gebhart/patrepeval huggingface dataset:
The VLSI Implementation of a Reed—Solomon Encoder Using Berlekamp's Bit-Serial Multiplier Algorithm (1984)

Berlekamp has developed for the California Institute of Technology Jet Propulsion Laboratory (JPL) a bit-serial multiplication algorithm for the encoding of Reed-Solomon (RS) codes, using a dual basis over a Galois field. The conventional RS encoder for long codes often requires lookup tables to perform multiplication of two field elements. Berlekamp's algorithm requires only shifting and EXCLUSIVE OR operations. It is shown in this paper that the new dual-basis (255,223) RS encoder can be realized readily on a single VLSI chip with NMOS technology.
Quantum annealing correction with minor embedding (2015)

Quantum annealing provides a promising route for the development of quantum optimization devices, but the usefulness of such devices will be limited in part by the range of implementable problems as dictated by hardware constraints. To overcome constraints imposed by restricted connectivity between qubits, a larger set of interactions can be approximated using minor embedding techniques whereby several physical qubits are used to represent a single logical qubit. However, minor embedding introduces new types of errors due to its approximate nature. We introduce and study quantum annealing correction schemes designed to improve the performance of quantum annealers in conjunction with minor embedding, thus leading to a hybrid scheme defined over an encoded graph. We argue that this scheme can be efficiently decoded using an energy minimization technique provided the density of errors does not exceed the per-site percolation threshold of the encoded graph. We test the hybrid scheme using a D-Wave Two processor on problems for which the encoded graph is a two-level grid and the Ising model is known to be NP-hard. The problems we consider are frustrated Ising model problem instances with ``planted'' (a priori known) solutions. Applied in conjunction with optimized energy penalties and decoding techniques, we find that this approach enables the quantum annealer to solve minor embedded instances with significantly higher success probability than it would without error correction. Our work demonstrates that quantum annealing correction can and should be used to improve the robustness of quantum annealing not only for natively embeddable problems but also when minor embedding is used to extend the connectivity of physical devices.
Gene Therapy for Osteoarthritis: Pharmacokinetics of Intra-Articular Self-Complementary Adeno-Associated Virus Interleukin-1 Receptor Antagonist Delivery in an Equine Model (2018)

Toward the treatment of osteoarthritis (OA), the authors have been investigating self-complementary adeno-associated virus (scAAV) for intra-articular delivery of therapeutic gene products. As OA frequently affects weight-bearing joints, pharmacokinetic studies of scAAV gene delivery were performed in the joints of the equine forelimb to identify parameters relevant to clinical translation in humans. Using interleukin-1 receptor antagonist (IL-1Ra) as a secreted therapeutic reporter, scAAV vector plasmids containing codon-optimized cDNA for equine IL-1Ra (eqIL-1Ra) were generated, which produced eqIL-1Ra at levels 30- to 50-fold higher than the native sequence. The most efficient cDNA was packaged in AAV2.5 capsid, and following characterization in vitro, the virus was injected into the carpal and metacarpophalangeal joints of horses over a 100-fold dose range. A putative ceiling dose of 5 × 10<sup>12</sup> viral genomes was identified that elevated the steady-state eqIL-1Ra in the synovial fluids of injected joints by >40-fold over endogenous levels and was sustained for at least 6 months. No adverse effects were seen, and eqIL-1Ra in serum and urine remained at background levels throughout. Using the 5 × 10<sup>12</sup> viral genome dose of scAAV, and green fluorescent protein as a cytologic marker, the local and systemic distribution of vector and transduced cells following intra-articular injection scAAV.GFP were compared in healthy equine joints and in those with late-stage, naturally occurring OA. In both cases, 99.7% of the vector remained within the injected joint. Strikingly, the pathologies characteristic of OA (synovitis, osteophyte formation, and cartilage erosion) were associated with a substantial increase in transgenic expression relative to tissues in healthy joints. This was most notable in regions of articular cartilage with visible damage, where foci of brilliantly fluorescent chondrocytes were observed. Overall, these data suggest that AAV-mediated gene transfer can provide relatively safe, sustained protein drug delivery to joints of human proportions.
Abstract 543: Clinical Development of Cardiac Reprogramming Gene Therapy (2020)

