gebhart/patrepeval huggingface dataset:
1015. Induction of Protective Immunity to Anthrax Lethal Toxin with a Chimpanzee Adenovirus-Based Vaccine Carrier in the Presence of Pre-Existing Anti-Human Adenovirus Immunity (2004)

An intentional release of anthrax spores could result in widespread inhalational anthrax and a socioeconomic disaster, and thus development of a effective, rapidly acting vaccine is essential to protect susceptible individuals. The current vaccine licensed for use in the US has limited availability and requires multiple administrations for full protection. We have recently demonstrated (Tan et al, Hum Gene Ther. 2003, 14:1673) that a single intramuscular administration of a recombinant serotype 5 adenovirus (Ad) vector expressing protective antigen (PA), a component of anthrax lethal toxin, provides rapid protection against lethal toxin challenge in BALB/c mice. However, approximately 35 to 50% of humans have pre-existing neutralizing antibodies against Ad5 and this may limit the utility of the Ad5-based vaccine. Based on the concept that “seroswitch” of an Ad vector could circumvent pre-existing anti-Ad5 immunity, this study assesses the hypothesis that a recombinant adenoviral vector based on the chimpanzee-derived serotype AdC7 expressing the secreted form of PA (AdC7secPA) will protect against anthrax lethal toxin in the presence of pre-existing anti-Ad5 immunity. BALB/c mice (n=5/group) were immunized intramuscularly with 109 particle units (pu) AdC7secPA, Ad5secPA (a human serotype Ad5-based vector expressing a secreted form of PA) or AdNull (an Ad5 vector with no transgene). At 4 wk post-administration, anti-PA reciprocal titers were assessed by ELISA. Serum anti-PA antibody titers for Ad5secPA-immunized mice were 8800 ± 1600 (mean ± standard error). Serum antibody titers in response to AdC7secPA immunization were 130 ± 62 at a dose of 109 pu, 3000 ± 1300 at 1010 pu, and 14,000 ± 3400 at 1011 pu. No anti-PA titers were detectable for the AdNull control group. To assess the effect of pre-existing anti-Ad5 immunity on anti-PA antibody titers, mice were injected intramuscularly with 1010 pu of a control Ad5 vector to induce anti-Ad immunity. At 4 wk post-administration, with anti-Ad5 neutralizing titers of 84 ± 13, the pre-immunized mice received 1010 pu AdC7secPA. Four wk later, the reciprocal anti-PA antibody titers in Ad5 pre-immunized mice were 1300 ± 490, demonstrating the efficacy of AdC7secPA at stimulating anti-PA titers in the presence of anti-Ad5 immunity. To assess protection in vivo, AdC7secPA- and Ad5secPA-immunized mice were challenged with a lethal intravenous dose of B. anthracis lethal toxin. After 6 wk, 100% of Ad5sechPA (109 pu)-immunized mice survived, whereas 100% of naive control mice died. A dose of 109 pu AdC7secPA protected 60% of immunized mice and a dose of 1010 pu resulted in 100% survival. In Ad5 pre-immunized, AdC7secPA-vaccinated mice, survival after lethal toxin challenge was 100%. These data demonstrate that in the presence of pre-existing anti-Ad5 immunity, the chimpanzee based vector AdC7secPA is an effective vaccine for the development of protective immunity against PA.
Lifting-based invertible motion adaptive transform (LIMAT) framework for highly scalable video compression (2003)

