gebhart/patrepeval huggingface dataset:
Purification of the regulatory protein AlgR1 and its binding in the far upstream region of the algD promoter in Pseudomonas aeruginosa. (1991)

A regulatory protein AlgR1, previously suggested to be a member of a two-component sensory transduction system because of its homology to OmpR and NtrC and its ability to allow activation of the algD promoter under conditions of high osmolarity, has been hyperproduced in Escherichia coli after deletion of the upstream region including part of the Shine-Dalgarno sequence of the algR1 gene and its subsequent cloning under the tac promoter. The AlgR1 protein is purified as a monomer, and the sequence of the nine N-terminal amino acids of the monomer matches with that predicted from the DNA sequence of the algR1 gene. The purified AlgR1 protein binds to two separate DNA fragments of the algD upstream region. DNase protection experiments identify these two DNA segments as 14-mer sequences centered at -382 and -458 regions, which contain a common CCGT-TCGTC sequence in them. While the presence of at least one AlgR1 binding site is important for the activation of the algD promoter, the presence of both of the binding sites in the upstream region leads to a higher level of activation.
Recognition of insulin-like-growth-factor-binding proteins in serum and amniotic fluid by an antiserum against a low-molecular-mass insulin-like-growth-factor-inhibitor/binding protein (1990)

An antiserum (R8) raised against a purified specific low-Mr (16,000-18,000) insulin-like-growth-factor (IGF)-inhibitor/binding protein, which is immunologically related to the native growth hormone (GH)-dependent Mr-150,000 IGF-binding protein in serum, has been used to probe a possible additional relationship to the predominant non-GH-dependent IGF-binding protein (Mr approximately 30,000) of human amniotic fluid. Amniotic-fluid fractions and an IGF-inhibitory fraction of serum were analysed by covalent cross-linking, ligand-blotting and immunoblotting techniques. Western blotting of the serum fraction using the R8 antiserum gave five immunoreactive (ir) bands, of which at least three (Mr 38,000, 34,000 and 23,000) possessed IGF-binding activity, as indicated by ligand (125I-IGF-I) blotting. Western blotting of two differently prepared amniotic-fluid fractions, which both showed potent IGF-inhibitory bioactivity, gave several (Mr range 14,500-73,000) ir bands, of which two (Mr 28,000 and 17,000) were most prominent. Ligand-blotting analysis gave a single intensely labelled band at Mr 28,000, consistent with the major presence of the Mr-28,000-30,000 amniotic-fluid IGF-binding protein. Covalent cross-linking of the amniotic-fluid fractions to 125I-IGF-I gave three specifically cross-linked complexes (Mr 36,000, 32,000 and 23,000), which, assuming a 1:1 binding stoichiometry with IGF (Mr 7500), represent binding proteins of Mr 28,500, 24,500 and 15,500 respectively. The Mr-15,500 binding protein, very similar to the Mr-17,000 ir band, in all likelihood represents the IGF-inhibitor protein. Our results indicate that inhibitor-sized binding proteins and IGF-inhibitor bioactivity are present in human amniotic fluid, and that the IGF-inhibitor protein (Mr 16,000) and amniotic-fluid IGF-binding protein (Mr 28,000) are immunologically related. Since the IGF-inhibitor protein is also immunologically and structurally related to the native, GH-dependent, Mr-150,000 binding protein in serum, our data suggest a heretofore-unrecognized immunological similarity between the Mr-150,000 binding protein and the amniotic-fluid binding protein and its serum analogue, the Mr approximately 30,000, non-GH-dependent, binding protein.
Light Activated Patterning of Dye-Labeled Molecules on Surfaces (2003)

This Communication describes a novel method for patterning proteins, ligands, or other organic/inorganic species onto solid substrates. The process works by linking the moiety of interest to a fluorophore that can be subsequently photobleached and bound to the interface. The technique can be performed in aqueous solution and allows several species to be addressed onto the surface simultaneously by using different frequencies of light. Because the method can be used with fluorophores excited by visible light, shorter and more damaging wavelengths can be avoided.
[Limited but potential efficacy by graft-versus-leukemia (GVL) for Pro T-ALL]. (2008)

