gebhart/patrepeval huggingface dataset:
Construction and Evaluation of Internal Control DNA for PCR Amplification of Chlamydia trachomatis DNA from Urine Samples (2003)

An internal control DNA (ICD) with the same primer binding sequences as the target Chlamydia trachomatis DNA was constructed and evaluated in a PCR assay with immunoenzymatic detection. One hundred urine specimens were tested, and 23 were found to contain inhibitors of the PCR, if not subjected to DNA extraction prior to amplification. Coamplification and detection of the ICD appeared to be a useful method for estimating the effects of inhibitors on C. trachomatis DNA amplification.
Numerical analysis of the shape anisotropy and anisotropy dispersion in thin film permalloy magnetoresistors (1983)

Thin film permalloy magnetoresistors are frequently used in read heads and magnetometers. This paper presents a numerical model of a magnetoresistor, taking into account the shape anisotropy and the anisotropy dispersion. The results of computations for such complex model and a simpler one are compared with experimental data. The agreement for proposed complex model is almost perfect.
Obesity-Associated Autoantibody Production Requires AIM to Retain the Immunoglobulin M Immune Complex on Follicular Dendritic Cells (2013)

Natural immunoglobulin M (IgM) is reactive to autoantigens and is believed to be important for autoimmunity. Blood pentameric IgM loaded with antigens forms a large immune complex (IC) that contains various elements, including apoptosis inhibitor of macrophage (AIM). Here we demonstrate that this IgM-AIM association contributes to autoantibody production under obese conditions. In mice fed a high-fat diet, natural IgM increased through B cell TLR4 stimulation. AIM associated with IgM and protected AIM from renal excretion, increasing blood AIM levels along with the obesity-induced IgM augmentation. Meanwhile, the AIM association inhibited IgM binding to the Fcα/μ receptor on splenic follicular dendritic cells, thereby protecting the IgM IC from Fcα/μ receptor-mediated internalization. This supported IgM-dependent autoantigen presentation to B cells, stimulating IgG autoantibody production. Accordingly, in obese AIM-deficient (AIM(-/-)) mice, the increase of multiple IgG autoantibodies observed in obese wild-type mice was abrogated. Thus, the AIM-IgM association plays a critical role in the obesity-associated autoimmune process.
Taper isolated dynamic gain RAM cell (1978)

This paper describes a one-transistor only, ROM-like dynamic RAM cell, which operates on the principle of a dynamic change in gain or threshold of the device constituting the cell. There is no capacitor in this cell. This concept is radically different from the principle of operation of the conventional one-transistor storage memory cell, which actually consists of a storage capacitor in addition to one transistor, and which stores and senses a fixed charge packet.
Ranking Sentences for Extractive Summarization with Reinforcement Learning (2018)

Shashi Narayan, Shay B. Cohen, Mirella Lapata. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
Floating-body concerns for SOI dynamic random access memory (DRAM) (2002)

Summary form only given. As operating voltages are reduced it becomes increasingly challenging to write a usable signal into the DRAM storage capacitor because of the nonscalability of threshold voltage, due to the limiting effects of subthreshold slope and substrate sensitivity. Since the maximum wordline voltage is limited by reliability considerations, it is extremely important that the threshold voltage of the DRAM array MOSFET be made as low as possible while meeting the static off-current objective for charge retention. SOI, compared to bulk CMOS, appears attractive for a low-voltage (<2 V) DRAM because its superior subthreshold slope and low substrate sensitivity yield a lower source-follower threshold voltage, resulting in increased logical 1 level to be written for the same operating conditions. However, transient effects of the floating body must be considered when designing for long data retention time and low active power. Although earlier work has considered dynamic retention problems for SOI DRAM during normal read/write operations, simulation results presented in this paper address a transient SOI DRAM leakage mechanism which appears during page mode operation, for both partially and fully depleted designs. Two novel solutions for suppressing the transient leakage mechanism have been investigated.
Towards an Elastic and Autonomic Multitenant Database (2011)

The success of cloud computing as a platform for deploying webapplications has led to a deluge of applications characterized by small data footprints with unpredictable access patterns. A scalable multitenant database management system (DBMS) is therefore an important component of the software stack for platforms supporting these applications. Elastic load balancing and efficient database migration techniques are key requirements for effective resource utilization and operational cost minimization. Our vision is a DBMS where multitenancy is viewed as virtualization in the database layer, and elasticity is a first class notion with the same stature as scalability, availability etc. We analyze the various models of database multitenancy, formalize the forms of migration, and identify the design space and research goals for an autonomic and elastic multitenant database.
Multiporosity/multipermeability approach to the simulation of naturally fractured reservoirs (1993)

