gebhart/patrepeval huggingface dataset:
CD40 Signaling Is Impaired in L. major–infected Macrophages and Is Rescued by a p38MAPK Activator Establishing a Host-protective Memory T Cell Response (2003)

Leishmania, a protozoan parasite, lives and multiplies as amastigote within macrophages. It is proposed that the macrophage expressed CD40 interacts with CD40 ligand on T cells to induce IFN-gamma, a Th1-type cytokine that restricts the amastigote growth. Here, we demonstrate that CD40 cross-linking early after infection resulted in inducible nitric oxide synthetase type-2 (iNOS2) induction and iNOS2-dependent amastigote elimination. Although CD40 expression remained unaltered on L. major-infected macrophages, delay in the treatment of macrophages or of mice with anti-CD40 antibody resulted in significant reduction in iNOS2 expression and leishmanicidal function suggesting impaired CD40 signaling in Leishmania infection. The inhibition of CD40-induced iNOS2 expression by SB203580, a p38-mitogen activated protein kinase (p38MAPK)-specific inhibitor, and the reversal of the inhibition by anisomycin, a p38MAPK activator, suggested a crucial role of p38MAPK in CD40 signaling. Indeed, the CD40-induced p38MAPK phosphorylation, iNOS2 expression and anti-leishmanial function were impaired in Leishmania-infected macrophages but were restored by anisomycin. Anisomycin's effects were reversed by SB203580 emphasizing the role of p38MAPK in CD40-induced iNOS2-dependent leishmanicidal function. Anisomycin administration in L. major-infected BALB/c mice resulted in significant reduction in the parasite load and established a host-protective Th1-type memory response. Also implicated in these findings is a scientific rationale to define novel anti-parasite drug targets and to bypass the problem of drug resistance.
Effects of co-solvents on peptide hydration water structure and dynamics (2009)

We evaluate the molecular response of hydration water as a function of temperature and proximity to the surface of the peptide N-acetyl-leucine-methylamide (NALMA) when in the presence of the kosmotrope co-solvent glycerol or the chaotrope co-solvent dimethyl sulfoxide (DMSO), using molecular dynamics simulation with a polarizable force field. These detailed microscopic studies complement established thermodynamic analysis on the role of co-solvents in shifting the equilibrium for proteins away from or towards the native folded state. We find that the structure of the water at the peptide interfaces reflects an increase in hydration number in the glycerol solution and a decrease in hydration numbers in the DMSO solution. While the water dynamics around NALMA in the presence of both co-solvents is slower than that observed with the water solvent alone, in the DMSO mixture we no longer measure a separation in water motion time scales at low temperatures as is seen in the pure water solvent, but rather one single relaxation time. In the glycerol, however, we do observe a separation of time scales at low temperatures, supporting the hypothesis that hydration water near a hydrophobic solute evolves on a separate time scale than the extensive hydrogen-bonding network of more bulk-like water. Our simulation studies highlight the differences in the two co-solvent solutions due to the relative frequency of water contacts with the hydrophobic vs. hydrophilic peptide surface, and direct water interactions with the co-solvents.
IL-17 Stimulates Granulopoiesis in Mice: Use of an Alternate, Novel Gene Therapy-Derived Method for In Vivo Evaluation of Cytokines (1998)

