gebhart/patrepeval huggingface dataset:
Encoding of Complex Valued Composite Functions onto Spatial Light Modulators in Real-Time (2000)

Abstract : Spatial light modulators (SLM) are used as real-time programmable diffractive optics for potential applications to multi-object laser designation of moving objects. For real-time situations in which prior knowledge is unavailable, fast on-line design algorithms are required. The time requirements rule out many iterative design methods currently used for fixed pattern diffractive optics. Instead, encoding methods that map desired complex values onto the available modulation values provide the fastest realizations. As time permits, designs improved through limited iteration can be mapped to the SLM. Such a system, built around pseudorandom encoding (PRE) and its extensions was developed and experimentally demonstrated during the study. The most significant extension to PRE is the development of a method of complex-valued encoding that can be accomplished with as few as three discrete modulation values, and which can be generalized to any modulator characteristic. The pairwise blending of PRE with three other encoding algorithms (minimum distance encoding-MDE, modified minimum distance encoding-mMDE, error diffusion-ED) provides one or two parameters that can be adjusted quickly to produce better performance than either algorithm produces individually. The new design methods were experimentally demonstrated together with demonstrations of real-time design and continuous scanning of multiple spots on arbitrary and independent trajectories.
Characterization of a<i>Borrelia burgdorferi</i>VlsE Invariable Region Useful in Canine Lyme Disease Serodiagnosis by Enzyme-Linked Immunosorbent Assay (2000)

Sera collected from dogs experimentally infected with Borrelia burgdorferi by tick inoculation were analyzed for an antibody response to each of the six invariable regions (IRs; i.e., IR(1) to IR(6)) of VlsE, the variable surface antigen of B. burgdorferi. Six synthetic peptides (C(1) to C(6)), which reproduced the six IR sequences were used as peptide-based, enzyme-linked immunosorbent assay (ELISA) antigens. Two IRs, IR(2) and IR(6), were found to be immunodominant. Studies with serially collected serum samples from experimentally infected dogs revealed that the antibody response to IR(6) appears earlier and is stronger than that to IR(2). Thus, the IR(6) sequence alone appeared to be sufficient for serodiagnosis. When C(6) alone was used as antigen, the peptide-based ELISA was positive in 7 of 23 dogs (30%) as early as 3 weeks postinfection. All dogs (n = 33) became strongly positive 1 or 2 weeks later, and this response persisted for the entire study, which lasted for 69 weeks. Of 55 sera submitted by veterinarians from dogs suspected of having Lyme disease, 19 were also positive by the C(6) ELISA, compared to 20 positives detected by immunoblot analysis using cultured B. burgdorferi lysates as antigen. The sensitivity of using C(2) and C(6) together for detecting specific antibody in both experimentally infected and clinically diagnosed dogs was not better than sensitivity with C(6) alone, confirming that C(6) suffices as a diagnostic probe. Moreover, the C(6) ELISA yielded 100% specificity with serum samples collected from 70 healthy dogs, 14 dogs with infections other than B. burgdorferi, and 15 animals vaccinated with either outer surface protein A, whole-spirochete vaccines, or the common puppy-vaccines. Therefore, this C(6) ELISA was both sensitive and specific for the serodiagnosis of canine Lyme disease and could be used with vaccinated dogs.
Solvothermal recovery of carbon fibers from thermoset polymer-based carbon fiber reinforced polymers (2015)

Clean, undamaged carbon fibers were easily separated from thermoset epoxy-based carbon fiber reinforced polymers through a two-step solvothermal method by using propanol or benzyl alcohol as solvents. The recovered carbon fibers were characterized by thermal gravity analysis, Fourier transform infrared spectroscopy, scanning electron microscopy, and mechanical tensile strength tests together with the digital photos. Results show that solvothermal temperature and duration, as well as pretreatment in dichloromethane play important roles in recovering carbon fiber. In addition, the tensile strength of the recovered carbon fibers remains approximately 94.5–98% of virgin carbon fibers.
1,2-Dihydropyrido[3,4-b]pyrazines: structure-activity relationships (1983)

