gebhart/patrepeval huggingface dataset:
Human NK Cells Express CC Chemokine Receptors 4 and 8 and Respond to Thymus and Activation-Regulated Chemokine, Macrophage-Derived Chemokine, and I-309 (2000)

NK cells respond to various chemokines, suggesting that they express receptors for these chemokines. In this paper, we show that IL-2-activated NK (IANK) cells express CC chemokine receptor 4 (CCR4) and CCR8, as determined by flow cytometric, immunoblot, and RNase protection assays. Macrophage-derived chemokine (MDC), the ligand for CCR4, induces the phosphorylation of CCR4 within 0.5 min of activating IANK cells with this ligand. This is corroborated with the recruitment of G protein-coupled receptor kinases 2 and 3 and their association with CCR4 in IANK cell membranes. Also, CCR4 is internalized between 5 and 45 min but reappears in the membranes after 60 min of stimulation with MDC. MDC, thymus and activation-regulated chemokine (TARC), and I-309 induce the chemotaxis of IANK cells, an activity that is inhibited upon pretreatment of these cells with pertussis toxin, suggesting that receptors for these chemokines are coupled to pertussis toxin-sensitive G proteins. In the calcium release assay, cross-desensitization experiments showed that TARC completely desensitizes the calcium flux response induced by MDC or I-309, whereas both MDC and I-309 partially desensitize the calcium flux response induced by TARC. These results suggest that TARC utilizes CCR4 and CCR8. Our results are the first to show that IL-2-activated NK cells express CCR4 and CCR8, suggesting that these receptors are not exclusive for Th2 cells.
Encapsulation of S. cerevisiae in Poly(glycerol) Silicate Derived Matrices: Effect of Matrix Additives and Cell Metabolic Phase on Long-Term Viability and Rate of Gene Expression (2011)

Bioencapsulation of living cells into silica materials derived from the sol–gel process has resulted in novel hybrid living materials with exciting functionalities. Despite the many successes in this field, long-term viability and activity of the encapsulated cells remain a significant obstacle to producing practical and robust devices, e.g., whole-cell-based biosensors. We report the first study on the effects of various media additives and the metabolic phase of encapsulated cells on long-term viability and the rate of inducible gene expression. Saccharomyces cerevisiae (S. cerevisiae) cells, genetically engineered to produce yellow fluorescent protein (YFP) in response to galactose, were encapsulated in poly(glycerol) silicate derived matrices. Surprisingly, we find that addition of media components to the glycerol-silica matrix adversely impacted long-term viability in all cases studied, with a 1.3, 1.4, or 5.4 fold decrease in viability after only 9 days of storage in matrices containing yeast peptone dextrose (YPD), yeast peptone (YP, no glucose), or Synthetic Complete (SC) +2% glucose media, respectively. These findings are attributed to the media components inducing exit of the cells from the more robust quiescent state, and the metabolic production of toxic byproducts. Encapsulated cells from exponential culture exhibited inducible reporter gene expression rates approximately 33% higher than cells from stationary cultures. Addition of media components to the silica matrix increased gene expression rates under certain conditions. These results further elaborate on other silica matrix encapsulated living cell studies, and provide important design parameters for developing effective living cell-based biosensors for case-specific detection applications.
Acoustic microscopy of living cells. (1981)

This paper reports preliminary results of the observation by acoustic microscopy of living cells in vitro. The scanning acoustic microscope uses high-frequency sound waves to produce images with submicrometer resolution. The contrast observed in acoustic micrographs of living cells depends on the acoustic properties (i.e., density, stiffness, and attenuation) and on the topographic contour of the cell. Variation in distance separating the acoustic lens and the viewed cell also has a profound effect on the image. When the substratum is located at the focal plane, thick regions of the cell show a darkening that can be related to cellular acoustic attenuation (a function of cytoplasmic viscosity). When the top of the cell is placed near the focal plane, concentric bright and dark rings appear in the image. The location of the rings can be related to cell topography, and the ring contrast can be correlated to the stiffness and density of the cell. In addition, the character of the images of single cells varies dramatically when the substratum upon which they are grown is changed to a different material. By careful selection of the substratum, the information content of the acoustic images can be increased. Our analysis of acoustic images of actively motile cells indicates that leading lamella are less dense or stiff than the quiescent trailing processes of the cells.
Intracoronary Application of C1 Esterase Inhibitor Improves Cardiac Function and Reduces Myocardial Necrosis in an Experimental Model of Ischemia and Reperfusion (1997)

