gebhart/patrepeval huggingface dataset:
Deregulated expression of HOXB4 enhances the primitive growth activity of human hematopoietic cells (2002)

Identification of the molecular mechanisms that can promote human hematopoietic stem cell amplification is a major goal in experimental and clinical hematology. Recent data indicate that a variety of regulatory molecules active in early development may also play a role in the maintenance of hematopoietic stem cells with repopulating activity. One important class of early developmental genes determining hematopoietic development are homeobox transcription factors. Here, we report that retrovirally mediated expression of the homeobox gene HOXB4 rapidly triggers an increase in the number of human hematopoietic cord blood cells with stem cell and progenitor cell properties detected both by in vitro and in vivo assays. This growth enhancement extended across primitive myeloid-erythroid and B-lymphoid progenitors but did not lead to alterations in the balance of lymphomyeloid reconstitution in vivo, suggesting that HOXB4 does not affect control of end-cell output. These findings reveal HOXB4 as a novel, positive regulator of the primitive growth activity of human hematopoietic progenitor cells and underline the relevance of early developmental factors for stem cell fate decisions.
Inhibition of pulmonary fibrosis in mice by CXCL10 requires glycosaminoglycan binding and syndecan-4 (2010)

Pulmonary fibrosis is a progressive, dysregulated response to injury culminating in compromised lung function due to excess extracellular matrix production. The heparan sulfate proteoglycan syndecan-4 is important in mediating fibroblast-matrix interactions, but its role in pulmonary fibrosis has not been explored. To investigate this issue, we used intratracheal instillation of bleomycin as a model of acute lung injury and fibrosis. We found that bleomycin treatment increased syndecan-4 expression. Moreover, we observed a marked decrease in neutrophil recruitment and an increase in both myofibroblast recruitment and interstitial fibrosis in bleomycin-treated syndecan-4-null (Sdc4-/-) mice. Subsequently, we identified a direct interaction between CXCL10, an antifibrotic chemokine, and syndecan-4 that inhibited primary lung fibroblast migration during fibrosis; mutation of the heparin-binding domain, but not the CXCR3 domain, of CXCL10 diminished this effect. Similarly, migration of fibroblasts from patients with pulmonary fibrosis was inhibited in the presence of CXCL10 protein defective in CXCR3 binding. Furthermore, administration of recombinant CXCL10 protein inhibited fibrosis in WT mice, but not in Sdc4-/- mice. Collectively, these data suggest that the direct interaction of syndecan-4 and CXCL10 in the lung interstitial compartment serves to inhibit fibroblast recruitment and subsequent fibrosis. Thus, administration of CXCL10 protein defective in CXCR3 binding may represent a novel therapy for pulmonary fibrosis.
[Current status of nuclear medicine in Japan]. (1999)

Radionuclides have been used for the diagnosis and therapy of cancers. In Japan, about 1.8 million studies are performed annually, especially on bone, the heart, the brain and cancer. In contrast to anatomical studies with X-ray, US or CT, nuclear medicine provides physiological or metabolic images. The characteristics of nuclear medicine come from the use of tracer studies employing various radiopharmaceuticals. The most commonly used radionuclides for cancer studies are 67Ga and 201T1. Recently, however, many other radiopharmaceuticals with tumor specificity have been developed, such as 99mTc labeled monoclonal antibodies and 111In labeled octreotide. 18F-FDG, which images glucose metabolism, is very useful in the management of lung, colorectal and other cancers. Furthermore, radionuclides are also employed in the therapy of cancer, such 131I-labeled anti-CD20 antibody for the B-cell lymphoma and 89Sr for the palliation of bone pain caused by prostate and breast cancer metastases.
LAT-mediated signaling in CD4+CD25+ regulatory T cell development (2005)

