gebhart/patrepeval huggingface dataset:
30 OXYGEN DEPRIVATION DOES NOT FURTHER AUGMENT MITOCHONDRIAL MEMBRANE POTENTIAL IN PHARMACOLOGICALLY TREATED FIBROBLASTS FOR USE IN SOMATIC CELL NUCLEAR TRANSFER (2016)

Somatic cells commonly used in nuclear transfer primarily utilise the tricarboxylic acid cycle and cellular respiration for energy production. Comparatively, the metabolism of somatic cells contrasts that of cells within early embryos, which predominantly use glycolysis and exhibit Warburg Effect (WE)-like characteristics. We hypothesised that fibroblast cells can become more blastomere-like if driven either pharmacologically or by oxygen constraint and could result in improved in vitro embryonic development after somatic cell nuclear transfer (SCNT). The pharmaceuticals used (PS48 and CPI-613) should decrease mitochondrial use of the tricarboxylic acid (TCA) cycle and promote the PI3K pathway, respectively. Furthermore, we hypothesised that oxygen constraint (1.3%) would hinder TCA cycle activity and promote glycolysis. The goal was to achieve a WE-like effect in donor cells before nuclear transfer (NT) by treating Day 35 porcine fetal fibroblasts with CPI-613 (100 µM), PS48 (10 µM), both drugs combined (MIX), or as controls (CON, 0 µM) for 7 days under stepwise oxygen constraint (OC; 1.3%) or under normal conditions (ON; 5%). Three biological replicates were collected and data were analysed for main effect of treatment via GLM procedure of SAS 9.4 (SAS Institute Inc., Cary, NC, USA). To determine if our treatments affected mitochondria respiratory capacity (thereby TCA cycle capability) within embryos, we measured mitochondrial membrane potential (??m) using JC-10, a biphasic cationic dye. Mitotracker green (MTG) was used to estimate mitochondrial quantity. The percentage of cells with low ??m was increased (P = 0.02) with any CPI or MIX treatment (treatments = 95%) compared with OC-PS48 and both control (ON and OC) treatments (treatments = 77.4%), whereas ON-PS48 had an intermediate level (90.4%; error = 4.9%). Contrary to our prediction, MTG intensity was lower across all ON treatments compared with OC treatments (NO treatments = 736 AU v. OC treatments = 872 AU; error = 23 AU; P &amp;lt; 0.01). Regardless of oxygen level, controls and PS48 treatments yielded the highest percentages of viable cells (treatments = 94%) and OC-CPI and NO-MIX the lowest (treatments = 86%) with NO-CPI and OC-MIX being intermediate (treatments = 90%; error = 3%; P &amp;lt; 0.01). Oxygen constraint did not promote a reduction in mitochondrial membrane potential in pharmacologically treated fibroblasts. Additionally, intensity of MTG was increased in fibroblasts cultured under oxygen constraint compared with those cultured in 5% oxygen. Our results warrant further investigation of the mitochondrial changes occurring with oxygen deprivation in donor-cells. Experiments are underway to determine if gene expression in cells treated pharmacologically and with oxygen constraint are augmented, and whether these treatments will result in better development after SCNT. This study was funded by Food for the 21stCentury and NIH R01HD080636.
Cryogenic Characterization and Modeling of 14 nm Bulk FinFET Technology (2021)

In this work, we report the characterization and modeling of a 14 nm bulk FinFET technology from room-temperature down to 4.6 K. A cryogenic device model is used which shows excellent fit to measured data and can accurately predict the performance of the devices at low temperatures. The nMOS device showed subthreshold swing of 20 mV/decade, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$V_{\mathrm{T}}$</tex> shift of 80 mV and gm enhancement of 30%, all at 4.6 K. These results show that a tailored cryogenic FinFET technology, i.e. one accounting for the change in V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> and SS, could achieve a sharp reduction of dissipated power by reducing the drive bias. Such technology has potential for strong impact e.g. in quantum computing, by enabling integration of dense advanced cryogenic ICs inside the cryostat.
Increased Fibrosis in White Adipose Tissue of Male and Female bGH Transgenic Mice Appears Independent of TGF-β Action (2023)

