gebhart/patrepeval huggingface dataset:
Ligand Binding Sites of Inducible Costimulator and High Avidity Mutants with Improved Function (2002)

Interaction between inducible costimulator (ICOS) and its ligand is implicated in the induction of cell-mediated and humoral immune responses. However, the molecular details of this interaction are unknown. We report here a mutagenesis analysis of residues in ICOS that are critical for ligand binding. A three-dimensional model of the extracellular immunoglobulin-like domain of ICOS was used to map the residues conserved within the CD28 family. This analysis identified a surface patch containing the characteristic "PPP" sequence and is conserved in human and mouse ICOS. Mutations in this region of human ICOS reduce or abolish ligand binding. Our results suggest that the ligand binding site in ICOS maps to a region overlapping yet distinct from the CD80/CD86 binding sites in CD28 and cytotoxic T lymphocyte antigen (CTLA)-4. Thus, the analysis suggests that differences in ligand binding specificity between these related costimulatory molecules have evolved by utilization of overlapping regions with different patterns of conserved and nonconserved residues. Two site-specific mutants generated in the course of our studies bound ICOS ligand with higher avidity than wild-type ICOS. An S76E mutant protein of ICOS blocked T cell costimulatory function of ICOS ligand and inhibited T cell response to allogeneic antigens superior to wild-type ICOS. Our studies thus identified critical residues involving in ICOS receptor-ligand interaction and provide new modulators for immune responses.
Portal imaging with a CsI(Tl) transparent scintillator x-ray detector (1998)

In a previous paper, a portal imaging system was described that used a 101 mm diameter, 3 mm thick CsI (Tl) transparent scintillating screen coupled to a liquid-nitrogen-cooled slow- scan CCD-TV camera with a 40 mm f1.0 macro lens with a 5:1 demagnification. Meanwhile, improved images have been acquired using a 50 mm f1.1 macro lens with a 7:1 demagnification. These images were presented at an AAPM International Symposium on Electronic Portal Imaging in Detroit, MI, in May, 1997. Since the Detroit meeting, a 203 mm diameter, 13 mm thick CsI(Tl) crystal has been purchased from Bicron. This transparent screen has been used with a Nikkor 35 mm f1.4 lens to show the whole 203 mm circular field at 0.53 mm pixel size with the existing Astromed liquid nitrogen cooled CCD TV camera system. The geometry of the imaging system has been optimized to achieve high spatial resolution (1 lp/mm) in spite of the increased thickness of the screen. This increased thickness allows the high image quality achieved with the older screen at 72 MU to be maintained with the newer screen while reducing the dose to 1 MU. Images have been acquired with the new screen of lead bar patterns, low-contrast hole patterns in Lucite blocks, and anthropomorphic phantoms.
Transfer of proteins across membranes. II. Reconstitution of functional rough microsomes from heterologous components. (1975)

The data presented in this paper demonstrate that native small ribosomal subunits from reticulocytes (containing initiation factors) and large ribosomal subunits derived from free polysomes of reticulocytes by the puromycin-KCl procedures can function with stripped microsomes derived from dog pancreas rough microsomes in a protein-synthesizing system in vitro in response to added IgG light chain mRNA so as to segregate the translation product in a proteolysis-resistant space. No such segregation took place for the translation product of globin mRNA. In addition to their ability to segregate the translation product of a specific heterologous mRNA, native dog pancreas rough microsomes as well as derived stripped microsomes were able to proteolytically process the larger, primary translation product in an apparently correct manner, as evidenced by the identical mol wt of the segregated translation product and the authentic secreted light chain. Segregation as well as proteolytic processing by native and stripped microsomes occurred only during ongoing translation but not after completion of translation. Attempts to solubilize the proteolytic processing activity, presumably localized in the microsomal membrane by detergent treatment, and to achieve proteolytic processing of the completed light chain precursor protein failed. Taken together, these results establish unequivocally that the information for segregation of a translation product is encoded in the mRNA itself, not in the protein-synthesizing apparatus; this provides strong evidence in support of the signal hypothesis.
Subtilisin from psychrophilic antarctic bacteria: characterization and site-directed mutagenesis of residues possibly involved in the adaptation to cold (1997)