C1-INH significantly protects ischemic tissue from reperfusion damage, reduces myocardial necrosis, and improves local cardiac function.
Gene Expression Profiling of Primary Cutaneous Melanoma and Clinical Outcome (2006)

Background: Gene expression profiling data for human primary cutaneous melanomas are scarce because of the lack of retrospective collections of frozen tumors. To identify differentially expressed genes that may be involved in melanoma progression and prognosis, we investigated the relationship between gene expression profiles and clinical outcome in a cohort of patients with primary melanoma. Methods: Labeled complementary RNA (cRNA) from each tissue sample was hybridized to a pangenomic 44K 60-mer oligonucleotide microarray. Class comparison and class prediction analyses were performed to identify genes whose expression in primary melanomas was associated with 4-year distant metastasis–free survival among 58 patients with at least 4 years of follow-up, distant metastasis, or death. Results were validated immunohistochemically at the protein level in 176 independent primary melanomas from patients with a median clinical follow-up of 8.5 years. Survival was analyzed with a Cox multivariable model and stratified log-rank test. All statistical tests were two-sided. Results: We identified 254 genes that were associated with distant metastasis–free survival of patients with primary melanoma. These 254 genes include genes involved in activating DNA replication origins, such as minichromosome maintenance genes and geminin. Twenty-three of these genes were studied at the protein level; expression of five (MCM4, P = .002; MCM3, P = .030; MCM6, P = .004; KPNA2, P = .021; and geminin, P = .004) was statistically significantly associated with overall survival in the validation set. In a multivariable Cox model adjusted for tumor thickness, ulceration, age, and sex, expression of MCM4 (hazard ratio [HR] of death = 4.04, 95% confidence interval [CI] = 1.39 to 11.76; P = .010) and MCM6 (HR of death = 7.42, 95% CI = 1.99 to 27.64; P = .003) proteins was still statistically significantly associated with overall survival. Conclusion: We identified 254 genes whose expression was associated with metastatic dissemination of cutaneous melanomas. These genes may shed light on the molecular mechanisms underlying poor prognosis in melanoma patients.
Analysis of a second bacteriophage hyaluronidase gene from Streptococcus pyogenes: evidence for a third hyaluronidase involved in extracellular enzymatic activity (1995)

The hyaluronidase gene (hylP2) from a second group A streptococcal bacteriophage was isolated from ATCC T-type-22 hyaluronidase-producing strain 10403, a strain known to produce increased amounts of extracellular hyaluronidase. Sequence analysis of hylP2 and alignment with the previously described bacteriophage hyaluronidase gene (hylP) showed a high degree of similarity; however, hylP2 had deletions of regions specifying 34 amino acids. Twenty-eight of the deleted amino acids were in a region of HylP containing a series of collagen-like Gly-X-Y repeating units. By employing primers for both hylP and hylP2, PCR amplification resulted in fragments of appropriate sizes in 97% of the strains tested, with some strains producing two fragments, indicating the presence of at least two phages. When the hylP2 gene was introduced via a plasmid vector into a non-hyaluronidase-producing Streptococcus pyogenes strain, this strain was still unable to produce extracellular hyaluronidase, although intracellular hyaluronidase was present. These results, along with the absence of a typical N-terminal signal peptide, indicate that HylP2 is unable to be secreted into the extracellular milieu. Examination of more than 100 strains for production of hyaluronidase showed that only 23% of the strains produced extracellular hyaluronidase. One of these strains (strain 10403) contains a single bacteriophage hyaluronidase gene (hylP2) which, when inactivated by allelic replacement, still produces large amounts of extracellular hyaluronidase. These results suggest the presence of a different hyaluronidase gene encoding a protein that is actively secreted into the extracellular milieu.
New concepts in human sperm-zona pellucida interaction (1995)

