gebhart/patrepeval huggingface dataset:
MXene–Graphene Field-Effect Transistor Sensing of Influenza Virus and SARS-CoV-2 (2021)

An MXene-graphene field-effect transistor (FET) sensor for both influenza virus and 2019-nCoV sensing was developed and characterized. The developed sensor combines the high chemical sensitivity of MXene and the continuity of large-area high-quality graphene to form an ultra-sensitive virus-sensing transduction material (VSTM). Through polymer linking, we are able to utilize antibody-antigen binding to achieve electrochemical signal transduction when viruses are deposited onto the VSTM surface. The MXene-graphene VSTM was integrated into a microfluidic channel that can directly receive viruses in solution. The developed sensor was tested with various concentrations of antigens from two viruses: inactivated influenza A (H1N1) HA virus ranging from 125 to 250,000 copies/mL and a recombinant 2019-nCoV spike protein ranging from 1 fg/mL to 10 pg/mL. The average response time was about ∼50 ms, which is significantly faster than the existing real-time reverse transcription-polymerase chain reaction method (>3 h). The low limit of detection (125 copies/mL for the influenza virus and 1 fg/mL for the recombinant 2019-nCoV spike protein) has demonstrated the sensitivity of the MXene-graphene VSTM on the FET platform to virus sensing. Especially, the high signal-to-viral load ratio (∼10% change in source-drain current and gate voltage) also demonstrates the ultra-sensitivity of the developed MXene-graphene FET sensor. In addition, the specificity of the sensor was also demonstrated by depositing the inactivated influenza A (H1N1) HA virus and the recombinant 2019-nCoV spike protein onto microfluidic channels with opposite antibodies, producing signal differences that are about 10 times lower. Thus, we have successfully fabricated a relatively low-cost, ultrasensitive, fast-responding, and specific inactivated influenza A (H1N1) and 2019-nCoV sensor with the MXene-graphene VSTM.
Nafion/TiO2 Proton Conductive Composite Membranes for PEM Fuel Cells Operating at Elevated Temperature and Reduced Relative Humidity (2006)

Abstract not Available.
Combining grease trap and Moringa Oleifera as adsorbent to treat wastewater restaurant (2021)

This research's main goal is to decrease the concentration of fats and oils, phosphorus, and organic material in the wastewater. This study, therefore, explored the use of activated Moringa oleifera as an alternative adsorbent for decreasing the phosphate concentration and organic material as BOD5 via the adsorption process. A grease trap was used to catch fats and oils, separated into three compartments. The use of these three compartments aimed to improve the efficiency of grease traps. In the meantime, adsorption was used to decrease the concentration of BOD5 and phosphate. moringa oleifera and commercial activated carbon (Powdered Activated Carbon, that produced from carbonaceous raw materials, coconut shell, and wood) were the adsorption media used in this analysis. The findings of this study showed the grease trap capability in which it could remove 89.83% of fats and oils by using three compartments. When considering the optimum condition achieved by using moringa oleifera as the adsorbent, it was found that more than 85% of both BOD5 and phosphate can be removed with an adsorbent height of 15 cm and an adsorption tube diameter of 15 cm. Additionally, Thomas Model was fitted by moringa oleifera and commercial adsorbents to explain the pattern of adsorption of BOD5 and phosphate in wastewater. The results of the model showed a maximum reduction in BOD5 690 mg/g and phosphate 0.215 mg/g by moringa oleivera adsorbents. This research investigated the effectiveness of Moringa oleifera as an adsorbent, cnsidering the basic surface area characteristics, pore diameter, and pore volume of Moringa oleifera as an adsorbent.
Attack Pattern Discovery in Forensic Investigation of Network Attacks (2011)

We mine the logs of network traffic data to find the contexts of attacks; we call them attack patterns. We propose an iterative algorithm for discovering attack patterns via a feedback mechanism, with the degrees of belief for attack instances propagated to the next iteration to further refine the search. Our simulations verify that the algorithm achieves accuracy in discovering attack patterns. Our attack pattern discovery has the additional advantage of being an unsupervised algorithm, e.g., it does not require a priori user-defined thresholds.
Types of Stem Cells in Regenerative Medicine: A Review (2014)

