effect of tumor necrosis factor alpha (TNF-alpha) in endotoxin-induced uveitis. (1993)

Unlike its apparent participation in the systemic effect of endotoxin, TNF-alpha is not directly involved in the pathogenesis of EIU and may even protect against the inflammatory processes of this disease.
An enhancer at the 3′ end of the mouse immunoglobulin heavy chain locus (1991)

A tissue-specific enhancer (E mu) lies between the joining (JH) and mu constant region (C mu) gene segments of the immunoglobulin heavy chain (IgH) locus. Since mouse endogenous IgH genes are efficiently transcribed in its absence, the normal function of this enhancer remains ill-defined. Recently, another lymphoid-specific enhancer of equal strength has been identified 3' of the rat IgH locus. We have isolated an analogous sequence from mouse and have mapped it 12.5 kb 3' of the 3'-most constant region gene (C alpha-membrane) of the BALB/c mouse locus. The mouse and rat sequences are 82% homologous and share with other enhancers several DNA sequence motifs capable of binding protein. However, in transient transfection assays, the mouse sequence behaves as a weaker enhancer. The role of this distant element in the expression of endogenous IgH genes, both in E mu-deficient, Ig-producing cell lines and during normal B cell development, is discussed.
Transcriptional Activities of the Orphan Nuclear Receptor ERRα (Estrogen Receptor-Related Receptor-α) (1999)

Estrogen receptor-related receptor alpha (ERR alpha) is an orphan nuclear receptor closely related to the estrogen receptor (ER), whose expression covers various stages of embryonic development and persists in certain adult tissues. We show that ERR alpha binds as a homodimer on a specific target sequence, the SFRE (SF-1 response element), already known to respond to the orphan nuclear receptor SF-1. Target sequences that are related to the SFRE and that discriminate between ERR alpha and SF-1 were identified. We have also analyzed the transcriptional properties of the ERR alpha originating from various species. All ERR alpha orthologs act as potent transactivators through the consensus SFRE. ERR alpha activity depends on the putative AF2AD domain, as well as on a serum compound that is withdrawn by charcoal treatment, suggesting the existence of a critical regulating factor brought by serum.
Systemic lupus erythematosus in three ethnic groups. XII. Risk factors for lupus nephritis after diagnosis (2002)

The purpose of this study was to determine the cumulative incidence of lupus nephritis (LN) and the factors predictive of its occurrence in a multiethnic systemic lupus erythematosus (SLE) cohort. We studied 353 SLE patients as defined by the American College of Rheumatology (ACR) criteria (65 Hispanics, 93 African-Americans and 91 Caucasians). First, we determined the cumulative incidence of LN in all patients. Next, we determined the predictors for LN in those with nephritis occurring after diagnosis. The dependent variable, LN, was defined by: (1) A renal biopsy demonstrating World Health Organization (WHO), class II-V histopathology; and/or (2) proteinuria > or = 0.5 g/24 h or 3+ proteinuria attributable to SLE; and/or (3) one of the following features also attributable to SLE and present on two or more visits, which were performed at least 6 months apart--proteinuria > or = 2+, serum creatinine > or = 1.4 mg/dl, creatinine clearance < or = 79 ml/min, > or = 10 RBCs or WBCs per high power field (hpf), or > or = 3 granular or cellular casts per hpf. Independent variables assessed at diagnosis, and if absent, at baseline, were from four domains: sociodemographic, clinical, immunologic and immunogenetic (including the complete antibody profile and MHC class II alleles), and health habits. Variables with P < 0.05 by chi square analyses were entered into domain-specific stepwise logistic regression analyses controlling for disease duration, with LN as the dependent variable. Significant domain-specific regression variables (P < or = 0.1) were then entered into an overall model. The cumulative incidence of LN was 54.3% in all patients, and 35.3% for those developing LN after diagnosis. LN after diagnosis occurred in 43.1% of 65 Hispanics, 50.5% of 93 African-Americans, and 14.3% of 91 Caucasians, P < 0.0001. The duration of follow-up for those with LN after diagnosis was 5.5+/-2.4 vs 4.0+/-2.9 years for those without LN. Hispanic (odds ratio (OR) = 2.71, 95% confidence limits (CL) = 1.07-6.87, P < 0.04) and African-American ethnicities (OR = 3.13, 95% CL = 1.21-8.09, P < 0.02), not married or living together (OR = 3.45, 95% CL = 1.69-7.69, P < 0.0003), higher SLAM score (OR = 1.11, 95% CL = 1.02-1.19, P < 0.007), anti-dsDNA (OR = 3.14, 95% CL = 1.50-6.57, P < 0.0001) and anti-RNP (OR = 4.24, CL = 1.98-9.07, P < 0.0001) antibodies were shown to be significant predictors of the occurrence of LN. Repeated analyses excluding the patients with missing HLA data showed that absence of HLA-DQB1*0201 was also a significant predictor for the occurrence of LN (OR = 2.34, CL = 1.13-5.26, P < 0.04). In conclusion, LN occurred significantly more often in Hispanics and African-Americans with SLE. Sociodemographic, clinical and immunologic/immunogenetic factors seem to be predictive of LN occurring after the diagnosis of SLE has been made.
Horizontal wells and steam‐assisted gravity drainage (1991)

Abstract Petroleum can be produced more efficiently using horizontal wells instead of conventional wells. For a typical 16 hectare well spacing, the pressure drawdown is as small as one‐fiftieth of that for conventional wells. In some cases, where coning is a problem in conventional production, horizontal wells allow operation with much less coproduction of the displacing fluid. In the thermal recovery of bitumen and heavy oils, the Steam‐Assisted Gravity Drainage process with horizontal production wells allows the systematic sweeping of the reservoir with economic production rates and without steam bypass. This paper described and reviews the application of horizontal wells to the production of heavy crude oils and bitumen by both non‐thermal and thermal methods.
Disinfection of drinking water by using a novel electrochemical reactor employing carbon-cloth electrodes (1992)

A novel electrochemical reactor employing carbon-cloth electrodes was constructed for disinfection of drinking water. Escherichia coli K-12 (10(2) cells per cm3) was sterilized when a cell suspension was passed through the reactor at a dilution rate of 6.0 h-1, and a potential of 0.7 V versus a saturated calomel electrode was applied to an electrode. The survival ratio increased with increasing dilution rate but was less than 0.1% at dilution rates of less than 6.0 h-1. Although the survival ratio increased with increasing cell concentration above 10(3) cells per cm3, the disinfection rate also increased. The disinfection rate was 6.0 x 10(2) cells per cm3 per h at a cell concentration of 10(2) cells per cm3. Continuous sterilization of E. coli cells was carried out for 24 h. Sterilization is based on an electrochemical reaction between the electrode and the cell which is mediated by intracellular coenzyme A. Sterilization of drinking water by using this reactor was successfully performed, demonstrating the potential of such a reactor for clean and efficient water purification.
Iteratively reweighted least-squares state estimation through Givens Rotations (1999)

This paper presents a robust iteratively reweighted least squares (IRLS) method for power system state estimation (PSSE). An orthogonal implementation through Givens Rotations to solve estimators based on nonquadratic criteria is introduced. The nonquadratic criteria are defined based on the robust statistical theory. The weights associated with the measurements include the effects of measurement variances and the location where each measurement is taken. Bad data identification is a byproduct of the proposed method. After bad data identification, no reprocessing is required in order to obtain the correct estimates. The method is validated by using the 14-bus, 30-bus and 118-bus IEEE test systems, in addition to a 340-bus realistic system.