gebhart/patrepeval huggingface dataset:
Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture (2012)

Improvements in technology have reduced the cost of DNA sequencing to the point that the limiting factor for many experiments is the time and reagent cost of sample preparation. We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at a cost of about $15 per sample. These libraries are effective not only for low-pass whole-genome sequencing, but also for simultaneously enriching them in pools of approximately 100 individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study.
Analysis of linear microstrip using an arbitrary ferromagnetic substance as the substrate (1969)

A Green&apos;s function of the vector potential for a microstrip is derived on the basis of the image theory after Silvester and the duality property of electric and magnetic fields of the TEM mode. It is also shown that the stationary equation similar to the variational equation for the electrostatic capacitance of the microstrip is given for its inductance with a magnetic substrate.
Transdermal photopolymerization for minimally invasive implantation (1999)

Photopolymerizations are widely used in medicine to create polymer networks for use in applications such as bone restorations and coatings for artificial implants. These photopolymerizations occur by directly exposing materials to light in "open" environments such as the oral cavity or during invasive procedures such as surgery. We hypothesized that light, which penetrates tissue including skin, could cause a photopolymerization indirectly. Liquid materials then could be injected s.c. and solidified by exposing the exterior surface of the skin to light. To test this hypothesis, the penetration of UVA and visible light through skin was studied. Modeling predicted the feasibility of transdermal polymerization with only 2 min of light exposure required to photopolymerize an implant underneath human skin. To establish the validity of these modeling studies, transdermal photopolymerization first was applied to tissue engineering by using "injectable" cartilage as a model system. Polymer/chondrocyte constructs were injected s.c. and transdermally photopolymerized. Implants harvested at 2, 4, and 7 weeks demonstrated collagen and proteoglycan production and histology with tissue structure comparable to native neocartilage. To further examine this phenomenon and test the applicability of transdermal photopolymerization for drug release devices, albumin, a model protein, was released for 1 week from photopolymerized hydrogels. With further study, transdermal photpolymerization potentially could be used to create a variety of new, minimally invasive surgical procedures in applications ranging from plastic and orthopedic surgery to tissue engineering and drug delivery.
A compact phage display human scFv library for selection of antibodies to a wide variety of antigens (2009)

These results suggested that by using an optimized protocol and very high repertoire diversity, a compact and efficient phage antibody library can be generated. This advanced method could be adopted by any molecular biology laboratory to generate both naïve or immunized libraries for particular targets as well as for high-throughput applications.
Low temperature InP∕Si wafer bonding using boride treated surface (2007)

An approach for InP∕Si wafer bonding based on boride-solution treatment was presented. The bonding energy is higher than the InP fracture energy by annealing at 280°C. An In0.53Ga0.47As∕InP multiple-quantum-well (MQW) structure grown on InP was transferred onto Si substrate via the bonding process. X-ray diffraction and photoluminescence reveal that crystal quality of the bonded MQW was preserved. A thin B2O3–POx–SiO2 oxide layer of about 28nm thick at the bonding interface was detected. X-ray photoelectron spectroscopy and Raman analyses indicate that the formation of oxygen bridging bonds by boride treatment is responsible for the strong fusion obtained at such low temperature.
Atomic-Resolution Visualization of Distinctive Chemical Mixing Behavior of Ni, Co, and Mn with Li in Layered Lithium Transition-Metal Oxide Cathode Materials (2015)

Capacity and voltage fading of layered structured cathode based on lithium transition-metal oxide is closely related to the lattice position and migration behavior of the transition-metal ions. However, it is scarcely clear about the behavior of each of these transition-metal ions in this category of cathode material. We report direct atomic resolution visualization of interatomic layer mixing of transition metals (Ni, Co, Mn) and lithium ions in layered structured oxide cathodes for lithium-ion batteries. Using chemical imaging with an aberration-corrected scanning transmission electron microscope (STEM) and density function theory calculations, we discovered that, in the layered cathodes, Mn and Co tend to reside almost exclusively at the lattice site of transition-metal (TM) layer in the structure or little interlayer mixing with Li. In contrast, Ni shows a high degree of interlayer mixing with Li. The fraction of Ni ions resides in the Li layer followed by a near linear dependence on total Ni concentration before reaching saturation. The observed distinctively different behavior of Ni with respect to Co and Mn provides new insights on both capacity and voltage fade in this class of cathode materials based on lithium and TM oxides, therefore providing scientific basis for selective tailoring of oxide cathode materials for enhanced performance.
Synthesis of New, Pyrene-Containing, Metal-Chelating Lipids and Sensing of Cupric Ions (2002)

