gebhart/patrepeval huggingface dataset:
Recent Developments in the Use of Liquid Crystal Coatings for Full-Surface Shear Stress Vector Measurements (1995)

Under normal white-light illumination and oblique observation, liquid crystal coating (LCC) color-change response to shear depends on both shear stress magnitude as well as the direction of the applied shear relative to the observer's line of sight. These color-change responses were quantified by subjecting a LCC to a wall-jet shear flow and measuring scattered-light spectra using a fiber optic probe and spectrophotometer. At any fixed shear stress magnitude, the maximum color change was measured when the shear vector was aligned with and directed away from the observer; changes in the relative in-plane view angle to either side of this vector/observer aligned position resulted in symmetric Gaussian reductions in measured color change. For this vector/observer aligned orientation, color change was found to scale linearly with increasing shear stress magnitude over an eight-fold range. Based on these results, a surface shear stress vector measurement methodology, involving multiple oblique-view observations of the test surface, was formulated. In the present paper, the experimental approach and data analysis procedure required to extend this vector measurement methodology to full-surface applications will be outlined and progress towards demonstrating this areal capability will be reviewed.
Genetic inactivation of <i>AKT1</i> , <i>AKT2</i> , and <i>PDPK1</i> in human colorectal cancer cells clarifies their roles in tumor growth regulation (2010)

Phosphotidylinositol-3-kinase (PI3K) signaling is altered in the majority of human cancers. To gain insight into the roles of members of this pathway in growth regulation, we inactivated AKT1 , AKT2 , or PDPK1 genes by targeted homologous recombination in human colon cancer cell lines. Knockout of either AKT1 or AKT2 had minimum effects on cell growth or downstream signaling. In contrast, knockout of both AKT1 and AKT2 resulted in markedly reduced proliferation in vitro when growth factors were limiting and severely affected experimental metastasis in mice. Unexpectedly, AKT1 and AKT2 appeared to regulate growth through FOXO proteins, but not through either GSK3β or mTOR. In contrast, inactivation of PDPK1 affected GSK3β and mTOR activation. These findings show that the PI3K signaling pathway is wired differently in human cancer cells than in other cell types or organisms, which has important implications for the design and testing of drugs that target this pathway.
A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides (2002)

Aiming to facilitate the analysis of human genetic variations in the context of disease susceptibility and varied drug response, we have developed a genotyping method that entails incorporation of a chemically labile nucleotide by PCR followed by specific chemical cleavage of the resulting amplicon at the modified bases. The identity of the cleaved fragments determines the genotype of the DNA. This method, termed Incorporation and Complete Chemical Cleavage, utilizes modified nucleotides 7-deaza-7-nitro-dATP, 7-deaza-7-nitro-dGTP, 5-hydroxy-dCTP, and 5-hydroxy-dUTP, which have increased chemical reactivity but are able to form standard Watson-Crick base pairs. Thus one analog is substituted for the corresponding nucleotide during PCR, generating amplicons that contain nucleotide analogs at each occurrence of the selected base throughout the target DNA except for the primer sequences. Subsequent treatment with an oxidant followed by an organic base results in chemical cleavage at each site of modification, which produces fragments of different lengths and/or molecular weights that reflect the genotype of the original DNA sample at the site of interest. This incorporation and cleavage chemistry are widely applicable to many existing nucleic acid analysis platforms, including gel electrophoresis and mass spectrometry. By combining DNA amplification and analog incorporation into one step, this strategy eliminates preamplification, DNA-strand separation, primer extension, and purification procedures associated with traditional chain-termination chemistry and therefore presents significant advantages in terms of speed, cost, and simplicity of genotyping.
Mucosal vaccine adjuvants update (2012)

Mucosal vaccination, capable of inducing protective immune responses both in the mucosal and systemic immune compartments, has many advantages and is regarded as a blue ocean in the vaccine industry. Mucosal vaccines can offer lower costs, better accessability, needle-free delivery, and higher capacity of mass immunizations during pandemics. However, only very limited number of mucosal vaccines was approved for human use in the market yet. Generally, induction of immune responses following mucosal immunization requires the co-administration of appropriate adjuvants that can initiate and support the effective collaboration between innate and adaptive immunity. Classically, adjuvant researches were rather empirical than keenly scientific. However, during last several years, fundamental scientific achievements in innate immunity have been translated into the development of new mucosal adjuvants. This review focuses on recent developments in the concepts of adjuvants and innate immunity, mucosal immunity with special interest of vaccine development, and basic and applied researches in mucosal adjuvant.
Molecular cloning and characterization of the structural gene for the major iron-regulated protein expressed by Neisseria gonorrhoeae. (1990)