Binding of spermatozoa to the zona pellucida is an initial, crucial recognition event leading to fertilization. In the mouse, the best species characterized so far, the zona pellucida protein 3 (ZP3) has a central role as the specific, primary sperm receptor on the zona and as the inducer of the acrosome reaction. This sequence of events is not clearly understood as it relates to human gametes. The ideal test for the evaluation of sperm-zona pellucida interaction is one that can examine these events in a sequential fashion (i.e. binding followed by the acrosome reaction) in a standardized and specific bioassay. Here we have used the hemizona assay as an internally controlled test to examine human sperm-zona pellucida interaction. Results presented show that: (i) the hemizona assay has an excellent predictive power for IVF outcome and for the identification of male infertility; (ii) using a specific anti-ZP3 antiserum in immunocytochemical studies, the hemizona assay allows for the identification of structural/functional anomalies of the protein backbone of human ZP3 (identification of oocyte anomalies); and (iii) glycobiological studies using the hemizona assay model indicate that the initial sperm-zona pellucida binding requires a seletin-like interaction between the human gametes. These efforts may help us to characterize the cellular and molecular mechanisms involved in human gametes and their dysfunctions in infertile patients.
Isoelectrophoretic Characterization of Protein Antigens Present in Mycobacterial Culture Filtrates and Recognized by Monoclonal Antibodies Directed Against the Mycobacterium bovis BCG Antigen 85 Complex (1992)

Nine monoclonal antibodies (MoAbs) were produced against Mycobacterium bovis BCG antigen 85 complex. Using isoelectric focusing combined with Western (immunoblot) blot analysis, antigenically related proteins could be identified in culture filtrates from M. tuberculosis, M. bovis, M. Kansasii, M. avium, M. xenopi, M. gordonae, M. fortuitum, M. phlei and M. smegmatis. Most of the MoAbs were found to be broadly cross-reactive between the various mycobacterial species, albeit some minor differences were observed. These MoAbs reacted generally, in each species, with different components. One MoAb (VID1-14) was found to be specifically directed only against antigen 85B from M. bovis, M. tuberculosis and M. kansasii.
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse (2006)

Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. RHA1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in a linear chromosome and three linear plasmids. A targeted insertion methodology was developed to determine the telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich in oxygenases (203) and ligases (192). Many of the oxygenases occur in the numerous pathways predicted to degrade aromatic compounds (30) or steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes, six of which exceed 25 kbp, and seven polyketide synthase genes, providing evidence that rhodococci harbor an extensive secondary metabolism. Among sequenced genomes, RHA1 is most similar to those of nocardial and mycobacterial strains. The genome contains few recent gene duplications. Moreover, three different analyses indicate that RHA1 has acquired fewer genes by recent horizontal transfer than most bacteria characterized to date and far fewer than Burkholderia xenovorans LB400, whose genome size and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear to demonstrate that ecologically similar bacteria can evolve large genomes by different means. Overall, RHA1 appears to have evolved to simultaneously catabolize a diverse range of plant-derived compounds in an O(2)-rich environment. In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms.
Markov random fields with efficient approximations (2002)

