gebhart/patrepeval huggingface dataset:
Involvement of Antilipoarabinomannan Antibodies in Classical Complement Activation in Tuberculosis (1998)

We examined alternative and classical complement activation induced by whole bacilli of Mycobacterium bovis BCG and Mycobacterium tuberculosis products. After exposure to BCG, there were higher levels of the terminal complement complex in sera from Indian tuberculosis patients than in sera from healthy controls. The addition of BCG with or without EGTA to these sera indicated that approximately 70 to 85% of the total levels of the terminal complement complex was formed by classical activation. Sera from Indian tuberculosis patients contained more antibody to lipoarabinomannan (LAM) than sera from healthy Indians. Levels of anti-LAM immunoglobulin G2 (IgG2), but not anti-LAM IgM, correlated positively with classical activation induced by BCG in the sera. By flow cytometry, deposition of C3 and terminal complement complex on bacilli incubated with normal human serum was demonstrated. The anticomplement staining was significantly reduced in the presence of EGTA and EDTA. Flow cytometry also revealed the binding of complement to BCG incubated with rabbit anti-LAM and then with factor B-depleted serum. This indicates that classical activation plays a major role in complement activation induced by mycobacteria and that anti-LAM IgG on the bacilli can mediate this response. Classical complement activation may be important for the extent of phagocytosis of M. tuberculosis by mononuclear phagocytes, which may influence the course after infection.
Metabolic manifestations of insulin deficiency do not occur without glucagon action (2012)

To determine unambiguously if suppression of glucagon action will eliminate manifestations of diabetes, we expressed glucagon receptors in livers of glucagon receptor-null (GcgR(-/-)) mice before and after β-cell destruction by high-dose streptozotocin. Wild type (WT) mice developed fatal diabetic ketoacidosis after streptozotocin, whereas GcgR(-/-) mice with similar β-cell destruction remained clinically normal without hyperglycemia, impaired glucose tolerance, or hepatic glycogen depletion. Restoration of receptor expression using adenovirus containing the GcgR cDNA restored hepatic GcgR, phospho-cAMP response element binding protein (P-CREB), and phosphoenol pyruvate carboxykinase, markers of glucagon action, rose dramatically and severe hyperglycemia appeared. When GcgR mRNA spontaneously disappeared 7 d later, P-CREB declined and hyperglycemia disappeared. In conclusion, the metabolic manifestations of diabetes cannot occur without glucagon action and, once present, disappear promptly when glucagon action is abolished. Glucagon suppression should be a major therapeutic goal in diabetes.
Polymorphisms of Genes in the Lipid Metabolism Pathway and Risk of Biliary Tract Cancers and Stones: A Population-Based Case-Control Study in Shanghai, China (2008)

Biliary tract cancers, encompassing the gallbladder, extrahepatic bile duct, and ampulla of Vater, are uncommon yet highly fatal malignancies. Gallstones, the primary risk factor for biliary cancers, are linked with hyperlipidemia. We examined the associations of 12 single nucleotide polymorphisms of five genes in the lipid metabolism pathway with the risks of biliary cancers and stones in a population-based case-control study in Shanghai, China. We included 235 gallbladder, 125 extrahepatic bile duct, and 46 ampulla of Vater cancer cases, 880 biliary stone cases, and 779 population controls. Subjects completed an in-person interview and gave blood. Genotyping was conducted by TaqMan assay using DNA from buffy coats. The effects of APOE IVS1+69 (rs440446) and APOB IVS6+360C>T (rs520354) markers were limited to men. Men carrying the G allele of APOE IVS1+69 had a 1.7-fold risk of stones [95% confidence interval (95% CI), 1.2-2.4], a 1.8-fold risk of gallbladder cancer (95% CI, 1.0-3.3), a 3.7-fold risk of bile duct cancer (95% CI, 2.0-7.0), and a 4-fold risk of ampullary cancer (95% CI, 1.4-12.4). Male carriers of the T allele of APOB IVS6+360C>T had a 2-fold risk of bile duct cancer (95% CI, 1.2-3.4). The APOB T-T haplotype (APOB IVS6+360C>T, EX4+56C>T) was associated with a 1.6-fold risk of bile duct cancer (95% CI, 1.1-2.3). Male and female carriers of the T allele of LDLR IVS9-30C>T (rs1003723) had a 1.5-fold risk of bile duct cancer. Our findings suggest that gene variants in the lipid metabolism pathway contribute to the risk of biliary tract stones and cancers, particularly of the bile duct.
Impact of Inverted Terminal Repeat Integrity on rAAV8 Production Using the Baculovirus/Sf9 Cells System (2017)

