gebhart/patrepeval huggingface dataset:
Identification of dAven, aDrosophila melanogasterortholog of the cell cycle regulator Aven (2011)

Aven is a regulator of the DNA-damage response and G2/M cell cycle progression. Overexpression of Aven is associated with poor prognosis in patients with childhood acute lymphoblastic leukemia and acute myeloid leukemia, and altered intracellular Aven distribution is associated with inﬁltrating ductal carcinoma and papillary carcinoma breast cancer subtypes. Although Aven orthologs have been identified in most vertebrate species, no Aven gene has been reported in invertebrates. Here, we describe a Drosophila melanogaster open reading frame (ORF) that shares sequence and functional similarities with vertebrate Aven genes. The protein encoded by this ORF, which we named dAven, contains several domains that are highly conserved among Aven proteins of fish, amphibian, bird and mammalian origins. In flies, knockdown of dAven by RNA interference (RNAi) resulted in lethality when its expression was reduced either ubiquitously or in fat cells using Gal4 drivers. Animals undergoing moderate dAven knockdown in the fat body had smaller fat cells displaying condensed chromosomes and increased levels of the mitotic marker phosphorylated histone H3 (PHH3), suggesting that dAven was required for normal cell cycle progression in this tissue. Remarkably, expression of dAven in Xenopus egg extracts resulted in G2/M arrest that was comparable to that caused by human Aven. Taken together, these results suggest that, like its vertebrate counterparts, dAven plays a role in cell cycle regulation. Drosophila could be an excellent model for studying the function of Aven and identifying cellular factors that influence its activity, revealing information that may be relevant to human disease.
Comparison of compensatory reserve during lower-body negative pressure and hemorrhage in nonhuman primates (2016)

Compensatory reserve was measured in baboons (n = 13) during hemorrhage (Hem) and lower-body negative pressure (LBNP) using a machine-learning algorithm developed to estimate compensatory reserve by detecting reductions in central blood volume during LBNP. The algorithm calculates compensatory reserve index (CRI) from normovolemia (CRI = 1) to cardiovascular decompensation (CRI = 0). The hypothesis was that Hem and LBNP will elicit similar CRI values and that CRI would have higher specificity than stroke volume (SV) in predicting decompensation. Blood was removed in four steps: 6.25%, 12.5%, 18.75%, and 25% of total blood volume. Four weeks after Hem, the same animals were subjected to four levels of LBNP that was matched on the basis of their central venous pressure. Data (mean ± 95% confidence interval) indicate that CRI decreased (P < 0.001) from baseline during Hem (0.69 ± 0.10, 0.57 ± 0.09, 0.36 ± 0.10, 0.16 ± 0.08, and 0.08 ± 0.03) and LBNP (0.76 ± 0.05, 0.66 ± 0.08, 0.36 ± 0.13, 0.23 ± 0.11, and 0.14 ± 0.09). CRI was not different between Hem and LBNP (P = 0.20). Linear regression analysis between Hem CRI and LBNP CRI revealed a slope of 1.03 and a correlation coefficient of 0.96. CRI exhibited greater specificity than SV in both Hem (92.3 vs. 82.1) and LBNP (94.8 vs. 83.1) and greater ROC AUC in Hem (0.94 vs. 0.84) and LBNP (0.94 vs. 0.92). These data support the hypothesis that Hem and LBNP elicited the same CRI response, suggesting that measurement of compensatory reserve is superior to SV as a predictor of cardiovascular decompensation.
Optically Compensated In‐Plane‐Switching‐Mode TFT‐LCD Panel (1998)

Abstract An optically compensated in‐plane‐switching‐mode TFT‐LCD panel was developed. The panel has an optical compensation film between a liquid crystal layer and a polarizer, and shows a significantly high‐contrast viewing angle, good gray‐scale capability, small color shift, and a large tolerance for cell gap non‐uniformity compared with a conventional in‐plane‐switching‐mode LCD.
Z-membranes: artificial organelles for overexpressing recombinant integral membrane proteins. (1996)

