gebhart/patrepeval huggingface dataset:
Staphylococcal Protein A Contributes to Persistent Colonization of Mice with Staphylococcus aureus (2018)

<i>Staphylococcus aureus</i> persistently colonizes the nasopharynx in humans, which increases the risk for invasive diseases, such as skin infection and bacteremia. Nasal colonization triggers IgG responses against staphylococcal surface antigens; however, these antibodies cannot prevent subsequent colonization or disease. Here, we describe <i>S. aureus</i> WU1, a multilocus sequence type 88 (ST88) isolate that persistently colonizes the nasopharynx in mice. We report that staphylococcal protein A (SpA) is required for persistence of <i>S. aureus</i> WU1 in the nasopharynx. Compared to animals colonized by wild-type <i>S. aureus</i>, mice colonized with the Δ<i>spa</i> variant mount increased IgG responses against staphylococcal colonization determinants. Immunization of mice with a nontoxigenic SpA variant, which cannot cross-link B cell receptors and divert antibody responses, elicits protein A-neutralizing antibodies that promote IgG responses against colonizing <i>S. aureus</i> and diminish pathogen persistence.<b>IMPORTANCE</b><i>Staphylococcus aureus</i> persistently colonizes the nasopharynx in about one-third of the human population, thereby promoting community- and hospital-acquired infections. Antibiotics are currently used for decolonization of individuals at increased risk of infection. However, the efficacy of antibiotics is limited by recolonization and selection for drug-resistant strains. Here, we propose a model of how staphylococcal protein A (SpA), a B cell superantigen, modifies host immune responses during colonization to support continued persistence of <i>S. aureus</i> in the nasopharynx. We show that this mechanism can be thwarted by vaccine-induced anti-SpA antibodies that promote IgG responses against staphylococcal antigens and diminish colonization.
ChemInform Abstract: VINYLIC RADICALS ARE INTERMEDIATES IN THE OXIDATION OF VINYLIC LITHIUM REAGENTS TO LITHIUM ENOLATES BY DIOXYGEN, BUT NOT BY LITHIUM TERT‐BUTYL PEROXIDE (1977)

Abstract Die isomeren Vinyllithiumverbindungen (I) und (IV) reagieren mit O 2 unter partiellem Verlust der Stereochemie an der Doppelbindung und mit Li‐tert.‐butylperoxid unter Retention der Konfiguration.
Incremental Segmentation and Decoding Strategies for Simultaneous Translation (2013)

Simultaneous translation is the challenging task of listening to source language speech, and at the same time, producing target language speech. Human interpreters achieve this task routinely and effortlessly, using different strategies in order to minimize the latency in producing target language. Toward modeling the human interpretation process, we propose a novel input segmentation method using the phrase alignment structure of the language pair. We compare and contrast three incremental decoding and two different input segmentation strategies, including our proposed method, for simultaneous translation. We present accuracy and latency tradeoffs for each of the decoding strategies when applied to audio lectures from the TED collection.
Oxygen “Getter” Effects on Microstructure and Carrier Transport in Low Temperature Combustion-Processed a-InXZnO (X = Ga, Sc, Y, La) Transistors (2013)

In oxide semiconductors, such as those based on indium zinc oxide (IXZO), a strong oxygen binding metal ion ("oxygen getter"), X, functions to control O vacancies and enhance lattice formation, hence tune carrier concentration and transport properties. Here we systematically study, in the IXZO series, the role of X = Ga(3+) versus the progression X = Sc(3+) → Y(3+) → La(3+), having similar chemical characteristics but increasing ionic radii. IXZO films are prepared from solution over broad composition ranges for the first time via low-temperature combustion synthesis. The films are characterized via thermal analysis of the precursor solutions, grazing incidence angle X-ray diffraction (GIAXRD), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and scanning transmission electron microscopy (STEM) with high angle annular dark field (HAADF) imaging. Excellent thin-film transistor (TFT) performance is achieved for all X, with optimal compositions after 300 °C processing exhibiting electron mobilities of 5.4, 2.6, 2.4, and 1.8 cm(2) V(-1) s(-1) for Ga(3+), Sc(3+), Y(3+), and La(3+), respectively, and with I(on)/I(off) = 10(7)-10(8). Analysis of the IXZO TFT positive bias stress response shows X = Ga(3+) to be superior with mobilities (μ) retaining >95% of the prestress values and threshold voltage shifts (ΔV(T)) of <1.6 V, versus <85% μ retention and ΔV(T) ≈ 20 V for the other trivalent ions. Detailed microstructural analysis indicates that Ga(3+) most effectively promotes oxide lattice formation. We conclude that the metal oxide lattice formation enthalpy (ΔH(L)) and metal ionic radius are the best predictors of IXZO oxygen getter efficacy.
ChemInform Abstract: STEREOCHEMICAL STUDIES OF ADRENERGIC DRUGS. OPTICALLY ACTIVE DERIVATIVES OF IMIDAZOLINES (1977)

