gebhart/patrepeval huggingface dataset:
Neurotrophic Factors, Their Receptors, and the Signal Transduction Pathways They Activate (1990)

Our studies of the spatiotemporal availability of neurotrophic factors, coupled with tagged ligand binding assays that identify cell bearing receptors for these factors, should lead toward defining the physiological roles of these molecules in the animal. The use of the tagged ligands to identify factor-responsive cell lines has also provided new model systems for the examination of ligand-receptor interactions, as well as for the study of the subsequent induction of intracellular response pathways. To obtain insights into such intracellular pathways, we have molecularly cloned genes encoding a family of serine-threonine protein kinases, most closely related to kinases involved in the yeast response to pheromones. These kinases may be crucial regulators of early steps in the response of mammalian cells to neurotrophic factors as well as other extracellular signals.
Response Tailored Protocol Versus the Fixed 12 Weeks Course of Dual Sofosbuvir/Daclatasvir Treatment in Egyptian Patients With Chronic Hepatitis C Genotype-4 Infection: A Randomized, Open-label, Non-inferiority Trial (2017)

Shortening the duration of therapy based on observed vRVR could provide a prudent basis to avoid unnecessary long treatment courses. This could not only reduce the drug exposure and the risk of adverse drug reactions, but also cut the cost of full treatment course with such expensive medications by one third. This could economize the treatment budget at the individual out-of-pocket level as well as the public health services and insurance levels and allow for better utilization of public health resources.
An Evaluation of Cross-Sectional Image Generation Schemes in the Selective Inhibition Sintering (SIS) Process (2014)

Selective Inhibition Sintering of metal alloys (SIS-metal) has been proven effective in the additive manufacture (AM) of low resolution bronze parts. The use of high precision inkjet print heads represents a significant advancement in the SIS-metal process. The fabrication of complex three-dimensional metallic parts requires SIS-metal compatible, cross-sectional image processing based on the part boundary profile. Thus, three candidate layer-processing approaches were identified and validated for rudimentary geometries. These approaches were identified from previous research as well as preliminary investigations. The validation criteria is based upon maintaining part integrity, the amount of powder waste produced, processing time, the ability to handle various part geometries, and the ease of access to inhibited regions. Results are discussed for deploying the three candidate layer processing approaches for rudimentary shapes, and a preliminary evaluation is presented for their use on more complex geometries.
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data (2005)

Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether individual genes are significantly activated or repressed by a particular stimulus. We have previously presented two Bayesian statistical methods for this level of analysis, collectively known as variance-modeled posterior inference with regional exponentials (VAMPIRE). These methods each require a sophisticated modeling step followed by integration of a posterior probability density. We present here a publicly available, web-based platform that allows users to easily load data, associate related samples and identify differentially expressed features using the VAMPIRE statistical framework. In addition, this suite of tools seamlessly integrates a novel gene annotation tool, known as GOby, which identifies statistically overrepresented gene groups. Unlike other tools in this genre, GOby can localize enrichment while respecting the hierarchical structure of annotation systems like Gene Ontology (GO). By identifying statistically significant enrichment of GO terms, Kyoto Encyclopedia of Genes and Genomes pathways, and TRANSFAC transcription factor binding sites, users can gain substantial insight into the physiological significance of sets of differentially expressed genes. The VAMPIRE microarray suite can be accessed at http://genome.ucsd.edu/microarray.
Ankrd26 Gene Disruption Enhances Adipogenesis of Mouse Embryonic Fibroblasts (2011)