Fibrosis is a pathological state caused by excess deposition of extracellular matrix proteins in a tissue. Male bovine growth hormone (bGH) transgenic mice experience metabolic dysfunction with a marked decrease in lifespan and with increased fibrosis in several tissues including white adipose tissue (WAT), which is more pronounced in the subcutaneous (Sc) depot. The current study expanded on these initial findings to evaluate WAT fibrosis in female bGH mice and the role of transforming growth factor (TGF)-β in the development of WAT fibrosis. Our findings established that female bGH mice, like males, experience a depot-dependent increase in WAT fibrosis, and bGH mice of both sexes have elevated circulating levels of several markers of collagen turnover. Using various methods, TGF-β signaling was found unchanged or decreased-as opposed to an expected increase-despite the marked fibrosis in WAT of bGH mice. However, acute GH treatments in vivo, in vitro, or ex vivo did elicit a modest increase in TGF-β signaling in some experimental systems. Finally, single nucleus RNA sequencing confirmed no perturbation in TGF-β or its receptor gene expression in any WAT cell subpopulations of Sc bGH WAT; however, a striking increase in B lymphocyte infiltration in bGH WAT was observed. Overall, these data suggest that bGH WAT fibrosis is independent of the action of TGF-β and reveals an intriguing shift in immune cells in bGH WAT that should be further explored considering the increasing importance of B cell-mediated WAT fibrosis and pathology.
Schottky barrier formed by network of screw dislocations in SrTiO3 (2005)

A network of screw dislocations was artificially created in SrTiO3, and characterized by transmission electron microscopy (TEM). Slight expansion of the dislocation core was observed by TEM. The composition of the dislocation core was quantified by electron energy loss spectroscopy, which reveals a 13±5% Ti∕O ratio increase but no Sr∕Ti ratio change in the core, demonstrating an oxygen deficiency or oxygen vacancy surplus in the dislocation core. The vacancy surplus was estimated to be about one vacancy every unit cell along the core. The dislocation core is positively charged; therefore, oxygen vacancies and holes are expelled from the dislocation network, forming a double Schottky barrier, which blocks charge carrier transports across the network. The Schottky barrier height at T=823K and PO2=2Pa was determined to be ∼0.48V.
Cooperative Spectrum Sensing in the Presence of Correlated and Malicious Cognitive Radios (2015)

While cooperative spectrum sensing improves sensing reliability when secondary users (SUs) have independent measurements, these gains are limited in the presence of correlated or malicious SUs. In this paper, we propose algorithms to improve spectrum sensing performance when the system contains both honest and malicious SUs all of whom may be experiencing correlated fading channels. We show that, when the SUs' reports at each time slot are independent and identically distributed, it is impossible to distinguish between malicious collaboration, i.e., collusion, and correlations caused by the environment. Thus, the optimal test statistic for cooperative spectrum sensing depends on the correlations in the SU reports but not on the source of these correlations. We propose two algorithms: one to identify SUs whose reports are correlated and another to infer the spectrum occupancy by using the learned structure of correlations. Groups of SUs whose reports are correlated are identified by learning the structure of the underlying Bayesian network model. This structure is implemented as a factor graph to infer the spectrum occupancy using a loopy belief propagation algorithm. We derive an upper bound of the error probability of the proposed structure learning algorithm and prove convergence of our loopy belief propagation algorithm.
On comparing the performance of object recognition systems (2002)

We give a methodology for the evaluation and comparison of object recognition systems. The methodology is based on indicators of two kinds: (1) statistical and (2) algorithmic. Statistical indicators measure the significance of the performance difference between different systems and rank the performances when the difference is significant. Of the various statistical indicators, we use the Kruskal-Wallis H test. Algorithmic indicators include the usual space and time complexity measures, and various performance curves in variables of error and test data sample size. We illustrate the methodology to evaluate a number of pattern classifiers.
Fast ultra-wideband microwave spectral scanning utilizing photonic wavelength- and time-division multiplexing (2017)

