gebhart/patrepeval huggingface dataset:
Identification of Candidate Driver Genes in Common Focal Chromosomal Aberrations of Microsatellite Stable Colorectal Cancer (2013)

Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Chromosomal instability (CIN) is a major driving force of microsatellite stable (MSS) sporadic CRC. CIN tumours are characterised by a large number of somatic chromosomal copy number aberrations (SCNA) that frequently affect oncogenes and tumour suppressor genes. The main aim of this work was to identify novel candidate CRC driver genes affected by recurrent and focal SCNA. High resolution genome-wide comparative genome hybridisation (CGH) arrays were used to compare tumour and normal DNA for 53 sporadic CRC cases. Context corrected common aberration (COCA) analysis and custom algorithms identified 64 deletions and 32 gains of focal minimal common regions (FMCR) at high frequency (>10%). Comparison of these FMCR with published genomic profiles from CRC revealed common overlap (42.2% of deletions and 34.4% of copy gains). Pathway analysis showed that apoptosis and p53 signalling pathways were commonly affected by deleted FMCR, and MAPK and potassium channel pathways by gains of FMCR. Candidate tumour suppressor genes in deleted FMCR included RASSF3, IFNAR1, IFNAR2 and NFKBIA and candidate oncogenes in gained FMCR included PRDM16, TNS1, RPA3 and KCNMA1. In conclusion, this study confirms some previously identified aberrations in MSS CRC and provides in silico evidence for some novel candidate driver genes.
A Convenient Preparation of <i>meso</i>-Tetra(4-sulfonatophenyl)porphyrin (1975)

The sulfonation of meso-tetraphenylporphyrin, in concentrated sulfuric acid followed by neutralization and dialysis, provides an efficient and convenient route to meso-tetra(4-sulfonatophenyl)porphyrin.
In vivo responses of macrophages and perisinusoidal cells to cholestatic liver injury. (1993)

We investigated the response of macrophages and perisinusoidal (Ito) cells (PSCs) during the development of secondary biliary cirrhosis after ligation and division of the common bile duct. Liver tissue was obtained from three groups of male Wistar rats: 1) untreated controls (n = 3); 2) common bile duct-ligated (CBDL) animals (n = 15); and 3) sham-operated controls (n = 15). Material from animal groups 2 and 3 was obtained on days 3, 7, 14, 21, and 28 after operation; in all animals 5-bromo-2-deoxyuridine was administered intraperitoneally before death. Monocytes and macrophages were detected using the monoclonal antibody ED1 and tissue macrophages using the antibody ED2. Cell proliferation within the macrophage population was demonstrated by double labeling for ED2 and incorporated 5-bromo-2-deoxyuridine. PSCs were demonstrated in tissue sections by immunolocalization of desmin; proliferating PSCs were identified by double labeling for desmin and incorporated 5-bromo-2-deoxyuridine. Evidence of phenotypic modulation of PSCs was sought using anti-alpha-smooth muscle actin (alpha-SMA) antibody. Increased numbers of ED1- and ED2-positive cells were seen in CBDL animals at all time points. Local proliferation of macrophages could be identified and reached a peak at day 3, thereafter falling toward control values. Compared with those of controls, livers of CBDL animals showed increased numbers of desmin-positive PSCs in periportal zones from day 3 on, reaching a peak at day 14 (127.8 +/- 10.99 cells/0.635 mm2) and followed by a plateau. PSC proliferation peaked at days 3 and 7 (labeling indices 11.2% and 11.2%, respectively) and thereafter fell toward control values; no expansion of the PSC population was seen in sham-operated rats. Increased alpha-SMA-positive cells were also noted from day 3, with a peak at day 21 (231.1 +/- 11.52 cells/0.635 mm2) and followed by a plateau. En face labeling experiments in days 14, 21, and 28 CBDL animals showed cells co-expressing alpha-SMA and desmin and cells expressing alpha-SMA alone. These results indicate that in response to chronic cholestatic liver injury, PSCs proliferate and undergo phenotypic modulation toward "myofibroblast-like" cells. The kinetics of the response are similar to those of the ED2-positive cell population in keeping with a hypothesis that PSC proliferation and activation may be mediated by factors released by macrophages in response to various forms of liver injury. We conclude that the responses of macrophages and PSCs to cholestatic injury are similar to those after toxin-induced hepatocyte necrosis.
An on-line data collection and analysis system for VLSI devices at wafer probe and final test (2002)