This report describes the cloning and sequencing of the major iron-regulated protein (termed Fbp) of Neisseria gonorrhoeae strain F62. Attempts to identify recombinants expressing the Fbp using specific antibody proved unsuccessful. Therefore, an alternative cloning strategy using oligonucleotide probes derived from NH2-terminal and tryptic fragments of this protein was used to identify short fragments of the gene. Using this methodology, the gene encoding the precursor of Fbp was cloned on three separate overlapping fragments and sequenced, and the amino acid sequence was deduced. These data were unambiguously confirmed by the known NH2-terminal amino acid sequence and were supported by the sequences from tryptic fragments that lie outside of this region. Using oligonucleotide probes, we were unable to obtain clones encoding the potential regulatory region of this protein. Therefore, the technique of inverse polymerase chain reaction was used to amplify a fragment containing an additional 200 bp. This fragment was cloned and sequenced and found to contain a consensus ribosome binding site and potential -10 and -35 sequences. Hybridization analysis of genomic DNA from gonococcal strain F62 indicated that only a single copy of the Fbp gene exists per genome. These results complement the biochemical characterization of the Fbp expressed by gonococci and further suggest that it has a role in iron-acquisition.
Window-time-space flow control (WTFC) (2002)

End to end flow control will be essential for data communications in the near future B-ISDN network, because of its heterogeneous structure. The network is considered a black box from the transmitters point of view, and modeled with G/G/I queuing system. The window bounded D/D/1/W model and window-time (WT) plane are defined using the previous result, that with lowering variance and keeping QoS constant, network delay curve approaches the D/D/1 one. On this basis, a new window-time-space flow control (WTFC) is developed, which enables the transmitter to estimate its optimal packet sending rate and window, under condition that total network (path) capacity is known. The total capacity can be signaled from the network or estimated by the transmitter. Simulation measurement results are presented and analyzed.
A Clinical and Biological Guide for Understanding Chemotherapy-Induced Alopecia and Its Prevention (2017)

Chemotherapy-induced alopecia (CIA) represents perhaps the most distressing side effect of chemotherapeutic agents and is of huge concern to the majority of patients. Scalp cooling is currently the only safe option to combat CIA. Clinical and biological evidence suggests improvements can be made, including efficacy in delivering adequately low temperature to the scalp and patient-specific cap design. The increased use of scalp cooling, an understanding of how to deliver it most effectively, and biological evidence-based approaches to improve its efficacy have enormous potential to ease the psychological burden of CIA, as this could lead to improvements in treatment and patient quality-of-life.
Microarray analysis reveals genetic pathways modulated by tipifarnib in acute myeloid leukemia (2004)

The genetic networks derived from these studies illuminate some of the biological pathways affected by FTI treatment while providing a proof of principle for identifying candidate genes that might be used as surrogate biomarkers of drug activity.
In-band impairment measurement via varied-SOP polarization-resolved optical spectrum analysis (2011)

We review a novel measurement concept, based on the acquisition of multiple polarization-analyzed optical spectra corresponding to different polarization-analyzer orientations, or equivalently to varied states of polarization (SOPs) of the light impinging upon the analyzer. This approach denoted Varied-SOP polarization-resolved Optical Spectrum Analysis (VSOP-OSA), enables several types of in-band optical impairments to be quantified. In particular, it permits accurate and rapid measurement of optical signal to noise ratio (OSNR), differential group delay (DGD), and interchannel-induced nonlinear effects (NLE) in term of NLE-induced signal depolarization. (8 pages)
Deep network packet filter design for reconfigurable devices (2008)

Most network routers and switches provide some protection against the network attacks. However, the rapidly increasing amount of damages reported over the past few years indicates the urgent need for tougher security. Deep-packet inspection is one of the solutions to capture packets that can not be identified using the traditional methods. It uses a list of signatures to scan the entire content of the packet, providing the means to filter harmful packets out of the network. Since one signature does not depend on the other, the filtering process has a high degree of parallelism. Most software and hardware deep-packet filters that are in use today execute the tasks under Von Neuman architecture. Such architecture can not fully take advantage of the parallelism. For instance, one of the most widely used network intrusion-detection systems, Snort, configured with 845 patterns, running on a dual 1-GHz Pentium III system, can sustain a throughput of only 50 Mbps. The poor performance is because of the fact that the processor is programmed to execute several tasks sequentially instead of simultaneously. We designed scalable deep-packet filters on field-programmable gate arrays (FPGAs) to search for all data-independent patterns simultaneously. With FPGAs, we have the ability to reprogram the filter when there are any changes to the signature set. The smallest full-pattern matcher implementation for the latest Snort NIDS fits in a single 400k Xilinx FPGA (Spartan 3-XC3S400) with a sustained throughput of 1.6 Gbps. Given a larger FPGA, the design can scale linearly to support a greater number of patterns, as well as higher data throughput.
Identification of Genomic Features in Environmentally Induced Epigenetic Transgenerational Inherited Sperm Epimutations (2014)