The syntheses of several saturated, pyrene-containing, metal-chelating lipids are described. These lipids are capable of strongly binding to transition metal ions employing the metal-chelating headgroup. The excimer-to-monomer ratio of the pyrene groups changes with addition of cupric ions to the liposomes. Three other transition metal ions (Zn(2+), Ni(2+), and Hg(2+)) did not cause any appreciable changes in the excimer-to-monomer ratio. [reaction--see text]
Deterministic analysis of oversampled A/D conversion and decoding improvement based on consistent estimates (1994)

Discusses the deterministic analysis of oversampled A/D conversion (ADC), the properties derivable from such an analysis, and the consequences on reconstruction using nonlinear decoding. Given a band-limited input X producing a quantized version C, the authors consider the set of all input signals that are band-limited and produce C. They call any element of this set a consistent estimate of X. Regardless of the type of encoder (simple, predictive, or noise-shaping), they show that this set is convex, and as a consequence, any nonconsistent estimate can be improved. They also show that the classical linear decoding estimates are not necessarily consistent. Numerical tests performed on simple ADC, single-loop, and multiloop /spl Sigma//spl Delta/ modulation show that consistent estimates yield a mean square error (MSE) that decreases asymptotically with the oversampling ratio faster than the linear decoding MSE by approximately 3 dB/octave. This implies an asymptotic MSE of the order of /spl Oscr/(R/sup /spl minus/(2n+2/)) instead of /spl Oscr/(R/sup /spl minus/(2n+1/)) in linear decoding, where R is the oversampling ratio and n the order of the modulator. Methods of improvement of nonconsistent estimates based on the deterministic knowledge of the quantized signal are proposed for simple ADC, predictive ADC, single-loop, and multiloop /spl Sigma//spl Delta/ modulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Using adaptive tracking to classify and monitor activities in a site (2002)

We describe a vision system that monitors activity in a site over extended periods of time. The system uses a distributed set of sensors to cover the site, and an adaptive tracker detects multiple moving objects in the sensors. Our hypothesis is that motion tracking is sufficient to support a range of computations about site activities. We demonstrate using the tracked motion data to calibrate the distributed sensors, to construct rough site models, to classify detected objects, to learn common patterns of activity for different object classes, and to detect unusual activities.
Advanced Cyber Attack Modeling Analysis and Visualization (2010)

Abstract : This project delivers an approach for visualization, correlation, and prediction of potentially large and complex attack graphs. These attack graphs show multi-step cyber attacks against networks, based on system vulnerabilities, network connectivity, and potential attacker exploits. We introduce a new paradigm for attack graph analysis that augments the traditional graph-centric view, based on graph adjacency matrices. In our approach, the analysis includes all known network attack paths, while still keeping complexity manageable. It supports pre-attack network hardening, correlation of detected attack events, and attack origin/impact prediction for post-attack responses. The goal of this system is to transform large quantities of network security data into actionable intelligence. The utility of organizing combinations of network attacks as graphs is well established. Traditionally, such attack graphs have been formed manually by security red teams (penetration testers). We have demonstrated the capability for computational generation of attack graphs, rather than relying on manual creation. This approach is based on models of network security conditions and potential attacker exploits. Because of vulnerability interdependencies across networks, a topological attack graph approach is needed, especially for proactive defense against insidious multi-step attacks. The traditional approach that treats network data and events in isolation, without the context provided by attack graphs, is clearly insufficient.
Swelling and pressure-volume relationships in the dermis measured by osmotic-stress technique (2009)