This paper describes a flexible software system for the collection of parametric, functional pattern fail, and bitmap data on-line during production testing of VLSI devices. The data is automatically loaded into a relational database for subsequent analysis by process and yield improvement software. The user can control the type and amount of data that is collected at each stage of a product's life. By enabling data collection on every test, the same system can be used for engineering and debug analysis.
Characterization of flat revertant cells isolated from simian virus 40-transformed mouse and rat cells which contain multiple copies of viral genomes (1981)

Eight clones of flat revertants were isolated by negative selection from simian virus 40 (SV40)-transformed mouse and rat cell lines in which two and six viral genome equivalents per cell were integrated, respectively. These revertants showed either a normal cell phenotype or a phenotype intermediate between normal and transformed cells as to cellular morphology and saturation density and were unable to grow in soft agar medium. One revertant derived from SV40-transformed mouse cells was T antigen positive, whereas the other seven revertants were T antigen negative. SV40 could be rescued only from the T-antigen-positive revertant by fusion with permissive monkey cells. The susceptibility of the revertants to retransformation by wild-type SV40 was variable among these revertants. T-antigen-negative revertants from SV40-transformed mouse cells were retransformed at a frequency of 3 to 10 times higher than their grandparental untransformed cells. In contrast, T-antigen-negative revertants from SV40-transformed rat cells could not be retransformed. The arrangement of viral genomes was analyzed by digestion of cellular DNA with restriction enzymes of different specificity, followed by detection of DNA fragments containing a viral sequence and rat cells were serially arranged within the length of about 30 kilobases, with at least two intervening cellular sequences. A head-to-tail tandem array of unit length viral genomes was present in at least one insertion site in the transformed rat cells. All of the revertants had undergone a deletion(s), and only a part of the viral genome was retained in T-antigen-negative revertants. A relatively high frequency of reversion in the transformed rat cells suggests that reversion occurs by homologous recombination between the integrated viral genomes.
Nanocrystalline Manganese Oxides for Electrochemical Capacitors with Neutral Electrolytes (2002)

With an objective to develop inexpensive electrode materials for electrochemical redox capacitors, nanocrystalline manganese oxides have been synthesized by reducing aqueous solution with various reducing agents such as potassium borohydride, sodium dithionite, sodium hypophosphite, and hydrochloric acid under various controlled pH conditions. The products have been characterized by X-ray diffraction, thermogravimetric analysis, surface area measurements, and cyclic voltametry in various neutral electrolytes such as aqueous NaCl, KCl, LiCl, and Optimized samples exhibit specific capacitance values of around 250 F/g in the range of 0-1 V vs. SCE with excellent cyclability in 2 M NaCl electrolyte. © 2002 The Electrochemical Society. All rights reserved.
The Catalytic Activity of Metals Produced by the Reduction of Salts in Liquid Ammonia. II. Nickel<sup>1</sup> (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Catalytic Activity of Metals Produced by the Reduction of Salts in Liquid Ammonia. II. Nickel1George W. Watt, Wilbur F. Roper, and Sidney G. ParkerCite this: J. Am. Chem. Soc. 1951, 73, 12, 5791–5793Publication Date (Print):December 1, 1951Publication History Published online1 May 2002Published inissue 1 December 1951https://pubs.acs.org/doi/10.1021/ja01156a093https://doi.org/10.1021/ja01156a093research-articleACS PublicationsRequest reuse permissionsArticle Views47Altmetric-Citations9LEARN 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
Condensation of Therapeutic Oligodeoxynucleotides and Plasmid DNA with PPI Dendrimers and PPI-Modified Gold Nanoparticles (2006)

