gebhart/patrepeval huggingface dataset:
Genetic regulation of formate hydrogenlyase of Escherichia coli: role of the fhlA gene product as a transcriptional activator for a new regulatory gene, fhlB (1990)

A new gene whose product is required for the production of formate hydrogenlyase (FHL) has been identified in Escherichia coli. This gene, termed fhlB, maps between the frdA (94.4 min) and argI (96.6 min) genes on the E. coli chromosome and is transcribed in a clockwise direction toward argI. Biochemical analysis of an FhlB- mutant, strain SE-2011 [phi(fhlB-lacZ+)], revealed that the mutant lacks formate dehydrogenase activity associated with FHL (FDH-H) and hydrogenase activity. As a result of these defects, fermentative hydrogen production and hydrogen uptake reactions were undetectable in strain SE-2011. Fumarate reductase activity of this mutant was also reduced to about 15% of the levels of the parent (strain MC4100), and strain SE-2011 did not produce succinate as a fermentation end product. Regulation of expression of the fhlB gene, studied as production of beta-galactosidase activity by strain SE-2011, revealed that the operon is expressed at low levels under aerobic conditions. Under anaerobic growth conditions, this activity increased by two- to threefold. Addition of formate enhanced the differential rate of synthesis of the fhlB gene product to as high as 130 U of beta-galactosidase specific activity per microgram of cell protein, but only under anaerobic conditions. Formate-dependent expression of phi(fhlB-lacZ+) required the sigma 54 subunit of RNA polymerase and the fhlA gene product. The concentration of formate required for maximum expression of the fhlB gene was about 15 mM; this value decreased to about 3 mM in the presence of plasmid pSE-133, which carries the fhlA gene in a multicopy plasmid. DNA sequence analysis of the fhlA gene showed that the FhlA protein is 686 amino acids long and has an anhydrous molecular weight of 78,086. On the basis of sequence homology with other transcriptional activators such as NtrC, HydG, and Klebsiella pneumoniae NifA proteins, the FhlA protein was deduced to be a transcriptional activator controlling the production of FHL. It is proposed that formate interacts with the FhlA protein and that this active complex initiates transcription of the fhlB gene. The FhlA and FhlB proteins act as a cascade in regulating the production of FDH-H and the FHL-linked hydrogenase and ultimately the production of FHL and fermentative hydrogen.
Cloning, sequencing, expression, and protective capacity of the oma87 gene encoding the Pasteurella multocida 87-kilodalton outer membrane antigen (1996)

Membrane proteins of Pasteurella multocida have been shown previously to elicit protective immunity. We have identified an 87-kDa outer membrane antigen, Oma87, which is present in all 16 serotypes of P. multocida. The gene encoding this protein was cloned and sequenced and found to have significant similarity to the D15 protective surface antigen of Haemophilus influenzae. Oma87 was localized to the outer membrane of the cell, and proteinase K treatment suggested that the protein is surface exposed. Native and recombinant Oma87 were strongly immunostained by convalescent-phase antiserum, indicating that the protein is expressed in vivo. Specific Oma87 antiserum protected mice against homologous, lethal P. multocida challenge. These results suggest that Oma87 is a protective outer membrane antigen of P. multocida.
Reovirus serotype 1 intestinal infection: a novel replicative cycle with ileal disease (1985)

After oral inoculation, reovirus serotype 1 strain Lang was shown to specifically infect the epithelial cells of the ileum, while sparing the epithelial cells in the duodenum, jejunum, and colon. The initial site of replication was localized in cells of the crypts of Lieberkühn adjacent to Peyer's patches. Virus was subsequently found by immunoperoxidase staining in cells migrating up the crypt-villus complex throughout the ileum. The severity of the pathological changes in the ileum was proportional to the concentration of the viral inoculum. This site-specific infection of the ileum by reovirus may provide a model for diseases that are restricted to specific sites in the intestine.
Near-Field Scanning Optical Microscopy (1987)