Water transfer across the extracellular matrix (ECM) involves interstitial osmotic forces in as yet unclear ways. In particular, the traditional values of Starling forces cannot adequately explain fluid transfer rates. Here, we reassess these forces by analyzing fluid transfer in live pig and human dermal explants. Pressure potentials were controlled with inert polymers adjusted by membrane osmometry (range = 3-219 mmHg), and fluid transfer in and out of the explants was followed by sequential precision weighing. Water motional freedom in the dermis was examined by NMR. In pigs, mean hydration pressure (HP; the pressure at which volume did not change) was 107 +/- 22 and 47 +/- 12 (SE) mmHg at 4 degrees C and 37 degrees C (P = 0.012, paired t-test, n = 7). Volume changes observed in response to pressure potential were reversible. The equation, Volume change = V(max)/[1+(time/T(1/2))(d)], where V(max) is maximal volume change; T(1/2), time at volume = 1/2 V(max); and d, a rate parameter, was fitted to experimental progression curves (r(2) > 0.9), yielding V(max) values linearly related to pressure, with mean slopes -3.5 +/- 0.28 and -2.6 +/- 0.21(SE) mul.g(-1).mmHg(-1) at 4 degrees C and 37 degrees C. NMR spin-spin relaxation times (T(2)) varied within 200- to 400-mum distances in directions perpendicular to the epidermis, with slopes reaching 0.03 ms/mum. Results support a mechanism in which fluid transport across the ECM is locally regulated at micrometer scales by cell- and fiber-gel-dependent osmomechanical forces. The large HP helps to explain the fast interstitial in/out flow rates observed clinically.
Two types of septic shock classified by the plasma levels of cytokines and endotoxin. (1992)

We investigated plasma levels of cytokines and endotoxin in septic shock to clarify the roles of various cytokines in this type of shock. Endotoxemia was observed in 16 of 22 septic shock patients. Plasma levels of tumor necrosis factor-alpha (TNF-alpha), interleukin 1 beta (IL-1 beta) IL-2, and IL-6 were significantly higher in septic shock than in sepsis without shock. Strong correlations were noted between TNF-alpha and IL-2 levels and between IL-1 beta and IL-6 levels. Patients with high TNF-alpha and IL-2 levels also showed endotoxemia. We defined two types of septic shock from these data, i.e., endotoxin+TNF-alpha + IL-2 shock and IL-beta + IL-6 shock. In the former type, high TNF-alpha and IL-2 levels were present before the onset of shock, and shock itself was associated with endotoxemia. The second type showed simultaneous elevation of IL-1 beta and IL-6 levels at the onset of septic shock, and endotoxin was detected in some of them. These results suggest that endotoxin and extremely high levels of TNF-alpha and IL-2, or the simultaneous elevation of IL-1 beta and IL-6, are related to the onset of septic shock.
Human apolipoprotein E mRNA. cDNA cloning and nucleotide sequencing of a new variant. (1984)

The complete nucleotide sequences of three cloned cDNAs corresponding to human liver apolipoprotein E (apo-E) mRNA were determined. Analysis of the longest cDNA showed that it contained 1157 nucleotides of mRNA sequence with a 5'-terminal nontranslated region of 61 nucleotides, a signal peptide region corresponding to 18 amino acids, a mature protein region corresponding to 299 amino acids, and a 3'-terminal nontranslated region of 142 nucleotides. The inferred amino acid sequences from two cDNAs were identical and corresponded to the amino acid sequence for plasma apo-E3 that has been reported previously ( Rall , S. C., Jr., Weisgraber , K. H., and Mahley , R. W. (1982) J. Biol. Chem. 257, 4171-4178). The third cDNA differed from the other two cDNAs in five nucleotide positions. Three of these differences occurred in the third nucleotide position of amino acid codons, resulting in no change in the corresponding amino acids at residues Val-85, Ser-223, and Gln-248. The other two altered nucleotides occurred in the first nucleotide position of codons, leading to changes in the amino acids encoded. In the variant sequence, a threonine replaced the normal alanine at residue 99 and a proline replaced the normal alanine at residue 152. We have concluded that the human liver donor was heterozygous for the epsilon 3 genotype. The variant cDNA corresponds to a new, previously undescribed variant form of apo-E in which the amino acid substitutions of the protein are electrophoretically silent; it would probably be undetectable by standard apo-E phenotyping methods. The amino acid substitution at position 152 occurs in a region of apo-E that appears to be important for receptor binding, and it may have clinical significance.
Cephalosporins. V. Synthesis and in vitro activity of some 7-(2-methoxymino-(substituted thio)alkanoyl)amino cephalosporanic acid derivatives. (1982)

