gebhart/patrepeval huggingface dataset:
Improved Myoelectric Prosthesis Control Using Targeted Reinnervation Surgery: A Case Series (2008)

Targeted reinnervation is a surgical technique developed to increase the number of myoelectric input sites available to control an upper-limb prosthesis. Because signals from the nerves related to specific movements are used to control those missing degrees-of-freedom, the control of a prosthesis using this procedure is more physiologically appropriate compared to conventional control. This procedure has successfully been performed on three people with a shoulder disarticulation level amputation and three people with a transhumeral level amputation. Performance on timed tests, including the box-and-blocks test and clothespin test, has increased two to six times. Options for new control strategies are discussed.
Deep ocean long range underwater navigation with ocean circulation model corrections (2023)

An underwater navigation algorithm that provides a "cold start" (CSA) geographic position, geo-position, underwater while submerged using travel times measured from a constellation of acoustic sources is described in Mikhalevsky, Sperry, Woolfe, Dzieciuch, and Worcester [J. Acoust. Soc. Am. 147(4), 2365 - 2382 (2020)]. The CSA geo-position is used as the receive position in the ocean for acoustic modeling runs using an ocean general circulation model (GCM). A different geo-position is calculated using adjusted ranges from the travel time offsets between the data and modeled arrival times for each source. Because the CSA geo-position is close to the true position, the source to CSA position propagation model path and the source to true vehicle position data path of the acoustic arrivals are nearly coincident, enabling accurate measurement of travel time offsets. The cold start with model (CSAM) processing reduced the CSA geo-position errors from a mean of 58 to 25 m. A simulation is developed to estimate CSA and CSAM performances as a function of group speed variability between the source paths. The CSAM geolocation accuracy can be calculated from and is controlled by the accuracy of the GCM.
Growth Evolution and Time-Resolved Photoluminescence Studies of III-Nitride Light-Emitting Diodes Grown by Abbreviated Growth Mode on Patterned AGOG Substrate (2010)

Abbreviated growth mode of InGaN-based light-emitting diodes on nano-patterned sapphire leads to reduction in dislocation density and non-radiative recombination rate, and 37% increase in internal quantum efficiency.
ACOUSTICS2008/603 extracting dispersion curves of acoustic data with continuous wavelet transform (2008)

Group and phase velocity (i.e. dispersion) of acoustic data carry important information about the acoustic state of the rock and are important tools for interpretation and for quantitative inversion. In this paper we propose an approach to automatically extract the velocity dispersion (group and phase) of acoustic waves received by an array of receivers without the use of any physical model, user inputs or supervision. The first step consists in applying the continuous wavelet transform to the waveforms recorded by each receiver. Then, the peak on the modulus map is used to determine the time locus of the energy of each mode as a function of frequency. At each frequency, a method of data association is used to find the corresponding loci for all receivers. A straight line is fit to these loci and its slope is used as an estimate for the group velocity at that frequency. Moreover the rate of change of the phase of the complex wavelet coecients at the locations corresponding to this best-fit straight line can be used to compute an estimate of the phase slowness at the same frequency. Repeating this for all frequencies and all separated modes of interest yields the desired dispersion curves for these modes.
Modulation of Acetone-Butanol-Ethanol Fermentation by Carbon Monoxide and Organic Acids (1985)

Metabolic modulation of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum with carbon monoxide (CO) and organic acids is described. CO, which is a known inhibitor of hydrogenase, was found to be effective in the concentration range of dissolved CO corresponding to a CO partial pressure of 0.1 to 0.2 atm. Metabolic modulation by CO was particularly effective when organic acids such as acetic and butyric acids were added to the fermentation as electron sinks. The uptake of organic acids was enhanced, and increases in butyric acid uptake by 50 to 200% over control were observed. Hydrogen production could be reduced by 50% and the ratio of solvents could be controlled by CO modulation and organic acid addition. Acetone production could be eliminated if desired. Butanol yield could be increased by 10 to 15%. Total solvent yield could be increased 1 to 3% and the electron efficiency to acetone-butanol-ethanol solvents could be increased from 73 to 78% for controls to 80 to 85% for CO- and organic acid-modulated fermentations. Based on these results, the dynamic nature of electron flow in this fermentation has been elucidated and mechanisms for metabolic control have been hypothesized.
A query mining model for the design of content and structure in a Web site (2006)

