gebhart/patrepeval huggingface dataset:
Tregalizumab – A Monoclonal Antibody to Target Regulatory T Cells (2016)

Regulatory T cells (Tregs) represent a subpopulation of CD4+ T cells, which are essential for the maintenance of immunological tolerance. The absence or dysfunction of Tregs can lead to autoimmunity and allergies. The restoration of functional Tregs and/or Treg cell numbers represents a novel and attractive approach for the treatment of autoimmune diseases, e.g. rheumatoid arthritis (RA). The CD4 cell surface receptor is a target for modulation of T cell function. Monoclonal antibodies (mAbs) against CD4 have previously been tested for the treatment of autoimmune diseases including RA. Furthermore, in model systems, anti-CD4 antibodies are able to induce tolerance and mediate immunomodulatory effects through a variety of mechanisms. Despite the availability of innovative and effective therapies for RA, many patients still have persistently active disease or experience adverse events which can limit use. A growing body of evidence suggests that Treg modulation could offer a new therapeutic strategy in RA and other autoimmune disorders. Here we describe tregalizumab (BT-061), which is a novel, non-depleting IgG1 mAb that binds to a unique epitope of CD4. Tregalizumab represents the first humanized anti-CD4 mAb that selectively induces Treg activation
Characterization of the Human Folate Receptor Alpha Via Novel Antibody-Based Probes (2011)

Folate receptor alpha (FRA) is a cell surface protein whose aberrant expression in malignant cells has resulted in its pursuit as a therapeutic target and marker for diagnosis of cancer. The development of immune-based reagents that can reproducibly detect FRA from patient tissue processed by varying methods has been difficult due to the complex post-translational structure of the protein whereby most reagents developed to date are highly structure-sensitive and have resulted in equivocal expression results across independent studies. The aim of the present study was to generate novel monoclonal antibodies (mAbs) using modified full length FRA protein as immunogen in order to develop a panel of mAbs to various, non-overlapping epitopes that may serve as diagnostic reagents able to robustly detect FRA-positive disease. Here we report the development of a panel of FRA-specific mAbs that are able to specifically detect FRA using an array of diagnostic platforms and methods. In addition, the methods used to develop these mAbs and their diverse binding properties provide additional information on the three dimensional structure of FRA in its native cell surface configuration.
Update on the use of rituximab for intractable rheumatoid arthritis (2009)

It has been 3 years since rituximab, a mouse x human chimeric anti-CD20 monoclonal antibody that selectively depleted B cells, was approved by the FDA for the treatment of moderate to severe rheumatoid arthritis (RA) with an inadequate response to anti-TNF therapies. Since approval rituximab has become a part of standard treatment, and additional data have become available on long-term efficacy and safety both from clinical trials and from post-marketing surveillance. In open long-term follow-up from clinical trials, patients treated with multiple courses of rituximab continued to respond in terms of signs and symptoms, and damage assessed radiographically was significantly inhibited. Moreover, the rate of serious infectious events was not increased as the number of courses increased. However, because of case reports of progressive multifocal leukoencephalopathy in patients treated with rituximab for non-malignant conditions, a black box warning has been added. Studies on the immunologic correlates of response to rituximab treatment including B cell subsets in peripheral blood and synovial biopsies are providing clues into how rituximab works for autoimmune disease. However, at this time we are not able to explain why some patients do not respond and cannot predict who will respond. Future challenges for the further development of rituximab for intractable RA will be discussed.
CCL2 and CXCL1 trigger calcitonin gene-related peptide release by exciting primary nociceptive neurons (2005)

