gebhart/patrepeval huggingface dataset:
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis (2012)

The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein-protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein's location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.
A cellular-band CDMA 0.25&#x03BC;m CMOS LNA linearized using active post-distortion (2005)

The theory of a linearization method using active post-distortion (APD) is explained. The method was used in a 0.25/spl mu/m CMOS LNA, designed for cellular band CDMA applications. The LNA achieves 1.2dB NF, 16.2dB power gain, and +8dBm IIP3 while consuming 12mA current from 2.6V supply voltage. It shows 5.7dBm improvement in IIP3 performance with 0.15dB NF penalty in comparison with an LNA which does not use APD.
Moving forward in HIV-associated cancer (2020)

Cancer has been linked to HIV since the earliest days of the epidemic. The unusually frequent occurrence of Kaposi sarcoma (KS) among men who have sex with men (MSM) in 1981 was a sentinel observation leading to the inclusion of KS in the first AIDS case definition.1,2 More than three decades later, major research investments have led to striking advances in understanding HIV pathogenesis, with antiretroviral therapy (ART) reducing AIDS complications and allowing HIV-infected individuals to experience life expectancy approaching that of persons without HIV.
Functional equivalence of hairpins in the RNA subunits of RNase MRP and RNase P in Saccharomyces cerevisiae (2000)

RNase MRP and RNase P are both ribonucleoprotein enzymes performing endonucleolytic cleavage of RNA. RNase MRP cleaves at a specific site in the precursor-rRNA transcript to initiate processing of the 5.8S rRNA. RNase P cleaves precursor tRNAs to create the 5' end of the mature tRNAs. In spite of their different specificities, the two RNases have significant structural similarities. For example, the two enzymes in Saccharomyces cerevisiae share eight protein subunits; only one protein is unique to each enzyme. The RNA components of the two nucleases also show striking secondary-structure similarity. To begin to characterize the role of the RNA subunits in enzyme function and substrate specificity, we swapped two hairpin structures (MRP3 and P3) between RNase MRP RNA and RNase P RNA of S. cerevisiae. The hairpins in the two enzymes could be exchanged without loss of function or specificity. On the other hand, when the MRP3 hairpin in RNase MRP of S. cerevisiae was replaced with the corresponding hairpin from the RNA of Schizosaccharomyces pombe or human RNase MRP, no functional enzyme was assembled. We propose that the MRP3 and P3 hairpins in S. cerevisiae perform similar functions and have coevolved to maintain common features that are different from those of MRP3 and P3 hairpins in other species.
Improved zero-tree coder research based on wavelet coefficients (2009)

By analyzing the characteristics of degree zerotree, both the EZW wavelet coder and SPIHT wavelet coder have advantages and disadvantages. Combined with the characteristics of wavelet coefficients, a zerotree based on hybrid encoder program was found. With the wavelet zerotree definition, taking the pre-processing zerotree before the zerotree coding, the identification of suitable programs of zerotree encoder comes out. The simulation results show that comparing with the separate use of EZW or SPIHT encoder, the hybrid encoder's encoding algorithm can effectively enhance the efficiency of code compression PSNR.
A Unification of Models of Tethered Satellites (2011)

In this paper, different conservative models of tethered satellites are related mathematically, and it is established in what limit they may provide useful insight into the underlying dynamics. An infinite dimensional model is linked to a finite dimensional model, the slack-spring model, through a conjecture on the singular perturbation of tether thickness. The slack-spring model is then naturally related to a billiard model in the limit of an inextensible spring. Next, the motion of a dumbbell model, which is lowest in the hierarchy of models, is identified within the motion of the billiard model through a theorem on the existence of invariant curves by exploiting Moser's twist map theorem. Finally, numerical computations provide insight into the dynamics of the billiard model.
[Urate transporter and renal hypouricemia]. (2003)

Urate, a purine metabolite, is a cause of gout(hyperuricemia), which is an independent risk factor for cardiovascular disease. Urate is a scavenger of reactive oxygen radicals that are involved in numerous diseases. Because humans have a renal urate reabsorption system and have lost hepatic uricase by mutational silencing in evolution, urate is present in human blood at high levels. We identified the long-hypothesized urate transporter in the human kidney (URAT1, encoded by SLC22A12), a urate anion exchanger regulating blood urate levels and targeted it with uricosuric and antiuricosuric agents. Moreover, we demonstrated that patients with renal hypouricemia have mutational defects in SLC22A12.
On the use of principal component analysis in the entropy based detection of denial‐of‐service attacks (2021)