: Two basic and clinical researches accomplished during the recent years on embryonic and adult stem cells constituted a mutation in regenerative therapy. These cells can be used for treating some degenerative diseases. Between them, age-related functional defects, hematopoietic and immune system disorders, heart failures, chronic liver injuries, diabetes, Parkinsonâs and Alzheimerâs diseases, arthritis and muscular, skin, lung, eye, and digestive disorders, aggressive and regressive cancers can be treated by cell therapies. This review focused on types of stem cells used in regenerative medicine.
Regulatory Loop between Redox Sensing of the NADH/NAD <sup>+</sup> Ratio by Rex (YdiH) and Oxidation of NADH by NADH Dehydrogenase Ndh in <i>Bacillus subtilis</i> (2006)

NADH dehydrogenase is a key component of the respiratory chain. It catalyzes the oxidation of NADH by transferring electrons to ubiquinone and establishes a proton motive force across the cell membrane. The yjlD (renamed ndh) gene of Bacillus subtilis is predicted to encode an enzyme similar to the NADH dehydrogenase II of Escherichia coli, encoded by the ndh gene. We have shown that the yjlC-ndh operon is negatively regulated by YdiH (renamed Rex), a homolog of Rex in Streptomyces coelicolor, and a redox-sensing transcriptional regulator that responds to the NADH/NAD(+) ratio. The ndh gene regulates expression of the yjlC-ndh operon, as indicated by the fact that mutation in ndh causes a higher NADH/NAD(+) ratio. An in vitro study showed that Rex binds to the downstream region of the yjlC-ndh promoter and that NAD(+) enhances the binding of Rex to the putative Rex-binding sites in the yjlC-ndh operon as well as in the cydABCD operon. These results indicated that Rex and Ndh together form a regulatory loop which functions to prevent a large fluctuation in the NADH/NAD(+) ratio in B. subtilis.
Amyloid precursor protein beta-secretase (BACE) mRNA expression in human neural cell lines following induction of neuronal differentiation and exposure to cytokines and growth factors (2000)

Recently, a novel amyloid precursor protein beta-secretase (designated BACE) was identified. Because activated microglia and astrocytes play a role in amyloidogenesis in Alzheimer's disease, the constitutive and glial cytokine/growth factor-regulated expression of BACE was studied in human neural cell lines. By reverse transcription-polymerase chain reaction (RT-PCR) analysis, BACE mRNA expression was identified in various human neural and non-neural cell lines. By northern blot analysis, the expression of BACE mRNA composed of five distinct transcripts (>8.0, 7.0, 6.0, 4.4 and 2.6 kb) was elevated markedly in NTera2 teratocarcinoma cells following retinoic acid-induced neuronal differentiation. But the levels of three major BACE mRNA species (7.0, 6.0 and 4.4 kb) were not significantly altered in NTera2-derived neurons, SK-N-SH neuroblastoma or U-373MG astrocytoma following exposure to tumor necrosis factor-alpha, interleukin (IL)-1beta, IL-6, interferon-gamma, transforming growth factor-beta1, epidermal growth factor, basic fibroblast growth factor, brain-derived neurotrophic factor, dibutyryl cyclic adenosine monophosphate or phorbol 12-myristate 13-acetate. These results indicate that BACE mRNA is expressed constitutively in human neural cells and its expression is upregulated during neuronal differentiation, but it is unlikely to be regulated by activated glia-derived cytokines and growth factors.
Effect of oxygenation of transperitoneal ventilation on the death time after asphyxiation in rabbits. (2010)

These results suggest that transperitoneal ventilation can markedly prolong the death time of asphyxiated rabbits.
Recovery of Alkaline Earth Metals from Desalination Brine for Carbon Capture and Sodium Removal (2021)