Chemokines are important mediators in immune responses and inflammatory processes. Calcitonin gene-related peptide (CGRP) is produced in dorsal root ganglion (DRG) neurons. In this study, CGRP radioimmunoassay was used to investigate whether the chemokines CCL2 and CXCL1 could trigger CGRP release from cultured DRG neurons of neonatal rats and, if so, which cellular signaling pathway was involved. The results showed that CCL2 and CXCL1 ( approximately 5-100 ng/ml) evoked CGRP release and intracellular calcium elevation in a pertussis toxin (PTX)-sensitive manner. The CGRP release by CCL2 and CXCL1 was significantly inhibited by EGTA, omega-conotoxin GVIA (an N-type calcium channel blocker), thapsigargin, and ryanodine. Pretreatment of DRG neurons for 30 min with the inhibitors of phospholipase C (PLC) and protein kinase C (PKC) but not mitogen-activated protein kinases (MAPKs) significantly reduced CCL2- or CXCL1-induced CGRP release and intracellular calcium elevation. Intraplantar injection of CCL2 or CXCL1 produced hyperalgesia to thermal and mechanical stimulation in rats. These data suggest that CCL2 and CXCL1 can stimulate CGRP release and intracellular calcium elevation in DRG neurons. PLC-, PKC-, and calcium-induced calcium release from ryanodine-sensitive calcium stores signaling pathways are involved in CCL2- and CXCL1-induced CGRP release from primary nociceptive neurons, in which chemokines produce painful effects via direct actions on chemokine receptors expressed by nociceptive neurons.
Expression Profiles of mRNAs for Osteoblast and Osteoclast Proteins as Indicators of Bone Loss in Mouse Immobilization Osteopenia Model (1999)

An experimental mouse model for disuse osteopenia was developed using unilateral cast immobilization. Analysis of the distal femurs and proximal tibias by quantitative histomorphometry revealed significant osteopenia within 10-21 days of immobilization. At 3 weeks, bone loss was also demonstrated with peripheral quantitative computed tomography as diminished bone mineral content and as concomitant reduction in the cross-sectional moment of inertia. These structural and geometrical alterations resulted in decreased strength of the distal femurs tested by cantilever bending. Analysis of the underlying cellular and molecular mechanisms of bone loss revealed a rapid increase in bone resorption within 3 days of immobilization. The mRNA levels for cathepsin K, matrix metalloproteinase-9, and tartrate resistant acid phosphatase were all significantly increased during the 21-day immobilization period, but with different expression profiles. These increases were paralleled by an increased number of osteoclasts as measured by histomorphometry. By day 6 of immobilization, the balance of bone turnover was further shifted toward net bone loss as the mRNA levels for major bone components (type I collagen and osteocalcin) were decreased. In histomorphometric analysis this was observed as reduced rates of mineral apposition and bone formation after 10 days of immobilization. The results of this study demonstrate that immobilization has a dual negative effect on bone turnover involving both depressed bone formation and enhanced bone resorption.
Bootstrapping A System For Phoneme Recognition And Keyword Spotting In Unaccompanied Singing. (2016)

[TODO] Add abstract here.
Abundant expression of polyomavirus middle T antigen and dihydrofolate reductase in an adenovirus recombinant (1987)

A modular gene with a cDNA encoding the polyomavirus middle T antigen positioned behind the adenovirus type 2 major late promoter and tripartite leader was substituted for the E1a region in an adenovirus vector. Permissive human cells infected with this recombinant produce middle T protein at levels as high as those of the most abundant late adenoviral proteins, e.g., hexon or fiber. This level represents at least a 40-fold increase over that observed in a polyomavirus lytic infection of murine cells. Partial proteolytic mapping showed that this protein has the same primary structure as middle T protein produced in polyomavirus-infected murine cells. The adenovirus recombinant-generated middle T protein exhibited in vitro kinase activity, although at an approximately 10-fold-lower specific activity than that of middle T protein from polyomavirus-infected murine cells. Comparison of the expression levels of this middle T antigen-containing adenovirus vector with a similar construction encoding dihydrofolate reductase suggested that the translation efficiency of the inserted gene was dependent upon the proximity of its initiation codon to the tripartite leader. We tested this possibility by comparing three dihydrofolate reductase recombinants among which the spacing between the initiation codon and tripartite leader varied from 188 to 36 nucleotides. The efficiency of expression of dihydrofolate reductase protein dramatically increased as this spacing was reduced.
Blind subjects implanted with the Argus II retinal prosthesis are able to improve performance in a spatial-motor task (2010)

In a study on the largest cohort of visual prosthesis recipients to date, we found that artificial vision augments information from existing vision in a spatial-motor task. Clinical trials registry no NCT00407602.
Molecular Characterization of the Locus Encoding Biosynthesis of the Lipopolysaccharide O Antigen of Escherichia coli Serotype O113 (1999)