IL-17 is a novel cytokine secreted principally by CD4+ T cells. It has been shown to support the growth of hemopoietic progenitors in vitro; however, its in vivo effects are presently unknown. Adenovirus-mediated gene transfer of the murine IL-17 cDNA targeted to the liver (5 x 10(9) plaque-forming units (PFU) intravenous) resulted in a transiently transgenic phenotype, with dramatic effects on in vivo granulopoiesis. Initially, there was a significant increase (fivefold) in the peripheral white blood count (WBC), including a 10-fold rise in the absolute neutrophil count. This was associated with a doubling in the spleen size over 7-14 days after gene transfer, which returned to near baseline by day 21, although the white blood cell count remained elevated. There was a profound stimulation of splenic hemopoiesis as demonstrated by an increase in total cellularity by 50% 7 days after gene transfer and an increase in hemopoietic colony formation. A maximal increase in frequency of high proliferative potential colonies (HPPC) (11-fold) and CFU-granulocyte-macrophage (GM) and CFU-granulocyte-erythrocyte-megakaryocyte-monocyte (GEMM) (CFU) (6-fold) was seen on day 3 after IL-17 gene transfer. Both CFU and HPPC remained significantly elevated in the spleen throughout day 21, but at reduced levels compared with day 3. Bone marrow CFU and HPPC were elevated on day 3 only by 75% and 25%, respectively, without changes in total cellularity. Thus, murine IL-17 is a cytokine that can stimulate granulopoiesis in vivo. Since IL-17 is principally produced by CD4+ T cells, this cytokine could have therapeutic implications in AIDS-related bone marrow failure and opportunistic infections.
Bronchial Circulation in Severe Multiple Peripheral Pulmonary Artery Stenosis (1965)

In an infant with severe, multiple, peripheral pulmonary artery stenoses angiography clearly demonstrated enlarged tortuous bronchial arteries, especially in the right lung, where a major tortuosity corresponded closely to the point of maximal intensity of a loud continuous murmur. Increased bronchial circulation may be responsible for continuous murmurs in patients with severe multiple peripheral pulmonary artery stenosis.
Building a Thermostable Membrane Protein (2000)

The poor stability of membrane proteins in detergent solution is one of the main technical barriers to their structural and functional characterization. Here we describe a solution to this problem for diacylglycerol kinase (DGK), an integral membrane protein from Escherichia coli. Twelve enhanced stability mutants of DGK were obtained using a simple screen. Four of the mutations were combined to create a quadruple mutant that had improved stability in a wide range of detergents. In n-octylglucoside, the wild-type DGK had a thermal inactivation half-life of 6 min at 55 degrees C, while the quadruple mutant displayed a half-life of 35 min at 80 degrees C. In addition, the quadruple mutant had improved thermodynamic stability. Our approach should be applicable to other membrane proteins that can be conveniently assayed.
Characterization of the interaction between serum mannan-binding protein and nucleic acid ligands (2009)

Serum MBP, also known as MBL, is a C-type lectin that is known to be a soluble host defense factor involved in innate immunity. It has been well established that dying microbes and apoptotic cells release highly viscous DNA that induces inflammation and septic shock, and apoptotic cells display fragmented DNA on their surfaces. However, PRRs that mediate the recognition and clearance of free DNA and fragmented DNA in apoptotic cells have not been characterized clearly. Although MBP was reported recently to bind DNA as a novel ligand, binding characterization and the recognition implications have not been addressed yet. In this study, we show that MBP can bind DNA and RNA in a calcium-dependent manner from a variety of origins, including bacteria, plasmids, synthetic oligonucleotides, and fragmented DNA of apoptotic cells. Direct binding and competition studies indicate that MBP binds nucleic acids via its CRD to varying degrees and that MBP binds dsDNA more effectively than ssDNA and ssRNA. Furthermore, we reveal that the MBP-DNA complex does not trigger complement activation via the MBP lectin pathway, and the lectin pathway of complement activation is required for MBP-mediated enhancement of phagocytosis of targets bearing MBP ligands and that MBP can recognize the fragmented DNA presented on apoptotic cells. Therefore, we propose that the MBP lectin pathway may support effective recognition and clearance of cellular debris by facilitating phagocytosis, possibly through immunomodulatory mechanisms, thus preventing autoimmunity.
A Solution to the Hidden-Line Problem for Computer-Drawn Polyhedra (1970)

