gebhart/patrepeval huggingface dataset:
Fluorescence in situ hybridization deletion mapping at 4p16.3 in bladder cancer cell lines refines the localisation of the critical interval to 30 kb (1996)

An allelotype analysis of transitional cell carcinoma of the bladder identified loss of heterozygosity (LOH) on chromosome arm 4p in 22% of tumours. In a more detailed LOH study of 178 bladder carcinomas, a 750 kb common region of deletion was identified between the markers D4S43 and D4S127 just telomeric to the Huntington disease locus. To refine this region of deletion at 4p16.3, we have carried out detailed fluorescence in situ hybridisation (FISH) analysis of 12 bladder cancer cell lines by using a chromosome 4 centromeric probe combined with a series of cosmid probes from contigs spanning the 750 kb region of deletion. A common 30 kb region of deletion was identified at 4p16.3 in over one-third of the bladder cancer cell lines analysed. The present study has refined the localisation of the critical region of deletion from 750 kb to approximately 30 kb, providing a precise starting point for positional cloning of the gene(s) involved in bladder cancer from within a very gene-rich region on chromosome band 4p16.3. This study demonstrates that FISH can be used for fine deletion mapping of potential tumour suppressor gene regions. The utilisation of FISH analysis to map chromosomal deletions should facilitate positional cloning of other genes as bacterial artificial chromosome (BAC) and yeast artificial chromosome (YAC) contigs of the human genome are established.
Nanoparticle Vaccines Encompassing the Respiratory Syncytial Virus (RSV) G Protein CX3C Chemokine Motif Induce Robust Immunity Protecting from Challenge and Disease (2013)

Nanoparticle vaccines were produced using layer-by-layer fabrication and incorporating respiratory syncytial virus (RSV) G protein polypeptides comprising the CX3C chemokine motif. BALB/c mice immunized with G protein nanoparticle vaccines produced a neutralizing antibody response that inhibited RSV replication in the lungs following RSV challenge. ELISPOT analysis showed that G nanoparticle vaccinated mice had increased levels of RSV G protein-specific IL-4 and IFN-γ secreting cells compared to controls following RSV challenge. Remarkably, RSV challenge of G protein nanoparticle vaccinated mice resulted in increased RSV M2-specific IL-4 and IFN-γ secreting T cells, and increased M2-specific H-2Kd-tetramer positive CD8(+) T cells in the lungs compared to controls. Cell type analysis showed vaccination was not associated with increased pulmonary eosinophilia following RSV challenge. These results demonstrate that vaccination of mice with the RSV G protein nanoparticle vaccines induces a potent neutralizing antibody response, increased G protein- and M2-specific T cell responses, and a reduction in RSV disease pathogenesis.
Synthesis and properties of an oligodeoxynucleotide containing a polycyclic aromatic hydrocarbon site specifically bound to the N2 amino group of a 2'-deoxyguanosine residue (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and properties of an oligodeoxynucleotide containing a polycyclic aromatic hydrocarbon site specifically bound to the N2 amino group of a 2'-deoxyguanosine residueRalph Casale and Larry W. McLaughlinCite this: J. Am. Chem. Soc. 1990, 112, 13, 5264–5271Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ja00169a039https://doi.org/10.1021/ja00169a039research-articleACS PublicationsRequest reuse permissionsArticle Views181Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Synthesis of recombinant blood coagulation factor VIII (FVIII) heavy and light chains and reconstitution of active form of FVIII (1999)

