gebhart/patrepeval huggingface dataset:
Virus-Dependent Phosphorylation of the IRF-3 Transcription Factor Regulates Nuclear Translocation, Transactivation Potential, and Proteasome-Mediated Degradation (1998)

The interferon regulatory factors (IRF) consist of a growing family of related transcription proteins first identified as regulators of the alpha beta interferon (IFN-alpha/beta) gene promoters, as well as the interferon-stimulated response element (ISRE) of some IFN-stimulated genes. IRF-3 was originally identified as a member of the IRF family based on homology with other IRF family members and on binding to the ISRE of the ISG15 promoter. IRF-3 is expressed constitutively in a variety of tissues, and the relative levels of IRF-3 mRNA do not change in virus-infected or IFN-treated cells. In the present study, we demonstrate that following Sendai virus infection, IRF-3 is posttranslationally modified by protein phosphorylation at multiple serine and threonine residues, which are located in the carboxy terminus of IRF-3. A combination of IRF-3 deletion and point mutations localized the inducible phosphorylation sites to the region -ISNSHPLSLTSDQ- between amino acids 395 and 407; point mutation of residues Ser-396 and Ser-398 eliminated virus-induced phosphorylation of IRF-3 protein, although residues Ser-402, Thr-404, and Ser-405 were also targets. Phosphorylation results in the cytoplasm-to-nucleus translocation of IRF-3, DNA binding, and increased transcriptional activation. Substitution of the Ser-Thr sites with the phosphomimetic Asp generated a constitutively active form of IRF-3 that functioned as a very strong activator of promoters containing PRDI-PRDIII or ISRE regulatory elements. Phosphorylation also appears to represent a signal for virus-mediated degradation, since the virus-induced turnover of IRF-3 was prevented by mutation of the IRF-3 Ser-Thr cluster or by proteasome inhibitors. Interestingly, virus infection resulted in the association of IRF-3 with the CREB binding protein (CBP) coactivator, as detected by coimmunoprecipitation with anti-CBP antibody, an interaction mediated by the C-terminal domains of both proteins. Mutation of residues Ser-396 and Ser-398 in IRF-3 abrogated its binding to CBP. These results are discussed in terms of a model in which virus-inducible, C-terminal phosphorylation of IRF-3 alters protein conformation to permit nuclear translocation, association with transcriptional partners, and primary activation of IFN- and IFN-responsive genes.
ABX-EGF monotherapy in patients (pts) with metastatic colorectal cancer (mCRC): An updated analysis (2004)

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Sensitivity of fresh acute myeloid leukemia cells to etoposide: relationship with cell growth characteristics and DNA single-strand breaks (1992)

In this study, we evaluated the individual in vitro sensitivity of fresh acute myeloid leukemia (AML) cells to VP-16, and attempted to correlate VP-16 cytotoxicity with AML cell growth characteristics and drug-induced DNA single-strand breaks (SSB). Primary (PE1) colony inhibition assays allowed us to characterize two distinct groups of AML: group I (patients 1 through 6), which displayed sensitivity to VP- 16 similar to that of normal CFU-GM (IC90 of 20.52 +/- 2.44 micrograms/mL v 20.48 +/- 2.23 micrograms/mL after 1 hour drug exposure, respectively); and group II (patients 7 through 11), which was more sensitive to VP-16 (IC90 of 7.26 +/- 2.93 micrograms/mL, P = .004). Subsequently, groups I and II were termed normosensitive and hypersensitive, respectively. This objective VP-16 sensitivity classification, as determined by PE1, remained unaltered when assessed by secondary (PE2) colony inhibition assay (evaluating the self-renewal fraction of AML progenitors), or by cytofluorometric viability assay (evaluating the ultimately differentiated blast cell population). These findings would suggest that individual sensitivity to VP-16 of a particular cell population is maintained throughout CFU-AML differentiation. Finally, we report that sensitivity of AML cells to VP- 16 did not correlate either with cell growth characteristics or with SSB generation. Indeed, AML cell sensitivity to VP-16 appeared more closely related to DNA repair kinetics after drug removal, ie, hypersensitivity being essentially characterized by a prolonged retention of SSB during the posttreatment period. Interestingly, the established HL-60 cell line, which presented greater sensitivity to VP- 16 cytotoxicity than KG1, HEL, and K562, was also found to exhibit delayed DNA SSB repair kinetics, as compared with the other AML cell lines. These results suggest that hypersensitivity to VP-16 of some AML cells may be related to a deficient DNA-repair mechanism.
Isolation of a candidate human hematopoietic stem-cell population. (1992)