Shiga toxigenic Escherichia coli (STEC) strains are a diverse group of organisms capable of causing severe gastrointestinal disease in humans. Within the STEC family, eae-positive STEC strains, particularly those belonging to serogroups O157 and O111, appear to have greater virulence for humans. However, in spite of being eae negative, STEC strains belonging to serogroup O113 have frequently been associated with cases of severe STEC disease, including hemolytic-uremic syndrome (HUS). Western blot analysis with convalescent-phase serum from a patient with HUS caused by an O113:H21 STEC strain indicated that human immune responses were directed principally against lipopolysaccharide O antigen. Accordingly, the serum was used to isolate a clone expressing O113 O antigen from a cosmid library of O113:H21 DNA constructed in E. coli K-12. Sequence analysis indicated that the O113 O-antigen biosynthesis (rfb) locus contains a cluster of nine genes which may be cotranscribed. Comparison with sequence databases identified candidate genes for four glycosyl transferases, an O-acetyl transferase, an O-unit flippase, and an O-antigen polymerase, as well as copies of galE and gnd. Two additional, separately transcribed genes downstream of the O113 rfb region were predicted to encode enzymes involved in synthesis of activated sugar precursors, one of which (designated wbnF) was essential for O113 O-antigen synthesis, and so is clearly a part of the O113 rfb locus. Interestingly, expression of O113 O antigen by E. coli K-12 significantly increased in vitro adherence to both HEp-2 and Henle 407 cells.
Fetal Expressed Gene Analysis in Maternal Blood: A New Tool for Noninvasive Study of the Fetus (2003)

Noninvasive approaches to prenatal diagnosis can avoid the risk of fetal loss associated with invasive procedures such as chorionic villus sampling, amniocentesis, and cordocentesis. Isolation of fetal cells from maternal blood requires further improvements before it can be applied in a clinical setting (1), but the reliability of cell-free fetal DNA analysis in maternal plasma or serum is now well established (2)(3)(4). As a result, it is currently used in specialized centers for the determination of fetal sex and fetal RhD status for the management of pregnant women at risk for X-linked disorders (5) or RhD alloimmunization (6). Because fetal DNA in maternal serum is circulating in an excess background of maternal DNA, clinical applications are restricted mainly to the detection of fetal sequences distinct from the mother’s DNA sequences.

Fetal RNA in maternal blood may be an alternative source of fetal nucleic acids. Al-Mufti et al. (7) detected specific RhD mRNA in mononuclear fetal cells isolated from blood of RhD-negative pregnant women, and Lo’s group demonstrated the presence of Y-chromosome-specific ( ZFY ) mRNA in maternal plasma of women carrying a male fetus (8). These two applications, however, again require fetal sequences that differ from the mother’s.

We have investigated the presence in maternal blood of fetal transcripts that may have the same sequence as that of the mother. Human chorionic gonadotropin (hCG) mRNA is a good candidate because it is a pregnancy-specific polypeptide hormone produced by the placenta and is specifically expressed in the fetal syncytiotrophoblast.

We studied 43 pregnant women and 20 nonpregnant women who had previously given birth to at least one neonate. After receiving informed consent, we collected blood (2.5 mL) into PAXgeneTM tubes to reduce RNA degradation (9). All pregnancy samples were obtained before …
Enhanced Kerr Nonlinearity via Atomic Coherence in a Three-Level Atomic System (2001)

We measure the Kerr-nonlinear index of refraction of a three-level Lambda-type atomic system inside an optical ring cavity. The Kerr nonlinearity is modified and greatly enhanced near atomic resonant conditions for both probe and coupling beams. The Kerr nonlinear coefficient n(2) changes sign when the coupling beam frequency detuning switches sign, which can lead to interesting applications in optical devices such as all-optical switches.
Antibacterial mechanisms of lysozyme on Streptococcus mutans. (1990)

Lysozyme is a dominant member of the antibacterial complex of human saliva and has the potential to kill bacteria by direct lysis or by mechanisms (not completely understood) that are independent of its muramidase activity. The muramidase-independent bactericidal activity appears to depend upon its cationic character. Bacterial death may be due to inhibition of nutrient transport (eg. glucose) and disruption of membrane integrity. This review also describes common bactericidal mechanisms of several cationic peptides/proteins to support the cationic-dependent bactericidal model of lysozyme.
Tumor metabolism: cancer cells give and take lactate (2008)