Heart failure affects an estimated 38 million people worldwide and is typically caused by cardiomyocyte (CM) loss or dysfunction. Although CMs have limited ability to regenerate, a large pool of non-myocytes, including cardiac fibroblasts (CFs), exist in the postnatal heart. In vivo reprogramming of non-myocytes into functional CMs is emerging as a potential new approach to treat heart failure and substantial proof-of-concept has been achieved in this new field. However, challenges remain in terms of clinical application. First, reported human reprogramming cocktails often consist of five to seven factors that require multiple AAV vectors for delivery. Thus, a less complex cocktail that is able to fit into one AAV vector is needed for this technology to impact human health. Second, the lack of specificity in AAV tropism further complicates the safety and regulatory landscape. A means to limit the expression of reprogramming factors to target cells is critical for maximizing long-term safety. Lastly, although promising studies in small animals have already been reported, safety and efficacy results in large animal MI models are critical to justify cardiac reprogramming in human clinical trials. We have developed a novel human cardiac reprogramming cocktail that consists of only two transcription factors and one miRNA. This new cocktail has been engineered into a single AAV cassette to efficiently reprogram human CFs into cardiomyocytes. We also substantially improved transduction of hCFs through AAV capsid engineering and eliminated CMs expression through a microRNA de-targeting method. Moreover, our novel cardiac reprogramming gene therapy improved cardiac function in both rat and swine MI models upon delivery at various time-points after MI without inducing arrhythmias. Given these promising safety and efficacy results in larger animals, we endeavor to translate direct cardiac reprogramming for clinical application.
Electrospray Ionization with a Pointed Carbon Fiber Emitter (2004)

A new type of electrospray ionization emitter employing a pointed carbon fiber has been developed for interfacing nanoliquid sampling techniques to mass spectrometry. The pointed carbon fiber protruding from an orifice with a surrounding hydrophobic surface confines a small Taylor cone at the tip, which generates a stable electrospray at the tip point. The small Taylor cone improves the electrospray efficiency thereby enhancing the detection limit. This emitter is rugged and able to generate stable electrospray over a wide range of flow rate, ESI voltage, and surface tension variation. Using a solution of angiotensin I, the carbon fiber emitter in 75-microm-i.d. fused-silica tubing was shown to give ion current comparable to that from a commercial 8 microm orifice nanospray emitter. Use of the emitter for ESI-MS/MS analysis of peptides was examined by infusing a mixture of cytochrome c and myoglobin tryptic digest peptides. Protein identification was demonstrated at the level of less than 1 fmol of the peptide consumed. The use of the carbon fiber emitter for interfacing monolithic capillary HPLC to MS was also demonstrated.
Compression ratio and decompression overhead tradeoffs in code compression for VLIW architectures (2002)

Memory has been one of the most restricted resources in embedded system design. Therefore, code compression has been one of the approaches to reduce the system costs. Many code compression methods try to improve the compression ratio but ignore the decompression overhead. In this paper, we take advantage of the separation of coding and modeling in arithmetic coding and study the tradeoffs between compression ratio and decompression overhead by exploring different probability models. Designs of the decompression unit for different models are discussed. Our work shows that simpler models result in smaller decompression overhead in code compression for VLIW, at the expense of compression ratio.
Phase 2 Trial of Ibudilast in Progressive Multiple Sclerosis (2018)

In a phase 2 trial involving patients with progressive multiple sclerosis, ibudilast was associated with slower progression of brain atrophy than placebo but was associated with higher rates of gastrointestinal side effects, headache, and depression. (Funded by the National Institute of Neurological Disorders and Stroke and others; NN102/SPRINT-MS ClinicalTrials.gov number, NCT01982942 .).
Controlling QoS by Integrated Power Control and Link Adaptation in Broadband Wireless Networks (2000)