The "hidden-line problem" for computer-drawn polyhedra is the problem of determining which edges, or parts of edges, of a polyhedra are visible from a given vantage point. This is an important problem in computer graphics, and its fast solution is especially critical for on-line CRT display applications. The method presented here for solving this problem is believed to be faster than previously known methods. An edge classification scheme is described that eliminates at once most of the totally invisible edges. The remaining, potentially visible edges are then tested in paths, which eventually cover the whole polyhedra. These paths are synthesized in such a way as to minimize the number of calculations. Both the case of a cluster of polyhedra and the illumination problem in which a polyhedron is illuminated from a point source of light are treated as applications of the general algorithm. Several illustrative examples are included.
Optimizations of Stored Vbr Video Transmission on Cbr Channel (1997)

In this paper, a new method is proposed to optimize stored VBR (variable-bit-rate) video transmission on CBR (constant-bit-rate) channel. The proposed method can minimize both the buffer requirement and workahead for a given peak transmission rate. Besides, the network utilization is maximized with the minimum service connection time. These problem parameters are not optimized at the same time in the conventional approaches. In this paper, we at first present the Lazy scheme to determine the minimum buffer and workahead required for a given peak transmission rate. Then, the Aggressive scheme is applied to maximize the system resource utilization (e.g., network bandwidth). The proposed schemes can be easily extended to transmit the VBR video with the minimum rate variability, or to resolve the buffer-constrained transmission problem with the minimum peak transmission rate for a given buffer size. Experiments to many well-known benchmark video traces show that the proposed method can obt...
Digital case library: a resource for teaching, learning, and diagnosis support in radiology. (1995)

The authors compiled a digital case library, a database of cases for intracranial masses, that can be used as an electronic teaching file and image source for case-based teaching applications, electronic textbooks, and diagnosis support tools. The library is a relational database with a feature-coded image archive that is structured around relevant radiologic findings. Its index for coding image content is structured as a hierarchical image description index that uses the relational format. Rules that control the search direction within the library and that generate lists of diagnostic hypotheses for decision support tools are embedded within the database structure. Currently, the library consists of 200 cases and 1,100 images that present intracranial masses on radiographs, computed tomograms, magnetic resonance images, and angiograms. Each image in the library is indexed according to its radiologic content. The user may search for reference images that contain particular radiologic features by formulating image content-based queries. The hierarchical index of radiologic findings allows multilevel query formulation that depends on the user's level of experience.
The synthesis of heterobifunctional linkers for the conjugation of ligands to molecular probes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe synthesis of heterobifunctional linkers for the conjugation of ligands to molecular probesCarolyn R. Bertozzi and Mark D. BednarskiCite this: J. Org. Chem. 1991, 56, 13, 4326–4329Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/jo00013a053https://doi.org/10.1021/jo00013a053research-articleACS PublicationsRequest reuse permissionsArticle Views2257Altmetric-Citations59LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Nonlinear response functions for the three-dimensional spectroscopies (2001)

Theoretical descriptions of the three-dimensional spectroscopies are presented in this paper by calculating the associated nonlinear response function. Previously, the harmonic approximation with the Wick’s theorem was used to obtain theoretical expression of the three-dimensional vibrational response function, by treating the mechanical and electrical anharmonicities perturbatively. However, the bath-induced memory effect and anharmonicity-induced frequency shift were not correctly taken into account by the previous theory. By incorporating the system–bath interaction properly, the general nonlinear response functions for the three-dimensional vibrational, vibrational-electronic, or electronic spectroscopies are obtained and discussed in detail. By using the resultant nonlinear response function, two-color vibrational photon echo, three-dimensional sum- and difference-frequency generation spectroscopies, and two-color infrared pump–probe spectroscopy are theoretically proposed.
Tri(n-Butyl) Phosphate/Detergent Treatment ofLicensed Therapeutic and Experimental Blood Derivatives (1987)