Abstract This paper investigates some possibilities for the use of the principal component analysis (PCA) algorithm in the detection of denial‐of‐service (DoS) attacks. Two simple traffic features that are widely used for the detection of DoS attacks are source and destination ports of packets. In this paper, we show that by using only the principal component of these two features as the input for detection a powerful detector can be built. Shannon entropy formula and two generalized entropy formulas have been used in combination with PCA. The input dataset is generated in an emulation testbed. The type of attack that is investigated is SYN flood.
Forward Technology Solar Cell Experiment First On-Orbit Data (2007)

This paper presents first on orbit measured data from the Forward Technology Solar Cell Experiment (FTSCE). FTSCE is a space experiment housed within the 5th Materials on the International Space Station Experiment (MISSE-5). MISSE-5 was launched aboard the Shuttle return to flight mission (STS-114) on July 26, 2005 and deployed on the exterior of the International Space Station (ISS). The experiment will remain in orbit for nominally one year, after which it will be returned to Earth for post-flight testing and analysis. While on orbit, the experiment is designed to measure a 36 point current vs. voltage (IV) curve on each of the experimental solar cells, and the data is continuously telemetered to Earth. The experiment also measures the solar cell temperature and the orientation of the solar cells to the sun. A range of solar cell technologies are included in the experiment including state-of-the-art triple junction InGaP/GaAs/Ge solar cells from several vendors, thin film amorphous Si and CuIn(Ga)Se2 cells, and next-generation technologies like single-junction GaAs cells grown on Si wafers and metamorphic InGaP/InGaAs/Ge triple-junction cells. In addition to FTSCE, MISSE-5 also contains a Thin-Film Materials experiment. This is a passive experiment that will provide data on the effect of the space environment on more than 200 different materials. FTSCE was initially conceived in response to various on-orbit and ground test anomalies associated with space power systems. The Department of Defense (DoD) required a method of rapidly obtaining on orbit validation data for new space solar cell technologies, and NRL was tasked to devise an experiment to meet this requirement. Rapid access to space was provided by the MISSE Program which is a NASA Langley Research Center program. MISSE-5 is a completely self-contained experiment system with its own power generation and storage system and communications system. The communications system, referred to as PCSat, transmits and receives in the Amateur Radio band providing a node on the Amateur Radio Satellite Service. This paper presents an overview of the various aspects of MISSE-5 and a sample of the first measured on orbit data.
Cell Membranes As Barriers for The Use of Antisense Therapeutic Agents (2002)

Antisense oligonucleotides are promising therapeutical agents for numerous diseases resulting from overexpression of genes, expression of mutant genes and viral infections. As most oligonucleotides are polyanions they can not readily pass cellular membranes in adequate amounts to show activity. Therefore, different types of carrier systems and modifications have been developed to enhance absorption and distribution at the level of tissues and cells. The current state of delivery systems will be reviewed with a major part devoted to the commonly used cationic lipids.
Phosphate Adsorption onto TiO2 from Aqueous Solutions:  An in Situ Internal Reflection Infrared Spectroscopic Study (1999)

The adsorption of phosphate ions from aqueous solution onto thin films of colloidal TiO2 has been studied for the first time by in situ internal reflection infrared spectroscopy. Phosphate binds strongly to TiO2, as evidenced by the large changes in the PO stretching band structure in the infrared spectrum of the adsorbed species compared with the solution species. The Langmuir binding constant for phosphate onto TiO2 at pH = 2.3 is (3.8 ± 0.8) × 104 dm3 mol-1, which is similar to the binding constants onto TiO2 for bidentate ligand species such as oxalate and catechol. The strength of the binding is also apparent in the kinetics of adsorption, showing fast adsorption and much slower desorption, as expected for a strongly bound species. The kinetics data at pH = 8.3 have indicated coverage-dependent phosphate adsorption and desorption. Experiments with substituted phosphate species have confirmed the bidentate binding of phosphate to Ti(IV) ions at the TiO2 surface.
Measurement of DC electric fields using the electro-optic effect (1985)

The linear electro-optic effect (Pockels effect) has been used to measure DC electric fields of order 105 Vm?1. Both lithium-niobate and bismuth-germanate crystals have been tried and their performances compared. A double-pass optical configuration was used, the ultimate aim being a single-ended probe capable of operation in a space-charge environment.
Tunneling Reaction Kinetics for the Hydrogen Abstraction Reaction H + H2S → H2 + HS in the Interstellar Medium (2017)

