gebhart/patrepeval huggingface dataset:
Antibodies that protect humans against Plasmodium falciparum blood stages do not on their own inhibit parasite growth and invasion in vitro, but act in cooperation with monocytes. (1990)

IgG extracted from the sera of African adults immune to malaria were injected intravenously into eight Plasmodium falciparum-infected nonimmune Thai patients. Clinical and parasitological improvement was reproducibly obtained in each case. After the disappearance of the transferred Ig, recrudescent parasites were equally susceptible to the same Ig preparation. High levels of antibodies to most parasite proteins were detected by Western blots in the receivers' sera (taken before transfer) as in the donors' Ig, thus indicating that the difference was qualitative rather than quantitative between donors and receivers. In vitro, the clinically effective Ig had no detectable inhibitory effect on either penetration or intra-erythrocytic development of the parasite. On the contrary, they sometimes increased parasite growth. In contrast, these IgG, as the receivers' Ig collected 4 d after transfer, but not those collected before transfer, proved able to exert an antibody-dependent cellular inhibitory (ADCI) effect in cooperation with normal blood monocytes. Results were consistent among the seven isolates studied in vitro, as with the recrudescent parasites. Thus, the results obtained in the ADCI assay correlate closely with clinical and parasitological observations.
The R‐form of DNA does exist (1994)

Oligonucleotide 5'-d(CATGCTAACT)-L-d(AGTTAGCATG)-L-d(CATGCTAACT)-3' [L = pO(CH2CH2O)3p] is shown to fold back on itself twice forming at pH 7 a sufficiently stable triplex (Tm is about 30 degrees C) with parallel-orientated identical strands (the recombinant or R-form of DNA). Experimental evidence was obtained by studying thermal denaturation, chemical modification and binding of fluorescent probes. The stability of the R-triplex increases in the presence of divalent ions or spermidine. Its structure is characterized by a certain heterogeneity that causes the cooperativity of a triplex-to-duplex transition to decrease. On the basis of conformational modeling, the possible types of base tripling in all four triplets are proposed. The experimental data as well as the molecular mechanic calculations indicate that the stabilities of triplets in the R-triplex decrease in the order: G:C-G = A:T-A >> T:A-T > C:G-C.
Postmenopausal hormone therapy: new questions and the case for new clinical trials (2006)

Observational studies suggest that postmenopausal hormone therapy (HT) prevents coronary heart disease, whereas randomized clinical trials have not confirmed a cardioprotective effect. Although observational studies may have overestimated the coronary benefit conferred by postmenopausal hormone use, there are other plausible explanations for the apparent discrepancy between previous results and the less favorable findings from clinical trials such as the large Women's Health Initiative. There is now a critical mass of data to support the hypothesis that age or time since menopause may importantly influence the benefit-risk ratio associated with HT, especially with respect to cardiovascular outcomes, and that the method of administration, dose, and formulation of exogenous hormones may also be relevant. Although the weight of the evidence indicates that older women and those with subclinical or overt coronary heart disease should not take HT, estrogen remains the most effective treatment currently available for vasomotor symptoms, and its effects on the development of coronary disease in newly postmenopausal women remain unclear. Moreover, effects of HT on quality of life and cognitive function in recently postmenopausal women merit further study. These unresolved clinical issues provide the rationale for the design of the Kronos Early Estrogen Prevention Study, a 5-year randomized trial that will evaluate the effectiveness of low-dose oral estrogen and transdermal estradiol in preventing progression of atherosclerosis in recently postmenopausal women.
Morphological Considerations in the Pathogenesis of Paratuberculosis in Goats (2005)

Paratuberculosis is a chronic granulomatous enteritis and lymphadenitis in ruminants caused by Mycobacterium avium subsp. paratuberuclosis . To investigate the efficacy of assays for early diagnosis, experimental infections were performed in goat kids. Oral doses of M. a. paratuberculosis were administered to goat kids over extended periods and the resulting infection was followed for 12–24 months. Complementary experiments were performed on goat kids vaccinated against M. a. paratuberculosis . Immunological, pathological and morphological examinations were undertaken in both these experimental systems. The analysis of results from these experiment series provided novel insights into the influence of the biology of gut‐associated lymphoid tissue on the progress of disease, into the character of the tissue granuloma and its dominance of the local tissue response and into the relationship between the local and systemic immune responses.
Recursive deconvolution of combinatorial chemical libraries. (1994)