Certain derivatives containing the 1,2-dihydropyrido[3,4-b]pyrazine (1-deaza-7,8-dihydropteridine) ring system are active against experimental neoplasms in mice. The mechanism of action of these agents has been attributed to the accumulation of cells at mitosis. Identification of the structural features that are necessary for activity was accomplished by evaluation of modified 1-deazapteridines and ring and ring-opened analogues. Relative to ethyl 4-amino-1-deaza-7,8-dihydro-6-[(N-methylanilino)methyl]pteridine-2-carbamate (11) and the corresponding 6-phenyl compound (12), no antitumor activity was observed with 7,8-dihydropteridines, 3-deaza-7,8-dihydropteridines, and the corresponding heteroaromatic compounds. Also, activity was diminished or destroyed when 1-deaza-7,8-dihydropteridines were oxidized to 1-deazapteridines or reduced to 1-deaza-5,6,7,8-tetrahydropteridines. In addition, replacement of the 4-amino group with other substituents destroyed activity. The presence of a 6-substituent containing an aryl group appeared to be necessary for activity, which was increased when a methyl group was substituted at the 7-position.
Electrical Detection, Identification, and Quantification of Exosomes (2018)

Exosomes are intercellular communication vehicles containing cell-specific molecules that can be quantified using different biochemical or biophysical techniques. This paper explores the use of capacitance-voltage electrical measurements for the label-free detection, identification, and quantifications of exosomes. With the application of voltage, an interface effective layer is formed because of the interaction between the exosome surface and its surrounding media. The exosomes store electrical energy when electrically polarized, thus enabling its electrical detection. A specific electrical capacitance-voltage profile is attributed to the precise nature of the respective exosomes, which helps in both identification and quantification. The exosome count is estimated by calculating the impurities inside a defined volume by observing the changes in electrical parameters extracted from the capacitance-voltage measurements. This technique could be applied to count suspended silica and liposomes nanoparticles as well. This approach was found to be faster and less expensive than other existing techniques.
Biochemical studies on capped RNA primers identify a class of oligonucleotide inhibitors of the influenza virus RNA polymerase. (1994)

A synthetic 67-nt RNA substrate, containing a 32P-labeled cap-1 structure (m7G32pppGm) was specifically cleaved by the influenza virus RNA polymerase (EC 2.7.7.48) to yield a single capped 11-nt fragment capable of directly priming transcription. An analysis of systematic truncations of this RNA substrate demonstrated that an additional nucleotide beyond this cleavage site was required for cleavage. The minimal RNA chain length required for priming activity was found to be 9 nt, while in contrast an RNA chain length of at least 4 nt was required for efficient binding to the viral polymerase. On the basis of these chain length requirements we show that a pool of capped oligonucleotides too short to prime transcription, but long enough to bind with high affinity to the viral polymerase, are potent inhibitors of cap-dependent transcription in vitro.
One-Pot Synthesis of 1,4,7,10,13,16,21,24-Octaazabicyclo[8.8.8]hexacosane - The Peraza Analogue of [2.2.2]Cryptand (2006)

The peraza analogue of polyether cryptand [2.2.2], 1,4,7,10,13,16,21,24-octaazabicyclo[8.8.8]hexacosane, has been synthesized in 70% yield via a two-step one-pot procedure by the condensation of tris(2-aminoethyl)amine (tren) with glyoxal in isopropanol at -78 °C followed by reduction of the intermediate with Na/liquid NH3. This preparation is significantly faster, simpler, and higher yielding than the previously reported two-step procedure, with its lengthy isolation process and 45% overall yield.
Stable electro-optic frequency comb generation using an ultrahigh finesse etalon filtered optoelectronic oscillator (2018)