Because carbon dioxide adsorbs the radiation from the Sun and the Earth’s surface, global warming has become a severe problem in this century. Global warming causes many environmental problems such as heatwave, desertification, and erratic rainfall. Above all, erratic rainfall makes people have insufficient freshwater. To solve this problem, desalination technology has been developed in many countries. Although desalination technology can provide freshwater, it produces brine as well (producing 1 L of freshwater would result in 1 L of brine). The brine will decrease the dissolved oxygen in the sea and affect the organism’s habitat. In this study, magnesium and calcium from desalination brine were recovered in the form of magnesium hydroxide and calcium hydroxide by adjusting the pH value for carbon capture and sodium removal. Magnesium hydroxide would turn into magnesium carbonate through contacting CO2 in saturated amine carriers. Calcium hydroxide was added to the brine and reacted with CO2 (modified Solvay process). Sodium in brine would then be precipitated in the form of sodium bicarbonate. After removing sodium, brine can be released back into the ocean, or other valuable metals can be extracted from brine without the side effect of sodium. The results revealed that 288 K of 3-Amino-1-propanol could capture 15 L (26.9 g) of CO2 and that 25 g/L of Ca(OH)2 at 288 K was the optimal parameter to remove 7000 ppm sodium and adsorb 16 L (28.7 g) of CO2 in the modified Solvay process. In a nutshell, this research aims to simultaneously treat the issue of CO2 emission and desalination brine by combining the amines carrier method and the modified Solvay process.
Surface-engineered substrates for improved human pluripotent stem cell culture under fully defined conditions (2011)

The current gold standard for the culture of human pluripotent stem cells requires the use of a feeder layer of cells. Here, we develop a spatially defined culture system based on UV/ozone radiation modification of typical cell culture plastics to define a favorable surface environment for human pluripotent stem cell culture. Chemical and geometrical optimization of the surfaces enables control of early cell aggregation from fully dissociated cells, as predicted from a numerical model of cell migration, and results in significant increases in cell growth of undifferentiated cells. These chemically defined xeno-free substrates generate more than three times the number of cells than feeder-containing substrates per surface area. Further, reprogramming and typical gene-targeting protocols can be readily performed on these engineered surfaces. These substrates provide an attractive cell culture platform for the production of clinically relevant factor-free reprogrammed cells from patient tissue samples and facilitate the definition of standardized scale-up friendly methods for disease modeling and cell therapeutic applications.
Pixel Circuits and Driving Schemes for Active-Matrix Organic Light-Emitting Diode Displays (2007)

Rapid progress over the last decade on thin film transistor (TFT) active matrix organic light emitting (AMOLED) displays led to the emergence of high-performance, low-power, low-cost flat panel displays. Despite the shortcomings of the active matrix that are associated with the instability and low mobility of TFTs, the amorphous silicon TFT technology still remains the primary solution for the AMOLED backplane. To take advantage of this technology, it is crucial to develop driving schemes and circuit techniques to compensate for the limitations of the TFTs. \nThe driving schemes proposed in this thesis address these challenges, in which, the sensitivity of the OLED current to the transistor variations is reduced significantly. This is achieved by comparing the data signal with a feedback signal associated with the pixel current by means of an external driving circuit through a column feedback line. Depending on the nature of the feedback signal, (i.e. current or voltage) several pixel circuits and external drivers are proposed. \nNew AMOLED pixel circuits with voltage and current feedback are designed, simulated, fabricated, and tested. The performance of these circuits is analyzed in terms of their stability, settling time, power efficiency, noise, and temperature-dependence. For the pixel circuits with current feedback, an operational transresistance amplifier is designed and implemented in a high-voltage CMOS process. Measurement results for both voltage and current feedback driving schemes indicate less than a 2%/V sensitivity to shifts in the threshold voltage of the TFTs. By using current feedback and an accelerating pulse, programming times less than 50 s are achieved.
Majorana bound state in a coupled quantum-dot hybrid-nanowire system (2016)

Hybrid nanowires combining semiconductor and superconductor materials appear well suited for the creation, detection, and control of Majorana bound states (MBSs). We demonstrate the emergence of MBSs from coalescing Andreev bound states (ABSs) in a hybrid InAs nanowire with epitaxial Al, using a quantum dot at the end of the nanowire as a spectrometer. Electrostatic gating tuned the nanowire density to a regime of one or a few ABSs. In an applied axial magnetic field, a topological phase emerges in which ABSs move to zero energy and remain there, forming MBSs. We observed hybridization of the MBS with the end-dot bound state, which is in agreement with a numerical model. The ABS/MBS spectra provide parameters that are useful for understanding topological superconductivity in this system.
Microneedle-mediated vaccine delivery: Harnessing cutaneous immunobiology to improve efficacy (2012)