A high-speed ultra-wideband microwave spectral scanning system is proposed and experimentally demonstrated. Utilizing coherent dual electro-optical frequency combs and a recirculating optical frequency shifter, the proposed system realizes wavelength- and time-division multiplexing at the same time, offering flexibility between scan speed and size, weight and power requirements (SWaP). High-speed spectral scanning spanning from ~1 to 8 GHz with ~1.2 MHz spectral resolution is achieved experimentally within 14 µs. The system can be easily scaled to higher bandwidth coverage, faster scanning speed or finer spectral resolution with suitable hardware.
Bifunctional Sensing Characteristics of Chemical Vapor Deposition Synthesized Atomic-Layered MoS2 (2015)

Two-dimensional (2D) molybdenum disulfide (MoS2) atomic layers have a strong potential to be adopted for 2D electronic components due to extraordinary and novel properties not available in their bulk foams. Unique properties of the MoS2, including quasi-2D crystallinity, ultrahigh surface-to-volume, and a high absorption coefficient, have enabled high-performance sensor applications. However, implementation of only a single-functional sensor presents a limitation for various advanced multifunctional sensor applications within a single device. Here, we demonstrate the charge-transfer-based sensitive (detection of 120 ppb of NO2) and selective gas-sensing capability of the chemical vapor deposition synthesized MoS2 and good photosensing characteristics, including moderate photoresponsivity (∼71 mA/W), reliable photoresponse, and rapid photoswitching (<500 ms). A bifunctional sensor within a single MoS2 device to detect photons and gas molecules in sequence is finally demonstrated, paving a way toward a versatile sensing platform for a futuristic multifunctional sensor.
Sampling over shift-invariant unions (2014)

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On the shape and structure of the murine pulmonary heart valve (2021)

Abstract Murine animal models are an established standard in translational research and provides a potential platform for studying heart valve disease. To date, studies on heart valve disease using murine models have been hindered by a lack of appropriate methodologies due to their small scale. In the present study, we developed a multi-scale, imaging-based approach to extract the functional structure and geometry for the murine heart valve. We chose the pulmonary valve (PV) to study, due to its importance in congenital heart valve disease. Excised pulmonary outflow tracts from eleven 1-year old C57BL/6J mice were fixed at 10, 20, and 30 mmHg to simulate physiological loading. Micro-computed tomography was used to reconstruct the 3D organ-level PV geometry, which was then spatially correlated with serial en-face scanning electron microscopy imaging to quantify local collagen fiber distributions. From the acquired volume renderings, we obtained the geometric descriptors of the murine PV under increasing transvalvular pressures, which demonstrated remarkable consistency. We also observed that the preferred collagen orientation was predominantly in the circumferential direction, as in larger mammalian valves. The present study represents a first step in establishing organ-level murine models for the study of heart valve disease.
DNA Microarray Analyses of the Long-Term Adaptive Response ofEscherichia colito Acetate and Propionate (2003)

In its natural environment, Escherichia coli is exposed to short-chain fatty acids, such as acetic acid or propionic acid, which can be utilized as carbon sources but which inhibit growth at higher concentrations. DNA microarray experiments revealed expression changes during exponential growth on complex medium due to the presence of sodium acetate or sodium propionate at a neutral external pH. The adaptive responses to acetate and propionate were similar and involved genes in three categories. First, the RNA levels for chemotaxis and flagellum genes increased. Accordingly, the expression of chromosomal fliC'-'lacZ and flhDC'-'lacZ fusions and swimming motility increased after adaptation to acetate or propionate. Second, the expression of many genes that are involved in the uptake and utilization of carbon sources decreased, indicating some kind of catabolite repression by acetate and propionate. Third, the expression of some genes of the general stress response increased, but the increases were more pronounced after short-term exposure for this response than for the adaptive response. Adaptation to propionate but not to acetate involved increased expression of threonine and isoleucine biosynthetic genes. The gene expression changes after adaptation to acetate or propionate were not caused solely by uncoupling or osmotic effects but represented specific characteristics of the long-term response of E. coli to either compound.
TRIANGULATING POLYGONS WITHOUT LARGE ANGLES (1995)