We present a 22-year-old male diagnosed with pro T-acute lymphoblastic leukemia (ALL). His laboratory test showed 181,900/microL of WBC complicated with lymphoadenopathy, pleural effusion, pericardial effusion and hepatosplenomegaly at the onset. Flow cytometry analysis of the leukemic cells showed cCD3+, CD7+, CD2+, CD1a-, CD3-, CD5-, CD4-, CD8-, CD34+, and HLA-DR+ as a pro T-cell phenotype. The patient was treated with induction therapy followed by 3 courses of consolidation therapy and achieved his first complete remission. He underwent up-front stem cell transplantation (SCT) from an HLA-full matched sibling, with early relapse just before transplantation. The conditioning regimen consisted of fludarabine (100 mg/m2) and melphalan (180 mg/m2). He relapsed with an extramedullary mass (gingival, testis, and femoral muscles) 1 year after transplantation. Since bone marrow involvement was not apparent, he received involved field radiation therapy (25.2 Gy/14 frequencies) in each mass. Six months after extramedullary relapse, bone marrow relapse occurred, and the patient died of sepsis due to Pseudomonas aeruginosa during re-induction therapies. Based on the immature T cell phenotype frequently with myeloid markers, a graft-versus- leukemic effect might be expected after allogeneic SCT for Pro T-ALL and a positive indication of SCT for this disease should be considered.
cGAS and Ifi204 Cooperate To Produce Type I IFNs in Response to Francisella Infection (2015)

Type I IFN production is an important host immune response against viral and bacterial infections. However, little is known about the ligands and corresponding host receptors that trigger type I IFN production during bacterial infections. We used a model intracellular pathogen, Francisella novicida, to begin characterizing the type I IFN response to bacterial pathogens. F. novicida replicates in the cytosol of host cells and elicits a robust type I IFN response that is largely TLR independent, but is dependent on the adapter molecule STING, suggesting that the type I IFN stimulus during F. novicida infection is cytosolic. In this study, we report that the cytosolic DNA sensors, cyclic GMP-AMP synthase (cGAS) and Ifi204, are both required for the STING-dependent type I IFN response to F. novicida infection in both primary and immortalized murine macrophages. We created cGAS, Ifi204, and Sting functional knockouts in RAW264.7 macrophages and demonstrated that cGAS and Ifi204 cooperate to sense dsDNA and activate the STING-dependent type I IFN pathway. In addition, we show that dsDNA from F. novicida is an important type I IFN stimulating ligand. One outcome of cGAS-STING signaling is the activation of the absent in melanoma 2 inflammasome in response to F. novicida infection. Whereas the absent in melanoma 2 inflammasome is beneficial to the host during F. novicida infection, type I IFN signaling by STING and IFN regulatory factor 3 is detrimental to the host during F. novicida infection. Collectively, our studies indicate that cGAS and Ifi204 cooperate to sense cytosolic dsDNA and F. novicida infection to produce a strong type I IFN response.
Magnetic Resonance Neurography (1992)

We have made cross-sectional image "neurograms" in which peripheral nerve has a greater signal intensity than that of other tissue. Neurographic images of the rabbit forelimb were obtained using a spin-echo magnetic resonance imaging (MRI) technique that combines fat suppression and diffusion weighting. After fat suppression the nerve shows up in relative isolation and is brighter than the surrounding tissue due to its longer T2 relaxation time of approximately 50 ms compared to approximately 27 ms for muscle. The addition of pulsed gradients for diffusion weighting of the MR signal further enhances the intensity of the nerve signal relative to that of surrounding muscle tissue. The greater diffusional anisotropy of nerve tissue (D parallel/D perpendicular = 3.1) compared to that of muscle (D parallel/D perpendicular = 1.9) allows further enhancement of the nerve by a subtraction of two diffusion-weighted images, one with the gradients oriented parallel and one with the gradients oriented perpendicular to the nerve orientation. We show that by manipulation of the MRI parameters, either echo time or pulsed gradient strength, the nerves can be made to show up as the most intense feature. This verifies the feasibility of generating three-dimensional "neurographic" images, analogous to angiograms, but which demonstrate the peripheral nerve tracts in apparent isolation.
Solubilization Of Nimesulide; Use Of Co-Solvents (2003)

