gebhart/patrepeval huggingface dataset:
Soaker hose versus compact nonporous windscreen: A comparison of performance at infrasonic frequencies (2005)

A compact nonporous windscreen described previously [J. Acoust. Soc. Am. 114, No. 4, Pt. 2, 2323 (2003)] was tested in the field against a soaker hose array to compare performance at infrasonic frequencies. The cylindrically shaped compact windscreen, made of closed-cell polyurethane foam, had dimensions 0.0762 m i.d. ×0.2286 m height ×0.0127 m wall (3×9×0.5 in.). The low acoustic impedance of the foam permits the propagation of infrasound through the walls of the windscreen with a transmission coefficient near unity. The soaker hoses were 15.24-m (50 ft.) long and coupled to a Chaparral model 5 low-frequency microphone. The hose plenum was removed and replaced with the compact windscreen for testing. A sonic boom simulator, located at a distance of 400 m (1/4 mile) from the microphone, generated tones at 3, 4, 5, and 6 Hz. Analysis of the signals received by the interior microphone revealed that the tones transmitted through the windscreen, as well as the reduction of background noise due to naturally occurring wind-generated turbulence, were nearly identical for the two types of windscreen.
Binding Specificity and Mutational Analysis of the Phosphotyrosine Binding Domain of the Brain-specific Adaptor Protein ShcC (1996)

Shc proteins (hereafter referred to as ShcA) represent major substrates of tyrosine phosphorylation by a wide variety of growth factors and cytokines. We have recently described a novel ShcA-like protein, ShcC, which like ShcA contains an NH2-terminal phosphotyrosine binding domain (PTB), a central effector region (CH1) and a COOH-terminal Src homology 2 domain (SH2). Both the SH2 and PTB domains of ShcC bind a similar profile of proteins as the comparable regions of ShcA. In an effort to define the functional differences or similarities between ShcA and ShcC, we have further characterized the PTB domain of ShcC. Using a degenerate phosphopeptide library screen, we show that the PTB domain of ShcC preferentially binds the sequence His-hydrophobic-Asn/hydrophobic-Asn-Pro-Ser/Thr-Tyr(P). This sequence is similar to the binding site for the ShcA PTB domain, suggesting that these two proteins may have overlapping specificities. In addition, random mutagenesis of the ShcC PTB domain has identified several amino acids important for PTB function (Gly32, Glu63, Ala136, Gly139, and Asp140). Mutation of these amino acids dramatically reduces the affinity of the ShcC PTB domain for the activated epidermal growth factor receptor in vitro.
Glycoproteomic probes for fluorescent imaging of fucosylated glycans <i>in vivo</i> (2006)

Glycomics is emerging as a new field for the biology of complex glycoproteins and glycoconjugates. The lack of versatile glycan-labeling methods has presented a major obstacle to visualizing at the cellular level and studying glycoconjugates. To address this issue, we developed a fluorescent labeling technique based on the Cu(I)-catalyzed [3 + 2] cycloaddition, or click chemistry, which allows rapid, versatile, and specific covalent labeling of cellular glycans bearing azide groups. The method entails generating a fluorescent probe from a nonfluorescent precursor, 4-ethynyl-N-ethyl-1,8-naphthalimide, by clicking the fluorescent trigger, the alkyne at the 4 position, with an azido-modified sugar. Using this click-activated fluorescent probe, we demonstrate incorporation of an azido-containing fucose analog into glycoproteins via the fucose salvage pathway. Distinct fluorescent signals were observed by flow cytometry when cells treated with 6-azidofucose were labeled with the click-activated fluorogenic probe or biotinylated alkyne. The intracellular localization of fucosylated glycoconjugates was visualized by using fluorescence microscopy. This technique will allow dynamic imaging of cellular fucosylation and facilitate studies of fucosylated glycoproteins and glycolipids.
Single-Photon Camera Guided Extreme Dynamic Range Imaging (2022)

