gebhart/patrepeval huggingface dataset:
Supplemental Table 1 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Supplemental Table 1&lt;/p&gt;
Phenotypic Expression in Escherichia coli and Nucleotide Sequence of Two Chinese Hamster Lung Cell cDNAs Encoding Different Dihydrofolate Reductases (1984)

Nucleotide sequence analysis of two cDNA clones, one shown to direct the synthesis in Escherichia coli of the pI 6.7 form of the 20,000-molecular-weight class of Chinese hamster lung cell dihydrofolate reductase, and the other shown to direct the synthesis of the pI 6.5 form of the 21,000-molecular-weight class of the enzyme, has revealed the following: (i) the differences in physical and enzymatic properties displayed by these two proteins are due to two variations in their respective amino acid sequences with the conversion of Leu to Phe at position 22 probably responsible for the differential sensitivity of these two enzymes to methotrexate and methasquin; (ii) the multiple mRNAs responsible for the synthesis of each of these proteins differ in size due, at least in part, to a length heterogeneity at their 3' ends; (iii) these two proteins are encoded by different genes; and (iv) the sequence AAATATA appears to be a major polyadenylation signal in one Chinese hamster lung cell dihydrofolate reductase gene and a minor signal in another.
1.6 Gb/s/pin 4-PAM signaling and circuits for a multidrop bus (2001)

A 1.6 Gb/s/pin 4-pulse-amplitude-modulated (PAM) multidrop signaling system has been designed. The motivation for multi-PAM signaling is discussed. The system uses single-ended+reference current-mode signaling with three dc references for maximum bandwidth per pin. A test chip with six I/O pins was fabricated in 0.35-/spl mu/m CMOS and tested in a 28-/spl Omega/ evaluation system using on-chip 2/sup 10/ pseudorandom bit sequence (PRBS) generator/checkers. Two different 4-PAM transmitter structures were designed and measured. A high-gain windowed integrating input receiver with wide common-mode range was designed in order to improve signal-to-noise ratio when operating with smaller 4-PAM input levels. Gray coding allowed a folded preamplifier architecture to be used in the LSB input receiver to minimize area and power. In-system margins are measured via system voltage and timing shmoos with a master communicating with two slave devices.
Gray-level image recognition on a dynamically reconfigurable vision architecture (2012)

Recently, for use in autonomous vehicles and robots, demand has been increasing for high-speed image recognition that is superior to that of the human eye. However, to recognize numerous images quickly, such system requires many template images to be read out dynamically from memory. They must then be sent to a processor quickly. Realizing such high-speed real-time image recognition operation is difficflt because of the bottleneck of transfer speed between the memory and the processor. Therefore, to improve the bottleneck, a dynamically reconfigurable vision architecture that can recognize binarized images has been presented. However, to date, no dynamically reconfigurable vision architecture that can recognize gray-level images has ever been presented. Therefore, this paper presents experimentation related to a more advanced dynamically reconfigurable vision architecture that can recognize gray-level images.
Bit-interleaved polar-coded OFDM for low-latency M2M wireless communications (2017)

Machine-to-machine (M2M) communications play an important role for applications that involve connections between a massive number of heterogeneous devices in home and industrial networks. For M2M networks, realizing low latency and high reliability is of great importance. In this paper, we show the great potential of polar-coded orthogonal frequency-division multiplexing (OFDM) to fulfill those requirements. We show that polar codes with list decoding plus cyclic redundancy check (CRC) can outperform state-of-the-art low-density parity-check (LDPC) codes at short block lengths. In addition, we introduce an efficient interleaver and constellation shaping for polar-coded high-order modulations, where a coded sequence is carefully mapped across subcarriers and modulation bits to exploit non-uniform reliability for higher diversity gains. Through computer simulations, we demonstrate that a significant gain greater than 2 dB can be achieved by quadratic polynomial permutation (QPP) interleaver with optimized parameters in comparison to the conventional random interleaver for high-order 256-ary quadrature-amplitude modulation (QAM) OFDM transmission in frequency-selective wireless channels.
Genetic variation across the human olfactory receptor repertoire alters odor perception (2019)

