gebhart/patrepeval huggingface dataset:
Protective effect of complement factor B and complement component 2 variants in age-related macular degeneration (2007)

Age-related macular degeneration (AMD) is a devastating disorder of the central retina, causing significant visual impairment for 7.5 million elderly Americans. Abnormal regulation of the complement system likely caused by the Y402H polymorphism in the complement factor H gene is a recognized risk factor for AMD, as is the A69S variant in the poorly characterized LOC387715 gene. Recently, polymorphisms in the factor B (CFB) and complement component 2 (CC2) genes were associated with decreased susceptibility to AMD. To validate this association in independent family-based and case-control Caucasian data sets, we genotyped two single-nucleotide polymorphisms (SNPs) in CC2 and four SNPs in CFB. The R32Q variant of CFB was significantly associated with protection from AMD in the family-based data set (P = 0.025). Three SNPs in CC2 and CFB were strongly associated with decreased risk of AMD in the case-control data set (CC2 E318D: P = 0.02; CC2 rs547154: P = 9 x 10(-6); and CFB R32Q P = 2 x 10(-5)). The minor alleles at CC2 rs547154 and CFB R32Q are present in 4% of cases versus 10% of controls, and as these SNPs are in strong linkage disequilibrium (r(2)=0.92), these results likely represent the same protective signal. After controlling for age, Y402H, A69S and smoking, the effect of CFB R32Q remained quite strong (OR 0.21, 95% confidence interval 0.11-0.39; P < 10(-4)). Likelihood ratio testing and conditional analyses in the case-control data set suggest that a weaker, independent protective effect exists for CC2 E318D.
Mutational Analysis of the Assembly Domain of the HIV-1 Envelope Glycoprotein (1993)

The amino-terminal 129 amino acids of gp41 of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) glycoprotein constitute the assembly domain required for efficient oligomer formation and stability. Point mutations in highly conserved structural features including cysteine residues, potential N-linked glycosylation sites, and a leucine zipper motif have been made in a soluble secreted form of Env (Envsec). No single point mutation had adverse effects on Env protein oligomerization. However, truncation of the C terminus of gp41 from 129 amino acids to 68 amino acids drastically reduced oligomerization efficiency, indicating that amino acids 68-129 are essential for assembly.
Extracorporeal CO2 Removal by Respiratory Electrodialysis (2015)

We previously described a highly efficient extracorporeal CO2 removal technique called respiratory electrodialysis (R-ED). Respiratory electrodialysis was composed of a hemodiafilter and a membrane lung (ML) positioned along the extracorporeal blood circuit, and an electrodialysis (ED) cell positioned on the hemodiafiltrate. The ED regionally increased blood chloride concentration to convert bicarbonate to CO2 upstream the ML, thus enhancing ML CO2 extraction (VCO2ML). In this in vitro study, with an aqueous polyelectrolytic carbonated solution mimicking blood, we tested a new R-ED setup, featuring an ML positioned on the hemodiafiltrate after the ED, at increasing ED current levels (0, 2, 4, 6, and 8 A). We measured VCO2ML, electrolytes concentrations, and pH of the extracorporeal circuit. Raising levels of ED-current increased chloride concentration from 107.5 ± 1.6 to 114.6 ± 1.3 mEq/L (0 vs. 8 A, p < 0.001) and reduced pH from 7.48 ± 0.01 to 6.51 ± 0.05 (0 vs. 8 A, p < 0.001) of the hemodiafiltrate entering the ML. Subsequently, VCO2ML increased from 27 ± 1.7 to 91.3 ± 1.5 ml/min (0 vs. 8 A, p < 0.001). Respiratory electrodialysis is efficient in increasing VCO2ML of an extracorporeal circuit featuring an ML perfused by hemodiafiltrate. During R-ED, the VCO2ML can be significantly enhanced by increasing the ED current.
Monitoring time course of human whole blood coagulation using a microfluidic dielectric sensor with a 3D capacitive structure (2015)

