gebhart/patrepeval huggingface dataset:
Isolation of Recombinant Protective Helicobacter pylori Antigens (1999)

A total of seven clones producing both new and previously described Helicobacter pylori proteins were isolated from a library of H. pylori genomic DNA. The screening approach by which these proteins were detected relied on the use of antisera raised in mice vaccinated with Helicobacter felis sonicate plus cholera toxin, a regimen which protects mice from H. pylori challenge. This strategy was designed to maximize the possibility of obtaining antigens which might be capable of conferring protection from H. pylori infection. Two of the clones were shown to encode the urease enzyme and the heat shock protein HspB, which have already been identified as protective antigens. The other five clones were sequenced, protein coding regions were deduced, and these sequences were amplified by PCR for incorporation into Escherichia coli expression vectors. The proteins produced from these expression systems were purified to allow testing for protective efficacy in an H. pylori mouse model. All five proteins were able to facilitate the clearance of a challenge with H. pylori, as judged by an assay of gastric urease activity and light microscopy on stomach sections. These results clearly indicate that the screening strategy has successfully identified candidate vaccine antigens.
Direct Addition of TMS-acetylene to Aldimines Catalyzed by a Simple, Commercially Available Ir(I) Complex (2001)

A new, convenient procedure for the addition reaction of trimethylsilylacetylene to imines is described. Simply treating a solution of aldimine and trimethylsilyl acetylene with catalytic [IrCl(COD)](2) furnishes the adduct in preparatively useful yields. Interestingly, the reaction may be conducted in the absence of solvent. [reaction: see text]
Control by H-2 genes of the Th1 response induced against a foreign antigen expressed by attenuated Salmonella typhimurium (1996)

Attenuated salmonellae represent an attractive vehicle for the delivery of heterologous protective antigens to the immune system. Here, we have investigated the influence of the genetic background of the host which regulates the growth and elimination of Salmonella cells on the cellular response induced against a foreign antigen delivered by an aroA Salmonella strain. We have tested CD4+ T-cell responses (cell proliferation and cytokine production) in various mouse strains following immunization with Salmonella typhimurium SL3261 expressing a high level of the recombinant Escherichia coli MalE protein. We were able to detect a CD4+ T-cell response against the recombinant MalE protein only in a restricted number of mouse strains, whereas all mice produced good levels of anti-MalE immunoglobulin G antibodies. The Ity gene did not play a major role in these differences in T-cell responses, since both Ity-resistant and -susceptible strains of mice were found to be unresponsive to MalE delivered by recombinant salmonellae. In contrast, when B10 congenic mice were used, a correlation was established between MalE-specific T-cell unresponsiveness and H-2 genes. The discrepancies described in this paper in the ability of various strains of mice to develop an efficient Th1 response against a recombinant antigen displayed by a live Salmonella vaccine underscore the difficulties that can be encountered in the vaccination of human populations by such a strategy.
Haptic rendering (1995)

Haptic rendering is the process of computing and generating forces in response to user interactions with virtual objects. Recent efforts by our team at MIT's AI laboratory have resulted in the development of haptic interface devices and algorithms for generating the forces of interaction with virtual objects. This paper focuses on the software techniques needed to generate sensations of contact interaction and material properties. In particular, the techniques we describe are appropriate for use with the Phantom haptic interface, a force generating display device developed in our laboratory. We also briefly describe a technique for representing and rendering the feel of arbitrary polyhedral shapes and address issues related to rendering the feel of non-homogeneous materials. A number of demonstrations of simple haptic tasks which combine our rendering techniques are also described.
Caspase Cleavage of Initiation Factor 4E-Binding Protein 1 Yields a Dominant Inhibitor of Cap-Dependent Translation and Reveals a Novel Regulatory Motif (2002)

