gebhart/patrepeval huggingface dataset:
Data from <i>FGFR1</i> Amplification Mediates Endocrine Resistance but Retains TORC Sensitivity in Metastatic Hormone Receptor–Positive (HR<sup>+</sup>) Breast Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;While &lt;i&gt;FGFR1&lt;/i&gt; amplification has been described in breast cancer, the optimal treatment approach for &lt;i&gt;FGFR1&lt;/i&gt;-amplified (FGFR1&lt;sup&gt;+&lt;/sup&gt;) metastatic breast cancer (MBC) remains undefined.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We evaluated clinical response to endocrine and targeted therapies in a cohort of patients with hormone receptor–positive (HR&lt;sup&gt;+&lt;/sup&gt;)/HER2&lt;sup&gt;−&lt;/sup&gt; MBC and validated the functional role of &lt;i&gt;FGFR1&lt;/i&gt;-amplification in mediating response/resistance to hormone therapy &lt;i&gt;in vitro&lt;/i&gt;.&lt;/p&gt;Results:&lt;p&gt;In the clinical cohort (&lt;i&gt;N&lt;/i&gt; = 110), we identified that patients with FGFR1&lt;sup&gt;+&lt;/sup&gt; tumors were more likely to have progesterone receptor (PR)-negative disease (47% vs. 20%; &lt;i&gt;P&lt;/i&gt; = 0.005), coexisting &lt;i&gt;TP53&lt;/i&gt; mutations (41% vs. 21%; &lt;i&gt;P&lt;/i&gt; = 0.05), and exhibited shorter time to progression with endocrine therapy alone and in combination with CDK4/6 inhibitor, but not with a mTOR inhibitor (everolimus), adjusting for key prognostic variables in multivariate analysis. Furthermore, mTOR-based therapy resulted in a sustained radiological and molecular response in an index case of FGFR1&lt;sup&gt;+&lt;/sup&gt; HR&lt;sup&gt;+&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt; MBC. In preclinical models, estrogen receptor–positive (ER&lt;sup&gt;+&lt;/sup&gt;)/&lt;i&gt;FGFR1&lt;/i&gt;-amplified CAMA1 human breast cancer cells were only partially sensitive to fulvestrant, palbociclib, and alpelisib, but highly sensitive to everolimus. In addition, transduction of an FGFR1 expression vector into ER&lt;sup&gt;+&lt;/sup&gt; T47D cells induced resistance to fulvestrant that could be overcome by added TORC1 inhibition, but not PI3K or CDK4/6 inhibition.&lt;/p&gt;Conclusions:&lt;p&gt;Collectively, these findings suggest that while &lt;i&gt;FGFR1&lt;/i&gt; amplification confers broad resistance to ER, PI3K, and CDK4/6 inhibitors, mTOR inhibitors might have a unique therapeutic role in the treatment of patients with ER&lt;sup&gt;+&lt;/sup&gt;/FGFR1&lt;sup&gt;+&lt;/sup&gt; MBC.&lt;/p&gt;&lt;/div&gt;
Biophysical Properties of Australia Antigen (1969)

Biophysical studies with Australia complement-fixing (CF) antigen showed it to be a particle with a buoyant density of 1.20 g/cm(3) in CsCl, a sedimentation coefficient of 110, and an average diameter of 25 nm. The CF antigen was not inactivated by ether, 1% deoxycholate, 1% Tween 80 or overnight heating at 56 C. The antigen was unstable when treated with 1% sodium dodecyl sulfate. A procedure is described for the isolation and partial purification of Australia antigen from serum by using isopycnic banding and rate separation techniques. Treatment of the 1.20 g/cm(3) Australia antigen with 1% Tween 80 yielded a minor peak of CF activity with a buoyant density of 1.39 g/cm(3) in CsCl.
Prospective Randomized Study Comparing MEMID with a Chop-Like Regimen in Elderly Patients with Aggressive Non-Hodgkin’s Lymphoma (2005)

The increased toxicity without survival benefit confirms the superiority of CHOP and CHOP-like regimens for elderly patient with aggressive NHL.
A simple distributed loop-free routing strategy for computer communication networks (1993)