Abstract Aus der Aminosäure (I) entstehen die Ester‐hydrochloride (II), die über die Amide (III) zu den Antipoden des 1,2‐Diamino‐propans (IVa) und (IVb) reduziert werden.
Mid-infrared imaging- and spectro-polarimetric subarcsecond observations of NGC 1068 (2016)

We present subarcsecond 7.5–13 μm imaging- and spectro-polarimetric observations of NGC 1068 using CanariCam on the 10.4-m Gran Telescopio CANARIAS. At all wavelengths, we find: (1) A 90 × 60 pc extended polarized feature in the northern ionization cone, with a uniform ∼44|$^\circ$| polarization angle. Its polarization arises from dust and gas emission in the ionization cone, heated by the active nucleus and jet, and further extinguished by aligned dust grains in the host galaxy. The polarization spectrum of the jet–molecular cloud interaction at ∼24 pc from the core is highly polarized, and does not show a silicate feature, suggesting that the dust grains are different from those in the interstellar medium. (2) A southern polarized feature at ∼9.6 pc from the core. Its polarization arises from a dust emission component extinguished by a large concentration of dust in the galaxy disc. We cannot distinguish between dust emission from magnetically aligned dust grains directly heated by the jet close to the core, and aligned dust grains in the dusty obscuring material surrounding the central engine. Silicate-like grains reproduce the polarized dust emission in this feature, suggesting different dust compositions in both ionization cones. (3) An upper limit of polarization degree of 0.3 per cent in the core. Based on our polarization model, the expected polarization of the obscuring dusty material is ≲0.1 per cent in the 8–13 μm wavelength range. This low polarization may be arising from the passage of radiation through aligned dust grains in the shielded edges of the clumps.
Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib (2023)

&lt;p&gt;PDF file 249K, Effect of pazopanib on S6K1 phosphorylation in cells expressing activating MTOR mutations&lt;/p&gt;
Understanding Within-Content Engagement through Pattern Analysis of Mouse Gestures (2014)

The availability of large volumes of interaction data and scalable data mining techniques have made possible to study the online behaviour for millions of Web users. Part of the efforts have focused on understanding how users interact and engage with web content. However, the measurement of within-content engagement remains a difficult and unsolved task. This is because of the lack of standardised, well-validated methods for measuring engagement, especially in an online context. To address this gap, we perform a controlled user study where we observe how users respond to online news in the presence or lack of interest. We collect mouse tracking data, which are known to correlate with visual attention, and examine how cursor behaviour can inform user engagement measures. The proposed method does not use any pre-determined concepts to characterise the cursor patterns. We, rather, follow an unsupervised approach and use a large set of features engineered from our data to extract the cursor patterns. Our findings support the connection between gaze and cursor behaviour but also, and more importantly, reveal other dependencies, such as the correlation between cursor activity and experienced affect. Finally, we demonstrate the value of our method by predicting the outcome of online news reading experiences.
Peri-strut low-intensity areas in optical coherence tomography correlate with peri-strut inflammation and neointimal proliferation (2014)

The presence of PLI in OCT correlates with neointimal thickness and appears to have a diagnostic value in the recognition of peri-strut inflammation, therefore possibly serving as a surrogate for in-vivo assessment of stent efficacy.
The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression (2021)

