gebhart/patrepeval huggingface dataset:
Efficient blind deconvolution of audio-frequency signal (2004)

A signal processing algorithm has been developed in which a filter function is extracted fromdegradeddata throughmathematical operations. The filter function can be used to restore much of the degraded content of the data through use of a deconvolution process. The operation can be performed without prior knowledge of the detection system, a technique known as blind deconvolution. The extraction process, designated Selfdeconvolving Data Reconstruction Algorithm (SeDDaRA), is applied here to audio-frequency signals showing significant qualitative improvement. Degradation arising from the process of electronic recording and reproduction is significantly reduced.
Comparative study of cerebrospinal fluid α‐synuclein seeding aggregation assays for diagnosis of Parkinson's disease (2019)

These α-synuclein seeding aggregation assays are reliable and reproducible for PD diagnosis. Assay parameters did not correlate with clinical parameters, including disease severity or duration. This assay is highly accurate for PD diagnosis and may impact clinical practice and clinical trials. © 2019 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Clustered Checkpointing and Partial Rollbacks for Reducing Conflict Costs in STMs (2010)

A Software Transactional Memory is a concurrency control mechanism that executes multiple concurrent, optimistic, lockfree, atomic transactions, thus alleviating many problems associated with conventional mutual exclusion primitives such as monitors and locks. With the advent of massive multi-cores, more transactions can be initiated concurrently, however resulting in an increase in the percentage of conflicting transactions. Each time a transaction conflicts, it imposes a significant cost on the system, originating from the need to abort and redo all the operations, including the costly shared memory read operations, thus making the overall system significantly heavy and impractical. We present an algorithm, Clustered Checkpointing and Partial Rollback (CCPR), for reducing the conflict costs of transactions in the face of increasing conflicts. The algorithm is based on intelligent checkpointing of transactions as they proceed, and, in case of conflict, rolling them back to a safe, consistent, intermediate checkpoint, thus reducing conflict costs. The intelligence of the algorithm lies in the fact that as conflicts decrease, the checkpointing costs go low, however, when conflicts increase, the checkpointing costs increase but are still pretty much less than the amount of savings obtained by the partial rollback of the conflicting transactions. We simulated several applications in the CCPR framework and found that it can result in as good as 17% reduction in the conflict costs originating from the need to redo all the shared memory read operations.
MICROX-an all-silicon technology for monolithic microwave integrated circuits (1993)

An improved silicon-on-insulator (SOI) approach offers devices and circuits operating to 10 GHz by providing formerly unattainable capabilities in bulk silicon: reduced junction-to-substrate capacitances in FETs and bipolar transistors, inherent electrical isolation between devices, and low-loss microstrip lines. The concept, called MICROX (patent pending), is based on the SIMOX process, but uses very-high-resistivity (typically>10000 Omega -cm) silicon substrates, MICROX NMOS transistors of effective gate length 0.25 mu m give a maximum frequency of operation, f/sub max/, of 32 GHz and f/sub T/ of 23.6 GHz in large-periphery (4 mu m*50 mu m) devices with no correction for the parasitic effects of the pads. The measured minimum noise figure is 1.5 dB at 2 GHz with associated gain of 17.5 dB, an improvement over previously reported values for silicon FETs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Use of Recombinant DNA Techniques to Study Tylosin Biosynthesis and Resistance in Streptomyces fradiae (1986)