This paper reports on the design, fabrication, and testing of a microfluidic sensor for dielectric spectroscopy (DS) of human whole blood during coagulation. The sensor employs a three-dimensional (3D), parallel-plate, capacitive sensing structure with a floating electrode integrated into a microfluidic channel. Using an impedance analyzer and after a 5-point calibration, the sensor is shown to measure the real part of complex relative dielectric permittivity of human whole blood in a frequency range of 10kHz to 100MHz. The temporal variation of dielectric permittivity at 1MHz for human whole blood from three different healthy donors shows a peak in permittivity at ~ 4 to 5 minutes, which also corresponds to the onset of CaCl2-initiated coagulation of the blood sample verified visually.
STAGE: an Integrated Environment for Statistical Test Script Generation (2004)

This work describes STAGE, an integrated environment for statistical test case generation and scripting, developed at the CPTS (Software Testing Research Center). The key contributions of the system are the use of stochastic automata networks (SANs) for representing the usage model and an intermediate model (called the Interface Event-State Model) to map the abstract usage model into the implemented interface components. SANs allow modular representation of systems with complex non-deterministic behavior, minimizing the state-space explosion found in Markov chains. The use of a separate model for the implementation has the advantage of making changes in the interface and generating the script automatically without affecting the abstract usage model. We implemented the technique into the STAGE environment; the experiments indicate that the performance of test case and script generation with SANs is at least compatible with Markov-based generation.
Omnidirecitional wireless power transfer for portable devices (2017)

In this paper, omnidirectional wireless power transfer system proposed by Intel and the University of Hong Kong are evaluated first based on FEA simulation and numerical model. The analysis results show that their systems cannot generate preferred omnidirectional magnetic field. Then, a new transmitter coil structure with preferred omnidirectional magnetic field is proposed. Two modulation methods of the excitation current are also studied and compared. Finally, three 6.78MHz LCL resonant converters are built to drive the transmitter coils and generate omnidirectional magnetic field. Near field probe is used to measure the magnetic field to verify both the proposed transmitter coil structure and modulation methods.
QD-FRET-based biosensing of small molecule analytes using transcription factor-DNA binding (2019)

An alternative molecular recognition approach was developed for sensing small molecule analytes using the differential binding of an allosteric transcription factor (TF, specifically TetR) to its cognate DNA as the molecular recognition element coupled with fluorescent resonance energy transfer (FRET) to yield an internally calibrated optical signal transduction mechanism. Sensors were evaluated comprising Cy5-modified DNA (FRET acceptor) with either a tdTomato-TetR fusion protein (FP-TF) or quantum dot-TetR conjugate (QD-TF) as the FRET donor by measuring the ratio of acceptor and donor fluorescence intensities (FA/FD) with titrations of a derivative of the antibiotic tetracycline, anhydrous tetracycline (aTc). A proof-of-concept FRET-based biosensor was successfully demonstrated through the modulation of FA/FD signal intensities based on varying analyte concentrations. Sensor design parameters affecting overall signal-to-noise ratio and sensitivity of the sensors are also identified.
Vacuum Packaging of MEMS With Multiple Internal Seal Rings (2008)

A proposed method of design and fabrication of vacuum-packaged microelectromechanical systems (MEMS) and of individual microelectromechanical devices involves the use of multiple internal seal rings (MISRs) in conjunction with vias (through holes plated with metal for electrical contacts). The proposed method is compatible with mass production in a wafer-level fabrication process, in which the dozens of MEMS or individual microelectromechanical devices on a typical wafer are simultaneously vacuum packaged by bonding a capping wafer before the devices are singulated (cut apart by use of a dicing saw). In addition to being compatible with mass production, the proposed method would eliminate the need for some complex and expensive production steps and would yield more reliable vacuum seals. Conventionally, each MEMS or individual microelectromechanical device is fabricated as one of many identical units on a device wafer. Vacuum packaging is accomplished by bonding the device wafer to a capping wafer with metal seal rings (one ring surrounding each unit) that have been formed on the capping wafer. The electrical leads of each unit are laid out on what would otherwise be a flat surface of the device wafer, against which the seal ring is to be pressed for sealing. The resulting pattern of metal lines and their insulating oxide coverings presents a very rough and uneven surface, upon which it is difficult to pattern the sealing metal. Consequently, the seal is prone to leakage unless additional costly and complex planarization steps are performed before patterning the seal ring and bonding the wafers.
Synthesis and Thermal Conductivity of Exfoliated Hexagonal Boron Nitride/Alumina Ceramic Composite (2017)