The loops resulting from either component failures or load changes in a computer communication network degrade the performance and the adaptability of conventional distributed adaptive routing strategies, such as ARPANET's previous routing strategy (APRS). The authors develop distributed loop-free routing strategy by adding only one additional piece of information-the total number of minimum-delay paths-to the commonly used routing messages and tables. The proposed routing strategy requires only easily obtainable information, yet removes loops completely. It is far more efficient in both time and space than its conventional counterparts, especially for sparse computer networks. The authors prove the correctness of the proposed strategy, and give several illustrative examples. The performance of this strategy is shown to be better than, or at least as good as, that of APRS and any multiorder routing strategies, in which the order of a routing strategy is determined by the amount of routing information carried in each routing message.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Leukotriene E4 Activates Human Th2 Cells for Exaggerated Proinflammatory Cytokine Production in Response to Prostaglandin D2 (2011)

PGD(2) exerts a number of proinflammatory responses through a high-affinity interaction with chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2) and has been detected at high concentrations at sites of allergic inflammation. Because cysteinyl leukotrienes (cysLTs) are also produced during the allergic response, we investigated the possibility that cysLTs may modulate the response of human Th2 cells to PGD(2). PGD(2) induced concentration-dependent Th2 cytokine production in the absence of TCR stimulation. Leukotrienes D(4) and E(4) (LTE(4)) also stimulated the cytokine production but were much less active than PGD(2). However, when combined with PGD(2), cysLTs caused a greater than additive enhancement of the response, with LTE(4) being most effective in activating Th2 cells. LTE(4) enhanced calcium mobilization in response to PGD(2) in Th2 cells without affecting endogenous PGD(2) production or CRTH2 receptor expression. The effect of LTE(4) was inhibited by montelukast but not by the P2Y(12) antagonist methylthioadenosine 5'-monophosphate. The enhancing effect was also evident with endogenous cysLTs produced from immunologically activated mast cells because inhibition of cysLT action by montelukast or cysLT synthesis by MK886, an inhibitor of 5-lipoxygenase-activating protein, reduced the response of Th2 cells to the levels produced by PGD(2) alone. These findings reveal that cysLTs, in particular LTE(4), have a significant proinflammatory impact on T cells and demonstrate their effects on Th2 cells are mediated by a montelukast-sensitive receptor.
Written Language Profile of Children and Youth with Asperger Syndrome: From Research to Practice (2003)

The current study investigated written language skills of children and youth with Asperger Syndrome (AS). Sixteen children and youth with AS and 16 neurotypical peers were compared on a standardized test of written language skills and legibility of handwriting. To investigate more detailed characteristics, informal analyses were also made for written samples from these standardized tests. In written language skills, significant differences were not found between standardized scores of both groups; however, in hand writing skills, the group of individuals with AS produced significantly less legible letters and words than the neurotypical group. Informal analyses of written samples further reveal that the group of children and youth with AS appear to be able write quantitatively similar to their neurotypical peers with using grammatical rules but had difficulty producing qualitative writing. Implications for translating research to practice in teaching writing skills for children and youth with AS are discussed.
Further polymorphism of the MICA gene (2002)

Summary The MHC class I chain‐related (MIC) gene family constitutes an interesting genetic group that is related to major histocompatibility complex (MHC) class I genes and is located within the MHC. The MIC gene products, MICA and MICB, have similar structures to HLA class I molecules. So far over 50 MICA alleles have been reported, which suggests that this genetic system is highly polymorphic. In order to investigate further the extent of MICA polymorphism we have studied exons 2–5 of the MICA gene in over 200 homozygous and heterozygous cell lines. Altogether we have identified 11 new MICA alleles and report 13 new nucleotide variations, one in exon 2, four in exon 3, four in exon 4, two in intron 1, one in intron 4 and one (a deletion) in exon 4. Eight of the 10 exonic variations are non‐synonymous. The deletion in exon 4 leads to a frame‐shift mutation and the introduction of a repeat of 12 leucine residues encoded by the microsatellite in exon 5. This study provides further evidence that the MICA gene is highly polymorphic. In contrast to MHC class I molecules, the polymorphic sites in MICA are predominantly within the α 2 and α 3 domains. The distribution of synonymous and non‐synonymous substitutions suggests that there is selection for the polymorphic positions, which therefore define potential functional sites in the protein. We were also able to determine the association between MICA and HLA‐B alleles in a number of homozygous cell lines bearing extended haplotypes.
Ultrafast absorption in free-standing porous silicon films (1995)

