gebhart/patrepeval huggingface dataset:
Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases (2011)

Identification of differentially expressed pathways from expression data is an important problem because it allows us to gain insights into the functional working mechanism of cells beyond the detection of differentially expressed genes. In this paper we present a brief guide to methods for the pathway analysis of expression data. Despite the vast amount of different statistical methods that have been developed so far, there is a considerable similarity among them, allowing a systematic classification and a reduction to a few null hypotheses that are effectively tested.

Systems biology aims to find emergent phenomena by the integration of heterogeneous data. In general, data integration itself is a part of any scientific inference: its elementary steps are the integration of observations (measurements) into the context of biological knowledge. However, in the case of systems biology, the scale of integration is many folds higher, resulting in a prodigious number of new computational approaches for the simultaneous analyses of heterogeneous data. In this paper we discuss one popular way of integrating biological knowledge into large-scale genome-wide measurements, namely the identification of functionally related genes (pathways) enriched or differentially expressed in gene expression data [1]. It should be noted that the approaches discussed are also applicable to the analyses of, e.g., RNA-seq, metabolomics or proteomics data and, generally, different types of biological measurements when preexisting biological knowledge is available.

In the early stages of methodological developments for gene expression data analyses, most approaches were focused on producing so-called gene lists. This is a set of individual genes called differentially expressed as identified by univariate test statistics (e.g., a t-test) [2]–[4]. Instead, more recent approaches clearly reflect systems biology's trend of data integration and interpretation [5]–[7], focusing on sets of functionally related genes (e.g., from the same signaling or metabolic pathway) rather than individual genes.

The purpose of this paper is to provide a brief guide to methods for the analysis of differentially expressed pathways or gene sets, which we simply call pathway-based methods. For this reason, we emphasize an illustration of the methods rather than their technical description. The reader is encouraged to follow the cited literature for technical details.
A Novel Pressure Transducer Using Mechanical Resonance (1978)

A novel electromechanical pressure transducer, suitable for telemetering, is proposed. It transforms an absolute static pressure into a frequency signal, using acoustical resonance due to the stiffness of a fluid in a cavity and the mass of a vibrating plate. The relation between the period of the output frequency T and the normalized input pressure p is theoretically given by T2 = A + B/p, where A and B are constants. This relation is verified experimentally by constructing two kinds of models. The advantages and disadvantages of the transducer are discussed.
Coronavirus disease 2019 may be driven by an overactivation of the renin-angiotensin-aldosterone system (2020)

Abstract SARS-CoV-2 enters the cell through the ACE2 receptor, which is considered one of the main inhibitors in the Renin-Angiotensin-Aldosterone System (RAAS).1​ ,2 The virus has been shown to downregulate the ACE2 receptor, leading to a subsequent increase in the vasopressoragentangiotensinII.3​ Evidently,criticalcoronavirusdisease2019(COVID-19)is thought to be due to a dysregulated immune response, causing a cytokine-release syndrome eventually leading to acute respiratory distress syndrome (ARDS).4​ ,5 ​However, several reports on clinical laboratory features and case-descriptions of critically ill patients with COVID-19 show discrepancies compared to typical ARDS. Here, we show that infusing swines with angiotensin II induces a pathophysiological syndrome closely resembling that of patients with RT-PCR-positive COVID-19. By using multimodal clinical imaging of patients, comparing laboratory data and translational histological features, we show that it is highly likely that an increase in RAAS is one, if not the main, pathogenic feature in critical COVID-19. Furthermore, it is plausible that this large animal model can be used to screen for potential new treatments for patients with severe COVID-19 and that MRI lung perfusion can be used to evaluate the outcome of potential treatments targeting the pathophysiological syndrome.
Monochromatic all-sky observations and auroral precipitation patterns (1976)