Tumors contain well-oxygenated (aerobic) and poorly oxygenated (hypoxic) regions, which were thought to utilize glucose for oxidative and glycolytic metabolism, respectively. In this issue of the JCI, Sonveaux et al. show that human cancer cells cultured under hypoxic conditions convert glucose to lactate and extrude it, whereas aerobic cancer cells take up lactate via monocarboxylate transporter 1 (MCT1) and utilize it for oxidative phosphorylation (see the related article beginning on page 3930). When MCT1 is inhibited, aerobic cancer cells take up glucose rather than lactate, and hypoxic cancer cells die due to glucose deprivation. Treatment of tumor-bearing mice with an inhibitor of MCT1 retarded tumor growth. MCT1 expression was detected exclusively in nonhypoxic regions of human cancer biopsy samples, and in combination, these data suggest that MCT1 inhibition holds potential as a novel cancer therapy.
Selective perfusion of the upper and lower body under different levels of hypothermia in a patient with coronary artery disease and dissecting thoracoabdominal aortic aneurysm. (2004)

Hypothermia is known to protect the myocardium and the spinal cord during ischemia. However the risk of complications increases with lower hypothermic conditions. In this paper we report a 62-year-old male patient with concomitant coronary artery disease who was surgically treated for a thoracoabdominal aortic aneurysm and an abdominal paraanastomotic pseudoaneurysm using selective perfusion of the upper and lower body under mild and deep hypothermia respectively. The patient was discharged uneventfully and only experienced transient delirium. We believe this novel modality may be a promising alternative in selected candidates.
Potent inhibitory effects of steroids in an in vitro model of angiogenesis (1996)

The regulation of angiogenesis in the ovarian follicle and corpus luteum is unclear. Steroids are produced at very high concentrations in these tissues and we therefore examined the effect of steroids on angiogenesis in vitro. Explants of rat aorta were embedded in collagen gel and cultured in serum-free medium. Capillary-like microvessels were produced from the explants and microvessel number and length were measured in the presence and absence of steroids. At a concentration of 10 micrograms/ml, cortisol, progesterone, 17 alpha-hydroxyprogesterone and medroxyprogesterone acetate produced degeneration of microvessels after 7 days of steroid treatment (P < 0.01). Androstenedione and tetrahydro-S-(11-deoxytetrahydrocortisol) (tetrahydro S) produced degeneration at a slower rate: androstenedione inhibited microvessel growth after 11 days (P < 0.01) and tetrahydro S after 14 days (P < 0.05). Oestriol had no effect on microvessels; oestrone had a slow degenerative effect with significant inhibition seen after 14 days (P < 0.01). Oestradiol-17 beta at a concentration of 10 micrograms/ml completely inhibited microvessel growth from the explant cultures (P < 0.01) while at 1 microgram/ml it caused degenerative effects on growing microvessels. The effects of oestradiol and cortisol were reversible on removal of steroid-containing medium and replacement with 10% serum. We conclude that oestradiol may modulate angiogenesis in tissues in which the steroid concentration is high.
Steric hindrances in protein permeation through the basement membrane studied in acellular kidney. (1987)

Acellular kidney preparations were used for studying the steric hindrances in the glomerular basement barrier. In accordance with the reports of other authors our data have provided evidence that, in this model the basement membrane does not suffer from gross ruptures and also preserves its integrity with regard to the proteoglycan moiety. Detergent treatment of the passing protein solution (used for the removal of cellular elements) results in abolishing charge differences. Under such conditions the molar percentage of proteins passing through the GBM barrier is inversely proportional to the logarithm of relative molecular mass. Application of different detergents in preparing the acellular kidney (Triton X-100 and sarcosyl) and in the treatment of individual proteins under study leads to linear relationships of different slopes which is ascribed to the differences in electrostatic repulsive forces introduced by the detergent. The proportion of molecules passing through the GBM barrier increases with increasing protein concentration in the perfusate approaching a limiting value at very high concentrations (0.1 mmol/l). This indicates that the individual protein molecules compete for the free space in basement membrane channels, a conclusion further supported by the fact that permeation of a protein through the barrier can be effectively blocked by increasing the overall protein concentration in the perfusate with another protein species.
Fas (CD95) expression and death-mediating function are induced by CD4 cross-linking on CD4+ T cells. (1996)

