gebhart/patrepeval huggingface dataset:
Interleukin-5–producing group 2 innate lymphoid cells control eosinophilia induced by interleukin-2 therapy (2014)

Interleukin (IL)-2 promotes regulatory T-cell development and function, and treatment with IL-2 is being tested as therapy for some autoimmune diseases. However, patients receiving IL-2 treatment also experience eosinophilia due to an unknown mechanism. Here, we show that patients receiving low-dose IL-2 have elevated levels of serum IL-5, and this correlates with their degree of eosinophilia. In mice, low-dose IL-2-anti-IL-2 antibody complexes drove group 2 innate lymphoid cells (ILC2) to produce IL-5 and proliferate. Using genetic approaches in mice, we demonstrate that activation of ILC2 was responsible for the eosinophilia observed with IL-2 therapy. These observations reveal a novel cellular network that is activated during IL-2 treatment. A better understanding of the cross talk between these cell populations may lead to more effective targeting of IL-2 to treat autoimmune disease.
Improving tangential resolution with a modified delay-and-sum reconstruction algorithm in photoacoustic and thermoacoustic tomography (2014)

Spatial resolution in photoacoustic and thermoacoustic tomography is ultrasound transducer (detector) bandwidth limited. For a circular scanning geometry the axial (radial) resolution is not affected by the detector aperture, but the tangential (lateral) resolution is highly dependent on the aperture size, and it is also spatially varying (depending on the location relative to the scanning center). Several approaches have been reported to counter this problem by physically attaching a negative acoustic lens in front of the nonfocused transducer or by using virtual point detectors. Here, we have implemented a modified delay-and-sum reconstruction method, which takes into account the large aperture of the detector, leading to more than fivefold improvement in the tangential resolution in photoacoustic (and thermoacoustic) tomography. Three different types of numerical phantoms were used to validate our reconstruction method. It is also shown that we were able to preserve the shape of the reconstructed objects with the modified algorithm.
Functional polymorphism of each of the two HLA-DR beta chain loci demonstrated with antigen-specific DR3- and DRw52-restricted T cell clones. (1988)

HLA-DR3- and HLA-DRw52-associated functional polymorphism was investigated with selected tetanus toxoid (TT)-specific T cell clones. We have shown earlier that HLA-DR antigens are encoded by two distinct loci, DR beta I and DR beta III. The alloantigenic determinant(s) defined by the serological HLA-DR3 specificity map to the former, while the supratypic HLA-DRw52 determinants map to DR beta III. Furthermore, we have recently recognized by DNA sequencing three alleles of HLA-DRw52 at locus DR beta III, referred to as 52 a, b, and c. Our objective was to correlate the pattern of T cell restriction with the gene products of individual DR beta chain loci and with the three newly described alleles of locus DR beta III. Among the selected T cell clones, 5 reacted exclusively when TT was presented by HLA-DR3+ APCs (TT-DR3-APC). In contrast, two T cell clones were stimulated by TT-DRw52-APC. More specifically, these two T cell clones (Clones 10 and 16) were stimulated by different subsets of TT-DRw52-APC. Clone 16 responded to some DR3 and TT-DRw6-APC, while clone 10 was stimulated by other TT-DR3 and TT-DRw6, and all TT-DR5-APC. This same pattern of DRw52 restriction was found in panel, as well as in family studies. Because this suggested a correlation with the pattern of DRw52 polymorphism observed earlier by DNA sequencing and oligonucleotide hybridization, the APC used in these experiments were typed for the 52 a, b, and c alleles of locus DR beta III by allele-specific oligonucleotide probes. This distribution overlapped exactly with the stimulation pattern defined by the T cell clones. Clone 16 responded to TT-52a-APC, clone 10 to TT-52b-APC, and both clones to a TT-52c-APC. The response of the T cell clones was inhibited differentially by mAbs to DR. Raising TT concentration, or increasing HLA-class II expression with INF-gamma both affected the magnitude of response of the TT-specific clones but did not modify their specificities. These results demonstrate that a restriction specificity can be attributed to the DR beta III locus and illustrate the functional relevance of the polymorphism observed at this locus. This is of special interest in view of the striking difference in the pattern of structural diversity among alleles of DR beta I and DR beta III.
Epithelial sodium channels: function, structure, and regulation (1997)

