gebhart/patrepeval huggingface dataset:
Identification and characterization of MTR1, a novel gene with homology to melastatin (MLSN1) and the trp gene family located in the BWS-WT2 critical region on chromosome 11p15.5 and showing allele-specific expression (2000)

Alterations within human chromosomal region 11p15.5 are associated with the Beckwith-Wiedemann syndrome (BWS) and predisposition to a variety of neoplasias, including Wilms' tumors (WTs), rhabdoid tumors and rhabdomyosarcomas. To identify candidate genes for 11p15. 5-related diseases we compared human genomic sequence with expressed sequence tag and protein databases from different organisms to discover evolutionarily conserved sequences. Herein we describe the identification and characterization of a novel human transcript related to a putative Caenorhabditis elegans protein and the trp (transient receptor potential) gene. The highest homologies are observed with the human TRPC7 and with melastatin 1 ( MLSN1 ), whose transcript is downregulated in metastatic melanomas. Other genes related to and interacting with the trp family include the Grc gene, which codes for a growth factor-regulated channel protein, and PKD1/PKD2, involved in polycystic kidney disease. The novel gene presented here (named MTR1 for MLSN1 - and TRP -related gene 1) resides between TSSC4 and KvLQT1. MTR1 is expressed as a 4.5 kb transcript in a variety of fetal and adult tissues. The putative open reading frame is encoded in 24 exons, one of which is alternatively spliced leading to two possible proteins of 872 or 1165 amino acids with several predicted membrane-spanning domains in both versions. MTR1 transcripts are present in a large proportion of WTs and rhabdomyosarcomas. RT-PCR analysis of somatic cell hybrids harboring a single human chromosome 11 demonstrated exclusive expression of MTR1 in cell lines carrying a paternal chromosome 11, indicating allele-specific inactivation of the maternal copy by genomic imprinting.
CDH1 and CDH13 methylation in serum is an independent prognostic marker in cervical cancer patients (2003)

Cervical cancer is the principal cause of death due to cancer in women. Five-year survival rate ranges from 15-80%, depending on the extent of the disease. New predictive markers for relapse may increase survival rates by improving treatment of patients at high risk for relapse. The gene products of CDH1 and CDH13, namely E-cadherin and H-cadherin, play a key role in cell-cell adhesion. Inactivation of the cadherin-mediated cell adhesion system, caused by aberrant methylation, is a common finding in human cancers. To test the hypothesis that CDH1/CDH13 methylation is a prognostic marker in cervical cancer we determined the methylation status of CDH1/CDH13 in serum samples from 93 cervical cancer patients. Methylation analysis was carried out using MethyLight. Aberrant methylation of the 5'-region of CDH1 or CDH13 was observed in 43% (40 of 93) of the patients. Cervical cancer patients with unmethylated CDH1/CDH13 in serum samples showed significantly better disease-free survival in univariate and multivariate analysis. Median disease-free survival for CDH1/CDH13 methylation negative and positive patients was 4.3 years and 1.2 years, respectively. Our results suggest that detection of aberrant methylation of CDH1/CDH13 may be of potential use as a marker for selecting cervical cancer patients at high risk for relapse who could benefit from additional systemic therapy.
Dihydrofolate reductase as a therapeutic target (1990)

The folate antagonists are an important class of therapeutic compounds, as evidenced by their use as antiinfective, antineoplastic, and antiinflammatory drugs. Thus far, all of the clinically useful drugs of this class have been inhibitors of dihydrofolate reductase (DHFR), a key enzyme in the synthesis of thymidylate, and therefore, of DNA. The basis of the antiinfective selectivity of these compounds is clear; the antifolates trimethoprim and pyrimethamine are potent inhibitors of bacterial and protozoal DHFRs, respectively, but are only weak inhibitors of mammalian DHFRs. These species-selective agents apparently exploit the differences in the active site regions of the parasite and host enzymes. Methotrexate is the DHFR inhibitor used most often in a clinical setting as an anticancer drug and as an antiinflammatory and immunosuppressive agent. Considerable progress has been made recently in understanding the biochemical basis for the selectivity of this drug and the biochemical mechanism (or mechanisms) responsible for the development of resistance to treatment with the drug. This understanding has led to a new generation of DHFR inhibitors that are now in clinical trials.
9-(1,3-Dihydroxy-2-propoxymethyl)guanine: a new potent and selective antiherpes agent (1983)

