gebhart/patrepeval huggingface dataset:
Detection of Lawsonia intracellularis in diagnostic specimens by one-step PCR (2000)

Lawsonia intracellularis is not culturable with a standard bacteriologic culture. One step PCR assay as a clinical diagnostic method was developed for the rapid detection of porcine proliferative enteritis (PPE) caused by L. intracellularis. Primers were designed based on the p78 DNA clone of L. intracellularis. The one step PCR resulted in the formation of a specific 210-bp DNA product derived from L. intracellularis. The nonspecific amplification product was not detected with swine genomic DNA or other bacterial strains causing similar symptoms to L. intracellularis infection. The one step PCR was as sensitive as 100 pg of L. intracellularis genomic DNA. We applied this method to field specimens diagnosed as PPE by macroscopic observation. Of 17 mucosal scraping specimens, 16 (94%) were identified as positive to PPE and 15 (88%) of 17 feces specimens. These results suggest that the one step PCR can be used as a rapid diagnostic method for L. intracellularis infection.
Organización y características sociodemográficas de las unidades domésticas de producción campesina. (2000)

La organización de las Unidades Domésticas de Producción Campesina (UDPC) responde a diversos procesos históricos y sociales, donde las necesidades de producción y reproducción social de los campesinos se enfrentan con un medio que es transformado por la expansión del capital; en este sentido, la UDPC debe ser contemplada como un concepto dinámico que se transforma en el tiempo y en el espacio. Además, en la UDPC se trata de utilizar de la manera más adecuada el insumo fuerza de trabajo familiar, por lo que todos sus miembros encuentran una función útil, ya sea bajo el esquema de producción o de reproducción dentro de la unidad, o bien, mandándolos a trabajar fuera de ella. Así pues, resulta de fundamental importancia conocer las características de organización interna de estos hogares, dadas por su estructura, tamaño y ciclo vital, así como por las características sociodemográficas de los jefes y de sus miembros.
Evidence for shared recognition of a peptide ligand by a diverse panel of non-obese diabetic mice-derived, islet-specific, diabetogenic T cell clones (2002)

MHC class II-restricted autoreactive T cells play a major role in the development of autoimmune diabetes mellitus in both human and mouse. Two of our groups previously established panels of islet-reactive CD4+ T cell clones from prediabetic non-obese diabetic (NOD) mice. These clones express distinct sets of TCR V alpha , V beta , J alpha and J beta , and also differ in the structure of the junctional region of TCR. All of the T cell clones have been shown to cause insulitis and several induce diabetes when transferred to various recipients. The antigen specificities of these T cell clones have not been determined, but they do not react with defined islet cell antigens such as glutamic acid decarboxylase. To identify the peptide ligands recognized by these clones, we examined the reactivity of the T cell clones to peptide mixtures in which anchor residues for H2-A g7 were fixed. Most of the clones showed similar reactivity to the peptide mixtures. To further determine the peptide ligands of the T cell clones, we synthesized several peptides based on the favored amino acid motifs and examined clone reactivity to the synthetic peptides. Some of the peptides, e.g. HLAI-RM and HIPI-RM, could stimulate most of the T cell clones tested, even though the clones expressed different TCR. The results suggest that our islet-reactive T cell clones recognize in islet beta cells a natural ligand that is similar to these peptides.
11β-Hydroxysteroid dehydrogenase and the pre-receptor regulation of corticosteroid hormone action (2005)

