gebhart/patrepeval huggingface dataset:
Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C (2015)

Soybean cyst nematode (SCN, <i>Heterodera glycine</i> Ichinohe), southern root-knot nematode [SRKN, <i>Meloidogyne incognita</i> (Kofoid and White) Chitwood] and reniform nematode (RN, <i>Rotylenchulus reniformis</i> Linford and Oliveira) are three important plant-parasitic pests in soybean. Previous study showed that plant introduction (PI) 567516C harbored novel quantitative trait loci (QTL) conferring SCN resistance to soybean. However, QTL underlying resistance to SRKN and RN in PI 567516C remain unknown. The objectives of this study were to identify QTL for resistance to SRKN and RN in PI 567516C. Two hundred and forty-seven F<sub>6:9</sub> recombinant inbred lines, derived from a cross between cultivar Magellan and PI 567516C, were evaluated for resistance to SRKN and RN. Two hundred and thirty-eight simple sequence repeats and 687 single nucleotide polymorphism markers were used to construct a genetic linkage map. Three significant QTL associated with resistance to SRKN were mapped on chromosomes (Chrs.) 10, 13 and 17. Two significant QTL associated with resistance to RN were detected on Chrs. 11 and 18. Whole-genome resequencing revealed that there might be Peking-type <i>Rhg1</i> in PI 567516C. Our study provides useful information to employ PI 567516C in soybean breeding in order to develop new cultivars with resistance to multiple nematodes.
Strand displacement applied to assays with nucleic acid probes. (1986)

This novel method for the detection of specific nucleic acid sequences has potential applications to clinical diagnosis. During hybridization, a signal-bearing nucleic acid strand is displaced by the target nucleic acid from a partially single-stranded complementary probe strand of nucleic acid. The probe:signal strand complex is prepared by hybridizing single-stranded probe that is entirely complementary to the target nucleic acid with a shorter signal sequence that is complementary to a portion of the probe strand. The sample nucleic acid is added to this hybrid complex under hybridization conditions. The target sequence, if present in the sample, will hybridize first to the unoccupied probe sequences, and then will displace the labeled strand by branch migration. By this "strand displacement" the signal strands are freed in solution, where they may be separated from those still hybridized; the quantity of label measured is directly proportional to the amount of analyte sequences in the sample. This method, demonstrated here for model and synthetic DNAs, can easily be adapted for the detection of any RNA or DNA sequence and obviates the need for immobilization of sample. A wide variety of labeling techniques can be used, and the displacement can be performed in solution or with the hybrid complex attached to a solid support. This assay circumvents nonspecific binding of label to the filter matrix and the laborious washing steps inherent in other assays involving nucleic acid probes.
Dual-illumination mode, wide-field probe imaging scheme for imaging irido-corneal angle region inside eye (2015)

Noninvasive medical imaging techniques have generated great interest and high potential in the research and development of ocular imaging and follow up procedures. It is well known that angle closure glaucoma is one of the major ocular diseases/ conditions that causes blindness. The identification and treatment of this disease are related primarily to angle assessment techniques. In this paper, we illustrate a probe-based imaging approach to obtain the images of the angle region in eye. The proposed probe consists of a micro CCD camera and LED/NIR laser light sources and they are configured at the distal end to enable imaging of iridocorneal region inside eye. With this proposed dualmodal probe, imaging is performed in light (white visible LED ON) and dark (NIR laser light source alone) conditions and the angle region is noticeable in both cases. The imaging using NIR sources have major significance in anterior chamber imaging since it evades pupil constriction due to the bright light and thereby the artificial altering of anterior chamber angle. The proposed methodology and developed scheme are expected to find potential application in glaucoma disease detection and diagnosis.
Augmentation of the CD8+ T Cell Response by IFN-γ in IL-12-Deficient Mice During <i>Toxoplasma gondii</i> Infection (1999)