Eukaryotic initiation factor 4E (eIF4E) binding proteins (4E-BPs) regulate the assembly of initiation complexes required for cap-dependent mRNA translation. 4E-BP1 undergoes insulin-stimulated phosphorylation, resulting in its release from eIF4E, allowing initiation complex assembly. 4E-BP1 undergoes caspase-dependent cleavage in cells undergoing apoptosis. Here we show that cleavage occurs after Asp24, giving rise to the N-terminally truncated polypeptide Delta4E-BP1, which possesses the eIF4E-binding site and all the known phosphorylation sites. Delta4E-BP1 binds to eIF4E and fails to become sufficiently phosphorylated upon insulin stimulation to bring about its release from eIF4E. Therefore, Delta4E-BP1 acts as a potent inhibitor of cap-dependent translation. Using a mutagenesis approach, we identify a novel regulatory motif of four amino acids (RAIP) which lies within the first 24 residues of 4E-BP1 and which is necessary for efficient phosphorylation of 4E-BP1. This motif is conserved among sequences of 4E-BP1 and 4E-BP2 but is absent from 4E-BP3. Insulin increased the phosphorylation of 4E-BP3 but not sufficiently to cause its release from eIF4E. However, a chimeric protein that was generated by replacing the N terminus of 4E-BP3 with the N-terminal sequence of 4E-BP1 (containing this RAIP motif) underwent a higher degree of phosphorylation and was released from eIF4E. This suggests that the N-terminal sequence of 4E-BP1 is required for optimal regulation of 4E-BPs by insulin.
Metal-Enhanced Fluorescence of Phycobiliproteins from Heterogeneous Plasmonic Nanostructures (2007)

We report here the use of plasmonic metal nanostructures in the form of silver island films (SiFs) to enhance the fluorescence emission of five different phycobiliproteins. Our findings clearly show that the phycobiliproteins display up to a 9-fold increase in fluorescence emission intensity, with a maximum 7-fold decrease in lifetime when they are assembled as a monolayer above SiFs, as compared to a monolayer assembled on the surface of amine-terminated glass slides of the control sample. The study was also repeated with a thin liquid layer of the phycobiliproteins sandwiched between two glass substrates (and a SiFs and a glass substrate) clamped together. Similarly, the results show a maximum 10-fold increase in fluorescence emission intensity coupled with a 2-fold decrease in lifetime of the phycobiliproteins in the SiF-glass setup as compared to the glass control sample, implying that near-field enhancement of phycobiliprotein emission can be attained both with and without chemical linkage of the proteins to the SiFs. Hence, our results clearly show that metal-enhanced fluorescence (MEF) can potentially be employed to increase the sensitivity and detection limit of the plethora of bioassays that employ phycobiliproteins as fluorescence labels, such as in fluoro-immunoassays where the assay can be tethered on the surface of SiFs, and also in flow cytometry where analytes in the liquid phase could potentially flow through channels coated with SiFs without actually being attached to the silver.
IL2-PE664Glu, a new chimeric protein cytotoxic to human-activated T lymphocytes. (1990)

To produce a molecule that will kill activated T cells as well as lymphomas and leukemias expressing interleukin 2 (IL2) receptors, we have created a recombinant chimeric protein in which IL2 is attached in peptide linkage to a truncated mutant form of Pseudomonas exotoxin (PE) (Lorberboum-Galski, H., FitzGerald, D.J.P., Chandhary, V.K., Adhya, S., and Pastan, I. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1922-1926). Although this molecule was very active on rodent cells, it had lower activity on some human cell types. A new chimeric protein termed IL2-PE664Glu has been constructed that is extremely toxic to both phytohemagglutinin blasts and mixed leukocyte reaction blasts prepared from monkey and human lymphocytes. The chimeric gene encoding this protein was constructed by fusing a cDNA clone for human interleukin 2 to the 5' end of a mutated cDNA encoding a full-length PE molecule. Four amino acids in domain I of PE were changed thus decreasing its nonspecific toxicity. IL2-PE664Glu is a much more active cytotoxic molecule for primate and human-activated T cells than IL2-PE40 which is a chimeric protein that was found to be an effective immunosuppressive agent in rodent models. Our results indicate that IL2-PE664Glu should be evaluated as an immunosuppressive agent for the treatment of human immune disorders in which activated T cells expressing the IL2 receptor are prominent.
Biochemical and functional analysis of an adenovirus-based ligand complex for gene transfer (1994)