The introduction of the methoxyimino group next to the carbonyl of the 7-position side chain in some alkylthioacetamido and vinylenethioaeetamido cephalosporins, and its effect on the in vitro antimicrobial activity, are described.
Wordspotting using a predictive neural model for the telephone speech corpus (2002)

We describe a wordspotting algorithm based on a predictive neural model for a telephone speech corpus. Each keyword is modeled as a whole word. For keyword detection scoring we used a minimum accumulated prediction residual. We computed empirically a threshold value for rejecting non-keyword speech in place of building non-keyword models. We tested the algorithm with the TUBTEL telephone speech corpus and compared it with other algorithms like the standard DTW-based wordspotting algorithm and the two-stage wordspotting algorithm based on a DTW and a multilayer perceptron.
Association of block copolymers in selective solvents, 1. Measurements on hydrogenated poly(styrene‐isoprene) in decane and in trans‐decalin (1979)

Abstract The dilute solution properties and association of hydrogenated poly(styrene‐isoprene) two‐block copolymers in decane and trans ‐decalin have been studied by means of viscosity, diffusion and light‐scattering measurements. Data were obtained for two samples with molecular weights of 48 000 and 80 000, and both with a styrene content of 38%. In trans ‐decalin the normal behaviour of a non‐associating polymer is found. Association occurs in decane with the formation of compact micelles, composed (at ambient temperatures) of about 80 molecules. In contrast to what is observed in other associating two‐block systems, the transition to the completely dissociated state at elevated temperatures causes a drop of the intrinsic viscosity. Moreover, and this is not evident from the viscometric results, the diffusion and light scattering studies reveal that in the intermediate region between association and dissociation another kind of structure with very large dimensions is formed that exists over an extended temperature range. A qualitative description of the observed phenomena is given.
Three Protein Cocktails Mediate Delayed-Type Hypersensitivity Responses Indistinguishable from That Elicited by Purified Protein Derivative in the Guinea Pig Model ofMycobacterium tuberculosisInfection (2010)

Purified protein derivative (PPD) is a widely used reagent for the diagnosis of Mycobacterium tuberculosis infection. Recently, the molecular composition of PPD was defined, with hundreds of mycobacterial protein representatives making up PPD. Which, if any, of these specific products drive the potency of PPD remains in question. In this study, two proteins (DnaK and GroEL2) previously identified as dominant proteins in PPD were tested for the capacity to induce delayed-type hypersensitivity (DTH) responses in H37Rv-infected or BCG-vaccinated guinea pigs. These two proteins were used in pull-down assays to identify interacting PPD products. Six proteins were identified as interacting partners with DnaK and GroEL2, i.e., Rv0009, Rv0475, Rv0569, Rv0685, Rv2626c, and Rv2632c. These six proteins were tested alone and in combination with DnaK and GroEL2 for the capacity to induce a DTH response in the guinea pig model. From these studies, two cocktails, DnaK/GroEL2/Rv0009 and DnaK/GroEL2/Rv0685, were found to induce DTH responses in H37Rv-infected or BCG-vaccinated guinea pigs that were indistinguishable from DTH responses driven by a PPD injection. The mechanism by which DTH responses were induced was elucidated by histologic examination, analysis of activated CD4(+)/CD8(+) T cells, and cytokine mRNA expression at the site of the DTH response. PPD and the protein cocktails tested induced strong DTH responses in H37Rv-infected guinea pigs. Ex vivo phenotyping of T cells at the DTH site indicated that this response is mediated by activated CD4(+) and CD8(+) T cells, with increases in gamma interferon and tumor necrosis factor alpha, but not interleukin-10, at the site of the DTH response. Our results demonstrate for the first time that the PPD response can be mimicked at the molecular level with defined protein cocktails. The use of this defined product will allow a more thorough understanding of the DTH response and may provide a platform for more rapid and sensitive second-generation skin test reagents for the diagnosis of M. tuberculosis infection.
Superconductivity at 93 K in a new mixed-phase Y-Ba-Cu-O compound system at ambient pressure (1987)

