gebhart/patrepeval huggingface dataset:
Inducible Expression of the ΔNGFr/F12Nef Fusion Protein as a New Tool for Anti-Human Immunodeficiency Virus Type 1 Gene Therapy (2002)

Expression of the human immunodeficiency virus type 1 (HIV-1) Nef triple mutant F12Nef strongly inhibits HIV-1 replication. We exploited such a unique feature in a novel anti-HIV-1 gene therapy design by constructing an HIV-1 Tat-defective lentivirus vector expressing the product of fusion between the low-affinity human nerve growth factor receptor truncated in its intracytoplasmic domain (deltaNGFr, NH(2) moiety), and F12Nef (COOH moiety), under the control of the HIV-1 long terminal repeats. In this manner, both the selection marker (deltaNGFr) and the anti-HIV-1 effector are comprised in the same fusion protein, the expression of which is targetable by HIV-1 infection. Such a vector was proved to transduce human cells efficiently and, on HIV-1 infection, it expressed high levels of the fusion protein. In addition, strong antiviral activity of the deltaNGFr/F12Nef-expressing vector was demonstrated in cell lines as well as in primary cell cultures challenged with T- or M-tropic HIV-1 isolates. Thus, the HIV-1-targetable expression of the deltaNGFr/F12Nef fusion protein represents a novel and powerful tool for an effective anti-HIV-1 gene therapy strategy.
Rotavirus VP8*: Phylogeny, Host Range, and Interaction with Histo-Blood Group Antigens (2012)

The distal portion of rotavirus (RV) VP4 spike protein (VP8*) is implicated in binding to cellular receptors, thereby facilitating viral attachment and entry. While VP8* of some animal RVs engage sialic acid, human RVs often attach to and enter cells in a sialic acid-independent manner. A recent study demonstrated that the major human RVs (P[4], P[6], and P[8]) recognize human histo-blood group antigens (HBGAs). In this study, we performed a phylogenetic analysis of RVs and showed further variations of RV interaction with HBGAs. On the basis of the VP8* sequences, RVs are grouped into five P genogroups (P[I] to P[V]), of which P[I], P[IV], and P[V] mainly infect animals, P[II] infects humans, and P[III] infects both animals and humans. The sialic acid-dependent RVs (P[1], P[2], P[3], and P[7]) form a subcluster within P[I], while all three major P genotypes of human RVs (P[4], P[6], and P[8]) are clustered in P[II]. We then characterized three human RVs (P[9], P[14], and P[25]) in P[III] and observed a new pattern of binding to the type A antigen which is distinct from that of the P[II] RVs. The binding was demonstrated by hemagglutination and saliva binding assay using recombinant VP8* and native RVs. Homology modeling and mutagenesis study showed that the locations of the carbohydrate binding interfaces are shared with the sialic acid-dependent RVs, although different amino acids are involved. The P[III] VP8* proteins also bind the A antigens of the porcine and bovine mucins, suggesting the A antigen as a possible factor for cross-species transmission of RVs. Our study suggests that HBGAs play an important role in RV infection and evolution.
Whole genome sequencing revealed new molecular characteristics in multidrug resistant staphylococci recovered from high frequency touched surfaces in London (2019)

The rise of antibiotic resistance (AMR) is one of the most important public health threats worldwide.Today, increasing attention is being paid to multidrug resistant staphylococci isolated from healthcare and non-healthcare environments as the treatment of these bacteria has become increasingly difficult. In this study, we compared staphylococci isolates recovered from high frequency touched surfaces from public areas in the community and hospitals in East and West London. 281 out of 600 (46.83%) staphylococci isolates recovered were multidrug resistant, of which 49 (8.17%) were mecA positive. There was significantly higher proportion of multidrug resistant staphylococci (P = 0.0002) in East London (56.7%) compared to West London (49.96%). The most common species identified as multidrug resistant were S. epidermidis, S. haemolyticus and S. hominis, whereas penicillin, fusidic acid and erythromycin were the most frequent antibiotics the isolates were resistant to. Whole genome sequenced of mecA positive isolates revealed that S. sciuri isolates carried the mecA1 gene, which has only 84.43% homology with mecA. In addition, other frequently identified resistance genes included blaZ, qacA/B and dfrC. We have also identified a diverse range of SCCmec types, many of which were untypable due to carrying a novel combination of ccr genes or multiple ccr complexes.
Rule Modeling Engine for Optimizing Complex Event Processing Patterns (2009)

