gebhart/patrepeval huggingface dataset:
Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels (2020)

IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.
Clinical Effects of Whole-body Hyperthermia in Advanced Malignancy (1974)

Fifty-one patients in the terminal stages of cancer have been treated with whole-body hyperthermia either alone (38 cases) or in combination with chemotherapy (13 cases). Altogether 227 treatment sessions were held averaging four hours each. The most sensitive tumours were those of the gastrointestinal tract and sarcomas. Breast and genitourinary tumours did not respond, and lung tumours and melanomas were only partially responsive. Major complications were remarkably few.
The RTX cytotoxin-related FrpA protein of Neisseria meningitidis is secreted extracellularly by meningococci and by HlyBD+ Escherichia coli (1993)

Neisseria meningitidis produces proteins (FrpA and FrpC) related to the RTX cytotoxin family. In meningococcal strain FAM20 these proteins were both localized in the outer membrane and secreted into the extracellular medium. An Escherichia coli strain with wild-type hemolysin secretion genes hlyB and hlyD and containing a cloned frpA gene secreted FrpA, whereas an isogenic hlyBD mutant strain did not. Low-stringency DNA hybridization revealed hlyBD-like sequences in N. meningitidis FAM20, suggesting that a similar RTX secretion system exists in meningococci. Structural features found at the C termini of other RTX proteins and thought to be important for their secretion were also found at the C terminus of FrpA. The secretion of FrpA from E. coli by heterologous RTX transport proteins further demonstrates the relation of the FrpA protein to RTX toxins.
Detection of clonality in follicular lymphoma using formalin-fixed, paraffin-embedded tissue samples and BIOMED-2 immunoglobulin primers (2010)

An improved PCR protocol for detection of clonality in FFPE samples using BIOMED-2 IG primers is presented. For best performance, a combination of IGH and IGK analyses is recommended.
Strongly coupled critical current density values achieved in Y1Ba2Cu3O7−δ coated conductors with near-single-crystal texture (2003)

One of the most intensely researched subjects in the development of YBa2Cu3O7−δ (YBCO)-based coated conductors is the methodology for achieving ever-sharper film texture on flexible metal substrates. This is a critical issue due to the intrinsic weak-link behavior that results in depressed critical current density (Jc) in polycrystalline YBCO. Using ion-beam-assisted deposition of magnesium oxide, we have achieved YBCO texture on superalloy substrates approaching that on single-crystal oxide substrates. This advance has allowed us to fabricate coated conductor samples with Jcs that are as high as for films on oxide crystals; for example, &amp;gt;2 MA/cm2 (75 K, self-field) at a YBCO thickness of ∼1.5 μm.
Studies on Effects of Drugs upon Protoscoleces of Echinococcus granulosus in Vitro : II Scolicidal Effect of Antibiotics, Antineoplastic and Other Agents against Echinococcus granulosus in Vitro (1979)

departmental bulletin paper
Agonist Anti-Human CD27 Monoclonal Antibody Induces T Cell Activation and Tumor Immunity in Human CD27–Transgenic Mice (2013)

The CD70/CD27 pathway plays a significant role in the control of immunity and tolerance, and previous studies demonstrated that targeting murine CD27 (mCD27) with agonist mAbs can mediate antitumor efficacy. We sought to exploit the potential of this pathway for immunotherapy by developing 1F5, a fully human IgG1 mAb to human CD27 (hCD27) with agonist activity. We developed transgenic mice expressing hCD27 under control of its native promoter for in vivo testing of the Ab. The expression and regulation of hCD27 in hCD27-transgenic (hCD27-Tg) mice were consistent with the understood biology of CD27 in humans. In vitro, 1F5 effectively induced proliferation and cytokine production from hCD27-Tg-derived T cells when combined with TCR stimulation. Administration of 1F5 to hCD27-Tg mice enhanced Ag-specific CD8(+) T cell responses to protein vaccination comparably to an agonist anti-mCD27 mAb. In syngeneic mouse tumor models, 1F5 showed potent antitumor efficacy and induction of protective immunity, which was dependent on CD4(+) and CD8(+) T cells. The requirement of FcR engagement for the agonistic and antitumor activities of 1F5 was demonstrated using an aglycosylated version of the 1F5 mAb. These data with regard to the targeting of hCD27 are consistent with previous reports on targeting mCD27 and provide a rationale for the clinical development of the 1F5 mAb, for which studies in advanced cancer patients have been initiated under the name CDX-1127.
In vitro and in vivo anti-Candida activity and toxicology of LY121019. (1984)