This paper presents an array of deformation‐dependent flow models of various porosities and permeabilities relevant to the characterization of naturally fractured reservoirs. A unified multiporosity multipermeability formulation is proposed as a generalization of the porosity‐ or permeability‐oriented models of specific degree. Some new relationships are identified in the parametric investigation for both single‐porosity and dual‐porosity models. A formula is derived to express Skempton's constant B by Biot's coefficient H and relative compressibility ϕ*. It is found that the recovery of the original expression for Skempton's constant B is largely dependent on the choice of ϕ*, representing relative compressibility. The dual‐porosity/dual‐permeability model is evaluated through an alternative finite element approximation. The deformation‐dependent fracture flow mechanism is introduced where the rock matrix possesses low permeability and fracture flow is dominant. A preliminary study of the reservoir simulation identifies the strong coupling between the fluid flow and solid deformation.
A Modified Percutaneous Outpatient Bladder Neck Suspension System (1994)

During the last 8 years the original percutaneous needle suspension of Pereyra has been enhanced with the goal to reestablish safely and simply support of the pubocervical fascia in a reproducible and secure manner. Refinements include changes in points of suture attachment, limitation of suture tension and devices to perform the procedure simply and anchor the suspending suture in bone. A path along 2 planes of landmarks is used to guide the needle in capturing a maximum amount of mobile pubocervical fascia with a minimum risk of injury to the bladder or ureter. In 3 years over 150 patients have undergone this procedure. Early problems included suture breakage and inaccurate anchor placement. There have been no cases of chronic urinary retention. During the last 2 years the procedure has been performed on an outpatient basis. When suprapubic infection has been suspected, symptoms and signs have resolved with antibiotics. No sutures have been removed and osteitis pubis has not been noted. Any improvement in long-term durability has not yet been determined due to the history of ongoing refinements and the need for subsequent long-term followup. The specifics of this suspension system are described.
Strategies for the Structural Determination of G Protein-coupled Receptors: From an Example of Histamine H<sub>1</sub> Receptor (2013)

G protein-coupled receptors (GPCRs) are major therapeutic drug targets and represent more than 30% of the market share of all prescription drugs. The high-resolution three-dimensional structures of the target receptors provide good initial models for structure-based approaches to drug screening and drug design, which are considered to accelerate drug discovery. However, significant bottlenecks at the expression, purification and crystallization stages of structure determination of GPCRs have existed. Here, we review recent techniques for the determination of GPCR structures. In particular, we focus on the protein engineering techniques that have been used to overcome bottlenecks in expression/purification and crystallization, including our development of a platform using budding yeast for the rapid construction and evaluation of GPCR variants for structural studies. We also present our success in determining the crystal structure of the histamine H₁ receptor (H₁R) in complex with doxepin, an inverse agonist antihistamine. The H₁R structure revealed the low selectivity of doxepin to aminergic receptors and provides key information that should aid the development of highly selective antihistamines.
Structure and Regulation of KGD1, the Structural Gene for Yeast α-Ketoglutarate Dehydrogenase (1989)

