gebhart/patrepeval huggingface dataset:
Endogenous Protein “Barcode” for Data Validation and Normalization in Quantitative MS Analysis (2014)

Quantitative proteomic experiments with mass spectrometry detection are typically conducted by using stable isotope labeling and label-free quantitation approaches. Proteins with housekeeping functions and stable expression level such actin, tubulin, and glyceraldehyde-3-phosphate dehydrogenase are frequently used as endogenous controls. Recent studies have shown that the expression level of such common housekeeping proteins is, in fact, dependent on various factors such as cell type, cell cycle, or disease status and can change in response to a biochemical stimulation. The interference of such phenomena can, therefore, substantially compromise their use for data validation, alter the interpretation of results, and lead to erroneous conclusions. In this work, we advance the concept of a protein "barcode" for data normalization and validation in quantitative proteomic experiments. The barcode comprises a novel set of proteins that was generated from cell cycle experiments performed with MCF7, an estrogen receptor positive breast cancer cell line, and MCF10A, a nontumorigenic immortalized breast cell line. The protein set was selected from a list of ~3700 proteins identified in different cellular subfractions and cell cycle stages of MCF7/MCF10A cells, based on the stability of spectral count data generated with an LTQ ion trap mass spectrometer. A total of 11 proteins qualified as endogenous standards for the nuclear and 62 for the cytoplasmic barcode, respectively. The validation of the protein sets was performed with a complementary SKBR3/Her2+ cell line.
The 3942-cm−1optical band in irradiated silicon (1987)

Uniaxial stress perturbations are reported on the 3942-${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ (488-meV) zero-phonon line common to irradiated Czochralski-grown silicon. We show that the line occurs at a monoclinic I center, with the electric dipole perpendicular to the principal axis of the center. Carbon and oxygen isotope doping experiments show that the optical center contains at least one carbon atom and at least one oxygen atom. Irradiation of tin-doped Czochralski-grown Si reduces the rate of production of 3942-${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ absorption, suggesting that vacancies may also be required in the formation of the centers. We find no evidence for other electronic states of the 3942-${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ center with energies similar to the states taking part in the 3942-${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ transition. Consequently this center provides the first opportunity to apply simple vibronic sideband theory to an absorption band in silicon. We show that the shape of the phonon sideband, its temperature dependence, and the temperature dependence of the zero-phonon intensity may all be understood with use of established theory. However, we draw attention to the problem of trying to understand the temperature dependence of the width and of the energy of the zero-phonon line, and also its isotope shift. In samples which have received relatively low irradiation doses compared with their carbon content, the 3942-${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ absorption increases upon annealing near 150?deC, before being destroyed at \ensuremath{\sim}225 \ifmmode^\circ\else\textdegree\fi{}C. This effect is not understood.
RESEARCH ON ANTI-ROLLING FLOATING STRUCTURES (2001)

While floating structures have many advantages such as environment-friendly, their rolling vibration caused by waves makes people indisposed and stevedoring inefficient. It is necessary to improve working efficiency on them by reducing their vibration to spread floating structures. We have developed vibration reduction systems. This paper shows validity of those systems by numerical analysis and experiments, and design methods of them.
PCM Storage System with Integrated Active Heat Pipe (2014)