In Complex Event Processing (CEP), we deal with how to search through a sequence of incoming events to find a specified and desired pattern. CEP has a broad use in today enterprise. It can act on sent and/or received events. The result can generate other events that can be used in different layers of an enterprise system. Growing number of areas dealing with arisen events like Business Activity Monitoring (BAM), Fraud detection and intrusion detection makes CEP a hot topic for researchers.Generating efficient high-performance patterns is the issue which has been addressed in this paper. The pattern can be made from any query given by user. The user defined query is CQL (Continuous Query Language)which is relevant for time series data. NFA (Nondeterministic Finite Automaton) is used for modeling patterns although it has some defects which are addressed.The focus of this paper is on developing a rule modeling engine and taking into account the role of historical data to make efficient patterns. We developed some algorithms for each component of proposed model. The results are optimized patterns produced based on historical data and queries given by user. Finally we show that these techniques can be efficient when we deal with high volume event-base data.
Unmanned Aerial Vehicles (2023)

Unmanned aerial vehicles (UAVs) are recognized as very useful tools to replace, help, or assist humans in various tasks, such as inspection and monitoring, surveillance, search and rescue, exploration, logistics and transportation, etc. Practical uses for such missions in both civilian and defense contexts have experienced a significant growth as a result of recent technological progresses. Nevertheless, some challenges and open issues regarding ensuring a full operational use of UAVs remain unanswered.This reprint aims to present recent advances in technologies and algorithms to improve the levels of autonomy, reliability, and safety of UAVs. Different topics are addressed, covering vehicle design and characterization (aerodynamics, flight dynamics, design optimization, communications), algorithms for autonomy (guidance and control, path planning, machine learning, computer vision, perception), traffic and risk management (unmanned traffic management, reliability, risk assessment). Open issues related to new missions such as precision agriculture or telecommunication relays are also considered.
An Interaction-Based Test Sequence Generation Approach for Testing Web Applications (2008)

Web applications often use dynamic pages that interact with each other by accessing shared objects, e.g., session objects. Interactions between dynamic pages need to be carefully tested, as they may give rise to subtle faults that cannot be detected by testing individual pages in isolation. Since it is impractical to test all possible interactions, a trade-off must be made between test coverage (in terms of number of interactions covered in the tests) and test effort. In this paper, we present a test sequence generation approach to cover all pairwise interactions, i.e., interactions between any two pages. Intuitively, if a page P could reach another page Ppsila, there must exist a test sequence in which both P and Ppsila are visited in the given order. We report a test sequence generation algorithm and two case studies in which test sequences are generated to achieve pairwise interaction coverage for two Web applications. The empirical results indicate that our approach achieves good code coverage and is effective for detecting interaction faults in the subject applications.
Double parallel-aligned cells for high speed liquid crystal displays (1993)

Double parallel-aligned nematic liquid crystal cells with crossed directors: one serves as a tunable phase compensator and another as a master cell, exhibits a fast response time, improved viewing angle, reasonably high white-to-black contrast ratio, and low operation voltage. The flexibility in choosing an appropriate operation voltage enables the device to be operated at its optimal condition. This operational mode can be used for both color-sequential projection and direct view displays.
Guided teaching interactions with robots: embodied queries and teaching heuristics (2012)