A substantial amount of information on the biosynthesis of tylosin has been obtained over the past ten years. Physiological studies and experiments with tylosin-blocked (tyl) mutants have suggested the probable pathway by which tylactone is converted to tylosin. The development of recombinant DNA methodology for streptomycetes in general, and for Streptomyces fradiae in particular, has allowed us to apply gene cloning techniques in further studies of tylosin biosynthesis in S. fradiae. The macrocin O-methyltransferase (MOMT), which catalyzes the last step in tylosin biosynthesis, was purified, and the sequence of the 35 amino acids at its amino-terminus was determined. A synthetic 44 base oligonucleotide probe was constructed on the basis of the amino acid sequence. The probe was used to identify sequences containing the MOMT structural gene in bacteriophage and cosmid libraries of S. fradiae DNA. Complementation of tyl mutants with the cloned DNA sequences identified nine tyl biosynthetic genes (tylC, D, E, F, H, J, K, L, and M) in a 42 kb stretch of DNA. Genes complementing four mutant classes, tylA, B, G, and I were not found. A tylosin-resistance gene, tlrB, was located just left of the tyl gene cluster. Tylosin-sensitive mutants of S. fradiae, which were isolated from regenerated protoplasts and which have pleiotropic deficiencies in tylosin biosynthesis, contained deletions which included at least some of the identified tyl loci and one or both of two tylosin-resistance genes, tlrB and tlrC. Possible schemes for the functional organization of the tyl region of the S. fradiae genome are discussed.
A Simulated Annealing Accelerated Bayesian Optimization (SAABO) for Real-Time Deep Neural Network Model with Range Constraints (2018)

optimization issues in many fields involve finding optimal solutions over surfaces that are highly non-linear, discontinuous and lumpy. They also necessitate integration of domain-specific reduced form physics-based engineering models with data-driven optimization techniques. Real-time drilling modeling and optimization is used as a prototype for demonstrating the new algorithm but can be applied to several real-time systems. This paper provides a new real-time model with deep neural network (DNN) automated closed loop control drilling optimization using a new simulated annealing accelerated Bayesian optimization (SAABO) algorithm. This approach offers an improved and efficient methodology to arrive at the maximum for optimization surfaces that are highly non-linear and lumpy (i.e., might contain multiple local minima). This method was applied to predict rate of penetration (ROP) with automatic optimum parameter tuning of weight on bit (WOB) and rotations per minute (RPM) for drilling optimization along with range constraints. These range constraints are obtained from the engineering models produced from domain insight. Thus, the optimization integrates reduced form physics-based engineering models into its framework. As such, the new real-time ROP DNN model used for optimization is a hybrid engineering and data-driven model. The hybrid DNN model uses real-time data and the generated data from the engineering model. The generated data are needed to fill the void space in the surface not covered by the real-time measured data. The stochastic optimization algorithm SAABO is fast, as the exploration points needed for Bayesian optimization (BO) are obtained from the simulated annealing (SA)-based algorithm. SAABO uses the distribution of exploration points from SA to speed up the convergence and improve the accuracy of the BO algorithm to optimize the ROP with constraints. The methodology comprising real-time ROP model prediction and stochastic optimization is fast and efficient for the computation of the necessary optimum controllable parameters for drilling. The new hybrid modeling approach and the SAABO algorithm developed in this paper can be applied to any real-time modeling system with optimization and closed loop control.
Externally hazard-free implementations of asynchronous circuits (1995)

We present a new sum-of-product based asynchronous architecture, called the N-SHOT architecture, that operates correctly under internal hazardous responses and guarantees hazard-freeness at the observable non-input signals. We formally prove that within this architecture a very wide class of semi-modular state graphs with input choices (either distributive or non-distributive) that satisfy the complete state coding property always admit a correct implementation. As with synchronous circuits, we permit internal hazards in the combinational logic core, which means we can make use of conventional combinational logic minimization methods to produce the sum-of-product implementation. This represents a significant departure from most existing methods that require the combinational logic to be hazard-free and are mainly valid for distributive behaviors.
Epithelial attachment alters the outcome of <i>Helicobacter pylori</i> infection (1998)

Genetically defined in vivo models are needed to assess the importance of target cell attachment in bacterial pathogenesis. Gastric colonization by Helicobacter pylori in human populations is common and persistent, and has various outcomes including peptic ulcers and cancer. The impact of attachment on the course of infection was examined in transgenic mice expressing a human receptor for H. pylori in their gastric epithelium. Persistent infection by a clinical isolate occurred at comparable microbial densities in transgenic and nontransgenic littermates. However, microbial attachment in transgenic mice resulted in production of autoantibodies to Lewisx carbohydrate epitopes shared by bacteria and acid-secreting parietal cells, chronic gastritis, and parietal cell loss. This model should help identify bacterial and host genes that produce attachment-related pathology.
Polymerization-Crosslinking of N-Methylolacrylamide in Cotton Fabric (1978)

