gebhart/patrepeval huggingface dataset:
Optimized Memristor-Based Multipliers (2017)

Since memristors came to the forefront of research, minimal work has explored their application to computer arithmetic. This paper proposes two memristor-based implementations of an N-bit shift-and-add multiplier, one using IMPLY operations and a second using MAD operations. The optimized IMPLY-based implementation reduces the baseline delay from 2N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + 29N steps and 17N+3 memristors to 2N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + 21N steps and 7N+1 memristors. A second implementation is proposed that is constructed from MAD gates, a lower-area, lower-delay alternative to IMPLY logic. This design performs an N-bit multiplication in N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + N steps with 5N memristors and 3N+2 drivers. Both designs require fewer steps and less than 1/6 of the number of components of a traditional CMOS design. Finally, both of the implementations are extended to implement radix-2 Booth multipliers. The IMPLY design only increases by 1 step per iteration and 2N memristors and drivers. The MAD design increases by N memristors and 6N switches but maintains the same delay as the shift-and-add multiplier. Both designs maintain a lower area and lower delay than the CMOS equivalent.
Holographic fixing, readout, and storage dynamics in photorefractive materials (1995)

Holographic gratings in photorefractive crystals that are based on charge redistribution inevitably decay as a result of ionic and electronic conduction. Under certain and restricted conditions these decay times can be acceptably long. Relevant decay rates and transient hologram field expressions are derived with special reference to LiNbO(3). Some experimental data are presented.
Cloning and sequence analysis of cytadhesin P1 gene from Mycoplasma pneumoniae (1987)

Mycoplasma pneumoniae cytadhesin P1 was purified by monoclonal antibody affinity chromatography followed by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The N-terminal 18-amino-acid sequence of P1 was determined and used to design two synthetic oligonucleotides, a 14-mer corresponding to amino acids 1 to 5 and an 18-mer corresponding to amino acids 7 to 12. These oligonucleotides served as hybridization probes for the identification of the P1 gene by Southern blot analysis of M. pneumoniae DNA. The P1 gene was cloned into plasmid pUC19 and mapped by using appropriate restriction endonucleases. The DNA sequence of the entire P1 gene was determined by subcloning appropriate DNA fragments into bacteriophage M13 and sequencing the DNA by the dideoxy-chain-termination method. The P1 gene contains an open reading frame of 4,881 nucleotides coding for a protein of 1,627 amino acids with a calculated molecular weight of 176,288. Properties of the amino-terminal sequence suggest that protein P1 may be synthesized as a precursor with subsequent processing to a mature protein of a calculated molecular weight of 169,758. Potential antigenic sites were determined by hydrophilicity plots. A computer search revealed that part of the predicted P1 sequence is homologous to cytoskeletal keratin of mammalian species and human fibrinogen alpha chain precursor. These results demonstrate the uniqueness of P1 as a cytadhesin and virulence determinant.
A non-blocking parallel spatial join algorithm (2003)

Interest in incremental and adaptive query processing has led to the investigation of equijoin evaluation algorithms that are non-blocking. This investigation has yielded a number of algorithms, including the symmetric hash join, the XJoin, the Ripple Join, and their variants. However, to our knowledge no one has proposed a nonblocking spatial join algorithm. In this paper, we propose a parallel non-blocking spatial join algorithm that uses duplicate avoidance rather than duplicate elimination. Results from a prototype implementation in a commercial parallel object-relational DBMS show that it generates answer tuples steadily even in the presence of memory overflow, and that its rate of producing answer tuples scales with the number of processors. Also, when allowed to run to completion, its performance is comparable with the state-of-the-art blocking parallel spatial join algorithm.
Association of Breast Cancer DNA Methylation Profiles with Hormone Receptor Status and Response to Tamoxifen (2004)

