gebhart/patrepeval huggingface dataset:
High Throughput Identification of Potential Arabidopsis Mitogen-activated Protein Kinases Substrates (2005)

Mitogen-activated protein kinase (MAPK) cascades are universal and highly conserved signal transduction modules in eucaryotes, including plants. These protein phosphorylation cascades link extracellular stimuli to a wide range of cellular responses. However, the underlying mechanisms are so far unknown as information about phosphorylation substrates of plant MAPKs is lacking. In this study we addressed the challenging task of identifying potential substrates for Arabidopsis thaliana mitogen-activated protein kinases MPK3 and MPK6, which are activated by many environmental stress factors. For this purpose, we developed a novel protein microarray-based proteomic method allowing high throughput study of protein phosphorylation. We generated protein microarrays including 1,690 Arabidopsis proteins, which were obtained from the expression of an almost nonredundant uniclone set derived from an inflorescence meristem cDNA expression library. Microarrays were incubated with MAPKs in the presence of radioactive ATP. Using a threshold-based quantification method to evaluate the microarray results, we were able to identify 48 potential substrates of MPK3 and 39 of MPK6. 26 of them are common for both kinases. One of the identified MPK6 substrates, 1-aminocyclopropane-1-carboxylic acid synthase-6, was just recently shown as the first plant MAPK substrate in vivo, demonstrating the potential of our method to identify substrates with physiological relevance. Furthermore we revealed transcription factors, transcription regulators, splicing factors, receptors, histones, and others as candidate substrates indicating that regulation in response to MAPK signaling is very complex and not restricted to the transcriptional level. Nearly all of the 48 potential MPK3 substrates were confirmed by other in vitro methods. As a whole, our approach makes it possible to shortlist candidate substrates of mitogen-activated protein kinases as well as those of other protein kinases for further analysis. Follow-up in vivo experiments are essential to evaluate their physiological relevance.
Data from Gene Expression Profiling in Cervical Cancer: An Exploration of Intratumor Heterogeneity (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To explore intratumor heterogeneity in gene expression profiles from patients with cervical cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; A total of 33 biopsies were obtained from 11 patients, sampling between two and five different areas for each tumor. The extracted RNA was hybridized onto the Affymetrix U133 Plus 2.0 oligonucleotide chip. The variance of expression within a patient (&lt;i&gt;W&lt;/i&gt;), between patients (&lt;i&gt;B&lt;/i&gt;) and the total variance (&lt;i&gt;T&lt;/i&gt; = &lt;i&gt;W&lt;/i&gt; + &lt;i&gt;B&lt;/i&gt;) were calculated for each ProbeSet, and the ratio &lt;i&gt;W/T&lt;/i&gt; was used as a measure of intratumor heterogeneity. Gene Ontology functional analysis was done to assess the function of genes that had high &lt;i&gt;W/T&lt;/i&gt; (top 10%) and low &lt;i&gt;W/T&lt;/i&gt; (bottom 10%) values.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In total, 448 ProbeSets (2.2% of the total) had &lt;i&gt;W/T&lt;/i&gt; &lt; 0.10, indicating low intratumor heterogeneity, and 537 ProbeSets (2.7% of the total) had &lt;i&gt;W/T&lt;/i&gt; &gt; 0.90, indicating high intratumor heterogeneity. In total 14,473 ProbeSets (72.4%) had higher intertumor than intratumor heterogeneity (&lt;i&gt;W/T&lt;/i&gt; &lt; 0.5). Genes with low intratumor heterogeneity were characterized by a statistically significant enrichment of immune-related functions (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001). Genes with high intratumor heterogeneity were characterized by a significant tendency towards nuclear localization and nucleic acid binding (both &lt;i&gt;P&lt;/i&gt; &lt; 0.0001). For genes with &lt;i&gt;W/T&lt;/i&gt; &gt; 0.5, more than six biopsies would be required to minimize the intratumoral heterogeneity to &lt;0.15; if &lt;i&gt;W/T&lt;/i&gt; is 0.3 to 0.4, four biopsies are required; and for low &lt;i&gt;W/T&lt;/i&gt; of 0.16 to 0.3, only two to three biopsies would be needed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Although the intratumor heterogeneity was low for the majority of the tested ProbeSets, for many genes, multiple biopsies are required to obtain a reliable estimate of gene expression.&lt;/p&gt;&lt;/div&gt;
Investigating the effects of processing parameters on poly(lactic acid) properties – a central composite design approach (2019)