Several variations of polymerization-crosslinking of N-methylolacrylamide (NMA) in cotton were explored to clarify factors critical to achievement of resilience with superior retentions of strength and abrasion resistance in fabric. Per sulfate catalysis simultaneously initiated both polymerization and crosslinking reactions of NMA in cotton fabric; the results from dry-cure reactions fell in the conventional range of textile performance properties achieved by treatment of cotton fabric with agents such as dimethyloldihydroxyethyleneurea. Wet-cure reactions carried out in scaled bags at or above 100°C resulted in low resilience, high retentions of strength-abrasion resistance, and large increases in stiffness, the last attributed to fiber bonding in yarns. Wet-cure reactions conducted at or below 80°C caused little stiffness, and only in these cases was a subsequent catalyzed dry-cure reaction effective in raising resilience with good retentions of strength and abrasion resistance. Inclusion of alkali metal phosphates in the persulfate-initiated reaction of NMA with cotton in a pad-dry-cure caused retentions of abrasion resistance to be very substantially improved and retentions in breaking and tearing strengths to be significantly improved at durable-press appearance ratings of 4.5. These results are attributed to relatively sequential but rapid polymerization and crosslinking reactions, to reduction in formation of oxymethylene crosslinks, and possibly to reduced molccular degradation of the cellulose.
Electrochemical Capacitors Using Hydrous Ruthenium Oxide and Hydrogen Inserted Ruthenium Oxide (1998)

Electrochemical capacitors made with hydrous ruthenium oxide and hydrogen inserted hydrous ruthenium oxide electrode materials were investigated. The electrochemical behavior of in the potential range of −0.2 to 1.3 V vs. saturated calomel electrode (SCE) was characterized using a cyclic voltammetry technique. It was found that, electrochemically, amorphous electrodes behave quite differently from crystalline . The potentials of both the positive and the negative electrodes of the capacitors were monitored relative to SCE. For capacitors made with electrode material, gas evolution and an increase of cell resistance were observed in the first few charge/discharge cycles. This was due to the fact that the potentials of the starting materials were close to the oxidation limit of the potential window. Hydrogen inserted hydrous ruthenium oxide with potentials near the center of the potential window were prepared using both electrochemical and chemical methods. It was demonstrated that capacitors made of hydrogen inserted ruthenium oxide electrodes exhibited high efficiency, high energy, and high power through a cycle life over 60,000 times.
A Novel Glycosphingolipid Hydrolyzing Enzyme, Glycosphingolipid Ceramide Deacylase, Which Cleaves the Linkage between the Fatty Acid and Sphingosine Base in Glycosphingolipids (1988)

It has been demonstrated that the GM2 ganglioside cannot be cleaved by exo-beta-N-acetylhexosaminidases isolated from molds or bacterial sources. Here, a novel GM2 ganglioside-degrading enzyme was found in cells of Nocardia sp. This enzyme releases free fatty acids from the GM2 ganglioside. The chemical structure of the resultant lyso-GM2 ganglioside has been characterized by fast atom bombardment mass spectrometry, gas chromatography, and proton nuclear magnetic resonance spectroscopy. Using 14C-labeled GM2, at the fatty acid moiety, with stearic acid as the substrate, the optimum pH was determined to be 5.8. The enzyme was demonstrated to be capable of releasing fatty acids from GM3, GM2, GM1, and GD1a, and from neutral glycosphingolipids including Gb3-Cer, asialo-GM2, and asialo-GM1, but not from sphingolipids including Cer, Gal-Cer, Glc-Cer, and Lac-Cer. This enzyme, tentatively called glycosphingolipid ceramide deacylase, was found to be a tightly membrane-bound enzyme.
Enabling Correct Interest Forwarding and Retransmissions in a Content Centric Network - eScholarship (2015)