We propose a new framework for highly scalable video compression, using a lifting-based invertible motion adaptive transform (LIMAT). We use motion-compensated lifting steps to implement the temporal wavelet transform, which preserves invertibility, regardless of the motion model. By contrast, the invertibility requirement has restricted previous approaches to either block-based or global motion compensation. We show that the proposed framework effectively applies the temporal wavelet transform along a set of motion trajectories. An implementation demonstrates high coding gain from a finely embedded, scalable compressed bit-stream. Results also demonstrate the effectiveness of temporal wavelet kernels other than the simple Haar, and the benefits of complex motion modeling, using a deformable triangular mesh. These advances are either incompatible or difficult to achieve with previously proposed strategies for scalable video compression. Video sequences reconstructed at reduced frame-rates, from subsets of the compressed bit-stream, demonstrate the visually pleasing properties expected from low-pass filtering along the motion trajectories. The paper also describes a compact representation for the motion parameters, having motion overhead comparable to that of motion-compensated predictive coders. Our experimental results compare favorably to others reported in the literature, however, our principal objective is to motivate a new framework for highly scalable video compression.
Capillary electrophoresis: a powerful microanalytical technique for biologically active molecules. (1993)

Capillary electrophoresis (CE) is a versatile microanalytical technique that has gained much attention, particularly from those working with biologically active molecules. Its appealing characteristics include unprecedented sensitivity and the ability for automating the rapid electrophoretic separation of a number of low-volume samples in a reproducible manner, with relatively short analysis times. The picomole-femtomole (10(-12)-10(-15) mol) sensitivity of UV-CE has been enhanced tremendously by the interfacing of detection systems such as laser-induced fluorescence, which has extended the sensitivity into the attomole-zeptomole (10(-18)-10(-21) mol) range. Fluorescence detection has shown great potential for the CE analysis of a wide range of biomolecules including peptides, proteins and DNA. CE research and development has taken on directions focused primarily on improving detection, understanding and exploiting the basic chemistry of CE and devising new applications.
Effect of Dietary Yeast Culture on Milk Yield, Composition, and Component Yields at Commercial Dairies (1997)

A field trial was conducted to evaluate the effect of dietary yeast culture on milk yield, composition, and component yields at 11 commercial dairies in Wisconsin. Rolling herd averages ranged from 10,000 to 12,800 kg per cow. Yeast culture was added to total mixed rations to allow an average daily intake of 57 g over two 30-d Dairy Herd Improvement (DHI) test periods. Production data from the 30-d DHI test periods immediately before and after the yeast culture feeding period were used as the control. There were 585 cows (245 primiparous and 340 multiparous) that completed the four 30-d period feeding sequence (OFF-ON-ON-OFF). Average days in milk were similar for the yeast and control feeding periods (140.0 vs 140.5, respectively). Dietary yeast culture increased (P<0.001) actual and 150 d adjusted milk yields 0.90 kg/d. Milk fat content was lower (P<0.001) for cows fed yeast culture (3.55 vs 3.65%), but milk fat yield was similar. Dietary yeast culture reduced (P<0.05) milk protein content 0.02 percentage units, but protein yield was higher (P<0.01) for cows fed yeast culture (1.17 vs 1.14 kg/d). The milk yield response was positive in 8 of 11 herds (herd by treatment interaction; P<0.001). These data indicate that under the conditions of this study the addition of yeast culture to total mixed rations for mid lactation dairy cows in high producing commercial herds increases milk and protein yield.
Enhancement of Candida albicans killing activity of separated human epidermal cells by ultraviolet radiation (1987)

Ultraviolet irradiation enhanced the Candida albicans killing activity of freshly separated human epidermal cells in vitro. The stimulation was dose-dependent and was not due to soluble extracellular factors acting on non-irradiated epidermal cells. The enhancement of the killing activity remained unchanged when epidermal cells were depleted of Langerhans cells. Protein synthesis inhibitors and prostaglandin antagonists abrogated the ultraviolet-induced augmentation of killing activity.
The in vitro response of phenotypically defined mouse stem cells and myeloerythroid progenitors to single or multiple growth factors. (1991)

