gebhart/patrepeval huggingface dataset:
Evidence for a Shift from a Type I Lymphocyte Pattern with HIV Disease Progression (1995)

Whether a shift from a type I (cell mediated) immune profile occurs with progressive HIV-related immune dysfunction is a matter of heated debate. We analyzed data for 333 HIV antibody-positive (HIV+) and -negative (HIV-) hemophilic children/adolescents, to examine whether the relationships among immunologic parameters and vaccine-related serology supported a shift with advancing HIV infection. In stepwise logistic regression analysis of HIV+ children's data, anergy to a panel of delayed hypersensitivity skin test antigens was positively associated with serum immunoglobulin A (IgA) levels (p = 0.012) and CD8+ cell counts (p = 0.021) and negatively associated with CD4+ cell counts (p = 0.002). Modeling supported anergy as a positive correlate of log IgA level (p = 0.046) and CD4+ lymphocyte count as a negative correlate, for HIV+ participants only (p < 0.0001). For mumps, the proportion of vaccinated HIV+ participants with protective IgG antibody titers was higher among those with CD4+ lymphocyte counts < 200 cells/mm3 (p = 0.058). For HIV+ participants < 14 years of age, this same trend was seen for measles and rubella, but was not seen in any age group for bacterial vaccine antigens. The intercorrelations among skin test anergy, CD4+ lymphocyte counts, serum IgA levels, and viral vaccine antigen-related serologic titers for HIV+ participants are consistent with an association between progressive HIV-related immune dysfunction and a predominance of type II (humoral immunity) or Type 0 (mixed immunity), relative to type I, lymphocyte profiles.
Contact dermatitis caused by ECG electrode jelly (1977)

A 4-year-old boy was seen because of contact dermatitis that resulted from the use of an ECG electrode jelly (Cambridge). Patch tests proved that gum tragacanth in the jelly was responsible for the eruption. This agent is found in many different products, including foods, troches, cosmetics, toothpastes, and textile sizings. <h3>Report of Case</h3> A 4-year-old boy was seen on March 23, 1976 because of persistent dermatitis on his chest and extremities. He had developed the eruption two months previously, shortly after an ECG had been taken. The eruption was confined to the areas where the electrode jelly had been used for contact between the skin and the electrodes. A diagnosis of contact dermatitis was made. The eruption resolved after topical treatment with steroids. Patch tests were performed, and the patient was found to be allergic to the electrode jelly and one of its constituents, gum tragacanth (Table). The commercially prepared
In Vitro Characterization of the Interaction between HIV-1 Gag and Human Lysyl-tRNA Synthetase (2006)

Human immunodeficiency virus type 1 (HIV-1) viral assembly is mediated by multiple protein-protein and protein-nucleic acid interactions. Human tRNA(Lys3) is used as the primer for HIV reverse transcription, and HIV Gag and GagPol are required for packaging of the tRNA into virions. Human lysyl-tRNA synthetase (LysRS) is also specifically packaged into HIV, suggesting a role for LysRS in tRNA packaging. Gag alone is sufficient for packaging of LysRS, and these two proteins have been shown to interact in vitro using glutathione S-transferase pull-down assays. In vitro pull-down assays using truncated constructs have also revealed that residues important for homodimerization of Gag and LysRS are critical for the Gag/LysRS interaction. In this work, we report further in vitro characterization of the interaction between HIV Gag and human LysRS using affinity pull-down assays, fluorescence anisotropy measurements and gel chromatography. An equilibrium binding constant of 310 +/- 80 nM was measured for the Gag/LysRS interaction. We also show that capsid alone binds to LysRS with a similar affinity as full-length Gag. Point mutations that disrupt the homodimerization of LysRS and Gag in vitro do not affect their interaction. These results suggest that dimerization of each protein per se is not required for the interaction but that residues involved in forming the homodimer interfaces contribute to heterodimer formation. Gel chromatography studies further support the formation of a Gag/LysRS heterodimer.
Future caries susceptibility in children with early childhood caries following treatment under general anesthesia. (2000)

Despite increased preventive measures implemented for children who experienced ECC, this study concluded that this group of children is still highly predisposed to greater caries incidence in later years. These findings strongly suggest that more aggressive preventive therapies may be required to prevent the future development of carious lesions in children who experienced ECC.
Characterization of a Covalent Monoadduct of Neocarzinostatin Chromophore at a DNA Bulge (1997)