We show how to triangulate polygonal regions—adding extra vertices as necessary— with triangles of guaranteed quality. Using only O(n) triangles, we can guarantee that the smallest height (shortest dimension) of a triangle in a triangulation of an n-vertex polygon (with holes) is a constant fraction of the largest possible. Using O(n log n) triangles for simple polygons or O(n 3/2 ) triangles for polygons with holes, we can guarantee that the largest angle is no greater than 150°. We can add the guarantee on smallest height to these no-large-angle results, without increasing the asymptotic complexity of the triangulation. Finally we give a nonobtuse triangulation algorithm for convex polygons that uses O(n 1.85 ) triangles.
Linearized electro-optic modulators based on a two-section Y-fed directional coupler (2010)

We experimentally demonstrate a linearized Y-fed directional coupler (DC) modulator based on an electro-optic (EO) polymer waveguide. The spurious free dynamic range of 119 dB/Hz2/3, which is 11 dB higher than that of the conventional Mach-Zehnder modulator, is achieved by introducing the reversed Δβ technique in the two-section Y-fed DC. The in-device EO coefficient (r33) of the fabricated device is as high as 79 pm/V in 1.55 μm wavelength, which is 88% of a single film r33 of LPD-80/APC.
Synthesis of β-lactamase inhibitors (1990)

Twenty-two compounds of the type R¹C₆H₄CH₂(CO)NHCHR²(CO)OCHR³COOH, where R¹ = H or OH, R² = H or Me, and R³ = H, Me, Et, i-Pr, Ph, or CH₂COOH, have been synthesized for testing as β-lactamase inhibitors. All of the intermediates and products were characterized by NMR, and mass spectra were run on some of the final products.
Genetic variants in PLCB4/PLCB1 as susceptibility loci for coronary artery aneurysm formation in Kawasaki disease in Han Chinese in Taiwan (2015)

Kawasaki disease (KD) is an acute, inflammatory, and self-limited vasculitis affecting infants and young children. Coronary artery aneurysm (CAA) formation is the major complication of KD and the leading cause of acquired cardiovascular disease among children. To identify susceptible loci that might predispose patients with KD to CAA formation, a genome-wide association screen was performed in a Taiwanese KD cohort. Patients with both KD and CAA had longer fever duration and delayed intravenous immunoglobulin treatment time. After adjusting for these factors, 100 susceptibility loci were identified. Four genes were identified from a single cluster of 35 using the Ingenuity Pathway Analysis (IPA) Knowledge Base. Silencing KCNQ5, PLCB1, PLCB4, and PLCL1 inhibited the effect of lipopolysaccharide-induced endothelial cell inflammation with varying degrees of proinflammatory cytokine expression. PLCB1 showed the most significant inhibition. Endothelial cell inflammation was also inhibited by using a phospholipase C (PLC) inhibitor. The single nucleotide polymorphism rs6140791 was identified between PLCB4 and PLCB1. Plasma PLC levels were higher in patients with KD and CC+CG rs6140791genotypes, and these genotypes were more prevalent in patients with KD who also had CAA. Our results suggest that polymorphism of the PLCB4/B1 genes might be involved in the CAA pathogenesis of KD.
Controlled thin-film deposition of α or β Ga2O3 by ion-beam sputtering (2020)

The wide bandgap of oxide semiconductors enables solid-state devices with functionalities beyond the reach of technologically more well-established materials such as silicon, germanium, or gallium nitride. These functionalities, among others, include optical transparency paving the way for transparent (opto-)electronics like ultraviolet light emitters or solar-blind detectors as well as large breakdown fields enabling high-power electronic applications. In particular, Ga2O3 is considered as oxide compatible with the nitride III-V materials. As a particular challenge, Ga2O3 may crystallize in different polymorphs. All possess large optical bandgaps beyond 4.8 eV and, thus, are of great interest for such devices. Nowadays, Ga2O3 thin films are prepared by a plethora of different synthesis methods including physical as well as chemical variants, however, reports on a controlled manufacturing process of individual Ga2O3 phases with sputtering techniques are currently scarce. Here, we grow Ga2O3 thin films by ion-beam sputtering on sapphire substrates of different orientation and demonstrate that selective controlled synthesis of different Ga2O3 polymorphs is feasible. The monoclinic β-phase and the corundum-type α-phase are stabilized when deposited on (0001) and (10–10) sapphire substrates, respectively. A stacking rather than a mixture of both phases is observed when thin films of α-phase exceed a certain thickness. Thus, thickness control enables the transition between the two phases. The proposed technique holds promise for ion-beam sputter methods to be employed in Ga2O3-related device build-up.
An alternative method for delivering exogenous material into developing zebrafish embryos (2007)

