gebhart/patrepeval huggingface dataset:
Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease (2005)

The propensity for developing atherosclerosis is dependent on underlying genetic risk and varies as a function of age and exposure to environmental risk factors. Employing three mouse models with different disease susceptibility, two diets, and a longitudinal experimental design, it was possible to manipulate each of these factors to focus analysis on genes most likely to have a specific disease-related function. To identify differences in longitudinal gene expression patterns of atherosclerosis, we have developed and employed a statistical algorithm that relies on generalized regression and permutation analysis. Comprehensive annotation of the array with ontology and pathway terms has allowed rigorous identification of molecular and biological processes that underlie disease pathophysiology. The repertoire of atherosclerosis-related immunomodulatory genes has been extended, and additional fundamental pathways have been identified. This highly disease-specific group of mouse genes was combined with an extensive human coronary artery data set to identify a shared group of genes differentially regulated among atherosclerotic tissues from different species and different vascular beds. A small core subset of these differentially regulated genes was sufficient to accurately classify various stages of the disease in mouse. The same gene subset was also found to accurately classify human coronary lesion severity. In addition, this classifier gene set was able to distinguish with high accuracy atherectomy specimens from native coronary artery disease vs. those collected from in-stent restenosis lesions, thus identifying molecular differences between these two processes. These studies significantly focus efforts aimed at identifying central gene regulatory pathways that mediate atherosclerotic disease, and the identification of classification gene sets offers unique insights into potential diagnostic and therapeutic strategies in atherosclerotic disease.
Zeamatin, an antifungal protein from maize with membrane-permeabilizing activity (1990)

A 22 kDa antifungal protein (zeamatin) was purified from Zea mays seeds. It was identified and assayed by its unusual property of acting synergistically with nikkomycin to inhibit growth of Candida albicans. Alone, it inhibited growth in suspension culture of C. albicans, Neurospora crassa and Trichoderma reesei. Zeamatin contained no detectable chitinase, 1,3-β-glucanase or ribosome-inactivating protein activity, enzymes present in a variety of plants that have been shown to have antifungal properties. At low concentrations zeamatin caused the rapid release of cytoplasmic material from C. albicans and N. crassa. This was confirmed microscopically by observing zeamatin-induced hyphal rupture of these fungi. These results suggest that zeamatin permeabilizes the fungal plasma membrane. We believe zeamatin to be a representative of a previously unrecognized class of plant antifungal proteins.
Mapping of Replication Initiation Sites in Human Ribosomal DNA by Nascent-Strand Abundance Analysis (1995)

New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E.M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R.D. Little, T.H.K. Platt, and C.L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit.
Hybrid human immunodeficiency virus Gag particles as an antigen carrier system: induction of cytotoxic T-cell and humoral responses by a Gag:V3 fusion (1993)

In attempts to increase the immunogenicity of recombinant antigens, a number of particulate antigen presentation systems have been developed. In this study, we used human immunodeficiency virus Gag particles as carriers for the human immunodeficiency virus envelope V3 region. Gag:V3 fusion proteins were expressed from baculovirus expression vectors; they migrated to the insect cell membrane and budded from the cells as hybrid particles. An immunization study carried out with rats showed that the particles elicited a strong anti-Gag antibody response and a weak antibody response to the V3 region. A strong anti-V3 cytolytic T-cell response was elicited in immunized mice. These data show that retroviral Gag particles can be used as antigen presentation vehicles.
Adenovirus infection after allogeneic stem cell transplantation (2007)