A recursive strategy that solves for the active members of a chemical library is presented. A pentapeptide library with an alphabet of Gly, Leu, Phe, and Tyr (1024 members) was constructed on a solid support by the method of split synthesis. One member of this library (NH2-Tyr-Gly-Gly-Phe-Leu) is a native binder to a beta-endorphin antibody. A variation of the split synthesis approach is used to build the combinatorial library. In four vials, a member of the library's alphabet is coupled to a solid support. After each coupling, a portion of the resin from each of the four reaction vials was set aside and catalogued. The solid support from each vial is then combined, mixed, and redivided. The steps of (i) coupling, (ii) saving and cataloging, and (iii) randomizing were repeated until a pentapeptide library was obtained. The four pentapeptide libraries where the N-terminal amino acid is defined were screened against the beta-endorphin antibody and quantitated via an ELISA. The amino acid of the four pools that demonstrated the most binding was then coupled to the four tetrapeptide partial libraries that had been set aside and catalogued during the split synthesis. This recursive deconvolution was repeated until the best binders were deduced. Besides the anticipated native binder, two other members of the library displayed significant binding. This recursive method of deconvolution does not use a molecular tag, requires only one split synthesis, and can be applied to the deconvolution of nonlinear small-molecule combinatorial libraries and linear oligomeric combinatorial libraries, since it is based only on the procedure of the synthesis.
Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis (2008)

The emerging field of synthetic genomics is expected to facilitate the generation of microorganisms with the potential to achieve a sustainable society. One approach towards this goal is the reduction of microbial genomes by rationally designed deletions to create simplified cells with predictable behavior that act as a platform to build in various genetic systems for specific purposes. We report a novel Bacillus subtilis strain, MBG874, depleted of 874 kb (20%) of the genomic sequence. When compared with wild-type cells, the regulatory network of gene expression of the mutant strain is reorganized after entry into the transition state due to the synergistic effect of multiple deletions, and productivity of extracellular cellulase and protease from transformed plasmids harboring the corresponding genes is remarkably enhanced. To our knowledge, this is the first report demonstrating that genome reduction actually contributes to the creation of bacterial cells with a practical application in industry. Further systematic analysis of changes in the transcriptional regulatory network of MGB874 cells in relation to protein productivity should facilitate the generation of improved B. subtilis cells as hosts of industrial protein production.
Semantic Parsing via Paraphrasing (2014)

A central challenge in semantic parsing is handling the myriad ways in which knowledge base predicates can be expressed. Traditionally, semantic parsers are trained primarily from text paired with knowledge base information. Our goal is to exploit the much larger amounts of raw text not tied to any knowledge base. In this paper, we turn semantic parsing on its head. Given an input utterance, we first use a simple method to deterministically generate a set of candidate logical forms with a canonical realization in natural language for each. Then, we use a paraphrase model to choose the realization that best paraphrases the input, and output the corresponding logical form. We present two simple paraphrase models, an association model and a vector space model, and train them jointly from question-answer pairs. Our system PARASEMPRE improves stateof-the-art accuracies on two recently released question-answering datasets.
Applications of photoacoustic sensing techniques (1986)

This paper reviews the theory and applications of photoacoustic (also called optoacoustic) methods belonging to the more general area of photothermal measurement techniques. The theory covers excitation of gaseous or condensed samples with modulated continuous light beams or pulsed light beams. The applications of photoacoustic methods include spectroscopy, monitoring deexcitation processes, probing physical properties of materials, and generating mechanical motions. Several other related photothermal methods, as well as particle-acoustics and wave-acoustics methods are also described. This review complements an earlier and narrower review [Rev. Mod. Phys. 53, 517 (1981)] that is mainly concerned with sensitive detection by pulsed photoacoustic spectroscopy in condensed matter.
Cellular Signaling and Volume Control in Stomatal Movements in Plants (2000)