Adeno-associated virus (AAV) inverted terminal repeats (ITRs) are key elements of AAV. These guanine-cytosine-rich structures are involved in the replication and encapsidation of the AAV genome, along with its integration in and excision from the host genome. These sequences are the only AAV-derived DNA sequences conserved in recombinant AAV (rAAV), as they allow its replication, encapsidation, and long-term maintenance and expression in target cells. Due to the original vector design, plasmids containing the gene of interest flanked by ITRs and used for rAAV production often present incomplete, truncated, or imperfect ITR sequences. For example, pSUB201 and its derivatives harbor a truncated (14 nt missing on the external part of the ITR), flop-orientated ITR plus 46 bp of non-ITR viral DNA at each end of the rAAV genome. It has been shown that rAAV genomes can be replicated, even with incomplete, truncated, or imperfect ITR sequences, leading to the production of rAAV vectors in transfection experiments. Nonetheless, it was hypothesized that unmodified wild-type (WT) ITR sequences could lead to a higher yield of rAAV, with less non-rAAV encapsidated DNA originating from the production cells and/or baculovirus shuttle vector genomes. This work studied the impact of imperfect ITRs on the level of encapsidated rAAV genomes and baculovirus-derived DNA sequences using the baculovirus/Sf9 cells production system. Replacement of truncated ITRs with WT and additional wtAAV2 sequences has an impact on the two major features of rAAV production: (1) a rise from 10% to 40% of full capsids obtained, and (2) up to a 10-fold reduction in non-rAAV encapsidated DNA. Furthermore, this study considered the impact on these major parameters of additional ITR elements and ITRs coupled with various regulatory elements of different origins. Implementation of the use of complete ITRs in the frame of the baculovirus-based rAAV expression system is one step that will be required to optimize the quality of rAAV-based gene therapy drugs.
Recombinant IL 2 but not recombinant interferon-gamma stimulates both proliferation and IgM secretion in a Ly-1+ clone of neoplastic murine B cells (BCL1). (1986)

We have used a lymphokine-responsive clone (3B3) of B leukemia cells (BCL1) to examine the effects of several recombinant and purified lymphokines. Cells from BCL1-3B3 were induced to secrete IgM in the presence of recombinant interleukin 2 (rIL 2) (10 to 50 U/ml); a concomitant increase in proliferation was observed. Recombinant interferon-gamma (rIFN-gamma) was a potent inhibitor of proliferation. In addition, rIFN-gamma did not induce an increase in IgM secretion and, when added to rIL 2-stimulated BCL1-3B3 cells, completely blocked IgM secretion at a concentration of 10 U/ml. Purified and recombinant IL 1 (rIL 1) had no significant effect on differentiation either alone or in combination with rIL 2 and/or rIFN-gamma. However, rIL 1 was able to synergize with rIL 2 in enhancing the proliferation of BCL1-3B3. The ability of cells to respond to rIL 2 was limited to the in vitro (Ly-1+) clones of BCL1 cells since the in vivo derived (Ly-1-) BCL1 cells did not differentiate in response to IL 2. Consistent with their functional response to rIL 2, cells from the in vitro clone (3B3) are IL 2-receptor-positive (IL-2R+) and the in vivo derived BCL1 cells are IL-2R-. A second set of neoplastic B cell clones derived from the AKR 225 lymphoma did not respond to rIL 2 even though they expressed receptors for IL 2 and could be induced by T cell supernatant to secrete IgM, thus indicating that expression of IL 2R is not the sole requirement for IL 2 responsiveness. The monoclonal anti-IL 2R antibody (7D4) mimicked IL 2 in its ability to stimulate differentiation of BCL1-3B3 cells. These data suggest that rIL 2 and the monoclonal anti-IL-2R antibody are capable of inducing a differentiative response in the Ly-1+ BCL1-3B3 cells that is functionally equivalent to the response evoked by the previously described lymphokine B cell differentiation factor for IgM (BCDF mu). Thus, two distinct lymphokines appear to be providing a similar signal to a clonal neoplastic B cell population. Furthermore, rIL 2 is capable of providing both a proliferative and a differentiative signal.
Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. (2000)