We have identified a rare (0.05-0.1%) subset of human fetal bone marrow cells that contains multipotent hematopoietic precursors. The population of human precursor cells that express Thy-1 and CD34 but no known lineage markers is enriched for clonogenic activity that establishes long-term, multilineage (myelomonocytic and B lymphoid) cultures on mouse marrow stromal lines. Further, the Thy-1+CD34+ subset that takes up little of the fluorescent mitochondrial dye rhodamine 123 contains virtually all the cells that establish long-term cultures. In human fetal thymus transplanted into SCID (severe combined immunodeficiency) mice, Thy-1+CD34+ fetal bone marrow cells differentiate into T lymphocytes. In two of nine cases, allogeneic Thy-1+CD34+ cells could engraft intact human fetal bone marrow grown in SCID mice, resulting in donor-derived myeloid and B cells. By extrapolation, the rare human Thy-1+Lin-CD34+ cell population contains pluripotent hematopoietic progenitors; we propose that it is highly enriched for candidate hematopoietic stem cells.
Electrically Facilitated Translocations of Proteins through Silicon Nitride Nanopores: Conjoint and Competitive Action of Diffusion, Electrophoresis, and Electroosmosis (2010)

Solid-state nanopores bear great potential to be used to probe single proteins; however, the passage of proteins through nanopores was found to be complex, and unexpected translocation behavior with respect to the passage direction, rate, and duration was observed. Here we study the translocation of a model protein (avidin) through silicon nitride nanopores focusing on the electrokinetic effects that facilitate protein transport across the pore. The nanopore zeta potential zeta(pore) and the protein zeta potential zeta(protein) are measured independently as a function of solution pH. Our results reveal that electroosmotic transport may enhance or dominate and reverse electrophoretic transport in nanopores. The translocation behavior is rationalized by accounting for the charging states of the protein and the pore, respectively; the resulting translocation direction can be predicted according to the difference in zeta potentials, zeta(protein) - zeta(pore). When electrophoresis and electroosmosis cancel each other out, diffusion becomes an effective (and bias-independent) mechanism which facilitates protein transport across the pore at a significant rate.
Video puppetry (2008)

We present a video-based interface that allows users of all skill levels to quickly create cutout-style animations by performing the character motions. The puppeteer first creates a cast of physical puppets using paper, markers and scissors. He then physically moves these puppets to tell a story. Using an inexpensive overhead camera our system tracks the motions of the puppets and renders them on a new background while removing the puppeteer's hands. Our system runs in real-time (at 30 fps) so that the puppeteer and the audience can immediately see the animation that is created. Our system also supports a variety of constraints and effects including articulated characters, multi-track animation, scene changes, camera controls, 2 1/2-D environments, shadows, and animation cycles. Users have evaluated our system both quantitatively and qualitatively: In tests of low-level dexterity, our system has similar accuracy to a mouse interface. For simple story telling, users prefer our system over either a mouse interface or traditional puppetry. We demonstrate that even first-time users, including an eleven-year-old, can use our system to quickly turn an original story idea into an animation.
Recent advances in immobilization methods of antibodies on solid supports (2008)

Antibody immobilization on a solid support is an essential process for the development of most immune-based assay systems. The choice of the immobilization method greatly affects antibody-antigen interactions on the assay surface. For the past several years, numerous strategies have been reported to control antibody immobilization, mainly by directing the orientation, stability, and density of bound antibodies on different assay platforms. Here we discuss recent developments in antibody immobilization methods with a particular focus on the strengths and limitations of reported approaches, and thereby provide a useful guideline for the selection of suitable antibody coupling procedures.
HLA B37 determines an influenza A virus nucleoprotein epitope recognized by cytotoxic T lymphocytes. (1986)

Human influenza A virus-specific, cytotoxic T cells have been shown previously to recognize the virus nucleoprotein on infected cells. CTL preparations from four HLA B37-positive donors were shown to recognize a synthetic peptide that corresponded to amino acids 335-349 of the nucleoprotein sequence. Influenza-specific CTL from 10 donors of other HLA types failed to recognize this epitope. CD8+ CTL lines were derived from lymphocytes of two HLA B37-positive donors and used to show that the peptide was represented on virus-infected cells and to determine the probable boundaries of the epitope.
Cellular expression of bone‐related proteins during in vitro osteogenesis in rat bone marrow stromal cell cultures (1994)