FVIII is synthesized as a single chain precursor of approximately 280 kD with the domain structure of A1-A2-B-A3-C1-C2 and it circulates as a series of metal ion-linked heterodimers that result from cleavages at B-A3 junction as well as additional cleavages within B domain. Factor VIII is converted to its active form, factor VIIIa, upon proteolytic cleavages by thrombin and is a heterotrimer composed of the A1, A2, and A3-C1-C2 subunits. A1 subunits of factor VIIIa terminates with 36 residue segment (Met337-Arg372) rich in acidic residues. This segment is removed after cleavages at Arg336 by activated protein C, which results in inactivation of the cofactor. In the present study, site-directed mutagenesis of FVIII at Arg336 to Gln336 was performed in order to produce an inactivation resistant mutant rFVIII (rFVIIIm) with an extended physiological stability. A recombinant mutant heavy chain of FVIII (rFVIII-Hm; Arg336 to Gln336) and wild-type light chain of FVIII (rFVIII-L) were expressed in Baculovirus-insect cell (Sf9) system, and a biologically active recombinant mutant FVIII (rFVIIIm) was reconstituted from rFVIII-Hm and rFVIII-L in the FVIII-depleted human plasma containing 40 mM CaCl2. The rFVIIIm exhibited cofactor activity of FVIIIa (2.85 x 10(-2) units/mg protein) that sustained the high level activity during in vitro incubation at 37 degrees C for 24 h, while the cofactor activity of normal plasma was declined steadily for the period. These results indicate that rFVIIIm (Arg336 to Gln336) expressed in Baculovirus-insect cell system is inactivation resistant in the plasma coagulation milieu and may be useful for the treatment of hemophilia A.
Hodgkin's lymphomas: classification, diagnosis, and grading. (1999)

Much has been learned in the past decade from the study of tissues involved by the disorder long known as Hodgkin's disease. Two important discoveries have prompted changes in classification and nomenclature: first, the recognition that there are two distinct lymphomas encompassed within this category (classical and nodular lymphocyte-predominant [NLP] types), and second, the discovery that the Reed-Sternberg (RS) cells in most cases are monoclonal B cells. Thus "Hodgkin's disease" comprises two distinct lymphomas, deserving of a name change, to "Hodgkin's lymphomas" (HLs). The immunophenotype and genetic features of both classical HL and NLPHL have been defined. These are useful in the subclassification of HL and in distinguishing HL from two recently described, aggressive lymphomas that were in the past often diagnosed as HL: anaplastic large-cell lymphoma, T-cell type (ALCL), and T-cell/histiocyte-rich large B-cell lymphoma (T/HRBCL). Despite the advances of recent years, many questions remain to be answered, and these will provide the challenges of the next decade.
Transcription Factor Nrf2 Coordinately Regulates a Group of Oxidative Stress-inducible Genes in Macrophages (2000)

Electrophiles and reactive oxygen species have been implicated in the pathogenesis of many diseases. Transcription factor Nrf2 was recently identified as a general regulator of one defense mechanism against such havoc. Nrf2 regulates the inducible expression of a group of detoxication enzymes, such as glutathione S-transferase and NAD(P)H:quinone oxidoreductase, via antioxidant response elements. Using peritoneal macrophages from Nrf2-deficient mice, we show here that Nrf2 also controls the expression of a group of electrophile- and oxidative stress-inducible proteins and activities, which includes heme oxygenase-1, A170, peroxiredoxin MSP23, and cystine membrane transport (system x(c)(-)) activity. The response to electrophilic and reactive oxygen species-producing agents was profoundly impaired in Nrf2-deficient cells. The lack of induction of system x(c)(-) activity resulted in the minimum level of intracellular glutathione, and Nrf2-deficient cells were more sensitive to toxic electrophiles. Several stress agents induced the DNA binding activity of Nrf2 in the nucleus without increasing its mRNA level. Thus Nrf2 regulates a wide-ranging metabolic response to oxidative stress.
Splitting of Pi and other 31 P NMR anomalies of skeletal muscle metabolites in canine muscular dystrophy (2012)

