gebhart/patrepeval huggingface dataset:
GFI1 functions in transcriptional control and cell fate determination require SNAG domain methylation to recruit LSD1 (2016)

Proper hematopoietic cell fate decisions require co-ordinated functions of transcription factors, their associated co-regulators, and histone-modifying enzymes. Growth factor independence 1 (GFI1) is a zinc finger transcriptional repressor and master regulator of normal and malignant hematopoiesis. While several GFI1-interacting proteins have been described, how GFI1 leverages these relationships to carry out transcriptional repression remains unclear. Here, we describe a functional axis involving GFI1, SMYD2, and LSD1 that is a critical contributor to GFI1-mediated transcriptional repression. SMYD2 methylates lysine-8 (K8) within a -(8)KSKK(11)- motif embedded in the GFI1 SNAG domain. Methylation-defective GFI1 SNAG domain lacks repressor function due to failure of LSD1 recruitment and persistence of promoter H3K4 di-methyl marks. Methylation-defective GFI1 also fails to complement GFI1 depletion phenotypes in developing zebrafish and lacks pro-growth and survival functions in lymphoid leukemia cells. Our data show a discrete methylation event in the GFI1 SNAG domain that facilitates recruitment of LSD1 to enable transcriptional repression and co-ordinate control of hematopoietic cell fate in both normal and malignant settings.
RAS gene mutations in childhood acute myeloid leukemia: A pediatric oncology group study (1990)

Mutations at codon 12, 13, and 61 of the HRAS, KRAS, and NRAS genes were evaluated in 99 cases of pediatric acute myeloid leukemia (AML) using oligonucleotide hybridization to polymerase chain reacted derived products. Twenty-four mutations were identified in the NRAS gene, 13 in the KRAS gene, and none in the HRAS gene. The mutations occurred in a broad spectrum of cases, and there was no specific association of RAS gene mutations with patient subsets defined on the basis of clinical or hematologic features. These data demonstrate that RAS gene mutations are at least as common in childhood AML as in adult AML and suggest that RAS gene mutations play a role in myeloid neoplasia in both age groups.
Treatment of experimental allergic encephalomyelitis in rabbits with alpha-fetoprotein. (1985)

We studied the ability of alpha-fetoprotein (AFP) to suppress experimental allergic encephalomyelitis (EAE) in rabbits. Animals were treated with daily injections of 50 micrograms of AFP following the onset of neurological signs. Clinical status, anti-myelin basic protein (MBP) antibody titers, and histopathological changes in the CNS were determined. Treatment with AFP significantly improved the clinical scores of the affected rabbits and inhibited the binding of anti-MBP antibodies to MBP in vitro. However, there was no significant difference in the titers of anti-MBP antibody, and no amelioration of histopathological changes between treated and control animals. We conclude that AFP is effective in improving the clinical status of animals with EAE, even after the appearance of clinical signs.
Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation (2007)

After encounter with antigen, the antibody repertoire is shaped by somatic hypermutation (SHM), which leads to an increase in the affinity of antibodies for the antigen, and class-switch recombination (CSR), which results in a change in the effector function of antibodies. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID), which deaminates deoxycytidine to deoxyuridine in single-stranded DNA (ssDNA). The precise mechanism responsible for the formation of ssDNA in V regions undergoing SHM has yet to be experimentally established. In this study, we searched for ssDNA in mutating V regions in which DNA-protein complexes were preserved in the context of chromatin in human B cell lines and in primary mouse B cells. We found that V regions that undergo SHM were enriched in short patches of ssDNA, rather than R loops, on both the coding and noncoding strands. Detection of these patches depended on the presence of DNA-associated proteins and required active transcription. Consistent with this, we found that both DNA strands in the V region were transcribed. We conclude that regions of DNA that are targets of SHM assemble protein-DNA complexes in which ssDNA is exposed, making it accessible to AID.
Glycosylation Variants of Mucins and CEACAMs As Candidate Biomarkers for the Diagnosis of Pancreatic Cystic Neoplasms (2010)