The synthesis of a new acyclic analogue of deoxyguanosine, 9-[(1,3-dihydroxy-2-propoxy)methyl]guanine (DHPG, 1), is described starting from epichlorohydrin via condensation of 2-O-(acetoxymethyl)-1,3-di-O-benzylglycerol (5) with N2,9-diacetylguanine (6). In vitro studies indicate that DHPG is a potent and broad-acting (herpes simplex virus types 1 and 2, cytomegalovirus, and Epstein-Barr virus) antiherpetic agent. In vivo studies indicate its lack of toxicity [LD50 (mice) = 1-2 g/kg, ip] and its superiority over acyclovir [oral ED50 = 7 (mg/kg)/day vs. 550 (mg/kg)/day in HSV-2 infected mice].
Multilabeled Pyrene-Functionalized 2‘-Amino-LNA Probes for Nucleic Acid Detection in Homogeneous Fluorescence Assays (2005)

Homogeneous fluorescence assays for detection of nucleic acids are widely used in biological sciences. Typically, probes such as molecular beacons that rely on distance-dependent fluorescence quenching are used for such assays. Less attention has been devoted to tethering a single kind of fluorophores to oligonucleotides and exploiting hybridization-induced modulation of fluorescence intensity for nucleic acid detection. Herein, thermal denaturation experiments and fluorescence properties of oligodeoxyribonucleotides containing one or more 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA monomer(s) X are described. These pyrene-functionalized 2'-amino-LNAs display large increases in thermal stability against DNA/RNA complements with excellent Watson-Crick mismatch discrimination. Upon duplex formation of appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA probes and complementary DNA/RNA, intensive fluorescence emission with quantum yields between 0.28 and 0.99 are observed. Quantum yields of such magnitudes are unprecedented among pyrene-labeled oligonucleotides. Molecular modeling studies suggest that the dioxabicyclo[2.2.1]heptane skeleton and amide linkage of monomer X fix the orientation of the pyrene moiety in the minor groove of a nucleic acid duplex. Interactions between pyrene and nucleobases, which typically lead to quenching of fluorescence, are thereby reduced. Duplexes between multiple modified probes and DNA/RNA complements exhibit additive increases in fluorescence intensity, while the fluorescence of single stranded probes becomes increasingly quenched. Up to 69-fold increase in fluorescence intensity (measured at lambda(em) = 383 nm) is observed upon hybridization to DNA/RNA. The emission from duplexes of multiple modified probes and DNA/RNA at concentrations down to less than 500 nM can easily be seen by the naked eye using standard illumination intensities.
Biologic activity in a fragment of recombinant human interferon alpha. (1984)

To attempt to locate functionally important regions of the interferon (IFN) molecule, recombinant human IFN-alpha 2 was subjected to proteolytic digestion. The bacterial proteinase thermolysin produced two major complementary fragments, HuIFN-alpha 2-(1-110) and HuIFN-alpha 2-(111-153). After reduction with 2-mercaptoethanol and separation of the two major fragments on NaDodSO4/polyacrylamide gel electrophoresis, antiviral activity persisted in the larger, Mr 12,000, fragment consisting of the amino-terminal 110 amino acids.
Application of champedak mannose‐binding lectin in the glycoproteomic profiling of serum samples unmasks reduced expression of alpha‐2 macroglobulin and complement factor B in patients with nasopharyngeal carcinoma (2010)