LY121019 (N-p-octyloxybenzoylechinocandin B nucleus) is a semisynthetic antifungal antibiotic that possesses potent anti-Candida activity. The MIC50 and the MIC90 for both LY121019 and amphotericin B were 0.625 and 1.25 micrograms/ml, respectively. Only an 8-fold increase in the MIC against C. albicans occurred during 34-day exposure to subinhibitory concentrations indicating that LY121019 has a low potential for causing resistance development. Scanning electron microscopic studies revealed that LY121019 caused severe damage to the C. albicans cell. The ED50's for LY121019 and amphotericin B administered parenterally to mice were 7.4 and 2.5 mg/kg, respectively. Parenterally administered LY121019 at doses of 6.25 mg/kg significantly reduced the recovery of C. albicans from infected mouse kidneys. Orally administered 50 and 100 mg/kg doses of LY121019 were effective in eliminating C. albicans from the gastrointestinal tract of infected mice. Topical application of 5% LY121019 was as effective as 3% nystatin in the treatment of superficial C. albicans infections. Local administration of LY121019, nystatin, or miconazole was effective against rat vaginal candidiasis. LY121019 was administered intravenously to dogs at doses up to 100 mg/kg/day, 5 days a week for 3 months; all dogs survived. Compound related effects included a histamine-like reaction, increased serum alkaline phosphatase and SGPT, fatty vacuolization of the liver, and some tissue damage at the injection site. The no effect dose in dog was 10 mg/kg. LY121019 had no more than 1/20 the toxicity of amphotericin B in the dog.
Fas and tumor necrosis factor receptor-mediated cell death: similarities and distinctions. (1994)

Fas antigen and two tumor necrosis factor receptors (TNFR), p55 and p75, are implicated in the triggering of cell death upon stimulation by natural ligands and specific monoclonal antibodies. However, the relative efficiency of each receptor, the mechanisms that regulate their function and the signaling pathways they employ, remain to be elucidated. In this study, fusion proteins, composed of the extracellular domain of CD40 and the intracellular and transmembrane domains of Fas, TNFRp55 and TNFRp75, were stably expressed in a human melanoma cell line that is deficient in Fas and TNFR expression. Transfectants were stimulated by a soluble recombinant form of the CD40 ligand gp39, and the effect on cell viability determined. Engagement of all three fusion proteins by the gp39 ligand induced lethal signals, but the rate at which cell death occurred was distinct. Fas-derived signals were observed to have the most rapid effect, killing most cells within hours of stimulation, whereas TNFRp55- and TNFRp75-associated signals resulted in cell death within 2-3 d after engagement by ligand. It is interesting to note that optimal cell killing by all three fusion proteins was dependent on a critical, low to intermediate, cell surface expression level. High levels of fusion protein expression, on the other hand, were associated with inhibition of cell death. Our results provide a model to study Fas and TNFR-mediated cell death and suggest a novel mechanism for the regulation of death signals triggered by members of the TNFR family.
Confocal compact scanning optical microscope based on compact disc technology (1991)

A compact scanning optical microscope (SOM) based on the optics and the mechanics of a compact disc (CD) player has been constructed. The low weight and compact construction of a CD player offer the possibility of scanning the entire microscope with respect to a stationary object. The compact scanning optical microscope is capable of measuring object-induced amplitude and phase changes of the light and is equipped with automatic focusing. The laser in the CD player is replaced by the endface of a single-mode fiber. The end face of the fiber acts both as the emitting source and as a point detector. Thus confocal detection is obtained without the problem of positioning a point detector with respect to a point source.
In Situ Hybridization of Human Erythropoietin in Pre -and Postnatal Kidneys (1995)