Ultrafast absorption studies on free-standing porous silicon films have been carried out at room temperature to investigate the carrier dynamics and the luminescence mechanism. Ultraviolet and visible excitations were used on an as-prepared sample and two annealed samples. Transient absorption curves of UV pumped, as-prepared samples contain a fast decay (τf) of 0.8±0.2 ps and a slower decay of ≳30 ps. τf is found to be shorter for both the 500 °C annealed sample with UV excitation and for the as-prepared sample with visible excitation. The faster decay rates suggest that the subpicosecond component of the transient absorption may be due to carrier thermalization rather than core-to-surface state excitation transfer.
Achieving Scale and Quality in School-to-Work Internships: Findings From Two Employer Surveys (2000)

Work-based learning is a central component of the school-to-work strategy. Yet, a widespread system of work-based learning in the form of internships or apprenticeships will need to involve thousands of employers willing to provide placements. This paper examines the issue of employer involvement in the school-to-work strategy through a survey of employers participating in five school-to-work programs and a survey of a comparison group of nonparticipating employers in those same labor markets. The motivations and potential motivations of employers are identified; the data suggest that participants are motivated by philanthropy, while firms in the nonparticipating sample indicate that they would need more bottom-line-oriented arguments to convince them to join up. We also explore the quality of work-based learning placements provided to try to identify the relationship between the characteristics and motivations of employers and the quality of the internships that they provide.
Progressive Point-Based Global Illumination (2011)

This paper proposes a progressive point-based global illumination algorithm to render complex scenes with limited time and memory. Our algorithm includes multi passes. The first pass is ray tracing, and the next passes are point cloud generating and point-based rendering passes. The point clouds are generating progressively, so that they can be generated as much as possible, without considering the limitation of the memory. With this method, we can find a proper size of point cloud. Then, we improve standard photon mapping with our progressive point-based global illumination. We progressively generate the point cloud storing indirect illumination computed by photon mapping and then render with point-based method. Our method costs less time than the standard photon mapping, it has higher quality and uses less memory than standard point-based global illumination.
Acidity, Complexing, Basicity and H‐Bonding of Organic Germanium, Tin and Lead Compounds: Experimental and Computational Results (1995)

This chapter contains sections titled: Abbreviations Outline Introduction H-bonding Introduction Reactions Germanium Alkyl- and Arylgermanes Germylamines and Germylimines Alkyl- and Arylhydridogermanium Metal Compounds Cyclic Compounds Tin Alkyl- and Arylstannanes Lead Complexing, Acidity and Basicity Introduction Complexing Complexing of Germanium, Tin and Lead in the Oxidation State +2 Complexing of Germanium, Tin and Lead in the Oxidation State +4 Germanium Tricoordinated Complexes Tetracoordinated Complexes Pentacoordinated Complexes Hexacoordinated Complexes Germanium Transition Metal Complexes Tin Tricoordinated Complexes Tetracoordinated Complexes Pentacoordinated Complexes Hexacoordinated Complexes Heptacoordinated Complexes Octacoordinated Complexes Lead Tetracoordinated Complexes Pentacoordinated Complexes Hexacoordinated Complexes Lead Transition Metal Complexes Relativistic Effects Computational Chemistry Introduction π-bonding in Group 14 The Heavier Congeners of Ethane: H3XYH3 (X,Y = C,Si,Ge,Sn,Pb) Cyclotrigermane and Cyclotristannane Acknowledgements References
[The applied research on neural network filtrated by rough-set in insect taxonomy]. (2006)