We previously reported that partial disruption of the Ankrd26 gene in mice leads to hyperphagia and leptin-resistant obesity. To determine whether the Ankrd26 mutation can affect the development of adipocytes, we studied mouse embryo fibroblasts (MEFs) from the mutant mice. We found that Ankrd26(-/-) MEFs have a higher rate of spontaneous adipogenesis than normal MEFs and that adipocyte formation is greatly increased when the cells are induced with troglitazone alone or with a mixture of troglitazone, insulin, dexamethasone, and methylisobutylxanthine. Increased adipogenesis was detected as an increase in lipid droplet formation and in the expression of several markers of adipogenesis. There was an increase in expression of early stage adipogenesis genes such as Krox20, KLF5, C/EBPβ, C/EBPδ, and late stage adipogenesis regulators KLF15, C/EBPα, PPARγ, and aP2. There was also an increase in adipocyte stem cell markers CD34 and Sca-1 and preadipocyte markers Gata2 and Pref-1, indicating an increase in both stem cells and progenitor cells in the mutant MEFs. Furthermore, ERK was found constitutively activated in Anrd26(-/-) MEFs, and the addition of MEK inhibitors to mutant cells blocked ERK activation, decreased adipogenesis induction, and significantly reduced expression of C/EBPδ, KLF15, PPARγ2, CD34, and Pref-1 genes. We conclude that Ankrd26 gene disruption promotes adipocyte differentiation at both the progenitor commitment and differentiation steps and that ERK activation plays a role in this process.
Explaining the gap between ASIC and custom power (2005)

Power dissipation is now both a key constraint and an application driver in VLSI systems. For a specific application, the energy efficiency of different implementations can differ by multiple orders of magnitude. This work surveys a range of techniques available to improve energy efficiency and highlights their cumulative benefit. Understanding, adopting and adapting selected techniques from full-custom solutions can help bridge the efficiency gap for the ASIC designs. Architecture and micro-architecture choices yield multiple-order of magnitude improvements in power dissipation by matching the structure of the design to the structure of the application and by providing multiple operating and power-down modes. The combination of methodology and full-custom circuit techniques and libraries provide benefits primarily due to reduced parasitic loading enabling the improved performance to be translated into the potential for factor-of-3 to factor-of-10 improvements in power.
Brush Gels: Where Theory, Simulations, and Experiments Meet (2022)

Polymer networks with brush-like (comb or bottlebrush) strands can have mechanical properties similar to biological tissues and can swell to larger volumes than their linear chain counterparts. We use a combination of the Flory–Rehner approach, scaling analysis, molecular dynamics simulations, and experimental data for poly(n-butyl acrylate) (PBA) networks swollen in toluene to elucidate the effect of brush strand architecture on the equilibrium swelling ratio, Qeq, the modulus of the swollen gel, Ggel(Qeq), and its relationship with the nonlinear modulus of the dry network, G(Qeq). Analysis of simulation data and experimental results for PBA gels demonstrates that the gel shear modulus monotonically decreases with increasing equilibrium swelling ratio as Ggel(Qeq) ∝ Qeq–3, which is consistent with a θ-solvent-like swelling behavior. There is a significant effect of the degree of polymerization nsc and grafting density 1/ng of the side chains on the gel modulus that manifests as mechanically diverse gels with the same solvent content. This unique behavior is explained by the architecture-controlled stiffening of the brush strands due to the swelling of the side chains in the gel state. In the framework of a scaling model, the effective Kuhn length of the swollen strands, bK,s, can be expressed in terms of the Kuhn length in the dry state, bK, and the ratio of shear modulus calculated in the framework of the Flory–Rehner approach, GgelFR(Qeq) = G(Qeq)/Qeq1/3, to the gel modulus Ggel(Qeq) such that bK,s ≈ bKGgelFR(Qeq)/Ggel(Qeq). The Kuhn length obtained from this analysis highlights different mechanisms of swollen brush rigidity.
Design and Optimization of a Low-e mpedance Pulsed-Power Marx Generator to Drive High-Power Releativistic X-Band Magnetron (2006)

In this paper, the design and optimization efforts aimed at reducing the intrinsic impedance of the Marx generator are discussed. By reducing the number of stages of the Marx's electrical circuit from the presently configured 11-stage Marx to a 7-stage Marx the inductance can be significantly decreased. In order to provide power from the Marx generator to an X-band relativistic magnetron, a coaxial transmission line and a vacuum-insulator interface will be used and the results of the design will be discussed.
Battery aging-aware energy management of green small cells powered by the smart grid (2017)