Neocarzinostatin chromophore (NCS-Chrom) induces highly efficient site-specific strand cleavage at the bulge of a folded single-stranded 31-mer DNA in the presence of oxygen [Kappen, L. S., and Goldberg, I. H. (1993) Science 261, 1319-1321]. Under anaerobic conditions, the major product is a material having gel mobility slower than that of the parent 31-mer. In order to characterize this product, it was stabilized by reduction with borane/pyridine, labeled with 32P at its 5' or 3' end, and subjected to chemical cleavage dependent on base elimination or modification, and the cleavage products were analyzed on a sequencing gel. A cleavage pattern comparable to that of the 31-mer was obtained until the bases on either side of T22 at the bulge. Cleaved fragments inclusive of T22 from the 5' or the 3' end had retarded and anomalous mobilities and appeared as a smear of bands closer to the starting material, presumably due to the presence of the covalently bound drug. Pyrimidine-specific agents such as hydrazine and potassium permanganate, but not the DNA sugar-specific probe thiol-activated NCS-Chrom, induced strand cleavage at T22. Mass spectral analysis of the presumed adduct isolated from anaerobic reactions containing NCS-Chrom and a bulge duplex substrate made up of a 10-mer and an 8-mer showed that the adduct contains one molecule of the drug and one molecule of the 10-mer. Taken together, the results show that (i) drug adduction is at T22 on the full-length substrate; (ii) the pyrimidine ring is accessible to base-specific chemical modifications, hence, presumably free of the drug; (iii) it is most likely that drug adduction is via its C6 position to the 5' carbon of T22, based on the current results and the known chemistry of the hydrogen abstraction by the drug in the presence or absence of oxygen; (iv) there is no involvement of the neighboring bases by way of inter- or intrastrand cross-linking; and (v) the product is a monoadduct.
Regeneration of peripheral nervous system axons (1995)

Abstract This chapter focuses on regeneration in mammals. It begins with an overview of regeneration. It then discusses axon sprouting, axonal elongation, cell body reaction and regeneration, environment of the regenerating peripheral axon, and restoration of function.
Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers (2014)

Exosomes are tiny vesicles (30-150 nm) constantly secreted by all healthy and abnormal cells, and found in abundance in all body fluids. These vesicles, loaded with unique RNA and protein cargo, have a wide range of biological functions, including cell-to-cell communication and signalling. As such, exosomes hold tremendous potential as biomarkers and could lead to the development of minimally invasive diagnostics and next generation therapies within the next few years. Here, we describe the strategies for isolation of exosomes from human blood serum and urine, characterization of their RNA cargo by sequencing, and present the initial data on exosome labelling and uptake tracing in a cell culture model. The value of exosomes for clinical applications is discussed with an emphasis on their potential for diagnosing and treating neurodegenerative diseases and brain cancer.
Oscillation of Cyclic Adenosine Monophosphate Concentration during the Myocardial Contraction Cycle (1973)

The concentration of adenosine 3',5'-monophosphate (cyclic AMP) rises and falls during each myocardial contraction cycle. Peak concentrations of cyclic AMP precede peak development of systolic tension. Epinephrine alters the normal oscillation in myocardial cyclic AMP and increases both diastolic and systolic concentrations of the cyclic nucleotide. These transient changes in myocardial cyclic AMP indicate a potential role for cyclic AMP as a beat-to-beat regulator of myocardial contractility.
Receptor-recognized α2-macroglobulin-methylamine elevates intracellular calcium, inositol phosphates and cyclic AMP in murine peritoneal macrophages (1993)