Many anomalies exist in the resting (31) P muscle spectra of boys with Duchenne muscular dystrophy (DMD) but few have been reported in Golden Retriever muscular dystrophy (GRMD), the closest existing animal model for DMD. Because GRMD is recommended for preclinical evaluation of therapies and quantitative outcome measures are needed, we investigated anomalies of (31) P NMRS in tibial cranial and biceps femoris muscles from 14 GRMD compared to 9 control (CONT) dogs. Alterations observed in DMD children - low phosphocreatine and high phospho-monoesters and -diesters - were all found in GRMD but increased pH was not. More surprisingly, inorganic phosphate (Pi) appeared to present a prominent splitting with an enhanced Pi(b) resonance at 0.3 ppm downfield of Pi(a) . Assuming that both resonances are Pi, the pH for Pi(a) in GRMD corresponded to a physiological intracellular pH(a) (6.97 ± 0.05), while pH(b) approached the extracellular range (7.27 ± 0.10) and correlated with pH(a) in GRMD (R(2) = 0.65). Both Pi(a) and Pi(b) were elevated compared to CONT and Pi(a) increased with age for GRMD (R(2) = 0.48, p < 0.001). Magnetisation transfer experiments between γATP and Pi were conducted to better characterise Pi pools. Equal T1 relaxation times for Pi(b) and Pi(a) did not support a mitochondrial origin of Pi(b) . We suggest that Pi(b) could originate from degenerating hypercontracted cells that have a leaky membrane and inadequate cell homeostasis and pH regulation. Pi(b) showed minimal chemical exchange in all dogs, while the exchange rate of Pi(a) was reduced in GRMD and might extraneously reflect low glycolytic activity in DMD. Taken together, the ensemble of (31) P NMRS alterations identifies muscle dysfunction and could provide useful biomarkers of therapeutic efficacy. Furthermore, among these, two might relate more specifically to dystrophic processes and merit further investigation: one is the existence of the enhanced alkaline Pi(b) pool; the other, mechanisms by which membrane disruption might increase phosphodiesters in dystrophy.
Incorporating FLT3 inhibitors into acute myeloid leukemia treatment regimens (2008)

FMS-Like-Tyrosine kinase-3 (FLT3) mutations are found in about 30% of cases of acute myeloid leukemia and confer an increased relapse rate and reduced overall survival. Targeting of this tyrosine kinase by direction inhibition is the focus of both preclinical and clinical research in AML. Several molecules in clinical development inhibit FLT3 with varying degrees of specificity. Preclinical models suggest that these compounds enhance the cytotoxicity of conventional chemotherapeutics against FLT3 mutant leukemia cells. The pharmacodynamic interactions between FLT3 inhibitors and chemotherapy appear to be sequence dependent. When the FLT3 inhibitor is used prior to chemotherapy, antagonism is displayed, while if FLT3 inhibition is instituted after to exposure to chemotherapy, synergistic cytotoxicity is seen. The combination of FLT3 inhibitors with chemotherapy is also complicated by potential pharmacokinetic obstacles, such as plasma protein binding and p-glycoprotein interactions. Ongoing and future studies are aimed at incorporating FLT3 inhibitors into conventional induction and consolidation therapy specifically for patients with FLT3 mutant AML.
Identification of Genes Upregulated in ALK -Positive and EGFR/KRAS/ALK -Negative Lung Adenocarcinomas (2011)

Activation of the EGFR, KRAS, and ALK oncogenes defines 3 different pathways of molecular pathogenesis in lung adenocarcinoma. However, many tumors lack activation of any pathway (triple-negative lung adenocarcinomas) posing a challenge for prognosis and treatment. Here, we report an extensive genome-wide expression profiling of 226 primary human stage I-II lung adenocarcinomas that elucidates molecular characteristics of tumors that harbor ALK mutations or that lack EGFR, KRAS, and ALK mutations, that is, triple-negative adenocarcinomas. One hundred and seventy-four genes were selected as being upregulated specifically in 79 lung adenocarcinomas without EGFR and KRAS mutations. Unsupervised clustering using a 174-gene signature, including ALK itself, classified these 2 groups of tumors into ALK-positive cases and 2 distinct groups of triple-negative cases (groups A and B). Notably, group A triple-negative cases had a worse prognosis for relapse and death, compared with cases with EGFR, KRAS, or ALK mutations or group B triple-negative cases. In ALK-positive tumors, 30 genes, including ALK and GRIN2A, were commonly overexpressed, whereas in group A triple-negative cases, 9 genes were commonly overexpressed, including a candidate diagnostic/therapeutic target DEPDC1, that were determined to be critical for predicting a worse prognosis. Our findings are important because they provide a molecular basis of ALK-positive lung adenocarcinomas and triple-negative lung adenocarcinomas and further stratify more or less aggressive subgroups of triple-negative lung ADC, possibly helping identify patients who may gain the most benefit from adjuvant chemotherapy after surgical resection.
DNA detection by surface enhanced resonance Raman scattering (SERRS) (2005)