Reconstruction of high-resolution extreme dynamic range images from a small number of low dynamic range (LDR) images is crucial for many computer vision applications. Current high dynamic range (HDR) cameras based on CMOS image sensor technology rely on multi-exposure bracketing which suffers from motion artifacts and signal-to-noise (SNR) dip artifacts in extreme dynamic range scenes. Recently, single-photon cameras (SPCs) have been shown to achieve orders of magnitude higher dynamic range for passive imaging than conventional CMOS sensors. SPCs are becoming increasingly available commercially, even in some consumer devices. Unfortunately, current SPCs suffer from low spatial resolution. To overcome the limitations of CMOS and SPC sensors, we propose a learning-based CMOS-SPC fusion method to recover high-resolution extreme dynamic range images. We compare the performance of our method against various traditional and state-of-the-art baselines using both synthetic and experimental data. Our method outperforms these baselines, both in terms of visual quality and quantitative metrics.
Human CD55 Expression Blocks Hyperacute Rejection and Restricts Complement Activation in Gal Knockout Cardiac Xenografts (2012)

HAR of GTKO hearts without hCD55 may occur. Expression of hCD55 seemed to restrict local complement activation but did not improve graft survival. Chronic vascular antibody deposition with evidence of protracted endothelial cell activation was seen. These observations suggest that non-Gal antibody-induced chronic endothelial cell activation coupled to possible hemostatic incompatibilities may be the primary stimulus for delayed xenograft rejection of GTKO hearts. To avoid possible HAR, future clinical studies should use donors expressing human complement regulatory proteins in the GTKO background.
Activities of heterodimers composed of DNA-binding- and transactivation-deficient subunits of the herpes simplex virus regulatory protein ICP4 (1991)

Two mutant strains (vi12 and vi13) of herpes simplex virus that contain insertion mutations in the sequences that encode the DNA-binding domain of viral regulatory protein ICP4 were generated. Both mutations disrupted specific DNA binding and resulted in transcriptionally inactive molecules; however, the ability of the mutant proteins to form dimers was retained. The mutant proteins formed heterodimers with an ICP4 deletion mutant (X25) that is nonfunctional but retains the ability to bind to consensus sites. Significantly elevated levels of early (E or beta) and "leaky late" (beta gamma or gamma 1) gene expression were observed upon coexpression of the insertion mutant and X25 ICP4 polypeptides. While the heterodimers composed of the vi13 and X25 peptides possessed DNA-binding activity, those composed of vi12 and X25 did not, indicating that DNA binding by the heterodimers may not be required for restored activity. Despite significant levels of early gene expression and viral DNA synthesis in vi12-infected X25 cells, true late (gamma 2) mRNA was not synthesized. This indicates that the structural requirements for ICP4 induction of different classes of viral genes may be different.
Long field-of-view MRI using continuous table motion (2004)

A method is presented for formation of an MK image of an arbitrarily long object. This is done by translating the object continuously through the magnetically homogenous volume of the MRI scanner, acquiring data during table motion, and accounting during the reconstruction for the relative displacement of the object for each cach measurement. The method is applied to MR imaging of the blood vessels of the abdomen, pelvis, and legs using intravenous administration of contrast material. Real-time reconstruction allows the operator to dynamically track the flow of contrast material through the legs and potentially adjust the table velocity interactively.
XNOR-SRAM (2019)

We present an in-memory computing SRAM macro for binary neural networks. The memory macro computes XNOR-and-accumulate for binary/ternary deep convolutional neural networks on the bitline without row-by-row data access. It achieves 33X better energy and 300X better energy-delay-product than digital ASIC and achieves high accuracy in machine learning tasks (98.3% for MNIST and 85.7% for CIFAR-10 datasets).
Abstract #5502: Inhibition of Notch signaling for the treatment of human carcinomas (2009)

