gebhart/patrepeval huggingface dataset:
Proton-Block Strategy for the Synthesis of Oligodeoxynucleotides without Base Protection, Capping Reaction, and P−N Bond Cleavage Reaction (2003)

A new N-unprotected phosphoramidite method called the "proton-block" approach was developed for the chemical synthesis of oligodeoxynucleotides based on the hitherto simplest and rational principle of acid-base reactions. This concept involves protection of the nucleobases of deoxycytidine and deoxyadenosine with "protons" to convert them to unreactive protonated bases during condensation by use of promoters having pK(a) values lower than 2.8. This strategy was applied to the synthesis of d[CpT] and d[ApT] to check the side reactions associated with the base residues. In this "proton-block" method, 5-nitrobenzimidazolium triflate (NBT) was found to be the best promoter, and THF was superior to CH(3)CN as the solvent so that the concomitant detritylation due to the inherent acidity of the promoter could be greatly suppressed. Application of this strategy to the solid-phase synthesis gave d[CpT], d[ApT], d[ApA], d[CpC], and d[GpT] as almost single peaks in HPLC analysis. Similarly, d[ApApApT] and d[CpCpCpT] were successfully synthesized without significant side reactions. Finally, d[CpCpCpCpCpCpT] and d[ApApApApApApT] were obtained as the main products. In the case of a longer oligomer, d[CpApGpTpCpApGpTpCpApGpT], a mixed solvent of CH(3)CN-N-methylpyrrolidone (1:1, v/v) was superior to THF so that the desired oligodeoxynucleotide could be isolated in a satisfactory yield. These results suggest that DNA synthesis can be carried out simply by using the protonated bases at the oligomer level not only without base protection but also without the capping reaction and the posttreatment of branched chains with MeOH-benzimidazolium triflate that previously was requisite. It is concluded that most of the reactions and solvent effects involved in this strategy can be explained in terms of simple acid-base reactions. Some problems associated with the previous posttreatment are also discussed with our own results.
A Classification Paradigm for Distributed Vertically Partitioned Data (2004)

In general, pattern classification algorithms assume that all the features are available during the construction of a classifier and its subsequent use. In many practical situations, data are recorded in different servers that are geographically apart, and each server observes features of local interest. The underlying infrastructure and other logistics (such as access control) in many cases do not permit continual synchronization. Each server thus has a partial view of the data in the sense that feature subsets (not necessarily disjoint) are available at each server. In this article, we present a classification algorithm for this distributed vertically partitioned data. We assume that local classifiers can be constructed based on the local partial views of the data available at each server. These local classifiers can be any one of the many standard classifiers (e.g., neural networks, decision tree, k nearest neighbor). Often these local classifiers are constructed to support decision making at each location, and our focus is not on these individual local classifiers. Rather, our focus is constructing a classifier that can use these local classifiers to achieve an error rate that is as close as possible to that of a classifier having access to the entire feature set. We empirically demonstrate the efficacy of the proposed algorithm and also provide theoretical results quantifying the loss that results as compared to the situation where the entire feature set is available to any single classifier.
Bi-directionally functional semiconductor laser (2003)

A quantum-cascade laser operating in both positive and negative bias-polarity is reported. Device properties in the two bias directions can be designed different or equal. We demonstrate a new laser with an emission wavelength dependent on bias-polarity.
Effects of SLM pixel dead zone on correlator performance (1988)

Spatial light modulators (SLMs) are generally pixeled structures with less than the full area of the pixel responding to the input signal. This inactive area, or dead zone, leads to distortions in optical correlator performance due to increased noise when the correlator uses SLMs in the input and filter planes. The problem is studied through computer simulation and by a closed form mathematical analysis. Three different correlation filter types are analyzed. Results are presented in the form of output SNR as a function of percent dead zone area.
Development of elevated temperature P/M aluminum alloy by rapid solidification processing. (1987)