Exfoliated hexagonal boron nitride (hBN)/alumina composite can be fabricated by following the process of (1) heating a mixture of hBN, AlCl3, and NaF in nitrogen for intercalation; (2) heating the intercalated product in air for exfoliation and at the same time converting the intercalate (AlCl3) into Al2O3, (3) rinsing the oxidized product, (4) coating individual exfoliated hBN platelets that contain Al2O3 with new layers of aluminum oxide, and finally, (5) hot pressing the product into the composite. The composite thus obtained has a composition of approximately 60 percent by weight hBN and 40 percent by weight alumina. Its in-plane and through-plane thermal conductivity were measured to be 86 and 18 watts per meter Kelvin, respectively, at room temperature.
Molecular Supracence Resolving Eight Colors in 300‐nm Width: Unprecedented Spectral Resolution (2020)

Abstract Monitoring multiple molecular probes simultaneously establishes their correlations and reveals the holistic mechanism. Current fluorescence imaging, however, is limited to about four colors because of typically circa 100‐nm spectral width. Herein, we show that molecular supracence imparts superior spectral resolution, resolving eight colors in 300‐nm width, about 37.5‐nm per color. A recently discovered light‐molecule interacting phenomenon, supracence only measures molecular emission above its excitation energy due to entanglement between atomic quantum system and electronic quantum system. As such, supracence takes advantage of sharp spectral edge of a single pathway and excitation specificity to produce narrow bands, whereas fluorescence has to deal with multiple pathways spilling out low‐energy long tail, that causes poor resolution. Thus, supracence enables myriad innovative molecular spectroscopy and microscopic imaging with profound impact broadly.
Pump-Power-Independent Double Slope-Assisted Distributed and Fast Brillouin Fiber-Optic Sensor (2014)

A small modification of the fast and distributed slope-assisted Brillouin time domain analysis (SA-BOTDA) method allows it to easily implement pump-power independent measurements of strain and/or temperature, using the ratio between readings taken on both slopes of the Brillouin gain spectrum. Employing this new double SA-BOTDA measurement technique, fast ( <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\sim}{\rm 100}~{\rm Hz}$</tex></formula> at <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">${\sim}{\rm 1}\hbox{-}{\rm kHz}$</tex></formula> effective sampling rate) strain measurements are shown to be immune to pump pulse power variations as large as 6 dB. At the expense of halving the sampling rate, this technique still maintains all the benefits of its SA-BOTDA predecessor. In particular, its ability to handle (Brillouin) longitudinally inhomogeneous fibers is demonstrated.
Host Recognition in the <i>Rhizobium</i>-Soybean Symbiosis (1984)

The mechanism of host-symbiont recognition in the soybean-Rhizobium symbiosis was investigated utilizing mutants of R. japonicum defective in nodulation. Soybeans were grown in clear plastic growth pouches allowing the identification of the area on the root most susceptible to Rhizobium nodulation; the area between the root tip (RT) and smallest emergent root hair (SERH). The location of nodules in relation to this developing zone is an indication of the rate of nodule initiation. Nodules were scored as to the distance from the RT mark made at the time of inoculation. Seventy-eight per cent of the plants nodulate above the RT mark when inoculated with the wild type R. japonicum strain 3I1b110 with the average distance of the uppermost nodule being approximately 2 millimeters above the RT mark. These data indicate that the wild type strain initiates nodulation rapidly within the RT-SERH zone following inoculation. However, inoculation with the slow-to-nodulate mutant strain HS111 resulted in 100% of the plants nodulating only below the RT mark with the average distance of the uppermost nodule being approximately 56 millimeters below the RT mark. Thus, mutant strain HS111 is defective in the ability to rapidly initiate infection leading to nodulation within the RT-SERH zone. The location of the nodules suggest that stain HS111 must ;adapt' to the root environment before nodulation can occur. To test this, strain HS111 was incubated in soybean root exudate prior to inoculation. In this case, 68% of the plants nodulated above the RT mark with the average distance of the uppermost nodule being approximately 1 millimeter below the RT mark. Experiments indicated that the change in nodule initiation by strain HS111 brought about by incubation in soybean root exudate was due to a phenotypic, rather than a genotypic change. The half-time of root exudate incubation for strain HS111 necessary for optimal nodulation enhancement was less than 6 hours. Heat sensitivity and trypsin sensitivity of the nodulation enhancement factor(s) in soybean root exudate indicate a protein was involved in the reversal of the delay in nodulation by mutant strain HS111.
System and method for refurbishing and processing parachutes (1980)