A stable and reproducible superconductivity transition between 80 and 93 K has been unambiguously observed both resistively and magnetically in a new Y-Ba-Cu-0 compound system at ambient pressure. An estimated upper critical field H, 2(0) between 80 and 180 T was obtained.
Interferon-gamma upregulates the susceptibility of human neuroblastoma cells to interleukin-2-activated natural killer cells. (1989)

The influence of interferon-gamma on the susceptibility of neuroblastoma cells in cell-mediated killing was investigated. Neuroblastoma cells were only weakly susceptible targets for peripheral mononuclear cells. However, enrichment of natural killer (NK) cells or activation of NK cells with interleukin-2 resulted in a considerable increase of neuroblastoma cell lysis. Pretreatment of neuroblastoma targets with interferon-gamma additionally increased the susceptibility to enriched NK cells as well as to interleukin-2-activated NK cells. The conjugate formation between enriched NK cells and the neuroblastoma targets was not affected by the pretreatment of the targets with interferon-gamma. Concomitantly, treatment of the neuroblastoma targets with interferon-gamma resulted in a strong induction of otherwise poorly expressed major histocompatibility complex (MHC) class I antigen expression. These results suggest that the increased expression of MHC class I antigens on target cells is not always correlated with decreased sensitivity for NK cells but can also be followed by an increased susceptibility for NK cells.
Inhibition of N-methyl-N-nitrosourea-induced mammary tumors in rats by the soybean isoflavones. (1997)

Soy-based diets, rich in the isoflavones genistein and daidzein, are thought to protect against breast and prostate cancer. We used the N-methyl-N-nitrosourea (MNU)-induced mammary carcinogenesis animal model to test the effectiveness of these two isoflavones as chemopreventive agents. Each isoflavone was injected daily into 35-day-old rats for six months while we monitored the animals' body weight and mammary tumor appearance. Genistein was effective in reducing tumor multiplicity, but it reduced tumor incidence only marginally. Daidzein was less effective in reducing both tumor incidence and multiplicity. To investigate genistein's mechanism of action, we determined the topoisomerase II (topo II) activity and detected the phosphotyrosine-containing peptides in the extracts of mammary tissues isolated from control and isoflavone-treated animals. Mammary tumors contained over 60-fold higher topo II enzymatic activity than the mammary glands. Similarly, more tyrosine phosphopeptides were detectable in mammary tumors than in mammary glands. Tissue samples from genistein treated animals contained similar topo II and protein tyrosine kinase (PTK) activities as the control group. These data suggest that mammary tumorigenesis is accompanied by an extensive increase in topo II and PTK activities. The mechanism of chemoprevention by genistein, however, is independent of topo II or PTK inhibition.
Learning basketball dribbling skills using trajectory optimization and deep reinforcement learning (2018)

Basketball is one of the world's most popular sports because of the agility and speed demonstrated by the players. This agility and speed makes designing controllers to realize robust control of basketball skills a challenge for physics-based character animation. The highly dynamic behaviors and precise manipulation of the ball that occur in the game are difficult to reproduce for simulated players. In this paper, we present an approach for learning robust basketball dribbling controllers from motion capture data. Our system decouples a basketball controller into locomotion control and arm control components and learns each component separately. To achieve robust control of the ball, we develop an efficient pipeline based on trajectory optimization and deep reinforcement learning and learn non-linear arm control policies. We also present a technique for learning skills and the transition between skills simultaneously. Our system is capable of learning robust controllers for various basketball dribbling skills, such as dribbling between the legs and crossover moves. The resulting control graphs enable a simulated player to perform transitions between these skills and respond to user interaction.