Pluripotential stem cells (Thylo Lin- Sca+; referred to as Sca+) and primitive myeloerythroid progenitor cells (Thylo Lin- Sca-; referred to as Sca-), defined by their in vivo repopulating properties, have been purified from mouse bone marrow. In this study, the growth factor requirements of these two subsets were compared in colony-forming assays. Sca- progenitor cells grew well in interleukin (IL) 3 alone and showed maximum growth when two factors, IL-3 plus IL-1 or IL-3 plus IL-6, were combined. In contrast, Sca+ stem cells were generally not responsive to any single factor tested. Some colony formation was found when IL-3 was paired with either IL-1 or IL-6, and this was significantly enhanced as additional factors were included. A remarkable frequency of as much as 1 colony per 1.7 input Sca+ cells was achieved when IL-1, IL-3, IL-6, and colony-stimulating factors were used together. These differences in factor requirements presumably reflect the need for multiple factor signaling in the more primitive stem cell population. In most other aspects of colony formation, Sca+ and Sca- cells were very similar. They generated colonies that had equivalent distributions in size and cellular composition. One notable difference was found in the kinetics of their response. Whereas nearly all Sca- cells formed colonies within 7 days, a significant fraction of Sca+ cells delayed colony formation for greater than 1 week. During this quiescent period, cell survival was absolutely dependent on the presence of factors in the medium.
Identification of a Polymorphic Gene, BCL2A1, Encoding Two Novel Hematopoietic Lineage-specific Minor Histocompatibility Antigens (2003)

We report the identification of two novel minor histocompatibility antigens (mHAgs), encoded by two separate single nucleotide polymorphisms on a single gene, BCL2A1, and restricted by human histocompatibility leukocyte antigen (HLA)-A*2402 (the most common HLA-A allele in Japanese) and B*4403, respectively. Two cytotoxic T lymphocyte (CTL) clones specific for these mHAgs were first isolated from two distinct recipients after hematopoietic cell transplantation. Both clones lyse only normal and malignant cells within the hematopoietic lineage. To localize the gene encoding the mHAgs, two-point linkage analysis was performed on the CTL lytic patterns of restricting HLA-transfected B lymphoblastoid cell lines obtained from Centre d'Etude du Polymorphisme Humain. Both CTL clones showed a completely identical lytic pattern for 4 pedigrees and the gene was localized within a 3.6-cM interval of 15q24.3-25.1 region that encodes at least 46 genes. Of those, only BCL2A1 has been reported to be expressed in hematopoietic cells and possess three nonsynonymous nucleotide changes. Minigene transfection and epitope reconstitution assays with synthetic peptides identified both HLA-A*2402- and B*4403-restricted mHAg epitopes to be encoded by distinct polymorphisms within BCL2A1.
Factor Analysis of the French Version of the 20-ltem Toronto Alexithymia Scale (TAS-20) (1996)

A French version of the Toronto Alexithymia Scale-20 Items (TAS-20) was factor-analyzed on a sample of 263 university students and its factor solution analyzed along with the studies using the Canadian version. Our results show a two-factor solution where the items rating the difficulty to identify feelings and the items rating the difficulty to describe feelings constitute a sole factor contrary to the Canadian version. These data are reviewed in the context of previous research and offer two subscales for future investigations utilizing the TAS-20.
Mammalian DNA polymerase beta can substitute for DNA polymerase I during DNA replication in Escherichia coli. (1992)

Mammalian DNA polymerase beta is the smallest known eukaryotic polymerase and is expressed as an active protein in Escherichia coli harboring a plasmid containing its cDNA. Since some catalytic functions of DNA polymerase beta and E. coli DNA polymerase I are similar, we wished to determine if DNA polymerase beta could substitute for DNA polymerase I in bacteria. We found that the expression of mammalian DNA polymerase beta in E. coli restored growth in a DNA polymerase I-defective bacterial mutant. Sucrose density gradient analysis revealed that DNA polymerase beta complements the replication defect in the mutant by increasing the rate of joining of Okazaki fragments. These findings demonstrate that DNA polymerase beta, believed to function in DNA repair in mammalian cells, can also function in DNA replication. Moreover, this complementation system will permit study of the in vivo function of altered species of DNA polymerase beta, an analysis currently precluded by the difficulty in isolating mutants in mammalian cells.
Colorgorical: Creating discriminable and preferable color palettes for information visualization (2016)