Rat bone marrow stromal cells comprise a heterogeneous mixture of cell lineages including osteoblastic cells. When grown in the presence of ascorbic acid, beta-glycerophosphate and 10(-8) M dexamethasone, osteoprogenitor cells within the population divide and differentiate to form bone nodules (Maniatopoulos et al., 1988, Cell Tissue Res., 254:317-330; Aubin et al., 1990, J. Bone Miner. Res., 5:S81) providing a useful model to investigate temporal and spatial changes in expression of osteoblastic markers. Immunocytochemistry was combined with Northern blotting, enzymatic assay, and radioimmunoassay to analyze the expression of bone-related proteins during the growth and differentiation sequence. By mRNA levels, protein production and/or enzymatic activity, expression of osteocalcin, bone sialoprotein, and alkaline phosphatase increased concomitantly with the development of bone nodules, while osteopontin mRNA levels decreased and those of SPARC/osteonectin did not change significantly. In older cultures with mineralizing nodules, mRNA levels for alkaline phosphatase and bone sialoprotein, but not osteocalcin, declined. Immunolabeling revealed that cells in early cultures stained poorly for SPARC/osteonectin and strongly for thrombospondin. Later, SPARC/osteonectin staining increased in most cells, while thrombospondin staining could be seen in both matrix and in cells, but with marked intercellular variability in intensity. At all time points studied, osteoblasts within bone nodules stained homogeneously for thrombospondin and alkaline phosphatase, and with marked heterogeneity of intensity amongst cells for SPARC/osteonectin and osteocalcin. Labelling with RCC455.4, a monoclonal antibody raised against rat calvaria cells which intensely labels osteoblasts and osteocytes (Turksen et al., 1992, J. Histochem. Cytochem., 40:1339-1352), co-localized with osteocalcin. Alkaline phosphatase activity and the amount of osteocalcin determined by both radioimmunoassay and immunolabelling decreased in very late cultures, a time corresponding to appearance of fully mineralized nodules. These studies indicate that the bone marrow stromal cell system is a useful model to study the temporal and spatial expression of bone-related proteins during osteogenesis and formation, mineralization, and maturation of bone nodules. Further, immunolabelling at the individual cell and single bone nodule level allowed discrimination of marked variability of expression of osteoblast markers during the differentiation sequence.
Treatment of ocular bacterial infections: an update. (1997)

Knowledge of the results of controlled antimicrobial studies and a review of standard practices in managing bacterial eye disease can provide the necessary background to help the eye care clinician make appropriate antimicrobial therapeutic decisions in patient care.
Infectious Agent from a Free-Living Soil Amoeba, Naegleria gruberi (1971)

A subcellular infectious material has been found in a strain of the amoeba Naegleria gruberi, strain EG, which is capable of infecting chick embryo cells and causing them to undergo cytopathic changes with the release of more infectious material. The material is present in two lines of the amoeba which were separated shortly after the isolation of the strain and subsequently maintained in separate laboratories.
Solution-Based Particle Formation of Pharmaceutical Powders by Supercritical or Compressed Fluid Co2and Cryogenic Spray-Freezing Technologies (2001)

Micronization is an important procedure used in the pharmaceutical industry to reduce the particle size of active pharmaceutical ingredients (APIs). The spray-drying and milling techniques presently used to micronize drug substances cannot be used to process thermolabile or physically unstable drug substances. Therefore, new micronization techniques, including particle precipitation with supercritical or compressed fluid CO2 and spray-freezing of drug solutions and suspensions into cryogenic gas to produce solid frozen microparticles, are currently being perfected for future use in the pharmaceutical industry. This review highlights the compressed gas and cryogenic liquid technologies being developed as potential solution-based particle formation technologies for drugs that cannot be processed by conventional micronization techniques.
A 0.06mm<sup>2</sup> 14nV/&#x221A;Hz chopper instrumentation amplifier with automatic differential-pair matching (2013)