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

Inhibition of Notch signaling for the treatment of human carcinomas Agamemnon Epenetos, Christina Kousparou, Spyros Stylianou Trojantec Ltd, the Bank of Cyprus Oncology Centre Nicosia, Cyprus Notch signaling is an evolutionary-conserved pathway in vertebrates and invertebrates which is involved many developmental processes, including cell fate decisions, apoptosis, proliferation, and stem-cell self renewal. There is increasing evidence that the same molecular pathways regulating the self renewal of stem cells are also being employed in cancer progression. The Notch signal transduction pathway has been implicated in the self-renewal of stem cells in hematopoietic, skin, neural, germ and breast tissue. Increasing evidence suggests that the Notch signaling pathway is frequently up regulated in many forms human malignancies including acute T-cell lymphoblastic leukemia, cervical, prostate, lung, breast and inhibition of the pathway could be a novel therapeutic approach for the treatment of human carcinomas. Furthermore, aberrant Notch regulation during the self-renewal of stem cells may cause certain human cancers. Thus, this pathway offers an attractive potential to target the cancer stem cells resulting in innovating cancer treatments. We have genetically engineered a fusion protein, consisting of the Drosophila transcription factor Antennapedia (ANTP) and with the truncated version of Mastermind-like (MAML) that behaves in a dominant negative (DN) fashion and inhibits Notch activation (ANTP/DN MAML, TR4). This novel fusion protein has been tested for its ability to target tumor cells in vitro and in vivo. Our data show that ANTP/DN MAML fusion protein, TR4 contains signals for proper cell targeting, internalization and nuclear transport. Furthermore, TR4 inhibits human mammary and colon xenograft tumor growth and metastases in immuno deficient mice. The immunogenicity and toxicity of TR4 was investigated in normal immuno-competent mice and the results indicate no immune responses or toxicity. Of interest, TR4 presence and activity was also detected in the brains of treated animals demonstrating that TR4 can cross the blood-brain barrier and potentially eliminate brain tumors and metastases, unlike other anticancer drugs and biologicals such as monoclonal antibodies that cannot cross the blood brain barrier.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 5502.
A theoretical investigation of the plasma klystron amplifier (1993)

The plasma klystron amplifier concept is investigated. The plasma klystron consists of a relativistic annular electron beam propagating through a space between a plasma column and drift tube wall. The annular electron beam, premodulated at the first cavity in the klystron, enters the space. An axial electric field accompanied by the modulated beam excites space charge waves in the plasma column, which acts like an inductive medium amplifying the electrostatic waves. The physical mechanism of self-amplification of the electrostatic waves is the two-stream instability, which is investigated in detail. Instability criteria indicate that the plasma should be opaque to sustain instability. A theoretical model to describe current modulation of the annular electron beam propagating through the space is developed. The electron beam current is modulated by the amplifying electric field fed by the plasma column. Saturation distance of the current modulation is a weakly dependent function of the initial energy modulation at the first cavity. Thus, a relatively low-power microwave input may well excite the two-stream instability and deliver a highly modulated beam to the extraction cavity. Due to a relatively large growth rate of the instability, required interaction length of the beam and plasma column is short for most applications.
The Effects Of Temperature On The Response Of A Porous Fiber Optic Humidity Sensor (1989)

Fiber optic waveguides based on porous glasses offer excellent sensitivity and specificity for remote chemical sensing. This paper examines the effect of temperature on the response of a porous fiber optic humidity sensor. Cobalt chloride is used as the colorimetric reagent, permeated into the porous segment of the fiber. The humidity response of the fiber has been evaluated over a temperature range of 25°C to 90°C. Temperature effects appear to result both from changes in the extinction coefficient of cobalt chloride as well as differences in the sensing probe's equilibrium constants. The basic temperature dependence of the humidity sensor has been modeled in an effort to provide compensation for the measurement probe in a real world environment.
Modular mechatronic system for stationary bicycles interfaced with virtual environment for rehabilitation (2014)

The VRACK system, a virtual reality mechatronic bicycle rehabilitation modular system was designed to convert most bicycles in virtual reality (VR) cycles. Preliminary testing of the augmented reality bicycle system was successful in demonstrating that a modular mechatronic kit can monitor and record kinetic and kinematic parameters of several riders.
Optimizing multiphoton fluorescence microscopy light collection from living tissue by noncontact total emission detection (epiTED) (2010)

