gebhart/patrepeval huggingface dataset:
Information-theoretically optimal compressed sensing via spatial coupling and approximate message passing (2012)

We study the compressed sensing reconstruction problem for a broad class of random, band-diagonal sensing matrices. This construction is inspired by the idea of spatial coupling in coding theory. As demonstrated heuristically and numerically by Krzakala et al. [11], message passing algorithms can effectively solve the reconstruction problem for spatially coupled measurements with undersampling rates close to the fraction of non-zero coordinates. We use an approximate message passing (AMP) algorithm and analyze it through the state evolution method. We give a rigorous proof that this approach is successful as soon as the undersampling rate δ exceeds the (upper) Rényi information dimension of the signal, d̅(p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> ). More precisely, for a sequence of signals of diverging dimension n whose empirical distribution converges to p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> , reconstruction is with high probability successful from d̅(p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> )n+o(n) measurements taken according to a band diagonal matrix. For sparse signals, i.e. sequences of dimension n and k(n) non-zero entries, this implies reconstruction from k(n) + o(n) measurements. For `discrete' signals, i.e. signals whose coordinates take a fixed finite set of values, this implies reconstruction from o(n) measurements. The result is robust with respect to noise, does not apply uniquely to random signals, but requires the knowledge of the empirical distribution of the signal p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> .
A Reconfigurable Antenna-Based Solution for Stationary Device Authentication in Wireless Networks (2012)

Applying channel information for user authentication is gaining attention in the area of wireless network security. Similarly, reconfigurable antennas capable of generating multiple decorrelated channel realizations have become increasingly popular in wireless systems. In this paper we propose and evaluate a channel-based authentication scheme that applies the capabilities of a pattern reconfigurable antenna for improved performance in user authentication. Field measurements of the channel frequency response employing such an antenna were performed to quantify the performance of the proposed scheme. Based on these measurements, we show the effect of correlation that exists between the different modes on the authentication performance. Furthermore, the performance gain that can be achieved by the scheme is studied as a function of the number of antenna modes. Offline mode analysis is performed to give a loose upper bound on performance while online mode analysis results are presented to quantify achievable authentication performance in realtime. A general guideline on how to choose the different elements of the decision metric in order to realize better performance for physical layer-based authentication schemes based on any diversity scheme is also developed.
Development of high efficiency GaN-based multiquantum-well light-emitting diodes and their applications (2002)

Highly efficient GaInN-GaN multiple quantum-well (MQW) light-emitting diodes (LEDs) were successfully developed by the low-temperature AlN buffer layer method for metal-organic vapor phase epitaxy (MOVPE). The light-emitting layer of the GaInN-GaN MQW drastically enhances the performance of GaN-based LEDs in terms of the efficiency and spectrums. Flip-chip (FC) type MQW LEDs have been newly developed to increase efficiency in extracting light from the GaN-based crystal to the outside. The luminous intensities of FC type blue and green LEDs are typically 6 and 14 cd, respectively, at 20 mA. The output power of the FC-type LEDs was 14 mW at 20 mA, which was approximately two times higher than that of the conventional face-up type blue LEDs. The external quantum efficiency of blue FC-type LEDs was as high as 20% at 20 mA. New multicolor package was developed using these high performance nitride-based LEDs and commercial AlGaInP-based red LEDs, the color range of which is the largest among other flat panel display devices.
Prediction of postoperative intraocular lens tilt using swept-source optical coherence tomography (2017)

The correlations between crystalline lens tilt and IOL tilt using whole-eye scanning indicate that preoperative tilt determination using SS-OCT could help predict postoperative IOL tilt, assist in IOL (toric) power calculations, and potentially improve visual outcomes.
Resource Aware Routing Protocol in Heterogeneous Wireless Machine-to-Machine Networks (2015)