We have expressed a fusion protein formed between the avian infectious bronchitis virus M protein and the bacterial enzyme beta-glucuronidase in transgenic tobacco cells. Electron microscope images of such cells demonstrate that overexpression of this fusion protein gives rise to a type of endoplasmic reticulum membrane domain in which adjacent membranes become zippered together apparently as a consequence of the oligomerizing action of beta-glucuronidase. These zippered (Z-) membranes lack markers of the endoplasmic reticulum (NADH cytochrome c reductase and ribosomes) and accumulate in the cells in the form of multilayered scroll-like structures (up to 2 micrometers in diameter; 20-50 per cell) without affecting plant growth. The discovery of Z-membranes has broad implications for biology and biotechnology in that they provide a means for accumulating large quantities of recombinant membrane proteins within discrete domains of native membranes.
The Expanding Diversity of Mycobacterium tuberculosis Drug Targets (2018)

After decades of relative inactivity, a large increase in efforts to discover antitubercular therapeutics has brought insights into the biology of Mycobacterium tuberculosis (Mtb) and promising new drugs such as bedaquiline, which inhibits ATP synthase, and the nitroimidazoles delamanid and pretomanid, which inhibit both mycolic acid synthesis and energy production. Despite these advances, the drug discovery pipeline remains underpopulated. The field desperately needs compounds with novel mechanisms of action capable of inhibiting multi- and extensively drug -resistant Mtb (M/XDR-TB) and, potentially, nonreplicating Mtb with the hope of shortening the duration of required therapy. New knowledge about Mtb, along with new methods and technologies, has driven exploration into novel target areas, such as energy production and central metabolism, that diverge from the classical targets in macromolecular synthesis. Here, we review new small molecule drug candidates that act on these novel targets to highlight the methods and perspectives advancing the field. These new targets bring with them the aspiration of shortening treatment duration as well as a pipeline of effective regimens against XDR-TB, positioning Mtb drug discovery to become a model for anti-infective discovery.
A steady-state analysis of bi-directional inductive power transfer systems (2013)

The modeling and analysis of bi-directional inductive power transfer (BD-IPT) systems are relatively complicated as they consist of high order resonant circuits, which are complex in nature and sensitive to variations in system parameters and control variables. Consequently, an accurate model that can predict the behavior of BD-IPT systems under different operating conditions has not been reported to-date. This paper therefore proposes a mathematical model through which the steady-state behavior of BD-IPT systems can be accurately characterized. The proposed mathematical model is comprehensive as it accounts for the effects of harmonics and sensitivity to variations in system parameters and control variables. The validity of the proposed model, which is verified using the simulated results of a 7.5 kW system, provides a clear insight into the operation of BDIPT systems and is expected to be useful at both design and optimizations stages.
Abstract 5155: Increased longevity of continuous bone marrow cultures and radioresistance of bone marrow stromal cells from SOD193AALS (Amyotrophic Lateral Sclerosis) mice (2019)

Introduction: The SOD1G93A mouse model of ALS, demonstrates hind limb paralysis beginning at 90 - 100 days of age with stage 4 paralysis at 125 days of age and progressive neuromuscular loss.Materials and Methods: To determine whether deficiency of functional SOD1 influenced parameters of hematopoiesis, long-term bone marrow cultures were established from ALS and control mice. Bone marrow stromal cell lines derived from LTBMCs were tested for clonogenic radiation survival. We tested the effect of bone marrow transplant after total body irradiation on delay of paralysis.Results: SOD1G93A marrow cultures demonstrated significant increase in production of hematopoietic progenitor cells (p < 0.0001) and overall longevity of production of hematopoietic cells (p = 0.0354), and bone marrow stromal cell lines were significantly radioresistant (D0 = 1.33 ± 0.09, and ñ = 8.57 ± 1.8) compared to control C57BL/6J mice (D0 = 1.59 ± 0.11, p = 0.117; and ñ = 3.4 ± 0.4, p= 0.0466). Total body irradiation and bone marrow transplantation with GFP+ donor marrow demonstrated a significant increase in paralysis free interval from 129.2 ± 3.0 to 240.7 ± 21.1 days (p = 0.0010), normalization of blood/brain barrier permeability, and increase in M2 marrow origin microglial cells in proximity to degenerating anterior horn cell/motor neurons. Isolated brain and spinal cord irradiation did not prolong the paralysis free interval (129.0 ± 2.7 days, p = 0.7748).Conclusions: The results of hematopoiesis in LTBMCs in the absence of functional SOD1 showed improved LTBMC longevity and radioresistance of marrow stromal cells both unexpected pleiotropic effects of the SOD1G93A genotype. Marrow transplant after TBI prolonged the paralysis free interval in ALS mice.Citation Format: Andrew Henderson, Michael W. Epperly, Renee Fisher, Donna Shields, Lora Rigatti, Christopher Donnelly, Simon Watkins, Joel S. Greenberger. Increased longevity of continuous bone marrow cultures and radioresistance of bone marrow stromal cells from SOD193A ALS (Amyotrophic Lateral Sclerosis) mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5155.
ChemInform Abstract: WO3/70% TBHP/Aqueous NaOH: An Efficient Catalytic Combination for the Selective Oxidation of Methylarenes and Alkyl Aryl Ketones to Benzoic Acids. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Backward wave oscillators for terahertz applications (2004)