An all-sky imaging system capable of fast monochromatic imaging at very low light levels is described; the system allows real time display of regions of proton precipitation and of soft and hard electron precipitation in the auroral zone. Sample data illustrate various auroral types previously classified from photometric data and/or from particle data from satellites. Time-lapse film throughout an entire night shows the position and intensity of plasma sheet precipitation, superposition of a harder electron aurora, the relative positions of proton aurora and diffuse aurora, and the changing character of the aurora as a function of local time and substorm activity. These patterns are discussed in terms of the substorm injection boundary model (McIlwain, 1974).
Dual hydrophobe and phenylboronic acid-grafted poly(vinylpyrrolidone) polymers as shear-thinning and mucoadhesive eyedrop formulations (2016)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
Search for new particles decaying to two jets with the D0 detector (1997)

Results from a search for new particles decaying to dijets in $\sqrt{s} = 1.8 TeV$ $p\bar{p}$ collisions using the D0 1992-93 and 1994-95 data samples (104 pb$^{-1}$ are presented. We exclude at the 95% confidence level the production of excited quarks with masses below 725 GeV/c$^2$, an additional standard model W boson with masses between 340 and 680 GeV/c$^2$ and an additional standard model Z boson with masses between 365 and 615 GeV/c$^2$.
Development of mutome-specific personalized vaccines for pancreatic cancer (2013)

Meeting abstracts A major obstacle to the development of immunotherapy for pancreatic ductal adenocarcinoma (PDA) has been identifying immune relevant antigens that are not expressed by normal cells. DNA sequencing technologies that allow for the genome-wide identification of tumor mutations have
Coherent control of radiationless transitions: Simultaneous excitation and decay of overlapping resonances (2013)

We develop a simple analytical theory for the study of coherent control of radiationless transitions, and in particular, internal conversion leading to dissociation, in molecules possessing overlapping resonances. The method is applied to a model diatomic system. In contrast to previous studies, we consider here the control of a molecule that is allowed to decay during and after the preparation process. We use this theory to derive the shape of the laser pulse that creates the specific excited wave packet that best enhances or suppresses the radiationless transitions process. The results show the importance of resonance overlap in the molecule in order to achieve efficient coherent control over radiationless transitions via laser excitation. Specifically, resonance overlap is proven to be crucial in order to alter interference contributions to the controlled observable, and hence to achieve efficient coherent control by varying the phase of the laser field.
Electro-optic waveguide TE ↔ TM mode converter with low drive voltage (1980)

We have achieved complete electro-optic TE <--> TM mode conversion in Ti-diffused lithium niobate waveguides with as little as a 2.5-V drive. Because, for birefringent substrates like lithium niobate, TE <--> TM conversion is wavelength dependent, our method is potentially useful for wavelength multiplexing and demultiplexing. Three independently controlled mode converters, each with a 15-A filter bandwidth and with center wavelengths separated by 80 A, have been fabricated on a single substrate.
Cycloalkanones. I. Stereochemistry of .alpha.,.alpha.'-dibenzylcycloalkanones (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCycloalkanones. I. Stereochemistry of .alpha.,.alpha.'-dibenzylcycloalkanonesJohn L. Irvine, Iris H. Hall, Gerald L. Carlson, and Claude PiantadosiCite this: J. Org. Chem. 1972, 37, 12, 2033–2034Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/jo00977a037https://doi.org/10.1021/jo00977a037research-articleACS PublicationsRequest reuse permissionsArticle Views65Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effect of beak movement in singing Bengalese finches (<i>Lonchura striata</i> var. <i>domestica</i>) (1996)

In human vocal production, the lungs produce energy for the voice, the vocal folds have a function of a sound source, and the vocal tract functions as a resonator. Birds have the syrinx for the sound source, but they do not have the vocal folds. In birdsong, the syrinx had been thought to act alone in song production, and vocal tract played no role. However, when a bird sings in helium, harmonic overtones emerge [Nowichi (1989)]. For this reason, it is suggested that the vocal tract may play an important role as a vocal filter in birdsong production. In this study, beam movements were measured in the Bengalese finches while they were singing, and the correlation between fundamental frequencies in the song and the beak gape was examined. This correlation was significantly high (r=0.890), the wider beak gape corresponding to a higher fundamental frequency. The result suggests that in Bengalese finches beak movement formulas a dynamic filter which modifies the frequency composition of the syringeal output. Thus sound production in songbirds may be comparable to that in humans.
ACTIVE IMMUNITY TO POLIOMYELITIS IN CHIMPANZEES FOLLOWING SUBCLINICAL INFECTION (1947)