The spatial resolution of most of the imaging or microcharacterization methods presently in use are fundamentally limited by the wavelength of the exciting or the emitted radiation being used. In general, the smaller the wavelength of the exciting probe, the greater the structural damage to the sample under study. Thus, the requirements of minimal sample alteration and high spatial resolution seem to be at odds with one another. However, the reason for this wavelength resolution limit is due to the far field methods for producing or detecting the radiation of interest. If one does not use far field optics, but rather the method of near field imaging, the spatial resolution attainable can be much smaller than the wavelength of the radiation used. This method of near field imaging has a general applicability for all wave probes.
Herding dynamical weights to learn (2009)

A new "herding" algorithm is proposed which directly converts observed moments into a sequence of pseudo-samples. The pseudo-samples respect the moment constraints and may be used to estimate (unobserved) quantities of interest. The procedure allows us to sidestep the usual approach of first learning a joint model (which is intractable) and then sampling from that model (which can easily get stuck in a local mode). Moreover, the algorithm is fully deterministic, avoiding random number generation) and does not need expensive operations such as exponentiation.
Evaluating serum anti-cyclin B1 antibodies as a biomarker for prevalent, early lung cancer in a population at high-risk for lung cancer (2006)

4549 Purpose: The primary aims of this study are to assess serum cyclin B1 antibody titers as effective diagnostic or screening tools for the identification of prevalent, early lung cancer cases within a population at-risk for lung cancer using a case-control study design. Background: Detecting lung cancer early creates the opportunity for more successful treatment outcomes. In order to identify early stage lung cancer, screening of at-risk populations may need to be implemented. The immune system is capable of responding to tumor antigens arising from altered host factors and may provide an early readout for the presence of cancer. Antibodies to the tumor antigen cyclin B1 are present in lung cancer patients. Unscheduled overexpression of this cell cycle regulator occurs early in tumorigenesis and might be detected by the immune system long before clinical diagnosis of cancer. Serum cyclin B1 antibody titer screening would be safe and likely acceptable to subjects/patients if antibody titers prove to be a sufficiently sensitive and specific biomarker of prevalent lung cancer. Methods: Antibodies recognizing cyclin B1 were measured using semi-automated ELISAs in sera samples from subjects with and without computed tomography- (CT-) detectable lung cancer enrolled in the Pittsburgh Lung Screening Study (PLuSS), a longitudinal study of long-term smokers over age 50. Total anti-cyclin B1 serum antibody titers and isotype-specific anti-cyclin B1 antibody titers were assessed for 37 PLuSS lung cancer cancers and 74 matched PLuSS control subject. Association of presence of anti-cyclin B1 antibody with cancer case status was evaluated using STATA V.9 conditional logistic regression analysis. Results: Total and isotype-specific anti-cyclin B1 antibodies were present in a small subset of cases and at-risk subjects without CT-detectable lung cancer. These positive outliers will be of special interest as the cohort is followed prospectively, as anti-cyclin B1 antibody levels may be of prognostic importance regarding disease outcomes for cases and future disease occurrence for at-risk controls. For prevalent CT-detectable cancer versus age-matched at-risk controls, presence of anti-cyclin B1 antibodies was not significantly associated with cancer case status. These findings differ from previous reports and may be a result of using lung cancer cases that were identified through a concerted screening effort rather than presenting as symptomatic lung cancer.
Non-small cell lung cancer and estrogen plus progestin use in postmenopausal women in the Women's Health Initiative randomized clinical trial (2009)