Mobile operators are deploying energy-harvesting heterogeneous networks due to their foreseen advantages such as self-sustainable capability and reduced operating expenditure, which cannot be offered by conventional grid powered communications. However, the used energy storage is subject to irreversible aging mechanisms, requiring intelligent management that considers both the energy cost and battery life cycle. In this paper, we propose a cognitive energy management strategy for small cell base stations powered by local renewable energy, a battery, and the smart grid to simultaneously minimize electricity expenditures of the mobile operators and enhance the life span of the storage device. Non-linear battery models and aging processes are considered to formulate the energy cost optimization problem. Simulation results in different configurations show that a degradation-aware policy significantly improves the battery lifetime, while achieving considerable cost savings.
Gender Differences in Spatial Learning, Synaptic Activity, and Long-Term Potentiation in the Hippocampus in Rats: Molecular Mechanisms (2015)

In tests of spatial ability, males outperform females both in rats and in humans. The mechanism underlying this gender differential learning ability and memory in spatial tasks remains unknown. Long-term potentiation (LTP) in the hippocampus is considered the basis for spatial learning and memory. The aims of this work were (a) to assess spatial learning and memory in male and female rats in the radial and Morris mazes; (b) to assess whether basal synaptic activity and LTP in the hippocampus are different in male and female rats; and (c) to identify the molecular mechanisms responsible for the gender differences in LTP. We analyzed in young male and female rats (a) performance in spatial tasks in the radial and Morris water mazes; (b) basal synaptic activity in hippocampal slices; and (c) LTP and some mechanisms modulating its magnitude. The results reported allow us to conclude that female rats show larger AMPA receptor-mediate synaptic responses under basal conditions, likely due to enhanced phosphorylation of GluR2 in Ser880 and increased amounts of GluR2-containing AMPA receptors in postsynaptic densities. In contrast, the magnitude of tetanus-induced LTP was lower in females than in males. This is due to reduced activation of soluble guanylate cyclase and the formation of cGMP, leading to lower activation of cGMP-dependent protein kinase and phosphorylation of GluR1 in Ser845, which results in lower insertion of AMPA receptors in the synaptic membrane and a lower magnitude of LTP. These mechanisms may contribute to the reduced performance of females in the radial and Morris water mazes.
Photosynthetic Apparatus in Roseateles depolymerans 61A Is Transcriptionally Induced by Carbon Limitation (2002)

Production of a photosynthetic apparatus in Roseateles depolymerans 61A, a recently discovered freshwater beta-Proteobacterium showing characteristics of aerobic phototrophic bacteria, was observed when the cells were subjected to a sudden decrease in carbon sources (e.g., when cells grown with 0.1 to 0.4% Casamino Acids were diluted or transferred into medium containing <or=0.04% Casamino Acids). Accumulation of bacteriochlorophyll (BChl) a was observed in the presence of oxygen and was enhanced under semiaerobic conditions (2% oxygen) but was reduced in the presence of light. Similarly to what has been reported regarding some aerobic phototrophic bacteria belonging to the alpha subclass of the Proteobacteria, viability of the cells in the carbon source-free medium was prolonged under aerobic-light (10 W m(-2)) conditions, possibly due to photosynthetic energy conversion, but was not prolonged under aerobic-dark conditions. The puf operon, which encodes most of the apoproteins of light-harvesting and reaction center complexes, was sequenced, and the effect of changes in Casamino Acids concentrations, oxygen, and light on its expression was estimated by the accumulation of its mRNA. The expression of the puf operon was induced by the decrease in carbon sources, similarly to what was observed for the accumulation of BChl a under aerobic and semiaerobic conditions (>or=0.2% O(2)), and was reduced in the presence of light. Transcription of the R. depolymerans puf operon is considered to be controlled by changes in carbon nutrients in addition to oxygen tension and light intensity.
Fosmanogepix: A Review of the First-in-Class Broad Spectrum Agent for the Treatment of Invasive Fungal Infections (2020)