A system and method for refurbishing and processing parachutes is disclosed including an overhead monorail conveyor system on which the parachute is suspended for horizontal conveyance. The parachute is first suspended in a partially opened tented configuration wherein open inspection of the canopy is permitted to remove debris and inspect all areas. Following inspection, the parachute is transported by the monorail conveyor to a washing and drying station with the parachute canopy mounted on the conveyor in a systematic arrangement which permits water and air to pass through the ribbon-like materials of the canopy. Following drying, the chute is conveyed into an interior space where it is finally inspected and removed from the monorial conveyor for folding. The chute is once again mounted on the conveyor and conveyed to a packing area.
Generic beamforming structure for adaptive schemes implemented in two- and three-dimensional arrays of sensors (1997)

The concept for implementing successfully adaptive schemes in two-dimensional (2-D) and three-dimensional (3-D) arrays of sensors, such as planar, circular, cylindrical, and spherical arrays, is similar to that of line arrays. In particular, the basic step is to minimize the number of degrees of freedom associated with the adaptation process. The present investigation has been centered on the definition of a generic beamforming structure that decomposes the beamforming process of 2- and 3-D sensor arrays into subsets of coherent processes. The approach is to separate the computationally intensive multidimensional beamforming into two simple modules, which are line and circular array beamformers. Thus the multidimensional beamforming process can now be divided into coherent subprocesses which lead to efficient implementation in real-time sonar and radar systems. Furthermore, the application of spatial shading to reduce the side-lobe structures can now be easily incorporated. Moreover, the new approach makes the implementation of adaptive schemes in multidimensional sensor arrays practically achievable. The investigation includes also the definition of generic sub-aperture schemes for 2- and 3-D sensor arrays. This approach leads to minimization of the associated convergence period and makes the implementation of adaptive schemes in multidimensional sensor arrays practically feasible. [Work supported by NSERC-STR181039.]
Chiral Porous Hybrid Solids for Practical Heterogeneous Asymmetric Hydrogenation of Aromatic Ketones. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
IBM Mastor: Multilingual Automatic Speech-To-Speech Translator (2006)

In this paper, we describe the IBM MASTOR systems which handle spontaneous free-form speech-to-speech translation on both laptop and hand-held PDAs. Challenges include speech recognition and machine translation in adverse environments, lack of data and linguistic resources for under-studied languages, and the need to rapidly develop capabilities for new languages. Importantly, the code and models must fit within the limited memory and computational resources of hand-held devices. We describe our approaches, experience, and success in building working free-form S2S systems that can handle two language pairs (including a low-resource language).
The zebrafish mutant gene chardonnay (cdy) encodes divalent metal transporter 1 (DMT1) (2002)