The apical (outward-facing) membranes of high-resistance epithelia contain Na+ channels, traditionally identified by their sensitivity to block by the K(+)-sparing diuretic amiloride. Such channels have been characterized in amphibian skin and urinary bladder, renal collecting duct, distal colon, sweat and salivary glands, lung, and taste buds. They mediate the first step of active Na+ reabsorption and play a major role in the maintenance of electrolyte and water homeostasis in all vertebrates. In the past, these channels were classified according to their biophysical and pharmacological properties. The recent cloning of the three homologous channel subunits denoted alpha-, beta-, and gamma-epithelial Na+ channels (ENaC) has provided a molecular definition of at least one class of amiloride-blockable channels. Subsequent studies have established that ENaC is a major Na(+)-conducting pathway in both absorbing and secretory epithelia and is related to one type of channel involved in mechanosensation. This review summarizes the biophysical characteristics, molecular properties, and regulatory mechanisms of epithelial amiloride-blockable Na+ channels. Special emphasis is given to recent studies utilizing cloned ENaC subunits and purified amiloride-binding proteins.
Identification of Conserved cis-Elements and Transcription Factors Required for Sterol-regulated Transcription of Stearoyl-CoA Desaturase 1 and 2 (1999)

We previously identified stearoyl-CoA desaturase 2 (SCD2) as a new member of the family of genes that are transcriptionally regulated in response to changing levels of nuclear sterol regulatory element binding proteins (SREBPs) or adipocyte determination and differentiation factor 1 (ADD1). A novel sterol regulatory element (SRE) (5'-AGCAGATTGTG-3') identified in the proximal promoter of the mouse SCD2 gene is required for induction of SCD2 promoter-reporter genes in response to cellular sterol depletion (Tabor, D. E., Kim, J. B., Spiegelman, B. M., and Edwards, P. A. (1998) J. Biol. Chem. 273, 22052-22058). In this report, we demonstrate that this novel SRE is both present in the promoter of the SCD1 gene and is critical for the sterol-dependent transcription of SCD1 promoter-reporter genes. Two conserved cis elements (5'-CCAAT-3') lie 5 and 48 base pairs 3' of the novel SREs in the promoters of both the SCD1 and SCD2 murine genes. Mutation of either of these putative NF-Y binding sites attenuates the transcriptional activation of SCD1 or SCD2 promoter-reporter genes in response to cellular sterol deprivation. Induction of both reporter genes is also attenuated when cells are cotransfected with dominant-negative forms of either NF-Y or SREBP. In addition, we demonstrate that the induction of SCD1 and SCD2 mRNAs that occurs during the differentiation of 3T3-L1 preadipocytes to adipocytes is paralleled by an increase in the levels of ADD1/SREBP-1c and that the SCD1 and SCD2 mRNAs are induced to even higher levels in response to ectopic expression of ADD1/SREBP-1c. We conclude that transcription of both SCD1 and SCD2 genes is responsive to cellular sterol levels and to the levels of nuclear SREBP/ADD1 and that transcriptional induction requires three spatially conserved cis elements, that bind SREBP and NF-Y. Additional studies demonstrate that maximal transcriptional repression of SCD2 reporter genes in response to an exogenous polyunsaturated fatty acid is dependent upon the SRE and the adjacent CCAAT motif.
Effect of oral nutritional supplementation on wound healing in diabetic foot ulcers: a prospective randomized controlled trial (2014)

While no differences in healing were identified with supplementation in non-ischaemic patients or those with normal albumin, addition of arginine, glutamine and β-hydroxy-β-methylbutyrate as an adjunct to standard of care may improve healing of diabetic foot ulcers in patients with risk of poor limb perfusion and/or low albumin levels. Further investigation involving arginine, glutamine and β-hydroxy-β-methylbutyrate in these high-risk subgroups might prove clinically valuable.
Isolation and characterization of indole acetic acid (IAA) producing Klebsiella pneumoniae strains from rhizosphere of wheat (Triticum aestivum) and their effect on plant growth. (2009)

The present study was undertaken for isolation of Klebsiella strains from rhizosphere of wheat (T. aestivum), screening and characterization of these strains for in vitro indole acetic acid (IAA) production and studying the effect of these strains on plant growth under gnotobiotic conditions. Nine strains of Klebsiella were isolated from rhizosphere of wheat (var. Lokwan) and identified as K. pneumoniae by 16S rRNA gene sequencing. Six K. pneumoniae strains showed in vitro IAA production. Colorimetric analysis showed that K8 produced maximum IAA (27.5 mg l(-1)) in the presence of tryptophan (1 mg ml(-1)) at 72 h of incubation with optimum conditions as pH 8.0, 37 degrees C and 0.5% (w/v) NaCl concentration. GC-MS analysis and IR studies confirmed presence of IAA in the cell filtrates of strain K8. Effect of six IAA producing Klebsiella strains on plant growth was studied by performing series of seed germination tests using moth bean seeds under axenic conditions and pot experiments using sterilized soil and wheat seeds (var. Lokwan). Strain K11 and K42 demonstrated increase in root length of inoculated moth beans (approximately 92.71% over the control). Results of pot experiments indicated that almost all the six IAA producing Klebsiella strains significantly increased the root length and shoot height of inoculated wheat seedlings over the control. The results suggest that these are promising isolates from wheat rhizosphere and merits research on appliance of these strains in agriculture.
Cloning and sequence analysis of a novel β2related integrin transcript from T lymphocytes: homology of integrin cysteine-rich repeats to domain III of laminin B chains (1990)