Fosmanogepix is a first-in-class antifungal currently in Phase 2 clinical trials for the treatment of invasive fungal infections caused by <i>Candida, Aspergillus</i> and rare molds. Fosmanogepix is the N-phosphonooxymethylene prodrug of manogepix, an inhibitor of the fungal enzyme Gwt1. Manogepix demonstrates broad spectrum in vitro activity against yeasts and molds, including difficult to treat pathogens. Because of its novel mechanism of action, manogepix retains potency against many resistant strains including echinocandin-resistant <i>Candida</i> and azole-resistant <i>Aspergillus.</i> Manogepix is also active against pathogens that demonstrate intrinsic resistance to other drug classes, such as <i>Scedosporium</i><i>,</i> <i>Lomentospora</i> <i>prolificans</i>, and <i>Fusarium</i> with variable activity against Mucorales. Fosmanogepix demonstrates significant in vivo efficacy in mouse and rabbit disseminated infection models due to <i>C. albicans, C. glabrata, C.</i> <i>auris</i><i>, C. tropicalis, Coccidioides</i> <i>immitis</i><i>,</i> and <i>F.</i> <i>solani</i> as well as pulmonary infection models of <i>A. fumigatus, A. flavus, S.</i> <i>prolificans</i><i>, S.</i> <i>apiospermum</i> and <i>Rhizopus</i> <i>arrhizus</i><i>.</i> Clinical trials demonstrated high oral bioavailability (>90%), enabling switching between fosmanogepix intravenous and oral formulations without compromising blood levels. Favorable drug-drug interaction, tolerability, and wide tissue distribution profiles are observed making fosmanogepix an attractive option for the treatment of invasive fungal infections. This systematic review summarizes the findings of published data on fosmanogepix.
New Method for Nanofabrication of Structures Analogous to “Core-Shell” Vesicles (1999)

The one-step synthesis of “core–shell” vesicle analogues using sonochemistry is described. The formation of such vesicles generally occurs in two steps—either the inorganic core is formed first, around which the shell is generated, or the empty shell is used as a microreactor for the crystallization of the inorganic core. Here ultrasound irradiation is used to simultaneously decompose Fe(CO)5 and form siloxane polymer chains from (CH3)3SiCl to produce micrometer-dimension vesicles containing monodisperse spindles.
Conversion cathodes for rechargeable lithium and lithium-ion batteries (2016)

Commercial lithium-ion (Li-ion) batteries built with Ni- and Co-based intercalation-type cathodes suffer from low specific energy, high toxicity and high cost. Conversion-type cathodes offer an opportunity to overcome such limitations.
Analysis of Potential Molecular Catalysts for the Hydroamination of Ethylene with Ammonia: A DFT Study with [Ir(PCP)] and [Ir(PSiP)] Complexes (2012)

Very few cases of oxidative addition of NH(3) to transition-metal complexes forming terminal amide hydrides have been experimentally observed. Here, two examples with the iridium pincer complexes [Ir(PCP)(NH(3))] A1 with PCP = [κ(3)-(tBu(2)P-C(2)H(4))(2)CH](-) and [Ir(PSiP)(NH(3))] B1 with PSiP = [κ(3)-(2-Cy(2)P-C(6)H(4))(2)SiMe](-) were investigated by DFT calculations applying the M06L density functional to successfully reproduce the trend of the experimentally observed thermochemical stabilities. According to the calculations, the corresponding hydrido-amido complexes A2 and B2 are more stable than the corresponding ammine complexes by ΔG = -2.8 and -2.6 kcal mol(-1), respectively. Complexes such as A2 and B2 are ideally suited entry points to catalytic cycles for the hydroamination of ethylene with ammonia. Therefore, the relevant stationary points of the potentially available cycles were studied computationally to verify if these complexes can catalyze the hydroamination. As a result, complex A2 will clearly not catalyze the hydroamination as all energy spans calculated range close to 40 kcal mol(-1) or higher. The energy spans obtained with B2 are significantly lower in some cases and range around 35 kcal mol(-1), further indicating that no turnover can be expected. By systematically varying the structure of B2, the energy span could be reduced to 28.8 kcal mol(-1) corresponding to a TOF of 17 h(-1) at a reaction temperature of 140 °C. A reoptimization of relevant structures under the inclusion of cyclohexane as a typical solvent reduces the calculated TOF to 6.0 h(-1).
13C NMR Analysis of α-Olefin Enchainment in Poly(α-olefins) Produced with Nickel and Palladium α-Diimine Catalysts (2007)