Engagement of the T cell receptor for antigen (TCR) induces formation of signaling complexes mediated through the transmembrane adaptor protein, the linker for activation of T cells (LAT). LAT plays an important role in T cell development, activation, and homeostasis. A knock-in mutation at Tyr136, which is the phospholipase C (PLC)-gamma1-binding site in LAT, leads to a severe autoimmune disease in mice. In this study, we show that CD4+CD25+ T reg cells that expressed Foxp3 transcription factor were nearly absent in both thymus and peripheral lymphoid organs of LAT(Y136F) mice. This defect was not a result of the autoimmune environment as LAT(Y136F) T reg cells also failed to develop in healthy LAT-/- mice that received mixed wild-type and LAT(Y136F) bone marrow cells. Moreover, adoptive transfer of normal CD4+CD25+ T reg cells protected neonatal LAT(Y136F) mice from developing this disease. These T reg cells effectively controlled expansion of CD4+ T cells in LAT(Y136F) mice likely via granzymes and/or TGF-beta-mediated suppression. Furthermore, ectopic expression of Foxp3 conferred a suppressive function in LAT(Y136F) T cells. Our data indicate that the LAT-PLC-gamma1 interaction plays a critical role in Foxp3 expression and the development of CD4+CD25+ T reg cells.
CD2 regulates responsiveness of activated T cells to interleukin 12. (1995)

Interleukin (IL) 12 is a 70-kD heterodimeric cytokine produced by antigen-presenting cells (APCs) such as macrophages in response to infectious pathogens and interferon (IFN) gamma. The varied immunomodulatory effects of IL-12 include the stimulation of proliferation and IFN-gamma production by T cells, and it also has a central role in the development of the T helper cell type 1 immune phenotype. We undertook the production of antibodies capable of modulating the response of T cells to IL-12, and in the process we discovered two antibodies that inhibited the ability of IL-12 to stimulate T cell proliferation. In this report, we demonstrate that these anti-bodies recognize CD2, and we show how antibodies directed toward either the adhesion domain of CD2 or its ligand, CD58, specifically inhibit IL-12 induced proliferation and IFN-gamma production by phytohemagglutinin-activated T cells, leaving the response to IL-12 unaffected. A three-to fourfold reduction in proliferation and IFN-gamma production was observed at IL-12 concentrations as high as 1 nM, with complete inhibition occurring at < or = 1 pM. This novel effect is not directly mediated at the level of the IL-12 receptor, as shown by the inability of these antibodies to block IL-12 binding to activated T cells. Furthermore, by using activating pairs of CD2 antibodies, we show that CD2 stimulation strongly synergizes with IL-12, even at 0.1 pM, in inducing both T cell proliferation and IFN-gamma production. Cytolytic T lymphocyte-associated antigen 4-immunoglobulin-mediated inhibition of the B7/CD28 interaction did not affect the T cell response to either IL-12 or IL-2, but the removal of APCs selectively diminished the proliferative response to IL-12. Based on this data, we hypothesize that CD2 has a central role in an IL-12/IFN-gamma positive feedback loop between T cell and APC, providing the key functional link via a CD2/CD58 interaction that controls T cell responsiveness to IL-12. This model provides a basis for future investigations aimed at defining the signaling mechanisms that mediate this cytokine-specific regulatory effect of CD2, and it offers insight into how a cytokine receptor and distinct adhesion molecule can interact to modulate responsiveness to that cytokine. In addition, it underscores the possibility that the clinical potential of an immunomodulatory drug like IL-12 may be governed by the presence or absence of specific costimulation.
Serial Recognition Memory by Retardates of Half or Whole Faces in Two Orientations (1973)

Sequences of whole faces and half faces, either upright or inverted, were shown to 24 educable retardates in a paced recognition memory procedure. Inverted faces were harder to recognize than upright faces and half faces were harder to recognize than whole faces. An interaction trend showed that the half-whole effect was more marked for the upright faces. The results, combined with earlier data, suggest that some factor in the upright whole face is crucial to the half-whole difference found with retarded Ss.
Glycosyltransferases: An Efficient Tool for the Enzymatic Synthesis of Oligosaccharides and Derivatives as well as Mimetics Thereof (2006)

