gebhart/patrepeval huggingface dataset:
Immunogenicity of Ty21a attenuated "Salmonella typhi" given with sodium bicarbonate or in enteric-coated capsules. (1983)

Ty21a, a stable attenuated mutant of Salmonella typhi, is a safe, protective oral vaccine when 3 doses of 10(9) cells in saline are taken after neutralization of gastric acidity by 1 g NaHCO3. To identify a more convenient method to administer vaccine and to determine the feasibility of immunizing with a single dose, we studied the immune response of children and adults to different formulations of Ty21a with a newly developed, sensitive, enzyme-linked immunosorbent assay (ELISA). In this ELISA, a rise in S. typhi O antibody was defined as a change in net optical density of greater than or equal to 0.15 (more than 3 SD from the mean difference in optical density in a negative control population). Three hundred and thirty-five Chilean children were given 3 doses of 10(9) Ty21a in 150 ml of milk with 0.8 g NaHCO3 or in enteric-coated capsules. In each group, 5% seroconverted by Widal O but 41% by IgG ELISA O antibody titers; mean antibody levels by group were identical. Studies were also carried out in healthy college students in a non-endemic area (U.S.A.) who had no history of prior typhoid immunization. In total, 141 U.S. adults received vaccine formulated in either one of two ways: 1) in gelatin capsules administered with two additional gelatin capsules containing a total of 0.8 gm NaHCO3 or 2) in enteric-coated capsules. Thirty-six persons received one dose, 30 got two doses and 16 ingested three doses of enteric-coated vaccines, while 44 persons receiving one dose and 15 got two doses of vaccine in the gelatin capsule formulation. Rates of seroconversion of ELISA O antibody were similar in all the groups. Ty21a vaccine was not recovered from multiple stool, jejunal fluid or blood cultures of the U.S. vaccine recipients. Based on these observations a large-scale field trial of efficacy has been initiated in 90.000 schoolchildren 6-20 years of age in Santiago, Chile, of whom one-third received one dose of enteric-coated vaccine, one-third got two doses and the remainder received placebo.
A Look at the Origin and Magnitude of the Chemical Contribution to the Enhancement Mechanism of Surface-Enhanced Raman Spectroscopy (SERS): Theory and Experiment (2013)

Normal and surface-enhanced Raman spectra for a set of substituted benzenethiols were measured experimentally and calculated from static polarizability derivatives determined with time-dependent density functional theory (TDDFT). Both silver and gold cluster–thiolate complexes were studied to investigate how the chemical enhancement varies with substituent. The experimental relative peak intensities and positions are well-matched by their theoretical counterparts. The static chemical enhancement of the ring stretching modes near 1600 cm–1 is determined experimentally and computationally for each derivative, and it is found that the experimental enhancement varies by a factor of 10 as a result of chemical substitution, with stronger electron donating groups on the benzene unit leading to higher enhancements. The calculated trends with substitution match experiment well, suggesting that TDDFT is describing the chemical effect qualitatively, if not quantitatively, in the static (low-frequency) limit. A two-state model is developed, providing qualitative insight into the results in terms of the variation of ligand-to-metal charge-transfer excitation energy with substitution.
Analysis and Optimal Design of a Packet-Voice Receiver (1980)

The analysis problems arising from a digital packet switched speech network are outlined in a wide statistical environment. The statistical models assumed are discussed with respect to practical applications. Particular attention is devoted to a formal description of the influence of the packet voice receiver on the system behavior in terms of the delay pdf. The optimization of the system performance, in order to obtain the best voice quality, is stated as an optimal control problem, and the analysis results play a central role in the construction of the objective functions. The problem is solved in a particular analytical environment. The outlined analytical results are supported by critical comments on their comparison with practical implementations, allowing the designer a better capability in handling any problems.
Heparin-induced osteopenia in pregnancy. (1980)

Multiple vertebral compression fractures occurred in a pregnant woman receiving heparin over nine months. This phenomenon may be more common than is clinically recognised and warrants careful re-examination of the indications and method of administration of anti-coagulants during pregnancy.
MPTP delta, a putative murine homolog of HPTP delta, is expressed in specialized regions of the brain and in the B-cell lineage. (1993)