Routing algorithm can significantly impact network performance. Routing in a network containing heterogeneous nodes differs from routing in a network with homogeneous nodes. If the routing algorithm is designed to fit less powerful nodes, the resources of more powerful nodes are wasted and network performance can be degraded. If the routing algorithm is developed to suit more powerful nodes, less powerful nodes may not have sufficient resources to run the algorithm and network may break down. Routing algorithms developed for homogeneous networks do not work well for heterogeneous networks. The IETF designed the IPv6 Routing Protocol for Low-Power and Lossy Networks (RPL) by taking into account resource heterogeneity and defined four modes of operation. However, RPL only allows one mode of operation for all routers in a network. This paper proposes a resource-aware adaptive mode RPL (RAM-RPL) to achieve adaptive mode of operation in heterogeneous wireless machine-to-machine (M2M) networks. RAM-RPL not only allows routers to have mixed modes of operation in a network but also allows routers to adaptively adjust their modes of operation during network operation. Acting parent and acting root techniques are introduced to realize adaptive mode of operation and route compression. RAM-RPL exploits resource heterogeneity and shifts routing workload from less powerful nodes to more powerful nodes. Simulation results show that RAM-RPL can improve data packet delivery rate by 26% and reduce control message overhead by 53% while maintaining similar packet latency.
Species-Independent Inhibition of Abnormal Prion Protein (PrP) Formation by a Peptide Containing a Conserved PrP Sequence (1999)

Conversion of the normal protease-sensitive prion protein (PrP) to its abnormal protease-resistant isoform (PrP-res) is a major feature of the pathogenesis associated with transmissible spongiform encephalopathy (TSE) diseases. In previous experiments, PrP conversion was inhibited by a peptide composed of hamster PrP residues 109 to 141, suggesting that this region of the PrP molecule plays a crucial role in the conversion process. In this study, we used PrP-res derived from animals infected with two different mouse scrapie strains and one hamster scrapie strain to investigate the species specificity of these conversion reactions. Conversion of PrP was found to be completely species specific; however, despite having three amino acid differences, peptides corresponding to the hamster and mouse PrP sequences from residues 109 to 141 inhibited both the mouse and hamster PrP conversion systems equally. Furthermore, a peptide corresponding to hamster PrP residues 119 to 136, which was identical in both mouse and hamster PrP, was able to inhibit PrP-res formation in both the mouse and hamster cell-free systems as well as in scrapie-infected mouse neuroblastoma cell cultures. Because the PrP region from 119 to 136 is very conserved in most species, this peptide may have inhibitory effects on PrP conversion in a wide variety of TSE diseases.
Novel <i>Bacillus thuringiensis</i> Binary Insecticidal Crystal Proteins Active on Western Corn Rootworm, <i>Diabrotica virgifera virgifera</i> LeConte (2002)

A new family of insecticidal crystal proteins was discovered by screening sporulated Bacillus thuringiensis cultures for oral activity against western corn rootworm (WCR) larvae. B. thuringiensis isolates PS80JJ1, PS149B1, and PS167H2 have WCR insecticidal activity attributable to parasporal inclusion bodies containing proteins with molecular masses of ca. 14 and 44 kDa. The genes encoding these polypeptides reside in apparent operons, and the 14-kDa protein open reading frame (ORF) precedes the 44-kDa protein ORF. Mutagenesis of either gene in the apparent operons dramatically reduced insecticidal activity of the corresponding recombinant B. thuringiensis strain. Bioassays performed with separately expressed, biochemically purified 14- and 44-kDa polypeptides also demonstrated that both proteins are required for WCR mortality. Sequence comparisons with other known B. thuringiensis insecticidal proteins failed to reveal homology with previously described Cry, Cyt, or Vip proteins. However, there is evidence that the 44-kDa polypeptide and the 41.9- and 51.4-kDa binary dipteran insecticidal proteins from Bacillus sphaericus are evolutionarily related. The 14- and 44-kDa polypeptides from isolates PS80JJ1, PS149B1, and PS167H2 have been designated Cry34Aa1, Cry34Ab1, and Cry34Ac1, respectively, and the 44-kDa polypeptides from these isolates have been designated Cry35Aa1, Cry35Ab1, and Cry35Ac1, respectively.
Discovery of the Serenex Hsp90 Inhibitor, SNX5422 (2013)