This article provides demonstrations and calculations, using rough-set theory and method, of the math-morphological features (MMFs), such as form parameter, lobation and sphericity, etc. drawn from 28 species of insects of the Hemiptera, Lepidoptera and Coleoptera based on their images. The results are compared with statistical analysis made by Zhao Hanqing, and also with the traditional classifications through the pattern recognition of neural network on the basis of the rough-set disposal. The result of the experiments showed that when used in categorical taxonomy, the importance of MMF was ranked from high to low: (roundness-likelihood. eccentricity) > (hot-hole number, sphericity, circularity) > (lobation, form parameter). The results of pattern recognition by neural network were completely identical with those of traditional classifications. Accordingly, the conclusion was that this theory applied in insect taxonomy was more idealistic compared with statistical analysis method, and it had great significance when used with rough-set neural network.
Quantization of Log-Likelihood Ratios to Maximize Mutual Information (2009)

We propose a quantization scheme for log-likelihood ratios which optimizes the trade-off between rate and accuracy in the sense of rate distortion theory: as distortion measure we use mutual information to determine quantization and decision levels maximizing mutual information for a given rate over a Gaussian channel. This approach is slightly superior to the previously proposed idea of applying the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Lloyd-Max</i> algorithm to the dasiasoft bitpsila density associated to the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</i> -values. A further data rate reduction can be achieved with <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">entropy</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">coding</i> , because the optimum quantization levels based on mutual information are used with pronounced unequal probabilities.
Recycling of a homogeneous catalyst using switchable water (2012)

Aqueous/organic biphasic catalysis allows easy separation of a homogeneous catalyst from product, but is often inefficient when hydrophobic substrates are used. A system based on switchable water is monophasic in the absence of CO2 and biphasic in its presence. Catalysis can be performed in the monophasic solvent, and then switched to a biphasic system, separating catalyst from product. Removal of CO2 allows for easy recycling of the catalyst. Hydroformylations have been achieved using this solvent system. The catalyst was recycled several times with minimal loss of activity.
A comparison of magnetite particles produced anaerobically by magnetotactic and dissimilatory iron‐reducing bacteria (1989)

We compare the magnetic properties of fine‐grained magnetite produced by two newly isolated anaerobic bacteria, a magnetotactic bacterium (MV‐1) and a dissimilatory iron‐reducing bacterium (GS‐15). Although room‐temperature magnetic properties are generally different between the two microorganisms, MV‐1 and GS‐15 magnetites can be most easily distinguished by the temperature variation of saturation remanence obtained at liquid helium temperatures. Magnetite produced by MV‐1 displays a sharp discontinuity in intensity at 100 K related to the Verwey transition. Magnetite produced by GS‐15 displays a gradual decrease in intensity with temperature due to the progressive unblocking of magnetization. The differing behavior is due exclusively to different grain size distributions produced by these microorganisms. MV‐1 produces magnetite with a narrow grain size distribution that is within the stable single domain size range at room temperature and below. GS‐15 produces magnetite with a wide grain size distribution extending into the superparamagnetic (SPM) size range. Our results show that a substantial fraction of particles produced by GS‐15 are SPM at room temperature.
The Effect of Inhaled Cannabis on Intraocular Pressure in Healthy Adult Subjects (2021)

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Inferring active cis-regulatory modules to predict functional regulatory elements (2019)

Abstract Transcription factors (TFs) often function as cis-regulatory modules (CRMs) including both master factors and mediator coactivators to activate enhancers or promoters and regulate target gene transcription. Cell type-specific ChIP-seq profiling of multiple TFs makes it feasible to infer functional CRMs for a particular cell type. Yet, approaches based on co-localization of TF ChIP-seq peaks to infer CRMs are applied but many weak binding events, especially of those mediators, are missed by peak callers, resulting in an incomplete identification of CRMs. We developed a ChIP -seq data-based CR M inference approach with G ibbs- S ampling (ChIP-GSM). In a Bayesian framework, ChIP-GSM samples read counts of TFs iteratively for the joint effect of each potential TF combination. Using inferred CRMs as novel features, ChIP-GSM employs a logistic regression model to predict active regulatory elements. Performance validation on FANTOM5 enhancer or promoter regions revealed the superior performance of CRMs on regulatory region activity prediction than TFs. Finally, integrating CRMs inferred for K562 cells and gene expression data we found that CRMs are likely to activate regulatory regions or genes at different time points to mediate distinct cellular functions. Author Summary Accurately inferring cis-regulatory modules (CRMs) from a large set of TFs is a challenging task because the binding signals of TFs are often weak, noisy and sensitive to the cellular environment. Nevertheless, investigating TF associations may help understand the difference between enhancer and promoter activation mechanisms. In this paper, we develop a computational method (ChIP-GSM) to infer CRMs acting on regulatory elements at enhancer and promote regions. The novel method is built upon a Bayesian framework with Gibbs sampling that can be used to infer CRMs reliably hence to predict regulatory elements. The performance of ChIP-GSM is compared to that of existing methods, demonstrating its improved performance. Experimental results demonstrate that CRMs identified by ChIP-GSM are likely activating regulatory regions at different time points to mediate distinct cellular functions.
Multi-photon microscopy with a low-cost and highly efficient Cr:LiCAF laser (2008)