In this article we present a model for mining queries in Web sites. This model relates the information provided by queries found in a site, with the site's usage, content and structure. The main goal of our model is to discover in simple way, valuable information on how to improve the structure and content of the site, allowing the site to become more intuitive and adequate to the needs of its users. This model proposes the analysis of different types of queries registered in the usage logs of site, such as queries sent by users in the site's internal search engine and queries submitted in global Web search engines, that lead to documents in the site. These queries provide useful information about the topics that interest users visiting a Web site, and their browsing patterns indicate if the documents found in the site were satisfactory to the users needs. This model additionally proposes a visual validation of the hierarchic organization of the site, given by links between documents and their contents.
Modified deep-learning-powered photonic analog-to-digital converter for wideband complicated signal receiving (2020)

We propose and demonstrate a modified deep-learning-powered photonic analog-to-digital converter (DL-PADC) in which a neural network is used to eliminate the signal distortions of the photonic system. This work broadens the receiving capability from simple waveforms to complicated waveforms via implementing a modified deep learning algorithm. Thus, the modified DL-PADC can be applied in real scenarios with wideband complicated signals. Testing results show that the trained neural network eliminates the signal distortions with high quality, improving the spur-free dynamic range by ∼20<i>d</i><i>B</i>. An experiment for echo detection is conducted as an example, which shows that the neural network enhances the quality of detailed target profile detection. Furthermore, the modified DL-PADC only comprises a low-complexity photonic system, which obviates the requirement for redundant hardware setup while maintaining the processing quality. It is expected that the modified DL-PADC can perform as a promising photonic wideband signal receiver with low hardware complexity.
Defects and diffusion in MeV implanted silicon (1999)

In this work we demonstrate that the defects that are created by 2-MeV Si ions can interact with dopant atoms both during implantation and during post-implant annealing. We show that the interstitials and vacancies created during MeV Si implantation result in a radiation enhanced diffusion of B and Sb markers, respectively, when the temperature of implantation is above the threshold temperature for formation of mobile dopant complexes. With the use of these dopant markers we also demonstrate that a vacancy-rich near surface region results during post-implant annealing of MeV implanted silicon. The depth distribution and the thermal evolution of clustered vacancies was measured by a Au labeling technique.
Lipidomic Profiling Links the Fanconi Anemia Pathway to Glycosphingolipid Metabolism in Head and Neck Cancer Cells (2018)

<b>Purpose:</b> Mutations in Fanconi anemia (FA) genes are common in sporadic squamous cell carcinoma of the head and neck (HNSCC), and we have previously demonstrated that FA pathway depletion in HNSCC cell lines stimulates invasion. The goal of our studies was to use a systems approach in order to define FA pathway-dependent lipid metabolism and to extract lipid-based signatures and effectors of invasion in FA-deficient cells.<b>Experimental Design:</b> We subjected FA-isogenic HNSCC keratinocyte cell lines to untargeted and targeted lipidomics analyses to discover novel biomarkers and candidate therapeutic targets in FA-deficient cells. Cellular invasion assays were carried out in the presence and absence of N-butyldeoxynojirimycin (NB-DNJ), a biosynthetic inhibitor of the newly identified class of gangliosides, to investigate the requirement of ganglioside upregulation in FA-deficient HNSCC cells.<b>Results:</b> The most notable element of the lipid profiling results was a consistent elevation of glycosphingolipids, and particularly the accumulation of gangliosides. Conversely, repression of this same class of lipids was observed upon genetic correction of FA patient-derived HNSCC cells. Functional studies demonstrate that ganglioside upregulation is required for HNSCC cell invasion driven by FA pathway loss. The motility of nontransformed keratinocytes in response to FA loss displayed a similar dependence, thus supporting early and late roles for the FA pathway in controlling keratinocyte invasion through lipid regulation.<b>Conclusions:</b> Elevation of glycosphingolipids including the ganglioside GM3 in response to FA loss stimulates invasive characteristics of immortalized and transformed keratinocytes. An inhibitor of glycosphingolipid biosynthesis NB-DNJ attenuates invasive characteristics of FA-deficient HNSCC cells. <i>Clin Cancer Res; 24(11); 2700-9. ©2018 AACR</i>.
Gallium nitride tunneling field-effect transistors exploiting polarization fields (2020)