The use of the latent heat of phase change materials (PCM) is considered a promising approach to store heat at a nearly constant temperature for direct steam generation (DSG), but the poor thermal conductivity of commonly available storage materials imposes severe limitations on storage performance. A new method is proposed to overcome the limitations of the low thermal conductivity. The approach is to physically decouple the evaporator pipes from the PCM, thus allowing independent sizing of each component. The thermal link between the two components is done via evaporation and condensation of a heat transfer fluid (HTF), according to the principle of a heat pipe. Pumping the liquid HTF provides active control of the heat pipe operation. The new concept is modeled and compared to the conventional design of conduction based PCM annulus around the steam pipe. An example case shows a significant advantage in performance of the active heat pipe configuration due to its reduced thermal resistance.
Data from Rapamycin inhibits multiple stages of c-Neu/ErbB2–induced tumor progression in a transgenic mouse model of HER2-positive breast cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Amplification of the HER2 (ErbB2, c-Neu) proto-oncogene in breast cancer is associated with poor prognosis and high relapse rates. HER2/ErbB2, in conjunction with ErbB3, signals through the Akt/phosphatidylinositol 3-kinase pathway and leads to the activation of mammalian target of rapamycin (mTOR), a critical mRNA translation regulator that controls cell growth. Gene expression analysis of mammary tumors collected from mouse mammary tumor virus-c-Neu transgenic mice revealed that mRNA levels of several mTOR pathway members were either up-regulated (p85/phosphatidylinositol 3-kinase and p70S6 kinase) or down-regulated (eIF-4E-BP1) in a manner expected to enhance signaling through this pathway. Treatment of these mice with the mTOR inhibitor rapamycin caused growth arrest and regression of primary tumors with no evidence of weight loss or generalized toxicity. The treatment effects were due to decreased proliferation, associated with reduced cyclin D1 expression, and increased cell death in primary tumors. Whereas many of the dead epithelial cells had the histopathologic characteristics of ischemic necrosis, rapamycin treatment was not associated with changes in microvascular density or apoptosis. Rapamycin also inhibited cellular proliferation in lung metastases. In summary, data from this preclinical model of ErbB2/Neu-induced breast cancer show that inhibition of the mTOR pathway with rapamycin blocks multiple stages of ErbB2/Neu-induced tumorigenic progression. [Mol Cancer Ther 2007;6(8):2188–97]&lt;/p&gt;&lt;/div&gt;
Impact of Applicability Domains to Generative Artificial Intelligence (2023)

Molecular generative artificial intelligence is drawing significant attention in the drug design community, with several experimentally validated proof of concepts already published. Nevertheless, generative models are known for sometimes generating unrealistic, unstable, unsynthesizable, or uninteresting structures. This calls for methods to constrain those algorithms to generate structures in drug-like portions of the chemical space. While the concept of applicability domains for predictive models is well studied, its counterpart for generative models is not yet well-defined. In this work, we empirically examine various possibilities and propose applicability domains suited for generative models. Using both public and internal data sets, we use generative methods to generate novel structures that are predicted to be actives by a corresponding quantitative structure-activity relationships model while constraining the generative model to stay within a given applicability domain. Our work looks at several applicability domain definitions, combining various criteria, such as structural similarity to the training set, similarity of physicochemical properties, unwanted substructures, and quantitative estimate of drug-likeness. We assess the structures generated from both qualitative and quantitative points of view and find that the applicability domain definitions have a strong influence on the drug-likeness of generated molecules. An extensive analysis of our results allows us to identify applicability domain definitions that are best suited for generating drug-like molecules with generative models. We anticipate that this work will help foster the adoption of generative models in an industrial context.
Hybrid chemometric approach for estimating the heat of detonation of aromatic energetic compounds (2019)

This work presents an elegant technique for estimating the heat of detonation (HD) of thirty organic energetic compounds by combining support vector regression (SVR) and gravitational search algorithm (GSA). The work shows that numbers of nitrogen and oxygen atoms as well as the compound molar mass are sufficient as descriptors. On the basis of three performance measuring parameters, the hybrid GSA-SVR outperforms Mortimer and Kamlet (1968), Mohammad and Hamid (2004) and Mohammad (2006) models with performance improvement of 93.951%, 86.197%, and 47.104%, respectively. The superior performance demonstrated by the proposed method would be of immense significance in containing the potential damage of the explosives through quick estimation of HD of organic energetic compounds without loss of experimental precision.
Robust channel estimation for switch-based mmWave MIMO systems (2017)