The hydrogen abstraction reaction between H and H<sub>2</sub>S, yielding HS and H<sub>2</sub> as products, has been studied within the framework of interstellar surface chemistry. High-temperature rate constants below 2000 K are calculated in the gas phase and are in agreement with previously reported values. Subsequently, low-temperature rate constants down to 55 K are presented for the first time that are of interest to astrochemistry, i.e., covering both bimolecular and unimolecular reaction mechanisms. For this, a so-called implicit surface model is used. In strict terms, this is a structural gas-phase model in which the restriction of the rotation in the solid state is taken into account. The calculated kinetic isotope effects are explained in terms of the difference in activation and delocalization. All rate constants are calculated at the UCCSD(T)-F12/cc-VTZ-F12 level of theory. Finally, we show that the energetics of the reaction is affected to an only small extent by the presence of H<sub>2</sub>O or H<sub>2</sub>S molecular clusters that simulate an ice surface, calculated at the MPWB1K/def2-TZVP level of theory.
Quantum state regeneration in entanglement based quantum key distribution protocols (2014)

Quantum Key Distribution (QKD) has been shown to be provably secure when certain idealized conditions are met in a physical realization. All implementations of QKD to date require non-orthogonal basis measurements to implement it; making it commonly assumed that measurement basis variation is fundamental to making QKD protocols secure from eavesdropping. We show here that in particular physical conditions this assumption is incorrect, and that provable security can be achieved without use of multiple bases. Basis setting information can in fact be shared with all potential eavesdroppers, as they are unable to use it to acquire or influence any part of the encryption key generation. Furthermore the key generation efficiency is limited to 100 % as compared with an inherent 50 % limit for alternating bases in BB84 or Entangled Ekert protocols.
Full-field optical sectioning and three-dimensional localization of fluorescent particles using focal plane modulation (2006)

We present a technique for imaging fluorescent particles based on the axial modulation of the objective's focal plane position. This technique provides full-field optical sectioning and can be used to localize the fluorophores in three dimensions. We describe the technique and apply it to image 200 nm diameter fluorescent beads immobilized in a gel. We show that full-field optical sectioning is obtained and that the beads are localized with a precision of 10 nm in the transverse plane and 14 nm in the axial direction.
Mesh Simplification and Adaptive LOD for Finite Element Mesh Generation (2006)

In this paper, we propose a new triangular finite element mesh generation method based on simplification of high-density mesh and adaptive level-of detail (LOD) methods for efficient CAE. Mesh simplification evaluating mesh properties is applied to control the mesh properties required for FE mesh, such as the number of triangular elements, element shape quality and size while keeping the specified approximation tolerance. Adaptive LOD methods based on vertex hierarchy according to curvature and region of interest, and global LOD method preserving density distributions are also proposed in order to construct a more appropriate FE mesh. These methods enable efficient generation of FE meshes with appropriate properties for analysis from a high-density mesh. Finally, the effectiveness of our approach is shown through evaluations of the FE meshes for practical use.
Wideband Beam Steering Antenna Array of Printed Cavity-Backed Elements With Integrated EBG Structure (2018)

The letter concerns the design of a wideband printed antenna array element based on a cavity-backed patch radiator with an incorporated U-slot. An additional 2 × 3 mushroom-like electromagnetic bandgap structure is introduced in the E-plane in close proximity to the patch element on the same single-layer substrate. The proposed array unit cell design is optimized for operation in the 12% relative bandwidth in C-band and the 80° conical beam steering sector. Both simulated and experimental data demonstrate considerable wideband beam steering performance improvement compared to the basic design (without isolating structure) characteristics, provided by achieved array elements decoupling. Research results predict for the 12% relative bandwidth broadside reflection coefficient magnitude |Γ| ≤ 0.3, and maximum for the 80° conical beam steering sector |Γ| ≤ 0.37.
Compact microLED optrode device for patterned inter-cortical optogenetics (Conference Presentation) (2020)

There is current demand for pattern programmable devices that can deliver light to deep brain structures for use in optogenetic experiments. Here we introduce a microLED optrode device with 181 individually addressable sites, each with the capability to optogenetically excite thousands of neurons in vivo. The device consists of a 10 x 10 glass microneedle array directly integrated with a custom fabricated microLED device. 100 microLEDs couple to the needle tips for intra-cortical light delivery and 81 microLEDs sit at interstitial points for surface illumination. Light delivery and thermal properties are comprehensively evaluated.
Current control for IPMSM drives: Direct discrete-time pole-placement design (2015)

This paper deals with discrete-time models and current control methods for synchronous motors with a magnetically anisotropic rotor structure, such as interior permanent-magnet synchronous motors (IPMSMs) and synchronous reluctance motors (SyRMs). Dynamic performance of current controllers based on continuous-time models is limited, especially if the ratio of the sampling frequency to the fundamental frequency is low. An exact closed-form hold-equivalent discrete motor model is derived. The zero-order hold of the stator-voltage input is modeled in stationary coordinates, where it physically is. An analytical discrete-time pole-placement design method for a two-degree-of-freedom state-space current controller with an integral action is proposed. The proposed method is easy to apply: only the desired closed-loop bandwidth and the three motor parameters (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> , L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> , L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</sub> ) are required. The robustness of the proposed current control design against parameter errors is analyzed. The controller is experimentally verified using a 6.7-kW SyRM drive.
Loop-Mediated Isothermal Amplification in a Core-Shell Bead Assay for the Detection of Tyrosine Kinase AXL Overexpression (2021)