In this work we investigate the overall stability of tunable, broadband electro-optic frequency combs created in an optoelectronic oscillator filtered with an ultra-high finesse Fabry-Perot etalon. Fractional frequency stability measurements show Allan deviations as low as 3E-13 for the comb central frequency of 193THz, and as low as 5E-10 on the 10.5GHz repetition frequency. At timescales of τ = 0.1s, the total frequency fluctuation of the outermost comb lines is calculated to be on the order of 388Hz. Individual comb line amplitude stability is also investigated, and the average amplitude fluctuation amongst all comb lines within 10dB amplitude deviation is measured to be ± 0.22dB standard deviation.
Filamentous Bacteriophage Produced by Pseudomonas aeruginosa Alters the Inflammatory Response and Promotes Noninvasive Infection<i>In Vivo</i> (2016)

Pseudomonas aeruginosa is an important opportunistic human pathogen that lives in biofilm-like cell aggregates at sites of chronic infection, such as those that occur in the lungs of patients with cystic fibrosis and nonhealing ulcers. During growth in a biofilm, P. aeruginosa dramatically increases the production of filamentous Pf bacteriophage (Pf phage). Previous work indicated that when in vivo Pf phage production was inhibited, P. aeruginosa was less virulent. However, it is not clear how the production of abundant quantities of Pf phage similar to those produced by biofilms under in vitro conditions affects pathogenesis. Here, using a murine pneumonia model, we show that the production of biofilm-relevant amounts of Pf phage prevents the dissemination of P. aeruginosa from the lung. Furthermore, filamentous phage promoted bacterial adhesion to mucin and inhibited bacterial invasion of airway epithelial cultures, suggesting that Pf phage traps P. aeruginosa within the lung. The in vivo production of Pf phage was also associated with reduced lung injury, reduced neutrophil recruitment, and lower cytokine levels. Additionally, when producing Pf phage, P. aeruginosa was less prone to phagocytosis by macrophages than bacteria not producing Pf phage. Collectively, these data suggest that filamentous Pf phage alters the progression of the inflammatory response and promotes phenotypes typically associated with chronic infection.
Design and evaluation of quantitative MRI phantoms to mimic the simultaneous presence of fat, iron, and fibrosis in the liver (2020)

Novel quantitative MRI phantoms that mimic the simultaneous presence of fat, iron, and fibrosis in the liver were successfully developed and validated.
Preparing rare earth-silicon-iron-aluminum alloys (1980)

As part of its mission to assure the maximum recovery and use of the Nation's mineral resources, the Bureau of Mines, investigated an improved procedure for producing rare earth-silicon alloys. For example, a charge consisting of 681 grams of mixed rare-earth oxides, 309 grams of ferrosilicon (75 wt-pct Si), and 182 grams of aluminum metal along with a flux consisting of 681 grams of CaO and 45 grams of MgO was reacted at 1500/sup 0/C in an induction furnace. Good slag-metal separation was achieved. The alloy product contained, in weight-percent, 53 RE, 28 Si, 11 Fe, and 4 Al with a rare earth recovery of 80 pct. In current industrial practice rare earth recoveries are usually about 60 pct in alloy products that contain approximately 30 wt-pct each of rare earths and silicon. Metallurgical evaluations showed the alloys prepared in this investigation to be as effective in controlling the detrimental effect of sulfur in steel and cast iron as the commercial rare earth-silicon-iron alloys presently used in the steel industry.
Network Aware Reliability Analysis for Distributed Storage Systems (2016)

It is hard to measure the reliability of a large distributed storage system, since it is influenced by low probability failure events that occur over time. Nevertheless, it is critical to be able to predict reliability in order to plan, deploy and operate the system. Existing approaches suffer from unrealistic assumptions regarding network bandwidth. This paper introduces a new framework that combines simulation and an analytic model to estimate durability for large distributed cloud storage systems. Our approach is the first that takes into account network bandwidth with a focus on the cumulative effect of simultaneous failures on repair time. Using our framework we evaluate the trade-offs between durability, network and storage costs for the OpenStack Swift object store, comparing various system configurations and resiliency schemes, including replication and erasure coding. In particular, we show that when accounting for the cumulative effect of simultaneous failures, the probability of data loss estimates can vary by two to four orders of magnitude.
Structural plasticity of a transmembrane peptide allows self-assembly into biologically active nanoparticles (2011)