The use of lectin affinity chromatography prior to 2-DE separation forms an alternative method to unmask the expression of targeted glycoproteins of lower abundance in serum samples. Reduced expression of alpha-2 macroglobulin (AMG) and complement factor B (CFB) was detected in sera of patients with nasopharyngeal carcinoma (NPC) when pooled serum samples of the patients and those of healthy individuals were subjected to affinity isolation using immobilized champedak mannose-binding lectin and analyzed by 2-DE and densitometry. The AMG and CFB spots were not detected in the 2-DE protein profiles when the same pooled serum samples were subjected to albumin and IgG depletion and neither were they detected when the depleted samples were analyzed by western blotting and lectin detection. Together with other acute-phase response proteins that were previously reported to be altered in expression in NPC patients, AMG and CFB may serve as useful complementary biomarkers for NPC.
Survey of Geodetic Mapping Methods: Geodetic Approaches to Mapping and the Relationship to Graph-Based SLAM (2014)

The ability to simultaneously localize a robot and build a map of the environment is central to most robotics applications, and the problem is often referred to as simultaneous localization and mapping (SLAM). Robotics researchers have proposed a large variety of solutions allowing robots to build maps and use them for navigation. In addition, the geodetic community has addressed large-scale map building for centuries, computing maps that span across continents. These large-scale mapping processes had to deal with several challenges that are similar to those of the robotics community. In this article, we explain key geodetic map building methods that we believe are relevant for robot mapping. We also aim at providing a geodetic perspective on current state-of-the-art SLAM methods and identifying similarities both in terms of challenges faced and the solutions proposed by both communities. The central goal of this article is to connect both fields and enable future synergies between them.
pH-Responsive Polymer Microspheres: Rapid Release of Encapsulated Material within the Range of Intracellular pH (2001)

Microspheres formed from a new poly(β-amino ester) degrade slowly at pH 7.4 (left fluorescence microscopy image) but dissolve quickly at pH values below 6.5 (right), to release encapsulated material rapidly and quantitatively. As the pH/solubility transition occurs within the intracellular pH range, these tiny spheres hold promise as intracellular drug delivery vehicles.
Fluoxymesterone Therapy in Advanced Breast Cancer (1958)

ANDROGENIC hormones have been effectively employed in the therapy of advanced breast cancer. Objective improvement occurs in approximately 25 per cent of patients with osseous metastases, with a lower rate of response in patients with soft-tissue lesions.1 Since the effects of castration in premenopausal women are far superior to those of androgenic therapy, the male hormones have been employed primarily for women of postmenopausal age. A continuing search for more effective androgenic compounds is under way. Testosterone propionate, administered intramuscularly in three divided doses of 150 to 300 mg. weekly, has become the standard agent in the evaluation by comparison . . .
Disulfiram implantation: a trial using placebo implants and two types of controls. (1980)

Both disulfiram and placebo implant patients abstained longer and had more intense disulfiram-ethanol reactions than did two control groups.
Genetically engineered fusion proteins for treatment of cancer. (2012)

In this review, we summarize approaches to treat cancer with genetically engineered fusion proteins. Such proteins can act as decoy receptors for several ligands or as recruiters of immune effector cells to tumor. Examples of interference with growth factor-mediated tumor growth and tumor-related angiogenesis with fusion proteins consisting of the extracellular domains, and in some cases also of entities of one or several receptors and the Fc part of human IgG1, are discussed. In addition, we present strategies for recruitment of immune effector cells to tumor with fusion proteins. This can be achieved with fusion proteins consisting of a tumor-related antibody and a cytokine or major histocompatibilty complex class-I-peptide complexes, by T-cell receptor cytokine fusion proteins or by combination of a T-cell-recruiting antibody with a tumor-related ligand or a defined T-cell receptor.
Defect‐Related Optical Behavior in Surface Modified TiO2 Nanostructures (2005)

Abstract The surface modification of TiO 2 nanostructures to incorporate nitrogen and form visible light absorbing titanium oxynitride centers is studied. Anatase TiO 2 structures in the 5–20 nm range, formed by a wet chemical technique, were surface modified and the nitridation of the highly reactive TiO 2 nanocolloid surface, as determined by X‐ray photoelectron spectroscopy (XPS) studies, is achieved by a quick and simple treatment in alkyl ammonium compounds. The nitriding process was also simultaneously accompanied by metal seeding resulting in a metal coating layer on the TiO 2 structures. The structure of the resultant titanium oxynitride nanostructures remains anatase. These freshly prepared samples exhibited a strong emission near 560 nm (2.21 eV), which red‐shifted to 660 nm (1.88 eV) and dropped in intensity with aging in the atmosphere. This behavior was also evident in some of the combined nitrogen doped and metal seeded TiO 2 nanocolloids. Electron spin resonance (ESR) performed on these samples identified a resonance at g = 2.0035, which increased significantly with nitridation. The resonance is attributed to an oxygen hole center created near the surface of the nanocolloid, which correlates well with the observed optical activity.
The response of normal and polyoma virus‐transformed BHK/21 cells to exogenous purines (1973)