Abstract We propose and analyze the performance of an algorithm for integrated power control and adaptive, modulationkoding to achieve a specitied range of packct error rate for real‐time applications in broadband wireless packet‐switched networks. The algorithm applies the Kalman‐filter method [I] for power control, and adapts packet transmission to an appropriate modulation level, according to the packet error requirement, and the radio and interference conditions. A new criterion for maintaining stable transmission power is derived. Based on the criterion, the proposed technique performs the link adaptation and adjusts transmission power to achieve the specified packet error rate. The effectiveness of the proposed method is dcmonstratcd by several numcrical examples.
Studies on waste potato starch and corn in urea-containing liquid supplements using in vitro rumen fermentation (1977)

Hydrothermally processed starch urea mixtures employed in urea-containing liquid supplements were shown to improve N use through in vitro rumen fermentation. Starch sources used were potatoes and corn. The starch source was blended with feed-grade urea (45% N) and water in a specific starch source-urea ratio, then hydrothermally processed. H/sub 3/PO/sub 4/ and EtCO/sub 2/H were added to lower pH and to act as an antifungal agent, respectively. In vitro microbial protein synthesis showed the 1.63:1 potato-based supplement on an as-is basis had more protein synthesized than did either the 1.90:1 potato- or 1.83:1 corn-based liquid supplement. However, on a dry basis, the corn-based supplement had more protein synthesized than either of the potato-based supplements. Compared with a 1.83:1 corn-based supplement, a 1.83:1 potato product performed equally well or better, based on microbial protein synthesized.
Reflection-type holographic disk memory with random phase shift multiplexing (2006)

A reflection-type holographic disk memory system with random phase shift multiplexing is proposed. The experimental results show that a binary data page of 18x17 bits is recorded successfully at intervals of 4 mum in a Fe:LiNbO3 crystal with a thickness of 0.5 mm when six data pages are superimposed. Numerical results show that random phase modulation can improve the shift selectivity in shift multiplexing recording as well as in data security. Experimental and numerical results show that reflection-type holographic disk memory has a high potential for terabyte storage capacity as in transmission-type memory.
Chip-Based Frequency Combs for High-Resolution Optical Coherence Tomography (2018)

We present a source for OCT based on chip-scale microresonators for sub-micrometer axial resolution and deep tissue penetration. Using the microresonators, we acquire OCT images of human tissue and show compatibility with standard OCT systems.
A novel method for detecting similar documents (2003)

We describe a system for rapidly determining document similarity among a set of documents obtained from an information retrieval (IR) system. We obtain a ranked list of the most important terms in each document using a rapid phrase recognizer system. We store these in a database and compute document similarity using a simple database query. If the number of terms found to not be contained in both documents is less than some predetermined threshold compared to the total number of terms in the document, these documents are determined to be very similar.
Clustered inter-phrase or word context-dependent models for continuously read Japanese. (1995)

This paper investigates methods to model inter-phrase or word context for continuous Japanese speech recognition. It is well known that in continuous speech, coarticulation between words or phrases induces allophonic variation of the beginning and ending phones in words or phrases. It was found that by compiling a network of contextdependent phonetic models which models these inter-word or inter-phrase context, recognition error reduction by 32 % can be achieved compared to models which do not account for inter-word context with task-dependent training, i.e. models that were trained with the same vocabulary as the test set. A more dramatic error reduction of up to 43% was possible with task-independent training. However, this will significantly increase the number of phonetic models required to model the vocabulary. With digit models, the increase in the number of models is 4 to 5 fold. To overcome this increase, we clustered the inter-word/phrase context into a few phonetic classes. Using one class for consonant inter-word context and two classes for vowel context, the recognition accuracy on digit string recognition was found to be virtually equal to the accuracy with unclustered models, while the number of phonetic models required was reduced by more than 50%.
Influence of growth temperature and scandium concentration on piezoelectric response of scandium aluminum nitride alloy thin films (2009)