Significant efforts have been devoted to the development of nanoparticular delivering systems targeting tumors. However, clinical application of nanoparticles is hampered by insufficient size homogeneity, difficulties in reproducible synthesis and manufacturing, frequent high uptake in the liver, systemic toxicity of the carriers (particularly for inorganic nanoparticles), and insufficient selectivity for tumor cells. We have found that properly modified synthetic analogs of transmembrane domains of membrane proteins can self-assemble into remarkably uniform spherical nanoparticles with innate biological activity. Self-assembly is driven by a structural transition of the peptide that adopts predominantly a beta-hairpin conformation in aqueous solutions, but folds into an alpha-helix upon spontaneous fusion of the nanoparticles with cell membrane. A 24-amino acid peptide corresponding to the second transmembrane helix of the CXCR4 forms self-assembled particles that inhibit CXCR4 function in vitro and hamper CXCR4-dependent tumor metastasis in vivo. Furthermore, such nanoparticles can encapsulate hydrophobic drugs, thus providing a delivery system with the potential for dual biological activity.
Collaborative Industrial Automation (2008)

This chapter summarizes our latest results concerning the development and the industrial application of the emerging “collaborative industrial automation” technology and its powerful meaning for facilitating the integration of a dynamic reconfigurable shop floor into a virtual factory. It argues, in this respect, that having a conglomerate of distributed, autonomous, intelligent, fault-tolerant, and reconfigurable production units, which operate as a set of cooperating entities, is one promising platform to achieve both local and global manufacturing objectives. Furthermore, the authors hope that understanding the underlying scientific and technological background through the development and industrial application of the collaborative automation paradigm will not only inform the academic, research, and industrial world of an emerging control and automation paradigm, but also assist in the understanding of a new vision of the manufacturing system of the 21st century [a mix of collaborative units, i.e., people, software systems, processes, and equipment (hardware), integrated into a virtual factory].
Functional Activity of Anti-Neisserial Surface Protein A Monoclonal Antibodies against Strains of<i>Neisseria meningitidis</i>Serogroup B (2001)

Neisserial surface protein A (NspA) is currently being investigated with humans as a candidate vaccine for the prevention of meningococcal disease. Although NspA is highly conserved, the ability of anti-NspA antibodies to bind to or elicit complement-mediated bactericidal activity against diverse Neisseria meningitidis serogroup B strains is controversial. To evaluate strain differences in NspA surface accessibility and susceptibility to bactericidal activity, we prepared murine immunoglobulin G2a anti-NspA monoclonal antibodies (MAbs) and evaluated their functional activity against 10 genetically diverse N. meningitidis serogroup B strains. By colony Western blot, all 10 strains expressed NspA as detected by one or more MAbs. By flow cytometry, two MAbs were found to bind to the bacterial surface of 6 of the 10 strains. In addition, two strains showed variable NspA surface accessibility for the MAbs despite being uniformly positive for NspA expression by colony Western blotting. Only 4 of the 10 strains were susceptible to anti-NspA complement-mediated bacteriolysis. Passively administered MAb protected infant rats from developing bacteremia after challenge with N. meningitidis serogroup B strain 8047 (surface binding positive, susceptible to anti-NspA bacteriolysis), was poorly protective against strain BZ232 (surface binding variable, resistant to bacteriolysis), and did not protect against strain M986 (surface binding negative, resistant to bacteriolysis). Finally, NspA does not appear to be critical for causing bacteremia, as an NspA knockout from strain 8047 was highly virulent in infant rats. Taken together, these findings suggest that an NspA-based vaccine will need to incorporate additional antigens to elicit broad protection against N. meningitidis serogroup B.
Use of Phenylacetyl Disulfide (PADS) in the Synthesis of Oligodeoxyribonucleotide Phosphorothioates (1999)