A novel anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium, strain PB(T), was isolated from a thermophilic (55 degrees C) anaerobic methanogenic reactor which had been treating kraft-pulp waste water. The bacterium oxidized acetate in co-culture with a thermophilic hydrogenotrophic methanogen. Strain PB(T), a gram-positive, spore-forming, rod-shaped bacterium grew optimally at 58 degrees C and pH 6.8. The bacterium grew acetogenically on several alcohols, methoxylated aromatics, pyruvate, glycine, cysteine, formate and hydrogen/CO2. Strain PB(T) also oxidized acetate with reduction of sulfate or thiosulfate as the electron acceptor. The bacterium contained MK-7 as the major quinone. The G+C content of the DNA was 53.5 mol%. Comparative 16S rDNA analysis indicated that strain PB(T) belongs to the Bacillus-Clostridium subphylum. However, it was distant from any known genera or micro-organism. The closest known relative was Thermoterrabacterium ferrireducens with 87.4% similarity. The name Thermacetogenium phaeum gen. nov., sp. nov. is proposed. The type strain is strain PBT (= DSM 12270T).
Non-Oral Poster 24 (2010)

OBJECTIVES: To assess the degree to which smoking, age, menopausal status, hormone replacement therapy, diabetes, body-mass index (BMI) and perioperative complications are associated with the risk of mesh erosion following transvaginal placement of polypropylene mesh for pelvic organ prolapse. MATERIALS AND METHODS: A matched case-control study was performed. Women with transvaginally placed polypropylene mesh for the repair of pelvic organ prolapse between January 1, 2004 and May 31, 2009 were included. Cases were all women treated at our tertiary care center with mesh erosion requiring surgical revision. Controls did not develop mesh erosion and were matched for similar date and type of surgery (location and brand of mesh). Cases were identified by CPT codes 57295 and 57296, indicating a surgical mesh revision from a vaginal or abdominal approach. Controls were identified by CPT code 57267, indicating the vaginal placement of mesh. Charts were manually reviewed to assess for all inclusion criteria. Patient demographics, characteristics, comorbidities, perioperative variables, complications and erosion status were ascertained from the medical records. Complications were those recorded by the surgeon, including: bleeding, transfusion, cystotomy, rectal injury, hematoma, sciatic pain, and urinary retention. A conditional logistic regression was used to control for matching; adjusted odds ratios (OR) with 95% confidence intervals (CI) were obtained from this model. The model included smoking status, menopausal status, hormone replacement therapy, diabetes status, BMI and age. A restricted cubic spline was used for BMI and age to relax assumptions of linearity in these variables. Analysis was performed with STATA version 9. RESULTS: Forty-eight cases were matched with 48 controls. The mean age for cases was 54.5 years and controls was 59.9 years. Parity, body mass index and menopausal status were similar between both groups (Mean parity 3; BMI 28.1 and 27.2, 38% and 40% menopausal, respectively). Results were inconclusive regarding the factors of interest and mesh erosion: The adjusted odds of developing mesh erosion were 3.4 fold higher among smokers than non-smokers (95% CI, 0.34 to 33.66), 2.3 fold higher among patients taking hormonal replacement therapy (95% CI, 0.57 to 9.19), and lower among those who were younger, (OR 0.96; 95% CI, 0.92 to 0.99), and those with diabetes (OR 0.46; 95% CI, 0.07 to 2.86). Mesh erosions tended to be more common among patients with perioperative complications, (OR, 6.04; 95% CI, 0.66 to 55.53). Complications among the cases included bleeding requiring transfusion (n = 1), cystotomy (n = 2), hematoma (n = 2), rectal perforation (n = 1), sciatic pain (n = 1) and urinary retention (n = 1). Only one control had a complication: postoperative urinary retention which resolved. CONCLUSION: Our results were inconclusive regarding whether smoking, age, menopausal status, hormone replacement therapy, diabetes and body-mass index are risk factors for the development of mesh erosion. There was a trend toward mesh erosion being more common after surgeries with perioperative complications.
A Study of a Weakly Ionized Rotating Plasma (1979)