Protein tyrosine phosphatases (PTPs), together with protein tyrosine kinases (PTKs), are involved in the regulation of cell activation, growth, and differentiation. To further elucidate the fine tuning of cell growth and differentiation through tyrosine phosphorylation, we tried to isolate mouse receptor-type PTP (RPTP) cDNA clones by screening mouse brain cDNA libraries with mouse CD45 PTP domain probes under reduced-stringency conditions. Characterization of isolated cDNA clones for RPTP showed that the cytoplasmic region contains two tandem repeats of PTP domain of about 230 amino acids with intrinsic phosphatase activity. The extracellular region was composed of immunoglobulin (Ig)-like domains and fibronectin type III (FN-III)-like domains. The gene was highly homologous to human PTP delta (HPTP delta) and thus was named MPTP delta (murine counterpart of HPTP delta). The MPTP delta gene appeared to generate at least three species of mRNA, which differ in the composition of the extracellular domain: type A, one Ig-like and four FN-III-like domains; type B, one Ig-like and eight FN-III-like domains; and type C, three Ig-like and eight FN-III-like domains. Interestingly, the 5' untranslated region and the leader peptide of types A and B were completely different from those of type C. Northern (RNA) blot analysis demonstrated that brain, kidney, and heart cells express three mRNA species of about 7 kb. Antibody directed against part of the extracellular domain of type A MPTP delta recognized a 210-kDa protein in brain and kidney lysates. In situ hybridization of brain samples revealed that MPTP delta mRNA is present in the hippocampus, thalamic reticular nucleus, and piriform cortex, where some Src family PTKs have been also demonstrated to exist. Although MPTP delta mRNA was not detected in lymphoid tissues, all of the pre-B-cell lines tested and one of three B-cell lines tested expressed MPTP delta mRNA, whereas antibody-producing B-cell hybridomas and T-cell and macrophage lines did not. Finally, the MPTP delta locus was tightly linked to the brown (b) locus on mouse chromosome 4.
Inflammation in Acute Kidney Injury (2008)

Ischemia-reperfusion injury (IRI) is one of the major causes of acute kidney injury (AKI) and evidence supporting the involvement of both innate and adaptive immunity in renal IRI has accumulated in recent years. In addition to leukocytes, kidney endothelial cells promote inflammation after IRI by increasing adhesion molecule expression and vascular permeability. Kidney tubular epithelial cells increase complement binding and upregulate toll-like receptors, both of which lead to cytokine/chemokine production in IRI. Activation of kidney resident dendritic cells, interferon-gamma-producing neutrophils, infiltrating macrophages, CD4+ T cells, B cells and invariant natural killer T cells are all implicated in the pathogenesis of AKI. The complex interplay between innate and adaptive immunity in renal IRI is still not completely understood, but major advances have been made. This review summarizes these recent advances to further our understanding of the immune mechanisms of acute kidney injury.
Consequences of DNA-Dependent Protein Kinase Catalytic Subunit Deficiency on Recombinant Adeno-Associated Virus Genome Circularization and Heterodimerization in Muscle Tissue (2003)

Circular concatemerization of the recombinant adeno-associated virus (rAAV) genome has been suggested as the predominant process facilitating long-term rAAV transduction in muscle. A recent study (S. Song, P. J. Laipis, K. I. Berns, and T. R. Flotte, Proc. Natl. Acad. Sci. USA 98:4084-4088, 2001) with SCID mice, which are defective in the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), has suggested that DNA-PKcs regulates the removal of free rAAV vector ends in muscle tissue. In the present study, we have sought to evaluate whether a lack of DNA-PKcs activity reduces circularization of rAAV genomes in SCID muscle and whether such a reduction alters the directivity of heterodimerization. Consistent with the previous report, linear rAAV genomes and free vector ends were detected only in DNA-PKcs-deficient muscle by Southern blotting. Appreciable amounts of circular rAAV genomes were detected in both DNA-PKcs-deficient and wild-type muscle samples by Southern blotting and bacterial trapping experiments. The existence of double-D inverted terminal repeat circular intermediates in SCID and wild-type muscles was also supported by their sensitivity to T7 endonuclease I digestion. However, DNA-PKcs-deficient muscle did demonstrate a approximately 50% reduction in the abundance of rescued circular genomes, despite equivalent levels of single rAAV transduction seen in wild-type animals. Dual trans-splicing lacZ vectors were used to functionally evaluate directional head-to-tail intermolecular viral genome concatamerization in vivo. Although AAV genomes are processed differently in SCID and wild-type muscles, a comparable level of trans-splicing-mediated beta-galactosidase expression was observed in both strains, suggesting that both circular and linear AAV concatemers may have contributed to the trans-splicing-mediated transgene expression. In summary, we have shown that SCID skeletal muscle retains a fairly high capacity to form circular genomes, despite a significant increase in linear vector genomes. Furthermore, the alteration in equilibrium between circular and linear concatemer genomes caused by the lack of DNA-PKcs activity does not appear to significantly affect the efficiency of dual-vector gene expression from head-to-tail linear and/or circular heterodimers.
[Cardiac manifestations of Lyme disease. Apropos of a case]. (1989)