In this paper Al-Fe system alloys were mainly investigated from the viewpoints of solid solubility, diffusion coefficient, temperature of liquidus and material cost. The mechanical properties at the room and elevated temperature were evaluated in the various Al-Fe system alloys. Al-8%Fe-2%V-2%Mo-1%Zr alloy was found to be superior to the conventional 2618 alloy in the room and elevated temperature-tensile strength, in the thermal stability of hardness, and in the fatigue and creep properties. The excellent properties mentioned above were due to the existense of Al-Fe-V-Mo, Al-Fe and Al-Zr system dispersoids.
Digital Optical Computing: Possibilities And Pitfalls (1986)

The potential development of digital optical computing systems is discussed. Previous approaches are reviewed and their shortcomings with respect to digital electronic circuitry are analyzed. Fundamental arguments are presented which indicate the potential advantages of optical logic over electronic logic. A generic classification of digital optical computing is presented.
Dual Capillary Electrophoresis Devices with Electrochemical Detection on a Single Platform (2005)

The purpose of this paper is to demonstrate the feasibility of developing a single lab-on-a-chip (LOC) platform capable of performing dual, simultaneous separation and detection of multiple analytes. Computational modeling was performed to determine optimum device geometry and performance. The soda-lime glass-based device was fabricated using traditional microtechnology processes, including UV photolithography, buffered oxide etch (BOE), electrode deposition and compression thermal bonding. The device was characterized with a mixture of dopamine (2mM) and catechol (2mM) in a phosphate buffer (20mM, 6.5 pH). Modeling results yielded migration velocities of 0.6 mm/s and 0.42 mm/s for dopamine (electrokinetic (EK) mobility=60,000 /spl mu/m/sup 2//V/spl middot/s) and catechol (EK mobility=42,000 /spl mu/m/sup 2//V/spl middot/s), respectively. Experimental results obtained from microchips exhibiting the same EK mobilities demonstrated identical electropherograms in both detection channels with migration velocities of 0.58 mm/s for dopamine and 0.41 mm/s for catechol.
Genetic Markers of Toxicity From Capecitabine and Other Fluorouracil-Based Regimens: Investigation in the QUASAR2 Study, Systematic Review, and Meta-Analysis (2014)

A panel of genetic biomarkers for capecitabine monotherapy toxicity would currently comprise only the four DPYD and TYMS variants above. We estimate this test could provide 26% sensitivity, 86% specificity, and 49% positive predictive value-better than most available commercial kits, but suboptimal for clinical use. The test panel might be extended to include additional, rare DPYD variants functionally equivalent to *2A and 2846A, though insufficient evidence supports its use in bolus, infusional, or combination FU. There remains a need to identify further markers of FU toxicity for all regimens.
P‐90: Large Scale Arrays of Microcavity Plasma Devices Based on Encapsulated Al/Al <sub>2</sub> O <sub>3</sub> Electrodes: Device Characteristics as a Plasma Display Pixel and Low Cost Wet Chemical Fabrication Processing (2007)

Abstract Addressable, large scale arrays of microcavity plasma devices have been fabricated by wet chemical processes. Dielectric encapsulated aluminum microcavity electrodes having cavities with a diameter of 100–200 μm are formed by wet electrochemical process suitable for low cost manufacturing. This presentation reports device structure and cell designs for high pressure Xe microplasmas.
A Potent, Neutralizing Human Monoclonal Antibody against a Unique Epitope Overlapping the CD4-Binding Site of HIV-1 gp120 That Is Broadly Conserved across North American and African Virus Isolates (1993)