Abstract Measurements are reported on a weakly ionized rotating argon plasma generated by two identical gas discharges facing each other. In each discharge a current up to 100 A is drawn between a point-like cathode and a ring-shaped anode. Axial magnetic fields up to 0.26 T are applied. All measurements have been done at 1 torr. For magnetic field strengths below 0.17 T the plasma has a more or less uniform radial distribution; above 0.17 T a contracted plasma column is present along the axis of the cylinder. In the symmetry plane between the two discharges measurements have been done on the rotational velocity of neutrals and ions, the electron density and temperature, the ion temperature, the plasma potential and the radial pressure distribution. The rotational velocity, the plasma potential and the pressure distribution are also calculated. The theoretical treatment is based on the theory developed by Klüber and Wilhelm and Hong. In the low magnetic field case velocities of 700 m/sec are found for ions as well as neutrals. The agreement between theory and experiment is good in this case. At high magnetic fields, the ions and neutrals are found to have azimuthal velocities of 1900 and 700 m/sec, respectively. The radial pressure enhancement due to the centrifugal forces is found to be approximately a factor of two whereas the theory predicts only a factor of 1.2. In a discharge in which a mixture of argon and xenon is used a relative separation factor of 2.15 is found.
Observation and Study of Dislocation Etch Pits in Molecular Beam Epitaxy Grown Gallium Nitride With the Use of Phosphoric Acid and Molten Potassium Hydroxide (2007)

Defects continue to challenge the functionality and reliability gallium nitride (GaN)-based devices. GaN grown on sapphire by molecular beam epitaxy was investigated by wet etching in hot phosphoric acid (H3PO4) and molten potassium hydroxide (KOH). Hexagonally shaped etch pits were formed on the etched sample surfaces. Etched samples were characterized with the use of atomic force microscopy (AFM) and scanning electron microscopy (SEM) and SEM cathode luminescence (SEM-CL). AFM images show dark spots indicating mixed dislocations. The densities of the mixed dislocations are almost ~3 x 108 cm 2. Observations were made about the three different types of etch pits distinguished as , , and . By comparing SEM and AFM, we made observations about a relationship between etch pits and dislocations. The origin of etch pits is the mixed dislocation, and the combination of KOH etching and AFM is found to be a better approach for a two dimensional evaluation of mixed dislocations. Results showed that both H3PO4 and molten KOH are good wet etchants for GaN and the pits created by H3PO4 were smaller and numerous when compared to the pits created by molten KOH.
Decoding the genome: a modified view (2004)

Transfer RNA's role in decoding the genome is critical to the accuracy and efficiency of protein synthesis. Though modified nucleosides were identified in RNA 50 years ago, only recently has their importance to tRNA's ability to decode cognate and wobble codons become apparent. RNA modifications are ubiquitous. To date, some 100 different posttranslational modifications have been identified. Modifications of tRNA are the most extensively investigated; however, many other RNAs have modified nucleosides. The modifications that occur at the first, or wobble position, of tRNA's anticodon and those 3'-adjacent to the anticodon are of particular interest. The tRNAs most affected by individual and combinations of modifications respond to codons in mixed codon boxes where distinction of the third codon base is important for discriminating between the correct cognate or wobble codons and the incorrect near-cognate codons (e.g. AAA/G for lysine versus AAU/C asparagine). In contrast, other modifications expand wobble codon recognition, such as U*U base pairing, for tRNAs that respond to multiple codons of a 4-fold degenerate codon box (e.g. GUU/A/C/G for valine). Whether restricting codon recognition, expanding wobble, enabling translocation, or maintaining the messenger RNA, reading frame modifications appear to reduce anticodon loop dynamics to that accepted by the ribosome. Therefore, we suggest that anticodon stem and loop domain nucleoside modifications allow a limited number of tRNAs to accurately and efficiently decode the 61 amino acid codons by selectively restricting some anticodon-codon interactions and expanding others.
Exosomes: an overview of biogenesis, composition and role in ovarian cancer (2014)