These results demonstrate the value of glycan variants for biomarker discovery and suggest that these biomarkers could greatly enhance the accuracy of differentiating pancreatic cystic tumors. Validation studies will be required to determine the clinical value of these markers.
Sialic Acid Residues Mediate Mycoplasma pneumoniae Attachment to Human and Sheep Erythrocytes (1982)

The adherence of Mycoplasma pneumoniae to human and sheep erythrocytes was directly related to the presence of sialyl residues on the erythrocytes. Competitive binding studies between M. pneumoniae and M. gallisepticum, known to bind to human erythrocytes via glycophorin, further reinforced the role of sialic acid in this recognition event.
Epigenetic reprogramming of melanoma cells by vitamin C treatment (2015)

Our data support the idea that vitamin C treatment increases 5hmC content in melanoma cells, while causing a decrease in tumor-cell invasiveness and clonogenic growth in soft agar. Thus, vitamin C could be a potential epigenetic treatment for melanoma.
Wnt-5a inhibits the canonical Wnt pathway by promoting GSK-3–independent β-catenin degradation (2003)

Wnts are secreted signaling molecules that can transduce their signals through several different pathways. Wnt-5a is considered a noncanonical Wnt as it does not signal by stabilizing beta-catenin in many biological systems. We have uncovered a new noncanonical pathway through which Wnt-5a antagonizes the canonical Wnt pathway by promoting the degradation of beta-catenin. This pathway is Siah2 and APC dependent, but GSK-3 and beta-TrCP independent. Furthermore, we provide evidence that Wnt-5a also acts in vivo to promote beta-catenin degradation in regulating mammalian limb development and possibly in suppressing tumor formation.
Heat stress regulates the human 70-kDa heat-shock gene through the 3'-untranslated region (1993)

Cells respond to a variety of stresses by synthesizing a family of proteins termed heat-shock proteins (HSP). Recently, the 3'-untranslated regions (UTRs) of some mRNAs have been shown to be important in the posttranscriptional regulation of protein production. Therefore, we hypothesized that heat could regulate HSP70 production through the HSP70 3'-UTR, in addition to its known effects on transcription. To test this hypothesis, cells were transfected with either a plasmid containing sequences encoding the human HSP70 or beta-globin 3'-untranslated region placed downstream of a chloramphenicol acetyltransferase (CAT) reporter gene. In both plasmids, the CAT gene was driven by an SV40 promoter. Following heat stress, cells transfected with the CAT construct containing the HSP70 3'-UTR showed increased CAT activity relative to the beta-globin 3'-UTR construct. This effect paralleled increases in HSP70 mRNA and levels of the inducible HSP70 protein by Western blot. These studies identify a heat-induced mechanism of posttranscriptional control of HSP70 synthesis utilizing the HSP70 3'-UTR, which may be important in the cells ability to regulate the heat-shock response.
Identification of AKAP‐4 as a new cancer/testis antigen for detection and immunotherapy of prostate cancer (2011)

We demonstrate the aberrant expression of AKAP-4 in PC, which will potentially be developed as a biomarker in PC. We provide evidence that AKAP-4 is a potential target for PC adoptive immunotherapy or anti-tumor vaccination.
Prophylactic neuroprotection for cerebral ischemia. (1994)

The possibility of ameliorating the consequences of an acute ischemic stroke by pretreating high-risk patients with appropriate neuroprotective agents needs to be explored. Several types of high-risk population for prophylactic neuroprotection can be envisioned and then studied in clinical trials.
Chondroitin 6-sulfate glycosaminoglycan is a major constituent of primate cone photoreceptor matrix sheaths (1987)

Recent work suggests that chemically and structurally distinct domains of the interphotoreceptor matrix ("cone matrix sheaths") surround cone photoreceptor outer segments and ellipsoids. This specific regionalization of at least some molecular constituents of the interphotoreceptor matrix may establish a unique cone-associated microenvironment. Previous histochemical and biochemical investigations have shown that a variety of glycosaminoglycans are components of the interphotoreceptor matrix and that the structural integrity of cone sheaths is slightly disrupted by glycosaminoglycan-degrading enzymes. In order to pursue the possibility that specific glycosaminoglycan species establish cone matrix sheath domains, monoclonal antibodies directed against various unsaturated glycosaminoglycans have been screened on sections of primate retina. The results of these studies identify chondroitin 6-sulfate glycosaminoglycan as a specific component of primate cone matrix sheaths.
Tissue homogenization with sterile reinforced polyethylene bags for quantitative culture of Candida albicans (1987)