α-Diimine complexes of palladium and nickel catalyze the polymerization of α-olefins to give new materials that range from low-Tg elastomers to low-melting, partially crystalline polymers. The 1H and 13C NMR spectra of the resulting polymers have been assigned in detail. Many unique microstructural features of the complex polymers have been identified. Mechanistic models that involve the 1,2- and 2,1-insertion of the α-olefins, chain walking, and insertion at certain points along the chain have been constructed. The complex microstructures can be explained using a small set of rules for palladium catalysts which is expanded slightly to account for the nickel catalysts.
A High Avidity Biosensor Reveals PI(3,4)P 2 is Predominantly a Class I PI3K Signaling Product (2018)

Abstract Class I PI 3-kinase (PI3K) signaling is central to animal growth and metabolism, and disruption of this pathway occurs frequently in cancer and diabetes. However, the specific spatial/temporal dynamics and signaling roles of its minor lipid messenger, phosphatidylinositol (3,4)-bisphosphate [PI(3,4)P 2 ], are not well understood. This owes principally to a lack of tools to study this scarce lipid. Here, we developed a high sensitivity genetically encoded biosensor for PI(3,4)P 2 , demonstrating high selectivity and specificity of the sensor for the lipid. We show that despite clear evidence for class II PI3K in PI(3,4)P 2 -driven function, the overwhelming majority of the lipid accumulates through degradation of class I PI3K-produced PIP 3 . However, we show that PI(3,4)P 2 is also subject to hydrolysis by the tumor suppressor lipid phosphatase PTEN. Collectively, our results show that PI(3,4)P 2 is potentially an important driver of class I PI3K-driven signaling, and provides powerful new tools to begin to resolve the biological functions of this lipid downstream of class I and II PI3K.
Automated Detection of Macular Diseases by Optical Coherence Tomography and Artificial Intelligence Machine Learning of Optical Coherence Tomography Images (2019)

Automated detection of macular diseases from OCT images might be feasible using the CNN model. Image augmentation might be effective to compensate for a small image number for training.
Breakthrough and desorption characteristics of a microtrap (2000)

Microtraps have been used as a concentrator cum injector in on-line gas chromatography, mass spectrometry, and in continuous nonmethane organic carbon (CNMOC) analysis. It is made by packing a narrow bore metal capillary with one or more adsorbents. The microtrap is heated with a pulse of electric current of 1–5 s duration depending upon the size of the trap. The concentration pulse desorbed from it is sharp enough to serve as an injection for high resolution gas chromatography (GC) separation. It has low thermal mass that allows it to be heated and cooled very rapidly. Breakthrough of volatile compounds, and quantitative desorption of large molecules are the major issues related to the microtrap. Parameters that effect breakthrough have been studied before, and variation in breakthrough volume as a function of analyte concentration is presented in this paper. Since the heating–cooling cycle is of the order of a few seconds, it is not easy to measure the microtrap temperature. An infrared thermocouple was used in this research to measure the microtrap temperature during its desorption. Desorption profiles and desorption efficiencies were studied under various conditions. © 2000 John Wiley & Sons, Inc. J Micro Sep 12: 267–275, 2000
Optimizing Computational and Communication Resources for MEC Network Empowered UAV-RIS Communications (2022)

&lt;p&gt;With the technological evolution and new applications, user equipment (UEs) has become a vital part of our lives. However, limited computational capabilities and finite battery life bottleneck the performance of computationally demanding applications. A practical solution to enhance the quality of experience (QoE) is to offload the extensive computation to the mobile edge cloud (MEC). Moreover, the network's performance can be further improved by deploying an unmanned aerial vehicle (UAV) integrated with intelligent reflective surfaces (IRS): an effective alternative to massive antenna systems to enhance the signal quality and suppress interference. In this work, the MEC network architecture is assisted by UAV-IRS to provide computational services to the UEs. To do so, a cost minimization problem in terms of computing time and hovering energy consumption is formulated.&lt;/p&gt; &lt;p&gt;Furthermore, to achieve an efficient solution to a formulated challenging problem, the original optimization problem is decoupled into sub-problems using the block-coordinate decent method. Moreover, numerical results are compared to baseline schemes to determine the effectiveness of the proposed scheme. Simulation results demonstrate that the optimal allocation of local computational resources results in minimizing tasks' computational time and hovering energy consumption.&lt;/p&gt;