This report is concerned with the production of subclinical poliomyelitis in the chimpanzee, and immunity to such infection. Subclinical infection was produced in eight chimpanzees by the administration of virus orally or intracutaneously, and was measured by the production of a virus carrier state and the development of neutralizing antibodies. Immunity was tested by attempting to induce the carrier state again by a challenge dose of virus by the same routes. With an homologous strain as the challenge virus, immunity as defined here was produced in each of four chimpanzees tested. Neutralizing antibodies to the homologous strain were present about 1 month following the first exposure to virus by either the oral or cutaneous route. In another group of two chimpanzees, one developed neutralizing antibodies and immunity to heterologous strains, and one did not.
Simulation of laser pulse driven terahertz generation in corrugated plasma channels (2015)

Intense, short laser pulses propagating through inhomogeneous plasma generate THz radiation. Full format PIC simulations and theoretical analysis are conducted to investigate two mechanisms of ponderomotively driven THz radiation: a transition radiation mechanism (TRM) occurring as a laser pulse crosses a plasma boundary, and a slow wave phase matching mechanism (SWPM) that occurs in corrugated plasma channels.
Highly Stereoselective Synthesis, Structure, and Application of (<i>E</i>)<i>-</i>9-[2-(Silyl)ethenyl]-9<i>H</i>-carbazoles (2005)

(E)-N-(Silyl)vinylcarbazole has been easily prepared via a new catalytic route, silylative coupling (SC) of vinylcarbazole with vinyltrisubstituted silanes catalyzed by [RuH(Cl)(CO)(PCy3)2]. X-ray structures of two silylvinylcarbazoles as first N-vinylcarbazole derivatives have been resolved. The Pd-catalyzed Hiyama coupling reaction (also as the tandem reaction with SC) of synthesized (E)-N-(triethoxysilyl)vinylcarbazole with iodobenzene has been performed to afford (E)-N-(phenylvinyl)carbazole with high yield and stereoselectivity.
Mitochondrial oxidative stress after carbon monoxide hypoxia in the rat brain. (1992)

To better understand the mechanisms of tissue injury during and after carbon monoxide (CO) hypoxia, we studied the generation of partially reduced oxygen species (PROS) in the brains of rats subjected to 1% CO for 30 min, and then reoxygenated on air for 0-180 min. By determining H2O2-dependent inactivation of catalase in the presence of 3-amino-1,2,4-triazole (ATZ), we found increased H2O2 production in the forebrain after reoxygenation. The localization of catalase to brain microperoxisomes indicated an intracellular site of H2O2 production; subsequent studies of forebrain mitochondria isolated during and after CO hypoxia implicated nearby mitochondria as the source of H2O2. In the mitochondria, two periods of PROS production were indicated by decreases in the ratio of reduced to oxidized glutathione (GSH/GSSG). These periods of oxidative stress occurred immediately after CO exposure and 120 min after reoxygenation, as indicated by 50 and 43% decreases in GSH/GSSG, respectively. The glutathione depletion data were supported by studies of hydroxyl radical generation using a salicylate probe. The salicylate hydroxylation products, 2,3 and 2,5-dihydroxybenzoic acid (DHBA), were detected in mitochondria from CO exposed rats in significantly increased amounts during the same time intervals as decreases in GSH/GSSG. The DHBA products were increased 3.4-fold immediately after CO exposure, and threefold after 120 min reoxygenation. Because these indications of oxidative stress were not prominent in the postmitochondrial fraction, we propose that PROS generated in the brain after CO hypoxia originate primarily from mitochondria. These PROS may contribute to CO-mediated neuronal damage during reoxygenation after severe CO intoxication.
An Oral Tyrosine Tolerance Test in Thyrotoxicosis and Myxedema (1965)