Nuclear respiratory-defective mutants of Saccharomyces cerevisiae have been screened for lesions in the mitochondrial alpha-ketoglutarate dehydrogenase complex. Strains assigned to complementation group G70 were ascertained to be deficient in enzyme activity due to mutations in the KGD1 gene coding for the alpha-ketoglutarate dehydrogenase component of the complex. The KGD1 gene has been cloned by transformation of a representative kgd1 mutant, C225/U1, with a recombinant plasmid library of wild-type yeast nuclear DNA. Transformants containing the gene on a multicopy plasmid had three- to four-times-higher alpha-ketoglutarate dehydrogenase activity than did wild-type S. cerevisiae. Substitution of the chromosomal copy of KGD1 with a disrupted allele (kgd1::URA3) induced a deficiency in alpha-ketoglutarate dehydrogenase. The sequence of the cloned region of DNA which complements kgd1 mutants was found to have an open reading frame of 3,042 nucleotides capable of coding for a protein of Mw 114,470. The encoded protein had 38% identical residues with the reported sequence of alpha-ketoglutarate dehydrogenase from Escherichia coli. Two lines of evidence indicated that transcription of KGD1 is catabolite repressed. Higher steady-state levels of KGD1 mRNA were detected in wild-type yeast grown on the nonrepressible sugar galactose than in yeast grown on high glucose. Regulation of KGD1 was also studied by fusing different 5'-flanking regions of KGD1 to the lacZ gene of E. coli and measuring the expression of beta-galactosidase in yeast. Transformants harboring a fusion of 693 nucleotides of the 5'-flanking sequence expressed 10 times more beta-galactosidase activity when grown under derepressed conditions. The response to the carbon source was reduced dramatically when the same lacZ fusion was present in a hap2 or hap3 mutant. The promoter element(s) responsible for the regulated expression of KGD1 has been mapped to the -354 to -143 region. This region contained several putative activation sites with sequences matching the core element proposed to be essential for binding of the HAP2 and HAP3 regulatory proteins.
Platelet-derived growth factor gene expression in human atherosclerotic plaques and normal artery wall. (1988)

We previously demonstrated that the B chain of platelet-derived growth factor (PDGF-B) is transcribed in human atherosclerotic plaques, indicating that production of growth factors within plaques could occur during atherogenesis. However, since atherosclerotic plaques are composed of several cell types and three of these--macrophages, endothelial cells, and smooth muscle cells--can express the PDGF genes, the cell type responsible for PDGF gene expression was not clear. In the present study we explore further the expression of PDGF-A and -B and identify transcriptionally active cell types. We assayed PDGF-A and -B mRNA levels in dissected fractions of carotid atherosclerotic plaques and normal artery and then sequentially rehybridized these blots with three cDNA probes that recognize cell type-specific markers: fms for macrophages, von Willebrand factor for endothelial cells, and smooth muscle alpha-actin for smooth muscle cells. In plaques, PDGF-A expression correlated with smooth muscle actin; PDGF-B expression correlated strongly with fms. PDGF-A expression correlated with smooth muscle actin. In normal vessel wall, PDGF-A expression was high in the media and again correlated with smooth muscle actin, whereas PDGF-B expression was high in the adventitia. Since transcripts from both PDGF genes are found in normal artery where cell turnover is very low, we suggest that PDGF gene expression does not necessarily function to produce smooth muscle cell proliferation. We propose that these genes may have an important nonmitogenic, maintenance function in normal arterial tissue and in the atherosclerotic plaque.
Lymphoid Chemokine B Cell-Attracting Chemokine-1 (CXCL13) Is Expressed in Germinal Center of Ectopic Lymphoid Follicles Within the Synovium of Chronic Arthritis Patients (2001)

A unique feature in inflammatory tissue of rheumatoid arthritis (RA) is the formation of ectopic lymphoid aggregates with germinal center (GC)-like structures that can be considered to contribute to the pathogenesis of RA, because local production of the autoantibody, rheumatoid factor, is thought to be a causative factor in tissue damage. However, the factors governing the formation of GC in RA are presently unknown. To begin to address this, the expression of B cell attracting chemokine (BCA-1) (CXCL13), a potent chemoattractant of B cells, was examined in the synovium of patients with RA or with osteoarthritis (OA). Expression of BCA-1 mRNA was detected in all RA samples, but in only one of five OA samples. Lymphoid follicles were observed in four of seven RA samples and in two of eight OA samples, and in most of them BCA-1 protein was detected in GC. BCA-1 was not detected in tissues lacking lymphoid follicles. Notably, BCA-1 was detected predominantly in follicular dendritic cells in GC. CD20-positive B cells were aggregated in regions of BCA-1 expression, but not T cells or macrophages. These data suggest that BCA-1 produced by follicular dendritic cells may attract B cells and contribute to the formation of GC-like structures in chronic arthritis.
Transcription of the segment-polarity gene wingless in the imaginal discs of Drosophila, and the phenotype of a pupal-lethal wg mutation (1988)