A new case of heart involvement in Lyme's disease is reported. Its originality lies in its strictly isolated nature, therefore revealing the disease; in its typical picture of myocardopericarditis combining, in various stages, infra-hissian conduction disorders, bouts of left ventricular insufficiency, pseudoischemic repolarisation disorders and finally a moderate pericardial shift; in the demonstration, during two successive heart explorations by NMR (Nuclear Magnetic Resonance), of a diffuse myocardial hypertrophy, subsiding in time, as the other symptoms of this patient.
Metastasis of Neuroendocrine Tumors Are Characterized by Increased Cell Proliferation and Reduced Expression of the ATM Gene (2012)

ATM down-regulation was strongly associated with metastatic NETs when compared with non-metastatic NETs and ATM may be a potential predictive marker for metastasis as well as a novel target in metastatic GEP-NETs.
Erythropoietin Increases Glutathione Peroxidase Enzyme Activity and Decreases Lipid Peroxidation Levels in Hypoxic-Ischemic Brain Injury in Neonatal Rats (2004)

These results suggest that Epo exerts neuroprotective effects against hypoxic-ischemic brain injury at least partially via the modulation of antioxidant enzyme activity.
Static and Dynamic Stereochemistry of Chiral Ln DOTA Analogues (2011)

Ln DOTA derivatives (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) are known to undergo relevant stereoisomeric equilibria in solution, which greatly modulate their chemical as well as their magnetic and optical properties. The subject is reviewed in terms of classical stereochemical description, with reference to conformational enthalpies. Yb is taken as the reference element because of its unique spectroscopic properties, namely, a small contact contribution to the paramagnetic shift and an intense near-infrared electronic circular dichroism, endowed with an easily recognizable fine structure.
Incidence of campylobacteriosis among patients with AIDS in Los Angeles County. (1991)

The incidence and characteristics of campylobacteriosis among patients with acquired immune deficiency syndrome (AIDS) in Los Angeles County were assessed by matching the Campylobacter and AIDS surveillance reporting registries for the years 1983-1987. Campylobacter infection was reported in 29 (0.7%) of 4,433 AIDS cases. The average annual incidence of Campylobacter among AIDS cases (519/100,000) exceeded the crude population rate by 39-fold and exceeded the rate among males aged 15-55 years by 35-fold. Campylobacter infection was more common in female AIDS patients than male patients (p = 0.065). A distinct seasonal variation was noted with peaks occurring in July and November. The median survival time for AIDS patients with Campylobacter (14 months) was lower than that for AIDS patients without Campylobacter (21 months); however, we were not able to assess potential confounders such as subsequent opportunistic infections or antiviral therapy and prophylactic regiment to validate this finding. Campylobacter cases with AIDS had higher rates of bacteremia and hospitalization than Campylobacter cases without AIDS. Attempts should be made to elucidate the sources of Campylobacter and other enteric infections among AIDS patients.
Stereoselectivity of Methyl Aryldiazoacetate Cyclopropanations of 1,1-Diarylethylene. Asymmetric Synthesis of a Cyclopropyl Analogue of Tamoxifen (2000)