Abstract The long non-coding RNA (lncRNA) EPB41L4A-AS1 is aberrantly expressed in various cancers and has been reported to be involved in metabolic reprogramming and as a repressor of the Warburg effect. Although the biological relevance of EPB41L4A-AS1 is evident, its functional role seems to vary depending on cell type and state of disease. By combining RNA sequencing and ChIP sequencing of cell cycle synchronized HaCaT cells we previously identified EPB41L4A-AS1 to be one of 59 lncRNAs with potential cell cycle functions. Here, we demonstrate that EPB41L4A-AS1 exists as bright foci and regulates gene expression in the nucleus in both cis and trans . Specifically, we find that EPB41L4A-AS1 positively regulates its sense overlapping gene EPB41L4A and influences expression of hundreds of other genes, including genes involved in cell proliferation. Finally, we show that EPB41L4A-AS1 affects cell cycle phase distribution, though these effects vary between cell types.
Single-polarization fiber with a high extinction ratio (2004)

An elliptical-core hole assisted single-polarization fiber was designed, fabricated, and characterized. Numerical modeling based on the vectorial Maxwell equation reveals the dependence of the single-polarization bandwidth on core delta and air-hole size. Several single-polarization fibers based on this design with their single-polarization operating windows centered between 0.9 and 1.5 microm were successfully demonstrated. A correlation between fiber birefringence and single-polarization operating bandwidth is qualitatively confirmed. A single-polarization bandwidth as high as 55 nm was observed. These fibers also show very high extinction ratios of 60 dB or higher at lengths much shorter than 1 m. Other properties such as the dependence on length of the single-polarization operating window were also measured.
Liquid Crystal Digital Beam Steering Device Based on Decoupled Birefringent Deflector and Polarization Rotator (2005)

ABSTRACT We describe digital beam deflectors (DBDs) based on liquid crystals. Each stage of the device comprises polarization rotator and birefringent prism deflector. We used prisms made of the uniaxial smectic A (SmA) liquid crystal and a solid yttrium orthovanadate crystal. SmA prisms have high birefringence and can be constructed in a variety of shapes. We address the challenges of uniform alignment of SmA, such as elimination of focal conic domains. Rotation of linear polarization is achieved by electrically switched twisted nematic or electrically controlled birefringent cell. We describe a four-stage DBD steering a normally incident laser beam within ±56 mrad range with 8 mrad steps.
A Switched-Coupling-Capacitor Equalizer for Series-Connected Battery Strings (2016)

Due to the low cost, small size, and easy control, the switched-capacitor (SC) equalizer is promising among all types of active cell balancing methods. However, the balancing speed is generally slow and the balancing efficiency is seriously low when the SC equalizer is applied into a long battery string. Therefore, an automatic switched-coupling-capacitor equalizer (SCCE) is proposed, which can realize the any-cells-to-any-cells equalization for a battery string. Only two switches and one capacitor are required for each battery cell. All mosfets are controlled by one pair of complementary pulse width modulation signals, and energy can be automatically and directly delivered from any higher voltage cells to any lower voltage ones without the need of cell monitoring circuits, leading to a high balancing efficiency and speed independent of the cell number and the initial cell voltages. Contrary to the conventional equalizers using additional components for the equalization among modules, the proposed equalizer shares a single converter for the equalization among cells and modules, resulting in smaller size and lower cost. A prototype for four lithium battery cells is implemented, and an experimental comparison between the proposed SCCE and the conventional SC equalizer is presented. Experimental results show the proposed topology exhibits a substantially improved balancing performance, and the measured peak efficiency is 92.7%.
Supplementary Data from Mutant p53 (G199V) Gains Antiapoptotic Function through Signal Transducer and Activator of Transcription 3 in Anaplastic Thyroid Cancer Cells (2023)

Supplementary Data from Mutant p53 (G199V) Gains Antiapoptotic Function through Signal Transducer and Activator of Transcription 3 in Anaplastic Thyroid Cancer Cells
The hunt for a global killer (2012)

As a veterinary student I always felt misplaced. Not until I attended a course in immunology did I really feel the urge and drive to dive into the matter. Almost by coincidence, as a brand new candidate, I had the fortune to get a position in Tuberculosis vaccine research, and never since have I doubted that it was the right choice for me. Since then I have been driven by scientific curiosity and the prospects of generating results that can be used for products for which there is a real need.
Studies on Image Fusion Techniques for Dynamic Applications (2008)