This study attempts to optimise poly(lactic acid) processing parameters using central composite design approach which is well known statistical tool in design of experiments. Three factors and five levels were chosen for carrying out the analysis. The parameters include mixing temperature (180–210°C), screw speed (50–100 rev min−1) and mixing time (5–10 min), which were varied independently. The results were evaluated based on maximum stress, tensile modulus, and impact strength under different conditions and the significant factors were determined using variance analysis (ANOVA). An optimum balance between the mechanical properties was obtained when the samples were blend at 180°C at 100 rev min−1 rotor speed for 10 min. Moreover, validation of the predicted results confirmed the optimised parameters, which were further complemented by morphological and thermal studies.
Identification of the Molecular Target of Small Molecule Inhibitors of HDL Receptor SR-BI Activity,, (2007)

Scavenger receptor, class B, type I (SR-BI), controls high-density lipoprotein (HDL) metabolism by mediating cellular selective uptake of lipids from HDL without the concomitant degradation of the lipoprotein particle. We previously identified in a high-throughput chemical screen of intact cells five compounds (BLT-1-5) that inhibit SR-BI-dependent lipid transport from HDL, but do not block HDL binding to SR-BI on the cell surface. Although these BLTs are widely used to examine the diverse functions of SR-BI, their direct target(s), SR-BI itself or some other component of the SR-BI pathway, has not been identified. Here we show that SR-BI in the context of a membrane lipid environment is the target of BLT-1, -3, -4, and -5. The analysis using intact cells and an in vitro system of purified SR-BI reconstituted into liposomes was aided by information derived from structure-activity relationship (SAR) analysis of the most potent of these BLTs, the thiosemicarbazone BLT-1. We found that the sulfur atom of BLT-1 was crucially important for its inhibitory activity, because changing it to an oxygen atom resulted in the isostructural, but essentially inactive, semicarbazone derivative BLT-1sc. SAR analysis also established the importance of BLT-1's hydrophobic tail. BLTs and their corresponding inactive compounds can be used to explore the mechanism and function of SR-BI-mediated selective lipid uptake in diverse mammalian experimental models. Consequently, BLTs may help determine the therapeutic potential of SR-BI-targeted pharmaceutical drugs.
Sleep Disorders (2008)

Sleep was once believed to be a static process where the brain shuts down during the night, and in the morning, the cevntral processes are aroused so that an individual can assume daily activities. The derangement of one or more of the physiological processes can result in a number of sleep disturbances such as insomnia, sleep apnea, circadian rhythm disorders, narcolepsy, and parasomnias. Excessive daytime sleepiness is common in individuals experiencing sleep disturbances. The general view of sleep regulation is that two main processes are integrated to control the amount and timing of sleep. Given the heterogenous state of the sleep/wake cycle, supplying an answer to the simple question as to why an organism sleeps is very complex, and several theories have been proposed. Several studies have evaluated the sleep-inducing and sleep-promoting effects of various H3 receptor agonists. Sleep apnea syndrome is characterized by frequent, repetitive disruptions in respiration during sleep, resulting in excessive arousal from sleep.
Data from Pattern of Serum Autoantibodies Allows Accurate Distinction between a Tumor and Pathologies of the Same Organ (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Recent studies impressively showed the diagnostic potential of seroreactivity patterns for different tumor types, offering the prospect for low-cost screening of numerous tumor types simultaneously. One of the major challenges toward this goal is to prove that seroreactivity profiles do not only allow for identifying a tumor but also allow for distinguishing tumors from other pathologies of the same organ.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We chose glioma as a model system and tested 325 sera (88 glioma, 95 intracranial tumors, 60 other brain pathologies, and 82 healthy controls) for seroreactivity on a panel of 35 antigens.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We were able to discriminate between glioma and all other sera with cross-validated specificity of 86.1%, sensitivity of 85.2%, and accuracy of 85.8%. We obtained comparably good results for the separation of glioma versus nontumor brain pathologies and glioma versus other intracranial tumors.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Our study provides first evidence that seroreactivity patterns allow for an accurate discrimination between a tumor and pathologies of the same organ even between different tumor types of the same organ.&lt;/p&gt;&lt;/div&gt;
Study of Fe- and Ni-Containing Lignins by Diffuse Reflectance IR Spectroscopy and X-ray Diffraction (2020)