We present an evaluation of Colorgorical, a web-based tool for creating discriminable and aesthetically preferable categorical color palettes. Colorgorical uses iterative semi-random sampling to pick colors from CIELAB space based on user-defined discriminability and preference importances. Colors are selected by assigning each a weighted sum score that applies the user-defined importances to Perceptual Distance, Name Difference, Name Uniqueness, and Pair Preference scoring functions, which compare a potential sample to already-picked palette colors. After, a color is added to the palette by randomly sampling from the highest scoring palettes. Users can also specify hue ranges or build off their own starting palettes. This procedure differs from previous approaches that do not allow customization (e.g., pre-made ColorBrewer palettes) or do not consider visualization design constraints (e.g., Adobe Color and ACE). In a Palette Score Evaluation, we verified that each scoring function measured different color information. Experiment 1 demonstrated that slider manipulation generates palettes that are consistent with the expected balance of discriminability and aesthetic preference for 3-, 5-, and 8-color palettes, and also shows that the number of colors may change the effectiveness of pair-based discriminability and preference scores. For instance, if the Pair Preference slider were upweighted, users would judge the palettes as more preferable on average. Experiment 2 compared Colorgorical palettes to benchmark palettes (ColorBrewer, Microsoft, Tableau, Random). Colorgorical palettes are as discriminable and are at least as preferable or more preferable than the alternative palette sets. In sum, Colorgorical allows users to make customized color palettes that are, on average, as effective as current industry standards by balancing the importance of discriminability and aesthetic preference.
Virus inactivation by grapes and wines (1976)

Infusions and extracts of different grapes inactivated poliovirus; agents responsible for this property resided in the skin of the grape. Commercial grape juice at both natural and neutral pH inactivate various enteric viruses and herpes simplex virus; a 1,000-fold reduction in poliovirus infectivity occurred after incubation with grape juice, pH 7.0, for 24 h at 4 degrees C. A variety of wines were antiviral but to a lesser extent than grape juice; red wines were more antiviral than white. Antiviral activity was demonstrable in fractions of grape juice varying in molecular weight from less than 1,000 to greater than 30,000 as determined by membrane filtration. Some restoration of poliovirus infectivity from virus-grape juice complexes was achieved with 1% gelatin, 0.1% Tween 80, 0.5% polyvinyl pyrrolidone, and 0.5% polyethylene glycol.
An Assay for Transforming Growth Factor-β Using Cells Transfected with a Plasminogen Activator Inhibitor-1 Promoter-Luciferase Construct (1994)

Transforming growth factor-beta (TGF-beta) is a potent regulator of cellular differentiation, proliferation, migration, and protein expression. These properties have been exploited to create a variety of bioassays for detecting the mature growth factor. In this paper, we describe a highly sensitive and specific, nonradioactive quantitative bioassay for TGF-beta based on its ability to induce plasminogen activator inhibitor-1 (PAI-1) expression. Mink lung epithelial cells (MLEC) were stably transfected with an expression construct containing a truncated PAI-1 promoter fused to the firefly luciferase reporter gene. Addition of TGF-beta (0.2 to > 30 pM) to the transfectants resulted in a dose-dependent increase in luciferase activity in the cell lysates. Although responsive to TGF-beta, this promoter fragment was only minimally influenced by other known inducers of PAI-1 expression. When compared to the widely used MLEC assay, this assay demonstrated greater sensitivity and specificity, allowing quantification of TGF-beta in complex biological solutions.
Improved siRNA/shRNA Functionality by Mismatched Duplex (2011)

siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity.
RSIP: address sharing with end-to-end security (2000)

Realm Speci#c IP #RSIP# is a new architecture under consideration in the Internet Engineering Task Force #IETF# that can potentially alleviate some of the problems associated with partitioning of the Internet address space due to, for example, the shortage of IPv4 addresses. It is being positioned as a replacement for Network Address Translation #NAT#, because, among other things, it can support endto -end security via IPsec, whichNAT cannot. This paper introduces the motivation behind RSIP, the RSIP architecture, and provides a basic overview of the RSIP protocol.
Modeling bipolar phase-shifted multielectrode catheter ablation (2002)