SNX 5422 is a synthetic orally bioavailable inhibitor of Hsp90 discovered by the biotechnology company Serenex Inc. (Durham NC, USA) using the chemoproteomic platform proteome mining. The molecule is derived from an indoline scaffold and is therefore structurally distinct from all other known Hsp90 inhibitors reported in the literature. The molecule also inhibits with nM potency the related heat-shock proteins GRP94 and TRAP-1, although it has yet to be established to what extent these actions contribute to its biological effects in vivo. SNX5422 is a pro-drug with oral bioavailability and is hydrolyzed to the active parent compound SNX2112 upon uptake. In cell-based and initial animal studies, and subsequent full pre-clinical work-up, SNX5422 exhibited all the hallmarks of a bona fide Hsp90 inhibitor (i.e. degradation of the expected portfolio of Hsp90-dependent clients, induction of Hsp70, tumor growth arrest). In general, the compound was well tolerated in animals, and showed potent efficacy in a variety of xenograph models of human cancer, both alone and in combination with other existing anticancer agents. The compound was therefore advanced to Phase I safety studies. At the time of writing SNX5422 had completed two Phase I clinical trials conducted by the National Cancer Institutes (Bethesda, MD, USA) and Pfizer (who acquired Serenex in 2008). Chapter 7 covers the discovery and development of SNX5422 and summarizes its biological activities in vivo.
Effects of Aging and Co Addition on Martensitic and Magnetic Transitions in Ni–Al–Fe β-based Shape Memory Alloys (2006)

Effects of low temperature aging and the addition of Co on the martensitic and magnetic transitions in the Ni–Al–Fe β (B2-type structure) alloy system were investigated using differential scanning calorimetry, transmission electron microscopy and vibrating sample magnetometry. The martensitic transition temperatures of a Ni57Al25Fe18 specimen homogenized at 1 473 K for 1 h were decreased by aging after homogenization, the maximum decrease by aging being observed at 573 K. On the other hand, the substitution of Co or Fe for Ni induced a decrease of the martensitic transition temperatures and an increase of the Curie temperature, while the substitution of Co for Fe resulted in an increase of the martensitic transition and Curie temperatures. Co was thus shown to be an effective element by which both the martensitic and magnetic transition temperatures can be controlled.
A pilot study identifying cancer-associated macrophage-like cells in the blood of cancer patients. (2014)

e22014 Background: Using a “liquid biopsy” to recover Circulating Tumor Cells (CTCs) has revealed an accompanying macrophage subset that may be a highly sensitive biomarker for solid tumors. This newly discovered cell type, defined as a circulating Cancer Associated Macrophage-Like cell (CAML), has been identified as a specialized cancer specific blood monocyte. We studied the peripheral blood of cancer patients to ascertain the prevalence of this cell in relation to CTCs. Here, we supply evidence that this previously unidentified circulating cell can be used in conjunction with CTCs to sequentially track cancer treatment and provide clinically relevant information in patients with solid tumors. Methods: Peripheral blood samples from 79 cancer patients were tested, with a patient distribution including, stage I - IV; breast, pancreatic, and prostate cancers; newly diagnosed/untreated patients; and patients undergoing systemic therapies. The study included 30 healthy controls. CellSieve microfilters were used to isolate both CTCs and CAMLs from 7.5 mL of whole peripheral blood. CTCs and CAMLs collected by this size exclusion technique were fixed, permeabilized, and stained with DAPI, antibody cocktail against cytokeratin 8, 18 and 19, EpCAM, and CD45. CAMLs were defined as enlarged, multinuclear cells with diffuse cytoplasmic cytokeratin, and CTCs were defined as filamentous cytokeratin cells that are not positive for CD45. Results: CAMLs were found in 97% patients with stage III/IV cancer, 83% with stage I/II and 92% of patients overall, regardless of cancer type. By comparison, CTCs were found in 54% of the same sample set. Specifically, CAMLs were found in 86% of prostate, 93% of pancreatic, and 97% of breast patient samples. CAMLs and CTCs were not found in controls. Conclusions: We present evidence that highly differentiated CAMLs can be found in the blood of most cancer patients, when tested by microfiltration. The presence of this cell expands the concept of using a “liquid biopsy” to indicate metastatic cancer and in sequentially tracking cancer treatment using circulating cells. Though preliminary, the presence of CAMLs in early stage patient samples suggests the possibility of using CAMLs as a biomarker for early stage cancer screening.
Skip-duty control method for minimizing switching stress in low-power multi-level Dc-Dc converters (2015)