Ligand-mediated approaches to gene transfer offer an alternative to viral vectors for both in vivo and in vitro applications. Although a significant percentage of the plasmid-based DNA complex is lost to lysosomal degradation following receptor-mediated endocytosis, simultaneous infection with adenovirus has been shown to increase the level of transgene expression [Curiel, Agarwal, Wagner and Cotten (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 8850-8854; Wagner, Zatloukal, Cotten, Kirlappos, Mechtler, Curiel and Birnstiel (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 6099-6103]. In this study we describe an adenovirus-based ligand complex where the plasmid DNA, polycation-ligand conjugate and adenovirus are contained within a single particle structure. At the core of the transfection particle is a replication-defective recombinant adenovirus encoding a cDNA minigene for human placenta alkaline phosphatase that was chemically modified with poly(L-lysine) (Ad-pLys). Electron microscopy of an adenovirus-based ligand complex formed by successively adding plasmid DNA and an asialo-orosomucoid-poly(L-lysine) conjugate to Ad-pLys revealed structures that appeared as intact viral particles coated with a dense biomolecular layer. Adenovirus-based ligand complexes containing either a luciferase or beta-galactosidase reporter plasmid were shown to efficiently deliver the plasmid transgene to cells that express the hepatic asialoglycoprotein receptor. Furthermore, the poly(L-lysine) modification greatly reduced the infectivity potential of the virus without causing a concomitant loss of augmented gene transfer. As an alternative to infectious virions, incomplete products of viral assembly were also considered as a source for endosomalytic activity. However, these defective virions were unable to significantly enhance plasmid transgene delivery.
SorLA/LR11 Regulates Processing of Amyloid Precursor Protein via Interaction with Adaptors GGA and PACS-1 (2007)

SorLA has been recognized as a novel sorting receptor that regulates trafficking and processing of the amyloid precursor protein (APP) and that represents a significant risk factor for sporadic Alzheimer disease. Here, we investigated the cellular mechanisms that control intracellular trafficking of sorLA and their relevance for APP processing. We demonstrate that sorLA acts as a retention factor for APP in trans-Golgi compartments/trans-Golgi network, preventing release of the precursor into regular processing pathways. Proper localization and activity of sorLA are dependent on functional interaction with GGA and PACS-1, adaptor proteins involved in protein transport to and from the trans-Golgi network. Aberrant targeting of sorLA to the recycling compartment or the plasma membrane causes faulty APP trafficking and imbalance in non-amyloidogenic and amyloidogenic processing fates. Thus, our findings identified altered routing of sorLA as a major cellular mechanism contributing to abnormal APP processing and enhanced amyloid beta-peptide formation.
The therapeutic potential of gut hormone peptide YY3-36 in the treatment of obesity (2005)

Many peptides are synthesised and released from the gastrointestinal tract. Although their roles in the regulation of gastrointestinal function have been known for some time, it has become increasingly evident that they also influence eating behaviour. Peptide YY (PYY) is released postprandially from gastrointestinal L-cells with glucagon-like peptide 1 (GLP-1) and oxyntomodulin. Following peripheral administration of PYY3-36, the circulating form of PYY, to mouse, rat or human there is marked inhibition of food intake. Obese subjects have lower basal fasting PYY levels and have a smaller postprandial rise. However, obesity does not appear to be associated with resistance to PYY (as it is with leptin) and exogenous infusion of PYY3-36 results in a reduction in food intake by 30% in an obese group and 31% in a lean group at a buffet meal. Overall PYY significantly reduced 24-h caloric intake in both obese (16.5%) and lean groups (23.5%). Obesity is the current major cause of premature death in the UK, killing almost 1000 people a week. Worldwide its prevalence is accelerating. The administration of the naturally occurring gut hormone may offer a long-term therapeutic approach to weight control. Here, the therapeutic potential of PYY is considered.
Toward Reliable Gold Nanoparticle Patterning On Self-Assembled DNA Nanoscaffold (2008)

Assembly of gold nanoparticles (AuNP) into designer architectures with reliablity is important for nanophotonics and nanoelectronics applications. Toward this goal we present a new strategy to prepare AuNPs monofunctionalized with lipoic acid modified DNA oligos. This strategy offers increased bonding strength between DNA oligos and AuNP surface. These conjugates are further selectively mixed with other DNA strands and assembled into fixed sized DNA nanostructures carring a discrete number of AuNPs at desired positions. Atomic force microscopy imaging reveals a dramatically improved yield of the AuNPs on DNA tile structure compared to the ensembles using monothiolate AuNP-DNA conjugates.
Antimicrobial Action of Citrus Oils (1967)