The electronic and phase states of Fe and Ni in catalysts supported on hydrolyzed lignin and sodium lignosulfonate are studied by spectral means (DRIFTS using CO adsorption and powder X-ray diffraction). Iron and nickel cations, along with zero-valent centers of iron and nickel metal species with sizes of around 7 nm are found to be present on the catalysts’ surfaces.
STABLE HIGH CONDUCTIVITY BILAYERED ELECTROLYTES FOR LOW TEMPERATURE SOLID OXIDE FUEL CELLS (2002)

A bilayer electrolyte consisting of acceptor-doped ceria (on the fuel/reducing side) and cubic-stabilized bismuth oxide (on the oxidizing side) was developed. The bilayer electrolyte that was developed showed significant improvement in open-circuit potential versus a typical ceria based SOFC. Moreover, the OCP of the bilayer cells increased as the thickness of the bismuth oxide layer increased relative to the ceria layer. Thereby, verifying the bilayer concept. Although, because of the absence of a suitable cathode (a problem we are still working assiduously to solve), we were unable to obtain power density curves, our modeling work predicts a reduction in electrolyte area specific resistance of two orders of magnitude over cubic-stabilized zirconia and projects a maximum power density of 9 W/m{sup 2} at 800 C and 0.09 W/m{sup 2} at 500 C. Towards the development of the bilayer electrolyte other significant strides were made. Among these were, first, the development of a, bismuth oxide based, oxide ion conductor with the highest conductivity (0.56 S/cm at 800 C and 0.043 S/cm at 500 C) known to date. Second, a physical model of the defect transport mechanisms and the driving forces for the ordering phenomena in bismuth oxide and other fluorite systems was developed. Third, a model for point defect transport in oxide mixed ionic-electronic conductors was developed, without the typical assumption of a uniform distribution of ions and including the effect of variable loads on the transport properties of an SOFC (with either a single or bilayer electrolyte).
Magnetic resonance guided optical spectroscopy imaging of human breast cancer using a combined frequency domain and continuous wave approach (2012)

Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is used to image high-risk patients for breast cancer because of its higher sensitivity to tumors (approaching 100%) than traditional x-ray mammography. We focus on Near Infrared Spectroscopy (NIRS) as an emerging functional and molecular imaging technique that non-invasively quantifies optical properties of total hemoglobin, oxygen saturation, water content, scattering, and lipid concentration to increase the relatively low specificity of DCE-MRI. Our optical imaging system combines six frequency domain wavelengths, measured using PMT detectors with three continuous wave wavelengths measured using CCD/spectrometers. We present methods on combining the synergistic attributes of DCE-MR and NIRS for in-vivo imaging of breast cancer in three dimensions using a custom optical MR breast coil and diffusion based light modeling software, NIRFAST. We present results from phantom studies, healthy subjects, and breast cancer patients. Preliminary results show contrast recovery within 10% in phantoms and spatial resolution less than 5mm. Images from healthy subjects were recovered with properties similar to literature values and previous studies. Patient images have shown elevated total hemoglobin values and water fraction, agreeing with histology and previous results. The additional information gained from NIRS may improve the ability to distinguish between malignant and benign lesions during MR imaging. These dual modality instruments will provide complex anatomical and molecular prognostic information, and may decrease the number of biopsies, thereby improving patient care.
Adjustable metal-semiconductor transition of FeS thin films by thermal annealing (2006)