Solubility of nimesulide in various solvents and solvent-co-solvent mixtures was determined in relatlon to the development of parenteral formulations. Solubility was low in aqueous solvents. Solubility Increased on solubilization of drug in semi-polar solvents and non-ionic surfactants. Solubility increased drastically (>70 mg/rnl) when polyethylene glycol 300 and polyethylene glycol 400 were used as solvents. The minimum concentration of polyethylene glycol required for solubility to be greater than 50 mg/ml was found to be 80%. It was recommended that solvent containing 90% polyethylene glycol and 10% co-solvent (alcohol, propylene glycol,Tween 80 and Brij 30) with solubility greater than 65 mg/ml can be used in parenteral formulations of nimesuilde. Alternatively 8% co-solvent can be mixed with 2% benzyl alcohol which acts as an anaesthetic agent.
TEWI Comparison of R744 and R134a Systems for Mobile Air Conditioning (1999)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper describes the comparison of the total equivalent warming impact (TEWI) of R744 and R134a mobile a/c systems. TEWI calculations were performed using experimental results obtained at typical idling and driving conditions instead of model predictions as in the published literature. The results show that for most of the regions in Europe, Japan and the US, the R744 system has a much lower TEWI than the R134a system that was tested.&lt;/div&gt;&lt;/div&gt;
A Rapid and Nondestructive Method for Microbiological Testing in Pharmaceutical Manufacturing (2006)

Improving the performance of pharmaceutical microbiological quality control (QC) testing is often included in the goals of the FDA’s Process Analytical Technology initiative. That a nineteenth century microbiologist would recognize the methods used by twenty-first century pharmaceutical manu facturers to detect and enumerate microbial contaminants, however, testifies to the glacial pace of technical change in microbiological QC. The persistence of the dominant detection technology, microbial culture, stems in large part from its numerous advantages. Culture tests use low-cost materials, minimize regulatory risk (they are the regulatory “gold standard”), demand low-level skills, deliver high sensitivity for culturable cells, yield pure cultures that can be used to identify contaminating microbes, and are useful for all of the key microbiological QC tests. But culture methods also bring some expensive drawbacks. Slow testing turnaround times (due to extensive cellular replication required for visual detection) are particularly costly to the industry. Lengthy testing cycles increase the costs of held inventory, the amount of discarded product, and the time required to get manufacturing plants up and running after a contamination event. Traditional culture methods can be subjective and require manual processing, laborious documentation, and cumbersome procedures to ensure regulatory compliance.
A review of current large‐scale mouse knockout efforts (2010)

After the successful completion of the human genome project (HGP), biological research in the postgenome era urgently needs an efficient approach for functional analysis of genes. Utilization of knockout mouse models has been powerful for elucidating the function of genes as well as finding new therapeutic interventions for human diseases. Gene trapping and gene targeting are two independent techniques for making knockout mice from embryonic stem (ES) cells. Gene trapping is high-throughput, random, and sequence-tagged while gene targeting enables the knockout of specific genes. It has been about 20 years since the first gene targeting and gene trapping mice were generated. In recent years, new tools have emerged for both gene targeting and gene trapping, and organizations have been formed to knock out genes in the mouse genome using either of the two methods. The knockout mouse project (KOMP) and the international gene trap consortium (IGTC) were initiated to create convenient resources for scientific research worldwide and knock out all the mouse genes. Organizers of KOMP regard it as important as the HGP. Gene targeting methods have changed from conventional gene targeting to high-throughput conditional gene targeting. The combined advantages of trapping and targeting elements are improving the gene trapping spectrum and gene targeting efficiency. As a newly-developed insertional mutation system, transposons have some advantages over retrovirus in trapping genes. Emergence of the international knockout mouse consortium (IKMP) is the beginning of a global collaboration to systematically knock out all the genes in the mouse genome for functional genomic research.
Th17, intestinal microbiota and the abnormal immune response in the pathogenesis of celiac disease. (2015)