Recently, a switch-based hybrid massive MIMO structure that aims to reduce the hardware complexity and power consumption has been proposed as a potential candidate for millimeter wave (mmWave) communications. In this paper, we investigate a matrix completion (MC)-based low-complexity channel estimator for such systems, which is compatible with the switch-based hybrid structure. We conduct a thorough comparison of the proposed scheme with state-of-the-art compressive sensing (CS)-based schemes. We show that our proposed scheme can achieve near-optimal spectral efficiency (SE) at significantly lower complexity. Furthermore, we demonstrate that the MC-based estimator, which does not need to assume a basis as required by CS estimators, is immune to array response mismatch which may arise from phase and amplitude errors.
Heart Transplantation Outcomes in Arrhythmogenic Right Ventricular Cardiomyopathy: A Contemporary National Analysis (2022)

In the largest series of HT in ARVC, we found that HT is increasingly performed in ARVC, with higher survival compared with other cardiomyopathy aetiologies. The right ventricular predominant pathophysiology may require unique considerations for heart failure management, including HT.
Prediction model for knee osteoarthritis based on genetic and clinical information (2010)

Our results showed that consideration of adjusted clinical information, as well as increases in the number of risk alleles to be integrated, is critical for OA prediction by using data from case-control studies. To the authors' knowledge, this is the first report of the OA-prediction model combining both genetic and clinical information.
Slot-loaded Dual-layer Artificial Magnetic Conductor (2011)

A dual-band artificial magnetic conductor (AMC) composed of two metallic patch layers with slot-loading is proposed. The slots inserted in the patches lengthen the current path on the patches, which increases the equivalent inductances. The equivalent circuit model of the dual-layer AMC is modified by the additional inductances due to the slot-loading, and the reflection phases calculated using the model is compared with full wave analysis results. The effects of the slot-loading on the reflection phase are discussed using the results. The method of controlling the reflection phase of the dual-layer AMC using slot-loading is expected to increase the degree of freedom in designing both AMC and electromagnetic gradient surface (EGS) structures.
Figure S4 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs (2023)

&lt;p&gt;Figure S4. Heat map analysis of the kinome screen generated by the Wilcoxon method.&lt;/p&gt;
Potential Use of Sox9 Gene Therapy for Intervertebral Degenerative Disc Disease (2003)

A novel adenoviral vector efficiently increased Sox9 and Type 2 collagen synthesis in cultured chondroblastic cells and human degenerated disc cells. In a rabbit model, sustained Sox9 production preserved the histologic appearance of the nucleus pulposus cells in vivo. These findings suggest a potential role for Sox9 gene therapy in the treatment of human degenerative disc disease.
Gold Catalysts: Nanoporous Gold Foams (2006)

No support: Unsupported nanoporous gold foams with a spongelike morphology (see images) are formed through the selective leaching of silver from a gold–silver alloy. These gold foams are highly active catalysts for CO oxidation at ambient pressures and temperatures down to −20 °C, and have potential applications as membrane catalysts.
Characterization of buffy coat‐derived granulocytes for clinical use: a comparison with granulocyte colony‐stimulating factor/dexamethasone‐pretreated donor‐derived products (2017)

The product described appears a promising alternative for transfusion purposes.
Decomposition of B2H6 on Ni(100) (1997)

The decomposition of diborane (B2H6) has been studied on the Ni(100) surface by means of thermal desorption spectrometry (TDS), x-ray photoelectron spectroscopy (XPS), and low-energy electron diffraction (LEED). At low gas exposures, decomposed B2H6 on the Ni(100) surface at low temperatures produces several peaks in the H2 TDS spectra. At high gas exposures, B4H10 was observed desorbing from the surface. The TDS spectra and XPS results for low gas exposures indicate that heating to 500 K results in complete decomposition of B2H6, leaving B bonded to the Ni(100) surface. Heating a thick boron film to 700 K results in a significant shift in the B [1s] and Ni [2p3/2] XPS peak positions, indicating that adsorbed B reacts with Ni(100) to form a nickel boride phase. This nickel boride phase is stable on the surface at temperatures up to 900 K. Nickel boride standards (NiB, Ni2B, Ni3B) were used for comparison with the surface nickel boride phase. XPS analysis of the standards led to the determination that the phase forming on the surface at 700 K was Ni2B. As the temperature is increased above 900 K, XPS results indicate that the boron diffuses rapidly into the bulk. It has also been found that high-temperature annealing in the presence of B2H6 results in the formation of a sharp (3×3) LEED pattern produced by 2/9 ML of B on the Ni(100) surface.
Measurements of x-ray emission from zinc and molybdenum transition radiators (1993)