FeS polycrystalline thin films were prepared on float glass at 500°C by radio-frequency reactive sputtering. The influence of vacuum annealing on the metal-semiconductor transition of FeS films was investigated. It has been found that with the increase of the annealing temperature from 360to600°C, the metal-semiconductor transition temperature of FeS films first decreases and then increases, associated with first a reduction and then an enhancement of hysteresis width. The thermal stress is considered to give rise to the abnormal change of the metal-semiconductor transition of the FeS film during annealing.
Measurement of the CP-violating weak phase ϕs and the decay width difference ΔΓs using the Bs0→J/ψϕ(1020) decay channel in pp collisions at s=8 TeV (2016)

Citation: Khachatryan, V., Sirunyan, A. M., Tumasyan, A., Adam, W., Asilar, E., Bergauer, T., . . . Woods, N. (2016). Measurement of the CP-violating weak phase ?s and the decay width difference ??c using the Bs 0?J/??(1020) decay channel in pp collisions at ? s=8 TeV. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, 757, 97-120. doi:10.1016/j.physletb.2016.03.046
Synthesis and structure analysis of 4-quinazolone derivatives from alkyl dicyanoacetates. (1991)

Cyclocondensation of alkyl dicyanoacetate alkali salts (NC)2C:C(OR)O- M+ (R = Me, Et, Bu, M = K; R = CH2Ph, M = Na) with anthranilic acids 3,2-R1(H2N)C6H3CO2H (R1 = H, Me) gave 4-quinazolones I in 23-46% yields. The structures of I were proved by 1H and 13C NMR and NOE's by 1- and 2-dimensional methods. The structure of I (R = Et, R1 = Me) was proved by x-ray crystallog.
Serum-Induced Differentiation of Human Meibomian Gland Epithelial Cells (2014)

Overall, our findings indicate that immortalized human meibomian gland epithelial cells may serve as an ideal preclinical model to identify factors that control cellular differentiation in the meibomian gland.
Epoxy/Glass and Polyimide (LaRC(TradeMark) PETI-8)/Carbon Fiber Metal Laminates Made by the VARTM Process (2010)

Recent work at NASA Langley Research Center (LaRC) has concentrated on developing new polyimide resin systems for advanced aerospace applications that can be processed without the use of an autoclave. Polyimide composites are very attractive for applications that require a high strength to weight ratio and thermal stability. Vacuum assisted resin transfer molding (VARTM) has shown the potential to reduce the manufacturing cost of composite structures. Fiber metal laminates (FML) made via this process with aluminum, glass fabric, and epoxy resins have been previously fabricated at LaRC. In this work, the VARTM process has been refined for epoxy/glass FMLs and extended to the fabrication of FM Ls with titanium/carbon fabric layers and a polyimide system developed at NASA, LARC(TradeMark) PETI-8. Resin flow pathways were introduced into the titanium foils to aid the infiltration of the polyimide resin. Injection temperatures in the range of 250-280 C were required to achieve the necessary VARTM viscosities (<10 Poise). Laminate quality and initial mechanical properties will be presented.
Nef Is Physically Recruited into the Immunological Synapse and Potentiates T Cell Activation Early after TCR Engagement (2005)

The HIV-1 protein Nef enhances viral pathogenicity and accelerates disease progression in vivo. Nef potentiates T cell activation by an unknown mechanism, probably by optimizing the intracellular environment for HIV replication. Using a new T cell reporter system, we have found that Nef more than doubles the number of cells expressing the transcription factors NF-kappaB and NFAT after TCR stimulation. This Nef-induced priming of TCR signaling pathways occurred independently of calcium signaling and involved a very proximal step before protein kinase C activation. Engagement of the TCR by MHC-bound Ag triggers the formation of the immunological synapse by recruiting detergent-resistant membrane microdomains, termed lipid rafts. Approximately 5-10% of the total cellular pool of Nef is localized within lipid rafts. Using confocal and real-time microscopy, we found that Nef in lipid rafts was recruited into the immunological synapse within minutes after Ab engagement of the TCR/CD3 and CD28 receptors. This recruitment was dependent on the N-terminal domain of Nef encompassing its myristoylation. Nef did not increase the number of cell surface lipid rafts or immunological synapses. Recently, studies have shown a specific interaction of Nef with an active subpopulation of p21-activated kinase-2 found only in the lipid rafts. Thus, the corecruitment of Nef and key cellular partners (e.g., activated p21-activated kinase-2) into the immunological synapse may underlie the increased frequency of cells expressing transcriptionally active forms of NF-kappaB and NFAT and the resultant changes in T cell activation.
Signal to Symbol Transformation Techniques for Robust Diagnosis in TRANSCEND (1999)