Adenovirus infection after allogeneic hematopoietic stem cell transplantation (HSCT) is an emerging pathogen causing relevant morbidity and mortality, with preponderance in children. During the last years, basic research on the biology of the virus and host immune response ameliorated the diagnostic, surveillance, and therapeutic strategies. Risk factors for infection commonly have an impact on T-cell reconstitution, such as T-cell depleted graft, unrelated or HLA-mismatched donor transplantation, and GvHD. Weekly surveillance by PCR in stool and blood till day 100 or longer post-HSCT and pre-emptive therapy with cidofovir are the mainstay of the current approach to adenoviral infections post-HSCT. Since a sufficient host T-cell response is essential to clear the virus, diagnostic procedures for detection of virus-specific T-cells have recently been developed to assess the risk of the infection. Furthermore, adoptive immunotherapy is a new treatment option for patients with absent specific T-cell response and present systemic adenoviral infection.
Hereditary deficiency of vitamin K-dependent coagulation factors with skeletal abnormalities (1996)

We describe a female infant who presented with severe intracranial bleeding and was found to have a hereditary deficiency of vitamin K-dependent coagulation factors. She also had mild stippling of the left femoral epiphysis and shortness of the distal phalanges of the fingers. We studied the possible relationship between these abnormalities and a peroxisomal defect and followed their responses to treatment with vitamin K. The level of vitamin K-dependent clotting factors returned to near-normal following treatment with pharmacological doses of vitamin K, but there was no effect on the skeletal abnormalities.
Patterns of Cancer Incidence, Mortality, and Prevalence Across Five Continents: Defining Priorities to Reduce Cancer Disparities in Different Geographic Regions of the World (2006)

Efforts to reduce global cancer disparities begin with an understanding of geographic patterns in cancer incidence, mortality, and prevalence. Using the GLOBOCAN (2002) and Cancer Incidence in Five Continents databases, we describe overall cancer incidence, mortality, and prevalence, age-adjusted temporal trends, and age-specific incidence patterns in selected geographic regions of the world. For the eight most common malignancies-cancers of lung, breast, colon and rectum, stomach, prostate, liver, cervix, and esophagus-the most important risk factors, cancer prevention and control measures are briefly reviewed. In 2002, an estimated 11 million new cancer cases and 7 million cancer deaths were reported worldwide; nearly 25 million persons were living with cancer. Among the eight most common cancers, global disparities in cancer incidence, mortality, and prevalence are evident, likely due to complex interactions of nonmodifiable (ie, genetic susceptibility and aging) and modifiable risk factors (ie, tobacco, infectious agents, diet, and physical activity). Indeed, when risk factors among populations are intertwined with differences in individual behaviors, cultural beliefs and practices, socioeconomic conditions, and health care systems, global cancer disparities are inevitable. For the eight most common cancers, priorities for reducing cancer disparities are discussed.
A cyclic peptide inhibitor of C-terminal binding protein dimerization links metabolism with mitotic fidelity in breast cancer cells (2013)

Identification of direct modulators of transcription factor protein-protein interactions is a key challenge for ligand discovery that promises to significantly advance current approaches to cancer therapy. Here, we report an inhibitor of NADH-dependent dimerization of the C-terminal binding protein (CtBP) transcriptional repressor, identified by screening genetically encoded cyclic peptide libraries of up to 64 million members. CtBP dimers form the core of transcription complexes associated with epigenetic regulation of multiple genes that control many characteristics of cancer cells, including proliferation, survival and migration. CtBP monomers also have distinct and critical cellular function, thus current experimental tools that deplete all forms of a targeted protein (<i>e.g.</i> siRNA) do not allow the cellular consequences of this metabolically regulated transcription factor to be deciphered. The most potent inhibitor from our screen (<i>cyclo</i>-SGWTVVRMY) is demonstrated to disrupt CtBP dimerization <i>in vitro</i> and in cells. This compound is used as a chemical tool to establish that the NADH-dependent dimerization of CtBPs regulates the maintenance of mitotic fidelity in cancer cells. Treatment of highly glycolytic breast cancer cell lines with the identified inhibitor significantly reduced their mitotic fidelity, proliferation and colony forming potential, whereas the compound does not affect mitotic fidelity of cells with lower glycolytic flux. This work not only links the altered metabolic state of transformed cells to a key determinant of the tumor cell phenotype, but the uncovered compound also serves as the starting point for the development of potential therapeutic agents that target tumors by disrupting the CtBP chromatin-modifying complex.
On the role of additives in alkyl–alkyl Negishi cross-couplings (2010)