Abstract The importance of IFN-γ in regulating the host CD8+ T cell response during microbial infection has not been delineated. Mice deficient for the p40 chain of the IL-12 heterodimer have impaired IFN-γ production and are susceptible to infection with the intracellular parasite Toxoplasma gondii. The administration of exogenous IFN-γ to parasite-infected p40−/− mice increases survival and up-regulates the depressed CD8+ T cell response following infection. CD8+ T cells isolated from cytokine-treated p40−/− mice exhibit an increase in both precursor CTL frequency and IFN-γ production compared with untreated controls. The enhancement of the CD8+ T cell response is independent of CD4+ T cell help. These CD8+ T cells induce protective immunity against a lethal challenge when adoptively transferred into naive p40−/− and IFN-γ−/− mice. These observations indicate that IFN-γ can regulate the CD8+ T cell response during T. gondii infection.
Imparting amphiphobicity on single-crystalline porous materials (2016)

Abstract The sophisticated control of surface wettability for target-specific applications has attracted widespread interest for use in a plethora of applications. Despite the recent advances in modification of non-porous materials, surface wettability control of porous materials, particularly single crystalline, remains undeveloped. Here we contribute a general method to impart amphiphobicity on single-crystalline porous materials as demonstrated by chemically coating the exterior of metal-organic framework (MOF) crystals with an amphiphobic surface. As amphiphobic porous materials, the resultant MOF crystals exhibit both superhydrophobicity and oleophobicity in addition to retaining high crystallinity and intact porosity. The chemical shielding effect resulting from the amphiphobicity of the MOFs is illustrated by their performances in water/organic vapour adsorption, as well as long-term ultrastability under highly humidified CO 2 environments and exceptional chemical stability in acid/base aqueous solutions. Our work thereby pioneers a perspective to protect crystalline porous materials under various chemical environments for numerous applications.
A temporal deep learning approach for MR perfusion parameter estimation in stroke (2016)

Perfusion magnetic resonance (MR) images are often used in the assessment of acute ischemic stroke to distinguish between salvageable tissue and infarcted core. Deconvolution methods such as singular value decomposition have been used to approximate model-based perfusion parameters from these images. However, studies have shown that these existing deconvolution algorithms can introduce distortions that may negatively influence the utility of these parameter maps. There is limited previous work on utilizing machine learning algorithms to estimate perfusion parameters. In this work, we present a novel bi-input convolutional neural network (bi-CNN) to approximate four perfusion parameters without using an explicit deconvolution method. These bi-CNNs produced good approximations for all four parameters, with relative average root-mean-square errors (ARMSEs) ≤ 5% of the maximum values. We further demonstrate the utility of the estimated perfusion maps for quantifying the salvageable tissue volume in stroke, with more than 80% agreement with the ground truth. These results show that deep learning techniques are a promising tool for perfusion parameter estimation without requiring a standard deconvolution process.
Non-interactive and non-malleable commitment (1998)

A commilmcnt protocol is a fundamental cryptographic primitive uacd a0 D basic building block throughout modem cryptography. In STOC 1991, Dolov Dwork and Naor showed that in many settings the Implemontotion of this fundamental primitive requires a strong non-malh6ility property in order not to be sueceptible to a certain clmoa of nttacke, In this paper, aeeuming that a common random ntrlng lo available to all playere, we show how to implement nonmalleablo commitment without any interaction and based on any one-way function, In contrast, all previous solutions required eithor logorlthmically many rounds of interaction or strong algebraic aaaumptlono, I lntroductlon COMMITMENT:
Automated detection of asynchrony in patient-ventilator interaction (2009)

An automated classification algorithm for the detection of expiratory ineffective efforts in patient-ventilator interaction is developed and validated. Using this algorithm, 5624 breaths from 23 patients in a pulmonary ward were examined. The participants (N = 23) underwent both conventional and non-invasive ventilation. Tracings of patient flow, pressure at the airway, and transdiaphragmatic pressure were manually labeled by an expert. Overall accuracy of 94.5% was achieved with sensitivity 58.7% and specificity 98.7%. The results demonstrate the viability of using pattern classification techniques to automatically detect the presence of asynchrony between a patient and their ventilator.
Multi-basis weighted memory polynomial for RF power amplifiers behavioral modeling (2016)