A subtilisin excreted by the Antarctic Bacillus TA39 has been purified to homogeneity and characterised. Two independent genes subt1 and subt2 are present but only subt1 is expressed significantly in the culture medium. The enzyme displays the usual characteristics of cold enzymes i.e. a high catalytic efficiency at low and moderate temperatures and an increased thermosensitivity originating from a 3D structure probably more flexible than its mesophilic counterpart. This is corroborated by the analysis of the computerized structure which shows a significant decrease in the number and strength of intramolecular weak bonds such as salt bridges and aromatic interactions. The affinity for calcium is also almost three orders of magnitude lower than that of mesophilic subtilisin and the interactions with the solvent are significantly higher thanks to a large increase in the number of Asp residues in the loops connecting secondary structures. The relation between flexibility and activity was investigated by site-directed mutagenesis tending mainly to increase the rigidity of the molecular edifice through the incorporation of additional salt bridge, disulfide bridge, aromatic interaction and by increasing the affinity of the enzyme for calcium. An important stabilization of the molecular structure was achieved through a modification of a calcium ligand T85D. The thermostability of the mutated product expressed in a mesophilic Bacillus reaches that of mesophilic subtilisin. Most important is the fact that this mutation further enhances the specific activity by a factor close to 2 when compared to the wild type enzyme so that the overall activity of the mutated cold enzyme is about 20 times higher than that of mesophilic subtilisin, illustrating the fact that thermostability is not systematically inversely related to specific activity. This opens new perspectives in the use of cold enzymes in biotechnology.
Development of a Natural Model of Cutaneous Leishmaniasis: Powerful Effects of  Vector Saliva and Saliva Preexposure on the Long-Term Outcome of Leishmania major Infection in the Mouse Ear Dermis (1998)

We have developed a model of cutaneous leishmaniasis due to Leishmania major that seeks to mimic the natural conditions of infection. 1,000 metacyclic promastigotes were coinoculated with a salivary gland sonicate (SGS) obtained from a natural vector, Phlebotomus papatasii, into the ear dermis of naive mice or of mice preexposed to SGS. The studies reveal a dramatic exacerbating effect of SGS on lesion development in the dermal site, and a complete abrogation of this effect in mice preexposed to salivary components. In both BALB/c and C57Bl/6 (B/6) mice, the dermal lesions appeared earlier, were more destructive, and contained greater numbers of parasites after infection in the presence of SGS. Furthermore, coinoculation of SGS converted B/6 mice into a nonhealing phenotype. No effect of SGS was seen in either IL-4- deficient or in SCID mice. Disease exacerbation in both BALB/c and B/6 mice was associated with an early (6 h) increase in the frequency of epidermal cells producing type 2 cytokines. SGS did not elicit type 2 cytokines in the epidermis of mice previously injected with SGS. These mice made antisaliva antibodies that were able to neutralize the ability of SGS to enhance infection and to elicit IL-4 and IL-5 responses in the epidermis. These results are the first to suggest that for individuals at risk of vector-borne infections, history of exposure to vector saliva might influence the outcome of exposure to transmitted parasites.
Analysis and measurement of birefringence in single-mode fibers using the backscattering method (1981)

The local parameters of linear, circular, and elliptical birefringence of backscattered light along a single-mode fiber are analyzed, and the twist-bending-induced elliptical birefringence in an extremely low birefringent single-mode fiber is measured using the backscattering method. The experimental results are in good agreement with the theoretical calculations. For a 130-microm-diameter fiber, twisted by 133 degrees /m and wound around a drum of 15-cm radius, the induced elliptical birefringence is |?| = 18 degrees /m at lambda = 904 nm.
4.3 Degradation and modification of cellulose acetates by biological systems (2004)