Microneedle-mediated vaccines hold enormous potential for patient benefit. However, in order for microneedle vaccine strategies to fulfill their potential, the proportion of an immune response that is due to the local action of delivered vaccines on skin antigen-presenting cells, and what is due to a systemic effect from vaccines reaching the systemic circulation, must be determined. Moreover, industry will need to invest significantly in new equipment and instrumentation in order to mass-produce microneedle vaccines consistently. Finally, microneedles will need to demonstrate consistent dose delivery across patient groups and match this to reliable immune responses before they will replace tried-and-tested needle-and-syringe-based approaches.
Simultaneous inversion of the background velocity and the perturbation in full-waveform inversion (2015)

ABSTRACT The gradient of standard full-waveform inversion (FWI) attempts to map the residuals in the data to perturbations in the model. Such perturbations may include smooth background updates from the transmission components and high wavenumber updates from the reflection components. However, if we fix the reflection components using imaging, the gradient of what is referred to as reflected-waveform inversion (RWI) admits mainly transmission background-type updates. The drawback of existing RWI methods is that they lack an optimal image capable of producing reflections within the convex region of the optimization. Because the influence of velocity on the data was given mainly by its background (propagator) and perturbed (reflectivity) components, we have optimized both components simultaneously using a modified objective function. Specifically, we used an objective function that combined the data generated from a source using the background velocity, and that by the perturbed velocity through Born modeling, to fit the observed data. When the initial velocity was smooth, the data modeled from the source using the background velocity will mainly be reflection free, and most of the reflections were obtained from the image (perturbed velocity). As the background velocity becomes more accurate and can produce reflections, the role of the image will slowly diminish, and the update will be dominated by the standard FWI gradient to obtain high resolution. Because the objective function was quadratic with respect to the image, the inversion for the image was fast. To update the background velocity smoothly, we have combined different components of the gradient linearly through solving a small optimization problem. Application to the Marmousi model found that this method converged starting with a linearly increasing velocity, and with data free of frequencies below 4 Hz. Application to the 2014 Chevron Gulf of Mexico imaging challenge data set demonstrated the potential of the proposed method.
OASIS: A Large-Scale Dataset for Single Image 3D in the Wild (2020)

Single-view 3D is the task of recovering 3D properties such as depth and surface normals from a single image. We hypothesize that a major obstacle to single-image 3D is data. We address this issue by presenting Open Annotations of Single Image Surfaces (OASIS), a dataset for single-image 3D in the wild consisting of annotations of detailed 3D geometry for 140,000 images. We train and evaluate leading models on a variety of single-image 3D tasks. We expect OASIS to be a useful resource for 3D vision research. Project site: https://pvl.cs.princeton.edu/OASIS.
Bayesian statistics in oncology (2009)

The rise of evidence-based medicine as well as important progress in statistical methods and computational power have led to a second birth of the >200-year-old Bayesian framework. The use of Bayesian techniques, in particular in the design and interpretation of clinical trials, offers several substantial advantages over the classical statistical approach. First, in contrast to classical statistics, Bayesian analysis allows a direct statement regarding the probability that a treatment was beneficial. Second, Bayesian statistics allow the researcher to incorporate any prior information in the analysis of the experimental results. Third, Bayesian methods can efficiently handle complex statistical models, which are suited for advanced clinical trial designs. Finally, Bayesian statistics encourage a thorough consideration and presentation of the assumptions underlying an analysis, which enables the reader to fully appraise the authors' conclusions. Both Bayesian and classical statistics have their respective strengths and limitations and should be viewed as being complementary to each other; we do not attempt to make a head-to-head comparison, as this is beyond the scope of the present review. Rather, the objective of the present article is to provide a nonmathematical, reader-friendly overview of the current practice of Bayesian statistics coupled with numerous intuitive examples from the field of oncology. It is hoped that this educational review will be a useful resource to the oncologist and result in a better understanding of the scope, strengths, and limitations of the Bayesian approach.
Bidirectional wavelength add-drop multiplexer using multiport optical circulators and fiber Bragg gratings (2000)