The CD4 receptor contributes to T-cell activation by coligating major histocompatibility complex class II on antigen presenting cells with the T-cell receptor (TCR)/CD3 complex, and triggering a cascade of signaling events including tyrosine phosphorylation of intracellular proteins. Paradoxically, CD3 cross-linking prior to TCR stimulation results in apoptotic cell death, as does injection of anti-CD4 antibodies in vivo of CD4 ligation by HIV glycoprotein (gp) 120. In this report we investigate the mechanism by which CD4 cross-linking induces cell death. We have found that CD4 cross-linking results in a small but rapid increase in levels of cell surface Fas, a member of the tumor necrosis factor receptor family implicated in apoptotic death and maintenance of immune homeostasis. Importantly, CD4 cross-linking triggered the ability of Fas to function as a death molecule. Subsequent to CD4 cross-linking, CD4+ splenocytes cultured overnight became sensitive to Fas-mediated death. Death was Fas-dependent, as demonstrated by cell survival in the absence of plate-bound anti-Fas antibody, and by the lack of CD4-induced death in cells from Fas-defective lymphoproliferative (lpr) mice. We demonstrate here that CD4 regulates the ability of Fas to induce cell death in Cd4+ T cells.
Binding to and Opsonophagocytic Activity of O-Antigen-Specific Monoclonal Antibodies against Encapsulated and NonencapsulatedKlebsiella pneumoniaeSerotype O1 Strains (2000)

The high mortality of nosocomial infections caused by Klebsiella spp. has acted as a stimulus to develop immunotherapeutic approaches targeted against surface molecules of these bacteria. Since O-antigen-specific antibodies may add to the protective effect of K antisera, we tested the functional and binding capacity of O-antigen-specific monoclonal antibodies (MAbs) raised against different Klebsiella O antigens. The MAbs tested were specific for the O-polysaccharide partial antigens D-galactan II (MAb Ru-O1), D-galactan I (MAb IV/4-5), or core oligosaccharide (MAb V/9-5) of the Klebsiella serogroup O1 antigen. In enzyme-linked immunosorbent assay binding experiments, we found that all MAbs recognized their epitopes on intact capsule-free bacteria; however, binding to encapsulated wild-type strains belonging to different K-antigen serotypes was significantly reduced. The K2 antigen acted as the strongest penetration barrier, while the K7 and K21 antigens allowed some, though diminished, antibody binding. In vitro phagocytic killing experiments showed that MAb Ru-O1 possessed significant opsonizing activity for nonencapsulated O1 serogroup strains and also, to a much lesser extent, for encapsulated strains belonging to the O1:K7 and O1:K21 serotypes. MAbs or antisera specific for the D-galactan II antigen may thus be the most promising agents for further efforts to develop a second-generation Klebsiella hyperimmune globulin comprising both K- and O-antigen specificities.
<p>Curcumin Modifies Epithelial–Mesenchymal Transition in Colorectal Cancer Through Regulation of miR-200c/EPM5</p> (2020)

Our data provide the first evidence that the curcumin inhibits EMT in CRC by upregulation of miR-200c and downregulation of EPM5, and the use of curcumin might be able to prevent or delay CRC progression.
Wound instillation--the next step in negative pressure wound therapy. Lessons learned from initial experiences. (2004)

Negative pressure wound therapy uses a reticulated sponge and subatmospheric pressure to facilitate healing of a variety of wounds. The therapy appears to assist wound healing by decreasing wound bacterial burden and edema while facilitating granulation tissue formation. The latest development in negative pressure wound therapy allows clinicians to instill a solution into the wound and is indicated for use when patients receiving negative pressure wound therapy would benefit from the controlled delivery of topical wound treatment solutions and suspensions. A retrospective analysis of five cases was conducted to describe initial experiences with instillation and negative pressure wound therapy (average treatment time on negative pressure wound therapy with instillation 15 days, range 5 to 24 days). In two of the five cases where traditional negative pressure wound therapy was tried, infected wounds improved and culture results became negative following instillation of antibiotics in a saline solution. In all cases where used, instillation of a topical anesthetic appeared to effectively minimize wound pain that is occasionally associated with negative pressure wound therapy. Negative pressure wound therapy with instillation and possibly hyperbaric oxygen therapy may be initiated from the onset of treatment to manage high-risk wounds that appear severely infected and may be limb-threatening if located on an extremity. Controlled clinical studies to ascertain the efficacy and cost-effectiveness of this treatment modality are needed.