In this paper, two multi-basis weighted memory polynomial models are proposed for radio frequency power amplifiers' behavioral modelling. In these models, the conventional memory polynomial function of the generalized and hybrid memory polynomial models is replaced by a weighted version of it. Experimental validation was performed on a power amplifier prototype exhibiting strong memory effects, and driven by a 20 MHz LTE signal with 1001 configuration. Proposed weighted generalized memory polynomial and hybrid memory polynomial models show superior performance when compared to their memory polynomial based conventional counterparts. Indeed, an NMSE improvement of 2 dB to 3 dB is obtained for the same complexity, and a reduction of almost 50% in the number of coefficients are achieved for the same performance.
Hypersonic Waverider Stream Surface Actuation for Variable Design Point Operation (2016)

A method of designing a hypersonic vehicle includes selecting a shock shape; tracing a leading edge along the shock shape; selecting a base plane defining endpoints of the leading edge and rearwardly displaced from a front of the leading edge; and tracing stream surfaces back from the leading edge along the shock to the base plane in order to define an upper surface and a lower surface, wherein the upper and lower surfaces and base plane enclose a volume representing internal volume of the hypersonic vehicle. The lower stream surface is controllably morphable.
Modeling and Analysis of Tire Dynamics with Respect to Wheel Torque Variations (2006)

Development of high-performance ABS, TCS, and vehicle dynamics control systems requires precise tire dynamics models. There are two tire vibration modes when considering the longitudinal tire force response with respect to wheel torque variations: (i) sidewall torsional compliance mode, and (ii) tread compliance mode. The recently developed LuGre tire friction model is exploited in this study to model the tire dynamics and analyze the tire vibrations. For the purpose of vibration analysis, the LuGre model is linearized and represented by an equivalent spring-damper system. The overall tire dynamics model is of fourth order. In order to find an analytical solution for vibration mode parameters, four approximate methods are proposed, analyzed, and compared.
Development of Low Dark Current SiGe Near-Infrared PIN Photodetectors on 300 mm Silicon Wafers (2016)

SiGe offers a low-cost alternative to conventional infrared sensor material systems such as InGaAs, InSb, and HgCdTe for developing near-infrared (NIR) photodetector devices that do not require cooling and can operate with relatively low dark current. As a result of the significant difference in thermal expansion coefficients between germanium (Ge) and silicon (Si), tensile strain incorporated into SiGe detector devices through specialized growth processes can extend their NIR wavelength range of operation. We have utilized high throughput, large-area complementary metal-oxide semiconductor (CMOS) technology to fabricate Ge based p-i-n (PIN) detector devices on 300 mm Si wafers. The two-step device fabrication process, designed to effectively reduce the density of defects and dislocations arising during deposition that form recombination centers which can result in higher dark current, involves low temperature epitaxial deposition of Ge to form a thin p+ seed layer, followed by higher temperature deposition of a thicker Ge intrinsic layer. Phosphorus was then ion-implanted to create devices with n+ regions of various doping concentrations. Secondary ion mass spectroscopy (SIMS) has been utilized to determine the doping profiles and material compositions of the layers. In addition, electrical characterization of the I-V photoresponse of different devices from the same wafer with various n+ region doping concentrations has demonstrated low dark current levels (down to below 1 nA at -1 V bias) and comparatively high photocurrent at reverse biases, with optimal response for doping concentration of 5 × 1019 cm-3.
Drop Size Stability Assessment of Fluorocarbon Emulsions (1992)

The aging of fluorocarbon emulsions prepared with natural egg yolk phospholipids (EYP) has been studied and a linear variation (r2 greater than 0.95) of the mean average volume of the droplets with time has been observed. The slope of the experimental lines, called "Stability Parameter, S" can thus be taken as a representation of the rate of aging of the emulsions. Examples are given of use of parameter S to assess the effect of formulation and processing parameters on the stability of diverse fluorocarbon emulsions. S is a useful tool to compare emulsions and ascertain any factors of stabilization/destabilization.
Heteroatom-Tolerant Delamination of Layered Zeolite Precursor Materials (2013)