A small-area low-power low-noise instrumentation amplifier (IA) is desired in arrayed sensor devices that are used for high-spatial-resolution biomedical and environment monitoring systems. This paper presents a 0.06mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> chopper-stabilized current-feedback IA with 13.5nV/√Hz input-referred noise and less than 3.5μV offset voltage. For significantly reducing the ripple due to chopping, the proposed IA uses a novel digital calibration scheme, namely, automatic differential-pair matching (ADPM), which enables a small die area and low-power operation. The proposed IA is implemented in a standard 0.18μm CMOS and achieves a noise efficiency factor (NEF) of 7.2 while drawing 194μA. The active area of the IA is 7.8× smaller than that of the state-of-the-art [1-5] while it maintains low output ripple, low noise, and low power.
Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: Potential use in diagnosis and prognosis (2003)

One hundred eighty-four serum samples from patients with ovarian cancer (n = 109), patients with benign tumors (n = 19), and healthy donors (n = 56) were analyzed on strong anion-exchange surfaces using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry technology. Univariate and multivariate statistical analyses applied to protein-profiling data obtained from 140 training serum samples identified three biomarker protein panels. The first panel of five candidate protein biomarkers, termed the screening biomarker panel, effectively diagnosed benign and malignant ovarian neoplasia [95.7% sensitivity, 82.6% specificity, 89.2% accuracy, and receiver operating characteristic (ROC) area under the curve of 0.94]. The other two panels, consisting of five and four candidate protein biomarkers each, effectively distinguished between benign and malignant ovarian neoplasia and were therefore referred to as validation biomarker panel I (81.5% sensitivity, 94.9% specificity, 88.2% accuracy, and ROC = 0.94) and validation biomarker panel II (72.8% sensitivity, 94.9% specificity, 83.9% accuracy, and ROC = 0.90). The three ovarian cancer biomarker protein panels correctly diagnosed 41 of the 44 blinded test samples: 21 of 22 malignant ovarian neoplasias [10 of 11 early-stage ovarian cancer (I/II) and 11 of 11 advanced-stage ovarian cancer (III/IV)], 6 of 6 low malignant potential, 5 of the 6 benign tumors, and 9 of 10 normal patient samples. In conclusion, we have discovered three ovarian cancer biomarker protein panels that, when used together, effectively distinguished serum samples from healthy controls and patients with either benign or malignant ovarian neoplasia.
Large system analysis of the Successive Encoding Successive Allocation Method for the MIMO BC (2010)

Analytical expressions for the average sum rate of signal processing algorithms which require full Channel State Information at the transmitter are hard to obtain in practice. In the large system limit, where at least two system parameters go to infinity at a finite fixed ratio, analytical expressions can often be obtained, which also serve as a good approximation in systems with finite parameters. In this paper we present a large system analysis of the Successive Encoding Successive Allocation Method (SESAM) with Minimum Mean Square Error (MMSE) filters, which can almost achieve the optimum sum capacity at drastically reduced complexity. An analytical approximation of the asymptotic sum rate for Rayleigh fading channels is derived and compared with simulations in finite systems.
Mutations in the RP1 gene causing autosomal dominant retinitis pigmentosa (1999)

Retinitis pigmentosa is a genetically heterogeneous form of retinal degeneration that affects approximately 1 in 3500 people worldwide. Recently we identified the gene responsible for the RP1 form of autosomal dominant retinitis pigmentosa (adRP) at 8q11-12 and found two different nonsense mutations in three families previously mapped to 8q. The RP1 gene is an unusually large protein, 2156 amino acids in length, but is comprised of four exons only. To determine the frequency and range of mutations in RP1 we screened probands from 56 large adRP families for mutations in the entire gene. After preliminary results indicated that mutations seem to cluster in a 442 nucleotide segment of exon 4, an additional 194 probands with adRP and 409 probands with other degenerative retinal diseases were tested for mutations in this region alone. We identified eight different disease-causing mutations in 17 of the 250 adRP probands tested. All of these mutations are either nonsense or frameshift mutations and lead to a severely truncated protein. Two of the eight different mutations, Arg677X and a 5 bp deletion of nucleotides 2280-2284, were reported previously, while the remaining six mutations are novel. We also identified two rare missense changes in two other families, one new polymorphic amino acid substitution, one silent substitution and a rare variant in the 5'-untranslated region that is not associated with disease. Based on this study, mutations in RP1 appear to cause at least 7% (17/250) of adRP. The 5 bp deletion of nucleotides 2280-2284 and the Arg677X nonsense mutation account for 59% (10/17) of these mutations. Further studies will determine whether missense changes in the RP1 gene are associated with disease, whether mutations in other regions of RP1 can cause forms of retinal disease other than adRP and whether the background variation in either the mutated or wild-type RP1 allele plays a role in the disease phenotype.
Deciphering the Reaction Dynamics Underlying Optimal Control Laser Fields (2003)