This article describes the measurements of x-ray power, spatial and spectral distributions from transition radiators whose spectra are narrowed by the foil material’s K-shell photoabsorption edge. We used two foil stacks, one composed of 15 foils of 3-μm-thick Zn and the other composed of 15 foils of 4-μm-thick Mo. At low average currents, the x-ray spectrum produced by transition radiation was measured by pulse height analysis to be between 5 and 9.7 keV for the Zn radiator and between 10 and 20.0 keV for the Mo radiator. These measurements compared well with calculations. The x-ray spatial distribution from the Zn radiator was measured using a silicon linear diode array. The x rays generated by the Zn radiator were found to be emitted in a forward-directed cone with half angle of ∼1.9 mrad with the center of the expected annulus filled. The power density in the peak of the annulus was found to be 50 mW/(mA cm2). At a high average electron-beam current of 12.5 μA, the x-ray power produced by a stack of ten Zn foils was measured in the spectral range between 5 and 9.66 keV to be 1.54 mW with the peak power in the 1 μs macropulse to be 8.5 W. Electron-beam energies between 249 and 282 MeV were used in these experiments.
LEEN: Locality/Fairness-Aware Key Partitioning for MapReduce in the Cloud (2010)

This paper investigates the problem of Partitioning Skew in MapReduce-based system. Our studies with Hadoop, a widely used MapReduce implementation, demonstrate that the presence of partitioning skew causes a huge amount of data transfer during the shuffle phase and leads to significant unfairness on the reduce input among different data nodes. As a result, the applications experience performance degradation due to the long data transfer during the shuffle phase along with the computation skew, particularly in reduce phase. We develop a novel algorithm named LEEN for locality-aware and fairness-aware key partitioning in MapReduce. LEEN embraces an asynchronous map and reduce scheme. All buffered intermediate keys are partitioned according to their frequencies and the fairness of the expected data distribution after the shuffle phase. We have integrated LEEN into Hadoop-0.18.0. Our experiments demonstrate that LEEN can efficiently achieve higher locality and reduce the amount of shuffled data. More importantly, LEEN guarantees fair distribution of the reduce inputs. As a result, LEEN achieves a performance improvement of up to 40% on different workloads.
Brother (and Sister) - Can you Spare a Dime? Losing Assets and Losing Income (2011)

In this chapter we look at the inside of the consumer’s mind, not for the pleasant factors of mental economics, but at the downside. When a person loses his job, loses his assets, we see that it’s possible to identify the different factors that drive both ability to cope and, in contrast anxiety. Whereas losing one’s job and one’s assets both provoke equal frequency of anxiety. Losing one’s house provokes the highest level of anxiety. In all cases thinking about the government and external forms of support, such as insurance, does not ameliorate anxiety. But there are things that do reduce anxiety. Belief in a personal God is a strong anxiety reducer for both situations, and is also important for other anxiety provoking situations. Some anxiety reducers are recognition of one’s friends and family, and the realization that other people are ‘in the same boat’, and one is not really alone.
A novel location-based key distribution scheme for large-scale stationary wireless networks (2015)

In this paper we study probabilistic key management schemes for large scale wireless multi-hop networks. We propose a novel method in which a probabilistic scheme combined with location information is used for distributing symmetric keys among the nodes. In order to apply the location information of the nodes in key distribution process, we partition the network into some regions and use graph coloring techniques to efficiently assign the keys. The proposed scheme has a superior scalability for large-scale stationary wireless networks using. This scheme elevates the probability of existence of a shared exclusive key among the nearby nodes, i.e., the probability of having an isolated node is significantly reduced in comparison with the existing probabilistic schemes. Our simulation results verify these terms.
Compliance to Screening Protocols for Multidrug-Resistant Microorganisms at the Emergency Departments of Two Academic Hospitals in the Dutch–German Cross-Border Region (2021)