[formula: see text] Dirhodium tetrakis(S-(N-dodecylbenzenesulfonyl)prolinate) (Rh2(S-DOSP)4)-catalyzed decomposition of methyl phenyldiazoacetate in the presence of 1,1-diarylethylenes results in intermolecular cyclopropanation with high enantioselectivity (up to 99% ee) and moderate diastereoselectivity (up to 80% de). The reaction was applied to the asymmetric synthesis of a cyclopropyl analogue of tamoxifen.
Identification of a Mouse Homologue of the Saccharomyces cerevisiae Recombination and Repair Gene, RAD52 (1994)

The product of the Saccharomyces cerevisiae RAD52 gene is implicated in DNA double-strand-break recombinational repair. Yeast strains lacking a functional RAD52 gene are extremely X-ray sensitive and deficient in mitotic and meiotic recombination. To identify RAD52 homologues exprsesed in higher eukaryotes, we have designed two degenerate polymerase chain reaction (PCR) primers corresponding to highly conserved sequences. The gene is evolutionarily conserved and comparative structure-function relationships may shed some light on the biology of this central recombinational protein. 13 refs., 3 figs.
Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins. (1992)

An interesting property of the Escherichia coli DNA polymerase II is the stimulation in DNA synthesis mediated by the DNA polymerase III accessory proteins beta,gamma complex. In this paper we have studied the basis for the stimulation in pol II activity and have concluded that these accessory proteins stimulate pol II activity by increasing the processivity of the enzyme between 150- and 600-fold. As is the case with pol III, processive synthesis by pol II requires both beta,gamma complex and SSB protein. Whereas the intrinsic velocity of synthesis by pol II is 20-30 nucleotides per s with or without the accessory proteins, the processivity of pol II is increased from approximately five nucleotides to greater than 1600 nucleotides incorporated per template binding event. The effect of the accessory proteins on the rate of replication is far greater on pol III than on pol II; pol III holoenzyme is able to complete replication of circular single-stranded M13 DNA in less than 20 s, whereas pol II in the presence of the gamma complex and beta requires approximately 5 min. We have investigated the effect of beta,gamma complex proteins on bypass of a site-specific abasic lesion by E. coli DNA polymerases I, II, and III. All three polymerases are extremely inefficient at bypass of the abasic lesion. We find limited bypass by pol I with no change upon addition of accessory proteins. pol II also shows limited bypass of the abasic site, dependent on the presence of beta,gamma complex and SSB. pol III shows no significant bypass of the abasic site with or without beta,gamma complex.
MPEG-2 video decoding on the TMS320C6X DSP architecture (2002)

This paper explores implementation of MPEG-2 decoding functions (bitstream parsing, IDCT: variable length decoding, motion compensation, dequantization) in software on the TI TMS320C6X architecture. We discuss cycle count estimates for these functions; our estimates are based on optimized, functionally accurate implementations in some cases, and on analysis of C implementations of the function in other cases. We describe how we arrive at these estimates in detail, and discuss how we were able to use automatic compilation effectively for certain functions. We also compare the C6x implementation to other MPEG-2 implementations that have been reported for general purpose CPUs that support a multimedia enhanced instruction set, such as Intel Pentium (MMX), SUN UltraSPARC (VIS), and HP PA (MAX).
Photonic Crystal Glucose-Sensing Material for Noninvasive Monitoring of Glucose in Tear Fluid (2004)

Abstract Background: We recently developed a photonic crystal glucose-sensing material (Alexeev et al., Anal Chem 2003;75:2316–23), which consists of a crystalline colloidal array embedded within a polymer network of a polyacrylamide-poly(ethylene glycol) hydrogel with pendent phenylboronic acid groups. The aim of the present work was to improve this approach for application to noninvasive or minimally invasive monitoring of glucose. Methods: We used new boronic acid derivatives such as 4-amino-3-fluorophenylboronic acid and 4-carboxy-3-fluorophenylboronic acid as the molecular recognition elements to achieve sensing at physiologic pH values. Results: The improved photonic glucose-sensing material sensed glucose in the range of the 100 μmol/L concentrations found in tear fluid. The detection limits were ∼1 μmol/L in synthetic tear fluid. The visually evident diffraction color shifted across the entire visible spectral region from red to blue over the physiologically relevant tear-fluid glucose concentrations. This sensing material is selective for glucose over galactose, mannose, and fructose. Conclusions: These new glucose sensors have properties appropriate for use in such glucose-sensing applications as ocular inserts or diagnostic contact lenses for patients with diabetes mellitus.
mixup: Beyond Empirical Risk Minimization (2017)