Wingless (wg) is a segment-polarity gene in Drosophila which is related to the murine proto-oncogene int1. In Drosophila embryos, wg transcription defines part of each parasegment. In situ hybridization shows that wg is also expressed in the imaginal discs which give rise to the adult during metamorphosis. Transcripts are localized in the apical cytoplasm of disc cells, and accumulate in different patterns in dorsal and ventral discs. The wgCX3 mutation produces morphological defect in the adult structures derived from these imaginal discs. The results show that wg is involved in the development of the adult, as well as the embryo, but that the imaginal discs do not express this segment-polarity gene in an identical pattern to the embryonic segments.
Glycosides from Chinese medicinal plant, Hemsleya panacis-scandens, and structure-taste relationship of cucurbitane glycosides. (1988)

From rhizomes of Hemsleya panacis-scandens collected in Yunnan, China, eight new cucurbitane glycosides named scandenosides R1-R7 and dihydrocucurbitacin F glucoside (2-O-β-D-glucopyranoside of 23, 24-dihydrocucurbitacin F) were isolated, along with six known cucurbitane glycosides. The structures of these new glycosides were determined on the basis of chemical and spectral data except for the configuration at C-20. Of these new glycosides, scandenoside R6 tastes sweet and R5 and dihydrocucurbitacin F glucoside taste bitter, while the others are tasteless. The structure-taste relationships of cucurbitane glycosides are discussed.
Measuring the Phase of Spatially Coherent Polychromatic Fields (2002)

Realistic optical fields are never completely monochromatic and the interpretation of the concept of phase is not straightforward. It has been pointed out by Wolf that, if a strict condition of spatial coherence is imposed, the statistically averaged behavior of a polychromatic field can be described by an associated monochromatic wave. We show that, for spatially coherent polychromatic optical fields, the measurement of the phase of the second-order correlations determines the phase of this associated, spatially coherent field. We verify this prediction using a novel interferometric technique for measuring the cross-spectral density of a steady-state optical field.
1,N6-etheno-2′ -deoxyadenosine and 3,N4-etheno-2′-deoxycytidine detected by monoclonal antibodies in lung and liver DNA of rats exposed to vinyl chloride (1989)

1,N6-Etheno-2'-deoxyadenosine (epsilon dAdo) and 3,N4-etheno-2'-deoxycytidine (epsilon dCyd) are formed in vitro by reaction of DNA with the electrophilic metabolites of vinyl chloride (VC), chloroethylene oxide and chloroacetaldehyde. To detect and quantitate these DNA adducts in vivo, we have raised a series of specific monoclonal antibodies (Mab). Among those, Mab EM-A-1 and Mab EM-C-1, respectively, were used for detection of epsilon dAdo and epsilon dCyd by competitive radioimmunoassay (RIA), following pre-separation of the etheno adducts from DNA hydrolysates by high performance liquid chromatography. At 50% inhibition of tracer-antibody binding, both Mab had a detection limit of 187 fmol and antibody affinity constants (K) of 2 x 10(9) l/mol. The levels of epsilon dAdo and epsilon dCyd were quantitated in the DNA of lung and liver tissue of young Sprague-Dawley rats exposed to 2000 p.p.m. of VC for 10 days. The epsilon dAdo/2'-deoxyadenosine and epsilon dCyd/2'-deoxycytidine molar ratios were 1.3 x 10(-7) and 3.3 x 10(-7), respectively, in lung DNA, and 5.0 x 10(-8) and 1.6 x 10(-7) in liver DNA. When hydrolysates of 3 mg of DNA were analyzed by RIA at 25% inhibition of tracer-antibody binding, epsilon dAdo and epsilon dCyd were not detected in liver DNA from untreated rats above the limiting epsilon dAdo/2'-deoxyadenosine and epsilon dCyd/2'-deoxycytidine molar ratios of 2.2 x 10(-8) and 3.1 x 10(-8), respectively.
Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin (1986)

Abstract Structural studies on serine proteinases have shown that hydrogen bonds are involved in stabilizing the charged tetrahedral intermediate in the transition-state complex. However, little is known about the quantitative contribution of these interactions to transition-state stabilization. X-ray crystallographic studies of subtilisin (Robertus, J. D., Kraut, J., Alden, R. A. &amp; Birktoft, J. J. Biochemistry, Wash. 11, 4293-4303 (1972)) have suggested that the amide side chain from asparagine-155 forms a hydrogen bond with the oxyanion produced on the substrate carbonyl oxygen in the tetrahedral intermediate. To study the importance of the Asn-155 hydrogen bond in stabilizing the tetrahedral intermediate, Asn-155 was substituted with Thr, His, Gin and Asp by using site-specific mutagenesis of the cloned subtilisin gene from B. amyloliquefaciens. These substitutions were intended to alter the position and charge of the potential hydrogen-bonding group at 155. Mutations of Asn-155 caused large decreases in substrate turnover, Kcat (200- to 4000-fold), with marginal decreases in substrate binding, KM (up to 7-fold). The most dramatic effects were seen with Thr-155, where Kcat was reduced 4000-fold with a slight increase in KM. Mutations of Asn-155 caused a loss in transition-state stabilization energy of 9.2-20 kJ mol-1 Simple enrichment methods are described which greatly facilitate the isolation of mutant sequences. These methods depend upon the introduction or elimination of a unique and silent restriction site near the site of mutagenesis.
A signature for the HMG‐1 box DNA‐binding proteins (1993)