Celiac disease (CD) is an autoimmune enteropathy induced by the ingestion of gluten in genetically predisposed individuals who carry the HLA-DQ2 or -DQ8 alleles. The immune response is abnormal in celiac disease with small intestinal epithelial damage via CD8+CD4- intraepithelial lymphocytes. The etiology is multifactorial involving genetic and environmental factors, an abnormal immune response, and intestinal dysbiosis. The innate and acquired T-cell mediated immunity play important roles in the pathogenesis of this disease, particularly CD4+ Th17 cells, which have been shown to have critical functions in host defense against bacterial pathogens and in the inflammatory responses to deamidated gluten peptides. We review what is known about the interaction between immune system and intestinal microbiota in the pathogenesis of celiac disease.
Pharmacophore Reassignment for Induction of the Immunosurveillance Cytokine TRAIL (2014)

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is an immunosurveillance cytokine that kills cancer cells but demonstrates little toxicity against normal cells. While investigating the TRAIL-inducing imidazolinopyrimidinone TIC10, a misassignment of its active structure was uncovered. Syntheses of the two isomers, corresponding to the published and reassigned structures, are reported. The ability of each to induce TRAIL expression in macrophages was investigated and it was found that only the compound corresponding to the reassigned structure shows the originally reported activity; the compound corresponding to the published structure is inactive. Importantly, this structural reassignment has furnished a previously unknown antitumor pharmacophore.
An assessment of the portability of ancestry informative markers between human populations (2009)

We find that BritAIMs are generally not useful to distinguish between continental groups or within continental groups distantly related to Britain. Moreover, our analyses suggest that the portability of AIMs across geographical scales (e.g. between Europe and Britain) can be limited and should therefore be taken into consideration in the design and interpretation of genetic association studies.
Sodium channels gone wild: resurgent current from neuronal and muscle channelopathies (2010)

Voltage-dependent sodium channels are the central players in the excitability of neurons, cardiac muscle, and skeletal muscle. Hundreds of mutations in sodium channels have been associated with human disease, particularly genetic forms of epilepsy, arrhythmias, myotonia, and periodic paralysis. In this issue of the JCI, Jarecki and colleagues present evidence suggesting that many such mutations alter the gating of sodium channels to produce resurgent sodium current, an unusual form of gating in which sodium channels reopen following an action potential, thus promoting the firing of another action potential (see the related article beginning on page 369). The results of this study suggest a widespread pathophysiological role for this mechanism, previously described to occur normally in only a few types of neurons.
Gold Nanoparticles Decorated with Oligo(ethylene glycol) Thiols:  Protein Resistance and Colloidal Stability (2007)

The interactions between proteins and gold colloids functionalized with protein-resistant oligo(ethylene glycol) (OEG) thiol, HS(CH2)11(OCH2CH2)6OMe (EG6OMe), in aqueous solution have been studied by small-angle X-ray scattering (SAXS) and UV-vis spectroscopy. The mean size, 2R, and the size distribution of the decorated gold colloids have been characterized by SAXS. The monolayer-protected gold colloids have no correlations due to the low volume fraction in solution and are stable in a wide range of temperatures (5-70 degrees C), pH (1.3-12.4), and ionic strength (0-1.0 M). In contrast, protein (bovine serum albumin) solutions with concentrations in the range of 60-200 mg/mL (4.6-14.5 vol %) show a pronounced correlation peak in SAXS, which results from the repulsive electrostatic interaction between charged proteins. These protein interactions show significant dependence on ionic strength, as would be expected for an electrostatic interaction (Zhang et al. J. Phys. Chem. B 2007, 111, 251). For a mixture of proteins and gold colloids, the protein-protein interaction changes little upon mixing with OEG-decorated gold colloids. In contrast, the colloid-colloid interaction is found to be strongly dependent on the protein concentration and the size of the colloid itself. Adding protein to a colloidal solution results in an attractive depletion interaction between functionalized gold colloids, and above a critical protein concentration, c*, the colloids form aggregates and flocculate. Adding salt to such mixtures enhances the depletion effect and decreases the critical protein concentration. The aggregation is a reversible process (i.e., diluting the solution leads to dissolution of aggregates). The results also indicate that the charge of the OEG self-assembled monolayer at a curved interface has a rather limited effect on the colloidal stabilization and the repulsive interaction with proteins.
Anti-synthetic peptide antibody reacting at the fusion junction of deletion-mutant epidermal growth factor receptors in human glioblastoma. (1990)