Large deep neural networks are powerful, but exhibit undesirable behaviors such as memorization and sensitivity to adversarial examples. In this work, we propose mixup, a simple learning principle to alleviate these issues. In essence, mixup trains a neural network on convex combinations of pairs of examples and their labels. By doing so, mixup regularizes the neural network to favor simple linear behavior in-between training examples. Our experiments on the ImageNet-2012, CIFAR-10, CIFAR-100, Google commands and UCI datasets show that mixup improves the generalization of state-of-the-art neural network architectures. We also find that mixup reduces the memorization of corrupt labels, increases the robustness to adversarial examples, and stabilizes the training of generative adversarial networks.
Mast Cell 5-Lipoxygenase Activity Promotes Intestinal Polyposis in APCΔ468 Mice (2011)

Arachidonic acid metabolism has been implicated in colon carcinogenesis, but the role of hematopoietic 5-lipoxygenase (5LO) that may impact tumor immunity in development of colon cancer has not been explored. Here we show that tissue-specific deletion of the 5LO gene in hematopoietic cells profoundly attenuates polyp development in the APC(Δ468) murine model of colon polyposis. In vitro analyses indicated that mast cells in particular utilized 5LO to limit proliferation of intestinal epithelial cells and to mobilize myeloid-derived suppressor cells (MDSCs). Mice lacking hemapoietic expression of 5LO exhibited reduced recruitment of MDSCs to the spleen, mesenteric lymph nodes, and primary tumor site. 5LO deficiency also reduced the activity in MDSCs of arginase-1, which is thought to be critical for MDSC function. Together, our results establish a pro-tumorigenic role of hematopoietic 5LO in the immune microenvironment and suggest 5LO inhibition as an avenue for future investigation in treatment of colorectal polyposis and cancer.
Evaluation of 13 short tandem repeat loci for use in personal identification applications. (1994)

Personal identification by using DNA typing methodologies has been an issue in the popular and scientific press for several years. We present a PCR-based DNA-typing method using 13 unlinked short tandem repeat (STR) loci. Validation of the loci and methodology has been performed to meet standards set by the forensic community and the accrediting organization for parentage testing. Extensive statistical analysis has addressed the issues surrounding the presentation of "match" statistics. We have found STR loci to provide a rapid, sensitive, and reliable method of DNA typing for parentage testing, forensic identification, and medical diagnostics. Valid statistical analysis is generally simpler than similar analysis of RFLP-VNTR results and provides powerful statistical evidence of the low frequency of random multilocus genotype matching.
Epigenetic alteration of SOCS family members is a possible pathogenetic mechanism in JAK2 wild type myeloproliferative diseases (2008)

In polycythemia vera (PV) and essential thrombocythemia (ET) specific JAK2 mutations constitutively activate the JAK-STAT pathway, explaining biologic findings such as endogenous erythroid colony (EECs) growth or PRV-1 RNA overexpression. Since these markers are detected also in JAK2 wild type patients, we hypothesized that, in these cases, the activation of the JAK-STAT pathway could be produced by a deregulation of the suppressor of cytokine signaling (SOCS) protein system. Eighty-one patients with PV and ET (53 adults and 28 children) were investigated for the methylation status of the SOCS-1, SOCS-2 and SOCS-3 CpG islands and for several myeloproliferative markers (including JAK2 and MPL mutations and clonality of hematopoiesis). SOCS-1 or SOCS-3 hypermethylation was identified in 23 patients and was associated with a significant decrease of SOCS-1 or SOCS-3 RNA and protein levels. The gene expression was restored by exposing cells to the demethylating agent 2-deoxyazacytidin. Interestingly, SOCS-1 or SOCS-3 hypermethylation was detected in 6 female patients, proved negative for JAK2 or MPL mutations and exhibiting monoclonal hematopoiesis. In conclusion, SOCS-1 or SOCS-3 hypermethylation can activate the JAK-STAT signaling pathway in alternative or together with JAK2 mutations. These alterations might represent a potential therapeutic target.
Luminescence Digital Imaging Microscopy (1989)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More