This paper addresses the problem of large sporadic transient voltages across the switches of low-power multi-level dc-dc converters and introduces a digital control-based method for their elimination. The physical origin of the large voltage transient spikes occurring at certain operating points, corresponding to zero current ripple operation, is explained. A control-based solution for the problem, based on the avoidance of the critical operating points, i.e. on skipping of critical duty ratio values, while maintaining tight voltage regulation and symmetric inductor current waveforms, is introduced. The effectiveness of the control method is demonstrated with a wide-input 10 V/ 3 A output, 1 MHz, three-level buck dc-dc experimental prototype, where it is shown that the skip-duty control completely eliminates the sporadic spikes.
Divergent PAM Specificity of a Highly-Similar SpCas9 Ortholog (2018)

RNA-guided DNA endonucleases of the CRISPR-Cas system are widely used for genome engineering and thus have numerous applications in a wide variety of fields. The range of sequences that CRISPR endonucleases can recognize, however, is constrained by the need for a specific protospacer adjacent motif (PAM) flanking the target site. In this study, we demonstrate the natural PAM plasticity of a highly-similar, yet previously uncharacterized, Cas9 from Streptococcus canis (ScCas9) through rational manipulation of distinguishing motif insertions. To this end, we report a divergent affinity to 5’-NNGT-3’ PAM sequences and demonstrate the editing capabilities of the ortholog in both bacterial and human cells. Finally, we build an automated bioinformatics pipeline, the Search for PAMs by ALignment Of Targets (SPAMALOT), which further explores the microbial PAM diversity of otherwise-overlooked Streptococcus Cas9 orthologs. Our results establish that ScCas9 can be utilized both as an alternative genome editing tool and as a functional platform to discover novel Streptococcus PAM specificities.
Modeling, Analysis, and Experimental Validation of a Bifurcation-Based Microsensor (2011)

Microelectromechanical chemical and biological sensors have garnered significant interest over the past two decades due to their ability to selectively detect very small amounts of added mass. Today, most resonant mass sensors utilize chemomechanically-induced shifts in the linear natural frequency for detection. In this paper, an alternative, amplitude-based sensing approach, which exploits dynamic transitions across saddle-node bifurcations that exist in a microresonator’s nonlinear frequency response, is investigated. In comparison to their more traditional, linear counterparts, these bifurcation-based sensors have the ability to provide improved sensor metrics, eliminate power-consuming hardware from final sensor implementations, and operate effectively at smaller (e.g. nano) scales. The present work details the ongoing development of a bifurcation-based mass sensor founded upon the near-resonant response of piezoelectrically-actuated microcantilevers. Specifically, the work details the modeling and analysis of these devices, their functionalization, and proof-of-concept mass sensing experiments which not only validate the proposed technique, but allow for the direct evaluation of pertinent sensor metrics.
Strontium and barium iodide high light yield scintillators (2008)

Europium-doped strontium and barium iodide are found to be readily growable by the Bridgman method and to produce high scintillation light yields. SrI2(Eu) emits into the Eu2+ band, centered at 435nm, with a decay time of 1.2μs and a light yield of ∼90000photons∕MeV. It offers energy resolution better than 4% full width at half maximum at 662keV, and exhibits excellent light yield proportionality. BaI2(Eu) produces &gt;30000photons∕MeV into the Eu2+ band at 420nm (&lt;1μs decay). An additional broad impurity-mediated recombination band is present at 550nm (&gt;3μs decay), unless high-purity feedstock is used.
Characterization of a Chemokine Receptor-Related Gene in Human Herpesvirus 8 and Its Expression in Kaposi's Sarcoma (1997)