Two isozymes of 11beta-hydroxysteroid dehydrogenase (11beta-HSD1 and 11beta-HSD2) catalyse the interconversion of hormonally active cortisol and inactive cortisone. The enzyme evolved from a metabolic pathway to a novel mechanism underpinning human disease with the elucidation of the role of the type 2 or 'kidney' isozyme and an inherited form of hypertension, 'apparent mineralocorticoid excess'. 'Cushing's disease of the kidney' arises because of a failure of 11beta-HSD2 to inactivate cortisol to cortisone resulting in cortisol-induced mineralocorticoid excess.Conversely, 11beta-HSD1 has been linked to human obesity and insulin resistance, but also to other diseases in which glucocorticoids have historically been implicated (osteoporosis, glaucoma). Here, the activation of cortisol from cortisone facilitates glucocorticoid hormone action at an autocrine level. The molecular basis for the putative human 11beta-HSD1 'knockout'--'cortisone reductase deficiency'--has recently been described, an observation that also answers a long standing conundrum relating to the set-point of 11beta-HSD1 activity. In each case, these clinical studies have been underpinned by studies in vitro and the manipulation of enzyme expression in vivo using recombinant mouse models.
Biosynthesis of fusarochromanone and its monoacetyl derivative by Fusarium equiseti (1989)

One fluorescent compound previously named TDP-2 was isolated and purified from a rice culture of Fusarium equiseti (Alaska 2-2). Mass spectral and nuclear magnetic resonance data indicated that it is a C-3'-N-acetyl derivative of fusarochromanone, a newly discovered mycotoxin. Time course studies of synthesis of these two compounds on autoclaved rice and Czapek-Dox medium enriched with soybean peptone indicated that fusarochromanone was converted to TDP-2 in the cultures. A high concentration of peptone in the liquid medium may stimulate both fusarochromanone synthesis and its conversion to TDP-2.
Measurement of Human Daily Physical Activity (2003)

IDEEA accurately measured duration, frequency, type, and intensity of a variety of daily PAs.
Anticytokine Strategies in the Treatment of the Systemic Inflammatory Response Syndrome (1993)

The systemic inflammatory response syndrome (SIRS) is an acute illness characterized by generalized activation of the endothelium. The most severe form of the syndrome is found in patients with shock due to gram-negative sepsis. We examined both animal and limited human data for the contribution of cytokines to this syndrome. Cytokines are endogenously produced proteins of small molecular weight and multiple biological effects. The cytokines interleukin 1 (IL-1) and tumor necrosis factor (TNF), as well as interferon-gamma and interleukin 8, are discussed. Laboratory investigations suggest that these cytokines play a critical role in SIRS by promoting the biochemical and clinical characteristics of SIRS. The biochemical changes induced by TNF and IL-1 include increased synthesis of nitric oxide, prostaglandins, platelet-activating factor, and endothelial cell adhesion molecules. Specific blockade of TNF using neutralizing antibodies or soluble receptors to TNF in animal models of SIRS reduces mortality and severity of disease. Similar results have been observed blocking IL-1 using soluble IL-1 receptors or IL-1 receptor antagonists. Preliminary clinical studies suggest that blockade may be useful in treating human SIRS. The various strategies for blocking IL-1 and TNF are presented; in addition, their mechanism(s) of action and safety in humans are discussed. We conclude that based on animal studies and preliminary clinical trials, strategies to block IL-1 or TNF may benefit patients with the syndrome, although thorough clinical trials have not been completed.
Transition network grammars for natural language analysis (1970)

The use of augmented transition network grammars for the analysis of natural language sentences is described. Structure-building actions associated with the arcs of the grammar network allow for the reordering, restructuring, and copying of constituents necessary to produce deep-structure representations of the type normally obtained from a transformational analysis, and conditions on the arcs allow for a powerful selectivity which can rule out meaningless analyses and take advantage of semantic information to guide the parsing. The advantages of this model for natural language analysis are discussed in detail and illustrated by examples. An implementation of an experimental parsing system for transition network grammars is briefly described.
A 22nm high performance embedded DRAM SoC technology featuring tri-gate transistors and MIMCAP COB (2013)