A survey of present methods and current techniques being pursued by the US Air Force for image fusion and registration is conducted. Formulating the problem within a signal detection theory framework provides a unique thrust.
An adaptive social network for information access: Theoretical and experimental results (2003)

We consider a social network of software agents who assist each other in helping their users find information.Unlike in most previous approaches, our architecture is fully distributed and includes agents who preserve the privacy and autonomy of their users.These agents learn models of each other in terms of expertise (ability to produce correct domain answers) and sociability (ability to produce accurate referrals).We study our framework experimentally to study how the social network evolves.Specifically, we find that under our multi-agent learning heuristic, the quality of the network improves with interactions: the quality is maximized when both expertise and sociability are considered; pivot agents further improve the quality of the network and have a catalytic effect on its quality even if they are ultimately removed.Moreover, the quality of the network improves when clustering decreases, reflecting the intuition that you need to talk to people outside your close circle to get the best information.
Data from Promoter Methylation of Genes in and around the Candidate Lung Cancer Susceptibility Locus <i>6q23-25</i> (2023)

&lt;div&gt;Abstract&lt;p&gt;Chromosomal aberrations associated with lung cancer are frequently observed in the long arm of chromosome 6. A candidate susceptibility locus at &lt;i&gt;6q23-25&lt;/i&gt; for lung cancer was recently identified; however, no tumor suppressor genes inactivated by mutation have been identified in this locus. Genetic, epigenetic, gene expression, and &lt;i&gt;in silico&lt;/i&gt; screening approaches were used to select 43 genes located in &lt;i&gt;6q12-27&lt;/i&gt; for characterization of methylation status. Twelve (28%) genes were methylated in at least one lung cancer cell line, and methylation of 8 genes was specific to lung cancer cell lines. Five of the 8 genes with the highest prevalence for methylation in cell lines (&lt;i&gt;TCF21, SYNE1, AKAP12, IL20RA&lt;/i&gt;, and &lt;i&gt;ACAT2&lt;/i&gt;) were examined in primary lung adenocarcinoma samples from smokers (&lt;i&gt;n&lt;/i&gt; = 100) and never smokers (&lt;i&gt;n&lt;/i&gt; = 75). The prevalence for methylation of these genes was 81%, 50%, 39%, 26%, and 14%, respectively, and did not differ by smoking status or age at diagnosis. Transcription of &lt;i&gt;SYNE1, AKAP12&lt;/i&gt;, and &lt;i&gt;IL20RA&lt;/i&gt; was completely silenced by hypermethylation and could be restored after treatment with 5-aza-2-deoxycytidine. Significant associations were found between methylation of &lt;i&gt;SYNE1&lt;/i&gt; and &lt;i&gt;TCF21, SYNE1&lt;/i&gt; and &lt;i&gt;AKAP12&lt;/i&gt;, and &lt;i&gt;AKAP12&lt;/i&gt; and &lt;i&gt;IL20RA&lt;/i&gt;, indicating a coordinated inactivation of these genes in tumors. A higher prevalence for methylation of these genes was not associated with early-onset lung cancer cases, most likely precluding their involvement in familial susceptibility to this disease. Together, our results indicate that frequent inactivation of multiple candidate tumor suppressor genes within chromosome &lt;i&gt;6q&lt;/i&gt; likely contributes to development of sporadic lung cancer. [Cancer Res 2008;68(6):1707–14]&lt;/p&gt;&lt;/div&gt;
Faculty Opinions recommendation of A mycobacterial lipoarabinomannan specific monoclonal antibody and its F(ab') fragment prolong survival of mice infected with Mycobacterium tuberculosis. (2004)

Read the full review for this Faculty Opinions recommended article: A mycobacterial lipoarabinomannan specific monoclonal antibody and its F(ab') fragment prolong survival of mice infected with Mycobacterium tuberculosis.
Causes of almond yield variations (1988)

Statistical analysis of regional, rainfall-related effects could help early-spring forecasting
Study and microwave applications of artificial periodic substrate PBG planar circuits (2003)