Humans use a family of more than 400 olfactory receptors (ORs) to detect odors, but there is currently no model that can predict olfactory perception from receptor activity patterns. Genetic variation in human ORs is abundant and alters receptor function, allowing us to examine the relationship between receptor function and perception. We sequenced the OR repertoire in 332 individuals and examined how genetic variation affected 276 olfactory phenotypes, including the perceived intensity and pleasantness of 68 odorants at two concentrations, detection thresholds of three odorants, and general olfactory acuity. Genetic variation in a single OR was frequently associated with changes in odorant perception, and we validated 10 cases in which in vitro OR function correlated with in vivo odorant perception using a functional assay. In 8 of these 10 cases, reduced receptor function was associated with reduced intensity perception. In addition, we used participant genotypes to quantify genetic ancestry and found that, in combination with single OR genotype, age, and gender, we can explain between 10% and 20% of the perceptual variation in 15 olfactory phenotypes, highlighting the importance of single OR genotype, ancestry, and demographic factors in the variation of olfactory perception.
Digital Coherent W-band MIMO Radio-over-Fiber Systems (2015)

We present digital coherent W-band MIMO RoF system and its collected digital signal processing for optical and wireless signal. Its high resilience of dual optical wireless link will find immediate application to disaster recovery.
Active Tuning of the Microresonator Coupling Condition with Coupled Rings (2023)

We demonstrate a novel approach to actively and continuously tune the coupling condition of microresonators. Our approach allows for wavelength-dependent coupling and dispersion modification after fabrication.
Message Passing Stein Variational Gradient Descent. (2018)

Stein variational gradient descent (SVGD) is a recently proposed particle-based Bayesian inference method, which has attracted a lot of interest due to its remarkable approximation ability and particle efficiency compared to traditional variational inference and Markov Chain Monte Carlo methods. However, we observed that particles of SVGD tend to collapse to modes of the target distribution, and this particle degeneracy phenomenon becomes more severe with higher dimensions. Our theoretical analysis finds out that there exists a negative correlation between the dimensionality and the repulsive force of SVGD which should be blamed for this phenomenon. We propose Message Passing SVGD (MP-SVGD) to solve this problem. By leveraging the conditional independence structure of probabilistic graphical models (PGMs), MP-SVGD converts the original high-dimensional global inference problem into a set of local ones over the Markov blanket with lower dimensions. Experimental results show its advantages of preventing vanishing repulsive force in high-dimensional space over SVGD, and its particle efficiency and approximation flexibility over other inference methods on graphical models.
Towards Single-Channel Unsupervised Source Separation of Speech Mixtures: The Layered Harmonics/Formants Separation-Tracking Model (2004)

Speaker models for blind source separation are typically based on HMMs consisting of vast numbers of states to capture source spectral variation, and trained on large amounts of isolated speech. Since observations can be similar between sources, inference relies on sequential constraints from the state transition matrix which are, however, quite weak. To avoid these problems, we propose a strategy of capturing local deformations of the time-frequency energy distribution. Since consecutive spectral frames are highly correlated, each frame can be accurately described as a nonuniform deformation of its predecessor. A smooth pattern of deformations is indicative of a single speaker, and the cliffs in the deformation fields may indicate a speaker switch. Further, the log-spectrum of speech can be decomposed into two additive layers, separately describing the harmonics and formant structure. We model smooth deformations as hidden transformation variables in both layers, using MRFs with overlapping subwindows as observations, assumed to be a noisy sum of the two layers. Loopy belief propagation provides for efficient inference. Without any pre-trained speech or speaker models, this approach can be used to fill in missing time-frequency observations, and the local entropy of the deformation fields indicate source boundaries for separation.
Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. (1984)