This report showcases a vertical tunnel field effect transistor (TFET) fabricated from a GaN/InGaN heterostructure and compares it to a gated vertical GaN p-n diode. By including a thin InGaN layer, the interband tunneling in the TFET is increased compared to the gated homojunction diode. This leads to an increased drain current of 57 μA/μm and a reduced subthreshold swing of 102 mV/dec, from 240 mV/dec. However, trap assisted tunneling prevents devices from realizing subthreshold slopes below the Boltzmann limit of 60 mV/dec. Nevertheless, this work shows the capability of tunnel field effect transistors to be realized in GaN by taking advantage of the spontaneous and piezoelectric polarization in the III-N material system.
Wide-Area Media Sharing with UPnP/DLNA (2008)

DLNA has defined schemes for interoperable content sharing between devices in a home network. In this paper we describe our architecture for extending UPnP and sharing content between devices using DLNA specified schemes across broadband wireless networks. The architecture relies only on end-points and does not require any service specific intelligence in network servers. We also describe how that same approach can also enable sharing between remote mobile devices and in-home off-the-shelf DLNA compatible devices.
Par j 1 and Par j 2, the major allergens from <i>Parietaria judaica</i> pollen, have similar immunoglobulin E epitopes (2003)

Three similar IgE-epitopes of major allergens from P. judaica have been described. They could be good candidates for designing of IgE haptens as therapeutic agents with reduced anaphylactic side-effects or for developing hypoallergenic variants of these major allergens.
Circular DNA tumor viruses make circular RNAs (2018)

Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV) cause ∼2% of all human cancers. RNase R-resistant RNA sequencing revealed that both gammaherpesviruses encode multiple, uniquely stable, circular RNAs (circRNA). EBV abundantly expressed both exon-only and exon-intron circRNAs from the BamHI A rightward transcript (BART) locus (circBARTs) formed from a spliced BART transcript and excluding the EBV miRNA region. The circBARTs were expressed in all verified EBV latency types, including EBV-positive posttransplant lymphoproliferative disease, Burkitt lymphoma, nasopharyngeal carcinoma, and AIDS-associated lymphoma tissues and cell lines. Only cells infected with the B95-8 EBV strain, with a 12-kb BART locus deletion, were negative for EBV circBARTs. Less abundant levels of EBV circRNAs originating from LMP2- and BHLF1-encoding genes were also identified. The circRNA sequencing of KSHV-infected primary effusion lymphoma cells revealed a KSHV-encoded circRNA from the vIRF4 locus (circvIRF4) that was constitutively expressed. In addition, KSHV polyadenylated nuclear (PAN) RNA locus generated a swarm (>100) of multiply backspliced, low-abundance RNase R-resistant circRNAs originating in both sense and antisense directions consistent with a novel hyperbacksplicing mechanism. In EBV and KSHV coinfected cells, exon-only EBV circBARTs were located more in the cytoplasm, whereas the intron-retaining circBARTs were found in the nuclear fraction. KSHV circvIRF4 and circPANs were detected in both nuclear and cytoplasmic fractions. Among viral circRNAs tested, none were found in polysome fractions from KSHV-EBV coinfected BC1 cells, although low-abundance protein translation from viral circRNAs could not be excluded. The circRNAs are a new class of viral transcripts expressed in gammaherpesvirus-related tumors that might contribute to viral oncogenesis.
Integrated Ammonia Recovery Technology in Conjunction with Dairy Anaerobic Digestion (2010)