IN patients with thyrotoxicosis the concentration of tyrosine in plasma has been shown to increase1 , 2 whereas concentrations of other amino acids except glutamic acid have been normal.3 When loads of tyrosine were fed to hyperthyroid patients, plasma levels of tyrosine measured hourly for six hours were elevated several times above levels found in euthyroid patients.3 In similar assays of oral tyrosine tolerance in hypothyroid subjects plasma levels after a tyrosine load were decreased below levels found in euthyroid subjects.The present investigation was intended to determine whether abnormal responses to orally administered loads of tyrosine are restricted to patients with . . .
Photoproduction of mesons from the nucleon (2003)

A general formalism is established for constructing models for the photoproduction of mesons from the nucleon. The essential ingredient is a mass operator which describes the coupling between meson-baryon, photon-baryon, and single-baryon channels. The most general forms for the mass operator interactions which produce these couplings are derived. These forms also provide generalizations of the Chew-Goldberger-Low-Nambu amplitudes for pion-nucleon photoproduction to any meson-baryon final state. The models lead to $S$-matrix elements that transform properly under inhomogeneous Lorentz transformations and are gauge invariant. The photoproduction amplitudes include final state interactions and satisfy Watson's theorem. A specific model is constructed by deriving the mass operator interactions from effective Lagrangians that describe the couplings of mesons, photons, and baryons. The electromagnetic interactions include direct and crossed nucleon contributions, as well as direct contributions from the ${P}_{33}(1232)$, ${P}_{11}(1440)$, ${D}_{13}(1520)$, and ${S}_{11}(1535)$ resonances. A contact term and exchange terms due to the $\ensuremath{\pi}$, $\ensuremath{\rho}$, and $\ensuremath{\omega}$ mesons are also included. The model gives a good fit to the significant multipoles in the energy range from the single-pion, photoproduction threshold up to a center-of-momentum energy of $W=1550\phantom{\rule{0.3em}{0ex}}\text{MeV}$, which corresponds to a photon lab energy of $810\phantom{\rule{0.3em}{0ex}}\text{MeV}$.
Molecular ion spectroscopy: Mass selected, resonant two-photon dissociation spectra of CH3I+ and CD3I+ (1988)

We present a new ion spectroscopic technique by which it is possible to investigate larger molecular ions by scanning an entire electronic state and coincidentally measuring and, hence, fixing the mass of the fragment ion observed. The technique involves primary resonance excitation together with secondary absorption followed by dissociation as detection process, employing the absorption of two photons in the ion. This method accesses the nondissociating vibronic levels of an electronic state rather than just the narrow range of predissociating levels, as in one-photon dissociation spectroscopy. Spectra of CH3I+ and CD3I+ over a range of 7000 cm−1, beginning at the origin of the Ã state, were recorded with progression bands up to n=21. These spectra allow for the first time an unambiguous assignment of the Ã←X̃ transition of CH3I+ and CD3I+. The exact positions of the electronic origin as well as of the origin of several progressions and new values for several vibrational constants of methyl iodide cations are reported. Some 300 bands in both ions were measured and assigned with this technique.
Selective Embedded Growth of Al<sub>x</sub>Ga<sub>1-x</sub>As by Low-Pressure Organometallic Vapor Phase Epitaxy (1986)

Selective embedded growth of Al x Ga 1- x As ( x ≤0.35) in grooves of patterned substrates has been achieved for the first time by low-pressure organometallic vapor phase epitaxy (LP-OMVPE). Epitaxial Al x Ga 1- x As layers are embedded only in chemically etched grooves, while no polycrystalline deposition occurs on the masked area. The layers grown in grooves with the reverse-mesa cross sections, formed in the [110] direction, are uniform in thickness and show flat-smooth surfaces throughout. These results indicate that LP-OMVPE is a very promising technique for monolithic device integration.
Ion tracer technique for airspeed measurement at low densities (1954)