The authors have investigated the influence of growth temperature and scandium concentration on the piezoelectric response of scandium aluminum nitride (ScxAl1−xN) films prepared by dual reactive cosputtering. The piezoelectric response strongly depends on the growth temperature and scandium concentration. The piezoelectric response of the films prepared at 400 °C gradually increases with increasing scandium concentration. On the other hand, the piezoelectric response of the films prepared at 580 °C drastically decreases and increases in the scandium concentration from 30% to 40%. We think that the drastic change of the piezoelectric response is due to the disordered grain growth.
Safety and long-term immunological effects of CryJ2-LAMP plasmid vaccine in Japanese red cedar atopic subjects: A phase I study (2017)

Japanese Red Cedar (JRC) pollen induced allergy affects one third of Japanese and the development of effective therapies remains an unachieved challenge. We designed a DNA vaccine encoding CryJ2 allergen from the JRC pollen and Lysosomal Associated Membrane Protein 1 (LAMP-1) to treat JRC allergy. These Phase IA and IB trials assessed safety and immunological effects of the investigational CryJ2-LAMP DNA vaccine in both non-sensitive and sensitive Japanese expatriates living in Honolulu, Hawaii. In the Phase IA trial, 6 JRC non-sensitive subjects and 9 JRC and/or Mountain Cedar (MC) sensitive subjects were given 4 vaccine doses (each 4mg/1ml) intramuscularly (IM) at 14-day intervals. Nine JRC and/or MC sensitive subjects were given 4 doses (2 mg/0.5 ml) IM at 14-day intervals. The safety and functional biomarkers were followed for 132 d. Following this, 17 of 24 subjects were recruited into the IB trial and received one booster dose (2 mg/0.5 ml) IM approximately 300 d after the first vaccination dose to which they were randomized in the first phase of the trial. All safety endpoints were met and all subjects tolerated CryJ2-LAMP vaccinations well. At the end of the IA trial, 10 out of 12 JRC sensitive and 6 out of 11 MC sensitive subjects experienced skin test negative conversion, possibly related to the CryJ2-LAMP vaccinations. Collectively, these data suggested that the CryJ2-LAMP DNA vaccine is safe and may be immunologically effective in treating JRC induced allergy.
Independent component analysis of gabor features for face recognition (2003)

We present an independent Gabor features (IGFs) method and its application to face recognition. The novelty of the IGF method comes from 1) the derivation of independent Gabor features in the feature extraction stage and 2) the development of an IGF features-based probabilistic reasoning model (PRM) classification method in the pattern recognition stage. In particular, the IGF method first derives a Gabor feature vector from a set of downsampled Gabor wavelet representations of face images, then reduces the dimensionality of the vector by means of principal component analysis, and finally defines the independent Gabor features based on the independent component analysis (ICA). The independence property of these Gabor features facilitates the application of the PRM method for classification. The rationale behind integrating the Gabor wavelets and the ICA is twofold. On the one hand, the Gabor transformed face images exhibit strong characteristics of spatial locality, scale, and orientation selectivity. These images can, thus, produce salient local features that are most suitable for face recognition. On the other hand, ICA would further reduce redundancy and represent independent features explicitly. These independent features are most useful for subsequent pattern discrimination and associative recall. Experiments on face recognition using the FacE REcognition Technology (FERET) and the ORL datasets, where the images vary in illumination, expression, pose, and scale, show the feasibility of the IGF method. In particular, the IGF method achieves 98.5% correct face recognition accuracy when using 180 features for the FERET dataset, and 100% accuracy for the ORL dataset using 88 features.
Mitigating the Cytotoxicity of Graphene Quantum Dots and Enhancing Their Applications in Bioimaging and Drug Delivery (2014)

Despite the promising photophysical properties of fluorescent graphene quantum dots (GQDs), their cellular toxicity needs to be addressed before their full potential could be completely realized in biomedicine. A simple method for mitigating the toxicity of GQDs by embedding them in PEG matrix is reported here. The enhanced biocompatibility of polymer modified, P-GQDs, is attributed to reduced reactive oxygen species generation, as measured by an intracellular ROS assay. We also demonstrate the enhanced loading and efficient intracellular delivery of therapeutics by P-GQDs.
Killing Two Birds with One Stone: Malicious Domain Detection with High Accuracy and Coverage (2017)