An additives study for the alkyl-alkyl Negishi reaction using an NHC-Pd catalyst revealed that bromide salts promote coupling while the cation is mechanistically benign. A double titration revealed that the cross-coupling begins at a 1 : 1 ratio of LiBr : (n)BuZnBr, suggesting that a higher-order zincate, presumably Li(m)Zn((n)Bu)Br(3)((2-m)-), is the active transmetalating agent.
&lt;i&gt;Estimation of Peanut Maturity Using Color Image Analysis&lt;/i&gt; (2018)

<b><sc>Abstract.</sc></b> Peanuts pods grow underground and mature unevenly, resulting that choosing the correct time to harvest is more complicated than other crops. Pod maturity can be determined by blasting with a pressure washer to remove outer skin of the pod (exocarp) to expose the color of the middle layer (mesocarp). The mesocarp color changes with maturity from white to yellow, orange, brown and finally black. The sum of percentage from orange, brown, and black mesocarp (OBB) color and black color (BL) represent the kernels are mature enough to harvest. The goal of this research is to identify methodologies to estimate OBB and BL of the pods using RGB images taken in the field and validate the proposed model using other pod images. The Mahalanobis distance classification method was used to process sets of images and calculate pods area (number of pixels) corresponding to two classes (mesocarp and background) with nine different color groups. The results showed a performance of 94% effectiveness for mesocarp using Mahalanobis distance classification. Statistical regression model for OBB and BL were developed based on 315 images of peanut pods taken from the field. The R<sup>2</sup> and root mean square error of predicted and actual OBB were 0.93 and 4.1%, respectively. The R<sup>2</sup> and root mean square error of predicted and actual BL were 0.88 and 1.8%, respectively. The validation of OBB using other images provided reasonable estimation (R<sup>2</sup> = 0.98 and RMSE = 2.73%). This approach proposed a simple, inexpensive, and non-destructive method for peanut maturity estimation.
Lift capabilities of hyaluronic acid fillers (2011)

The 24-mg/ml smooth, cohesive HA gel fillers achieve a high lift capacity by combining higher cohesivity with lower relative G' versus the 20-mg/ml granular consistency gel filler.
Reaction of Eugenol with Synthesis Gas. Synthesis of 5,6,7,8-Tetrahydro-3-methoxy-2-naphthol (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of Eugenol with Synthesis Gas. Synthesis of 5,6,7,8-Tetrahydro-3-methoxy-2-naphtholFranco Gaslini and Lucio Zion NahumCite this: J. Org. Chem. 1964, 29, 5, 1177–1180Publication Date (Print):May 1, 1964Publication History Published online1 May 2002Published inissue 1 May 1964https://pubs.acs.org/doi/10.1021/jo01028a045https://doi.org/10.1021/jo01028a045research-articleACS PublicationsRequest reuse permissionsArticle Views231Altmetric-Citations7LEARN 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
Probabilistic multimedia retrieval (2002)

We present a framework in which probabilistic models for textual and visual information retrieval can be integrated seamlessly. The framework facilitates searching for imagery using textual descriptions and visual examples simultaneously. The underlying Language Models for text and Gaussian Mixture Models for images have proven successful in various retrieval tasks.
Naturally occurring anhydrovitamin A2. Transformation into retinene2 (1966)