A variety of environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. The process involves exposure of a gestating female and the developing fetus to environmental factors that promote permanent alterations in the epigenetic programming of the germline. The molecular aspects of the phenomenon involve epigenetic modifications (epimutations) in the germline (e.g. sperm) that are transmitted to subsequent generations. The current study integrates previously described experimental epigenomic transgenerational data and web-based bioinformatic analyses to identify genomic features associated with these transgenerationally transmitted epimutations. A previously identified genomic feature associated with these epimutations is a low CpG density (<12/100bp). The current observations suggest the transgenerational differential DNA methylation regions (DMR) in sperm contain unique consensus DNA sequence motifs, zinc finger motifs and G-quadruplex sequences. Interaction of molecular factors with these sequences could alter chromatin structure and accessibility of proteins with DNA methyltransferases to alter de novo DNA methylation patterns. G-quadruplex regions can promote the opening of the chromatin that may influence the action of DNA methyltransferases, or factors interacting with them, for the establishment of epigenetic marks. Zinc finger binding factors can also promote this chromatin remodeling and influence the expression of non-coding RNA. The current study identified genomic features associated with sperm epimutations that may explain in part how these sites become susceptible for transgenerational programming.
Upf1p, Nmd2p, and Upf3p Regulate the Decapping and Exonucleolytic Degradation of both Nonsense-Containing mRNAs and Wild-Type mRNAs (2001)

In Saccharomyces cerevisiae, rapid degradation of nonsense-containing mRNAs requires the decapping enzyme Dcp1p, the 5'-to-3' exoribonuclease Xrn1p, and the three nonsense-mediated mRNA decay (NMD) factors, Upf1p, Nmd2p, and Upf3p. To identify specific functions for the NMD factors, we analyzed the mRNA decay phenotypes of yeast strains containing deletions of DCP1 or XRN1 and UPF1, NMD2, or UPF3. Our results indicate that Upf1p, Nmd2p, and Upf3p regulate decapping and exonucleolytic degradation of nonsense-containing mRNAs. In addition, we show that these factors also regulate the same processes in the degradation of wild-type mRNAs. The participation of the NMD factors in general mRNA degradation suggests that they may regulate an aspect of translation termination common to all transcripts.
Antibodies to Crucial Epitopes on HSV-2 Glycoprotein D as a Guide to Dosing an mRNA Genital Herpes Vaccine (2022)

The toxicity of mRNA-lipid nanoparticle (LNP) vaccines depends on the total mRNA-LNP dose. We established that the maximum tolerated dose of our trivalent mRNA-LNP genital herpes vaccine was 10 μg/immunization in mice. We then evaluated one of the mRNAs, gD2 mRNA-LNP, to determine how much of the 10 μg total dose to assign to this immunogen. We immunized mice with 0.3, 1.0, 3.0, or 10 μg of gD2 mRNA-LNP and measured serum IgG ELISA, neutralizing antibodies, and antibodies to six crucial gD2 epitopes involved in virus entry and spread. Antibodies to crucial gD2 epitopes peaked at 1 μg, while ELISA and neutralizing titers continued to increase at higher doses. The epitope results suggested no immunologic benefit above 1 μg of gD2 mRNA-LNP, while ELISA and neutralizing titers indicated higher doses may be useful. We challenged the gD2 mRNA-immunized mice intravaginally with HSV-2. The 1-μg dose provided total protection, confirming the epitope studies, and supported assigning less than one-third of the trivalent vaccine maximum dose of 10 μg to gD2 mRNA-LNP. Epitope mapping as performed in mice can also be accomplished in phase 1 human trials to help select the optimum dose of each immunogen in a multivalent vaccine.
A Computer Generated Model of Adenosine Receptors Rationalising Binding and Selectivity of Receptor Ligands (1991)

Computer graphic analyses on a broad spectrum of adenosine receptor ligands has shown that both the A1 and A2 adenosine receptors have three binding sites. The spatial relationship of these three binding sites has been defined. Adenosine orientation at A1 and A2 is different.
A carbon nanotube oscillator as a surface profiling device (2008)