We show that the mechanisms used in the name data networking (NDN) and the original content centric networking (CCN) architectures may not detect Interest loops, even if the network in which they operate is static and no faults occur. Furthermore, we show that no correct Interest forwarding strategy can be defined that allows Interest aggregation and attempts todetect Interest looping by identifying Interests uniquely. We introduce SIFAH (Strategy for Interest Forwarding and Aggregation with Hop-Counts), the first Interest forwarding strategy shown to be correct under any operational conditions of a content centric network. SIFAH operates by having forwarding information bases (FIBs) store the next hops and number of hops to named content, and by having each Interest state the name of the requested content and the hop count from the router forwarding an Interest to the content. We present the results of simulation experiments using the ndnSIM simulator comparing CCN and NDN with SIFAH. The results of these experiments illustrate the negative impact of undetected Interest looping when Interests are aggregated in CCN and NDN, and the performance advantages of using SIFAH.
Brominated Poly(2,6-diphenyl-1,4-phenylene oxide) and Its Silica Nanocomposite Membranes for Gas Separation (2007)

Brominated poly(2,6-diphenyl-1,4-phenylene oxide) (BPPOdp) is synthesized as a new membrane material for gas separation. BPPOdp forms flexible membranes with higher CO2 permeability (PCO2 = 78 Barrer) and selectivity (αCO2/N2 = 30) than poly(2,6-dimethyl-1,4-phenylene oxide) (PPOdm) membranes. BPPOdp also forms nanocomposite membranes with silica nanoparticles. The nanocomposite membranes have a greatly enhanced CO2 permeability while maintaining the CO2/N2 and CO2/CH4 selectivities of the pure BPPOdp membranes. The CO2 permeability increases as the silica content increases in the membrane. The 10-nm silica nanoparticles are more effective at increasing the CO2 permeability than the 30-nm silica nanoparticles. Mechanism studies show that the enhanced permeability results from the nanogaps between the silica nanoparticles and the polymer chains due to their incompatibility.
23814, an Inhibitory Antibody of Ligand-Mediated Notch1 Activation, Modulates Angiogenesis and Inhibits Tumor Growth without Gastrointestinal Toxicity (2015)

Dysregulation of Notch signaling has been implicated in the development of many different types of cancer. Notch inhibitors are being tested in the clinic, but in most cases gastrointestinal and other toxicities have limited the dosage and, therefore, the effectiveness of these therapies. Herein, we describe the generation of a monoclonal antibody against the ligand-binding domain of the Notch1 receptor that specifically blocks ligand-induced activation. This antibody, 23814, recognizes both human and murine Notch1 with similar affinity, enabling examination of the effects on both tumor and host tissue in preclinical models. 23814 blocked Notch1 function in vivo, inhibited functional angiogenesis, and inhibited tumor growth without causing gastrointestinal toxicity. The lack of toxicity allowed for combination of 23814 and the VEGFR inhibitor tivozanib, resulting in significant growth inhibition of several VEGFR inhibitor-resistant tumor models. Analysis of the gene expression profiles of an extensive collection of murine breast tumors enabled the successful prediction of which tumors were most likely to respond to the combination of 23814 and tivozanib. Therefore, the use of a specific Notch1 antibody that does not induce significant toxicity may allow combination treatment with angiogenesis inhibitors or other targeted agents to achieve enhanced therapeutic benefit.
Purification and characterization of exoenzyme S from Pseudomonas aeruginosa 388 (1993)

Exoenzyme S was purified > 1,500-fold from the culture supernatant fluid of Pseudomonas aeruginosa 388 at high yield without utilization of solvents or detergents. Two proteins, with apparent molecular sizes of 53 and 49 kDa, cofractionated with exoenzyme S activity. Rabbit anti-49-kDa-protein immunoglobulin G was prepared by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis-purified 49-kDa protein as immunogen. Anti-49-kDa-protein IgG inhibited the ADP-ribosyltransferase activity of purified exoenzyme S in a dose-dependent manner, which indicated a role for the 49-kDa protein in the ADP-ribosylation reaction. Analysis by ultrafiltration showed that exoenzyme S activity and the 53- and 49-kDa proteins cofractionated and that exoenzyme S was apparently > 300 kDa in size. Urea (8 M) and 1.0% Triton X-100 reversibly decreased the apparent molecular sizes of exoenzyme S activity and the 53- and 49-kDa proteins to between 30 and 100 kDa.
Investigating ion-surface collisions with a niobium superconducting tunnel junction detector in a time-of-flight mass spectrometer (2000)