Human plasma alpha 2-macroglobulin (alpha 2M) is a tetrameric proteinase inhibitor, which undergoes a conformational change upon reaction with either a proteinase or methylamine. As a result, a receptor recognition site is exposed on each subunit of the molecule enabling it to bind to its receptors on macrophages. We have used Fura-2-loaded murine peritoneal macrophages and digital video fluorescence microscopy to examine the effects of receptor binding on second messenger levels. alpha 2M-methylamine caused a rapid 2-4-fold increase in intracellular Ca2+ concentration ([Ca2+]i) within 5 s of binding to receptors. The agonists induced a focal increase in [Ca2+]i that spread out to other areas of the cell. The increase in [Ca2+]i was dependent on the alpha 2M-methylamine concentration and on the extracellular [Ca2+]. Both sinusoidal and transitory oscillations were observed, which varied from cell to cell. Neither alpha 2M nor boiled alpha 2M-methylamine, forms that are not recognized by the receptor, affected [Ca2+]i in peritoneal macrophages under identical conditions of incubation. The alpha 2M-methylamine-induced rise in [Ca2+]i was accompanied by a rapid and transient increase in macrophage inositol phosphates, including inositol tris- and tetrakis-phosphates. Native alpha 2M did not stimulate a rise in inositol phosphates. Finally, binding of alpha 2M-methylamine to macrophages increased cyclic AMP transiently. Thus receptor-recognized alpha-macroglobulins behave as agonists whose receptor binding causes stimulation of signal transduction pathways.
Solution Structure of the Immunodominant Domain of Protective Antigen GNA1870 of Neisseria meningitidis (2006)

GNA1870, a 28-kDa surface-exposed lipoprotein of Neisseria meningitidis recently discovered by reverse vaccinology, is one of the most potent antigens of Meningococcus and a promising candidate for a universal vaccine against a devastating disease. Previous studies of epitope mapping and genetic characterization identified residues critical for bactericidal response within the C-terminal domain of the molecule. To elucidate the conformation of protective epitopes, we used NMR spectroscopy to obtain the solution structure of the immunodominant 18-kDa C-terminal portion of GNA1870. The structure consists of an eight-stranded antiparallel beta-barrel overlaid by a short alpha-helix with an unstructured N-terminal end. Residues previously shown to be important for antibody recognition were mapped on loops facing the same ridge of the molecule. The sequence similarity of GNA1870 with members of the bacterial transferrin receptor family allows one to predict the folding of this class of well known bacterial antigens, providing the basis for the rational engineering of high affinity B cell epitopes.
Drug Target Discovery by Gene Expression Analysis Cell Cycle Genes (2001)

Gene expression microarrays and gene expression databases provide new opportunities for the discovery of drug targets and for determination of a drug's mode of action. We review gene expression analysis methods and describe studies that have identified cell cycle genes using differential expression analysis and co-expression analysis. We present an example of the identification of previously-unrecognized human cell cycle genes, CDCA1 through CDCA8, that are co-expressed with known cell cycle genes including CDC2, CDC7, CDC23, cyclin, MCAK, mki67a, topoisomerase II, and others.
Antimicrobial and antioxidant properties of some commercial essential oils (1998)

The essential oil composition of Cananga odorata, Boswellia thurifera, Cymbopogon citratus, Marjorana hortensis, Ocimum basilicum, Rosmarinus officinalis, Cinnamomum zeylanicum and Citrus limon was analysed by GC and GC–MS, and their antimicrobial and antioxidant activity tested. Twenty-five different genera of bacteria and one fungal species were used in this study as test organisms. These included animal and plant pathogens, food poisoning and spoilage bacteria and the spoilage fungus Aspergillus niger. The volatile oils exhibited considerable inhibitory effect against all the tested organisms. The oils also demonstrated antioxidant capacities, comparable with α-tocopherol and butylated hydroxytoluene (BHT). The method adopted in this study was the modified thiobarbituric acid reactive species (TBARS) assay. The antioxidant activity was carried out under different conditions by using egg yolk and rat liver in the absence and presence of the radical inducer 2,2′-azobis (2-amidinopropane) dihydrochloride (ABAP). © 1998 John Wiley & Sons, Ltd.
Flying Stiction, Lubricant Pick-Up and Carbon-Overcoat Wear of Magnetic Heads (1999)

Flying stiction, a high static friction force resulting from a magnetic head seeking/flying over a disk surface, has posed a new challenge in magnetic-disk tribology for low flying heights (˜30 nm or less), as demanded by high recording densities. Two types of magnetic heads were used in this study. A more than 10-fold increase in flying stiction force was observed for the carbon coated heads after a 24 hours of seeking/flying over the disk surface. Using Time of Flight Secondary Ion Mass Spectroscopy and a scanning micro-ellipsometer, we found that the lubricant pickup during seeking/flying operation was responsible for the observed 10-fold increase of the flying stiction force. A nearly exponential dependence of flying stiction force on lubricant amount picked up on the air bearing surface (ABS) of the magnetic heads was found. For 24 hours of seeking/flying time, the lubricant accumulated on the ABS surfaces can be up to 1.5 nm, comparable to the lubricant thickness on the disk surfaces. The lubricant amount was found quite uniformly distributed over the ABS surface of the head. Wear on the carbon overcoat of the magnetic heads was also measured, and was equivalent to approximately 1 nm carbon loss for a 24-hour seeking/flying period. The wear rate of the carbon overcoat was very fast for short periods of seeking time (˜2 hours) and slowed down to near-zero as lubricant built up on the ABS surface, indicating that the lubricant on the head protected carbon wear. The wear of carbon overcoat strongly suggests that intermittent physical contacts between the disk surface and head ABS occurred during seeking/flying operations.
Resveratrol and Its Glycon Piceid Are Stable Polyphenols (2006)