We demonstrated the formation of oligodeoxynucleotide (ODN) nanoparticles in the presence of polypropylenimine (PPI) dendrimers using total intensity light scattering (TILS) and atomic force microscopy (AFM). Based on the interesting observations during the ODN condensation, two competitive condensation mechanisms were proposed, which are very different from the condensation pathways of high molecular weight DNA polymers. Confocal microscopic analysis showed that the nanoparticles formed with G4 and G5 dendrimers could undergo facile cellular uptake in a breast cancer cell line, MDA-MB-231, whereas particles formed with G1-G3 dendrimers lacked this ability. Nanoparticles formed with G1-G3 dendrimers showed significantly lower zeta potentials (5.2-6.5 mV) than those (12-18 mV) of particles formed with G4 and G5 dendrimers. These results indicate an important effect of both the size and surface charge density of the dendrimers on ODN nanoparticle formation and cellular transport. Finally, we report a novel condensing approach to reach a goal of high efficiency and low/nontoxic transport of high concentration DNAs to cancer cells by using low-generation PPI dendrimers with gold nanoparticles as labile catalyst.
Transforming mechanism of the feline sarcoma virus encoded v-fms oncogene product. (1991)

The v-fms oncogene product encoded by the McDonough strain of feline sarcoma virus (SM-FeSV) is a transmembrane glycoprotein which belongs to the tyrosine kinase receptor family. The cellular counterpart, the c-fms product, is the receptor for macrophage colony stimulating factor (M-CSF or CSF-1). The v-fms and the c-fms product differ structurally only in seven point mutations and in their C-terminal domains. We have corrected the published sequence of the v-fms product and found that the new C-terminal end contains a threonine phosphorylation site (Thr939). This site is phosphorylated in vivo leading to an enhancement of the v-fms-specific tyrosine kinase activity. The extracellular domain of the v-fms product contains 11 N-glycosylation sites. Glycosylation and transport of the v-fms molecules to the plasma membrane are prerequisites for the transforming potential of the virus. Phosphorylation of the v-fms molecules in tyrosine, serine and threonine residues takes place only at the plasma membrane. Coexpression showed that the overexpression of M-CSF and c-fms in fibroblasts leads to cell transformation by an autocrine loop mechanism. This interaction between M-CSF and the c-fms protein also takes place at the plasma membrane. To study the v-fms transforming mechanisms, we have expressed the v-fms oncogene in chicken fibroblasts which are free of the cross-reactive M-CSF. The expression of the v-fms oncogene alone did not cause transformation. However, upon addition of M-CSF, these cells became completely transformed.(ABSTRACT TRUNCATED AT 250 WORDS)
Melamine Detection in Infant Formula Powder Using Near- and Mid-Infrared Spectroscopy (2009)

Near- and mid-infrared spectroscopy methods (NIR, FTIR-ATR, FTIR-DRIFT) were evaluated for the detection and quantification of melamine in infant formula powder. Partial least-squares (PLS) models were established for correlating spectral data to melamine concentration: R(2) > 0.99, RMSECV ≤ 0.9, and RPD ≥ 12. Factorization analysis of spectra was able to differentiate unadulterated infant formula powder from samples containing 1 ppm melamine with no misclassifications, a confidence level of 99.99%, and selectivity > 2. These nondestructive methods require little or no sample preparation. The NIR method has an assay time of 1 min, and a 2 min total time to detection. The FTIR methods require up to 5 min for melamine detection. Therefore, NIR and FTIR methods enable rapid detection of 1 ppm melamine in infant formula powder.
Alzheimer’s presenilin 1 modulates sorting of APP and its carboxyl‐terminal fragments in cerebral neurons <i>in vivo</i> (2007)