The vision of personal robot assistants continues to become more realistic with technological advances in robotics. The increase in the capabilities of robots, presents boundless opportunities for them to perform useful tasks for humans. \nHowever, it is not feasible for engineers to program robots for all possible uses. Instead, we envision general-purpose robots that can be programmed by their end-users.\n\nLearning from Demonstration (LfD), is an approach that allows users to program new capabilities on a robot by demonstrating what is required from the robot. Although LfD has become an established area of Robotics, many challenges remain in making it effective and intuitive for naive users. This thesis contributes to addressing these challenges in several ways. First, the problems that occur in teaching-learning interactions between humans and robots are characterized through human-subject experiments in three different domains. To address these problems, two mechanisms for guiding human teachers in their interactions are developed: embodied queries and teaching heuristics.\n\nEmbodied queries, inspired from Active Learning queries, are questions asked by the robot so as to steer the teacher towards providing more informative demonstrations. They leverage the robot's embodiment to physically manipulate the environment and to communicate the question. Two technical contributions are made in developing embodied queries. The first is Active Keyframe-based LfD -- a framework for learning human-segmented skills in continuous action spaces and producing four different types of embodied queries to improve learned skills. The second is Intermittently-Active Learning in which a learner makes queries selectively, so as to create balanced interactions with the benefits of fully-active learning. Empirical findings from five experiments with human subjects are presented. These identify interaction-related issues in generating embodied queries, characterize human question asking, and evaluate implementations of Intermittently-Active Learning and Active Keyframe-based LfD on the humanoid robot Simon.\n\nThe second mechanism, teaching heuristics, is a set of instructions given to human teachers in order to elicit more informative demonstrations from them. Such instructions are devised based on an understanding of what constitutes an optimal teacher for a given learner, with techniques grounded in Algorithmic Teaching. The utility of teaching heuristics is empirically demonstrated through six human-subject experiments, that involve teaching different concepts or tasks to a virtual agent, or teaching skills to Simon.\n\nWith a diverse set of human subject experiments, this thesis demonstrates the necessity for guiding humans in teaching interactions with robots, and verifies the utility of two proposed mechanisms in improving sample efficiency and final performance, while enhancing the user interaction.
Bacteriophage T7 late promoters with point mutations: quantitative footprinting and<i>in vivo</i>expression (1988)

Journal Article Bacteriophage T7 late promoters with point mutations: quantitative footprinting and in vivo expression Get access Kenneth A. Chapman, Kenneth A. Chapman * McArdle Laboratory for Cancer Research, University of WisconsinMadison, WI 53706, USA + Present addresses: MSU-DOE Plant Reseach Laboratory, Michigan State University, East Lansing, MI 48824 * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Samuel I. Gunderson, Samuel I. Gunderson McArdle Laboratory for Cancer Research, University of WisconsinMadison, WI 53706, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Anello, Michael Anello McArdle Laboratory for Cancer Research, University of WisconsinMadison, WI 53706, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert D. Wells, Robert D. Wells McArdle Laboratory for Cancer Research, University of WisconsinMadison, WI 53706, USA § Department of Biochemistry, University of Alabama at Birmingham, Schools of Medicine and Dentistry Birmingham, AL 35294, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard R. Burgess Richard R. Burgess McArdle Laboratory for Cancer Research, University of WisconsinMadison, WI 53706, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 10, 25 May 1988, Pages 4511–4524, https://doi.org/10.1093/nar/16.10.4511 Published: 25 May 1988 Article history Received: 12 January 1988 Revision received: 14 April 1988 Accepted: 14 April 1988 Published: 25 May 1988
Treatment of Obesity Hypoventilation Syndrome and Serum Leptin (2005)

Regular NIV use reduces serum leptin in OHS. Leptin may be a modulator of respiratory drive in patients with OHS.
A subset of human rapidly self-renewing marrow stromal cells preferentially engraft in mice (2005)