1. ;Naturally occurring anhydrovitamin A(2)' obtained from the liver oil of freshwater fish Bagarius bagarius yielded, after six-stage chromatography, a pure product showing characteristic bands at 350, 368 (E(1%) (1cm.) 1006) and 390mmu in ethanol, and producing a green colour with antimony trichloride (E(1%) (1cm.) 1884 at 693mmu). 2. On distribution of the material between light petroleum and 95% methanol, 70% of it is found in methanol, which points to its hydroxylic character. 3. It gives an acetyl derivative, from which the original hydroxy compound can be regenerated on hydrolysis. 4. The infrared spectrum shows, besides other bands, one at 3460cm.(-1) attributable to a hydroxy group. 5. On passing a light-petroleum solution of naturally occurring anhydrovitamin A(2) through manganese dioxide a 6% conversion into retinene(2) is observed. 6. A 3-hydroxyanhydroretinol structure is proposed for naturally occurring anhydrovitamin A(2) and a mechanism of its transformation into retinene(2) on this basis is suggested.
Evidence That Aging And Amyloid Promote Microglial Cell Senescence (2007)

Advanced age and presence of intracerebral amyloid deposits are known to be major risk factors for development of neurodegeneration in Alzheimer's disease (AD), and both have been associated with microglial activation. However, the specific role of activated microglia in AD pathogenesis remains unresolved. Here we report that microglial cells exhibit significant telomere shortening and reduction of telomerase activity with normal aging in rats, and that in humans there is a tendency toward telomere shortening with presence of dementia. Human brains containing high amyloid loads demonstrate a significantly higher degree of microglial dystrophy than nondemented, amyloid-free control subjects. Collectively, these findings show that microglial cell senescence associated with telomere shortening and normal aging is exacerbated by the presence of amyloid. They suggest that degeneration of microglia is a factor in the pathogenesis of AD.
Structure-based Design of High Affinity Peptides Inhibiting the Interaction of p53 with MDM2 and MDMX (2009)

MDM2 and MDMX function as key regulators of p53 by binding to its N terminus, inhibiting its transcriptional activity, and promoting degradation. MDM2 and MDMX overexpression or hyperactivation directly contributes to the loss of p53 function during the development of nearly 50% of human cancers. Recent studies showed that disrupting p53-MDM2 and p53-MDMX interactions can lead to robust activation of p53 but also revealed a need to develop novel dual specific or MDMX-specific inhibitors. Using phage display we identified a 12-residue peptide (pDI) with inhibitory activity against MDM2 and MDMX. The co-crystal structures of the pDI and a single mutant derivative (pDI6W) liganded with the N-terminal domains of human MDMX and MDM2 served as the basis for the design of 11 distinct pDI-derivative peptides that were tested for inhibitory potential. The best derivative (termed pDIQ) contained four amino acid substitutions and exhibited a 5-fold increase in potency over the parent peptide against both MDM2 (IC(50) = 8 nm) and MDMX (IC(50) = 110 nm). Further structural studies revealed key molecular features enabling the high affinity binding of the pDIQ to these proteins. These include large conformational changes of the pDIQ to reach into a hydrophobic site unique to MDMX. The findings suggest new strategies toward the rational design of small molecule inhibitors efficiently targeting MDMX.
THE EFFECT OF PARENTERAL TESTOSTERONE REPLACEMENT ON PROSTATE SPECIFIC ANTIGEN IN HYPOGONADAL MEN WITH ERECTILE DYSFUNCTION (1997)

Parenteral testosterone replacement in hypogonadal men with normal pretreatment digital rectal examination and serum PSA levels does not alter PSA or PSA velocity beyond established nontreatment norms. Thus, any significant increase in PSA or PSA velocity should not be attributed to testosterone replacement therapy and should be evaluated.
Origin of Substrate Specificity of Human and Rat 17β-Hydroxysteroid Dehydrogenase Type 1, Using Chimeric Enzymes and Site-Directed Substitutions* (1997)