Atrial fibrillation (AFIB) is a common clinical problem affecting approximately 0.5-1% of the United States population. Radio-frequency (RF) multielectrode catheter (MEC) ablation has successes in curing AFIB. We utilized finite-element method analysis to determine the myocardial temperature distribution after 30 s, 80 degrees C temperature-controlled unipolar ablation using three 7F 12.5-mm electrodes with 2-mm interelectrode spacing MEC. Numerical results demonstrated that cold spots occurred at the edges of the middle electrode and hot spots at the side electrodes. We introduced the bipolar phase-shifted technique for RF energy delivery of MEC ablation. We determined the optimal phase-shift (phi) between the two sinusoidal voltage sources of a simplified two-dimensional finite-element model. At the optimal phi, we can achieve a temperature distribution that minimizes the difference between temperatures at electrode edges. We also studied the effects of myocardial electric conductivity (sigma), thermal conductivity (k), and the electrode spacing on the optimal phi. When we varied sigma and kappa from 50% to 150%, optimal phi ranged from 29.5 degrees to 23.5 degrees, and in the vicinity of 26.5 degrees, respectively. The optimal phi for 3-mm spacing MEC was 30.5 degrees. We show the design of a simplified bipolar phase-shifted MEC ablation system.
Discovery of Novel and Potent Orally Active Calcium-Sensing Receptor Antagonists that Stimulate Pulselike Parathyroid Hormone Secretion: Synthesis and Structure−Activity Relationships of Tetrahydropyrazolopyrimidine Derivatives (2011)

As part of our research for novel calcium-sensing receptor (CaSR) antagonists that can function as oral bone anabolic agents, we recently reported the discovery of a tetrahydropyrazolopyrimidine derivative featuring adamantyl group 1b with potent CaSR antagonistic activity. To explore the potential of this calcilytic congener, we introduced the gem-dialkyl benzyl group at the 3-position of the tetrahydropyrazolopyrimidine ring, forming a bioisostere of the adamantyl group by mimicking the adamantyl group's lipophilicity and bulkiness. Optimization directed toward the improvement of solubility and metabolic stability led to the discovery of compound 9e, which stimulated transient PTH secretion when orally administered to normal rats. Further, compound 9e proved to be fully effective in an osteopenic ovariectomized rat model.
mTOR Inhibition Induces Upstream Receptor Tyrosine Kinase Signaling and Activates Akt (2006)

Stimulation of the insulin and insulin-like growth factor I (IGF-I) receptor activates the phosphoinositide-3-kinase/Akt/mTOR pathway causing pleiotropic cellular effects including an mTOR-dependent loss in insulin receptor substrate-1 expression leading to feedback down-regulation of signaling through the pathway. In model systems, tumors exhibiting mutational activation of phosphoinositide-3-kinase/Akt kinase, a common event in cancers, are hypersensitive to mTOR inhibitors, including rapamycin. Despite the activity in model systems, in patients, mTOR inhibitors exhibit more modest antitumor activity. We now show that mTOR inhibition induces insulin receptor substrate-1 expression and abrogates feedback inhibition of the pathway, resulting in Akt activation both in cancer cell lines and in patient tumors treated with the rapamycin derivative, RAD001. IGF-I receptor inhibition prevents rapamycin-induced Akt activation and sensitizes tumor cells to inhibition of mTOR. In contrast, IGF-I reverses the antiproliferative effects of rapamycin in serum-free medium. The data suggest that feedback down-regulation of receptor tyrosine kinase signaling is a frequent event in tumor cells with constitutive mTOR activation. Reversal of this feedback loop by rapamycin may attenuate its therapeutic effects, whereas combination therapy that ablates mTOR function and prevents Akt activation may have improved antitumor activity.