CRA1500 Background: Sex differences in lung cancer outcome suggest a potential hormonal influence; however, observational studies provide mixed findings regarding menopausal hormone therapy (HT) and lung cancer. Methods: Secondary analyses of the WHI randomized, placebo-controlled trial of daily conjugated equine estrogen (CEE, 0.625 mg) plus medroxyprogesterone acetate (MPA, 2.5 mg) in 16,608 multi-ethnic postmenopausal women, aged 50–79 were conducted on lung cancer incidence and mortality. Lung cancers were confirmed by medical record review. Results: Groups were balanced for age, race/ethnicity, and prior HT. Smoking status was also comparable (never 50%, past 40%, current 10% in both groups). Cumulative risk for lung cancer was highest in current (0.51%), compared to past (0.14%) and never (0.04%) smokers. After 5.6 years on trial intervention and 2.4 years additional follow-up (median), small cell lung cancer incidence was comparable between randomization groups (total n=26), as was subsequent small cell lung cancer mortality. Although a trend for more non-small cell lung cancer (NSCLC) diagnoses in the active hormone group was not significant (p=0.12), an apparent divergence emerged after five years, with more diagnoses in the CEE+MPA group. In addition, mortality after NSCLC diagnosis was significantly higher for the CEE+MPA group (46.3% vs 27.0%, respectively, hazard ratio (HR) 1.59, 95% CI 1.03–2.46, p=0.04). As a result, CEE+MPA group women were more likely to die from NSCLC than those on placebo (p=0.02). Conclusions: Use of CEE + MPA for over 5 years increases a woman's risk for NSCLC mortality, the leading cause of cancer death in women. These data, together with recent results indicating higher breast cancer risk (Cancer Res 2009;69(2):78s), suggest cancer impact should influence risk-to-benefit consideration for combined HT use. NSCLC outcomes (annualized %) by randomization group CEE+MPA Placebo HR 95% CI P-Value N % N % NSCLC Incidence 96 0.14% 72 0.11% 1.28 0.94, 1.73 0.12 NSCLC Mortality * 67 0.10% 39 0.06% 1.61 1.09–2.39 0.02 * Analyses begin at entry randomization Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Amgen, AstraZeneca, Eli Lilly, Novartis, Wyeth Amgen, AstraZeneca, Eli Lilly, Novartis, Wyeth Amgen
Chemokines in neurological disease models: correlation between chemokine expression patterns and inflammatory pathology (1997)

We have recently determined chemokine expression profiles in a variety of models of neural trauma and immune-inflammation. The results indicate the following: (1) Chemokine expression in posttraumatic inflammation is generally restricted to the monocyte chemoattractant MCP-1, and occurs before hematogenous cell entry into neural tissues. Therefore MCP-1 is an excellent candidate for a mediator of leukocyte recruitment in these settings. (2) Chemokine expression in immune-inflammation is diverse and includes both alpha- and beta-chemokines. Chemokine production can be attributed to parenchymal and infiltrating cell populations. Early signs of inflammation precede chemokine expression, which is believed to exert the crucial function of amplifying the immune-mediated inflammatory reaction. These observations provide a basis for evaluating model neurological disorders in transgenic mice that express chemokines ectopically or in mice that are deficient in chemokine ligands or receptors as a consequence of gene targeting. Ultimately, a clear definition of roles of chemokines and their receptors in neurological diseases will suggest rational intervention.
Cloning and characterization of rhesus cytomegalovirus glycoprotein B. (1997)

Rhesus cytomegalovirus (RhCMV) infection of rhesus macaques is an important model to investigate critical issues of cytomegalovirus biology. To better understand host immunological responses to viral glycoproteins, the glycoprotein B (gB) gene of RhCMV was molecularly cloned, sequenced and characterized. Transcription analysis revealed that RhCMV gB was transcribed as a late gene. The RhCMV gB gene encoded a predicted protein of 854 amino acids that was 60% identical/75% similar to the human CMV (HCMV) gB protein. The region of HCMV gB proposed to be responsible for virus binding to host cells, fusion and cell-to-cell spread was the most highly conserved region with RhCMV gB (74% identity/85% similarity). Conserved elements included 11 of 12 cysteine residues, 14 of 16 potential N-linked glycosylation sites and cross-reactive epitopes. Metabolic labelling experiments demonstrated that RhCMV gB was proteolytically processed similarly to HCMV gB. These results are critical for investigating virus-host relationships in CMV-infected primates.
An experimental 1-Mbit CMOS SRAM with configurable organization and operation (1988)