A simple method of tissue homogenization with sterile reinforced polyethylene bags for quantitative fungal cultures was evaluated with mice infected with Candida albicans. This new method correlated well with standard methods (P less than or equal to 0.01) for quantifying viable fungus in homogenates of brain, kidney, spleen, liver, and lungs and may be applicable in clinical and experimental mycology laboratories.
Regulation of human dioxin receptor function by indolocarbazoles, receptor ligands of dietary origin. (1994)

The intracellular basic helix-loop-helix (bHLH) dioxin receptor mediates signal transduction by dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin). In analogy to nuclear receptors that are members of the steroid hormone receptor superfamily the dioxin receptor is a ligand-inducible transcriptional regulator that directly binds to response elements within regulated genes. The most commonly studied dioxin receptor ligands are dioxin itself and structurally related environmental contaminants. A physiological ligand has not yet been identified. Interestingly, however, indolo[3,2-b]carbazole, a compound formed from precursors in the diet, has been shown to bind the murine dioxin receptor with high affinity in vitro. In the present study we show that this compound and its methylated derivative 5,11-dimethylindolo[3,2-b]carbazole very potently activated transcription from a dioxin or xenobiotic response element (XRE)-driven reporter gene in both murine and human hepatoma cells. This effect was not observed in mutant, dioxin-resistant hepatoma cells which are either deficient in expression of dioxin receptor or the bHLH receptor partner factor Arnt. In vitro indolocarbazoles induced XRE binding activity by the human dioxin receptor-Arnt complex in a dose-dependent manner. Thus, both dioxin- and indolocarbazole-activated forms of dioxin receptor regulate target gene expression by the same mechanism involving recruitment of the bHLH factor Arnt and recognition of the XRE element. Finally, the indolo[3,2-b]carbazole-activated human dioxin receptor appeared to generate more stable complexes with the XRE target sequence relative to those produced by the dioxin-activated receptor form, indicating interesting mechanistic differences between different classes of dioxin receptor ligands in their abilities to modulate human dioxin receptor function.
Early Interventional Treatment with Intranasal Mometasone Furoate in Japanese Cedar/Cypress Pollinosis: A Randomized Placebo-Controlled Trial (2012)

EIT with MFNS for JCCP is both safe and effective. This treatment can potentially lessen symptoms and help pollinosis patients remain in the intermittent state.
Fibroblast growth factor 23 and soluble klotho in children with chronic kidney disease (2012)

This study shows increasing FGF23 and reduced s-klotho levels with progressive renal failure even in a population of children with well-controlled P levels. Novel associations between FGF23 and serum Ca as well as 25(OH)D warrant further investigation.
Matrix Metalloproteinase 9 and Vascular Endothelial Growth Factor Are Essential for Osteoclast Recruitment into Developing Long Bones (2000)

Bone development requires the recruitment of osteoclast precursors from surrounding mesenchyme, thereby allowing the key events of bone growth such as marrow cavity formation, capillary invasion, and matrix remodeling. We demonstrate that mice deficient in gelatinase B/matrix metalloproteinase (MMP)-9 exhibit a delay in osteoclast recruitment. Histological analysis and specialized invasion and bone resorption models show that MMP-9 is specifically required for the invasion of osteoclasts and endothelial cells into the discontinuously mineralized hypertrophic cartilage that fills the core of the diaphysis. However, MMPs other than MMP-9 are required for the passage of the cells through unmineralized type I collagen of the nascent bone collar, and play a role in resorption of mineralized matrix. MMP-9 stimulates the solubilization of unmineralized cartilage by MMP-13, a collagenase highly expressed in hypertrophic cartilage before osteoclast invasion. Hypertrophic cartilage also expresses vascular endothelial growth factor (VEGF), which binds to extracellular matrix and is made bioavailable by MMP-9 (Bergers, G., R. Brekken, G. McMahon, T.H. Vu, T. Itoh, K. Tamaki, K. Tanzawa, P. Thorpe, S. Itohara, Z. Werb, and D. Hanahan. 2000. Nat. Cell Biol. 2:737-744). We show that VEGF is a chemoattractant for osteoclasts. Moreover, invasion of osteoclasts into the hypertrophic cartilage requires VEGF because it is inhibited by blocking VEGF function. These observations identify specific actions of MMP-9 and VEGF that are critical for early bone development.
Controlled Coupling and Occupation of Silicon Atomic Quantum Dots at Room Temperature (2009)