SUMMARY— The inhibitory effect of essential oils of orange and lemon oil and the antibiotics tylosin and nisin was tested on bacteria and fungi in nutrient media. Though the degree of inhibition varied with the culture, orange oil was a more effective antimicrobial agent than lemon oil. All other conditions being identical, 2, 000 ppm of orange oil had an effect similar to 10 ppm of tylosin, on all the gram‐positive cultures tried, including the spores of Bacillus subtilis. Moreover, orange oil was the only additive that showed inhibition of growth of the gram‐negative cultures, excepting Serratia marcescens. Yeasts, in general, were more sensitive than bacteria to orange oil, the effective dose being 500 ppm, at a cell concentration of 1 million/ml. This was a definite advantage over the antibiotics, which had no action on fungi. Though not so sensitive as the yeasts, the molds were also suppressed by orange oil at 2, 000 ppm. The possibility of using orange oil as a preservative in foods is indicated.
Differences in outcome according to Clostridium difficile testing method: a prospective multicentre diagnostic validation study of C difficile infection (2013)

We noted no increase in mortality when toxigenic C difficile alone was present. Toxin (cytotoxin assay) positivity correlated with clinical outcome, and so this reference method best defines true cases of C difficile infection. A new diagnostic category of potential C difficile excretor (cytotoxigenic culture positive but cytotoxin assay negative) could be used to characterise patients with diarrhoea that is probably not due to C difficile infection, but who can cause cross-infection.
Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions (2018)

The gut microbiota has an important role in the gut barrier, inflammation and metabolic functions. Studies have identified a close association between the intestinal barrier and metabolic diseases, including obesity and type 2 diabetes (T2D). Recently, Akkermansia muciniphila has been reported as a beneficial bacterium that reduces gut barrier disruption and insulin resistance. Here we evaluated the role of A. muciniphila-derived extracellular vesicles (AmEVs) in the regulation of gut permeability. We found that there are more AmEVs in the fecal samples of healthy controls compared with those of patients with T2D. In addition, AmEV administration enhanced tight junction function, reduced body weight gain and improved glucose tolerance in high-fat diet (HFD)-induced diabetic mice. To test the direct effect of AmEVs on human epithelial cells, cultured Caco-2 cells were treated with these vesicles. AmEVs decreased the gut permeability of lipopolysaccharide-treated Caco-2 cells, whereas Escherichia coli-derived EVs had no significant effect. Interestingly, the expression of occludin was increased by AmEV treatment. Overall, these results imply that AmEVs may act as a functional moiety for controlling gut permeability and that the regulation of intestinal barrier integrity can improve metabolic functions in HFD-fed mice.
Cyclohexanecarboxyl-Coenzyme A (CoA) and Cyclohex-1-ene-1-Carboxyl-CoA Dehydrogenases, Two Enzymes Involved in the Fermentation of Benzoate and Crotonate in Syntrophus aciditrophicus (2013)

The strictly anaerobic Syntrophus aciditrophicus is a fermenting deltaproteobacterium that is able to degrade benzoate or crotonate in the presence and in the absence of a hydrogen-consuming partner. During growth in pure culture, both substrates are dismutated to acetate and cyclohexane carboxylate. In this work, the unknown enzymes involved in the late steps of cyclohexane carboxylate formation were studied. Using enzyme assays monitoring the oxidative direction, a cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA)-forming cyclohexanecarboxyl-CoA (ChCoA) dehydrogenase was purified and characterized from S. aciditrophicus and after heterologous expression of its gene in Escherichia coli. In addition, a cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA)-forming Ch1CoA dehydrogenase was characterized after purification of the heterologously expressed gene. Both enzymes had a native molecular mass of 150 kDa and were composed of a single, 40- to 45-kDa subunit; both contained flavin adenine dinucleotide (FAD) as a cofactor. While the ChCoA dehydrogenase was competitively inhibited by Ch1CoA in the oxidative direction, Ch1CoA dehydrogenase further converted the product Ch1,5CoA to benzoyl-CoA. The results obtained suggest that Ch1,5CoA is a common intermediate in benzoate and crotonate fermentation that serves as an electron-accepting substrate for the two consecutively operating acyl-CoA dehydrogenases characterized in this work. In the case of benzoate fermentation, Ch1,5CoA is formed by a class II benzoyl-CoA reductase; in the case of crotonate fermentation, Ch1,5CoA is formed by reversing the reactions of the benzoyl-CoA degradation pathway that are also employed during the oxidative (degradative) branch of benzoate fermentation.
Fusarium solani on Soybean Roots: Nomenclature of the Causal Agent of Sudden Death Syndrome and Identity and Relevance of F. solani form B (1997)