Calabazas Creek Research, Inc. is funded by the National Aeronautics and Space Administration to develop advanced backward wave oscillators that incorporate energy recovery, air cooling and improved performance. An improved coupler transforms the generated RF power to a high-purity, Gaussian output mode. The construction of a 600-700 GHz BWO is currently underway with higher frequency sources in development. Simulations predict 6-8 mW of RF power over a 100 GHz bandwidth.
Hierarchical HIT Registries (2020)

This document describes using the registration protocol and registries
to support hierarchical HITs (HHITs). New and existing HIP parameters
are used to communicate Registry Policies and data about the HHIT
device and the Registries. Further Registries are expected to provide
RVS services for registered HHIT devices.
Intimal hyperplasia after vascular injury is inhibited by antisense cdk 2 kinase oligonucleotides. (1994)

The cell cycle regulatory enzyme, cdk (cyclin-dependent kinase) 2 kinase, is activated in the rat carotid artery after balloon angioplasty injury, and may mediate smooth muscle proliferation. To test the hypothesis that inhibition of the expression of this key enzyme can inhibit intimal hyperplasia, we studied the effect of antisense phosphorothioate oligodeoxynucleotides (ODN) against cdk 2 kinase administered by intraluminal delivery using hemagglutinating virus of Japan (HVJ)-liposome-mediated transfer. The specificity of antisense cdk 2 ODN was confirmed by the observation that mRNA level of cdk 2 kinase in injured vessels was markedly diminished by the antisense ODN treatment. At 2 wk after transfection, antisense cdk 2 ODN treatment (15 microM) resulted in a significant inhibition (60%) in neointima formation, compared with sense ODN-treated and untreated vessels. Since we have previously observed that cell division cycle 2 kinase mRNA was also activated after vascular injury, we administered the combination of antisense cdc 2 and cdk 2 ODN in this study. Antisense cdc 2 ODN alone (15 microM) only reduced intimal formation by 40%. Combined antisense treatment resulted in near complete inhibition of neointima formation. To understand the mechanism of the sustained effect of a single antisense ODN administration, we examined kinetics of ODN in the vessel wall. Using phosphorothioate FITC-labeled ODN, we transfected carotid artery using the HVJ-liposome method. Fluorescence localized immediately to the medial layer, and persisted up to 2 wk after transfection. These results demonstrate that a single intraluminal administration of antisense ODN directed to cell cycle regulatory genes (e.g., cdk 2 kinase) using the HVJ method can result in a sustained inhibition of neointima formation after balloon angioplasty in rat carotid injury model.
Antiproliferative Activity of Fucoidan Was Associated with the Induction of Apoptosis and Autophagy in AGS Human Gastric Cancer Cells (2011)