The integrins have been grouped into three subfamilies based on the utilization of three distinct beta chain subunits, beta 1, beta 2, and beta 3. The recent discovery of beta 4 and beta 5 subunits, and the sharing of alpha subunits between beta subfamilies reflects a greater structural and functional diversity of the integrin supergene family than first anticipated. We exploit integrin gene sequence homology for the identification of a new integrin beta chain. Oligonucleotide probes designed from the highly conserved Arg-Gly-Asp (RGD)-binding domain were used to amplify related transcripts from phytohaemagglutinin-activated human peripheral blood lymphocytes using the polymerase chain reaction (PCR). Five PCR products encoding beta 1, beta 2, beta 3, beta 4, and a new beta clone, designated beta 7, were identified. Full-length beta 7 cDNA was isolated from an activated human T lymphocyte library, using an oligonucleotide probe constructed from the beta 7 PCR product. The beta 7 cDNA contains a long open reading frame of 2391 bp which encodes a protein sequence consisting of 797 amino acids. The encoded sequence revealed a typical signal peptide, a predominantly hydrophilic 707 amino acid residue domain with 8 N-glycosylation sites, a transmembrane domain, and a C-terminal domain of 52 amino acids. The beta 7 sequence showed homology to known beta 1, beta 2, beta 3, beta 4, and beta 5 sequences of 43, 46, 38, 32, and 37% respectively. Four cysteine-rich homologous repeat sequences were found in beta 7 and were homologous to sequences in other integrin beta subunits, and to domain III of the laminin B chains. Part of this cysteine-rich region is homologous to proteins that contain epidermal growth factor-like repeat sequences. Northern analysis revealed that mature beta 7 mRNA is approximately 3.5 kb in size, and expression was restricted to T and B lymphocytes in the small panel of cell types examined. We conclude that beta 7 may be a new member of the leukocyte cell adhesion molecule subset of integrins, and is a candidate immunoregulatory molecule.
Synthesis, Characterization, Reactivity, and Electrochemistry of Palladium Monolayer Protected Clusters (2000)

This paper describes the synthesis, characterization, reactivity, and electrochemistry of monolayer-protected clusters (MPCs) of palladium that are passivated by monolayers of hexanethiolate or dodecanethiolate ligands. The synthetic product is sensitive to the thiol:Pd ratio used in the reaction mixture: a 1:1 ratio or smaller ratio produces metallic Pd(0) clusters that are similar to analogously prepared Au MPCs, but much more ligand-rich, whereas ≥2:1 ratios yield a very different material that is either extremely small Pd(0) clusters or a form of Pd(II) alkanethiolate complex. The monolayers of the metallic Pd(0) MPCs that are synthesized using small thiol:Pd ratios can be modified by ligand place-exchange and coupling reactions. The electrochemistry of the Pd core and of electroactive labels attached to the alkanethiolate ligands was studied. Quantized double-layer core charging is seen but less clearly than with Au MPCs. The Pd nanoparticles were examined using NMR, FTIR, UV−vis, TEM, TGA, and elemental analysis.
Effects of different molecular weight elastoviscous hyaluronan solutions on articular nociceptive afferents (2004)

We conclude that the elastoviscous properties of HA solutions are determining factors in reducing pain-eliciting nerve activity both in normal and in inflamed rat joints.
Trapping of the malaria vector Anopheles gambiae with odour-baited MM-X traps in semi-field conditions in western Kenya (2006)

These results are the first to report behavioural responses of an African malaria vector to human foot odour outside the laboratory, and further investigation of fractions and/or individual chemical components of this odour complex are called for. Semi-field systems offer the prospect of high-throughput screening of candidate kairomones, which may expedite the development of efficient trap-bait systems for this and other African mosquito species.
Expression of cell surface GPI-anchored human p97 in baculovirus-infected insect cells (1997)