We have generated DNA methylation profiles of 148 human breast tumors and found significant differences in hormone receptor (HR) status between clusters of DNA methylation profiles. Of 35 DNA methylation markers analyzed, the ESR1 gene, encoding estrogen receptor alpha, proved to be the best predictor of progesterone receptor status, whereas methylation of the PGR gene, encoding progesterone receptor, was the best predictor of estrogen receptor status. ESR1 methylation outperformed HR status as a predictor of clinical response in patients treated with the antiestrogen tamoxifen, whereas promoter methylation of the CYP1B1 gene, encoding a tamoxifen- and estradiol-metabolizing cytochrome p450, predicted response differentially in tamoxifen-treated and nontamoxifen-treated patients. High levels of promoter methylation of the ARHI gene, encoding a RAS-related small G-protein, were strongly predictive of good survival in patients who had not received tamoxifen therapy. Our results reveal an as yet unrecognized degree of interaction between DNA methylation and HR biology in breast cancer cells and suggest potentially clinically useful novel DNA methylation predictors of response to hormonal and non-hormonal breast cancer therapy.
A framework for identification of brain network dynamics using a novel binary noise modulated electrical stimulation pattern (2015)

Modeling and identification of brain network dynamics is of great importance both for understanding brain function and for closed-loop control of brain states. In this work, we present a multi-input-multi-output (MIMO) linear state-space model (LSSM) to describe the brain network dynamics in response to electrical stimulation. The LSSM maps the parameters of electrical stimulation, such as frequency, amplitude and pulse-width to recorded brain signals such as electrocorticography (ECoG) and electroencephalography (EEG). Effective identification of the LSSM in open-loop stimulation experiments, however, is strongly dependent on the open-loop input stimulation design. We propose a novel input design to accurately identify the LSSM by integrating the concept of binary noise (BN) with practical constraints on stimulation waveforms. The designed input pattern is a pulse train modulated by stochastic BN parameters. We show that this input pattern both satisfies the necessary spectral condition for accurate system identification and can incorporate any desired pulse shape. Using numerical experiments, we show that the quality of identification depends heavily on the input signal pattern and the proposed binary noise modulated pattern achieves satisfactory identification results, reducing the relative estimation error more than 300 times compared with step sequence modulated, single-sinusoid modulated and multi-sinusoids modulated input patterns.
Vocal Conversion from Speaking Voice to Singing Voice Using STRAIGHT (2007)

Our results show that CLU is a viable anabolic option by preserving power output with similar MPS stimulation when compared with the TRD condition in trained young adults.
Simulation and experimental characterization of a 2-D, 3-MHz capacitive micromachined ultrasonic transducer (CMUT) array element (2003)

In this paper, a 400-/spl mu/m/spl times/400-/spl mu/m, 2-D capacitive micromachined ultrasonic transducer array element is experimentally characterized, and the results are found to be in agreement with theoretical predictions. As a receiver the transducer has a 1.8/spl times/10/sup -7/ nm//spl radic/Hz displacement sensitivity, and, as a transmitter, it produces 16.4 kPa/V of output pressure at the transducer surface at 3 MHz. The transducer also has more than 100% fractional bandwidth around 3 MHz, which makes it suitable for ultrasound imaging. The radiation pattern measurements indicate a 3-dB acceptance angle of /spl plusmn/35 degrees in agreement with the theoretical predictions.
Computerized analysis of breast lesions in three dimensions using dynamic magnetic‐resonance imaging (1998)