Human herpesvirus 8 (HHV-8) is a recently discovered, virus that is highly associated with Kaposi's sarcoma (KS) and AIDS-associated body cavity lymphomas, although it is also found in some normal individuals. HHV-8 is related by nucleotide sequence homology to herpesvirus saimiri (HVS), which causes T cell lymphomas in some New World monkeys, and to Epstein-Barr virus (EBV), a human herpesvirus linked etiologically with Burkitt's lymphoma and nasopharyngeal carcinoma. We report that, like HVS but unlike EBV, HHV-8 contains a gene (ORF74) with significant sequence homology to the high-affinity IL-8 receptor, a member of the alpha (CXC) chemokine receptor family of transmembrane G protein-coupled receptors. We also show by reverse transcription PCR that the chemokine receptor-related HHV-8 gene is detectable in some RNA samples from KS tissue, and that its expression varies independently from that of ORF26, a minor capsid protein. The presence of a potential chemokine receptor in HHV-8 and its expression in KS tissue suggests that it may be important in the regulation of viral gene expression and may play a role in the etiology of KS and AIDS-related body cavity lymphomas.
Soft quality-of-service control for multimedia traffic on ATM networks (2002)

The provision of bandwidth-on-demand with quality-of-service (QoS) guarantees has long been a promise of ATM networks. However existing traffic management services provide only static traffic contracts bound to network-level QoS measured in terms of traffic engineering parameters. These parameters do not convey application-specific needs. As a result, the network does not consider the sensitivity of application performance to bandwidth allocation leading to inefficient use of bandwidth and poor end-to-end system performance. A novel traffic management framework for adaptive multimedia applications based on bandwidth renegotiation with soft QoS guarantees is presented. The design of a soft-QoS controller is given. Experimental results using interactive MPEG video applications show that the proposed framework allows the network to double the number of accepted connections while meeting their soft-QoS requirements for a wide range of bandwidth renegotiation requests.
A distributed wavelet compression algorithm for wireless sensor networks using lifting (2004)

We address the problem of compression for wireless sensor networks, where each of the sensors has limited power, and acquires data that should be sent to a remote central node. The final goal is to have a reconstructed version of the sampled field at the central node, with the sensors spending as little energy as possible. We propose a distributed wavelet algorithm, based on the lifting scheme, as a means to decorrelate data at the nodes by exchanging information between neighboring sensors. A key result of our work is that by using a locally adaptive distributed transform it is possible to optimize overall power consumption by operating at the right trade-off point between local processing and transmission costs.
FIBER OPTIC GYROSCOPES WITH DEPOLARIZED LIGHT; PATENT (1992)

A depolarized fiber optic gyroscope with a detector for detecting a rotation about an axis of rotation and a method therefor is disclosed. The gyroscope includes a depolarized light source for generating the depolarized light; a gyro coil for, conducting depolarized light about the axis of rotation, the gyro coil including a coil of a non-polarization preserving fiber having first and second ends; a depolarizer with first and second ports for eliminating birefringence induced scale factor variations caused by the non-polarization preserving fiber, the first port of the depolarizer being coupled to the first end of the gyro coil; and a coupler device for coupling the second end of the gyro coil, the second port of the depolarizer, the detector and the depolarized light source, without utilizing a polarizer.
Association of polymorphism at the type I collagen (COL1A1) locus with reduced bone mineral density, increased fracture risk, and increased collagen turnover (1999)

These data support the findings that the COL1A1 gene polymorphism is associated with low BMD and fracture risk, and suggest a possible physiologic effect on total body turnover of type I collagen.
Reliable Logic Circuit Elements that Exploit Nonlinearity in the Presence of a Noise Floor (2009)

The response of a noisy nonlinear system to deterministic input signals can be enhanced by cooperative phenomena. We show that when one presents two square waves as input to a two-state system, the response of the system can produce a logical output (NOR/OR) with a probability controlled by the noise intensity. As one increases the noise (for fixed threshold or nonlinearity), the probability of the output reflecting a NOR/OR operation increases to unity and then decreases. Changing the nonlinearity (or the thresholds) of the system changes the output into another logic operation (NAND/AND) whose probability displays analogous behavior. The interplay of nonlinearity and noise can yield logic behavior, and the emergent outcome of such systems is a logic gate. This "logical stochastic resonance" is demonstrated via an experimental realization of a two-state system with two (adjustable) thresholds.