Controversies have arisen as to whether adult stem cells or progenitor cells from bone marrow can engraft into nonhematopoietic tissues in vivo. To resolve some of the controversies, we developed a highly sensitive polymerase chain reaction-based single nucleotide polymorphism (PCR-SNP) assay for competitive engraftment of mixtures of stem/progenitor cells. We used the assay to follow engraftment in immunodeficient mice of subpopulations of the stem/progenitor cells from human bone marrow referred to as either mesenchymal stem cells or marrow stromal cells (MSCs). The engraftment into adult mice without induced tissue injury was low and variable, but there was preferential engraftment of a subpopulation of rapidly self-renewing MSCs (RS-MSCs) compared with a subpopulation of slowly renewing MSCs (SR-MSCs). After intravenous infusion, there was a tendency for the cells to engraft into the hippocampal region that was previously designated a "vascular niche." Migration assays suggested that preferential engraftment of RS-MSCs was in part explained by their expression of CXCR4 and CX3R1, the receptors for SDF-1 and fractalkine.
Erie As a Way of Life (2018)

This essay—presented as the keynote address to the University of Akron School of Law’s conference on “Erie at 80”—considers the impact of the Supreme Court’s decision in Erie Railroad Co. v. Tompkins on the broader landscape of American law. I begin with Erie’s contribution to our modern, positivist understanding of the nature of law. That understanding, however, is under threat from pervasive tendencies, on both the political Left and Right, to collapse the distinction between law as a set of positivist choices adopted by government and law as the principles that we think are just, right, and true. Second, I consider Erie’s understanding of the role of the federal courts as bodies that lack general lawmaking powers. This understanding shapes current debates about judicial activism. But it is also threatened by the advent of federal multi-district litigation, which stresses the importance of one federal court “to rule them all” in consolidating solutions to broad social problems. Third, I assess Erie’s role in defining contemporary American federalism, which rejects rigid subject-matter categories for state and national power and instead stresses the political and procedural checks on national lawmaking. Erie’s model, however, is increasingly circumvented by Executive lawmaking that circumvents national legislative channels. Finally, I examine Erie as the key exemplar of the Legal Process School’s way of thinking about law and political conflict. That school of jurisprudence responded to a breakdown of national consensus on substantive norms by stressing the value of legitimate procedures for resolving disputes. Although the Legal Process School is not much in fashion these days, agreement on legitimate institutional allocations of authority may offer a plausible antidote to political polarization and the breakdown of civil discourse over substantive values.
Ras-dependent oncolysis with an adenovirus VAI mutant. (2003)

Adenovirus synthesize proteins that interact with oncogene and tumor suppressor gene products to set the cell for virus replication. Mutant viruses defective in these functions replicate selectively in cancer cells and represent new tools to treat cancer. We report a selectivity strategy based on deletions of adenovirus Virus-Associated (VA) RNAs. In normal cells, these RNAs are necessary for virus replication because they inactivate the RNA-dependent protein kinase protein kinase R, a kinase that otherwise would block protein translation in response to infection. However, downstream effectors of Ras can also inactivate protein kinase R, and therefore, the need for VA RNA genes should be bypassed in cells with an active Ras pathway. We demonstrate here that a VAI RNA mutant presents a Ras-dependent replication and can be used for oncolytic virotherapy of pancreatic tumors.
Water Impact Resistant and Antireflective Superhydrophobic Surfaces Fabricated by Spray Coating of Nanoparticles: Interface Engineering via End-Grafted Polymers (2018)

Fully transparent and water impact resistant superhydrophobic coatings are of great importance for a range of applications including photovoltaics, photonics, automotive windshields, and building windows. A widely utilized approach to fabricate such coatings involves solution-based deposition of hydrophobic nanoparticles. A central challenge is that these coatings do not simultaneously offer high levels of water repellency, perfect transparence, and water impact resistance. Here we demonstrate that end-grafted polymers present excellent interfaces for spray-coated hydrophobic nanoparticles and enable fabrication of water impact resistant and antireflective superhydrophobic coatings (SHPARCs). Depending on the backbone chemistry and thickness, end-grafted polymers uniquely interacted with the fluorinated nanoparticles, resulting in nanostructured films that provided reduction of reflective losses and protection from the impact of water droplets. Counterintuitively, substrates modified with end-grafted hydrophilic polymers exhibited high water impact resistance: the sliding angle of SHPARC on 12 nm thick end-grafted poly(ethylene glycol) layer was <2° after exposure to 100000 water droplets. SHPARC increased the transparency of the glass substrate by ∼5% through omnidirectional antireflectivity. We finally demonstrate application of SHPARC on a large area (156 × 156 mm2) silicon solar cell without significant (<0.23%) reduction of the power conversion efficiency, illustrating the promise of the presented approach in fabrication of self-cleaning photovoltaic modules.
Olanzapine Augmentation of Fluoxetine in the Treatment of Refractory Obsessive-Compulsive Disorder (1998)