DNAs that contain specific yeast chromosomal sequences called ARSs transform Saccharomyces cerevisiae at high frequency and can replicate extrachromosomally as plasmids when introduced into S. cerevisiae by transformation. To determine the boundaries of the minimal sequences required for autonomous replication in S. cerevisiae, we have carried out in vitro mutagenesis of the first chromosomal ARS described, ARS1. Rather than identifying a distinct and continuous segment that mediates the ARS+ phenotype, we find three different functional domains within ARS1. We define domain A as the 11-base-pair (bp) sequence that is also found at most other ARS regions. It is necessary but not sufficient for high-frequency transformation. Domain B, which cannot mediate high-frequency transformation, or replicate by itself, is required for efficient, stable replication of plasmids containing domain A. Domain B, as we define it, is continuous with domain A in ARS1, but insertions of 4 bp between the two do not affect replication. The extent of domain B has an upper limit of 109 bp and a lower limit of 46 bp in size. There is no obvious sequence homology between domain B of ARS1 and any other ARS sequence. Finally, domain C is defined on the basis of our deletions as at least 200 bp flanking domain A on the opposite side from domain B and is also required for the stability of domain A in S. cerevisiae. The effect of deletions of domain C can be observed only in the absence of domain B, at least by the assays used in the current study, and the significance of this finding is discussed.
Hydrodynamic characterization of vasoactive intestinal peptide receptors extracted from rat lung membranes in Triton X-100 and n-octyl-beta-D-glucopyranoside. (1987)

Rat lung membrane vasoactive intestinal peptide (VIP) receptors were covalently labeled with 125I-VIP, extracted in Triton X-100 and n-octyl-beta-D-glucopyranoside, and analyzed by gel filtration and sucrose density gradient sedimentation. The fractions were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography, and the identity of the 125I-VIP.receptor complex was demonstrated by its co-migration with the covalently labeled 55-kDa receptor unit identified previously. Furthermore, the radioactivity in the peak corresponding to the 125I-VIP.receptor complex was displaced in the presence of unlabeled VIP in a dose-dependent manner. The following hydrodynamic properties were determined for VIP receptors in each detergent solution: in Triton X-100, Stokes radius of 6.1 +/- 0.4 nm, sedimentation coefficient (S20,w) of 7.35 +/- 0.45 S, and partial specific volume (v) of 0.809 +/- 0.015 ml/g; in n-octyl-beta-D-glucopyranoside, Stokes radius of 5.6 +/- 0.00 nm, S20,w of 10.87 +/- 0.22 S, and partial specific volume of 0.783 +/- 0.020 ml/g. The apparent molecular weight of the 125I-VIP.receptor.detergent complex was calculated as 270,000 +/- 36,000 in Triton X-100 and 320,000 +/- 32,000 in n-octyl-beta-D-glucopyranoside. The amount of detergent bound to the receptor was estimated by using the two sets of hydrodynamic data and the significantly different partial specific volumes of the two detergents. Thus, the molecular weight of the receptor alone was calculated as 54,600 daltons, indicating that approximately 3.9 g of Triton X-100 and 4.9 g of n-octyl-beta-D-glucopyranoside were bound per g of receptor. This species contained the 55-kDa binding unit and appeared to be glycosylated as evidenced by its specific binding to wheat germ agglutinin-Sepharose. These results indicate that the rat lung VIP receptor is a glycoprotein with a single polypeptide chain of 55 kDa. The large amount of detergent bound suggests that the receptor is extensively embedded in the membrane.
CO2reverse selective mixed matrix membranes for H2purification by incorporation of carbon–silica fillers (2012)

By filling a PDMS top layer with porous carbon–silica microspheres, a defect-free mixed matrix membrane was created with notable CO2 reverse selective separation properties. For the separation of CO2 over H2 at room temperature and 10 bar inlet pressure, these membranes demonstrate high CO2 gas fluxes up to 3 × 10−7 mol cm−2 s−1, in combination with ideal separation factors in the range of 6 to 9. The present separation data signify an important step forward in the removal of CO2 from H2 using a reverse selective separation strategy. Moreover, they elucidate the potential of such mixed matrix membranes in the emerging field of CO2 separation.
HYDration and Bicarbonate to Prevent Acute Renal Injury After Endovascular Aneurysm Repair With Suprarenal Fixation: Pilot/Feasibility Randomised Controlled Study (HYDRA Pilot Trial) (2018)