A human monoclonal antibody (HuMAb), 5145A, against HIV-1 gp120 was isolated from an asymptomatic, seropositive hemophiliac. The epitope of this HuMAb was destroyed by reduction of gp120 disulfide bonds, but not by removal of N-linked carbohydrates. This epitope overlaps the CD4-binding site of gp120, because binding of 5145A to gp120 is inhibited by soluble CD4 and by 1125H, a previously described HuMAb directed toward the CD4-binding site. However, the 5145A epitope differs from those of 1125H and other anti-CD4-binding site HuMAbs previously described, as documented by the viral strain specificity of 5145A and its reactivity with a panel of gp120 mutants. Specifically, 5145A reacted with 14 of 15 HIV-1 isolates tested, including 9 isolates from the Central African Republic, 6 of which were not recognized by 1125H. Partial epitope mapping of 5145A, using a series of gp120 mutants, demonstrated its lack of sensitivity to mutations in residues 257 and 427, contrasting with a marked sensitivity to mutations in residues 368 and 370. This pattern of reactivity distinguishes its epitope from that of any HuMAb against the CD4-binding site region described to date. In addition, 5145A exhibited potent and essentially equivalent neutralization of the MN, SF-2, IIIB, and RF strains and possessed significant neutralizing activity against three of three African strains tested. Finally, 5145A synergistically neutralized the MN and SF-2 strains of HIV-1 when combined with 4117C, a HuMAb against the V3 loop. The broad strain specificity and potent neutralizing activity of 5145A, together with its ability to synergize with an anti-V3 loop HuMAb in neutralizing HIV-1, indicate that 5145A has excellent potential as a passive immunotherapeutic agent against HIV-1.
Immunogenicity of Influenza Virus Vaccine Is Increased by Anti-Gal-Mediated Targeting to Antigen-Presenting Cells (2007)

This study describes a method for increasing the immunogenicity of influenza virus vaccines by exploiting the natural anti-Gal antibody to effectively target vaccines to antigen-presenting cells (APC). This method is based on enzymatic engineering of carbohydrate chains on virus envelope hemagglutinin to carry the alpha-Gal epitope (Gal alpha 1-3Gal beta 1-4GlcNAc-R). This epitope interacts with anti-Gal, the most abundant antibody in humans (1% of immunoglobulins). Influenza virus vaccine expressing alpha-Gal epitopes is opsonized in situ by anti-Gal immunoglobulin G. The Fc portion of opsonizing anti-Gal interacts with Fc gamma receptors on APC and induces effective uptake of the vaccine virus by APC. APC internalizes the opsonized virus to transport it to draining lymph nodes for stimulation of influenza virus-specific T cells, thereby eliciting a protective immune response. The efficacy of such an influenza vaccine was demonstrated in alpha 1,3galactosyltransferase (alpha 1,3GT) knockout mice, which produce anti-Gal, using the influenza virus strain A/Puerto Rico/8/34-H1N1 (PR8). Synthesis of alpha-Gal epitopes on carbohydrate chains of PR8 virus (PR8(alpha gal)) was catalyzed by recombinant alpha1,3GT, the glycosylation enzyme that synthesizes alpha-Gal epitopes in cells of nonprimate mammals. Mice immunized with PR8(alpha gal) displayed much higher numbers of PR8-specific CD8(+) and CD4(+) T cells (determined by intracellular cytokine staining and enzyme-linked immunospot assay) and produced anti-PR8 antibodies with much higher titers than mice immunized with PR8 lacking alpha-Gal epitopes. Mice immunized with PR8(alpha gal) also displayed a much higher level of protection than PR8 immunized mice after being challenged with lethal doses of live PR8 virus. We suggest that a similar method for increasing immunogenicity may be applicable to avian influenza vaccines.
Facile processing of clays into organically‐modified aerogels (2005)

Abstract A facile process for the conversion of clay powders to organically modified clay aerogels (OMCAs) is reported. The resultant clay aerogels are of potential interest for a variety of applications, by themselves, or as a component in composite materials. Freeze‐drying aqueous clay‐surfactant solutions isolates these highly organized materials. Robust OMCAs are formed from clay‐surfactant compositions that initially produce stable surfactant modified clay‐water suspensions. Characterization of the OMCA by FTIR, WAXD, and TGA confirms the retention of surfactant after freeze‐drying, while SEM and porosimetry data show a structural reorganization of clay sheet bundles. © 2005 American Institute of Chemical Engineers AIChE J, 2006
Microdeletions of chromosomal region 22q11 in patients with congenital conotruncal cardiac defects. (1993)