Multi-photon microscopy (MPM) is a powerful tool for biomedical imaging, enabling molecular contrast and integrated structural and functional imaging on the cellular and subcellular level. However, the cost and complexity of femtosecond laser sources that are required in MPM are significant hurdles to widespread adoption of this important imaging modality. In this work, we describe femtosecond diode pumped Cr:LiCAF laser technology as a low cost alternative to femtosecond Ti:Sapphire lasers for MPM. Using single mode pump diodes which cost only $150 each, a diode pumped Cr:LiCAF laser generates approximately 70-fs duration, 1.8-nJ pulses at approximately 800 nm wavelengths, with a repetition rate of 100 MHz and average output power of 180 mW. Representative examples of MPM imaging in neuroscience, immunology, endocrinology and cancer research using Cr:LiCAF laser technology are presented. These studies demonstrate the potential of this laser source for use in a broad range of MPM applications.
Observation of the Effect of Wetting Efficiency on a Flow of Liquids Impinging on Solid Substrates by Fluorescence Depolarization (2003)

Steady-state fluorescence depolarization has proven, in the past few years, to be a method sensitive to adhesion of thin liquid films flowing without boundaries on solid substrates of different chemical constitutions. This work extends our prior preliminary assessment of the efficiency of the method and the influence of experimental variables. Ten thin films of ethylene glycol (MEG) were mapped over 102 mm2 by polarized laser-induced fluorescence (PLF−FI) while flowing on substrates. The interfacial tension, ΓSL, was varied either by changing the chemical constitution of the substrate (borosilicate, tin dioxide, poly(vinyl alcohol) (PVA), and linear alkylbenzene sulfonate (LAS)) or by addition of tensoactives to MEG (sodium dodecyl sulfate (SDS) and poly(ethylene oxide) (PEO)). Contact angle measurements were employed to classify interfaces according to their static ΓSL, that is, their wetting efficiencies. PLF−FI experimental variables, such as laser power, film thickness, and impinging velocity profile, did not alter the data within the range studied, except for flow rates over 220 cm s-1. Average polarization (Pav) increased from 10.5% to 13.5% upon decreasing adhesion by varying the chemical constitution of the solid. When surfactants were dissolved in the liquid flow, polarization ranged from 5.4% to 3.8% while for surfactant as substrate it increased. Simple multivariate principal component analysis (PCA) was applied to downstream polarization averages (Pdown) for each map. The two principal components accounted for 95.6% of the variance, ordering the maps according to decreasing adhesion and gathering them into three groups: dissolved surfactants, liquid films flowing at the highest flow rate, and solid surfaces of different chemical composition. Hierarchic cluster analysis (HCA) showed that, as adhesion decreased, similarity among the polarization maps increased.
Low-Power Crossbar Switch With Two-Varistor Selected Complementary Atom Switch (2V-1CAS; Via-Switch) for Nonvolatile FPGA (2019)

A nonvolatile and programmable routing switch featuring two-varistor selected complementary atom switch (2V-1CAS also known as via-switch) is evaluated. The a-Si/SiN/a-Si varistor as a selector for the atom switch shows superior nonlinear current-voltage characteristics with high selectivity of ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> , which originates from the staircase barrier height in the layers. The two control lines connected to the varistors realize multiple fan-outs of the crossbar switch without select transistors. The 50 × 20 crossbar switch block is demonstrated, where the atom switch is placed at each cross point and programmed through the varistors. The developed via-switch crossbar switch is a strong candidate for achieving energy-efficient nonvolatile field-programmable gate array in the Internet-of-Things applications.