Abstract Adenosine (10 μM) stimulates the initial growth rate of BHK/21 cells seeded at low but not high density in monolayer culture; it does not affect final cell density or permit growth in agar. In labelling experiments With tritiated thymidine, adenosine also increases the response of quiescent cells to low concentrations of serum. Dialysis of serum to remove oxypurines only marginally reduces its effect on quiescent cell labelling or growth, indicating that BHK/21 cells are able to synthesise purines. The response of quiescent cells to 5% serum is inhibited by high MW (2 × 10 6 ) dextran sulphate at 2 μg per milliliter. Low MW dextran sulphate (30,000) and heparin at 20 μg per milliliter produce the same effect. Exogenous adenosine (10 μM) prevents this inhibition. Many other purine derivatives replace adenosine for all the above activities but xanthine is completely inactive in all. It, therefore, appears that nucleotide synthesis is a necessary function of these compounds. The growth of cells of a polyoma‐virus‐transformed BHK/21 line in monolayer is not stimulated by exogenous purine, though their colony‐forming ability in agar is increased five‐fold. The stimulating effects of exogenous purines on normal BHK/21 cells and the absolute requirement for them in the presence of polyanions is discussed in relation to possible mechanisms of growth control.
The Identity of Glutathione S -Transferase B with Ligandin, a Major Binding Protein of Liver (1974)

Evidence is presented that ligandin, an intracellular protein involved in the binding of such anions as bilirubin, indocyanine green, and penicillin, is identical to glutathione S -transferase B (EC 2.5.1.18), an enzyme catalyzing the conjugation of glutathione with such electrophiles as 1-chloro-2,4-dinitrobenzene, 1,2-dichloro-4-nitrobenzene, iodomethane, ethacrynic acid, and bromosulfophthalein. The proteins, isolated by distinct methods, have the same specificity for substrates and for ligands, react in identical fashion to antibody produced against ligandin, bear entirely similar physical characteristics and amino acid composition, and are both induced in response to phenobarbital. Indocyanine green, one of the ligands that is not effective as a substrate, was shown to competitively inhibit the conjugation reaction. It is suggested that specificity is directed toward compounds with electrophilic sites.
General Pattern Theory: A Mathematical Study of Regular Structures (1993)

PART I: PATTERN ALGEBRA PART II: PATTERN TOPOLOGY PART III: PATTERN DYNAMICS PART IV: METRIC PATTERN THEORY PART V: PATTERN DEFORMATIONS PART VI: PATTERN INFERENCE PART VII: CREATING REGULAR STRUCTURES
Safety analysis of vagal nerve stimulation for continuous nerve monitoring during thyroid surgery (2012)

VNS for CIONM resulted in increased vagal activity assessable via HRVA. The increased parasympathetic tone affected neither hemodynamics nor levels of the proinflammatory cytokine TNF-α. VNS for CIONM appears safe with the applied settings.
In Vitro Models of Human T Cell Development: Dishing Out Progenitor T Cells (2007)