Research over the past two decades has uncovered numerous biological roles for carbohydrates, e.g. in cell adhesion processes, signal transduction, malignant transformation, or viral and bacterial cell-surface recognition. Carbohydrates and structural analogues thereof are therefore considered as potential new leads. Although the chemical synthesis of carbohydrates is well established, the preparation of particular oligosaccharides still remains a costly and cumbersome challenge. A complementary approach to the chemical synthesis is the use of enzymatic methods. The transfer of monosaccharide moieties to natural substrates, catalyzed by glycosyltransferases, exhibits excellent chemo-, regio- and stereoselectivity. In addition, enzymatic glycosylations permit the synthesis of carbohydrate derivatives and even carbohydrate mimetics. Our results reveal a remarkable synthetic potential of fucosyltransferases VI (EC 2.4.1.65) and III (EC 2.4.1.65), and ? (2?3)-sialyltransferase ST3Gal III (EC 2.4.99.6). Their use for the preparative synthesis of oligosaccharides and derivatives as well as mimetics thereof is demonstrated.
Cell-free DNA (cfDNA) mutations from clonal hematopoiesis: Implications for interpretation of liquid biopsy tests. (2017)

11526 Background: A large fraction of cfDNA fragments are derived from hematopoietic sources. Somatic alterations in cfDNA can be tumor-derived but also could represent somatic changes associated with clonal hematopoiesis. We performed deep sequencing of both plasma cfDNA and matched white blood cell (WBC) genomic DNA (gDNA) to determine the contribution of clonal hematopoiesis to the variants observed in cfDNA. Four cohorts were investigated: metastatic breast (BC), non-small cell lung (NSCLC), castration-resistant prostate cancer (CRPC), and non-cancer participants (pts). Methods: Metastatic cancer pts with de novo or progressive disease were prospectively enrolled. Non-cancer pts were blood bank donors. Plasma cfDNA and matched WBC gDNA were sequenced using a targeted 508-gene panel (2 Mb) to &gt; 60,000X raw depth. Variant calling used a novel pipeline that employed molecular barcoding for error suppression followed by de novo assembly and graph-based variant calling. Results: Of 151 metastatic cancer pts (48 BC, 49 NSCLC, 54 CRPC), median age was 64 (30-87) with 53% female and 33% treatment naive. Of 47 non-cancer pts, median age was 61 (20-78) with 51% female. Analysis of cfDNA identified 1072 variants (AF &gt; 0.1%, &gt; 2 mutant reads, passing bioinformatic quality filters) which were also detected in WBC gDNA as non-germline ( &lt; 35% allele frequency [AF]) non-synonymous variants. For these cfDNA variants, AF ranged from 0.1-14.4% and correlated with AF in WBC gDNA (r 2 = 0.47, p &lt; 0.001). Mutated genes were consistent with clonal hematopoiesis, with the most frequently mutated genes being DNMT3A, TET2, PPM1D, and TP53 (215, 77, 45, and 36 variants, respectively). For both cancer and non-cancer pts (age &gt; 45), median number of overlapping variants was 5 per pt (range 0-22). The number of WBC gDNA and cfDNA variants per individual was positively associated with age (p &lt; 0.001) in both cancer and non-cancer pts (interaction p = 0.08). Conclusions: Somatic cfDNA variants are frequently derived from clonal hematopoiesis and increase with age. Accurate assessment of somatic alterations in cfDNA should account for this phenomenon to distinguish between tumor-derived and WBC-derived variants.
An Open-Label, Multicenter, Phase I/II Study of JNJ-40346527, a CSF-1R Inhibitor, in Patients with Relapsed or Refractory Hodgkin Lymphoma (2015)

JNJ-40346527, a selective inhibitor of CSF-1R was well tolerated, and preliminary antitumor results suggested limited activity in monotherapy for the treatment of cHL.
Lateral Hydrogen Diffusion at p-GaN Layers in Nitride-Based Light Emitting Diodes with Tunnel Junctions (2013)

We demonstrated lateral Mg activation along p-GaN layers underneath n-GaN surface layers in nitride-based light emitting diodes (LEDs) with GaInN tunnel junctions. A high temperature thermal annealing was effective for the lateral Mg activation when the p-GaN layers were partly exposed to an oxygen ambient as etched sidewalls. The activated regions gradually extended from the etched sidewalls to the centers with an increase of annealing time, observed as emission regions with current injection. These results suggest that hydrogen diffuses not vertically thorough the above n-GaN but laterally through the exposed portions of the p-GaN. The lowest voltage drop at the GaInN tunnel junction was estimated to be 0.9 V at 50 mA with the optimized annealing condition.
Antiviral Resistance in Influenza Viruses — Implications for Management and Pandemic Response (2006)