Due to the transient transcription of the gene of erythropoietin (EPO) in response to hypoxic stimuli, localization within the cell of origin in humans has not been possible. Under acutely induced transcription of the EPO gene, through severe bleeding (hematocrit < 10%), EPO transcripts were detected within renal interstitial cells in rodents. However, by immunohistochemistry or tissue culture, human tubular epithelial cells or glomerular mesangium have been shown to produce EPO, suggesting a species difference. Aiming to investigate the precise location of EPO in intact human kidneys, 38 fetal, infant, and adult kidneys were examined by in situ hybridization. Kidneys from patients with conditions predisposing to severe hypoxia and/or induced polycythemia were utilized, because under these conditions active EPO mRNA synthesis is expected. We found specific EPO mRNA transcripts within a small population of cortical interstitial cells of near-term or postnatal kidneys.
Four Functionally Distinct Populations of Human Effector-Memory CD8+ T Lymphocytes (2007)

In humans, the pathways of memory and effector T cell differentiation remain poorly defined. We have dissected the functional properties of ex vivo effector-memory (EM) CD45RA-CCR7- T lymphocytes present within the circulating CD8+ T cell pool of healthy individuals. Our studies show that EM T cells are heterogeneous and are subdivided based on differential CD27 and CD28 expression into four subsets. EM(1) (CD27+CD28+) and EM(4) (CD27-CD28+) T cells express low levels of effector mediators such as granzyme B and perforin and high levels of CD127/IL-7Ralpha. EM(1) cells also have a relatively short replicative history and display strong ex vivo telomerase activity. Therefore, these cells are closely related to central-memory (CD45RA-CCR7+) cells. In contrast, EM(2) (CD27+CD28-) and EM(3) (CD27-CD28-) cells express mediators characteristic of effector cells, whereby EM(3) cells display stronger ex vivo cytolytic activity and have experienced larger numbers of cell divisions, thus resembling differentiated effector (CD45RA+CCR7-) cells. These data indicate that progressive up-regulation of cytolytic activity and stepwise loss of CCR7, CD28, and CD27 both characterize CD8+ T cell differentiation. Finally, memory CD8+ T cells not only include central-memory cells but also EM(1) cells, which differ in CCR7 expression and may therefore confer memory functions in lymphoid and peripheral tissues, respectively.
Human Factor H-Related Protein 5 Has Cofactor Activity, Inhibits C3 Convertase Activity, Binds Heparin and C-Reactive Protein, and Associates with Lipoprotein (2005)

Factor H-related protein 5 (FHR-5) is a recently discovered member of the factor H (fH)-related protein family. FHR proteins are structurally similar to the complement regulator fH, but their biological functions remain poorly defined. FHR-5 is synthesized in the liver and consists of 9 short consensus repeats (SCRs), which display various degrees of homology to those of fH and the other FHR proteins. FHR-5 colocalizes with complement deposits in vivo and binds C3b in vitro, suggesting a role in complement regulation or localization. The current study examined whether rFHR-5 exhibits properties similar to those of fH, including heparin binding, CRP binding, cofactor activity for the factor I-mediated degradation of C3b and decay acceleration of the C3 convertase. rFHR-5 bound heparin-BSA and heparin-agarose and a defined series of truncations expressed in Pichia pastoris localized the heparin-binding region to within SCRs 5-7. rFHR-5 bound CRP, and this binding was also localized to SCRs 5-7. FHR-5 inhibited alternative pathway C3 convertase activity in a fluid phase assay; however, dissociation of the convertase was not observed in a solid phase assay. rFHR-5 displayed factor I-dependent cofactor activity for C3b cleavage, although it was apparently less effective than fH. In addition, we demonstrate association of FHR-5 with high density lipid lipoprotein complexes in human plasma. These results demonstrate that FHR-5 shares properties of heparin and CRP binding and lipoprotein association with one or more of the other FHRs but is unique among this family of proteins in possessing independent complement-regulatory activity.
Identification of the Depth of Burn Injury by Collagen Stainability (1984)

Heat-denatured collagen in burned skin stains red instead of blue in Masson's trichrome stain. This change in stainability corresponds to the loss of birefringence in slides examined in polarized light. The depth of the abnormal staining of the skin slices was proportional to the time and temperature of the heat exposure. It is concluded that the change in collagen stainability from blue to red relates to the loss of crystallinity or parallel alignment of the collagen fibers. It is further proposed that change in the stainability of collagen in the burns could be used to delineate the depth of the thermal skin injury or the effectiveness of the surgical excision or debridement of the wound by dressing materials.
Saponin and sapogenol. XXXIV. Chemical constituents of astragali radix, the root of Astragalus membranaceus Bunge. (1). Cycloastragenol, the 9,19-cyclolanostane-type aglycone of astragalosides, and the artifact aglycone astragenol. (1983)