With approximately 696 million tons of animal manure produced yearly in the United States, and 46% of that being generated on concentrated animal feeding operations (CAFOs) (Ribaudo et al., 2003), animal waste management is becoming an important environmental concern. It causes air and water quality concerns and climate impacts. In addition, many CAFOs generate more waste than can be disposed of without causing localized nutrient buildup. Although anaerobic digestion (AD) has been widely used in animal manure management for methane entrapment, reduction of volatile organics, solids reduction, chemical oxygen demand, vector reduction and pathogen removal, it does not reduce or recover nutrients. In fact, AD can make ammonia emissions even more problematic as it partially converts organic nitrogen to the ammonia form.
Almost linear speed-up of distributed discrete event simulations (2003)

A distributed simulation algorithm is presented which explores the topology of the simulated system using precomputed minimum propagation delays between subsystems. The algorithm also uses opaque periods which are the delays caused by the nonpreemptive states these subsystems can enter. The algorithm achieves Theta (N/log N) speed-up when run on an appropriate physically realizable N-processor parallel computer. No other algorithm for distributed discrete event simulation has been theoretically shown to achieve this level of efficiency. Experiments show speed-ups of greater than 20 on 25 processors of a shared memory MIMD computer and greater than 1900 on 2/sup 14/ processors of a SIMD computer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>gag</i> , <i>vif</i> , and <i>nef</i> Genes Contribute to the Homologous Viral Interference Induced by a Nonproducer Human Immunodeficiency Virus Type 1 (HIV-1) Variant: Identification of Novel HIV-1-Inhibiting Viral Protein Mutants (1998)

We previously demonstrated that expression of the nonproducer F12-human immunodeficiency virus type 1 (HIV-1) variant induces a block in the replication of superinfecting HIV that does not depend on the down-regulation of CD4 HIV receptors. In order to individuate the gene(s) involved in F12-HIV-induced interference, vectors expressing each of the nine F12-HIV proteins were transfected in HIV-susceptible HeLa CD4 cells. Pools of cell clones stably producing each viral protein were infected with HIV-1, and virus release was measured in terms of reverse transcriptase activity in supernatants. We hereby demonstrate that HeLa CD4 cells expressing the F12-HIV gag, vif, or nef gene were resistant, to different degrees, to infection with T-cell-line-adapted HIV-1 strains. Conversely, expression of either the tat, rev, or vpu F12-HIV gene increased the rate of HIV release, and no apparent effects on HIV replication were observed in cells expressing either the F12-HIV vpr, pol, or env gene. No variation of CD4 exposure was detected in any of the uninfected HeLa CD4 pools. These data indicate that F12-HIV homologous viral interference is the consequence of the synergistic anti-HIV effects of Gag, Vif, and Nef proteins. Retrovirus vectors expressing F12-HIV vif or nef allowed us to further establish that the expression of each mutated protein (i) inhibits the replication of clinical HIV-1 isolates as well, (ii) impairs the infectivity of the virus released by cells chronically infected with HIV-1, and (iii) limitedly to F12-HIV Vif protein, induces HIV resistance in both vif-permissive and vif-nonpermissive cells. The levels of action of F12-HIV vif and nef anti-HIV effects were also determined. We observed that HIV virions emerging from the first viral cycle on F12-HIV vif-expressing cells, although released in unaltered amounts, had a strongly reduced ability to initiate the retrotranscription process when they reinfected parental HeLa CD4 cells. Differently, we observed that expression of F12-HIV Nef protein affects the HIV life cycle at the level of viral assembling and/or release. For the first time, an inhibitory effect on the HIV life cycle in both acutely and chronically infected cells induced by mutated Vif and Nef HIV-1 proteins is described. These genes could thus be proposed as new useful reagents for anti-HIV gene therapy.
Correction of diverse muscular dystrophy mutations in human engineered heart muscle by single-site genome editing (2018)