Two morphological forms of Fusarium solani pathogenic on soybean, forms A and B, were further characterized and distinguished from other fungi. Questions regarding their identity were addressed. Soybean plants grown in the field and in a growth chamber were inoculated with Fusarium solani form A and F. solani f. sp. phaseoli. F. solani form A incited leaf symptoms typical of sudden death syndrome; F. solani f. sp. phaseoli did not. It was concluded that the two fungi are different and distinguishable on the basis of host specialization and the types of symptoms they incite on soybean. F. solani form A, the causal agent of sudden death syndrome, was designated F. solani (Mart.) Sacc. f. sp. glycines form. nov. Cultural and morphological characteristics of F. solani form B, the cause of seedling disease and root rot of soybean, and Plectosphaerella cucumerina were compared to determine the validity of a report indicating that they were conspecific. Results demonstrated that F. solani form B and P. cucumerina are distinctly different and not conspecific. The relevance of identifying and recognizing the two F. solani forms as separate and distinct members of the F. solani pathogen complex on soybean is discussed.
Duchenne muscular dystrophy: current cell therapies (2015)

Duchenne muscular dystrophy is a genetically determined X-linked disease and the most common, progressive pediatric muscle disorder. For decades, research has been conducted to find an effective therapy. This review presents current therapeutic methods for Duchenne muscular dystrophy, based on scientific articles in English published mainly in the period 2000 to 2014. We used the PubMed database to identify and review the most important studies. An analysis of contemporary studies of stem cell therapy and the use of granulocyte colony-stimulating factor (G-CSF) in muscular dystrophy was performed.
Quantitative selection and parallel characterization of aptamers (2013)

Significance The comprehensive functional mapping of the human proteome will require access to high-quality affinity reagents that specifically bind to their respective proteins with high affinities. Unfortunately, currently available antibodies can only target a small fraction of the proteome, and their affinity and specificity can vary considerably for each protein. Thus there is an urgent need for novel technologies capable of generating alternative, synthetic affinity reagents in a scalable and economical manner. Toward this end, we report a unique screening system (termed the “Quantitative Parallel Aptamer Selection System”) that can accelerate discovery of high-quality aptamer reagents by enabling simultaneous measurements of binding affinity ( K d ) and specificity for thousands of aptamers in parallel.
Association of Fetal Hormone Levels with Stem Cell Potential: Evidence for Early Life Roots of Human Cancer (2005)

Intrauterine and perinatal factors have been linked to risk of childhood leukemia, testicular cancer, and breast cancer in the offspring. The pool of stem cells in target tissue has been suggested as a critical factor linking early life exposures to cancer. We examined the relation between intrauterine hormone levels and measurements of stem cell potential in umbilical cord blood. Cord blood donors were 40 women, ages >/=18 years, who delivered, from August 2002 to June 2003, a singleton birth after a gestation of at least 37 weeks. We assayed plasma concentrations of estradiol, unconjugated estriol, testosterone, progesterone, prolactin, sex hormone binding globulin, insulin-like growth factor-I (IGF-I), and IGF binding protein-3. For stem cell potential, we measured concentrations of CD34(+) and CD34(+)CD38(-) cells and granulocyte-macrophage colony-forming unit (CFU-GM). We applied linear regression analysis and controlled for maternal and neonatal characteristics. We found strong positive associations between IGF-I and stem cell measures, 1 SD increase in IGF-I being associated with a 41% increase in CD34(+) (P = 0.008), a 109% increase in CD34(+)CD38(-) (P = 0.005), and a 94% increase in CFU-GM (P = 0.01). Similar associations were observed for IGF binding protein-3. Among steroid hormones, estriol and testosterone were significantly positively associated with CD34(+) and CFU-GM. These findings indicate that levels of growth factors and hormones are strongly associated with stem cell potential in human umbilical cord blood and point to a potential mechanism that may mediate the relationship between in utero exposure to hormones and cancer risk in the offspring.