▪ Abstract Stomatal guard cells are unique as a plant cell model and, because of the depth of present knowledge on ion transport and its regulation, offer a first look at signal integration in higher plants. A large body of data indicates that Ca 2+ and H + act independently, integrating with protein kinases and phosphatases, to control the gating of the K + and Cl − channels that mediate solute flux for stomatal movements. Oscillations in the cytosolic-free concentration of Ca 2+ contribute to a signaling cassette, integrated within these events through an unusual coupling with membrane voltage for solute homeostasis. Similar cassettes are anticipated to include control pathways linked to cytosolic pH. Additional developments during the last two years point to events in membrane traffic that play equally important roles in stomatal control. Research in these areas is now adding entirely new dimensions to our understanding of guard cell signaling.
Microbial Products Stimulate Human Toll-like Receptor 2 Expression through Histone Modification Surrounding a Proximal NF-κB-binding Site (2007)

Previous studies have yielded conflicting results regarding the ability of microbial products to activate TLR2 gene expression in human monocytes. In this study, we found that TLR2 mRNA was rapidly up-regulated in human monocytes treated with TLR2 and TLR4 agonists, and this corresponded to an increase in cell surface receptor levels. This induction was abrogated by actinomycin D as well as a pharmacologic inhibitor of NF-kappaB, suggesting that the TLR2 gene is transcriptionally activated via NF-kappaB. Microbial agonists were found to shift the transcription initiation site of the TLR2 gene, and sequence examination revealed a near-consensus NF-kappaB-binding element immediately upstream of this site. Electromobility shift assays confirmed that NF-kappaB bound to this putative site in vitro. However, luciferase reporter plasmids driven by the TLR2 promoter were not responsive to TLR2 agonists. Overexpression of the NF-kappaB p65 subunit was sufficient to induce expression of the endogenous TLR2 mRNA, and co-transfection of the CREB-binding protein and p300 co-activators further increased TLR2 mRNA levels. Chromatin immunoprecipitation analysis revealed that p65, CREB-binding protein, and p300 are recruited to the TLR2 promoter upon stimulation of human monocytes followed by histone hyperacetylation. Taken together, these results define a mechanism whereby histone modification and increased promoter access induce expression of human TLR2 following infection.
Myocardial triglyceride turnover and contribution to energy substrate utilization in isolated working rat hearts (1991)

The objective of this study was to determine the contribution of myocardial triglycerides to overall ATP production in isolated working rat hearts. Endogenous lipid pools were initially prelabeled (pulsed) by perfusing hearts for 60 min with Krebs-Henseleit buffer containing 1.2 mM [1-14C]palmitate. During a subsequent 60-min period (chase), hearts were perfused with either no fat, low fat (0.4 mM [9,10-3H] palmitate), or high fat (1.2 mM [9,10-3H]palmitate). All buffers contained 11 mM glucose. During the "chase," 14CO2 production (a measure of endogenous fatty acid oxidation) and 3H2O production (a measure of exogenous fatty acid oxidation) were determined. Oxidative rates of endogenous fatty acids during the chase were 279 +/- 50, 88 +/- 14, and 88 +/- 8 nmol of [14C]palmitate oxidized per g dry weight.min in the no fat, low fat, and high fat groups, respectively, compared to exogenous palmitate oxidation rates of 0, 361 +/- 68, and 633 +/- 60 nmol of [3H]palmitate/g dry weight.min, in the no fat, low fat, and high fat groups, respectively. Endogenous [14C]palmitate oxidation rates were matched by loss of [14C]palmitate from endogenous myocardial triglycerides. Overall triglyceride content decreased during the no fat and low fat chase perfusion but did not change during the high fat chase. Loss of triglyceride [14C]palmitate during the high fat chase was matched by incorporation of exogenous [3H]palmitate in triglycerides. In a second series of perfusions, three groups of hearts were perfused under similar conditions, except that unlabeled palmitate was used during the "pulse" and that 11 mM [2-3H/U-14C]glucose and unlabeled palmitate was present during the chase. During the chase, both glycolysis (3H2O production) and glucose oxidation (14CO2 production) rates were measured. Rates of glucose oxidation were inversely related to the fatty acid concentration in the perfusate (1257 +/- 158, 366 +/- 40, and 124 +/- 26 nmol of glucose oxidized per min.g dry weight in the no fat, low fat, and high fat groups, respectively), while rates of glycolysis were not significantly different between these groups. Calculation of overall ATP production from both oxidative and glycolytic sources determined that even in the presence of high concentrations of fatty acids, myocardial triglyceride turnover can provide over 11% of steady state ATP production in the aerobically perfused heart. In the absence of fatty acids, myocardial triglyceride fatty acids can become the major energy substrate of the heart.(ABSTRACT TRUNCATED AT 400 WORDS)
Detection of Epstein-Barr Virus Genome in Nasopharyngeal Carcinoma by In situ DNA Hybridization (1993)