We have investigated human gliomas that amplify and rearrange the epidermal growth factor receptor gene, with generation of an in-frame deletion mutation of 802 nucleotides in the external domain. This in-frame deletion mutation generates a local amino acid sequence at the fusion junction of what normally were distant polypeptide sequences in the intact epidermal growth factor receptor. This 14-amino acid peptide was chemically synthesized, coupled to keyhole limpet hemocyanin, and used as an immunogen in rabbits. The elicited antibody reacted specifically with the fusion peptide in ELISA. The anti-fusion junction peptide antibody was purified by passage of the antiserum over a peptide affinity column with acidic elution. The purified antibody selectively bound the glioma deletion mutant as compared to the intact epidermal growth factor receptor as assessed by immunocytochemistry, immunofluorescence, immunoprecipitation with gel electrophoresis, and binding experiments using radioiodinated antibody. These data indicate that it is feasible to generate site-specific anti-peptide antibodies that are highly selective for mutant proteins in human tumors. The anti-peptide antibody described here, and other mutation site-specific antibodies, should be ideal candidates for tumor immunoimaging and immunotherapy.
Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis (2011)

With the emergence and spread of multidrug resistant bacteria, effective methods to eliminate both planktonic bacteria and those embedded in surface-attached biofilms are needed. Electric currents at μA-mA/cm2 range are known to reduce the viability of bacteria. However, the mechanism of such effects is still not well understood. In this study, Bacillus subtilis was used as the model Gram-positive species to systematically investigate the effects of electrochemical currents on bacteria including the morphology, viability, and gene expression of planktonic cells, and viability of biofilm cells. The data suggest that weak electrochemical currents can effectively eliminate B. subtilis both as planktonic cells and in biofilms. DNA microarray results indicate that the genes associated with oxidative stress response, nutrient starvation, and membrane functions were induced by electrochemical currents. These findings suggest that ions and oxidative species generated by electrochemical reactions might be important for the killing effects of these currents.
Recent developments in multidimensional multirate systems (1993)

The authors review the fundamentals of multidimensional (M-D) multirate signal processing and present recent and new developments in M-D multirate systems. A method is presented for deriving all parallelepiped-shaped filters in M-D multirate applications from an appropriate 1-D filter. It is shown that the generalized-pseudocirculant property is necessary and sufficient for an M-D maximally decimated filter-bank system to be free from aliasing. It is shown how the Smith form, Smith-McMillan form, and the least common multiples of integer matrices can resolve many nonseparable M-D multirate problems. The condition for alias-free decimation and the multistage design of decimation systems are mentioned.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Superlattice of Octanethiol-Protected Copper Nanoparticles (2006)

The synthesis and spectroscopic characterizations of size-controlled Cu nanoparticles forming self-assembled 2D superlattices with hexagonal packing are described. The scanning electron microscopy (SEM), nuclear magnetic resonance (NMR), thermal gravimetric analysis (TGA), and electron spectroscopy for chemical analysis (ESCA) techniques were used to characterize the octanethiol-protected copper nanoparticles.
Long‐Term Safety and Efficacy of the RTS,S/AS02A Malaria Vaccine in Mozambican Children (2009)

These results show evidence that RTS,S/AS02A maintained protection during the 45-month surveillance period, and they highlight the feasibility of developing an effective vaccine against malaria. In combination with other malaria-control measures, such a vaccine could greatly contribute to reducing the intolerable global burden of this disease. Trial registration. ClinicalTrials.gov identifiers NCT00197041 and NCT00323622 .