Resistance to amantadine has been detected at an extraordinarily high frequency in isolates of influenza A virus. Dr. Frederick Hayden discusses the implications of resistance to antiviral agents for the current clinical management of influenza and for planning for a possible pandemic.
Randomised trial of intravenous infusion of ephedrine or mephentermine for management of hypotension during spinal anaesthesia for Caesarean section (2004)

This study compared the effects of intravenous infusions of ephedrine and mephentermine for maintenance of maternal arterial pressure and neonatal outcome in pregnant women receiving subarachnoid block for lower segment Caesarean section. Sixty patients who developed hypotension following subarachnoid block for Caesarean section were randomly divided into two groups of 30 each to receive an intravenous infusion of ephedrine or mephentermine. Hypotension was defined as a decrease in systolic blood pressure of > or = 20% from the baseline value or an absolute value of <100 mmHg, whichever was higher. The vasopressor infusion was titrated to maintain systolic blood pressure between 'hypotension' and baseline values. Baseline haemodynamic parameters, haemodynamic changes subsequent to the start of vasopressor infusion, duration of hypotension and amount of vasopressor required were statistically similar for both groups. Neonatal APGAR scores and acid-base profiles were also comparable. To conclude, mephentermine can be used as safely and effectively as ephedrine for the management of hypotension during spinal anaesthesia in patients undergoing elective Caesarean section.
Intramuscular Dexmedetomidine as Premedication for General Anesthesia (1993)

The results suggest that pretreatment with a single intramuscular injection of 2.5 micrograms/kg dexmedetomidine is efficacious, but significantly increases the incidence of intraoperative hypotension and bradycardia in ASA physical status 1 or 2 patients.
Alkaline imidazolium- and quaternary ammonium-functionalized anion exchange membranes for alkaline fuel cell applications (2011)

Alkaline imidazolium-type ionic liquids (ILs) and quaternary ammonium salt functionalized alkaline anion-exchange membranes (AEMs), with the same ion exchange capacity (IEC), were synthesized via in situ cross-linking of styrene, acrylonitrile, 1-methyl-3-(4-vinylbenzyl)imidazolium chloride ([MVBIm][Cl]), and N,N,N-trimethyl-1-(4-vinylphenyl) methanaminium chloride ([TMVPMA][Cl]), respectively. The water uptake, swelling ratio, conductivity, and alkaline stability of resultant cross-linked copolymer membranes were investigated. Both types of copolymer membranes exhibit hydroxide conductivity above 10−2 S cm−1 at room temperature. Alkaline imidazolium-type IL functionalized membranes showed an excellent chemical stability of up to 1000 h without obvious loss of ion conductivity, whereas the membranes based on quaternary ammonium salts degraded in high pH solution because of nucleophillic substitution on quaternary ammonium cations. The results of this study suggest that the AEMs based on alkaline imidazolium-type ILs are expected to promote the widespread use of alkaline fuel cells.
Missing Cells in Developmental Research. (1996)

The use of missing cells in longitudinal research is addressed and a sample is given using multiple linear regression for the solution. Applications of longitudinal research are discussed wherein logically missing cells occur.
Re-engineering multicloning sites for function and convenience (2011)

Multicloning sites (MCSs) in standard expression vectors are widely used and thought to be benign, non-interacting elements that exist for mere convenience. However, MCSs impose a necessary distance between promoter elements and genes of interest. As a result, the choice of cloning site defines the genetic context and may introduce significant mRNA secondary structure in the 5'-untranslated region leading to strong translation inhibition. Here, we demonstrate the first performance-based assessment of MCSs in yeast, showing that commonly used MCSs can induce dramatic reductions in protein expression, and that this inhibition is highly promoter and gene dependent. In response, we develop and apply a novel predictive model of structure-based translation inhibition to design improved MCSs for significantly higher and more consistent protein expression. In doing so, we were able to minimize the inhibitory effects of MCSs with the yeast TEF, CYC and GPD promoters. These results highlight the non-interchangeable nature of biological parts and represent the first complete, global redesign of a genetic circuit of such widespread importance as a multicloning site. The improved translational control offered by these designed MCSs is paramount to obtaining high titers of heterologous proteins in eukaryotes and to enabling precise control of genetic circuits.
Synthesis and pharmacological properties of some 2-(3-aminopropionyl)- and 2-(3-aminopropyl)-1-(3-pyridyl)-1,2,3,4-tetrahydro-beta-carbolines. (1989)