Fucoidan, a sulfated polysaccharide purified from brown algae, possesses a variety of pharmacologic effects, including antiinflammatory, antioxidant, and anticancer properties; however, the underlying action mechanisms are not completely understood. This study investigated the possible mechanisms through which fucoidan exerts its antiproliferative action in cultured AGS human gastric adenocarcinoma cells. We found that fucoidan effectively inhibits the growth of AGS cells by inducing autophagy, as well as apoptosis. Apoptosis by fucoidan treatment was associated with the downregulation of antiapoptotic Bcl-2 and Bcl-xL expression, loss of mitochondrial membrane potential, activation of caspases, and concomitant degradation of poly-(ADP-ribose) polymerase protein. In addition, the morphological study indicated a characteristic finding of autophagy, such as the formation of autophagosomes in fucoidan-treated AGS cells. Furthermore, markers of autophagy, namely, the conversion of microtubule-associated protein light chain 3 (LC3)-I to LC3-II and increased beclin-1 accumulation, were observed. Overall, the present data suggest that fucoidan induces apoptotic and autophagic cell death, and both apoptotic and autophagic mechanisms contribute to the fucoidan-induced AGS cell death.
SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development (2016)

1 Summary Recent advances in RNA sequencing enable the generation of genome-wide expression data at the single-cell level, opening up new avenues for transcriptomics and systems biology. A new application of single-cell whole-transcriptomics is the unbiased ordering of cells according to their progression along a dynamic process of interest. We introduce SCORPIUS, a method which can effectively reconstruct an ordering of individual cells without any prior information about the dynamic process. Comprehensive evaluation using ten scRNA-seq datasets shows that SCORPIUS consistently outperforms state-of-the-art techniques. We used SCORPIUS to generate novel hypotheses regarding dendritic cell development, which were subsequently validated in vivo . This work enables data-driven investigation and characterization of dynamic processes and lays the foundation for objective benchmarking of future trajectory inference methods.
Endogenous retroviral elements, but not exogenous retroviruses, are detected in CD30-positive lymphoproliferative disorders of the skin (2003)

Primary cutaneous CD30-positive lymphoproliferative disorders (LPD) comprise a spectrum of disorders including lymphomatoid papulosis (LyP) and CD30+ pleomorphic or anaplastic large T-cell lymphomas ( 1 – 3 ). LyP is a chronic, recurrent lymphoproliferative disorder which manifests clinically as papulonodular, spontaneously regressing skin lesions ( 4 ). Histologically, large pleomorphic and anaplastic tumor cells are found which are activated T-lymphocytes expressing the CD30 antigen ( 5 , 6 ). Viruses are known etiologic factors in the pathogenesis of non-Hodgkin’s lymphomas (NHL) ( 7 ). In particular, retroviruses such as human T-lymphotropic virus 1 and 2 (HTLV-1 and 2) have been linked to adult T-cell leukemia/lymphoma (ATLL) and other forms of NHL (for review see refs 8 and 9). Primary cutaneous lymphomas, especially cutaneous T-cell lymphomas, have been considered to be caused by viruses. Several reports of the detection of HTLV-1 or 2 sequences in cutaneous T-cell lymphomas (CTCL) ( 10 – 13 ) have not been confirmed in other studies ( 8 , 9 , 14 , 15 ).
Interoperability of magnetic pads with intermediate coils and different primaries (2022)

An interoperability study is performed for a three-coil system with double-d (DDP) magnetic topologies for the primary pad while keeping the secondary and intermediate pads as circular pads (CP). A mathematical model is provided for the three-coil system along with magnetic simulation results from Ansys Maxwell software. Using these results, calculations were carried out to establish the minimum primary apparent power required to transfer 10kW of power to the load. At the natural offset and maximum misalignment positions, the primary pad must exert 75.8kVA and 128.3kVA, respectively. Whereas, the intermediate apparent power is fixed at 185kVA within the misalignment constraints. At these power levels leakage magnetic fields produced were $7 \mu \mathrm{T}$ and $10 \mu \mathrm{T}$ in the worst leakage plane when measured 1050mm away from the center of the secondary pad. Finally, a comparison of employing a primary pad as a double-d or circular pad is presented.
Omicron-specific mRNA vaccine induced potent neutralizing antibody against Omicron but not other SARS-CoV-2 variants (2022)