T cells develop within the unique microenvironment provided by the thymus. T cell differentiation involves a series of commitment events and developmental checkpoints including T cell receptor (TCR) gene recombination and positive/negative selection of developing thymocytes to yield functionally mature T cells. These events occur in a sequential, temporal and spatial fashion, as developing thymocytes migrate through the thymus. In vitro studies to yield insights into human T cell development have classically employed the fetal thymic organ culture (FTOC) model system. This approach relies on the seeding of human hematopoietic stem cells (HSCs) and/or their progeny into host thymic lobes or thymic fragments, typically of mouse origin. Recently, a novel in vitro approach that makes use of the OP9 bone marrow stromal cell line expressing the Notch receptor ligand Delta-like-1 (OP9-DL1) effectively supported the generation of large numbers of human progenitor T cells from HSCs. In this review, we outline several in vitro systems employed for the generation and study of human T cells. Particular emphasis is dedicated to the OP9-DL1 coculture system. Finally, given the number of progenitor T cells that can be generated in vitro, we discuss the potential implications for the treatment of immune-related diseases such as cancer, immunedeficiency, and autoimmunity. Keywords: T cell development, Delta-like-1, progenitor T cells, cellular therapy, immune-reconstitution, hematopoietic stem cells
Selective killing of human malignant cell lines deficient in methylthioadenosine phosphorylase, a purine metabolic enzyme. (1981)

Seven out of 31 (23%) human malignant tumor cell lines had no detectable methylthioadenosine phosphorylase activity (less than 0.001 nmol/min per mg of protein), assayed with 5'-chloroadenosine as substrate. The enzyme-deficient cell lines were derived from five leukemias, one melanoma, and one breast cancer. None of 16 cell lines of nonmalignant origin, derived from lymphocytes, fibroblasts, and epithelial cells, lacked the enzyme (range, 0.156-1.447 nmol/min per mg of protein). As detected by autoradiography, intact enzyme-positive cell lines normal immature bone marrow cells, and four specimens of malignant tumor cells incorporated the adenine moiety of 5'-chloroadenosine into nucleic acids; however, no enzyme-deficient cell lines used 5'-chloroadenosine. When both types of cell lines were cultured in a medium containing 0.4 microM methotrexate, 16 microM uridine, and 16 microM thymidine (or 10 microM azaserine alone), no cells grew. If methylthioadenosine was added to the same medium, only enzyme-positive cells increased in number; most enzyme-deficient cells were dead after 3 days. Thus, human malignant tumor cell lines naturally deficient in methylthioadenosine phosphorylase could be selectively killed when de novo purine synthesis was inhibited and methylthioadenosine was the only exogenous source of purines.
Role of complement in inflammation and injury in the nervous system. (1997)

The complement (C) system plays important roles in host defence but activation at inappropriate sites or to an excessive degree can cause host tissue damage. C has been implicated as a factor in the causation or propagation of tissue injury in numerous diseases. The brain is an immunologically isolated site, sheltered from circulating cells and proteins of the immune system; nevertheless, there is a growing body of evidence implicating C in numerous brain diseases. In this brief article we review the evidence suggesting a role for C in diseases of the central and peripheral nervous system and discuss the possible sources of C at these sites. Some brain cells synthesise C and also express specific receptors; some are exquisitely sensitive to the lytic effects of C. The evidence suggests that C synthesis and activation in the brain are important in immune defence at this site but may also play a role in brain disease.
Stem cell mobilization with G-CSF analogs: a rational approach to separate GVHD and GVL? (2005)

The separation of graft-versus-host disease (GVHD) and graft-versus-leukemia (GVL) remains the "holy grail" of allogeneic stem cell transplantation, and improvements are urgently needed to allow more effective therapy of malignant disease. The use of G-CSF-mobilized peripheral blood as a clinical stem cell source is associated with enhanced GVL effects without amplification of significant acute GVHD. Preclinical studies have demonstrated that G-CSF modulates donor T cell function before transplantation, promoting T(H)2 differentiation and regulatory T cell function. In addition, the expansion of immature antigen-presenting cells (APCs) and plasmacytoid dendritic cells (DCs) favors the maintenance of this pattern of T cell differentiation after transplantation. Although these patterns of T cell differentiation attenuate acute GVHD, they do not have an impact on the cytolytic pathways of the CD8(+) T cells that are critical for effective GVL. Recently, it has been demonstrated that modification of G-CSF, either by pegylation of the native cytokine or conjugation to Flt-3L, results in the expansion and activation of donor iNKT cells, which significantly augment CD8(+) T cell-mediated cytotoxicity and GVL effects after transplantation. Given that these cytokines also enhance the expansion of regulatory T cells and APCs, they further separate GVHD and GVL, offering potential clinical advantages for the transplant recipient.