It is demonstrated that the silicon atom dangling bond (DB) state serves as a quantum dot. Coulomb repulsion causes DBs separated by less, similar2 nm to exhibit reduced localized charge, which enables electron tunnel coupling of DBs. Scanning tunneling microscopy measurements and theoretical modeling reveal that fabrication geometry of multi-DB assemblies determines net occupation and tunnel coupling strength among dots. Electron occupation of DB assemblies can be controlled at room temperature. Electrostatic control over charge distribution within assemblies is demonstrated.
Image de-noising by integer wavelet transforms and generalized cross validation (1999)

De-noising algorithms based on wavelet thresholding replace small wavelet coefficients by zero and keep or shrink the coefficients with absolute value above the threshold. The optimal threshold minimizes the error of the result as compared to the unknown, exact data. To estimate this optimal threshold, we use Generalized Cross Validation. This procedure has linear complexity and is fully automatic, i.e., it does not require an estimate for the noise energy. This paper uses the method for wavelet transforms that map integer gray-scale pixel values to integer wavelet coefficients. An image with artificial noise is used to illustrate the optimality properties of the estimator. Not all theoretical requirements for a successful application of the method are strictly fulfilled in the integer transform case. However, this has little influence on practical results.
Targeting Cancer-Derived Adenosine:New Therapeutic Approaches (2014)

High concentrations of immunosuppressive adenosine have been reported in cancers, and adenosine is implicated in the growth of tumors. This brief review delineates the current treatment strategies and tumor subtypes that will benefit from targeting adenosinergic pathways, alone or in combination with contemporary approaches to cancer treatment.
A general purpose multiple way partitioning algorithm (1991)

This paper presents a discussion of methods to solve multiple way partitioning problems under three different objective functions. A multicommodity flow fzeatmertt is proposed for partitioning without a size wmstrain~and an iterative improvement algorithm is proposed for partitioning with a size comt.rstint. This algoriti incorporates a top-down clustering technique to deal with the local minima problems in common heuristics, a novel multi-pin net model to capture the contributory moves, and a Primal-Dual iteration to enhance the iterative improvement.
A system for the delivery of interactive television programming (2002)

Interactive television is a technology for delivering television programming on demand to households and businesses. Rather than passively choosing from a predetermined set of programs at scheduled times, the viewer can request programming to be delivered to him individually on demand. This paper describes a system being developed by IBM that is in active use at customer trials. The system supports movies on demand as well as more interactive applications such as home shopping. This system as deployed today on IBM's RS/6000 series of computers supports in the hundreds of viewers, but running on the SP-2 supercomputer and its follow-ons, the system can be scaled to support thousands of interactive viewers.
THE POPULATION GENETICS OF ESCHERICHIA COLI (1984)