A benefit of multiphoton fluorescence microscopy is the inherent optical sectioning that occurs during excitation at the diffraction-limited spot. The scanned collection of fluorescence emission is incoherent; that is, no real image needs to be formed on the detector plane. The nearly isotropic emission of fluorescence excited at the focal spot allows for new detection schemes that efficiently funnel all attainable photons to detector(s). We previously showed [Combs, C.A., et al. (2007) Optimization of multiphoton excitation microscopy by total emission detection using a parabolic light reflector. J. Microsc. 228, 330-337] that parabolic mirrors and condensers could be combined to collect the totality of solid angle around the excitation spot for tissue blocks, leading to ∼8-fold signal gain. Using a similar approach, we have developed an in vivo total emission detection (epiTED) instrument modified to make noncontact images from outside of living tissue. Simulations suggest that a ∼4-fold enhancement may be possible (much larger with lower NA objectives than the 0.95 NA used here) with this approach, depending on objective characteristics, imaging depth and the characteristics of the sample being imaged. In our initial prototype, 2-fold improvements were demonstrated in the mouse brain and skeletal muscle as well as the rat kidney, using a variety of fluorophores and no compromise of spatial resolution. These results show this epiTED prototype effectively doubles emission signal in vivo; thus, it will maintain the image signal-to-noise ratio at two times the scan rate or enable full scan rate at approximately 30% reduced laser power (to minimize photo-damage).
Eventually Consistent Transactions (full version) (2011)

When distributed clients query or update shared data, eventual consistency can provide better availability than strong consistency models. However, programming and implementing such systems can be difficult unless we establish a reasonable consistency model, i.e. some minimal guarantees that programmers can understand and systems can provide effectively. To this end, we propose a novel consistency model based on eventually consistent transactions. Unlike serializable transactions, eventually consistent transactions are ordered by two order relations (visibility and arbitration) rather than a single order relation. To demonstrate that eventually consistent transactions can be effectively implemented, we establish a handful of simple operational rules for managing replicas, versions and updates, based on graphs called revision diagrams. We prove that these rules are sufficient to guarantee correct implementation of eventually consistent transactions. Finally, we present two operational models (single server and server pool) of systems that provide eventually consistent transactions.
Optical properties of mixed-oxide WO3/MoO3 electrochromic films (1977)

The electrochromic optical absorption of mixed-oxide WO3/MoO3 amorphous films occurs at higher energy than either pure oxide alone. The systematics of the energy shifts as a function of MoO3 concentration and coloration density is determined. The data is explained by the intervalency charge-transfer model if we assume that electrons trapped at Mo6+ ions lie 0.73 eV deeper than electrons on W6+ ions. Measurements of electron diffusion in mixed oxides support this hypothesis. The maximum absorption peak of mixed oxides is 2.15 eV compared with 1.4 eV for WO3. This is close to the peak in eye sensitivity, thereby leading to improved electrochromic display devices.
A Context-Aware Framework for Detecting Sensor-Based Threats on Smart Devices (2019)

Sensors (e.g., light, gyroscope, and accelerometer) and sensing-enabled applications on a smart device make the applications more user-friendly and efficient. However, the current permission-based sensor management systems of smart devices only focus on certain sensors and any App can get access to other sensors by just accessing the generic sensor Application Programming Interface (API). In this way, attackers can exploit these sensors in numerous ways: they can extract or leak users' sensitive information, transfer malware, or record or steal sensitive information from other nearby devices. In this paper, we propose 6thSense, a context-aware intrusion detection system which enhances the security of smart devices by observing changes in sensor data for different tasks of users and creating a contextual model to distinguish benign and malicious behavior of sensors. 6thSense utilizes three different Machine Learning-based detection mechanisms (i.e., Markov Chain, Naive Bayes, and LMT). We implemented 6thSense on several sensor-rich Android-based smart devices (i.e., smart watch and smartphone) and collected data from typical daily activities of 100 real users. Furthermore, we evaluated the performance of 6thSense against three sensor-based threats: (1) a malicious App that can be triggered via a sensor, (2) a malicious App that can leak information via a sensor, and (3) a malicious App that can steal data using sensors. Our extensive evaluations show that the 6thSense framework is an effective and practical approach to defeat growing sensor-based threats with an accuracy above 96 percent without compromising the normal functionality of the device. Moreover, our framework reveals minimal overhead.
Soybean Rust Genome Sequencing Project (2006)