Contrast-enhanced magnetic resonance imaging (MRI) of the breast is known to reveal breast cancer with higher sensitivity than mammography alone. The specificity is, however, compromised by the observation that several benign masses take up contrast agent in addition to malignant lesions. The aim of this study is to increase the objectivity of breast cancer diagnosis in contrast-enhanced MRI by developing automated methods for computer-aided diagnosis. Our database consists of 27 MR studies from 27 patients. In each study, at least four MR series of both breasts are obtained using FLASH three-dimensional (3D) acquisition at 90 s time intervals after injection of Gadopentetate dimeglumine (Gd-DTPA) contrast agent. Each series consists of 64 coronal slices with a typical thickness of 2 mm, and a pixel size of 1.25 mm. The study contains 13 benign and 15 malignant lesions from which features are automatically extracted in 3D. These features include margin descriptors and radial gradient analysis as a function of time and space. Stepwise multiple regression is employed to obtain an effective subset of combined features. A final estimate of likelihood of malignancy is determined by linear discriminant analysis, and the performance of classification by round-robin testing and receiver operating characteristics (ROC) analysis. To assess the efficacy of 3D analysis, the study is repeated in two-dimensions (2D) using a representative slice through the middle of the lesion. In 2D and in 3D, radial gradient analysis and analysis of margin sharpness were found to be an effective combination to distinguish between benign and malignant masses (resulting area under the ROC curve: 0.96). Feature analysis in 3D was found to result in higher performance of lesion characterization than 2D feature analysis for the majority of single and combined features. In conclusion, automated feature extraction and classification has the potential to complement the interpretation of radiologists in an objective, consistent, and accurate way.
The Electrode‐Tissue Interface: The Revolutionary Role of Steroid‐Elution (2014)

The electrode‐tissue interface is that area lying between the cathode of a low‐voltage implantable pacemaker or cardioverter‐defibrillator (ICD) lead and the endocardium or epi‐myocardium of the cardiac chamber being paced. The electrical stimulus that is delivered to this interface is responsible for myocyte depolarization with consequent cardiac contraction. The process by which this occurs is reasonably well understood and any explanation requires a basic understanding of the physics and cellular electrophysiology of pacing. The effective and efficient delivery of electrical energy to the myocardium via the lead is dependent on many factors to be discussed in this review. However, despite numerous evolutionary changes occurring in the cathode's material, design, and surface configuration, it was not until the incorporation of steroid‐elution to the electrode‐tissue interface that reliable and significantly low stimulation threshold cardiac pacing became possible.
Machine Learning Classifies Core and Outer Fucosylation of N-Glycoproteins Using Mass Spectrometry (2020)

Protein glycosylation is known to be involved in biological progresses such as cell recognition, growth, differentiation, and apoptosis. Fucosylation of glycoproteins plays an important role for structural stability and function of N-linked glycoproteins. Although many of biological and clinical studies of protein fucosylation by fucosyltransferases has been reported, structural classification of fucosylated N-glycoproteins such as core or outer isoforms remains a challenge. Here, we report for the first time the classification of N-glycopeptides as core- and outer-fucosylated types using tandem mass spectrometry (MS/MS) and machine learning algorithms such as the deep neural network (DNN) and support vector machine (SVM). Training and test sets of more than 800 MS/MS spectra of N-glycopeptides from the immunoglobulin gamma and alpha 1-acid-glycoprotein standards were selected for classification of the fucosylation types using supervised learning models. The best-performing model had an accuracy of more than 99% against manual characterization and area under the curve values greater than 0.99, which were calculated by probability scores from target and decoy datasets. Finally, this model was applied to classify fucosylated N-glycoproteins from human plasma. A total of 82N-glycopeptides, with 54 core-, 24 outer-, and 4 dual-fucosylation types derived from 54 glycoproteins, were commonly classified as the same type in both the DNN and SVM. Specifically, outer fucosylation was dominant in tri- and tetra-antennary N-glycopeptides, while core fucosylation was dominant in the mono-, bi-antennary and hybrid types of N-glycoproteins in human plasma. Thus, the machine learning methods can be combined with MS/MS to distinguish between different isoforms of fucosylated N-glycopeptides.
Mutating a Critical Lysine in ShK Toxin Alters Its Binding Configuration in the Pore−Vestibule Region of the Voltage-Gated Potassium Channel, Kv1.3 (2002)