Bolus high dose NaHCO<sub>3</sub> and hydration is a promising EVAR related AKI prevention method. This trial has confirmed the feasibility of delivering a definitive large RCT to confirm the efficacy of this novel intervention, in preventing EVAR related AKI.
Whole-genome sequencing of genotype VI Newcastle disease viruses from formalin-fixed paraffin-embedded tissues from wild pigeons reveals continuous evolution and previously unrecognized genetic diversity in the U.S. (2018)

This work reports the first successful evolutionary study using deep sequencing of complete NDV genomes from FFPE samples of wild bird origin. There are at least two distinct U.S. lineages of genotype VI NDV maintained in wild pigeons that are continuously evolving independently from each other and have no evident epidemiological connections to viruses circulating abroad. These findings support the hypothesis that columbids are serving as reservoirs of virulent NDV in the U.S.
Endothelial Insulin Receptors Promote VEGF-A Signaling via ERK1/2 and Sprouting Angiogenesis (2021)

Endothelial insulin receptors (Insr) promote sprouting angiogenesis, although the underpinning cellular and molecular mechanisms are unknown. Comparing mice with whole-body insulin receptor haploinsufficiency (Insr+/-) against littermate controls, we found impaired limb perfusion and muscle capillary density after inducing hind-limb ischemia; this was in spite of increased expression of the proangiogenic growth factor Vegfa. Insr+/- neonatal retinas exhibited reduced tip cell number and branching complexity during developmental angiogenesis, which was also found in separate studies of mice with endothelium-restricted Insr haploinsufficiency. Functional responses to vascular endothelial growth factor A (VEGF-A), including in vitro angiogenesis, were also impaired in aortic rings and pulmonary endothelial cells from Insr+/- mice. Human umbilical vein endothelial cells with shRNA-mediated knockdown of Insr also demonstrated impaired functional angiogenic responses to VEGF-A. VEGF-A signaling to Akt and endothelial nitric oxide synthase was intact, but downstream signaling to extracellular signal-reduced kinase 1/2 (ERK1/2) was impaired, as was VEGF receptor-2 (VEGFR-2) internalization, which is required specifically for signaling to ERK1/2. Hence, endothelial insulin receptors facilitate the functional response to VEGF-A during angiogenic sprouting and are required for appropriate signal transduction from VEGFR-2 to ERK1/2.
Conditions for minimum noise generation in backward-wave amplifiers (1958)

The noise figure of a backward-wave amplifier can be minimized by optimizing the standing-wave ratio and position of the standing wave of noise power on the beam in the precircuit region. These optimum conditions are presented as detailed functions of tube parameters for the common types of backward-wave amplifiers and are compared with the characteristics of conventional traveling-wave tubes. The problem of achieving maximum tuning range while maintaining a noise figure close to the theoretical minimum value is discussed and general design criteria and methods are evolved. Although the voltage-tuned characteristics of backward-wave amplitiers impose rigorous requirements on the noise space-charge-wave transducer, it is shown that wide low-noise tuning ranges are possible even with no programming of the noise reducing electrodes.
<title>Error diffusion using the web-safe colors: how good is it across platforms?</title> (1998)

Accurate color rendering across displays is complicated on the World Wide Web by the color-handling properties of individual web browsers. However, the major browsers have all adopted a minimal color palette of 216 RGB triples, called the `browser-safe' colors, suitable for use with web page backgrounds and text, logos, cartoons, and line drawings. For naturalistic or photographic images, however, simple quantization to 216 colors can produce images with altered hues or color banding. We show that dithering with the browser-safe colors is a good strategy for such images, especially at spatial resolutions above 150 dpi. However, even if the RGB image is transmitted and received unaltered, the system gamma will affect appearance. Ambient lighting contributes to the rendered image's appearance, but does not mask the effects of differences in monitor gammas. The need for an image-rendering convention traceable to the CIE is underscored by these results.
Molecular Characterization of the Microsomal Tamoxifen Binding Site (2004)