A 22 nm generation technology is described incorporating transistor and interconnects with performance suitable for the needs of both high density DRAM and high-performance logic devices. We have integrated a 0.029 μm2 DRAM cell capable of meeting >100μs retention at 95°C. Results will be reported for a test-vehicle with best-reported array density at 17.5Mb/mm2 based on a 128Mb macro. The process technology utilizes our leading edge 22nm 3-D tri-gate transistor as described previously [1,2]. The excellent leakage and performance characteristics of tri-gate transistors have been optimized for the access transistor, while maintaining the performance needed to enable high performance circuits in the same die. A high aspect-ratio, 3-D metal-insulator-metal capacitor trench has been integrated into the ultra-low-k interlayer dielectric and Cu metallization used for interconnect stacks. The previously described 22nm logic and SoC technology has been leveraged, with a 3-D MIM capacitor included in the ultra-low-k (ULK) ILD at the same level as the Metal-2 through Metal-4 interconnects. Excellent retention capability and yield have been demonstrated.
Hydroaminoalkylation: Early-Transition-Metal-Catalyzed α-Alkylation of Amines (2014)

The recent development and progress of early-transition-metal-catalyzed C–H alkylation adjacent to nitrogen of unprotected amines with alkenes are summarized. Group 4 and 5 metal complexes are very effective for hydroaminoalkylation catalysis, an emerging atom-economic C(sp<sup>3</sup>)–C(sp<sup>3</sup>) bond formation strategy. 1 Introduction 2 Group 4 Hydroaminoalkylation Catalysis 2.1 Intramolecular Hydroaminoalkylation 2.2 Intermolecular Hydroaminoalkylation 3 Group 5 Hydroaminoalkylation Catalysis 4 Conclusions and Outlook
Agar human T cell colony growth promoted by a B + null cell-derived lymphokine distinct from IL 2. (1985)

Human T cell agar colonies can be grown under PHA stimulation from either mature T cells or their E rosette-negative (E-), OKT3- peripheral blood and bone marrow precursors. Colonies comprise a majority of mature E+, OKT3+ cells and a minor (5 to 10%) population of immature E-, T3-, T8-, T4-, DR+, T10+, RFB1+ cells, which upon replating in subculture, can generate secondary colonies of OKT3+, E+, OKT4+, OKT8+ cells. Secondary colony formation can serve as a test for growth requirement of colony precursors, because it depends on the presence of both PHA and a colony-promoting activity (CPA) recovered in PHA-stimulated B + null or T + adherent cell supernatants. CPA production by B + null cells was not affected by their treatment with OKT3 or D66 (T11-like) monoclonal antibodies (MAB) + complement but was abolished by an anti-HLA-DR MAB + complement. However, B cells sorted by panning with the same anti-HLA-DR MAB did not release CPA, demonstrating the requirement of both B cells and null cells for CPA production. Neither IL 2 nor IL 1 could account for B + null cell-derived CPA.
A comparison and optimization of methods and factors affecting the transformation of Escherichia coli (2013)

DNA manipulation routinely requires competent bacteria that can be made using one of numerous methods. To determine the best methods, we compared four commonly used chemical methods (DMSO, MgCl2-CaCl2, CaCl2 and Hanahan's methods) on frequently used Escherichia coli (E. coli) strains: DH5α, XL-1 Blue, SCS110, JM109, TOP10 and BL21-(DE3)-PLysS. Hanahan's method was found to be most effective for DH5α, XL-1 Blue and JM109 strains (P<0.05), whilst the CaCl2 method was best for SCS110, TOP10 and BL21 strains (P<0.05). The use of SOB (super optimal broth) over LB [Luria-Bertani (broth)] growth media was found to enhance the competency of XL-1 Blue (P<0.05), dampened JM109's competency (P<0.05), and had no effect on the other strains (P>0.05). We found no significant differences between using 45 or 90 s heat shock across all the six strains (P>0.05). Through further optimization by means of concentrating the aliquots, we were able to get further increases in transformation efficiencies. Based on the optimized parameters and methods, these common laboratory E. coli strains attained high levels of TrE (transformation efficiency), thus facilitating the production of highly efficient and cost-effective competent bacteria.
Decreased Bioavailable Testosterone in Aging Normal and Impotent Men* (1986)