Exosomes are tiny membrane-bound vesicles that are over produced by most proliferating cell types during normal and pathological states. Their levels are up-regulated during pregnancy and disease states such as cancer. Exosomes contain a wide variety of proteins, lipids, RNAs, non-transcribed RNAs, microRNAs and small RNAs that are representative to their cellular origin and shuttle from a donor cell to a recipient cell. From intercellular communication to tumor proliferation, exosomes carry out a diverse range of functions, both helpful and harmful. Useful as biomarkers, exosomes may be applicable in diagnostic assessments as well as cell-free anti-tumor vaccines. Exosomes of ovarian cancer contain different set of proteins and miRNAs compared to exosomes of normal, cancer-free individuals. These molecules may be used as multiple "barcode" for the development of a diagnostic tool for early detection of ovarian cancer.
Molecular Oxygen Reduction in PEM Fuel Cell Conditions:  ToF-SIMS Analysis of Co-Based Electrocatalysts (2005)

A series of Co-based electrocatalysts for oxygen reduction in acid media has been prepared using two different Co precursors: cobalt acetate (CoAc) and a cobalt porphyrin (CoTMPP). These catalysts have been analyzed by ToF-SIMS to obtain information on the number and the structure of catalytic active sites in these materials. The results are compared with the results of a similar analysis already performed on a series of Fe-based electrocatalysts (J. Phys. Chem. B 2002, 106, 8705) also prepared with two different Fe precursors: iron acetate (FeAc) and an iron porphyrin (ClFeTMPP). The interpretation of ToF-SIMS data for Fe-based catalysts allowed us to conclude that whatever the Fe precursor was, the same catalytic sites (FeN2/C and FeN4/C, with their respective dominant ToF-SIMS signatures: FeN2C4+ and FeN4C8+ ions) were found. The comparison of the ToF-SIMS data with the activity of those catalysts led to the conclusion that the FeN2C catalytic site was more active than FeN4/C. When the same procedure is applied to ToF-SIMS data measured for Co-based catalysts, the following conclusions are drawn: (i) as for Fe precursors, both Co precursors also give similar results; (ii) as for Fe-based catalysts, the same four families of MetalNxCy+ ions, with 1, 2, 3, and 4 nitrogen atoms, are also found in the spectra of Co-based catalysts, but there is no dominant CoNxCy+ ion signature; (iii) only CoN4/C can be ascertained on the basis of ToF-SIMS measurements. There is no strong support from ToF-SIMS measurements for (or against) the existence of CoN2/C in Co-based catalysts as there is for FeN2/C in Fe-based catalysts; (iv) contrary to Fe-based catalysts, all catalytic sites (if there are any besides CoN4/C) are about equally active in Co-based electrocatalysts.
A common neutralizing epitope conserved between the hemagglutinins of influenza A virus H1 and H2 strains (1993)

When mice were immunized with the A/Okuda/57 (H2N2) strain of influenza virus, a unique monoclonal antibody designated C179 was obtained. Although C179 was confirmed to recognize the hemagglutinin (HA) glycoprotein by immunoprecipitation assays, it did not show hemagglutination inhibition activity to any of the strains of the three subtypes of influenza A virus. However, it neutralized all of the H1 and H2 strains but not the H3 strains. Moreover, it inhibited polykaryon formation induced by the H1 and H2 strains but not by the H3 strains. Two antigenic variants against C179 were obtained, and nucleotide sequence analysis revealed that amino acid sequences, from 318 to 322 of HA1 and from 47 to 58 of HA2, conserved among H1 and H2 strains were responsible for the recognition of C179. Since the two sites were located close to each other at the middle of the stem region of the HA molecule, C179 seemed to recognize these sites conformationally. These data indicated that binding of C179 to the stem region of HA inhibits the fusion activity of HA and thus results in virus neutralization and inhibition of cell-cell fusion. This is the first report which describes the presence of conserved antigenic sites on HA not only in a specific subtype but also in two subtypes of influenza A virus.
A Mutual-Information-Based Approach to Entity Reconciliation in Heterogeneous Databases (2008)

Entity reconciliation is crucial to data interoperability in heterogeneous databases. In our previous research works, we proposed an entities matching algorithm based on attribute entropy to identify the corresponding entities, which can resolve the limitations of present main approaches and improve the precision of entities matching obviously. By our further research, we find that some attributes with different importance in identifying the entities will obtain the same weights just according to attribute entropy. So in this paper we employ mutual information to quantify attribute weight due to mutual information well describes the correlation of probability distributions over two attributes. According to this idea, the final entropy computation algorithm and entity reconciliation algorithm based on mutual information are presented. The experimental results on real-world data show that our mutual-information-based approach can obtain better performance.