The synthesis of the first delaminated borosilicate layered zeolite precursor is described, along with its aluminosilicate analogue, which consists of Al-containing UCB-3 and B-containing UCB-4 from as-made SSZ-70. In addition, the delamination of PREFER (which is the precursor to ferrierite zeolite) under similar conditions yields delaminated layered zeolite precursors consisting of Al-containing UCB-5 and Ti-containing UCB-6. Multinuclear solid-state NMR spectroscopy (^(11)B and ^(27)Al), diffuse-reflectance UV-vis spectroscopy, and heteroatom/Si ratios measured via elemental analysis are consistent with a lack of heteroatom leaching from the framework following delamination. Such mild delamination conditions are achieved by swelling the zeolite precursor in a fluoride/chloride surfactant mixture in DMF solvent, followed by sonication. Powder X-ray diffraction, argon gas physisorption, and chemisorption of bulky base probes strongly suggest delamination, and demonstrate a 1.5-fold increase in the number density of external acid sites and surface area of calcined UCB-3, relative to calcined Al-SSZ-70. The synthesis of microporous pockets in materials UCB-3–UCB-5 suggests the possibility of interlayer porosity in SSZ-70, which is a layered zeolite precursor material whose structure remains currently unknown. The mildness of the delamination method presented here, as well as the lack of need for acidification in the synthesis procedure, enables the delamination of heteroatom-containing zeolites while preserving the framework integrity of labile heteroatoms, which could otherwise be leached under harsher conditions.
pH‐metric determination of acid values in vegetable oils without titration (1996)

Abstract A new method for determining acid values in vegetable oils has been developed for a nontitration pH‐metric technique with a reagent consisting of 0.20 M triethanolamine in a 1∶1 solution of water and isopropanol. The emulsive properties of this reagent provide rapid (within a minute) and quantitative extraction of free fatty acids from an oil into the solvent phase. Acid values were determined by measuring conditional pH of the emulsified reagent in a pH‐meter with an aqueous reference electrode. Three different applications of this technique are discussed.
N-Glycosylation of Campylobacter jejuni Surface Proteins Promotes Bacterial Fitness (2013)

Campylobacter jejuni is the etiologic agent of human bacterial gastroenteritis worldwide. In contrast, despite heavy colonization, C. jejuni maintains a commensal mode of existence in chickens. The consumption of contaminated chicken products is thought to be the principal mode of C. jejuni transmission to the human population. C. jejuni harbors a system for N-linked protein glycosylation that has been well characterized and modifies more than 60 periplasmic and membrane-bound proteins. However, the precise role of this modification in the biology of C. jejuni remains unexplored. We hypothesized that the N-glycans protect C. jejuni surface proteins from the action of gut proteases. The C. jejuni pglB mutant, deficient in the expression of the oligosaccharyltransferase, exhibited reduced growth in medium supplemented with chicken cecal contents (CCC) compared with that of wild-type (WT) cells. Inactivation of the cecal proteases by heat treatment or with protease inhibitors completely restored bacterial viability and partially rescued bacterial growth. Physiological concentrations of trypsin, but not chymotrypsin, also reduced C. jejuni pglB mutant CFU. Live or dead staining indicated that CCC preferentially influenced C. jejuni growth as opposed to bacterial viability. We identified multiple chicken cecal proteases by mass fingerprinting. The use of protease inhibitors that target specific classes indicated that both metalloproteases and serine proteases were involved in the attenuated growth of the oligosaccharyltransferase mutant. In conclusion, protein N-linked glycosylation of surface proteins may enhance C. jejuni fitness by protecting bacterial proteins from cleavage due to gut proteases.
Glass-based coatings for titanium implant alloys (1999)

Glass coatings on Ti6Al4V were prepared using a simple enameling technique. The composition of the glasses was tailored to match the thermal expansion of Ti6Al4V. By controlling the firing atmosphere, time, and temperature, it was possible to control the reactivity between the glass and the alloy and to fabricate coatings (25-150 micron thick) with excellent adhesion to the substrate. The optimum firing temperatures ranged between 800 and 840 degrees C at times up to 1 min in air or 15 min in N2. The same basic technique was used to prepare multilayered coatings with graded composition or with hydroxyapatite (HA) particles embedded in the outer layer. Some of these coatings presented excellent adhesion to the substrate and were able to form HA during in vitro tests in simulated body fluid.
Real-time estimation and dynamic renegotiation of UPC parameters for arbitrary traffic sources in ATM networks (1998)