Five derivatives of 2-(3-aminopropionyl)-1-(3-pyridyl)-1,2,3,4-tetrahydro-beta-carboline (2a-e) were obtained, which yielded, as a result of reduction with LiAlH4, five respective 2-aminopropyl-derivatives (3a-e). Pharmacological studies revealed that phenylpiperazine-derivatives 2d, 2e, 3d and 3e have sedative and analgesic properties. All compounds are devoided of neuroleptic, antidepressant, anxiolytic and antiparkinsonic activity.
Translational Mini-Review Series on Type 1 Diabetes: Systematic analysis of T cell epitopes in autoimmune diabetes (2007)

T cell epitopes represent the molecular code words through which the adaptive immune system communicates. In the context of a T cell-mediated autoimmune disease such as type 1 diabetes, CD4 and CD8 T cell recognition of islet autoantigenic epitopes is a key step in the autoimmune cascade. Epitope recognition takes place during the generation of tolerance, during its loss as the disease process is initiated, and during epitope spreading as islet cell damage is perpetuated. Epitope recognition is also a potentially critical element in therapeutic interventions such as antigen-specific immunotherapy. T cell epitope discovery, therefore, is an important component of type 1 diabetes research, in both human and murine models. With this in mind, in this review we present a comprehensive guide to epitopes that have been identified as T cell targets in autoimmune diabetes. Targets of both CD4 and CD8 T cells are listed for human type 1 diabetes, for humanized [human leucocyte antigen (HLA)-transgenic] mouse models, and for the major spontaneous disease model, the non-obese diabetic (NOD) mouse. Importantly, for each epitope we provide an analysis of the relative stringency with which it has been identified, including whether recognition is spontaneous or induced and whether there is evidence that the epitope is generated from the native protein by natural antigen processing. This analysis provides an important resource for investigating diabetes pathogenesis, for developing antigen-specific therapies, and for developing strategies for T cell monitoring during disease development and therapeutic intervention.
Molecular Design of Bioconjugated Cell Adhesion Peptide with a Water-Soluble Polymeric Modifier for Enhancement of Antimetastatic Effect (2002)

The adhesive interaction of tumor cells with various components of the extracellular matrix (ECM), such as laminin and fibronectin appears to play a crucial role in tumor metastasis. It has been reported that adhesive peptides, such as Tyr-Ile-Gly-Ser-Arg (YIGSR) in laminin and Arg-Gly-Asp (RGD), inhibited adhesion and invasion of various tumor cells to ECM in vitro, and exhibited inhibitory effects on pulmonary metastasis of B16-BL6 melanoma cells in mice. However, large doses of these peptides were required for significant anti-metastatic effects in vivo, probably due to their rapid degradation by various peptidases and their rapid excretion from the blood into the urine. To overcome these problems, the development of an appropriate drug delivery system (DDS) is required to improve in vivo stability and prolong plasma half-lives. Several strategies such as peptide-cyclization and D-amino acid substation have been reported to improve stability in blood by inhibiting enzymatic degradation. However, even these approaches have proven insufficient to overcome rapid renal clearance from the circulation. On the other hand, bioconjugation with water-soluble polymeric modifiers could markedly prolong the plasma half-lives by not only increasing peptidase resistance but also impeding renal excretion. In addition, it is possible to strictly control the in vivo pharmacokinetics of a peptide by introducing functional molecules with targeting or slow release capacities to the polymeric modifier. In this review we demonstrate with reference to our recent studies that bioconjugation of adhesive peptides with the appropriate polymeric modifier can enhance antimetastatic activity and may facilitate therapeutic use.