Plant extracts containing phytopolyphenols, including resveratrol, are extensively used as nutraceutical supplements. Recent reports allege their lack of stability at ambient conditions. We have studied the stability of resveratrol and its glycon piceid in a mixture with a whole grape extract for 2 years (long-term stability) under Good Manufacturing Practice pharmaceutical protocols (at 60% humidity and 25 degrees C). The neat compounds were followed for 4 years under conditions of "accelerated stability," at 75% humidity and 40 degrees C, all in the presence of ambient air. Chromatographic analysis did not detect any instability, thus disproving the claims to the opposite. No storage precautions are necessary for these nutritional supplements.
Comparison of Success of Antibiotic Therapy During Lactation and Results of Antimicrobial Susceptibility Tests for Bovine Mastitis (1997)

Antimicrobial susceptibility testing was conducted on a variety of mastitis pathogens. The infected quarters were subsequently treated during lactation with a commercially available product containing penicillin and novobiocin that was designed for lactating cows. Cows were treated as per the recommendations of the product manufacturer, and cures were determined by the absence of bacteria in both sets of duplicate quarter milk samples that were collected at 28 d posttreatment. Comparisons were made between the susceptibility of the bacteria and the therapeutic success or failure. All isolates tested were considered to be susceptible to the penicillin and novobiocin combination. Bacteriologic cure rates for newly acquired Staphylococcus aureus intramammary infection (IMI) (< 2 wk in duration) at 28 d posttreatment were 70%. Cure rates for chronic Staph. aureus IMI (> 4 wk duration) were much lower (35%), reaffirming previous reports of the intractable nature of chronic Staph. aureus IMI. Cure rates for subclinical IMI caused by other organisms were 90% for Streptococcus agalactiae, 91% for Streptococcus uberis, 90% for Streptococcus dysgalactiae, 77% for other Streptococcus spp., and 71% for Staphylococcus spp. other than Staph. aureus. In vitro testing was considered to be a predictor of therapy outcome for IMI caused by Staphylococcus spp., newly acquired Staph. aureus, Strep. uberis, Strep. dysgalactiae, and Strep. agalactiae, but was not considered to be a useful predictor of efficacy for chronic IMI caused by Staph. aureus.
Determination of muscimol and ibotenic acid in mushrooms of Amanitaceae by capillary electrophoresis (2014)

In this study, the CZE method for rapid quantitative and qualitative determination of ibotenic acid and muscimol in Amanita mushrooms naturally grown in Poland was developed. The investigations included the species of A. muscaria, A. pantherina, and A. citrina, collected in southern region of Poland. The studied hallucinogenic compounds were effectively extracted with a mixture of methanol and 1 mM sodium phosphate buffer at pH 3 (1:1 v/v) using ultrasound-assisted procedure. The obtained extracts were separated and determined by CZE utilizing a 25 mM sodium phosphate running buffer adjusted to pH 3 with 5% content of acetonitrile v/v. The calibration curves for both analytes were linear in the range of 2.5-7000 μg/mL. The intraday and interday variations of quantitative data were 1.0 and 2.5% RSD, respectively. The recovery values of analyzed compounds were over 87%. The identities of ibotenic acid and muscimol were confirmed by UV spectra, migration time, and measurements after addition of external standard.
Bacteria-associated hemophagocytic syndrome (1984)