Non-invasive manipulation of multicellular systems is important for medical and biological research. The ability to introduce, remove, or modify molecules in the intracellular environment is pivotal to our understanding of cellular structure and function. Herein, we report on an alternative method for introducing foreign material into developing embryos using the application of femtosecond (fs) laser pulses. When intense fs laser pulses are focused to a sub-micron spot, transient pores are formed, providing a transport pathway for the delivery of exogenous material into embryonic cells. In this study, zebrafish embryos were used as a model system to demonstrate the non-invasiveness of this applied delivery tool. Utilizing optically induced transient pores chorionated and dechorionated zebrafish embryos were successfully loaded with a fluorescent reporter molecule (fluorescein isothiocyanate), Streptavidin-conjugated quantum dots or DNA (Simian-CMV-EGFP). Pore formation was independent of the targeted location, with both blastomere-yolk interface and blastomere pores competent for delivery. Long-term survival of laser manipulated embryos to pec-fin stage was 89% and 100% for dechorionated and chorionated embryos, respectively. To our knowledge, this is the first report of DNA delivery into zebrafish embryos utilizing fs laser pulses.
Performance evaluation of single channel virtual-circuit MAC protocols for MANETs (2011)

In this paper, we develop and evaluate models for estimating various performance metrics for unicast traffic using a single frequency channel virtual-circuit Medium Access Control (MAC) protocol in mobile wireless ad-hoc networks. Time is divided into periodic frames with a portion reserved for control traffic and the rest divided into timeslots for data traffic. In order to avoid interference between neighboring links, the virtual-circuit MAC protocol uses a set of reservation rules to assign timeslots to links. One such virtual-circuit MAC protocol is the hard scheduling mode of the reservation based Unifying Slot Assignment Protocol (USAP) with the number of frequency channels in a frame set to one. USAP uses a set of generic reservation rules to avoid interference between neighboring links. We model the performance of a single frequency channel virtual-circuit MAC protocol using reduced load loss network models that couple the physical, MAC, and routing layers effects. The blocking probability of a call at a particular link is calculated by considering cliques of neighboring interfering links that cannot transmit simultaneously. These neighboring interfering links and the conflict graph are calculated using the virtual-circuit reservation rules. We compare our results with simulation and show good match for large networks across various offered loads.
Contrast in Multi-Beam-Interference Lithography for the Fabrication of Photonic Crystal Structures (2008)

Multi-beam-interference lithography can be contrast-optimized to provide an efficient means of fabricating photonic crystal structures. Comparison to light- and dark-field mask technology in conventional lithography is presented and experimentally verified.
Modulation of γ-secretase by EVP-0015962 reduces amyloid deposition and behavioral deficits in Tg2576 mice (2012)

EVP-0015962 is orally bioavailable, detected in brain, and a potent, selective γ-secretase modulator in vitro and in vivo. Chronic treatment with EVP-0015962 was well tolerated in mice and lowered the production of Aβ42, attenuated memory deficits, and reduced Aβ plaque formation and inflammation in Tg2576 transgenic animals. In summary, these data suggest that γ-secretase modulation with EVP-0015962 represents a viable therapeutic alternative for disease modification in Alzheimer's disease.
High-Fidelity Generative Image Compression (2020)

We extensively study how to combine Generative Adversarial Networks and learned compression to obtain a state-of-the-art generative lossy compression system. In particular, we investigate normalization layers, generator and discriminator architectures, training strategies, as well as perceptual losses. In contrast to previous work, i) we obtain visually pleasing reconstructions that are perceptually similar to the input, ii) we operate in a broad range of bitrates, and iii) our approach can be applied to high-resolution images. We bridge the gap between rate-distortion-perception theory and practice by evaluating our approach both quantitatively with various perceptual metrics, and with a user study. The study shows that our method is preferred to previous approaches even if they use more than 2x the bitrate.