Incubation of an AHF concentrate with 0.3% tri(n-butyl)phosphate (TNBP) and 0.2% sodium cholate was shown to inactivate at least 10,000 infectious doses of lipid-enveloped viruses, including hepatitis B and non-A, non-B viruses and HTLV-III [Prince et al., Lancet i, pp. 706-710, 1986]. The use of TNBP/detergent combinations for virus sterilization was evaluated further to determine its effect on the structure and function of a wide variety of blood proteins. Vesicular stormatitis and Sindbis viruses were used as markers of virus inactivation. TNBP/detergent treatment did not significantly alter the function of AHF, factor VII, factor IX, factor X, fibrinogen, factor XIII, fibronectin, anti-HBsAg and anti-HA in normal immune serum globulin, haptoglobin, tumor necrosis factor, a-interferon, and both native and chemically polymerized stroma-free hemoglobin. As compared with partially purified derivatives, the extent of virus sterilization of plasma and component cryoprecipitate with 0.3% TNBP and 0.2% sodium cholate at ambient temperature could be improved by raising the TNBP concentration and temperature. Virus sterilization by TNBP/detergent mixtures appears to be generally applicable to blood protein derivatives.
Identification of a new locus involved in expression of Haemophilus influenzae type b lipooligosaccharide (1994)

Previous studies have shown that changes in the expression of the Haemophilus influenzae type b (Hib) lipooligosaccharide (LOS) epitope reactive with monoclonal antibody (MAb) 5G8 can be correlated with alterations in the virulence of some Hib strains. To identify the locus involved in expression of this particular LOS epitope, a genomic library was constructed in the plasmid shuttle vector pGJB103 from Hib strain DL42, which constitutively expressed LOS reactive with MAb 5G8. This library was used to transform a second Hib strain (DL180) that normally does not express this LOS epitope, and a recombinant clone was identified that bound MAb 5G8. Subcloning of different regions of the Hib DL42 DNA insert in this recombinant plasmid determined that a 1.9-kb EcoRI fragment, designated lex-2, was responsible for transforming Hib strain DL180 to reactivity with MAb 5G8. Nucleotide sequence analysis revealed the presence of two contiguous open reading frames (ORFs) in lex-2, the first of which contained 18 tandem repeats of the nucleotide tetramer GCAA near its 5' end. Sequence analysis of PCR-derived products from MAb 5G8-reactive and -nonreactive Hib DL180 colonies established that 18 GCAA repeats were associated with expression of the LOS epitope that bound MAb 5G8. Mutational analysis determined that a functional ORF 2 was essential for expression of the MAb 5G8-reactive LOS epitope. The nucleotide tetramer GCAA repeat present in ORF 1 was also detected in at least two different chromosomal regions in all Hib strains tested. The availability of the cloned lex-2 locus should facilitate future analysis of the complex regulatory mechanisms involved in expression of LOS epitopes by this pathogen.
Phosphorylation of serine‐46 in HPr, a key regulatory protein in bacteria, results in stabilization of its solution structure (1995)

The serine-phosphorylated form of histidine-containing protein (HPr), a component of the phosphoenolpyruvate:sugar phosphotransferase system from Bacillus subtilis, has been characterized by NMR spectroscopy and solvent denaturation studies. The results indicate that phosphorylation of Ser 46, the N-cap of alpha-helix-B, does not cause a conformational change but rather stabilizes the helix. Amide proton exchange rates in helix-B are decreased and phosphorylation stabilizes the protein to solvent and thermal denaturation, with a delta delta G of 0.7-0.8 kcal mol-1. A mutant in which Ser 46 is replaced by aspartic acid shows a similar stabilization, indicating that an electrostatic interaction between the negatively charged groups and the helix macrodipole contributes significantly to the stabilization.
Uroplakin Gene Expression by Normal and Neoplastic Human Urothelium (1998)