A double wall carbon nanotube oscillator near an infinite surface with the nanotube axis perpendicular to the surface is investigated. The oscillatory motion is governed in part by the van der Waals forces in the system, and we use the Lennard-Jones approximation for their calculation. In addition, friction losses due to the proximity of the oscillating nanotube near the infinite surface are taken into account using a phenomenological model. Newton's equation is solved and the oscillatory motion is studied as a function of the nanotube-surface distance, the nanotube length, and the initial extrusion of the moving nanotube. A practical device for surface profiling is also proposed.
A model predictive control optimization environment for real-time commercial building application (2012)

A model predictive control (MPC) environment is described. The environment integrates Matlab and EnergyPlus with a modified particle swarm optimizer to predict optimal building control strategies. A supporting framework is described which couples the environment to a building automation system, allowing real-time optimization considering operator overrides and updated weather forecasts. Challenges unique to integration with EnergyPlus for real-time optimization are discussed. Application of the environment is demonstrated in two simulation cases. First, the environment is used to determine hourly cooling set points minimizing daily energy cost for EnergyPlus's Benchmark Large Office building. Results suggest 5% cost savings during the study period. Second, the environment is used to determine hourly supply water temperature and circulator availability that minimize daily energy consumption for a small office building having a thermally activated building system (TABS). Compared to the base case, energy savings up to 54% are reported, with often improved occupant comfort.
Going Towards Discretized Spectrum Space: Quantification of Spectrum Consumption Spaces and a Quantified Spectrum Access Paradigm (2014)

Dynamic spectrum sharing approach is a paradigm shift from the conventional static and exclusive approach to spectrum allocation. The existing methodologies to define use of the spectrum and quantify its efficiency are based on the static spectrum assignment paradigm and not suitable for the dynamic spectrum sharing paradigm. There is a need to separately quantify the spectrum consumed by the individual transmitters and receivers when multiple heterogeneous wireless networks are sharing the spectrum in time, space, and frequency dimensions. By discretizing the spectrum dimensions, we define a methodology for quantifying the spectrum consumption spaces. This is an attempt to adopt the discretized signal processing principle and apply it to spectrum management functions that would bring in simplicity, flexibility, and precision among other advantages.
Fault Localization in Large-Scale Network Policy Deployment (2018)

The recent advances in network management automation and Software-Defined Networking (SDN) facilitate network policy management tasks. At the same time, these new technologies create a new mode of failure in the management cycle itself. Network policies are presented in an abstract model at a centralized controller and deployed as low-level rules across network devices. Thus, any software and hardware element in that cycle can be a potential cause of underlying network problems. In this paper, we present and solve a network policy fault localization problem that arises in operating policy management frameworks for a production network. We formulate our problem via risk modeling and propose a greedy algorithm that quickly localizes faulty policy objects in the network policy. We then design and develop SCOUT-a fully-automated system that produces faulty policy objects and further pinpoints physical-level failures which made the objects faulty. Evaluation results using a real testbed and extensive simulations demonstrate that SCOUT detects faulty objects with small false positives and false negatives.
Gone in Seconds: Praxis, Performance, and Peculiarities of Ultrafast Chiral Liquid Chromatography with Superficially Porous Particles (2015)

A variety of brush-type chiral stationary phases (CSPs) were developed using superficially porous particles (SPPs). Given their high efficiencies and relatively low back pressures, columns containing these particles were particularly advantageous for ultrafast "chiral" separations in the 4-40 s range. Further, they were used in all mobile phase modes and with high flow rates and pressures to separate over 60 pairs of enantiomers. When operating under these conditions, both instrumentation and column packing must be modified or optimized so as not to limit separation performance and quality. Further, frictional heating results in axial thermal gradients of up to 16 °C and radial temperature gradients up to 8 °C, which can produce interesting secondary effects in enantiomeric separations. It is shown that the kinetic behavior of various CSPs can differ from one another as much as they differ from the well-studied C18 reversed phase media. Three additional interesting aspects of this work are (a) the first kinetic evidence of two different chiral recognition mechanisms, (b) a demonstration of increased efficiencies at higher flow rates for specific separations, and
Conclusive eavesdropping in quantum key distribution (2005)

It is argued that the BB84 (Bennett–Brassard 1984) protocol of quantum key distribution has a vulnerability similar to the well-known vulnerability of the B92 (Bennett 1992) protocol in the presence of losses. The quantum circuit and design are first reviewed for an optimized entangling probe attacking the BB84 protocol of quantum key distribution and yielding maximum information to the probe. Probe photon polarization states become optimally entangled with the signal states on their way between the legitimate transmitter and receiver. Although standard von Neumann projective measurements of the probe yield maximum information on the pre-privacy amplified key, if instead the probe measurements are performed with a certain positive operator valued measure, then the measurement results are unambiguous, at least some of the time, resulting in complete information gain by the probe for sufficient loss in the key distribution channel.