Congenital conotruncal cardiac defects occur with increased frequency in patients with DiGeorge syndrome (DGS). Previous studies have shown that the majority of patients with DGS or velocardiofacial syndrome (VCFS) have a microdeletion within chromosomal region 22q11. We hypothesised that patients with conotruncal defects who were not diagnosed with DGS or VCFS would also have 22q11 deletions. Seventeen non-syndromic patients with one of three types of conotruncal defects most commonly seen in DGS or VCFS were evaluated for a 22q11 deletion. DNA probes from within the DiGeorge critical region were used. Heterozygosity at a locus was assessed using restriction fragment length polymorphisms. Copy number was determined by dosage analysis using Southern blot analysis of fluorescence in situ hybridisation of metaphase spreads. Five of 17 patients were shown to have a 22q11 deletion when evaluated by dosage analysis. This study shows a genetic contribution to the development of some conotruncal cardiac malformations and alters knowledge regarding the risk of heritability of these defects in certain cases.
Islet Amyloid Polypeptide and Insulin Secretion From Isolated Perfused Pancreas of Fed, Fasted, Glucose-Treated, and Dexamethasone-Treated Rats (1991)

Rats from four experimental treatment groups, including fed controls, 24- to 30-h fasted, dexamethasone-treated, and intraperitoneal glucose-treated, were used to assess the effects of these treatments on the immunohistochemically detectable islet amyloid polypeptide (IAPP) content in the pancreatic islets. Isolated perfused pancreases from additional animals in these groups were used to assess insulin and IAPP secretion and relative amounts of these hormones secreted into the perfusate under low-glucose (2.75 mM) and high-glucose (16.7 mM) conditions. Insulin and IAPP concentrations in the perfusate were measured by radioimmunoassays. Titration of immunohistochemical staining revealed the highest levels of IAPP in the dexamethasone- and glucose-treated groups, followed by the fed controls; the least amount was observed in the fasted group. In the perfusion experiments, the dexamethasone-treated group had significantly higher IAPP secretion than did all of the other groups under stimulation with 16.7 mM glucose. In addition, both dexamethasone treatment and glucose treatment increased the relative amount of IAPP to insulin secretion during 16.7 mM glucose stimulation in comparison with fed controls and fasted groups. Fasting tended to have the opposite effect and significantly decreased the relative amount of IAPP to insulin secreted under stimulation with 16.7 mM glucose. In all groups, IAPP and insulin secretion were generally parallel, which is consistent with their colocalization in the beta-cell secretory vesicle and co-release after glucose stimulation. However, significant differences in the insulin-IAPP ratios between experimental groups is consistent with the hypothesis that production of IAPP and insulin are regulated differently in the beta-cell.(ABSTRACT TRUNCATED AT 250 WORDS)
Thermochemistry and Molecular Structure of a Remarkable Agostic Interaction in a Heterobifunctional Ruthenium−Boron Complex (2010)

A boron-pendant ruthenium species forms a unique agostic methyl bridge between the boron and ruthenium atoms in the presence of a ligating solvent, acetonitrile. NMR inversion-recovery experiments enabled the activation and equilibrium thermochemistry for formation of the agostic bridge to be measured. The mechanism for bridge formation involves displacement of an acetonitrile ligand; thus, this is a rare example of a case where an agostic C-H ligand competitively displaces another tightly binding ligand from a coordinatively saturated complex. Characterization of this complex gives unique insights into the development of C-H activation catalysis based on this ligand-metal bifunctional motif.
EFFICIENT DYNAMIC LOOKUP FOR BURSTY ACCESS PATTERNS (2004)

Internet (IP) packet forwarding is typically done by finding the longest prefix in a router table that matches the packet's destination address. Although significant effort has been devoted to the development of data structures for static and dynamic router-tables for random packet-access-patterns, considerably less effort has been expended in the development of such structures for bursty access-patterns (i.e., streams of packets in which destination addresses repeat frequently within localized windows of packets). In this paper, we first formulate a variant, ACRBT (alternative collection of red-black trees), of the CRBT (collection of red-black trees) data structure proposed earlier for dynamic router-tables. By replacing the red-black trees used in the ACRBT with splay trees, we obtain the CST (collection of splay trees) structure in which search, insert, and delete take O( log n) amortized time per operation, where n is the number of prefixes in the router table. By replacing the front end of the CST with biased skip lists, we obtain the BSLPT (biased skip lists with prefix trees) structure in which search, insert, and delete take O( log n) expected time. The CST and BSLPT structures are designed so as to perform much better when the access pattern is bursty than when it is not. Experimental results using real IPv4 routing databases and synthetically generated search sequences as well as trace sequences are presented. For extremely bursty access patterns, the CST structure is best. Otherwise, the ACRBT is recommended. Our experiments also indicate that a supernode implementation of the ACRBT usually has better search performance than does the traditional one-element-per-node implementation.
An Eighteen‐Membered Macrocyclic Ligand for Actinium‐225 Targeted Alpha Therapy (2017)