To elucidate the possible role of Epstein-Barr virus (EBV) in nasopharyngeal carcinoma (NPC), we investigated the EBV genome in NPC by in situ DNA hybridization using radioisotope- and and biotin-labeled EBV DNA probes. The EBV genome was detected in the tumor cells in all (100%) 60 cases, irrespective of histological type, but not in the lymphocytes. Silver grains, which reflected the copy number of the EBV genome, were more abundant in the nonkeratinizing, spindle cell, and undifferentiated carcinomas than in keratinizing squamous cell carcinoma. In the keratinizing carcinoma, which was poorly differentiated in this series, the EBV genome was usually detected in anaplastic tumor cells, and not in the keratinizing areas. The sensitivity of the radioisotopic technique was superior to that of the biotinylated probe method (100 vs. 81.7%, p < 0.0003). These results suggest that EBV is etiologically related to nasopharyngeal carcinogenesis and that the differentiation of tumor cells in vivo, and probably also in vitro, may become incompatible with EBV replication.
Hunting for Better Li-Based Electrode Materials via Low Temperature Inorganic Synthesis (2009)

International audience
Anti-inflammatory Activity of IVIG Mediated Through the Inhibitory Fc Receptor (2001)

The molecular basis for the anti-inflammatory property of intravenous gamma globulin (IVIG) was investigated in a murine model of immune thrombocytopenia. Administration of clinically protective doses of intact antibody or monomeric Fc fragments to wild-type or Fcgamma receptor-humanized mice prevented platelet consumption triggered by a pathogenic autoantibody. The inhibitory Fc receptor, FcgammaRIIB, was required for protection, because disruption either by genetic deletion or with a blocking monoclonal antibody reversed the therapeutic effect of IVIG. Protection was associated with the ability of IVIG administration to induce surface expression of FcgammaRIIB on splenic macrophages. Modulation of inhibitory signaling is thus a potent therapeutic strategy for attenuating autoantibody-triggered inflammatory diseases.
Characterizaton of Short Isoforms of the Leptin Receptor in Rat Cerebral Microvessels and of Brain Uptake of Leptin in Mouse Models of Obesity (2002)

Leptin deficiency causes obesity in rodents and humans, but circulating levels of leptin are paradoxically elevated in obesity. The mechanisms underlying this leptin resistance are unknown, but may involve reduced leptin transport across the blood-brain barrier via short isoforms of the leptin receptor (Ob-R). Here, we first quantified short Ob-R mRNA expression in isolated rat cerebral microvessels constituting the blood-brain barrier and found that Ob-Ra and Ob-Rc mRNA were abundantly expressed in similar amounts. Second, brain uptake of leptin was reduced in mice lacking Ob-R. Third, brain uptake of leptin in New Zealand Obese mice, a strain that responds to central, but not peripheral, leptin, was re-duced, suggesting that their obesity is at least partly due to deficient leptin transport into the brain. Fourth, brain uptake of leptin was significantly reduced in diet-induced obese mice. Neither New Zealand Obese mice nor diet-induced obese mice exhibited significant decreases in Ob-R mRNA expression in isolated cerebral microvessels. These data support the ideas that short isoforms of Ob-R are involved in brain uptake of leptin and that impaired blood-brain barrier function contributes to the pathogenesis of obesity. However, the mechanisms by which obesity-related deficits in brain uptake of leptin occur remain to be defined.
A Novel Lipolytic Enzyme Located in the Outer Membrane of Pseudomonas aeruginosa (1999)