We propose and experimentally demonstrate a new of bidirectional wavelength add-drop multiplexer using multiport optical circulators and fiber Bragg gratings. It has the efficient suppression of the unwanted light caused by Rayleigh backscattering and optical reflection and is economical for the effective use of multiport optical circulators.
Quantitative assessment of photoacoustic tomography systems integrating clinical ultrasound transducers using novel tissue-simulating phantoms (2015)

Photoacoustic Tomography (PAT) systems based on commercial ultrasound instruments have the benefit of dualmodality imaging, which increases their appeal from a clinical standpoint. However, factors that influence PAT system performance have not been thoroughly investigated and standardized test methods have not been established for image quality evaluation. To address these issues we have adapted phantom-based approaches from ultrasound imaging standards and implemented them to assess a PAT system developed for vascular imaging. Our system comprises a tunable near-infrared pulsed laser and a commercial ultrasound imaging system, including four interchangeable linear array clinical ultrasound transducers with varying center frequencies, acoustic bandwidths and geometries. Phantoms consisted of a customized polyvinyl chloride (PVC) plastisol gel that simulates both optical and acoustic properties of breast tissue. One phantom incorporates a sub-resolution filament array suitable for bimodal ultrasound-photoacoustic imaging, while another contains an array of hemoglobin-filled cylindrical inclusions at various depths. Key performance characteristics were evaluated, including spatial resolution, signal uniformity, contrast, and penetration depth. These characteristics were evaluated at 750 nm at radiant exposures below ANSI safety limits. Effects of transducer properties on imaging performance were evaluated. Axial and lateral resolution ranged from 0.27-0.83 mm and 0.28-1.8 mm, respectively, and penetration depths from 1.9-4.2 cm were achieved. These results demonstrate variation in PAT system performance based on clinical transducer selection, as well as the utility of realistic phantom-based test methods in performing benchtop evaluations of system performance.
Corrected settling time of the distributed parallel arbiter (1992)

In data buses used for interconnecting the constituent parts of a computer system, contention can arise if two or more of the modules attempt to acquire control of the bus at the same time. The distributed parallel arbiter is a widely-used means of resolving this contention; it consists of a combinational logic network distributed among all the modules. The time taken for the network to settle is the sum of two components, one representing delays through circuit elements, and the second, propagation delays along bus lines. An earlier calculation of the second of these delays has been found to be incorrect because it took no account of the glitches caused by logic hazards and by the electrical properties of the bus lines—‘wired-OR’ glitches. These errors are corrected, revised expressions for the delay are given, and a method is proposed for improving the performance by bypassing the arbitration process unless contention is actually present.
Effect of Cytochrome c on the Generation and Elimination of O<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.gif"><mml:msubsup><mml:mrow/><mml:mrow><mml:mn>2</mml:mn></mml:mrow><mml:mrow><mml:mo>⨪</mml:mo></mml:mrow></mml:msubsup></mml:math> and H2O2 in Mitochondria (2003)

The primary recognized function of cytochrome c is to act as an electron carrier transferring electrons from complex III to complex IV in the respiratory chain of mitochondria. Recent studies on cell apoptosis reveal that cytochrome c is responsible for the programmed cell death when it is released from mitochondria to cytoplasm. In this study we present evidence showing that cytochrome c plays an antioxidative role by acting on the generation and elimination of O(2)(*) and H(2)O(2) in mitochondria. The O(2)(*) and H(2)O(2) generation in cytochrome c-depleted Keilin-Hartree heart muscle preparation (HMP) is 7-8 times higher than that in normal HMP. The reconstitution of cytochrome c to the cytochrome c-depleted HMP causes the O(2)(*) and H(2)O(2) generation to exponentially decrease. An alternative electron-leak pathway of the respiratory chain is suggested to explain how cytochrome c affects on the generation and elimination of O(2)(*) and H(2)O(2) in mitochondria. Enough cytochrome c in the respiratory chain is needed for keeping O(2)(*) and H(2)O(2) at a lower physiological level. A dramatic increase of O(2)(*) and H(2)O(2) generation occurs when cytochrome c is released from the respiratory chain. The burst of O(2)(*) and H(2)O(2), which happens at the same time as cytochrome c release from the respiratory chain, should have some role in the early stage of cell apoptosis.