Note presenting a study of the aerodynamic and production-detection problems associated with ion tracer velocity measurement techniques, with particular emphasis on those aspects unique to low-density gas dynamics. A critical survey was made of the various techniques which have been employed and specific suggestions are offered relative to the successful use of ion tracer velocity measuring methods at low densities.
A DNA barcode reference library for marine fish of Portugal : design and annotation (2011)

Abstract can be found at: thttp://www.dnabarcodes2011.org/conference/program/abstract_page.php?uniqid=BTXlxj
Generation and modelling of megavoltage photon beams for contrast-enhanced radiation therapy (2006)

Contrast-enhanced radiation therapy (CERT) is a treatment approach involving the irradiation of tumours containing high atomic number (Z) contrast media, using low-quality x-ray beams. This work describes the experimental generation of x-ray beams using a linear accelerator with low-Z target materials (beryllium and aluminium), in order to produce photon energy spectra appropriate for CERT. Measurements were made to compare the experimental beams to conventional linear accelerator photon beams in terms of per cent depth dose. Monte Carlo simulation was used to model the generation of each beam, and models were validated against experimental measurement. Validated models were used to demonstrate changes in photon spectra as well as to quantify the variation of tumour dose enhancement with iodinated contrast medium concentration in a simulated tumour volume. Finally, the ratio of the linear attenuation coefficient for iodinated contrast medium relative to water was determined experimentally as a function of iodine concentration. Beams created with low-Z targets show significant changes in energy spectra compared to conventional beams. For the 4 MeV/Be beam, for example, 33% of photons have energies below 60 keV. Measurements and calculation show that both the linear attenuation coefficient ratio and dose enhancement factor (DEF) increase most rapidly at concentrations below 46 mg I ml(-1). There is a significant dependence of DEF on electron energy and a lesser dependence on target material. The 4 MeV/Be beam is the most promising in terms of magnitude of DEF - for example, DEF values of 1.16 and 1.29 are obtained for concentrations of 20 mg I ml(-1) and 50 mg I ml(-1), respectively. DEF will increase or decrease, respectively, for shallower or deeper tumours at a rate of approximately 1.1% cm(-1). In summary, we show that significant dose enhancement is possible by altering the linear accelerator target and filtration, but the magnitude is highly dependent on contrast medium concentration.
Raman Spectra of Formic Acid Gasification Products in Subcritical and Supercritical Water (2019)

Formic acid gasification was carried out in a continuous supercritical water reactor at temperatures from 300°C to 430°C, residence times between 4 s and 65 s, a constant pressure of 25 MPa, and a constant initial formic acid concentration of 3.6 wt%. Raman spectra of the reaction products in the reactor effluent stream were collected for each experimental condition. The intent is to use this Raman data to characterize reaction pathways and reaction rates of formic acid decomposition in subcritical and supercritical water. To do this, each Raman spectra can be used to calculate the molar concentration of each reaction product, which in this case includes hydrogen, carbon monoxide, carbon dioxide, and residual formic acid. All spectra were collected at 25 MPa and 20°C. Spectra were collected using a Raman flowcell from MarqMetrix (Seattle, WA) which includes a high-resolution fiber-optic Raman laser, and an optical cell with a sapphire ball lens, which allows for focusing the Raman laser into the effluent stream and collecting Raman spectra along the same axis in the backscatter configuration. The Raman laser used has an excitation wavelength of 785 nm, and was operated at 300 mW. For each experimental condition, five spectra were collected and averaged, with each spectra using a 20 s integration time. This was to minimize measurement noise. The "dark" signal was subtracted automatically with the MarqMetrix data collection software, and the fluorescent background signal was subtracted using a semi-manual MATLAB routine, which is included with this dataset. Spectra were normalized to the height of the prominent sapphire peak, to correct for any optical effects.