The baculovirus/insect cell system (Autographa californica multiple nuclear polyhedrosis virus/Spodoptera frugiperda Sf9 cells) was used to express the GPI-anchored human melanoma tumor antigen, melanotransferrin or p97. This system served to study the expression and productivity of recombinant GPI-anchored p97 by insect cells. The Sf9 cells expressed a cell surface GPI-anchored form of p97 as well as a soluble form of p97 that did not appear to be derived from the GPI-anchored form of p97. Both recombinant forms, although Endo H resistant, migrated slightly faster ( approximately 88 kDa) than the native p97 ( approximately 95-97 kDa). The insect GPI-anchored p97 was sensitive to PI-PLC, which exposed a detectable cross-reacting determinant. The Sf9 cell surface p97 expression was similar to that of human melanoma (SK-MEL-28) cells, whereas the Sf9 cell specific secretion rate was 10-fold higher. Also Sf9 cells retained considerably higher levels of p97 within the cell. The Sf9 cell surface expression of p97 varied with time after infection, with the maximum expression, which appeared independent of multiplicities of infection greater than 1, occurring at 48 h. After 48 h, levels of cell surface and secreted p97 fell whereas p97 retained within the cell increased, which possibly reflected the lytic nature of the expression system. The successful expression of GPI-anchored human p97 by the baculovirus/insect cell system not only provides a source of p97 for further research but also is the basis of an alternative method for the commercial production of GPI-anchored proteins.
Granulomatous lung disease: an approach to the differential diagnosis. (2010)

Most granulomas in the lung are caused by mycobacterial or fungal infection. The diagnosis requires familiarity with the tissue reaction as well as with the morphologic features of the organisms, including appropriate interpretation of special stains. The major noninfectious causes of granulomatous lung disease are sarcoidosis, Wegener granulomatosis, hypersensitivity pneumonitis, hot tub lung, aspiration pneumonia, and talc granulomatosis.
Somatic Afferent Regulation of Plasma Luteinizing Hormone and Testosterone in Anesthetized Rats. (1992)

The effects of cutaneous stimulation on plasma luteinizing hormone (LH) and testosterone were examined in adult male Wistar rats anesthetized with pentobarbital. Under the resting condition without somatic sensory stimulation, plasma LH and testosterone measured every 30 min between 1400 and 1730 h revealed no significant fluctuations. Nociceptive mechanical stimulation of bilateral hindpaws by pinching for 10 min significantly increased plasma LH and testosterone. Plasma LH was increased 30 and 60 min after stimulation, while plasma testosterone was increased 60-150 min after stimulation. However, innocuous mechanical stimulation of bilateral hindlimbs by brushing for 10 min did not significantly change either plasma LH or testosterone. These results indicate that, when emotional factors were eliminated by anesthetization, cutaneous nociceptive information led to the increased secretion of LH from the anterior pituitary, resulting in an increase in testosterone secretion from the testes into the plasma.
Methanotrophic bacteria. (1996)

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene.
Nucleic Acid Hybridization: A Rapid Method for the Diagnosis of Infectious Diseases (1989)

A new method is described for the rapid identification of microorganisms in clinical samples by DNA-DNA hybridization. In this procedure, nucleic acids are labelled nonradioisotopically in the sample, which is then incubated with a panel of immobilized unlabelled DNAs from different organisms as probes. The sample labelling is a photochemical reaction between the nucleic acids in cell lysates and an isopsoralen derivative covalently linked to a biotin moiety for detection. Results are given of the application of the procedure to the identification of pathogens in clinical specimens of urine and cerebrospinal fluid.
Rate control for an embedded wavelet video coder (1997)

Embedded coders provide a better rate-distortion tradeoff while the coded bit stream can be truncated at any point without a significant perceptible distortion. We investigate rate control for an embedded wavelet video coder by converting the rate control problem to a bit allocation problem for each frame. Then, a computationally efficient rate control algorithm is derived by exploiting the rate-distortion performance of the embedded wavelet coder and the frame dependency between the reference frame and the predictive frame. Experiments are performed to demonstrate the superior performance of the embedded wavelet video coder with the proposed rate control scheme. It is shown that the proposed rate control strategy outperforms the fixed allocation rate control by 0.1-0.4 dB for a variety of sequences, and the performance gain can be as large as 1.3-2.7 dB around scene changes.
Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme (2017)

Chemically regulated self-cleaving ribozymes, or aptazymes, are emerging as a promising class of genetic devices that allow dynamic control of gene expression in synthetic biology. However, further expansion of the limited repertoire of ribozymes and aptamers, and development of new strategies to couple the RNA elements to engineer functional aptazymes are highly desirable for synthetic biology applications. Here, we report aptazymes based on the recently identified self-cleaving pistol ribozyme class using a guanine aptamer as the molecular sensing element. Two aptazyme architectures were studied by constructing and assaying 17 728 mutants by deep sequencing. Although one of the architectures did not yield functional aptazymes, a novel aptazyme design in which the aptamer and the ribozyme were placed in tandem yielded a number of guanine-inhibited ribozymes. Detailed analysis of the extensive sequence-function data suggests a mechanism that involves a competition between two mutually exclusive RNA structures reminiscent of natural bacterial riboswitches.