Iron is an essential nutrient required for the function of all cells, most notably for the production of hemoglobin in red blood cells. Defects in the mechanisms of iron absorption, storage, or utilization can lead to disorders of iron-limited erythropoiesis or iron overload. In an effort to further understand these processes, we have used the zebrafish as a genetic system to study vertebrate iron metabolism. Here we characterized the phenotype of chardonnay (cdy), a zebrafish mutant with hypochromic, microcytic anemia, and positioned the mutant gene on linkage group 11. The cdy gene was isolated by a functional genomics approach in which we used a combination of expression studies, sequence analyses, and radiation hybrid panel mapping. We identified erythroid-specific genes using a whole embryo mRNA in situ hybridization screen and placed these genes on the zebrafish genomic map. One of these genes encoded the iron transporter divalent metal transporter 1 (DMT1) and colocalized with the cdy gene. We identified a nonsense mutation in the cdy allele and demonstrated that, whereas wild-type zebrafish DMT1 protein can transport iron, the truncated protein expressed in cdy mutants is not functional. Our studies further demonstrate the conservation of iron metabolism in vertebrates and suggest the existence of an alternative pathway of intestinal and red blood cell iron uptake.
A general framework for optimizing arterial spin labeling MRI experiments (2018)

The presented framework can effectively design ASL experiments to minimize measurement errors based on the requirements of the scan.
Design for enhanced thermo-electric pumping in light emitting diodes (2013)

We present a strategy for optimization of thermo-electric pumping in light emitting diodes (LEDs). We use a finite element model for charge transport in a GaInAsSb/GaSb double hetero-junction LED that is verified experimentally to consider optimal design and operation of low-bias LEDs. The wall-plug efficiency is shown to be enhanced by over 200× at nanowatt power levels and 20× at microwatt power levels. A design for room-temperature operation of a 2.2 μm LED with 100% efficiency is proposed—this represents a 110 °C reduction of the temperature required to observe unity efficiency.
Reversal of forward voltage drift in 4H-SiC p-i-n diodes via low temperature annealing (2007)

Recent reports have shown that Shockley stacking fault (SSF) growth in 4H-SiC may be reversed via low temperature (210–600°C) annealing. It is not clear if the associated drift in the forward voltage drop (Vf) is also reversed. Here we show that annealing of SSFs causes the complete and repeatable recovery of Vf. Furthermore, by looking at the time-dependent recovery of Vf during both the current stressing and thermal annealing of a single diode, we ascertain that the mechanisms for these two processes are different.
Development of Large-scaled FEM for Analysis of Mechanical Problems in Welding (2005)

Finite element method is a powerful tool for predicting welding distortion. However, the mechanical phenomena in welding are strong non-linear transient problems and thermal-elastic-plastic FE analysis requires very long computational times. To overcome this problem, an interactive substructure method is developed as a method to reduce the computational time in three-dimensional analysis. In this paper, by comparing with commercial software, the calculation accuracy and speed of this method is discussed. In order to confirm calculation efficiency for a large scale problem, calculation of the model with 670,000 degree of freedoms is performed. Further, calculation of the rotational distortion in FSW is performed and its applicability for practical problems is demonstrated.
25 Role of Myeloid Derived Suppressor Cells in Asthma (2012)

BACKGROUND: We know that a heterogeneous group of myeloid cells termed myeloid derived suppressor cells (MDSC) accumulate in almost all pathological conditions, which elicit an inflammatory signal. The exact role played by these cells in asthma is not known. In this study we investigated the function and role of these cells in asthma. METHODS: Accumulation of MDSC and other subsets of myeloid cells were analyzed from peripheral blood mononuclear cells from patients with non-severe asthma (FEV(1)) >60) and severe asthma (FEV(1) <60) by multicolor-flowcytometry and compared to healthy controls. Allergic mouse models were used to determine the role of microRNA-142 (miR-142) in regulation and expansion of MDSC. RESULTS: There is a significant increase in the proportion of MDSC in severe versus non-severe asthmatics and controls, corresponding to a decrease in myeloid dendritic cells. Allergic mice had significant increased levels of MDSC expansion which were associated with increased levels of IL-6 and downregulation of miR-142. miR-142 overexpression induced MDSC differentiation. CONCLUSIONS: An accumulation of MDSC is associated with severe asthma in humans and mice. In an allergic mouse model, IL-6 levels increase. miR-142 may play an important role in regulation and differentiation of MDSC, leading to altered immunity.