Tissue available (bioavailable) testosterone (T) includes circulating free T (FT) and albumin-bound T. A reasonable assessment of bioavailable T can be made by using 50% ammonium sulfate to precipitate sex hormone-binding globulin (SHBG)-bound T. The supernatant non-SHBG-bound T (non-SHBG-T) correlates well with physiological androgen activity. To assess bioavailable T in normal aging men, we analyzed serum samples from seven healthy aged men (65-83 yr old) and compared the results to samples from 13 young men (22-39 yr old). Mean serum T, FT, and LH concentrations were not significantly different in the 2 groups. However, the mean absolute non-SHBG-T level was significantly lower (P less than 0.005) in the older group. In a separate population of 20 impotent but otherwise healthy men (5 27-37 yr old, 10 48-64 yr old, and 5 66-69 yr old), the mean absolute non-SHBG-T concentration was lower in middle-aged (P less than .01) and elderly men (P less than 0.001) than in young men. The absolute FT was lower only in the elderly group (P less than 0.05), while mean LH and T levels were similar in all 3 age groups. These data suggest that serum concentrations of tissue available T are decreased in aged men and that non-SHBG-T measurement is a more sensitive indicator of this decrease than are serum T or serum FT measurements. These changes appear to begin by middle age.
Selective requantization for transcoding of MPEG compressed video (2002)

The paper addresses the problem of bit-rate conversion of MPEG compressed video. We present selective requantization, a method for reducing the requantization errors in transcoding. The proposed method is based on avoiding critical ratios of the two cascaded quantizations (encoding versus transcoding) that either lead to larger transcoding errors or require a higher bit budget. Results show that selective requantization improves the quality of the transcoded images. The presented method is simple to implement and does not require side information.
Efficient Expression of the Saccharomyces cerevisiae PGK Gene Depends on an Upstream Activation Sequence but Does Not Require TATA Sequences (1986)

The Saccharomyces cerevisiae PGK (phosphoglycerate kinase) gene encodes one of the most abundant mRNA and protein species in the cell. To identify the promoter sequences required for the efficient expression of PGK, we undertook a detailed internal deletion analysis of the 5' noncoding region of the gene. Our analysis revealed that PGK has an upstream activation sequence (UASPGK) located between 402 and 479 nucleotides upstream from the initiating ATG sequence which is required for full transcriptional activity. Deletion of this sequence caused a marked reduction in the levels of PGK transcription. We showed that PGK has no requirement for TATA sequences; deletion of one or both potential TATA sequences had no effect on either the levels of PGK expression or the accuracy of transcription initiation. We also showed that the UASPGK functions as efficiently when in the inverted orientation and that it can enhance transcription when placed upstream of a TRP1-IFN fusion gene comprising the promoter of TRP1 fused to the coding region of human interferon alpha-2.
Anti-vascular endothelial growth factor acts on retinal microglia/macrophage activation in a rat model of ocular inflammation. (2014)

Microglia and macrophages expressed VEGF receptors, and intravitreous anti-VEGF influenced the microglia and macrophage activation state. Taking into account that anti-VEGF drugs are repeatedly injected in the vitreous of patients with retinal diseases, part of their effects could result from unsuspected modulation of the microglia activation state. This should be further studied in other ocular pathogenic conditions and human pathology.
Mechanistic and structural studies on legumain explain its zymogenicity, distinct activation pathways, and regulation (2013)