A lipase-negative deletion mutant of Pseudomonas aeruginosa PAO1 still showed extracellular lipolytic activity toward short-chain p-nitrophenylesters. By screening a genomic DNA library of P. aeruginosa PAO1, an esterase gene, estA, was identified, cloned, and sequenced, revealing an open reading frame of 1,941 bp. The product of estA is a 69.5-kDa protein, which is probably processed by removal of an N-terminal signal peptide to yield a 67-kDa mature protein. A molecular mass of 66 kDa was determined for (35)S-labeled EstA by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. The amino acid sequence of EstA indicated that the esterase is a member of a novel GDSL family of lipolytic enzymes. The estA gene showed high similarity to an open reading frame of unknown function located in the trpE-trpG region of P. putida and to a gene encoding an outer membrane esterase of Salmonella typhimurium. Amino acid sequence alignments led us to predict that this esterase is an autotransporter protein which possesses a carboxy-terminal beta-barrel domain, allowing the secretion of the amino-terminal passenger domain harboring the catalytic activity. Expression of estA in P. aeruginosa and Escherichia coli and subsequent cell fractionation revealed that the enzyme was associated with the cellular membranes. Trypsin treatment of whole cells released a significant amount of esterase, indicating that the enzyme was located in the outer membrane with the catalytic domain exposed to the surface. To our knowledge, this esterase is unique in that it exemplifies in P. aeruginosa (i) the first enzyme identified in the outer membrane and (ii) the first example of a type IV secretion mechanism.
Prognostic value of p53 protein expression and clinicopathological factors in infiltrating ductal carcinoma of the breast. A study of 192 patients. (2001)

The p53 gene is located on the short arm of chromosome 17. It encodes a 53-kd nuclear protein (p53) found in scant amounts in normal tissue. Mutations of the p53 gene have been reported in different human tumours. In breast cancer, it has been noted that the overexpression of p53 protein in the nucleus is an indicator of poor prognosis, although there is a high degree of variability, which may be due to different immunohistochemical techniques, varying assessment of results and the type of monoclonal antibody used. This study is an immunohistochemical analysis of p53 expression in 192 cases of infiltrating ductal carcinoma of the breast, correlating it with clinicopathological factors and the clinical course of the disease. Of all the breast-cancer tissue analysed, stains for p53 antibody were found in 87 tumours (45.3%). The results of multivariate analysis show that the independent predictors related to recurrence are tumour size, lymph-node metastasis and p53, while those related to death are necrosis, lymph-node metastasis and p53. In summary, our series showed prognostic significance between the expression of p53 and shorter survival time and disease-free interval for all patients in general as well as those who presented lymph-node metastases at the time of diagnosis.
Characterization of Aldehyde-PEG Tethered Surfaces:  Influence of PEG Chain Length on the Specific Biorecognition (2004)

A functionalized poly(ethylene glycol) (PEG) layer possessing a reactive aldehyde group at the free end of the tethered PEG chain was constructed by simple coating on the substrate, using the acetal-PEG/poly(DL-lactide) block copolymer, followed by the hydrolysis of the acetal end group by an acid treatment. The reactivity of the aldehyde group at the distal end of the PEG tethered chain was evaluated via a reductive amination using 4-amino-2,2,6,6-tetramethylpiperidinyloxy as the model compound. Further conjugation of the aldehyde group with sugar moieties has demonstrated an increased recognition ability with lectins with an increasing PEG chain length, which was attributable to the mobility of the chain end. These results provide a novel idea for highly sensitive biorecognition, suggesting a method to create highly selective biosensing surfaces that are able to prevent the undesired nonspecific adsorption of biocomponents.
Randomized, Double-blind, Placebo-controlled Trial of ALD403, an anti-CGRP peptide antibody in the prevention of chronic migraine. (S52.003) (2017)

To evaluate the efficacy and safety of ALD403, an anti-CGRP antibody, for the prevention of chronic migraine.