This paper presents a robust and flexible real-time scheme for determining appropriate parameter values for usage parameter control (UPC) of an arbitrary source in an asynchronous transfer mode network. In our approach, the UPC parameters are chosen as a function of the statistical characteristics of the observed cell stream, the user's tolerance for traffic shaping, and a measure of the network cost. For this purpose, we develop an approximate statistical characterization for an arbitrary cell stream. The statistical characterization is mapped to a UPC descriptor that can be negotiated, with the network. The selected UPC descriptor is optimal in the sense of minimizing a network cost function, subject to meeting user-specified constraints on shaping delay. The UPC estimation scheme is extended to adapt to slow time-scale changes in traffic characteristics via dynamic renegotiation of the UPC parameters. We illustrate the effectiveness of our methodologies with examples taken from MPEG video sequences.
The mouse telomerase RNA 5'-end lies just upstream of the telomerase template sequence (1998)

Telomerase is a ribonucleoprotein enzyme with an essential RNA component. Embedded within the telomerase RNA is a template sequence for telomere synthesis. We have characterized the structure of the 5' regions of the human and mouse telomerase-RNA genes, and have found a striking difference in the location of the template sequence: Whereas the 5'-end of the human telomerase RNA lies 45 nt from the telomerase-RNA template sequence, the 5'-end of the mouse telomerase RNA lies just 2 nt from the telomerase-RNA template sequence. Analysis of genomic sequences flanking the 5'-end of the human and mouse telomerase RNA-coding sequences reveals similar promoter-element arrangements typical of mRNA-type promoters: a TATA box-like element and an upstream region containing a consensus CCAAT box. This putative promoter structure contrasts with that of the ciliate telomerase-RNA genes whose structure resembles RNA polymerase III U6 small nuclear RNA (snRNA) promoters. These and other comparisons suggest that, during evolution, both the RNA-polymerase specificity of telomerase RNA-gene promoters and, more recently, the position of the template sequence in the telomerase RNA changed.
Recent progress of THz-quantum cascade lasers using nitride-based materials (2015)

Nitride semiconductor is a material having potentials for realizing wide frequency range of quantum-cascade lasers (QCLs), i.e., 3～20 THz and 1～8 μm, including an unexplored terahertz frequency range from 5 to 12 THz, as well as realizing room temperature operation of THz-QCL. The merit of using an AlGaN-based semiconductor is that it has much higher longitudinal optical phonon energies (E<sub>LO</sub>> 90meV) than those of GaAs-based semiconductors (~ 36 meV). In this study, we demonstrate the first lasing action of GaN-based QCLs. We introduced an unique quantum design active region, i.e., “pure 3-level system design”, which is consisting of 2 quantum wells (QWs) per one period. We grew GaN/AlGaN QC structures by using molecular beam epitaxy (MBE). The layer structure of the GaN/AlGaN QCL was consisting of 100~200 periods of QC active layers sandwiched by Si-doped (Al)GaN upper and lower contact layers, which were grown on a high-quality AlGaN/AlN template grown on a c-plane sapphire substrate. After the crystal growth, we fabricated QCL sample with single metal plasmon waveguide structure. Lasing spectrum was obtained at 5.39 THz measured under pulsed current injection at 5.8K. The threshold current density J<sub>th</sub> and the threshold voltage V<sub>th</sub> were 1.75 kA/cm<sup>2</sup> and 14.5 V, respectively. We also fabricated similar design GaN/AlGaN QCL by metal organic chemical vapor deposition (MOCVD), and obtained lasing at 6.97 THz. The J<sub>th</sub> and V<sub>th</sub> of the MOCVD grown QCL were 0.75 kA/cm<sup>2</sup> and 27 V, respectively, measured at 5.2 K.
A Selective-Area Metal Bonding InGaAsP–Si Laser (2010)

A 1.55-μ m hybrid InGaAsP-Si laser was fabricated by the selective-area metal bonding method. Two Si blocking stripes, each with an excess-metals accommodated space, were used to separate the optical coupling area and the metal bonding areas. In such a structure, the air gap between the InGaAsP structure and Si waveguide has been reduced to be negligible. The laser operates with a threshold current density of 1.7 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a slope efficiency of 0.05 W/A under pulsed-wave operation. Room-temperature continuous lasing with a maximum output power of 0.45 mW is realized.