This Education article outlines the different ways in which surface enhanced resonance Raman scattering (SERRS) can be used for the detection of DNA. The use of various different SERRS detection strategies that have allowed both sensitive and selective detection to be obtained is covered. Detection of DNA by SERRS involves the use of a dye with the DNA, whether as an intercalator or by direct covalent attachment. This generates strong SERRS signals that indicate the presence of the specific DNA sequence. The SERRS detection of DNA in different molecular biological assays is also discussed.
Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase (2006)

Biological electron transfer is designed to connect catalytic clusters by chains of redox cofactors. A review of the characterized natural redox proteins with a critical eye for molecular scale measurement of variation and selection related to physiological function shows no statistically significant differences in the protein medium lying between cofactors engaged in physiologically beneficial or detrimental electron transfer. Instead, control of electron tunnelling over long distances relies overwhelmingly on less than 14 A spacing between the cofactors in a chain. Near catalytic clusters, shorter distances (commonly less than 7 A) appear to be selected to generate tunnelling frequencies sufficiently high to scale the barriers of multi-electron, bond-forming/-breaking catalysis at physiological rates. We illustrate this behaviour in a tunnelling network analysis of cytochrome c oxidase. In order to surmount the large, thermally activated, adiabatic barriers in the 5-10 kcal mol-1 range expected for H+ motion and O2 reduction at the binuclear centre of oxidase on the 10(3)-10(5) s-1 time-scale of respiration, electron access with a tunnelling frequency of 10(9) or 10(10) s-1 is required. This is provided by selecting closely placed redox centres, such as haem a (6.9 A) or tyrosine (4.9 A). A corollary is that more distantly placed redox centres, such as CuA, cannot rapidly scale the catalytic site barrier, but must send their electrons through more closely placed centres, avoiding direct short circuits that might circumvent proton pumping coupled to haems a to a3 electron transfer. The selection of distances and energetic barriers directs electron transfer from CuA to haem a rather than a3, without any need for delicate engineering of the protein medium to 'hard wire' electron transfer. Indeed, an examination of a large number of oxidoreductases provides no evidence of such naturally selected wiring of electron tunnelling pathways.
Similarity, probability and database organisation (2002)

The question of storing imperfect data within a database framework has been discussed in the literature almost since the time when the first formal database structure was proposed. The matter received an additional impetus with the advent of fuzzy sets and its promise of formally capturing the notion of imprecision. If the imperfection is one of uncertainty as to whether a certain data item (or data structure) is actually present in the database, then the use of probability would be natural. However, when the imperfection relates to the relative proximity of the actual data to some idealised value, the use of a fuzzy-like model (possibility or similarity) seems warranted. In practice, the choice of model appears to be a matter of personal preference for a researcher. Characteristically, there has been no attempt to utilise both possibility and probability within the same data model. This might be due, in part, to the difficulty of capturing, in a reasonable way, various interactions between the simultaneously present possibility and probability weights. This paper describes work in progress, dealing with our research in modelling the interaction between similarity among the tuples (a binary function) and the probabilities of the tuples in the relational data model. The importance of such a study is underlined by the ubiquity of situations which involve, in a natural fashion, both probabilistic and possibilistic considerations. We illustrate it on two examples.
Megakaryoblastic Leukemia-1/2, a Transcriptional Co-activator of Serum Response Factor, Is Required for Skeletal Myogenic Differentiation (2003)