Triterpene-oligoglycoside constituents of Astragali Radix, the root of Korean Astragalus membranaceus BUNGE (Leguminosae), were isolated. By means of enzymatic and chemical degradations, the 9, 19-cyclolanostane-type triterpene named cycloastragenol (1), which was the common genuine aglycone of ten of eleven astragalosides, and the lanost-9 (II)-ene-type counterpart named astragenol (5), which was an artifact aglycone secondarily formed from 1, were isolated. On the basis of chemical and physicochemical evidence, the structures of cycloastragenol and astragenol were elucidated as (20R, 24S)-3β, 6α, 16β, 25-tetrahydroxy-20, 24-epoxy-9, 19-cyclolanostane (1) and (20R, 24S)-3β, 6α, 16β, 25-tetrahydroxy-20, 24-epoxy-lanost-9 (11)-ene (5), respectively.
The functional role of tumor suppressor genes in gliomas (1998)

The ability to transfer exogenous genes to cancer cells has yielded a wealth of information about the neoplastic processes that occur at molecular and cellular levels. Current research focuses on defining the biochemical factors that govern the interplay between cell growth and cell death in gliomas. The identification of tumor suppressor genes has greatly enhanced our understanding of the molecular mechanism of brain tumors. Accomplishing the transition from basic science to clinical practice is a major challenge for the future of brain tumor research. The concept of tumor suppressor genes is examined, with particular emphasis on the functional studies of the role of the p53, p16, Rb, and PTEN/MMAC1 genes in gliomas. Moreover, recent advances linking tumor suppressor genes, apoptosis, and cell-cycle control pathways in brain tumors are reviewed. The ability to detect mutations in tumor suppressor genes plays an important role in cancer diagnosis and prognosis. Perhaps of greatest significance has been the realization that tumor suppressor genes may provide novel targets for development of specific anticancer therapies for brain tumors.
Predicting Sources of Dissolved Organic Nitrogen to an Estuary from an Agro-Urban Coastal Watershed (2016)

Dissolved organic nitrogen (DON) is the nitrogen (N)-containing component of dissolved organic matter (DOM) and in aquatic ecosystems is part of the biologically reactive nitrogen pool that can degrade water quality in N-sensitive waters. Unlike inorganic N (nitrate and ammonium) DON is comprised of many different molecules of variable reactivity. Few methods exist to track the sources of DON in watersheds. In this study, DOM excitation-emission matrix (EEM) fluorescence of eight discrete DON sources was measured and modeled with parallel factor analysis (PARAFAC) and the resulting model ("FluorMod") was fit to 516 EEMs measured in surface waters from the main stem of the Neuse River and its tributaries, located in eastern North Carolina. PARAFAC components were positively correlated to DON concentration. Principle components analysis (PCA) was used to confirm separation of the eight sources and model validation was achieved by measurement of source samples not included in the model development with an error of <10%. Application of FluorMod to surface waters of streams within the Neuse River Basin showed that while >70% of DON was attributed to natural sources, nonpoint sources, such as soil and poultry litter leachates and street runoff, accounted for the remaining 30%. This result was consistent with changes in land use from urbanized Raleigh metropolitan area to the largely agricultural Southeastern coastal plain. Overall, the predicted fraction of nonpoint DON sources was consistent with previous reports of increased organic N inputs in this river basin, which are suspected of impacting the water quality of its estuary.
Attenuation of Sound in Suspensions and Emulsions: Theory and Experiments (1972)