Abstract A survey is given on recent findings in the enzymology of cellulose acetate degradation. Acetyl esterases have been identified as the principal enzymes, initiating cellulose acetate degradation as a prerequisite for endoglucanase‐catalyzed cellulose acetate depolymerisation. Acetyl esterases are provided by nature to deacetylate naturally occurring partly acetylated polysaccharides, i.e. xylan and chitin. Accordingly they are not designed to attack high DS cellulose acetate. Under these circumstances acetyl esterases require a pretreatment of cellulose acetate, leading to some reduction in DS, in case highly substituted material should be degraded. One of these treatments is composting under the conditions of which a partial deacetylation may occur under the action of heat and high pH, facilitating the accessibility for acetyl esterases. However from the present knowledge it cannot be excluded that certain microbial specialists exist, being capable to degrade high DS cellulose acetate.
Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease (2013)

We have adapted a bacterial CRISPR RNA/Cas9 system to precisely engineer the Drosophila genome and report that Cas9-mediated genomic modifications are efficiently transmitted through the germline. This RNA-guided Cas9 system can be rapidly programmed to generate targeted alleles for probing gene function in Drosophila.
MicroRNA Biogenesis: Isolation and Characterization of the Microprocessor Complex (2006)

The recently discovered microRNAs (miRNAs) are a large family of small regulatory RNAs that have been implicated in controlling diverse pathways in a variety of organisms (1, 2). For posttranscriptional gene silencing, one strand of the miRNA is used to guide components of the RNA interference machinery, including Argonaute 2, to messenger RNAs (mRNAs) with complementary sequences (3, 4). Thus, targeted mRNAs are either cleaved by the endonuclease Argonaute 2 (5, 6), or protein synthesis is blocked by an as yet uncharacterized mechanism (7, 8). Genes encoding miRNAs are transcribed as long primary miRNAs (pri-miRNAs) that are sequentially processed by components of the nucleus and cytoplasm to yield a mature, approx 22-nucleotide (nt)-long miRNA (9). Two members of the ribonuclease (RNase) III endonuclease protein family, Drosha and Dicer, have been implicated in this two-step processing (10-13). To further our understanding of miRNA biogenesis and function it will be essential to identify the protein complexes involved. We were interested in defining the proteins required for the initial nuclear processing of pri-miRNAs to the approx 60- to 70-nt stem-loop intermediates known as precursor miRNAs (pre-miRNAs) (9, 10). This led to our identification of a protein complex we termed Microprocessor, which is necessary and sufficient for processing pri-miRNA to premiRNAs (14). The Microprocessor complex comprises Drosha and the double-stranded RNAbinding protein DiGeorge syndrome critical region 8 gene (DGCR8), which is deleted in DiGeorge syndrome (15, 16). In this chapter, we detail the methods used for the biochemical isolation and identification of the Microprocessor complex from human cells. We include a protocol for the in vitro analysis of pri-miRNA processing activity of the purified Microprocessor complex.
Disruption of Transcriptionally Active Stat3 Dimers with Non‐phosphorylated, Salicylic Acid‐Based Small Molecules: Potent in vitro and Tumor Cell Activities (2009)

Three's company: A library of analogues of the previously reported Stat3 inhibitor S3I-201 was prepared. The most active analogues, SF-1-066 (X=NCH3) and SF-1-121 (X=O), have shown impressive in vitro and whole-cell activities that possibly result from the successful occupation of a third, hydrophobic subpocket of the Stat3 SH2 domain. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Facile Large-Scale Synthesis of Monodisperse Mesoporous Silica Nanospheres with Tunable Pore Structure (2013)

Mesoporous silica nanoparticles (MSNs) are experiencing rapid development in the biomedical field for imaging and for use in heterogeneous catalysis. Although the synthesis of MSNs with various morphologies and particle sizes has been reported, synthesis of a pore network with monodispersion control below 200 nm is still challenging. We achieved this goal using mild conditions. The reaction occurred at atmospheric pressure with a templating sol-gel technique using cetyltrimethylammonium (CTA(+)) as the templating surfactant and small organic amines (SOAs) as the mineralizing agent. Production of small pore sizes was performed for the first time, using pure and redispersible monodispersed porous nanophases with either stellate (ST) or raspberry-like (RB) channel morphologies. Tosylate (Tos(-)) counterions favored ST and bromide (Br(-)) RB morphologies at ultralow SOA concentrations. Both anions yielded a worm-like (WO) morphology at high SOA concentrations. A three-step formation mechanism based on self-assembly and ion competition at the electrical palisade of micelles is proposed. Facile recovery and redispersion using specific SOAs allowed a high yield production at the kilogram scale. This novel technique has practical applications in industry.
<title>Image processing for computer-aided diagnosis of lung cancer screening system by CT (LSCT)</title> (1998)