Human 17beta-hydroxysteroid dehydrogenase (17-HSD) type 1 predominantly catalyzes the 17beta-reduction of estrone to estradiol. The present results, however, show that rat 17-HSD type 1 equally uses both estrone and androstenedione as substrates. Analyzing the activity of various rat/human chimeric enzymes indicated that the region between amino acids 148 and 268 is responsible for the difference in substrate specificity, which is in line with the structural data showing that the recognition end of the active site is primarily at residues 185-230. The enzymes are highly conserved between amino acids 148-191, and the data indicate that in this region Asn152HisAsp153Glu and Pro187Ala variations are most closely related to the differential steroid specificity. The structural analyses furthermore suggested that the presence of His instead of Asn at position 152 of the human enzyme might result in considerable rearrangement of the loop located close to the beta-face of the A- and B-rings of the bound substrate, and that the Pro187Ala variation could modify the flexible region involved in substrate recognition and access of the substrate to the active site. Altogether, our results indicate that the Asn152His and Pro187Ala variations, together with several amino acid variations at the recognition end of the catalytic cleft built by residues 190-230, alter the structure of the active site of rat 17-HSD type 1 to one more favorable to an androgenic substrate.
Three-dimensional finite element analysis of current density and temperature distributions during radio-frequency ablation (1995)

This study analyzed the influence of electrode geometry, tissue-electrode angle, and blood flow on current density and temperature distribution, lesion size, and power requirements during radio-frequency ablation. We used validated three-dimensional finite element models to perform these analyses. We found that the use of an electrically insulating layer over the junction between electrode and catheter body reduced the chances of charring and coagulation. The use of a thermistor at the tip of the ablation electrodes did not affect the current density decreased more slowly with distance from the electrode surface. We analyzed the effects of three tissue-electrode angles: 0, 45, and 90 degrees. More power was needed to reach a maximal tissue temperature of 95 degrees C after 120 s when the electrode-tissue angle was 45 degrees. Consequently, the lesions were larger and deeper for a tissue-electrode angle of 45 degrees than for 0 and 90 degrees. The lesion depth, volume, and required power increased with blood flow rate regardless of the tissue-electrode angle. The significant changes in power with the tissue-electrode angle suggest that it is safer and more efficient to ablate using temperature-controlled RF generators. The maximal temperature was reached at locations within the tissue, a fraction of a millimeter away from the electrode surface. These locations did not always coincide with the local current density maxima. The locations of these hottest spots and the difference between their temperature and the temperature read by a sensor placed at the electrode tip changed with blood flow rate and tissue-electrode angle.
Assembly and Enzymatic Properties of the Catalytic Domain of Human Complement Protease C1r (2001)

The catalytic properties of C1r, the protease that mediates activation of the C1 complex of complement, are mediated by its C-terminal region, comprising two complement control protein (CCP) modules followed by a serine protease (SP) domain. Baculovirus-mediated expression was used to produce fragments containing the SP domain and either 2 CCP modules (CCP1/2-SP) or only the second CCP module (CCP2-SP). In each case, the wild-type species and two mutants stabilized in the proenzyme form by mutations at the cleavage site (R446Q) or at the active site serine residue (S637A), were produced. Both wild-type fragments were recovered as two-chain, activated proteases, whereas all mutants retained a single-chain, proenzyme structure, providing the first experimental evidence that C1r activation is an autolytic process. As shown by sedimentation velocity analysis, all CCP1/2-SP fragments were dimers (5.5-5.6 S), and all CCP2-SP fragments were monomers (3.2-3.4 S). Thus, CCP1 is essential to the assembly of the dimer, but formation of a stable dimer is not a prerequisite for self-activation. Activation of the R446Q mutants could be achieved by extrinsic cleavage by thermolysin, which cleaved the CCP2-SP species more efficiently than the CCP1/2-SP species and yielded enzymes with C1s-cleaving activities similar to their active wild-type counterparts. C1r and its activated fragments all cleaved C1s, with relative efficiencies in the order C1r < CCP1/2-SP < CCP2-SP, indicating that CCP1 is not involved in C1s recognition.