cDNA sequences for human uroplakins UPIa, UPIb, UPII, and UPIII were cloned and used to investigate uroplakin transcription by normal and neoplastic urothelial cells. Normal urothelium expressed mRNA for all four uroplakins, although UPIII could be detected only by ribonuclease protection assay. By in situ hybridization, UPIa and UPII were confined to superficial cells and UPIb was also expressed by intermediate cells. Cultured normal human urothelial cells showed a proliferative basal/intermediate cell phenotype and constitutive expression of UPIb only. Uroplakin expression by transitional cell carcinoma cell lines was related to their differentiated phenotype in vitro. RT4 cells expressed all uroplakins, VM-CUB-3 expressed three uroplakins, RT112 and HT1376 cells expressed only UPIb in high abundance, and COLO232, KK47, and EJ cells had no detectable expression. These results correlated with patterns of uroplakin expression in tumors. UPIa and UPII were detected superficially only in well differentiated transitional cell carcinoma papillae. UPIb was positive in seven of nine and overexpressed in five of nine noninvasive transitional cell carcinomas and was also present in four of eight invasive transitional cell carcinomas. Lymph node metastases retained the same pattern of UPIb expression as the primary tumor. Unlike the three differentiation-regulated uroplakins, UPIb may have an alternative role in urothelial cell/tissue processes.
Full-Thickness Skin Wound Healing Using Human Placenta-Derived Extracellular Matrix Containing Bioactive Molecules (2012)

The human placenta, a complex organ, which facilitates exchange between the fetus and the mother, contains abundant extracellular matrix (ECM) components and well-preserved endogenous growth factors. In this study, we designed a new dermal substitute from human placentas for full-thickness wound healing. Highly porous, decellularized ECM sheets were fabricated from human placentas via homogenization, centrifugation, chemical and enzymatic treatments, molding, and freeze-drying. The physical structure and biological composition of human placenta-derived ECM sheets dramatically supported the regeneration of full-thickness wound in vivo. At the early stage, the ECM sheet efficiently absorbed wound exudates and tightly attached to the wound surface. Four weeks after implantation, the wound was completely closed, epidermic cells were well arranged and the bilayer structure of the epidermis and dermis was restored. Moreover, hair follicles and microvessels were newly formed in the ECM sheet-implanted wounds. Overall, the ECM sheet produced a dermal substitute with similar cellular organization to that of normal skin. These results suggest that human placenta-derived ECM sheets provide a microenvironment favorable to the growth and differentiation of cells, and positive modulate the healing of full-thickness wounds.
The 2013 British Menopause Society & Women’s Health Concern recommendations on hormone replacement therapy (2013)

The British Menopause Society (BMS) recommendations on hormone replacement therapy (HRT) are designed to complement the BMS Observations and Recommendations on menopause management, submitted to the Department of Health in the UK and published in full in Menopause International, The Journal of the British Menopause Society and in the Royal College of Obstetricians and Gynaecologists Expert Advisory Group Report, High Quality Women’s Health Care. Our key recommendation is that all women should be able to access advice on how they can optimise their menopause transition and beyond, with particular reference to lifestyle and diet and an opportunity to discuss the pros and cons of complementary therapies andHRT. The following information based on the latest available evidence can be used to provide guidance to prescribers of HRT and alternatives. An extensive reference section and links to useful websites provide an opportunity to access extensive evidence based information in each key area.
Preparation and properties of magnetic nano‐ and microsized particles for biological and environmental separations (2007)

The paper presents a critical overview on magnetic nanoparticles and microspheres used as separation media in different fields of chemistry, biochemistry, biology, and environment protection. The preparation of most widely used magnetic iron oxides in appropriate form, their coating or encapsulation in polymer microspheres, and functionalization is discussed in the first part. In the second part, new developments in the main application areas of magnetic composite particles for separation and catalytical purposes are briefly described. They cover separations and isolations of toxic inorganic and organic ions, proteins, and other biopolymers, cells, and microorganisms. Only selected number of relevant papers could be included due to the restricted extent of the review.
DESIGNING CLINICAL TRIALS FOR AGE-RELATED GEOGRAPHIC ATROPHY OF THE MACULA (2007)

These data should be helpful in planning future treatment trials for GA.