This paper presents the results of analytical study and numerical simulation as well as discusses various microwave applications of artificial periodic substrate photonic bandgap (PBG) circuits. The configurations considered are planar microstrip and coplanar line circuits on the high-density dielectric substrate containing finite-periodic groups of air blocks underneath the lines. Transmission matrix method has been applied for analyzing the transmission/reflection characteristics of the circuits and obtaining the stopband and passband conditions. Simulation results illustrating applications of PBG circuits as microwave bandpass filters and harmonic tuning elements are presented. The configurations discussed here provide certain advantages and promising solutions in the design of novel integrated antennas and adaptive arrays for the next-generation mobile communication systems.
Radiation and Convection Heat Transfer in Wildland Fire Environments (2009)

Wildland fire research has been extensive and on going since before 1950. The motivation behind this research is to prevent loss of property and lives. In spite of this research, the heat transfer of fuel ignition and flame spread is not well understood. This dissertation seeks to fill gaps in this understanding through modeling and also by experimentation. The effect of water vapor on the transmission of thermal radiation from the flame to the fuel was investigated. The Spectral Line Weighted-sum-of-gray-gases approach was adopted for treating the spectral nature of the radiation. The study reveals that water vapor has only a moderate effect even at 100 percent humidity. Experiments were conducted wherein wood shavings and Ponderosa pine needles in quiescent air were subjected to an imposed radiant heat flux. The internal temperature of these particles was measured and compared to steady-state model predictions. Excellent agreement was observed between the model predictions and the experimental data. Exercise of the model led to the conclusion that ignition of the fuel element by radiation heating alone is unlikely. Time-resolved radiation and convection heat flux were measured in a series of experimental laboratory fires designed to explore heat transfer behavior during combustion of discontinuous fuel beds. Convection heat flux was shown to fluctuate between positive and negative values during flame engulfment, indicating the presence of alternating packets of hot combustion gas and cool ambient air within the flame. Rapid temporal fluctuations were observed in both radiation and convection. Spectral analysis revealed content at frequencies as high as 150 to 200 Hz. Time-resolved radiation and convection heat flux histories were also collected on fourteen controlled burns and wildfires. The data reveal significant temporal fluctuations in both radiation and convection heat flux. Spectral analysis using a Fast Fourier Trans-form (FFT) revealed content as high as 100 Hz using data sets that were sampled at 500 Hz. The role of the higher frequency convective content in fuel thermal response was explored using a one-dimensional transient conduction model with a convective boundary condition. It was shown that high-frequency (i.e., short-duration) convective pulses can lead to fine fuel ignition.
Commentary: dissecting the PNPLA3 association with liver fat and stiffness, and interaction with diet – authors’ reply (2014)

We thank Stinton and Loomba for their commentary.1 Compared with previous papers on this topic, our study focused on the general Chinese population and used state-of-the art non-invasive assessment of hepatic steatosis and fibrosis, i.e. proton-magnetic resonance spectroscopy and transient elastography.2 The association between metabolic syndrome and non-alcoholic fatty liver disease (NAFLD) is well known.3 Seventy per cent of Chinese patients with biopsy-proven NAFLD suffered from metabolic syndrome, compared to 7% of those without NAFLD.4 Our current study further shows that metabolic syndrome remains the most important determinant of NAFLD in the general population.2 The additional effect of the patatin-like phospholipase domain-containing protein 3 (PNPLA3) rs738409 polymorphism on hepatic steatosis in people with metabolic syndrome was limited. In contrast, among subjects without metabolic syndrome, the prevalence of NAFLD increased from 12% in CC carriers to 34% in GG carriers. Stinton and Loomba also highlighted that PNPLA3 polymorphism did not affect liver stiffness in our cohort. However, the negative result may be explained by the low prevalence of advanced fibrosis and cirrhosis in the general population.5 In a meta-analysis of 16 studies, PNPLA3 polymorphism influenced not only hepatic steatosis but also the histological severity.6 When we further analysed our hospital cohort with liver biopsies,7 the GG genotype was associated with more severe hepatic steatosis and fibrosis (Figure 1). The authors’ declarations of personal and financial interests are unchanged from those in the original article.2
Suppression of detrusor overactivity in rats with bladder outlet obstruction by a type 4 phosphodiesterase inhibitor (2006)

A selective PDE4 inhibitor can effectively suppress detrusor overactivity in rats with BOO, at doses that have no effect on voiding bladder contractions. Thus, selective PDE4 inhibitors should be considered for the treatment of overactive bladder in patients with BOO.