In this paper, we report the image processing technique for computer-aided diagnosis of lung cancer screening system by CT (LSCT). LSCT is the newly developed mobile-type CT scanner for the mass screening of lung cancer by our project team. In this new LSCT system, one essential problem is the increase of image information to be diagnosed by a doctor to about 30 slices per patient from 1 X-ray film. To solve this difficult problem, we are trying to reduce the image information drastically to be displayed for the detector by image processing techniques. We propose a new method named Variable-New-Quoit filter for the automatic recognition of the pathological shadow candidates. Our computer aided diagnosis system can satisfactorily reduce the number of CT cross sections by this method, containing the abnormal shadow candidates.
Metal–organic frameworks for the storage and delivery of biologically active hydrogen sulfide (2012)

Hydrogen sulfide is an extremely toxic gas that is also of great interest for biological applications when delivered in the correct amount and at the desired rate. Here we show that the highly porous metal-organic frameworks with the CPO-27 structure can bind the hydrogen sulfide relatively strongly, allowing the storage of the gas for at least several months. Delivered gas is biologically active in preliminary vasodilation studies of porcine arteries, and the structure of the hydrogen sulfide molecules inside the framework has been elucidated using a combination of powder X-ray diffraction and pair distribution function analysis.
Modulation of the cannabinoid CB2 receptor in microglial cells in response to inflammatory stimuli (2005)

The cannabinoid system is known to be important in neuronal regulation, but is also capable of modulating immune function. Although the CNS resident microglial cells have been shown to express the CB2 subtype of cannabinoid receptor during non-immune-mediated pathological conditions, little is known about the expression of the cannabinoid system during immune-mediated CNS pathology. To examine this question, we measured CB2 receptor mRNA expression in the CNS of mice with experimental autoimmune encephalomyelitis (EAE) and, by real-time PCR, found a 100-fold increase in CB2 receptor mRNA expression during EAE onset. We next determined whether microglial cells specifically express the CB2 receptor during EAE, and found that activated microglial cells expressed 10-fold more CB2 receptor than microglia in the resting state. To determine the signals required for the up-regulation of the CB2 receptor, we cultured microglial cells with combinations of gamma-interferon (IFN-gamma) and granulocyte) macrophage-colony stimulating factor (GM-CSF), which both promote microglial cell activation and are expressed in the CNS during EAE, and found that they synergized, resulting in an eight to 10-fold increase in the CB2 receptor. We found no difference in the amount of the CB2 receptor ligand, 2-arachidonylglycerol (2-AG), in the spinal cord during EAE. These data demonstrate that microglial cell activation is accompanied by CB2 receptor up-regulation, suggesting that this receptor plays an important role in microglial cell function in the CNS during autoimmune-induced inflammation.
Selectivity Enhancement of Silica-Supported Sulfonic Acid Catalysts in Water by Coating of Ionic Liquid (2007)

Coating of silica-supported sulfonic acid catalysts with hydrophobic ionic liquid leads to a significant improvement of catalyst selectivity. Many organic reactions, including Prins cyclization, cycloaddition of epoxide to aldehyde, and dehydrative etherification of secondary benzyl alcohols, proceed well in formalin or pure water. In particular, tandem dehydration/Prins cyclization reactions of tertiary and secondary alcohols with formaldehyde were developed for the first time.
Effective Inhibitors of Hemagglutination by Influenza Virus Synthesized from Polymers Having Active Ester Groups. Insight into Mechanism of Inhibition (1995)