Studies in continuously cultured cells have established that familial Alzheimer's disease (FAD) mutant presenilin 1 (PS1) delays exit of the amyloid precursor protein (APP) from the trans-Golgi network (TGN). Here we report the first description of PS1-regulated APP trafficking in cerebral neurons in culture and in vivo. Using neurons from transgenic mice or a cell-free APP transport vesicle biogenesis system derived from the TGN of those neurons, we demonstrated that knocking-in an FAD-associated mutant PS1 transgene was associated with delayed kinetics of APP arrival at the cell surface. Apparently, this delay was at least partially attributable to impaired exit of APP from the TGN, which was documented in the cell-free APP transport vesicle biogenesis assay. To extend the study to APP and carboxyl terminal fragment (CTF) trafficking to cerebral neurons in vivo, we performed subcellular fractionation of brains from APP transgenic mice, some of which carried a second transgene encoding an FAD-associated mutant form of PS1. The presence of the FAD mutant PS1 was associated with a slight shift in the subcellular localization of both holoAPP and APP CTFs toward iodixanol density gradient fractions that were enriched in a marker for the TGN. In a parallel set of experiments, we used an APP : furin chimeric protein strategy to test the effect of artificially forcing TGN concentration of an APP : furin chimera that could be a substrate for beta- and gamma-cleavage. This chimeric substrate generated excess Abeta42 when compared with wildtype APP. These data indicate that the presence of an FAD-associated mutant human PS1 transgene is associated with redistribution of the APP and APP CTFs in brain neurons toward TGN-enriched fractions. The chimera experiment suggests that TGN-enrichment of a beta-/gamma-secretase substrate may play an integral role in the action of mutant PS1 to elevate brain levels of Abeta42.
OSCAR for bioinformatics clusters (2004)

Use the software that the big labs use, and put a decade of Linux cluster management experience to work for you.
Interleukin-17 Retinotoxicity Is Prevented by Gene Transfer of a Soluble Interleukin-17 Receptor Acting as a Cytokine Blocker: Implications for Age-Related Macular Degeneration (2014)

Age-related macular degeneration (AMD) is a common yet complex retinal degeneration that causes irreversible central blindness in the elderly. Pathology is widely believed to follow loss of retinal pigment epithelium (RPE) and photoreceptor degeneration. Here we report aberrant expression of interleukin-17A (IL17A) and the receptor IL17RC in the macula of AMD patients. In vitro, IL17A induces RPE cell death characterized by the accumulation of cytoplasmic lipids and autophagosomes with subsequent activation of pro-apoptotic Caspase-3 and Caspase-9. This pathology is reduced by siRNA knockdown of IL17RC. IL17-dependent retinal degeneration in a mouse model of focal retinal degeneration can be prevented by gene therapy with adeno-associated virus vector encoding soluble IL17 receptor. This intervention rescues RPE and photoreceptors in a MAPK-dependent process. The IL17 pathway plays a key role in RPE and photoreceptor degeneration and could hold therapeutic potential in AMD.
The Treatment of Melioidosis (2010)

Melioidosis is a complex bacterial infection, treatment of which combines the urgency of treating rapidly fatal Gram negative septicaemia with the need for eradication of long-term persistent disease in pulmonary, soft tissue, skeletal and other organ systems. Incremental improvements in treatment have been made as a result of multicentre collaboration across the main endemic region of Southeast Asia and northern Australia. There is an emerging consensus on the three main patterns of antimicrobial chemotherapy; initial (Phase 1) treatment, subsequent eradication (Phase 2) therapy and most recently post-exposure (Phase 0) prophylaxis. The combination of agents used, duration of therapy and need for adjunct modalities depends on the type, severity and antimicrobial susceptibility of infection. New antibiotic and adjunct therapies are at an investigational stage but on currently available data are unlikely to make a significant impact on this potentially fatal infection.
The potential of murine cytomegalovirus as a viral vector for immunocontraception (1994)