A 1-Mb SRAM (static random-access memory) configurable as a 128-kb*8, 256-kb*4, or 1-Mb*1 memory featuring asynchronous operation with static-column and chip-enable-access speedup modes or synchronous operation with a fast-page (toggle) or static-column mode is described. It has been fabricated in a double-metal, double-polysilicon CMOS process with 0.7- mu m geometry and special SRAM structures. The measured synchronous access of 29 ns with a fast-page mode access of 22 ns. Measured asynchronous access is 34 ns with a static-column access of 33 ns and a chip-select speedup access of 29 ns. The SRAMs six-transistor CMOS memory cell is 58.24 mu m/sup 2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structural basis for decreased induction of class IB PI3‐kinases expression by MIF inhibitors (2016)

Macrophage migration inhibitory factor (MIF) is a master regulator of proinflammatory cytokines and plays pathological roles when not properly regulated in rheumatoid arthritis, lupus, atherosclerosis, asthma and cancer. Unlike canonical cytokines, MIF has vestigial keto-enol tautomerase activity. Most of the current MIF inhibitors were screened for the inhibition of this enzymatic activity. However, only some of the enzymatic inhibitors inhibit receptor-mediated biological functions of MIF, such as cell recruitment, through an unknown molecular mechanism. The goal of this study was to understand the molecular basis underlying the pharmacological inhibition of biological functions of MIF. Here, we demonstrate how the structural changes caused upon inhibitor binding translate into the alteration of MIF-induced downstream signalling. Macrophage migration inhibitory factor activates phosphoinositide 3-kinases (PI3Ks) that play a pivotal role in immune cell recruitment in health and disease. There are several different PI3K isoforms, but little is known about how they respond to MIF. We demonstrate that MIF up-regulates the expression of Class IB PI3Ks in leucocytes. We also demonstrate that MIF tautomerase active site inhibitors down-regulate the expression of Class IB PI3Ks as well as leucocyte recruitment in vitro and in vivo. Finally, based on our MIF:inhibitor complex crystal structures, we hypothesize that the reduction in Class IB PI3K expression occurs because of the displacement of Pro1 towards the second loop of MIF upon inhibitor binding, which results in increased flexibility of the loop 2 and sub-optimal MIF binding to its receptors. These results will provide molecular insights for fine-tuning the biological functions of MIF.
Genetic Detoxification of Bacterial Toxins: A New Approach to Vaccine Development (1995)

Chemically detoxified bacterial toxins (toxoids) have been successfully used as vaccines for the prevention of many bacterial infectious diseases. Today, nontoxic derivatives of bacterial toxins can be obtained by mutagenesis of the toxin genes. These genetically inactivated toxins are superior to the classical toxoids both in safety and in immunogenicity and therefore they should replace the old toxoids in the existing vaccines. In addition, they represent a novel class of immunogens with unique properties, some of which may be used for innovative approaches to vaccination.
Effect of Cytarabine on the NMR Structure of a Model Okazaki Fragment from the SV40 Genome (1999)

Okazaki fragments occur as intermediates during lagging strand DNA replication. Alterations in Okazaki fragment structure may contribute to the anticancer activities of nucleoside analogues such as cytarabine, a potent anti-leukemic agent that inhibits lagging strand replication. We have determined the solution structures for two model Okazaki fragments, [OKA] and [ARAC]. These sequences are derived from a frequent initiation site for primase during replication of the SV-40 viral genome. The sequence of [ARAC] differs from [OKA] only by substitution of cytarabine for one deoxycytidine. The structure of each model Okazaki fragment was elucidated using NMR spectroscopy and restrained molecular dynamics simulations. The solution structures of [OKA] and [ARAC] each consist of two distinct domains: a DNA duplex region (DDR) and an RNA-DNA hybrid duplex region (HDR). The DDR of [OKA] adopts geometry similar to B-form except for variations in helical parameters, especially twist and roll, which occur in the purine tract, increasing base overlap among the five consecutive purines. The helical axes for the DDR and HDR of [OKA] are bent 22 degrees relative to one another. Although the local structures for the DDR and HDR of [ARAC] are similar to those in [OKA] (root-mean-square deviation (rmsd) approximately 0.8, 1.7 A), the bending at the junction is different (41 degrees for [ARAC] vs 22 degrees for [OKA]). Increased helical bending of cytarabine-substituted Okazaki fragments may contribute to the propensity of cytarabine to inhibit elongation of the lagging strand during DNA replication, and in effecting anticancer activity.
Data Warehousing: Strategies, Technologies, and Techniques (1996)