Potenza, Marc N. MD, PhD; Wasylink, Suzanne RNC; Longhurst, James G. MD; Epperson, C. Neill MD; McDougle, Christopher J. MD Author Information
Permeability of Organic-Rich Shale (2015)

Summary Measured permeability of an organic-rich shale sample varies significantly with applied laboratory conditions, such as the confining pressure, temperature, and the measurement fluid type. This indicates that the measured quantity is influenced by several mechanisms that add complexity to the measurement. The complexity is mainly caused by stress dependence of the matrix permeability. Also, it is because organic-rich shale holds significant volumes of fluids in sorbed (adsorbed, dissolved) states; sorption can also influence the permeability through its own storage and transport mechanisms. The stress-dependence and sorption effects on permeability could develop under the reservoir conditions and influence the production, although we currently do not have a predictive permeability model that considers their coexistence. In this work, this is accomplished by considering that the shale matrix consists of multiple continua with organic and inorganic pores. Stress dependency of the permeability comes along with slit-shaped pores, whereas the sorption effects are associated with nanoscale organic capillaries. A simple conceptual flow model with an apparent shale permeability is developed that couples the molecular-transport effects of the sorbed phase with the stress dependence of the slit-shaped pores. The simulation results show the impact of the permeability model on the production. Sensitivity analysis on the new permeability model shows that the stress dependence of the overall transport is significant at high pore pressure, when the effective stress is relatively low. Diffusive molecular transport of the sorbed phase becomes important as the stress gets larger and, hence, the slit-shaped pores close. The constructed apparent-permeability vs. pore-pressure curves show the dominance of the molecular transport as an increase in permeability characterized by appearance of a minimum permeability value at the intermediate values of the pressure. One can use the new permeability model easily in history matching a well performance and optimizing its production.
Longitudinal Assessment of Glycosylated Blood Protein Concentrations in Normal Pregnancy and Gestational Diabetes (1986)

Longitudinal changes in glycosylated hemoglobin concentration (GlyHb) and glycosylated serum protein concentration (GSP) in both normal pregnancy and pregnancy complicated by gestational diabetes were determined using affinity chromatography, a method in which nonenzymatically glycosylated proteins are specifically measured. At 7-10 wk gestation, GlyHb in women who developed diabetes (N = 21) was higher than GlyHb in normal women (N = 49) (6.7 +/- 0.2% versus 5.7 +/- 0.2%, respectively, P less than 0.001) and remained elevated throughout gestation. In normal pregnancy, GlyHb decreased to a nadir at 23-26 wk and returned to baseline concentration by 31-34 wk. In gestational diabetes, there was an initial increase in GlyHb to 7.1 +/- 0.5% at 11-14 wk followed by a steady decrease. At 7-10 wk, GSP in women who developed diabetes was not elevated compared with normal concentration, although at 11-14 wk there was significant difference between the two groups (P less than 0.02). In normal women, GSP remained constant throughout gestation. In gestational diabetes, GSP decreased to early pregnancy values (P less than 0.02). Glycosylated blood proteins were elevated in early gestation in women who developed gestational diabetes and may have predictive value in identifying women who will develop diabetes in pregnancy.
Effects of inositol on ovarian function and metabolic factors in women with PCOS: a randomized double blind placebo-controlled trial. (2004)

These data support a beneficial effect of inositol in improving ovarian function in women with oligomenorrhea and polycystic ovaries.