Histiocytic medullary reticulosis (HMR) was originally defined as a neoplastic disorder. Some cases reported as HMR have been characterized by a systemic proliferation of mature histiocytes showing hemophagocytosis, bone marrow necrosis, pancytopenia, hepatitis, and coagulopathy. Clinically, these patients have fever and constitutional symptoms and often have hepatosplenomegaly and lymphadenopathy. Although there is a high mortality rate, this process appears to be reactive and has been associated with active viral infection. Similar cases have been briefly described that were associated with other agents or disease processes, but concomitant viral infections were not excluded. Three characteristic examples of this hemophagocytic syndrome that were associated with bacterial sepsis are described. Active infection by those viruses that have previously been associated with the syndrome was excluded. It appears that the hemophagocytic syndrome may be associated with various types of active disseminated infections.
Biomimetic, synthetic HDL nanostructures for lymphoma (2013)

New therapies that challenge existing paradigms are needed for the treatment of cancer. We report a nanoparticle-enabled therapeutic approach to B-cell lymphoma using synthetic high density lipoprotein nanoparticles (HDL-NPs). HDL-NPs are synthesized using a gold nanoparticle template to control conjugate size and ensure a spherical shape. Like natural HDLs, biomimetic HDL-NPs target scavenger receptor type B-1, a high-affinity HDL receptor expressed by lymphoma cells. Functionally, compared with natural HDL, the gold NP template enables differential manipulation of cellular cholesterol flux in lymphoma cells, promoting cellular cholesterol efflux and limiting cholesterol delivery. This combination of scavenger receptor type B-1 binding and relative cholesterol starvation selectively induces apoptosis. HDL-NP treatment of mice bearing B-cell lymphoma xenografts selectively inhibits B-cell lymphoma growth. As such, HDL-NPs are biofunctional therapeutic agents, whose mechanism of action is enabled by the presence of a synthetic nanotemplate. HDL-NPs are active in B-cell lymphomas and potentially, other malignancies or diseases of pathologic cholesterol accumulation.
Cell Wall Attachment of a Widely Distributed Peptidoglycan Binding Domain Is Hindered by Cell Wall Constituents (2003)

The C-terminal region (cA) of the major autolysin AcmA of Lactococcus lactis contains three highly similar repeated regions of 45 amino acid residues (LysM domains), which are separated by nonhomologous sequences. The cA domain could be deleted without destroying the cell wall-hydrolyzing activity of the enzyme in vitro. This AcmA derivative was capable neither of binding to lactococcal cells nor of lysing these cells while separation of the producer cells was incomplete. The cA domain and a chimeric protein consisting of cA fused to the C terminus of MSA2, a malaria parasite surface antigen, bound to lactococcal cells specifically via cA. The fusion protein also bound to many other Gram-positive bacteria. By chemical treatment of purified cell walls of L. lactis and Bacillus subtilis, peptidoglycan was identified as the cell wall component interacting with cA. Immunofluorescence studies showed that binding is on specific locations on the surface of L. lactis, Enterococcus faecalis, Streptococcus thermophilus, B. subtilis, Lactobacillus sake, and Lactobacillus casei cells. Based on these studies, we propose that LysM-type repeats bind to peptidoglycan and that binding is hindered by other cell wall constituents, resulting in localized binding of AcmA. Lipoteichoic acid is a candidate hindering component. For L. lactis SK110, it is shown that lipoteichoic acids are not uniformly distributed over the cell surface and are mainly present at sites where no MSA2cA binding is observed.
An Integrated Genetic and Cytogenetic Map of the Cucumber Genome (2009)

The Cucurbitaceae includes important crops such as cucumber, melon, watermelon, squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular linkage maps. We report herein the development of highly polymorphic simple sequence repeat (SSR) markers originated from whole genome shotgun sequencing and the subsequent construction of a high-density genetic linkage map. This map includes 995 SSRs in seven linkage groups which spans in total 573 cM, and defines approximately 680 recombination breakpoints with an average of 0.58 cM between two markers. These linkage groups were then assigned to seven corresponding chromosomes using fluorescent in situ hybridization (FISH). FISH assays also revealed a chromosomal inversion between Cucumis subspecies [C. sativus var. sativus L. and var. hardwickii (R.) Alef], which resulted in marker clustering on the genetic map. A quarter of the mapped markers showed relatively high polymorphism levels among 11 inbred lines of cucumber. Among the 995 markers, 49%, 26% and 22% were conserved in melon, watermelon and pumpkin, respectively. This map will facilitate whole genome sequencing, positional cloning, and molecular breeding in cucumber, and enable the integration of knowledge of gene and trait in cucurbits.