Markov Random Fields (MRFs) can be used for a wide variety of vision problems. In this paper we focus on MRFs with two-valued clique potentials, which form a generalized Potts model. We show that the maximum a posteriori estimate of such an MRF can be obtained by solving a multiway minimum cut problem on a graph. We develop efficient algorithms for computing good approximations to the minimum multiway, cut. The visual correspondence problem can be formulated as an MRF in our framework; this yields quite promising results on real data with ground truth. We also apply our techniques to MRFs with linear clique potentials.
Intracellular trafficking of retroviral genomes during the early phase of infection: viral exploitation of cellular pathways (2001)

Retroviruses enter cells through specific cell-surface receptors and then embark on a journey that ultimately leads to the establishment of the integrated proviral DNA. The steps of the journey include the reverse transcription of the viral RNA into DNA, the trafficking of the viral protein-DNA complex through the cytoplasm, the entry of the complex into the nucleus, and the insertion of the linear viral DNA into the host genome. All these steps are likely to involve specific interactions of viral proteins with host machinery. Our knowledge of the details of these interactions is very limited but is rapidly expanding, and should provide a deeper understanding of the pathways and components used by the different classes of retroviruses. This knowledge in turn should enable the development of better and more efficient retroviral vectors for use in gene therapy protocols in vivo.
Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients (2016)

Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation epidermal growth factor receptor (EGFR) inhibitor rociletinib. We observe multiple resistance mechanisms in 46% of patients after treatment with first-line inhibitors, indicating frequent intra-patient heterogeneity. Rociletinib resistance recurrently involves MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We describe a novel EGFR L798I mutation and find that EGFR C797S, which arises in ∼33% of patients after osimertinib treatment, occurs in <3% after rociletinib. Increased MET copy number is the most frequent rociletinib resistance mechanism in this cohort and patients with multiple pre-existing mechanisms (T790M and MET) experience inferior responses. Similarly, rociletinib-resistant xenografts develop MET amplification that can be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumour heterogeneity in NSCLC and the utility of ctDNA-based resistance mechanism assessment.
High-anisotropy nanocluster films for high-density perpendicular recording (2005)

This paper reports results on the synthesis and magnetic properties of L1/sub 0/:X nanocomposite films, where L1/sub 0/=FePt, CoPt, and X=C, Ag, etc. Two fabrication methods are discussed: nonepitaxial growth of oriented perpendicular media, and monodispersed nanoparticle-assembled films grown with a gas-aggregation source. The magnetic properties are controllable through variations in the nanocluster properties and nanostructure. The films show promise for development as recording media at extremely high areal densities.
Proteins with SH2 domains: transducers in the tyrosine kinase signaling pathway. (1992)

SH22 domains are protein motifs consisting of approximately 100 amino acids which were originally described by Sadowski et a!. (1). This domain was discovered when the noncatalytic domains of cytoplasmic tyrosine kinases such as fps were compared to src (1) and subsequently described in the enzyme PLC-y (2, 3) and the oncogene v-ak (4). Interest in SH2 domains has heightened with the recent finding that these domains directly bind to protein sequences containing phosphotyrosmne (5). This finding, coupled with the fact that SH2 domains are found in molecules involved in growth factor mediated intracellular signaling and oncogenesis, indicates that SH2 domains are important in pathways utilized in growth control (6, 7). The focus of this review will be to discuss the general characteristics of 5H2 domains by reviewing several of the important SH2 domain containing proteins. In understanding the terminology of SH2 domains, it is instructive to examine the structure of src (Fig. 1 ). The tyrosine kinase domain of src represents src homology region 1, but this designation is not commonly utilized. Immediately amino-terminal to the tyrosine kinase domain lies the SH2 domain, which is designated in some other papers as the B and C box (3, 4). Next to the SH2 domain lies the SH3 domain, also known as the A box (3, 4). SH3 domains are approximately 50 amino acids long, and their function remains unknown, although they are found in cytoskeletal proteins such as spectnin (8). Proteins with SH2 domains often have accompanying SH3 domains (Fig. 1), and there is also a large group of proteins that have the SH3 domain only (5). Extensive comparisons of the amino acid sequence of SH2 domains have been published (5). Fig. 2 displays the amino acid sequence of a limited number of SH2 (Fig. 2A) and SH3 domains (Fig. 2B). Approximately 30 residues in SH2 domains are highly conserved, and three
Prolonged Shedding of Zika Virus RNA in Vaginal Secretions, Nicaragua (2019)