The performance of an energy sensitive, niobium superconducting tunnel junction (STJ) detector is investigated by measuring the pulse height produced by impacting molecular and atomic ions at different kinetic energies. Ions are produced by laser desorption and matrix-assisted laser desorption in a time-of-flight mass spectrometer. Our results show that the STJ detector pulse height decreases for increasing molecular ion mass, passes through a minimum at around 2000 Da, and then increases with increasing mass of molecular ions above 2000 Da. The detector does not show a decline in sensitivity for high mass ions as is observed with microchannel plate ion detectors. These detector plus height measurements are discussed in terms of several physical mechanisms involved in an ion-surface collision.
Liposoluble platinum(II) complexes with antitumor activity. (1986)

Seventeen liposoluble bis(carboxylato)-cyclohexane-1,2-diammineplatinum(II) and bis(carboxylato)-cis-diammineplatinum(II) complexes were synthesized and tested for antitumor activity against leukemia L1210 cells in mice. The former complexes had excellent antitumor activity without any toxicity to the host at the therapeutic dose when used with lipiodol as a carrier solvent. The latter complexes had neither antitumor activity nor toxicity in vivo. The former complexes were gradually released from lipiodol to saline in vitro; the latter were not. The activity depended on the chain length of the carboxylato residue and also on the molecular shape of the ligand part of the complexes.
16 GENETIC ANALYSIS IDENTIFIED NOVEL LOCI ASSOCIATED WITH IBD (2018)

More than 200 genetic loci have been identified in Inflammatory Bowel Disease (IBD). However, those loci do not explain the full hereditability of IBD, suggesting there are more genetics variants with weak or moderate effect sizes. To further expand our understanding of the biology of this complex disease, we screened for additional IBD loci in an independent cohort and replicated the findings in the IIBDGC cohort. 3,312 IBD cases from Cedars-Sinai Medical Center and 5,220 family and population-based controls with ImmunoChip data were included as the discovery cohort. Top SNPs were then replicated in the IIBDGC cohort (30179 cases and 29678 controls, having excluded all samples from the discovery stage). Inverse-variance Meta-Analysis was utilized to combine results from both cohorts. In addition to the known IBD genes including IL23R, HLA and NOD2, we identified multiple novel genes associated with IBD. Those genes include: CCL21 (in CD,OR=0.88, p=2.93E-8) which is a CCR7-binding chemokine that plays a vital role by modulating the circulation of T cells and dendritic cells; SEC61B (in all IBD, OR=0.93,p=1.68E-8) which is essential for nuclear transport of epidermal growth factor receptor (EGFR); RRM1(in CD, OR=0.91, p=3.64E-8) which plays an important role in DNA synthesis and damage repair; ETS1 (in all IBD, OR=1.08, p=4.39E-9) which codes for a sequence-specific transcription factor whose expression plays an important role in the development of hematopoietic cells, particularly in T- and natural killer (NK) lineages. eQTL analyses indicates that top SNP (rs10835755) in RRM1 is a strong eQTL of RRM1 gene itself (In GTEx, p = 3.20E-20, 6.20E-14 and 3.4E-6 in artery, Esophagus and Colon, respectively). More functional analyses of the novel loci are underway. Novel loci identified in current study strongly suggest that larger sample sizes are warranted to further understand the genetic basis of IBD.
Machining with flexible manipulator: toward improving robotic machining performance (2006)

This paper presents the critical issues and methodologies to improve robotic machining performance with flexible industrial robots. Compared with CNC machines, the stiffness of industrial robots is significantly lower, resulting in unacceptable quality and lower productivity. The problem is treated with a novel methodology that consists of stiffness modeling, real-time deformation compensation for quality and controlled material removal rate for efficiency. Experimental results show that higher productivity as well as better surface accuracy can be achieved, indicating a promising and practical use of industrial robots for machining applications that is not possible at present