Soybean rust is caused by two closely related fungal pathogens, Phakopsora pachyrhizi and P. meibomiae. The Asian soybean rust pathogen P. pachyrhizi (ASR) is highly aggressive and is responsible for significant losses of soybean crop in Africa, Asia, Australia and South America (Figure 1). It was discovered for the first time in the continental United States in Louisiana in November 2004. During 2005, the presence of ASR was confirmed in 138 counties across nine southern states. ASR poses a significant threat to the U.S. soybean industry (17 billion dollar anually), depending on the severity and extent of subsequent outbreaks. Currently, no commercial soybeans are resistant to ASR, and fungicides are generally recognized as the most effective means for controlling the disease. Very little is known about the molecular mechanisms involved in the soybean-rust interaction. In order to develop new strategies to control the disease, it is crucial to increase our understanding of the biology of the pathogen and the infection process. Here, we present strategies and preliminary results from the P. pachyrhizi Genome Sequencing Project, including the complete mitochondrial genome sequence and the comparative analysis of expressed sequence tags (ESTs) generated from four specific-stages of P. pachyrhizi.
Compact Ion Source for Mass Spectrometers (1982)

Cyclotron-resonance device uses miniature components and permanent magnet for small size, low weight, and low cost. Gas molecules are ionized by electrons from hot filament. Magnetic field, acting with electrostatic drift field, causes ions to move in circles with a superimposed drift perpendicular to both fields, toward the exit. Compact source can be used for studying ion-molecule reactions by ion cyclotron-resonance methods in conventional mass spectrometer with either magnetic sector or quadrupole sector.
Activation of enhancer sequences in type II human T-cell leukemia virus and bovine leukemia virus long terminal repeats by virus-associated trans-acting regulatory factors (1986)

The ability of the sequences present in the long terminal repeats (LTRs) of human T-cell leukemia viruses type I and II (HTLV-I and HTLV-II) and of bovine leukemia virus to function as enhancer elements was investigated. Recombinant plasmids that contained the HTLV-I, HTLV-II, and bovine leukemia virus LTRs at a distance from a simian virus 40 promoter element located 5' to the bacterial gene encoding chloramphenicol acetyltransferase (EC 2.3.1.28) were constructed. We report that all three LTR sequences contain enhancer elements capable of increasing the level of gene expression directed from a distal heterologous promoter. The enhancer present in the HTLV-I LTR was active in uninfected cells of lymphoid and nonlymphoid origin. In contrast, the enhancer activity of the HTLV-II and bovine leukemia virus LTR sequences was evident only in virus-infected cells. This activity is likely due to virus-associated trans-acting transcriptional factors previously shown to be present in HTLV- and bovine leukemia virus-infected cells. The implication of these observations for virus replication and transforming activity are discussed.
Computationally designed adeno-associated virus (AAV) Rep 78 is efficiently maintained within an adenovirus vector (2011)

Adeno-associated virus (AAV) is a single-stranded parvovirus retaining the unique capacity for site-specific integration into a transcriptionally silent region of the human genome, a characteristic requiring the functional properties of the Rep 78/68 polypeptide in conjunction with AAV terminal repeat integrating elements. Previous strategies designed to assemble these genetic elements into adenoviral (Ad) backbones have been limited by the general intolerability of AAV Rep sequences, prompting us to computationally reengineer the Rep gene by using synonymous codon pair recoding. Rep mutants generated by using de novo genome synthesis maintained the polypeptide sequence and endonuclease properties of Rep 78, while dramatically enhancing Ad replication and viral titer yields, characteristics indistinguishable from adenovirus lacking coexpressed Rep. Parallel approaches using domain swaps encompassing WT and recoded genomic segments, coupled with iterative computational algorithms, collectively established that 3' cis-acting Rep genetic elements (and not the Rep 78 polypeptide) retain dominant-acting sequences inhibiting Ad replication. These data provide insights into the molecular relationships of AAV Rep and Ad replication, while expanding the applicability of synonymous codon pair reengineering as a strategy to effect phenotypic endpoints.