Zika virus, an arthropod-borne flavivirus pathogen in humans, is unusual because it can be sexually transmitted and can be shed for prolonged periods in semen. We report viral shedding in vaginal secretions for up to 6 months, indicating the potential for sexual and vertical transmission by infected women.
Evaluation of the Effects of Dietary Organic Germanium, Ge-132, and Raffinose Supplementation on Caecal Flora in Rats (2012)

Poly-trans-[(2-carboxyethyl) germasesquioxane] (Ge-132) is the most common organic germanium compound. The ingestion of Ge-132 promotes bile secretion. We assessed the rat caecal characteristics after the administration of Ge-132 and raffinose, a prebiotic oligosaccharide, because both Ge-132 and some prebiotics can change the fecal color to yellow. We also compared the changes in the caecal flora caused by the two compounds. In addition, we evaluated the simultaneous administration of Ge-132 and raffinose and their effects on β-glucuronidase activity, which is known to be a factor related to colon cancer. Male Wistar rats (three weeks old) were given one of the following diets: 1) a control diet (control group), 2) a diet containing 0.05% Ge-132 (Ge-132 group), 3) a diet containing 5% raffinose (RAF group) or 4) a diet containing 0.05% Ge-132 + 5% raffinose (GeRAF group). The Bifidobacterium, Lactobacillus and total bacteria counts were significantly increased by the dietary raffinose, and Ge-132 did not suppress this increase. The raffinose intake increased caecal acetic acid production significantly. The activity of β-glucuronidase in the caecal contents was increased by dietary Ge-132, whereas dietary raffinose decreased the β-glucuronidase activity significantly. These results indicate that the simultaneous intake of dietary raffinose and Ge-132 does not inhibit the effects of either compound on intestinal fermentation and bile secretion. Additionally, the simultaneous intake of both raffinose and Ge-132 could abrogate the increase in β-glucuronidase activity induced by Ge-132 alone.
A novel resist and post-etch residue removal process using ozonated chemistries (2002)

A novel, environmentally friendly process is successfully applied for the removal of photoresist and organic post-etch residues from silicon surfaces. The moist ozone gasphase process described, greatly increases the organic removal efficiency. Improved performance over traditional processes is due to enhanced reactive ozone availability near the wafer surface. Additionally, OH radical scavengers such as acetic acid chemically enhance the process efficiency even further.
Effects of titanium‐coated micromachined grooved substrata on orienting layers of osteoblast‐like cells and collagen fibers in culture (2004)

Osteogenic cells from newborn rat calvariae were cultured on titanium surfaces on which cell orientation could be manipulated. Substrata included smooth surfaces and substrata with smooth regions (gaps) flanked by grooves of 47-microm pitch and 3-, 10-, or 30-microm depth. Orientation angles of the cells were measured over time using propidium-iodide staining and confocal laser scanning microscopy. In addition, collagen fibers were identified using picro-sirius staining and reflected light polarization microscopy. Grooves proved effective in orienting cells, but their orienting ability decreased above the ridge level. Cells on the smooth surface showed no preferred orientation. Cells in the gaps became oriented as a result of cell-cell interactions with the cells on the flanking grooves. Cells in grooves produced oriented collagen fibers, but in the gaps, fibers could be parallel, perpendicular, or diagonal to the grooves. Collagen fibers on the smooth surfaces formed arrays of parallel fibers in a crisscross pattern. In long-term cultures, bone-like nodules were formed, but mostly above the ridge level. These data demonstrate that grooved surfaces can influence cell orientation both in cell populations above the cells in contact with the grooves and in cell populations adjacent to the grooves.