The voltage-gated potassium channel in T lymphocytes, Kv1.3, an important target for immunosuppressants, is blocked by picomolar concentrations of the polypeptide ShK toxin and its analogue ShK-Dap22. ShK-Dap22 shows increased selectivity for Kv1.3, and our goal was to determine the molecular basis for this selectivity by probing the interactions of ShK and ShK-Dap22 with the pore and vestibule of Kv1.3. The free energies of interactions between toxin and channel residues were measured using mutant cycle analyses. These data, interpreted as approximate distance restraints, guided molecular dynamics simulations in which the toxins were docked with a model of Kv1.3 based on the crystal structure of the bacterial K(+)-channel KcsA. Despite the similar tertiary structures of the two ligands, the mutant cycle data imply that they make different contacts with Kv1.3, and they can be docked with the channel in configurations that are consistent with the mutant cycle data for each toxin but quite distinct from one another. ShK binds to Kv1.3 with Lys22 occupying the negatively charged pore of the channel, whereas the equivalent residue in ShK-Dap22 interacts with residues further out in the vestibule, producing a significant change in toxin orientation. The increased selectivity of ShK-Dap22 is achieved by strong interactions of Dap22 with His404 and Asp386 on Kv1.3, with only weak interactions between the channel pore and the toxin. Potent and specific blockade of Kv1.3 apparently occurs without insertion of a positively charged residue into the channel pore. Moreover, the finding that a single residue substitution alters the binding configuration emphasizes the need to obtain consistent data from multiple mutant cycle experiments in attempts to define protein interaction surfaces using these data.
Addressing, routing, and broadcasting in hexagonal mesh multiprocessors (1990)

A family of six-regular graphs, called hexagonal meshes or H-meshes, is considered as a multiprocessor interconnection network. Processing nodes on the periphery of an H-mesh are first wrapped around to achieve regularity and homogeneity. The diameter of a wrapped H-mesh is shown to be of O(p/sup 1/2/), where p is the number of nodes in the H-mesh. An elegant, distributed routing scheme is developed for wrapped H-meshes so that each node in an H-mesh can compute shortest paths from itself to any other node with a straightforward algorithm of O(1) using the addresses of the source-destination pair only, i.e. independent of the network's size. This is in sharp contrast with those previously known algorithms that rely on using routing tables. Furthermore, the authors also develop an efficient point-to-point broadcasting algorithm for the H-meshes which is proved to be optimal in the number of required communication steps. The wrapped H-meshes are compared against some other existing multiprocessor interconnection networks, such as hypercubes, trees, and square meshes. The comparison reinforces the attractiveness of the H-mesh architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Paper generators (2013)

We present a new energy harvesting technology that generates electrical energy from a user's interactions with paper-like materials. The energy harvesters are flexible, light, and inexpensive, and they utilize a user's gestures such as tapping, touching, rubbing and sliding to generate electrical energy. The harvested energy is then used to actuate LEDs, e-paper displays and various other devices to create novel interactive applications, such as enhancing books and other printed media with interactivity.
A novel reclosing algorithm considering the recovery time of a superconducting fault current limiter in a distribution system with distributed generation (2010)

Distributed generation (DG) technologies, such as wind turbines, fuel cells, and photovoltaic systems, are connected to a distribution system. A superconducting fault current limiter (SFCL) is also connected to a distribution system for fault current limitation. The connection of an SFCL causes protective coordination problems, especially for reclosing. In this work, a new reclosing algorithm is proposed considering the recovery time of an SFCL in a distribution system with DG. The main idea is that it uses a carrier signal to distinguish whether the fault is transient or permanent after the tripping of the line by a recloser. The distribution system, DG, and SFCL are modeled using an electromagnetic transient program (EMTP), and the simulations regarding the fault resistance, the recovery time of the SFCL, and the fault clearing time are performed. The simulation results show the validity and effectiveness of the proposed algorithm. (5 pages)
Glycan alterations on serum mucins in pancreatic cancer patients (2008)