Serum response factor (SRF) is required for the expression of a wide variety of muscle-specific genes that are expressed upon differentiation and is thus required for both striated and smooth muscle differentiation in addition to its role in regulating growth factor-inducible genes. A heart and smooth muscle-specific SRF co-activator, myocardin, has been shown to be required for cardiac development and smooth muscle differentiation. However, no such co-factors of SRF have been identified in the skeletal myogenic differentiation program. Myocardin and the related transcription factor megakaryoblastic leukemia-1 (MKL1/MAL/MRTF-A) can strongly potentiate the activity of SRF. Here we report the cloning of the third member of the myocardin/MKL family in humans, MKL2. MKL2 binds to and activates SRF similar to myocardin and MKL1. To determine the role of these factors in skeletal myogenic differentiation we used a dominant negative MKL2 to show that the MKL family of proteins is required for skeletal myogenic differentiation. Expression of the dominant negative protein in C2C12 skeletal myoblasts blocked the differentiation-induced expression of the SRF target genes skeletal alpha-actin and alpha-myosin heavy chain and blocked differentiation of the myoblasts to myotubes in vitro. C2C12 cells express both MKL1 and MKL2, but not myocardin, implicating MKL1 and/or MKL2 in the requirement for skeletal myogenic differentiation. MKL1 was predominantly cytoplasmic in C2C12 cells, with a small amount in the nucleus, however, no movement of MKL1 to the nucleus was observed upon differentiation.
A mathematical and physiological model for early distribution of radioiodide in man (1965)

A model is proposed for the early distribution of radioiodide in man. This model is formalized as a set of eight simultaneous differential equations, each predicting the rate of change of radioiodide in a compartment. These equations have been fitted by numerical integration on a digital computer to plasma curves from sessions with and without aspiration of gastric contents, curves of the aspirated radioiodide, and thyroidal and renal plasma clearance rates. In this model, plasma radioiodide is distributed reversibly to the erythrocytes, interstitial fluid (space E) and a “slowly diffusible space” (space C). Distribution to the thyroid and kidney is irreversible. Radioiodide distributed to the salivary glands and gastric mucosa must pass through a gastrointestinal cycle before eventual reabsorption from the intestine. Successive compartments of this cycle are the “inaccessible gastric space” (space M), free gastric juice (space S) and the intestine (space D). All of the modes of distribution mentioned are governed by rate constants except for transfer from space S to space D, which occurs as a complete transfer at a fixed interval tau. gastrointestinal iodide cycle; pooling of radioiodide in gastrointestinal tract; plasma radioiodide curve; multicompartment model; iterative solution of mathematical model Submitted on September 28, 1964
Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. (1994)

Genes located near telomeres in yeast are subject to position-effect variegation. To better understand the mechanism of this variegation, we investigated how a telomeric URA3 gene switches from a silent to an expressed state. We found that silencing of a telomeric URA3 gene was attributable to the elimination of its basal transcription. The reversal of that silencing was dependent on the presence of PPR1, the trans-activator protein of URA3. Maximum expression of URA3 required a higher concentration of PPR1 when URA3 was telomeric compared with when it was at a nontelomeric location. The ability of PPR1 to overcome silencing varied at different points in the cell cycle. In cells arrested in G2/metaphase, PPR1 was able to activate transcription of a telomeric URA3, but in cells arrested in G0, G1, or early S phase it was not. In comparison, a nontelomeric URA3 could be activated by PPR1 at all times. We conclude that once established, telomeric silent chromatin is a relatively stable structure, making a gene recalcitrant to activation. Following the disassembly of silent chromatin during DNA replication, competition of assembly ensues between components of telomeric chromatin, to establish a silent state, and the trans-activator, to establish gene expression. These results help explain the stochastic nature of phenotypic switching in variegated gene expression.