Tamoxifen is a selective estrogen receptor modulator widely used for the prophylactic treatment of breast cancer. In addition to the estrogen receptor (ER), tamoxifen binds with high affinity to the microsomal antiestrogen binding site (AEBS), which is involved in ER-independent effects of tamoxifen. In the present study, we investigate the modulation of the biosynthesis of cholesterol in tumor cell lines by AEBS ligands. As a consequence of the treatment with the antitumoral drugs tamoxifen or PBPE, a selective AEBS ligand, we show that tumor cells produced a significant concentration- and time-dependent accumulation of cholesterol precursors. Sterols have been purified by HPLC and gas chromatography, and their chemical structures determined by mass spectrometric analysis. The major metabolites identified were 5alpha-cholest-8-en-3beta-ol for tamoxifen treatment and 5alpha-cholest-8-en-3beta-ol and cholesta-5,7-dien-3beta-ol, for PBPE treatment, suggesting that these AEBS ligands affect at least two enzymatic steps: the 3beta-hydroxysterol-Delta8-Delta7-isomerase and the 3beta-hydroxysterol-Delta7-reductase. Steroidal antiestrogens such as ICI 182,780 and RU 58,668 did not affect these enzymatic steps, because they do not bind to the AEBS. Transient co-expression of human 3beta-hydroxysterol-Delta8-Delta7-isomerase and 3beta-hydroxysterol-Delta7-reductase and immunoprecipitation experiments showed that both enzymes were required to reconstitute the AEBS in mammalian cells. Altogether, these data provide strong evidence that the AEBS is a hetero-oligomeric complex including 3beta-hydroxysterol-Delta8-Delta7-isomerase and the 3beta-hydroxysterol-Delta7-reductase as subunits that are necessary and sufficient for tamoxifen binding in mammary cells. Furthermore, because selective AEBS ligands are antitumoral compounds, these data suggest a link between cholesterol metabolism at a post-lanosterol step and tumor growth control. These data afford both the identification of the AEBS and give new insight into a novel molecular mechanism of action for drugs of clinical value.
Laser action by optically depumping lower states (2023)

A method and apparatus for obtaining laser action between an upper energy level and a lower energy level of a gaseous medium, which comprises populating the upper energy level to some degree (short of achieving a conventional inverted population) by any suitable pumping means, and thereafter establishing an inverted population by transiently and selectively depumping the lower energy level such as by exposing the medium to an intense source of radiation which selectively causes the transformation of the lower energy level species to some other energy level. Thus, a thermally pumped/optically depumped gas laser system is produced.
Different expression of Lyt differentiation antigens and cell surface glycoproteins by a murine T lymphoma line and its highly metastatic variant (1982)

Cloned lines of the methylcholanthrene-induced DBA/2 T lymphoma Eb and its highly metastatic variant line ESb were analyzed for differences in the expression of serologically detectable cell surface differentiation markers. Flow cytofluorographic analysis of cells stained with fluorescein isothiocyanate-conjugated monoclonal rate anti-mouse Thy-1, Lyt-1, Lyt-2 and complement-dependent cytotoxicity with mouse alloantisera against Lyt-3.2 and Ly-6.2 revealed, for the parental low metastasizing line, Eb, a phenotype of Thy-1+, Lyt-1-, Lyt-2+, Lyt-3+, Ly-6+, whereas the highly metastasizing variant line typed as Thy-1-, Lyt-1+, Lyt-2-, Lyt-3-, Ly-6-. Analysis of galactose oxidase/NaB3H4-labeled glycoproteins from Eb and ESb clones by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate showed further phenotypic differences. Selective binding of radiolabeled glycoproteins to Helix pomatia or Vicia villosa-Sepharose, respectively, allowed the identification of T130 to be expressed on Eb cells and T145 to be expressed on some ESb clones. The latter antigen is expressed on murine cytotoxic T lymphocytes. Immune precipitation analysis revealed that Eb and ESb bear different molecular forms of the T200 antigen. Comparisons of iodinated surface proteins derived from tumor cells either treated or untreated with tunicamycin indicated that many of the differences in membrane proteins between Eb and ESb cells could be attributed to differences in glycosylation. Our results, derived from a defined tumor system of lymphoid origin, show that the progression from a low to a high malignant tumor line can be associated with changes in the expression of various defined cell surface differentiation antigens. The question of a possible relationship between tumor progression and cell differentiation or dedifferentiation is discussed.