Wild populations of house mice (Mus domesticus) regularly undergo population eruptions in the cereal growing regions of S.E. Australia, causing significant damage to crops. Rodenticides are costly and are of limited usefulness, and the need for a biological control agent is widely recognized. The options for the use of an infectious agent to control mouse populations are considered. The three main types are: infectious agents which establish lethal infection; those which directly interfere with fertility; and recombinant virus vectors encoding fertility-associated proteins such as zona pellucida or sperm antigens in order to induce immunocontraceptive responses in infected mice. Ectromelia, a murine pox virus, has the potential for reducing mouse populations by lethal infection but it is not present in wild mice in Australia. The disadvantages of using ectromelia are that it would pose a significant threat to colonies of laboratory mice, there appears to be substantial innate resistance in Australian wild mice and it may not be entirely mouse-specific, thus placing native rodents at risk. A number of factors influencing the selection of a virus as a vector for immunocontraception are discussed. The mouse-specific murine cytomegalovirus (MCMV) fits most of these criteria. Infection with MCMV is already widespread in Australia with 80-90% of Mus domesticus tested being seropositive. It is a large DNA virus which establishes persistent, non-lethal infection, it is a suitable vector for the insertion of foreign genes and has a number of properties, including the capacity for superinfection, that should assist the recombinant virus to persist in wild mouse populations and induce an immunocontraceptive effect.
Repensando a Literatura Comparada: Edward Said e Fredric Jameson (1997)

As obras de Edward Said e Fredric Jameson representam, no contexto da crítica literária e cultural da atualidade, projetos alternativos para restaurar a validade do estudo histórico na leitura de textos, e isto na dimensão de poder globalizante que compreende as culturas metropolitanas e periféricas. Enquanto Jameson tenta situar tais textos em suas desigualdades e no contexto de uma história única e última e do sistema ideológico que os explica de forma mais completa (o Marxismo), Said percebe tais textos a partir da prática relativamente livre do crítico que, em precário equilíbrio entre cultura e sistema de pensamento e munido de uma ética humanitária de valor universal, tenta produzir uma leitura em contraponto dirigida para a percepção das histórias do outro cultural reprimidas pelas estratégias discursivas imperiais.
Fan-beam reconstruction methods (1979)

In a previous paper a technique was developed for finding reconstruction algorithms for arbitrary ray-sampling schemes. The resulting algorithms use a general linear operator, the kernel of which depends on the details of the scanning geometry. Here this method is applied to the problem of reconstructing density distributions from arbitrary fan-beam data. The general fan-beam method is then specialized to a number of scanning geometries of practical importance. Included are two cases where the kernel of the general linear operator can be factored and rewritten as a function of the difference of coordinates only and the superposition integral consequently simplifies into a convolution integral. Algorithms for these special cases of the fan-beam problem have been developed previously by others. In the general case, however, Fourier transforms and convolutions do not apply, and linear space-variant operators must be used. As a demonstration, details of a fan-beam method for data obtained with uniform ray-sampling density are developed.
Emergence of Cytomegalovirus Disease in Patients Receiving Temozolomide: Report of Two Cases and Literature Review (2010)

Temozolomide chemotherapy has become part of the therapy used to treat glioblastoma multiforme and refractory anaplastic astrocytoma. Temozolomide frequently produces profound lymphopenia. We report 2 cases of cytomegalovirus disease that occurred in patients receiving temozolomide therapy and review 4 additional cases reported in the literature. Narrow monitoring with cytomegalovirus antigenemia assay should be considered for recommendation.
A mathematical model of the volume, pH, and ion content regulation in reticulocytes. Application to the pathophysiology of sickle cell dehydration. (1991)

We developed a mathematical model of the reticulocyte, seeking to explain how a cell with similar volume but much higher ionic traffic than the mature red cell (RBC) regulates its volume, pH, and ion content in physiological and abnormal conditions. Analysis of the fluxbalance required by reticulocytes to conserve volume and composition predicted the existence of previously unsuspected Na(+)-dependent Cl- entry mechanisms. Unlike mature RBCs, reticulocytes did not tend to return to their original state after brief perturbations. The model predicted hysteresis and drift in cell pH, volume, and ion contents after transient alterations in membrane permeability or medium composition; irreversible cell dehydration could thus occur by brief K+ permeabilization, transient medium acidification, or the replacement of external Na+ with an impermeant cation. Both the hysteresis and drift after perturbations were shown to depend on the pHi dependence of the K:Cl cotransport, a major reticulocyte transporter. This behavior suggested a novel mechanism for the generation of irreversibly sickled cells directly from reticulocytes, rather than in a stepwise, progressive manner from discocytes. Experimental tests of the model's predictions and the hypothesis are described in the following paper.