Abstract Oligodeoxyribonucleotide phosphorothioates, where one of the nonbridging oxygen of the internucleotide phosphate is formally replaced by a sulfur atom, are the first class to undergo human clinical trials. Ongoing phosphorothioate clinical trials against several disease targets has necessitated manufacture of very large quantities of oligonucleotide active pharmaceutical ingredient (API). Clinical trial and future market demands have stimulated effort towards developing cost efficient large scale synthesis of these complex bio-molecules. This effort has culminated in the routine synthesis of 20-mer oligodeoxyribonucleotide phosphorothioates at 150 mmole scale using only 1.75-fold molar excess of amidites in less than 8 h total synthesis time.
Human natural killer cells: their origin, receptors and function (2002)

The term of "natural killer" (NK) cells was originally assigned on a merely functional basis to lymphoid cells capable of lysing certain tumors in the absence of prior stimulation. However, both their origin and the molecular mechanism(s) involved in their function remained a mystery for many years 1. Regarding their origin, clear evidence has now been provided both in mouse and in man that NK and T cells may derive from a common precursor 2-5. Thus, mature NK cells can be obtained in vitro from CD34(+) cells isolated from umbilical cord blood, bone marrow (BM) and even human thymus 6 when cultured in the presence of appropriate feeder cells or IL-15. The molecular mechanism allowing NK cells to discriminate between normal and tumor cells, predicted by the "missing self hypothesis" 7, has been clarified only in recent years. Thus, NK cells recognize MHC class I molecules through surface receptors delivering signals that inhibit, rather than activate, NK cells. As a consequence, NK cells lyse target cells that have lost (or express insufficient amounts of) MHC class I molecules, as frequently occurs in tumors and in cells infected by certain viruses.
Using Topology for Spatial Reasoning (1997)

Several formalisms have been proposed for qualitative reasoning about regions and their topological relations in space. These formalisms, based on pairwise relations, do not allow sufficiently powerful inferences to be used for spatial reasoning tasks such as planning a collision-free path. In this paper, I show how considering relations between region triples, much more powerful reasoning techniques become possible. I show in particular that in two dimensions, purely topological reasoning is sufficient to compute a minimal place graph which represents all minimal and maximal region combinations, as well as all minimal paths between them. I illustrate how this could be applied to motion planning, showing that in spite of its qualitative nature, the formalism is powerful enough to solve problems of pratical interest. 1
Path specialization (2008)

As garbage collected languages become widely used, the quest for reducing collection overheads becomes essential. In this paper, we propose a compiler optimization called path specialization that shrinks the cost of memory barriers for a wide variety of garbage collectors including concurrent, incremental, and real-time collectors. Path specialization provides a non-trivial decrease in write-barrier overheads and a drastic reduction of read-barrier overheads. It is effective when used with collectors that go through various phases each employing a different barrier behavior, and is most effective for collectors that have an idle phase, in which no barrier activity is required. We have implemented path specialization in the Bartok compiler and runtime for C# and tested it with state-of-the-art concurrent and real-time collectors, demonstrating its efficacy.
Centralized Management of HVAC Energy in Large Multi-AHU Zones (2015)

HVAC control strategies that exploit temporal variations in zone occupancy have been well studied. However, at a given time, occupancy can also vary spatially within a single large zone with no internal wall partitions, that is served by multiple AHUs. We complement prior work by studying how spatial variations in a large zone can be leveraged to save energy and improve occupant comfort. Specifically, we propose a novel strategy for centralized reactive control of all the AHUs serving a large zone, MAZIC (Multi-AHU Zone Intelligent Control). To decide control outputs, we use a thermal model to capture the mixing of heat loads across different regions of the large zone served by different AHUs. We study MAZIC's performance in terms of energy consumption and comfort using real-world occupancy data. When the spatial skew in occupancy is high, MAZIC reduces energy consumption by 11% over individual PID controllers running at each AHU, while maintaining similar comfort levels. Sensing temperature and occupancy at finer spatial resolution helps both MAZIC and PID controllers to save more energy when the occupancy is skewed. Finer spatial sensing does not add much value when the occupancy is not so skewed. We also find that augmenting MAZIC with a MPC (Model Predictive Control) approach yields insignificant improvement (< 3%) during normal occupancy. With ON-OFF occupancy patterns, MPC improves energy savings by up to 6% over reactive MAZIC.