TRANSCEND uses qualitative transient analysis methods for monitoring and diagnosis of dynamic systems to overcome complexity and convergence issues that arise in numerical processing, especially for nonlinear systems. Generating qualitative features from real signals, the signal to symbol transformation problem, is a challenging task. This paper discusses model-driven methods for generating symbolic feature descriptions of magnitude and slope changes in noisy continuous data. Experiments have been successfully conducted on faults introduced into the cooling system of an automobile engine.
Densities of SiO 2 ‐Al 2 O 3 Melts (1979)

The densities of binary aluminosilicate melts were measured X‐radiographically as a function of Al 2 O 3 , concentration between 1800° and 2000°C. Within this temperature range, the density curves vary linearly and are parallel from fused SiO 2 to ≊30 to 45 mol% Al 2 O 3 , depending on the temperature. At higher Al 2 O 3 contents, negative deviation from linearity increases with increasing temperature. Recent supplementary research efforts on various aspects of the system SiO 2 ‐Al 2 O 3 indicate that the changing coordination and structural role of the aluminum ion may be a primary factor in determining the shapes of the density curves.
Glomerulosclerosis and body growth are mediated by different portions of bovine growth hormone. Studies in transgenic mice. (1993)

These data indicated that development of glomerulosclerosis and body growth promotion were mediated by different regions of the growth hormone molecule. The glomerular response to bGH was unique and consisted of increased size and glomerulosclerosis.
Entity reconciliation in a multi-camera network (2016)

Location traces are becoming fairly abundant with the introduction of various mobile devices such as smartphones, in-car navigation units, and video cameras. Each individual type of device generates different features about a mobile entity along with the location of that entity itself. For example, the smartphone can provide the motion (using accelerometer) of an individual, whereas a video camera can identify what type of clothing the person is wearing. A key challenge is to be able to fuse the data across different data sources and generate a unique view for each entity. This paper tackles a slice of this larger problem, which is to reconcile entities across a multi-camera network and a GPS trace from a smartphone and proposes a novel algorithm that can scale horizontally to adapt to new age distributed systems such as Apache Spark and IBM's InfoSphere Streams. We show through extensive experiments on a real-world dataset that our algorithm outperforms existing approaches and adapts to horizontally scalable distributed environments.
Continuous care intervention with carbohydrate restriction improves physical function of the knees among patients with type 2 diabetes: a non-randomized study (2022)

Clinical trial registration: NCT02519309 (10/08/2015).
Guided Interconnect - The Next-Generation Flex Circuits for High-Performance System Design (2018)

A high-performance and patent-pending [1] interconnect structure for flex circuits is described in this paper. It is termed Guided Interconnect, as its basic principle is to “guide” the electromagnetic wave of high-speed signaling in a closely-coupled manner. As a result, higher I/O density of up to 40% compared to conventional flexible printed circuits (FPC) can be achieved, while not jeopardizing the signal integrity performance. The above conclusion is supported by both analytical and measurement results, which are in excellent agreement with each other. In addition, this inventive structure also comes with significant mechanical benefit - its flexibility is experimentally demonstrated to be 3 times better than the meshed FPC. In short, this research work has served as an initial working model towards developing a candidate for high-speed, high-performance cables, small form-factor systems, such as tablets, smart phones or 2-in-1s.
Control Technology Readiness for Spaceborne Optical Interferometer Missions (1997)

This paper describes the Micro-Precision Interferometer (MPI) testbed and its major achievements to date related to mitigating risk for future spaceborne optical interferometer missions.