Inference based techniques are one of the major approaches to analyze DNS data and detecting malicious domains. The key idea of inference techniques is to first define associations between domains based on features extracted from DNS data. Then, an inference algorithm is deployed to infer potential malicious domains based on their direct/indirect associations with known malicious ones. The way associations are defined is key to the effectiveness of an inference technique. It is desirable to be both accurate (i.e., avoid falsely associating domains with no meaningful connections) and with good coverage (i.e., identify all associations between domains with meaningful connections). Due to the limited scope of information provided by DNS data, it becomes a challenge to design an association scheme that achieves both high accuracy and good coverage. In this paper, we propose a new association scheme to identify domains controlled by the same entity. Our key idea is an in-depth analysis of active DNS data to accurately separate public IPs from dedicated ones, which enables us to build high-quality associations between domains. Our scheme identifies many meaningful connections between domains that are discarded by existing state-of-the-art approaches. Our experimental results show that the proposed association scheme not only significantly improves the domain coverage compared to existing approaches but also achieves better detection accuracy. Existing path-based inference algorithm is specifically designed for DNS data analysis. It is effective but computationally expensive. As a solution, we investigate the effectiveness of combining our association scheme with the generic belief propagation algorithm. Through comprehensive experiments, we show that this approach offers significant efficiency and scalability improvement with only minor negative impact of detection accuracy.
A hybrid adaptive antenna array (2010)

Owing to the excessive demand on signal processing and space constraint, a full digital implementation of a large adaptive antenna array at millimeter wave frequencies is very challenging. Targeted at long range high data rate point-to-point link in the 70/80 GHz bands, a novel hybrid adaptive antenna array which consists of analogue subarrays followed by a digital beamformer is presented in this paper to overcome the digital implementation difficulty. Two subarray configurations, the interleaved subarray and the side-by-side subarray, are proposed, and two Doppler resilient adaptive angle-of-arrival estimation and beamforming algorithms, the differential beam tracking (DBT) and the differential beam search (DBS), are developed. Simulation results on the DBT and DBS performance are provided using a 64 element hybrid planar array of four 4 by 4 element subarrays with the two subarray configurations, respectively. Recursive mean square error (MSE) bounds of the developed algorithms are also analyzed and compared with simulated MSEs.
An 85-aa segment of the GB virus type C NS5A phosphoprotein inhibits HIV-1 replication in CD4 <sup>+</sup> Jurkat T cells (2006)

GB virus type C (GBV-C) is an apparently nonpathogenic virus that replicates in T and B lymphocytes and is a common cause of persistent human infection. Among HIV-1-infected individuals, persistent coinfection with GBV-C is associated with prolonged survival, and infection of blood mononuclear cells or CD4+ T cells with GBV-C and HIV in vitro results in significantly reduced HIV-1 replication. To date, the viral protein(s) that lead to HIV inhibition have not been identified. The GBV-C nonstructural phosphoprotein (NS5A) is predicted to have pleotropic effects on cells, including interactions with the IFN-induced dsRNA-activated protein kinase (PKR). We studied GBV-C NS5A to determine whether it is involved in inhibition of HIV replication. GBV-C NS5A protein from an isolate that was cleared by IFN therapy did not inhibit PKR, whereas NS5A from an isolate that was not cleared by IFN-inhibited PKR function in a yeast genetic system. Both of these GBV-C NS5A proteins were expressed in a CD4+ T cell line (Jurkat), and both induced a potent, dose-dependent inhibition of HIV-1 replication, thus the effect was independent of PKR inhibition. NS5A induced the release of the chemokine SDF-1 and decreased surface expression of the HIV coreceptor CXCR4, potentially explaining the HIV inhibition. Deletion mapping of the NS5A protein found that an 85-aa region between amino acids 152 and 237 inhibits HIV-1 replication. Thus, GBV-C NS5A protein alters the cellular milieu necessary for HIV-1 replication and may provide a previously undescribed therapeutic approach for anti-HIV therapy.