The absorption of sound in emulsions and suspensions is due to viscous and thermal transport processes occurring at the interface of the nonhomogeneities, as well as to the intrinsic absorption in the materials comprising the system. A complete description of these processes for systems of fluid particles suspended in fluid media was given by Epstein and Carhart [J. Acoust. Soc. Amer. 25, 553 (1953)]. However, subsequent investigators of liquid systems have generally neglected the thermal transport process. We show in this work that the Epstein-Carhart results provide a good description of our experimental attenuation data in emulsions, and that the thermal transport process can be the major factor in the attenuation. We have here also extended the theory further to include the attenuation in suspensions of solid particles, and good agreement is found between our theory and experimental results for aqueous suspensions of polystyrene spheres.
Chromosomal Deletion Formation System Based on Tn5 Double Transposition: Use For Making Minimal Genomes and Essential Gene Analysis (2003)

In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in the Escherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecular transposition events. Two similar transposons were developed. The first deletion transposon was utilized to create a consecutive set of deletions in the E. coli chromosome. The deletion procedure has been repeated 20 serial times to reduce the genome an average of 200 kb (averaging 10 kb per deletion). The second deletion transposon contains a conditional origin of replication that allows deleted chromosomal DNA to be captured as a complementary plasmid. By plating cells on media that do not support plasmid replication, the deleted chromosomal material is lost and if it is essential, the cells do not survive. This methodology was used to analyze 15 chromosomal regions and more than 100 open reading frames (ORFs). This provides a robust technology for identifying essential and dispensable genes.
Antimicrobial peptides: Resistant‐proof antibiotics of the new millennium (2004)

Abstract This review encompasses an update on the worldwide research activities made towards developing antimicrobials against the persistent threats from multidrug‐resistant gram‐negative infection. The lethality of endotoxin or lipopolysaccharide and its conserved bioactive moiety, lipid A, is discussed. We include documentation of our own research efforts towards the development of novel endotoxin antagonists and antimicrobials such as Sushi peptides, derived from the horseshoe crab Factor C, which show great promise for future prophylactic/therapeutic applications. The mechanism of microbicidal action of the Sushi peptides is postulated. In addition to Sushi peptides, we also present other approaches we have undertaken, such as screening for anti‐endotoxic peptides from a phage‐display library; a computational approach towards rational design of anti‐endotoxic and antimicrobial peptides; and finally, a novel alternative that is best analogized by the ancient Chinese medical practice of using “poison to kill poison,” which, in modern parlance, entails the innovative application of nonendotoxic Helicobacter pylori lipopolysaccharide/lipid A as a competitor to antagonize the endotoxicity of LPS, and hence, the display of antimicrobial properties. Drug Dev. Res. 62:317–335, 2004. © 2004 Wiley‐Liss, Inc.
Human prothrombinase complex assembly and function on isolated peripheral blood cell populations. (1985)

A membrane-bound Ca2+-dependent complex of the cofactor Factor Va and the enzyme Factor Xa comprises the prothrombinase coagulation complex which catalyzes the proteolytic conversion of prothrombin to thrombin. Analyses of the kinetics of prothrombin activation permit calculation of the stoichiometry and binding parameters governing the functional interactions of Factor Va and Factor Xa with isolated thrombin-activated human platelets and isolated leukocyte subpopulations. Our kinetic approach indicates that Factor Xa binds to approximately 2700 +/- 1000 (n = 8) functional sites on the surface of thrombin-activated platelets with an apparent dissociation constant (Kd) equal to 1.18 +/- 0.53 X 10(-10) M and kcat equal to 19 +/- 7 mol of thrombin/s/mol of Factor Xa bound. The store of Factor V in normal platelets prevents an analogous determination of the functional Factor Va platelet binding sites. Factor Va and Factor Xa titrations performed using platelets from a Factor V antigen-deficient individual indicate that Factor Va and Factor Xa form a 1:1 stoichiometric complex on the surface of thrombin-activated platelets. Both binding isotherms are governed by the same apparent Kd (approximately equal to 10(-10) M) and expressed the same kcat/site (14-17 s-1. Factor Xa-platelet binding parameters are not altered by the use of different platelet agonists, the choice of anticoagulant, or platelet washing procedure. Kinetics of prothrombin activation indicate also that monocytes, lymphocytes, and neutrophils possess, respectively, 16,000, 45,000, and 8,000 Factor Va-Factor Xa receptor sites/cell, which are all governed by apparent KdS approximately equal to 10(-10) M. Enzymatic complexes bound to monocytes or neutrophils exhibit kcat values similar to the platelet-bound complex. Complexes bound to lymphocytes are only 25% as active.