5513 The carbohydrate structures on certain mucins are frequently altered in pancreatic cancer patients. A characterization of the variation in those structures over many cancer patients could be used to assess their diagnostic value and to identify possible functional relationships with disease. Using a novel method of profiling glycans on native proteins using antibody arrays, we characterized certain glycan levels on several mucins (MUC1, MUC5ac, MUC16) in the sera of pancreatic cancer patients (n = 23) and control subjects (n = 23). Probing the proteins with 22 different glycan binding lectins or antibodies revealed several groups of glycans that were elevated in cancer, including Lewis antigens, T/Tn antigens, and fucose groups. Glycan detection greatly improved the discrimination between cancer and control samples relative to detecting the glycoprotein alone. For example, at a threshold defining an 87% specificity (3/23 control samples above the threshold), 7/23 cancer patients (30% sensitivity) showed an elevation in the MUC5ac core protein (AUC=0.72), but 23/23 cancer patients (100% sensitivity) showed an elevation in WGA binding on MUC5ac (AUC=0.90). Using a panel of the top six glycan measurements, we detected all but one (96% sensitivity) at a 100% specificity, which was an improvement over the use of CA 19-9 alone. These data provide the first look at the variability in glycan structures between people and molecules and have revealed previously unknown associations with cancer. These results also validate the concept of using glycan detection for improved biomarker accuracy and highlight the advantage of this approach for that research.
Durable and refreshable polymeric <i>N</i>‐halamine biocides containing 3‐(4′‐vinylbenzyl)‐5,5‐dimethylhydantoin (2001)

Abstract A novel vinyl‐hydantoin monomer, 3‐(4′‐vinylbenzyl)‐5,5‐dimethylhydantoin, was synthesized in a good yield and was fully characterized with Fourier transform infrared (FTIR) and 1 H NMR spectra. Its homopolymer and copolymers with several common acrylic and vinyl monomers, such as vinyl acetate, acrylonitrile, and methyl methacrylate, were readily prepared under mild conditions. The polymers were characterized with FTIR and 1 H NMR, and their thermal properties were analyzed with differential scanning calorimetry studies. The halogenated products of the corresponding copolymers exhibited potent antibacterial properties against Escherichia coli , and the antibacterial properties were durable and regenerable. The structure–property relationships of the polymers were further discussed. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3348–3355, 2001
Process for production of synthesis gas. [12 claims] (1977)

A process is described for the production of a synthesis gas, capable of being upgraded to a high BTU pipeline gas, by the partial oxidation and substantially complete gasification of a carbonaceous material under CO-promoting conditions wherein the carbonaceous material, oxygen, and recycled carbon doxide from the process are introduced into a molten salt containing an alkali metal carbonate and a minor portion of an alkali metal sulfide, the system being operated at a selected temperature and pressure between 1400 and 2000/sup 0/F and between 1 and 100 atmospheres. The molar ratio of carbon dioxide to oxygen employed is controlled at from about 0.6:1 to about 1.2:1 to control the CO production and also to maintain the molten salt at a desired operating temperature. Sulfur and ash introduced with the fuel are retained in the molten salt. The gaseous effluent, containing a molar ratio of carbon monoxide to carbon dioxide substantially greater than one, is reacted in a water gas shift reaction, followed by removal of the carbon dioxide present in the gaseous effluent from the shift reaction to produce the synthesis gas, capable of being reacted further under appropriate conditions to produce pipeline gas, methanol, ammonia, or gasoline. Atmore » least a portion of the removed carbon dioxide is recycled for admixture with the oxygen to form the feed gas to the molten salt containing the carbonaceous material. 12 claims, 5 figures.« less
Novel Solder Pads for Self-Aligned Flip-Chip Assembly (2019)

Self-alignment via solder-surface tension in flip-chip bonding opens the door to low-cost, high-throughput assembly of components with sub-micron accuracy. This is especially impactful to integrated photonics as used for high speed optical communication and sensors [1,2]. Assembly yield hinges on the details of solder-induced forces and on the geometry of the melted solder surface. Low curvature of melted solder is best to balance solder forces for optimal re-alignment yield but leads to shallow contact angles and solder de-wetting on traditional solder pads. We introduce and demonstrate the concept of recessed solder pads with shallow angled edges. Such geometry enables arbitrarily-low curvature of the molten solder surface and even flat or slightly concave shapes. The solder stays anchored at the angled edges of recessed pads and can be made to flow in long and narrow conduits. Both aspects are key to widening the fabrication and process window for the solder-induced chip-alignment technology.