E. coli is a successful and diverse group of organisms, well defined by DNA hybridization within the Enterobacteriacae and including the closely related organisms Shigella and the Alkalescens-Dispar biogroup. The primary habitat of E. coli is the lower intestinal tract of warm-blooded animals, which is colonized shortly after birth. At any one time, most normal individuals carry several strains of E. coli in their intestinal tract, including a small number of resident clones exhibiting a rate of replacement measured in weeks or months and a much larger number of transient clones that are replaced in a matter of days or weeks. The secondary habitats of E. coli are soil, sediment, and water, where its half life is thought to be only a few days. Pathogenic forms of E. coli are associated with diarrheal diseases, urinary tract infections, neonatal meningitis, nosocomial infections, and in infections of domesticated animals. E. coli populations contain much genetic diversity, more than is found in most eukaryotes. Genetic diversity has been studied from the standpoint of (a) serology with respect to surface antigens, (b) biogrouping with respect to variable characters such as nutritional versatility, antibiotic resistance, and bacteriophage susceptibility, (c) electrophoresis of enzymes of intermediary metabolism or outer membrane proteins, (d) DNA hybridization, (e) restriction-fragment length polymorphisms, (f) DNA sequences, (g) insertion sequences, and (h) plasmids. However identified, strains of E. coli appear to have a wide, but not totally indiscriminate, host range. Aside from genes directly associated with virulence, genetic divergence between pathogenic and nonpathogenic strains, although statistically significant, is not pronounced. Electrophoretic studies indicate that, while some serotypes may represent a single genetic clone almost exclusively, other serotypes may represent two or more genetically unrelated clones. Unrelated clones may therefore converge to the same or very similar serotypes. Electrophoresis has also been used to define three groups of clones among natural isolates, perhaps corresponding to subspecies of E. coli. These groups are worldwide in distribution and have a wide host range. E. coli populations exhibit great linkage disequilibrium, which occurs as highly nonrandom combinations of alleles at different loci. Reproduction is evidently largely asexual, with insufficient genetic recombination to dissipate linkage disequilibrium.(ABSTRACT TRUNCATED AT 400 WORDS)
Reputation and Commitment in Two-Person Repeated Games Without Discounting (1995)

Two-person repeated games with no discounting are considered where there is uncertainty about the type of the players. If there is a possibility that a player is an automaton committed to a particular pure or mixed stage -game action, then this provides a lower bound on the Nash equilibrium payoffs to a normal type of this player. The lower bound is the best available and is robust to the existence of other types. The results are extended to the case of two-sided uncertainty. This work extends Schmidt (1993) who analysed the restricted class of conflicting interest games.
Role of the prostaglandin E receptor subtype EP1 in colon carcinogenesis. (1999)

Although the cyclooxygenase pathway of the arachidonic acid cascade has been suggested to play an important role in colon carcinogenesis, the molecular species of prostanoids and receptors involved have not been fully elucidated yet. We examined the development of aberrant crypt foci (ACFs), putative preneoplastic lesions of the colon, in two lines of knockout mice, each deficient in prostaglandin E receptors, EP1 and EP3, by treatment with the colon carcinogen, azoxymethane. Formation of ACFs was decreased only in the EP1-knockout mice to approximately 60% of the level in wild-type mice. Administration of 250, 500, or 1000 ppm of a novel selective EP1 antagonist, ONO-8711, in the diet to azoxymethane-treated C57BL/6J mice also resulted in a dose-dependent reduction of ACF formation. Moreover, when Min mice, having a nonsense mutation in the adenomatous polyposis coli gene, were given 500 ppm ONO-8711 in the diet, the number of intestinal polyps was significantly reduced to 57% of that in the basal diet group. These results strongly suggest that prostaglandin E2 contributes to colon carcinogenesis to some extent through its action at the EP1 receptor. Thus, EP1 antagonists may be good candidates as chemopreventive agents for colon cancer.
Conformational Changes in Rhodopsin Probed by Surface Plasmon Resonance Spectroscopy (1994)

Surface plasmon resonance (SPR) spectroscopy has been used to follow incorporation and light-induced conformational changes in bovine rhodopsin reconstituted into an egg phosphatidylcholine bilayer deposited on a thin silver film. The magnitude of the SPR spectral changes caused by light varies with pH in a manner paralleling that in flash photolysis experiments, which monitor formation of metarhodopsin II. Irradiation produces an increase of approximately 4 A in the average thickness of the proteolipid layer, consistent with exposure of recognition sites for the G protein. The results demonstrate that the SPR technology described herein may be used to monitor conformational events in membrane-associated receptors such as rhodopsin.