Abstract The emerging SARS-CoV-2 variants of concern (VOC) harbor mutations associated with increasing transmission and immune escape, hence undermine the effectiveness of current COVID-19 vaccines. In late November of 2021, the Omicron (B.1.1.529) variant was identified in South Africa and rapidly spread across the globe. It was shown to exhibit significant resistance to neutralization by serum not only from convalescent patients, but also from individuals receiving currently used COVID-19 vaccines with multiple booster shots. Therefore, there is an urgent need to develop next generation vaccines against VOCs like Omicron. In this study, we develop a panel of mRNA-LNP-based vaccines using the receptor binding domain (RBD) of Omicron and Delta variants, which are dominant in the current wave of COVID-19. In addition to the Omicron- and Delta-specific vaccines, the panel also includes a “Hybrid” vaccine that uses the RBD containing all 16 point-mutations shown in Omicron and Delta RBD, as well as a bivalent vaccine composed of both Omicron and Delta RBD-LNP in half dose. Interestingly, both Omicron-specific and Hybrid RBD-LNP elicited extremely high titer of neutralizing antibody against Omicron itself, but few to none neutralizing antibody against other SARS-CoV-2 variants. The bivalent RBD-LNP, on the other hand, generated antibody with broadly neutralizing activity against the wild-type virus and all variants. Surprisingly, similar cross-protection was also shown by the Delta-specific RBD-LNP. Taken together, our data demonstrated that Omicron-specific mRNA vaccine can induce potent neutralizing antibody response against Omicron, but the inclusion of epitopes from other variants may be required for eliciting cross-protection. This study would lay a foundation for rational development of the next generation vaccines against SARS-CoV-2 VOCs.
Mapping of the mechanical response in Si/SiGe nanosheet device geometries (2022)

Abstract The performance of next-generation, nanoelectronic devices relies on a precise understanding of strain within the constituent materials. However, the increased flexibility inherent to these three-dimensional device geometries necessitates direct measurement of their deformation. Here we report synchrotron x-ray diffraction-based non-destructive nanoscale mapping of Si/SiGe nanosheets for gate-all-around structures. We identified two competing mechanisms at different length scales contributing to the deformation. One is consistent with the in-plane elastic relaxation due to the Ge lattice mismatch with the surrounding Si. The second is associated with the out-of-plane layering of the Si and SiGe regions at a length scale of film thickness. Complementary mechanical modeling corroborated the qualitative aspects of the deformation profiles observed across a variety of nanosheet sample widths. However, greater deformation is observed in the SiGe layers of the nanosheets than the predicted distributions. These insights could play a role in predicting carrier mobilities of future devices.
Optimal Periodic Variable Switching PWM for Harmonic Performance Enhancement in Grid-Connected Voltage Source Converters (2022)

Variable switching frequency PWM (VSFPWM) modulation can be advantageously implemented in industrial applications, such as renewable energy, motor drives, and uninterrupted power supply (UPS) systems, to reduce the injected current harmonic amplitudes, to suppress audible noise, and to improve semiconductor power efficiency. In this article, the usage of periodic VSFPWM methods in a voltage source converter (VSC) is proposed, analyzed, and benchmarked in terms of harmonic spectrum spreading, following the IEEE-519 current harmonic standard for the connection to the distribution grid. Particular attention is paid to the influence of VSFPWM on the ac filter design. First, the analytical model of the voltage harmonic spectrum generated by a three-phase three-wire two-level VSC implementing several periodic VSFPWM methods is derived. Subsequently, a design guideline for the commonly used <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LCL</i> filter in the grid-tied VSC application is proposed, which minimizes the size requirement of the necessary components. The voltage spectrum models of the proposed VSFPWM method and the optimal switching profiles are verified by MATLAB/Simulink simulations and a 5-kW three-phase two-level VSC hardware demonstrator. The study shows that the ac filter power density for the studied VSFPWM methods can be greatly increased when compared with the conventional and widely employed constant switching frequency continuous PWM strategies.
The Future of the Moving Image (2001)

Electronic cameras and projectors are improving at a rapid pace. Computational elements are increasing in power to the point where substantial processing can he applied to the image stream, and compression algorithms have improved to the level where very high quality can he maintained at high compression ratios. The combination of high resolution and high frame rate can bring unprecedented image clarity to an electronic imaging system. With high-quality compression as a central system element, image capture and presentation systems can realize their full technological potential. While it is evident that uncompressed digital video at standard definition is widely available for many video system elements, it is now becoming apparent that imaging systems are poised to jump orders of magnitude in quality beyond this. HDTV implementations of the last decade now look like a small step in comparison to the leap in quality that is anticipated.