The cysteine protease legumain plays important functions in immunity and cancer at different cellular locations, some of which appeared conflicting with its proteolytic activity and stability. Here, we report crystal structures of legumain in the zymogenic and fully activated form in complex with different substrate analogs. We show that the eponymous asparagine-specific endopeptidase activity is electrostatically generated by pH shift. Completely unexpectedly, the structure points toward a hidden carboxypeptidase activity that develops upon proteolytic activation with the release of an activation peptide. These activation routes reconcile the enigmatic pH stability of legumain, e.g., lysosomal, nuclear, and extracellular activities with relevance in immunology and cancer. Substrate access and turnover is controlled by selective protonation of the S1 pocket (KM) and the catalytic nucleophile (kcat), respectively. The multibranched and context-dependent activation process of legumain illustrates how proteases can act not only as signal transducers but as decision makers.
Ribozymes Targeted to Stearoyl–ACP Δ9 Desaturase mRNA Produce Heritable Increases of Stearic Acid in Transgenic Maize Leaves (1998)

Ribozymes are RNAs that can be designed to catalyze the specific cleavage or ligation of target RNAs. We have explored the possibility of using ribozymes in maize to downregulate the expression of the stearoyl-acyl carrier protein (Delta9) desaturase gene. Based on site accessibility and catalytic activity, several ribozyme constructs were designed and transformed into regenerable maize lines. One of these constructs, a multimer hammerhead ribozyme linked to a selectable marker gene, was shown to increase leaf stearate in two of 13 maize lines. There were concomitant decreases in Delta9 desaturase mRNA and protein. The plants with the altered stearate phenotype were shown to express ribozyme RNA. The ribozyme-mediated trait was heritable, as evidenced by stearate increases in the leaves of the R1 plants derived from a high-stearate line. The increase in stearate correlated with the presence of the ribozyme gene. A catalytically inactive version of this ribozyme did not produce any significant effect in transgenic maize. This is evidence that ribozymes can be used to modulate the expression of endogenous genes in maize.
A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution (2008)

The ability to monitor DNA polymerase activity with single-nucleotide resolution has been the cornerstone of a number of advanced single-molecule DNA sequencing concepts. Toward this goal, we report the first observation of the base-by-base DNA polymerase activity with single-base resolution at the single-molecule level. We describe the design and characterization of a supramolecular nanopore device capable of detecting up to nine consecutive DNA polymerase-catalyzed single-nucleotide primer extensions with high sensitivity and spatial resolution (<or=2.4 A). The device is assembled in a suspended lipid membrane by threading and mechanically capturing a single strand of DNA-PEG copolymer inside an alpha-hemolysin protein pore. Single-nucleotide primer extensions result in successive displacements of the template DNA strand within the protein pore, which can be monitored by the corresponding stepped changes in the ion current flowing through the pore under an applied transmembrane potential. The system described thus represents a promising advance toward nanopore-mediated single-molecule DNA sequencing concept and, in addition, might be applicable to studying a number of other biopolymer-protein interactions and dynamics.
A chemically cleavable biotinylated nucleotide: usefulness in the recovery of protein-DNA complexes from avidin affinity columns. (1985)

A biotinylated nucleotide analog containing a disulfide bond in the 12-atom linker joining biotin to the C-5 of the pyrimidine ring has been synthesized. This analog, Bio-SS-dUTP, is an efficient substrate for Escherichia coli DNA polymerase I. Bio-SS-dUTP supported DNA synthesis in a standard nick-translation reaction at 35%-40% the rate of an equal concentration of the normal nucleotide, TTP. DNA containing this analog was bound to an avidin-agarose affinity column and subsequently eluted after reduction of the disulfide bond by dithiothreitol. The ability to recover biotinylated DNA from an avidin affinity column under nondenaturing conditions should prove useful in the isolation of specific protein-DNA complexes. As a demonstration of this approach, Bio-SS-DNA was reconstituted with histones to form 11S monomer nucleosomes. Bio-SS-nucleosomes were shown to selectively bind to avidin-agarose. Ninety percent of the bound Bio-SS-nucleosomes were recovered from the affinity column by elution with buffer containing 50-500 mM dithiothreitol. The recovered nucleosomes were shown to be intact 11S particles as judged by velocity sedimentation in a sucrose gradient. This approach may prove to be generally useful in the isolation of protein-DNA complexes in a form suitable for further analysis of their native unperturbed structure.