From the Publisher:
Data warehouseing is key information management strategy for businesses that want to stay competitive into the next century. With this practical,information-packed sourcebook enterprise computing professionals will discover how to design and build an effective data warehousing system. Author Rob Mattison provides a well-organized,step-by-step plan and offers a valuable,vendor-independent examination of the available tools and products. He explains the key concepts of business process reengineering,client/server technology,systems architecture,online analytical processing (OLAP),and decision support systems (DS) that are critical to data warehousing.
Synthesis, Preclinical Validation, Dosimetry, and Toxicity of 68Ga-NOTA-Anti-HER2 Nanobodies for iPET Imaging of HER2 Receptor Expression in Cancer (2013)

A new anti-HER2 PET tracer, (68)Ga-NOTA-2Rs15d, was synthesized via a rapid procedure under mild conditions. Preclinical validation showed high-specific-contrast imaging of HER2-positive tumors with no observed toxicity. (68)Ga-NOTA-2Rs15d is ready for first-in-human clinical trials.
Immunogenetic analysis of the immune response to pneumococcal polysaccharide (2000)

Pneumococcal serotype-specific anti-capsular polysaccharide antibodies protect against invasive pneumococcal disease. Within an individual the diversity of these antibodies is limited. To evaluate the repertoire of antibodies to pneumococcus and determine whether oligoclonality is seen both between serotypes and between individuals, we sampled the B cell repertoire induced by polysaccharide and conjugate vaccine in adult volunteers. Fifteen hybridomas secreting pneumococcus-specific monoclonal antibodies were generated from five volunteers. Ten were isotype switched, six were IgG2 and four were IgA. These included two isotype switch variants of the same clone. V(H)3 and V(kappa)2 were used by 10/15 and 7/13 of the sequenced clones, respectively, with identical genes, V(H)3-48 and V(kappa)2-A17 used by a number of volunteers to a variety of serotypes. VDJ junctional characteristics and complementarity-determining region (CDR) 3 length were variable. High levels of somatic mutation in CDR1 and 2, inconsistent with a primary response, were found in 10/11 of the isotype-switched antibodies, including those induced by plain polysaccharide antigens. These data suggest that wild-type infection or nasopharyngeal carriage of Streptococcus pneumoniae in adults may induce memory and the response to subsequent immunization with plain polysaccharide or conjugate pneumococcal vaccines may have the characteristics of a secondary response.
LP‐1: Late‐News Poster: High Efficiency Reconfigurable 2D/3D Autostereoscopic Display (2003)

Abstract A novel architecture to enable flat panel displays to be electrically reconfigured between a full resolution 2D mode and a half resolution, low cross talk, autostereoscopic 3D mode is described. A Polarisation Activated Microlens comprising a high precision passive birefringent lens array and a commodity switchable polariser element is added to existing LCD panels with a low cost premium. The architecture enables high optical efficiency in 2D and 3D modes and is suitable for transmissive, reflective and transflective LCD devices. The implementation of the component on a transmissive TFT‐LCD is described and measured performance presented.
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples (2015)

Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.
Counterion-induced condensation of deoxyribonucleic acid. A light-scattering study (1979)

The addition of the trivalent or tetravalent cations spermidine or spermine to a solution of T7 DNA in aqueous solution causes an alteration of the DNA from its extended coil form to a condensed form. If performed at low DNA concentration and at low ionic strengths, this transformation results in a monomolecular collapse to form a particle with a hydrodynamic radius of about 500 A. We have monitored this change using quasielastic and total intensity light scattering. In a solution of 50% methanol in water, the divalent cations Mg2+ and putrescine also can cause the condensation of DNA. Using Manning's (1978) counterion condensation theory, we calculate a striking unity among these disparate ions: the collapse occurs in each case when from 89 to 90% of the DNA phosphate charges are neutralized by condensed counterions.