Femtosecond high-resolution pump-probe experiments have been used together with theoretical ab initio quantum calculations and wave packet dynamics simulations to decode an optimal femtosecond pulse that is generated from adaptive learning algorithms. This pulse is designed to maximize the yield of the organometallic ion CpMn(CO)3 while hindering the competing fragmentation. The sequential excitation and ionization of the target ion are accomplished by an optimized field consisting of two dominant subpulses with optimal frequencies and time delays.
Effet de la forme de présentation de l'orge sur la production et la composition du lait de vache (1995)

&mdash; L'effet de la forme de prsentation de l'orge (broye (B) ou aplatie (A)) a t tudi sur 22 vaches multipares en phase descendante de lactation, utilises dans un essai en inversion avec 2 priodes successives de 3 sem. Au cours de l'essai, tous les animaux ont reu une ration constitue d'un mlange 75/15/10 d'ensilage de mas, d'ensilage d'herbe et de drches de brasserie, et de foin offert volont, ainsi que de 2 kg de pulpes dshydrates. Les quantits d'aliment concentr fermier (mlange 75/25 d'orge et de tourteaux) ont t calcules en fonction du niveau de production des animaux et n'ont pas vari au cours de l'essai. Dans le traitement B, 100 g de substances tampons ont t ajouts la ration. En moyenne, les animaux ont ingr 8,2 kg/j de concentrs, dont 4,7 kg d'orge. La forme de prsentation de l'orge n'a eu d'effet ni sur la vitesse d'ingestion du concentr (240 g/min en moyenne), ni sur la production laitire (respectivement 33,1 et 32,7 kg/j dans les lots B et A), ni sur la composition chimique du lait, et en particulier le taux butyreux (38,4 et 37,7 dans les lots B et A). Le pH du jus de rumen et la proportion des principaux acides gras volatils du rumen ont t semblables dans les 2 lots. vache laitire / concentr / forme de prsentation Summary &mdash; Effect of grain processing on milk production and composition. The effect of grain processing (ground [GJ or rolled [RJ) was analysed on 22 multiparous cows in mid-lactation used in a 2 * 2 latin-square design experiment. During each 3-wk period, cows were offered a diet composed of a mixture of corn silage, grass silage and brewer's grain (75115110, ad libitum), of hay (ad libitum) and of dried sugar beet pulp (2 kgld). The quantities of concentrate (75% barley and 25% meal) were cal- culated according to milk production level and did not vary during the trial. In group G, 100 g/d of buffer compound was added to the diet. Grain processing had effect neither on time spent to eat the * Cette tude a t ralise avec la participation financire de l'association Gala.
Purification and Partial Characterization of Testicular Hyaluronidase (1968)

A new method is presented for the purification of testicular hyaluronidase involving ion exchange chromatography followed by gel filtration on Sephadex G-75. A highly purified hyaluronidase preparation has been obtained which contains 45,000 National Formulary activity units per mg, dry weight, and which migrates as a single component on polyacrylamide gel electrophoresis at pH 4.3. The enzyme has been shown to be a glycoprotein containing 5.00% mannose and 2.17% glucosamine (expressed as N-acetylglucosamine). The molecular weight of the purified hyaluronidase has been determined to be 61,000 by gel filtration methods. This value is in contrast to a molecular weight of 126,000 for the crude enzyme, as determined by similar techniques. This difference between the crude and purified enzyme could be due to association with a carrier protein in the crude testicular extract or to the existence of hyaluronidase as a dimer in the crude state. Only 76% of the weight of the purified hyaluronidase could be accounted for by its amino acid and carbohydrate composition.
Leptin Is a Risk Marker for First-Ever Hemorrhagic Stroke in a Population-Based Cohort (1999)

Plasma leptin is strongly associated with an increased risk for first-ever hemorrhagic stroke, independent of other risk markers for cardiovascular disease. Leptin may be an important link in the development of cardiovascular disease in obesity.