Highly effective sialic acid-containing inhibitors of influenza virus X-31 were synthesized using poly[N-(acryoyloxy)succinimide] (pNAS), a polymer preactivated by incorporation of active ester groups. Polymers containing two and three different components were prepared by sequential reaction of pNAS with two and three amines, respectively. This preparation of co- and terpolymers was synthetically more efficient than methods involving copolymerization of different monomers and gave polymers that were more easily compared than those generated by copolymerization. Polymers in this study (prepared from a single batch of pNAS) had a constant degree of polymerization (DP approximately 2000) and probably had a distribution of components that was more random than analogous polymers prepared by copolymerization. Use of C-glycosides of sialic acid made it possible to investigate inhibition by different polymers at temperatures ranging from 4 to 36 degrees C without artifacts due to the hydrolytic action of neuraminidase. The inhibitors were, in general, more effective at 36 degrees C than at 4 degrees C. The hemagglutination (HAI) assay was used to measure the value of the inhibition constant KHAIi each polymer. The value of KHAIi for the two-component polymer containing 20% sialic acid on a polyacrylamide backbone at 4 degrees C was 4 nM (in terms of the sialic acid moieties present in solution) and was approximately 50-fold more effective than the best inhibitors previously described and 25-fold more effective than the best naturally occurring inhibitor. The most effective inhibitor synthesized in this work contained 10% benzyl amine and 20% sialic acid on a polyacrylamide backbone, and its value of KHAIi was 600 pM at 36 degrees C. Approximately 100 polymers that differed in one or two components were assayed to distinguish between two limiting mechanisms for inhibition of the interaction between the surfaces of virus and erythrocytes: high-affinity binding through polyvalency, and steric stabilization. The results suggest that both mechanisms play an important role. The system comprising polyvalent inhibitors of agglutination of erythrocytes by influenza provides a system that may be useful as a model for inhibitors of other pathogen-host interactions, a large number of which are themselves polyvalent.
Rates of Lead Migration and Stimulation Lossin Spinal Cord Stimulation: A RetrospectiveComparison of Laminotomy VersusPercutaneous Implantation (2011)

Rates of stimulation loss and radiographic lead migration are similar for both laminotomy and percutaneous implantation. Time to loss of stimulation was not statistically different in either group, although there was a trend toward laminotomy leads migrating earlier. Lead type and laterality of symptoms do not affect lead migration rates. The effect of the level of implant and diagnosis was indeterminate.
Purification and Characterization of Active and Stable Recombinant Plasminogen‐Activator Inhibitor Accumulated at High Levels in Escherichia coli (1994)

Plasminogen-activator inhibitor type 1 (PAI-1), the primary physiological inhibitor of tissue-type plasminogen activator, is an unusual member of the serine protease inhibitor (serpin) superfamily in that it spontaneously converts to a latent form lacking activity. This latent form can be reactivated by denaturation and refolding, but the activation is usually incomplete and often leads to aggregation of the protein. In this study we have developed a high-level expression system that leads to the accumulation of PAI-1 at 30-50% total microbial protein. We have developed a single-step purification protocol which can be completed in a few hours, yielding approximately 20 mg purified recombinant PAI-1/litre culture. The purified PAI-1 was 80-100% active and was stable upon incubation at 37 degrees C with a half-life of approximately 48 h. At 20 degrees C, PAI-1 activity was stable for a week and at 4 degrees C it retained its activity completely for up to two months. Freezing caused significant loss of activity. The stability of PAI-1 activity was found to be dependent on pH and ionic strength, being most stable at pH 5.6 and at an ionic strength of 1 M salt. We show that by a combination of high-level expression and rapid purification under optimum conditions, it is possible to produce active and stable PAI-1 in high yield.
Cytokines in systemic juvenile idiopathic arthritis and haemophagocytic lymphohistiocytosis: tipping the balance between interleukin-18 and interferon-γ (2015)

Patients with active sJIA and HLH/MAS show distinct cytokine profiles, with highly elevated plasma levels of IFN-γ and IFN-γ-induced proteins typically found in HLH/MAS. In addition to PBMCs, histiocytes, endothelial cells and fibroblasts may contribute to an IFN-γ profile in plasma. Increasing levels of IFN-γ compared with IL-18 may raise suspicion about the development of MAS in sJIA.