The upregulated expression of tyrosine kinase AXL has been reported in several hematologic and solid human tumors, including gastric, breast, colorectal, prostate and ovarian cancers. Thus, AXL can potentially serve as a diagnostic and prognostic biomarker for various cancers. This paper reports the first ever loop-mediated isothermal amplification (LAMP) in a core-shell bead assay for the detection of AXL gene overexpression. We demonstrated simple instrumentation toward a point-of-care device to perform LAMP. This paper also reports the first ever use of core-shell beads as a microreactor to perform LAMP as an attempt to promote environmentally-friendly laboratory practices.
Linking atmospheric synoptic transport, cloud phase, surface energy fluxes, and sea-ice growth: observations of midwinter SHEBA conditions (2016)

Observations from the Surface Heat Budget of the Arctic Ocean (SHEBA) project are used to describe a sequence of events linking midwinter long-range advection of atmospheric heat and moisture into the Arctic Basin, formation of supercooled liquid water clouds, enhancement of net surface energy fluxes through increased downwelling longwave radiation, and reduction in near-surface conductive heat flux loss due to a warming of the surface, thereby leading to a reduction in sea-ice bottom growth. The analyses provide details of two events during Jan. 1–12, 1998, one entering the Arctic through Fram Strait and the other from northeast Siberia; winter statistics extend the results. Both deep, precipitating frontal clouds and post-frontal stratocumulus clouds impact the surface radiation and energy budget. Cloud liquid water, occurring preferentially in stratocumulus clouds extending into the base of the inversion, provides the strongest impact on surface radiation and hence modulates the surface forcing, as found previously. The observations suggest a minimum water vapor threshold, likely case dependent, for producing liquid water clouds. Through responses to the radiative forcing and surface warming, this cloud liquid water also modulates the turbulent and conductive heat fluxes, and produces a thermal wave penetrating into the sea ice. About 20–33 % of the observed variations of bottom ice growth can be directly linked to variations in surface conductive heat flux, with retarded ice growth occurring several days after these moisture plumes reduce the surface conductive heat flux. This sequence of events modulate pack-ice wintertime environmental conditions and total ice growth, and has implications for the annual sea-ice evolution, especially for the current conditions of extensive thinner ice.
Hitherto Unreported Malignant Melanomas in the Syrian Hamster: An Experimental Counterpart of the Human Malignant Melanomas (1958)

Summary 1.Primary melanotic and amelanotic malignant melanomas have been found in 10 or 1.9 per cent of 523 Syrian hamsters surviving 181 days and longer on the experiment. These tumors are of spontaneous origin. 2.Eight of the ten melanomas originated in males; nine of the ten melanomas demonstrated metastases; five of the ten animals with melanomas also had one or more additional primary tumors originating in other tissues. 3.This is the first experiment recorded in which malignant melanomas have been observed in the Syrian hamster. 4.The histogenesis of the hamster melanocarcinomas appears to be identical with that noted in malignant melanomas of humans—namely, origin from a junctional nevus. This identity seems not to have been demonstrated previously with tumors of this or other experimental animals. The macroscopic and histologic appearances and the growth characteristics of the malignant melanomas of hamsters correspond well with the features of this tumor in the human. 5.Four of the melanocarcinomas are now being carried in transplant form. These tumors are available to any interested investigator.
Repetitive Imaging of Reporter Gene Expression in the Lung (2003)

Positron emission tomographic imaging is emerging as a powerful technology to monitor reporter transgene expression in the lungs and other organs. However, little information is available about its usefulness for studying gene expression over time. Therefore, we infected 20 rats with a replication-deficient adenovirus containing a fusion gene encoding for a mutant Herpes simplex virus type-1 thymidine kinase and an enhanced green fluorescent protein. Five additional rats were infected with a control virus. Pulmonary gene transfer was performed via intratracheal administration of vector using a surfactant-based method. Imaging was performed 4–6 hr, and 4, 7, and 10 days after gene transfer, using 9-(4-[ 18 F]-fluoro-3-hydroxymethylbutyl)guanine, an imaging substrate for the mutant kinase. Lung tracer uptake assessed with imaging was moderately but significantly increased 4–6 hr after gene transfer, was maximal after 4 days, and was no longer detectable by 10 days. The temporal pattern of transgene expression measured ex vivo with in vitro assays of thymidine kinase activity and green fluorescent protein was similar to imaging. In conclusion, positron emission tomography is a reliable new tool to evaluate the onset and duration of reporter gene expression noninvasively in the lungs of intact animals.