A diverse group of DNA-binding regulatory proteins share a common structural domain which is homologous to the sequence of a highly conserved and abundant chromosomal protein, HMG-1. Proteins containing this HMG-1 box regulate various cellular functions involving DNA binding, suggesting that the target DNA sequences share a common structural element. Members of this protein family exhibit a dual DNA-binding specificity: each recognizes a unique sequence as well as a common DNA conformation. The highly conserved HMG-1/-2 proteins may modulate the binding of other HMG-1 box proteins to bent DNA. We examine the structural and functional relationships between the proteins, identify their signature and describe common features of their target DNA elements.
[In vitro culture of umbilical cord blood MNC and CD34+ selected cells]. (2002)

For in vitro studies, both CD34+ selected cell and mononuclear cell (MNC) can be used to expand hematopoietic stem/progenitor cells. To investigate the expansion characteristics of mononuclear cells (MNC) and CD34+ selected cells the two cell fractions were cultured in the medium containing cytokine cocktails of SCF + IL-3 + IL-6 + FL + Tpo. It was found that the CD34+ selected cells had presented a high proliferation potential. The expansion of CD34+ selected cells could be maintained for 8 weeks while that of MNCs declined after 4 weeks. During the culture period, the maximum expansion of total cells in CD34+ selected cell culture achieved 31,270.9 +/- 8640.5 times, while that of MNC reached 50.9 +/- 8.2 times only. In the culture of MNCs, the colony density and the proportion of CD34+ cells increased from day 0 to day 7. However, in the culture of CD34+ selected cells, both the colony density and the proportion of CD34+ cells declined continuously during the whole culture period. During the ex vivo culture of CD34+ selected cells, the maximum expansion of CFU-GM and CD34+ cells achieved 185.7 +/- 14.1 fold and 191.7 +/- 188.8 fold, respectively. They are much higher than that of MNC, which were 12.4 +/- 3.2 fold and 50.6 +/- 33.2 fold only. While the BFU-E of both cell fractions only expanded by few times, which were 7.2 +/- 5.2 and 10.1 +/- 3.4 times, respectively. The results showed that the CD34+ selected cells culture could obtain more CFU-GM cells and CD34+ cells during the whole culture period.
Mutants in the ADP-ribosyltransferase Cleft of Cholera Toxin Lack Diarrheagenicity but Retain Adjuvanticity (1997)

Cholera toxin (CT), the most commonly used mucosal adjuvant in experimental animals, is unsuitable for humans because of potent diarrhea-inducing properties. We have constructed two CT-A subunit mutants, e.g., serine-->phenylalanine at position 61 (S61F), and glutamic acid-->lysine at 112 (E112K) by site-directed mutagenesis. Neither mutant CT (mCT), in contrast to native CT (nCT), induced adenosine diphosphate-ribosylation, cyclic adenosine monophosphate formation, or fluid accumulation in ligated mouse ileal loops. Both mCTs retained adjuvant properties, since mice given ovalbumin (OVA) subcutaneously with mCTs or nCT, but not OVA alone developed high-titered serum anti-OVA immunoglobulin G (IgG) antibodies (Abs) which were largely of IgG1 and IgG2b subclasses. Although nCT induced brisk IgE Ab responses, both mCTs elicited lower anti-OVA IgE Abs. OVA-specific CD4+ T cells were induced by nCT and by mCTs, and quantitative analysis of secreted cytokines and mRNA revealed a T helper cell 2 (Th2)-type response. These results now show that the toxic properties of CT can be separated from adjuvanticity, and the mCTs induce Ab responses via a Th2 cell pathway.