Genome editing with CRISPR/Cas9 is a promising new approach for correcting or mitigating disease-causing mutations. Duchenne muscular dystrophy (DMD) is associated with lethal degeneration of cardiac and skeletal muscle caused by more than 3000 different mutations in the X-linked dystrophin gene (<i>DMD</i>). Most of these mutations are clustered in "hotspots." There is a fortuitous correspondence between the eukaryotic splice acceptor and splice donor sequences and the protospacer adjacent motif sequences that govern prokaryotic CRISPR/Cas9 target gene recognition and cleavage. Taking advantage of this correspondence, we screened for optimal guide RNAs capable of introducing insertion/deletion (indel) mutations by nonhomologous end joining that abolish conserved RNA splice sites in 12 exons that potentially allow skipping of the most common mutant or out-of-frame <i>DMD</i> exons within or nearby mutational hotspots. We refer to the correction of DMD mutations by exon skipping as myoediting. In proof-of-concept studies, we performed myoediting in representative induced pluripotent stem cells from multiple patients with large deletions, point mutations, or duplications within the <i>DMD</i> gene and efficiently restored dystrophin protein expression in derivative cardiomyocytes. In three-dimensional engineered heart muscle (EHM), myoediting of DMD mutations restored dystrophin expression and the corresponding mechanical force of contraction. Correcting only a subset of cardiomyocytes (30 to 50%) was sufficient to rescue the mutant EHM phenotype to near-normal control levels. We conclude that abolishing conserved RNA splicing acceptor/donor sites and directing the splicing machinery to skip mutant or out-of-frame exons through myoediting allow correction of the cardiac abnormalities associated with DMD by eliminating the underlying genetic basis of the disease.
Classification and quantitative estimation of cognitive stress from in-game keystroke analysis using EEG and GSR (2017)

This paper presents a novel approach to classify cognitive stress, at an inter-personal level, induced by a proposed Stroop-Tetris game using Electroencephalogram (EEG), Galvanic Skin Response (GSR) and Photoplethysmogram (PPG). Features are derived from each sensor aimed at discriminating low and high cognitive stress, followed by feature reduction. Leave-one-subject-out cross-validation across the data shows high median accuracies in classification individually for EEG, GSR and PPG analysis (72.75%, 69.30% and 64.75% respectively), which was further enhanced to 77.25% by employing feature level fusion. A novel metric derived from the keystrokes of the subjects is introduced to quantify real-time stress. An intra-personal regression model to relate EEG features with the real-time stress metric demonstrates high correlation and low p-value between predicted and actual values of this metric.
A sampled or superstructure grating tunable twin-guide laser for wide tunability with 2 tuning currents (2002)

A new widely tunable laser structure is proposed, a tunable twin guide (TTG) laser with 2 different sampled or superstructure gratings. This widely tunable laser only requires 2 instead of 3 tuning currents and has a much shorter cavity length than existing widely tunable laser diodes.
SecureNN: Efficient and Private Neural Network Training. (2018)

Neural Networks (NN) provide a powerful method for machine learning training and inference. To effectively train, it is desirable for multiple parties to combine their data — however, doing so conflicts with data privacy. In this work, we provide novel three-party secure computation protocols for various NN building blocks such as matrix multiplication, convolutions, Rectified Linear Units, Maxpool, normalization and so on. This enables us to construct three-party secure protocols for training and inference of several NN architectures such that no single party learns any information about the data. Experimentally, we implement our system over Amazon EC2 servers in different settings. Our work advances the state-of-the-art of secure computation for neural networks in three ways: Scalability: We are the first work to provide neural network training on Convolutional Neural Networks (CNNs) that have an accuracy of >99% on the MNIST dataset; Performance: For secure inference, our system outperforms prior 2 and 3-server works (SecureML, MiniONN, Chameleon, Gazelle) by 6x-113x (with larger gains obtained in more complex networks). Our total execution times are 2-4x faster than even just the online times of these works. For secure training, compared to the only prior work (SecureML) that considered a much smaller fully connected network, our protocols are 79x and 7x faster than their 2 and 3-server protocols. In the WAN setting, these improvements are more dramatic and we obtain an improvement of 553x! Security: Our protocols provide two kinds of security: full security (privacy and correctness) against one semi-honest corruption and the notion of privacy against one malicious corruption [Araki et al. CCS’16]. All prior works only provide semi-honest security and ours is the first system to provide any security against malicious adversaries for the secure computation of complex algorithms such as neural network inference and training. Our gains come from a significant improvement in communication through the elimination of expensive garbled circuits and oblivious transfer protocols.