Abstract The 18‐membered macrocycle H 2 macropa was investigated for 225 Ac chelation in targeted alpha therapy (TAT). Radiolabeling studies showed that macropa, at submicromolar concentration, complexed all 225 Ac (26 kBq) in 5 min at RT. [ 225 Ac(macropa)] + remained intact over 7 to 8 days when challenged with either excess La 3+ ions or human serum, and did not accumulate in any organ after 5 h in healthy mice. A bifunctional analogue, macropa‐NCS, was conjugated to trastuzumab as well as to the prostate‐specific membrane antigen‐targeting compound RPS‐070. Both constructs rapidly radiolabeled 225 Ac in just minutes at RT, and macropa‐Tmab retained >99 % of its 225 Ac in human serum after 7 days. In LNCaP xenograft mice, 225 Ac‐macropa‐RPS‐070 was selectively targeted to tumors and did not release free 225 Ac over 96 h. These findings establish macropa to be a highly promising ligand for 225 Ac chelation that will facilitate the clinical development of 225 Ac TAT for the treatment of soft‐tissue metastases.
Learning 6-DOF Grasping Interaction via Deep Geometry-Aware 3D Representations (2018)

This paper focuses on the problem of learning 6- DOF grasping with a parallel jaw gripper in simulation. Our key idea is constraining and regularizing grasping interaction learning through 3D geometry prediction. We introduce a deep geometry-aware grasping network (DGGN) that decomposes the learning into two steps. First, we learn to build mental geometry-aware representation by reconstructing the scene (i.e., 3D occupancy grid) from RGBD input via generative 3D shape modeling. Second, we learn to predict grasping outcome with its internal geometry-aware representation. The learned outcome prediction model is used to sequentially propose grasping solutions via analysis-by-synthesis optimization. Our contributions are fourfold: (1) To best of our knowledge, we are presenting for the first time a method to learn a 6-DOF grasping net from RGBD input; (2) We build a grasping dataset from demonstrations in virtual reality with rich sensory and interaction annotations. This dataset includes 101 everyday objects spread across 7 categories, additionally, we propose a data augmentation strategy for effective learning; (3) We demonstrate that the learned geometry-aware representation leads to about 10% relative performance improvement over the baseline CNN on grasping objects from our dataset. (4) We further demonstrate that the model generalizes to novel viewpoints and object instances.
Characterization of electrical conductivity in a zeolitelike material (2009)

We present the electrical characterization of a zeolitelike oxo-vanadium arsenate framework. The experimentally obtained electronic and ionic conductivities and their interactions are discussed. Further, we investigate the potential use of electrically conducting zeolitelike materials in electrical energy storage applications, in light of the material’s structural and electronic characteristics.
Neuromorphic computing with multi-memristive synapses (2018)

Neuromorphic computing has emerged as a promising avenue towards building the next generation of intelligent computing systems. It has been proposed that memristive devices, which exhibit history-dependent conductivity modulation, could efficiently represent the synaptic weights in artificial neural networks. However, precise modulation of the device conductance over a wide dynamic range, necessary to maintain high network accuracy, is proving to be challenging. To address this, we present a multi-memristive synaptic architecture with an efficient global counter-based arbitration scheme. We focus on phase change memory devices, develop a comprehensive model and demonstrate via simulations the effectiveness of the concept for both spiking and non-spiking neural networks. Moreover, we present experimental results involving over a million phase change memory devices for unsupervised learning of temporal correlations using a spiking neural network. The work presents a significant step towards the realization of large-scale and energy-efficient neuromorphic computing systems.