Infections caused by multidrug-resistant organisms (MDROs) are associated with prolonged hospitalization and higher risk of mortality. Patients arriving in the hospital via the emergency department (ED) are screened for the presence of MDROs in compliance with the screening protocols in order to apply the correct isolation measures. In the Dutch-German border region, local hospitals apply their own screening protocols which are based upon national screening protocols. The contents of the national and local MDRO screening protocols were compared on vancomycin-resistant enterococci (VRE), methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), and carbapenemase-producing and carbapenem-resistant <i>Enterobacteriaceae</i> (CPE/CRE). The practicality of the screening protocols was evaluated by performing an audit. As a result, the content of the MDRO screening protocols differed regarding risk factors for MDRO carriage, swab site, personal protective equipment, and isolation measures. The observations and questionnaires showed that the practicality was sufficient; however, the responsibility was not designated clearly and education regarding the screening protocols was deemed inappropriate. The differences between the MDRO screening protocols complicate patient care in the Dutch-German border region. Arrangements have to be made about the responsibility of the MDRO screening, and improvements are necessary concerning education regarding the MDRO screening protocols.
The En^a Antigen and AntibodyA Genetical Modification of Human Red Cells Affectingtheir Blood Grouping Reactions (1969)

The red cells from a 23-year-old pregnant woman gave very unusual blood grouping reactions and her serum contained a ‘new’ antibody active against a very high incidence antigen. The reactions of various unrelated blood group antigens are modified, in some cases enhanced and in others depressed, the total picture being strongly reminiscent of the effects of proteolytic enzyme treatment. It is suggested that these effects can only be due to some factor affecting the red cell structure possibly by modifying the cell envelope. This modifying factor is genetically determined and shows dosage effect. Of nine siblings three are apparently homozygous and four heterozygous for this factor, the other two being ‘normal’. It is extremely rare, no further examples having been found in 18,472 blood donors. The antibody is undoubtedly immune, probably due to a blood transfusion two years previously. 12,509 donors have been tested with it but the only compatible red cells are those of the three homozygous siblings, i.e. the propositus, one sister and one brother. The antibody is therefore related to the modifying factor. Two codominant genes En^a and En^b are postulated, En^b being exceedingly rare. It is suggested that these genes determine not only the presence of the corresponding antigens Ena and Enb but also the structure of the red cell. EnaEna = ‘Normal’. EnaEnb = ‘Single dose modified’. EnbEnb = ‘Double dose modified’. The antibody thus becomes anti-En^a.
The Measurement of Central Noradrenergic Activity in Spontaneously Hypertensive Rats: A Comparison of Free 3,4 ??? Dihydroxyphenylethyleneglycol Levels with FLA-63 Induced Noradrenaline Depletion (1985)

Noradrenergic activity was measured in the brainstem, hypothalamus and thoracic spinal cord of male and female spontaneously hypertensive (SHR) and Wistar-Kyoto (WKY) rats at 6 and 28-36 weeks of age. Two techniques were used, measurement of a major noradrenaline (NA) metabolite, free 3,4-dihydroxyphenylethyleneglycol (DHPG), and measurement of the rate of decline in brain NA levels following dopamine-beta-hydroxylase (DBH) inhibition by FLA-63. There was a good correlation between the changes with age in NA turnover measured by the two techniques. NA levels and NA turnover measured by both techniques fell with age in brainstem and thoracic spinal cord in both SHR and WKY rats. In both strains these falls in turnover were associated with increases in blood pressure. However, the increase in blood pressure in the SHR was greater than in the WKY, even though NA turnover fell to a similar extent in both strains. These data show a difference in the pattern of change in NA levels and turnover in the brainstem and thoracic spinal cord compared to other brain regions and may therefore be related to the development of higher levels of blood pressure in older rats in both strains. They do not offer a simple explanation for the much higher blood pressures seen at all ages in the SHR.