gebhart/patrepeval huggingface dataset:
The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status (2017)

Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. <i>Caenorhabditis elegans</i> XX animals are hermaphrodites that exhaust their sperm after 3 d of egg-laying. Even though <i>C. elegans</i> can live for many days after cessation of egg-laying, the molecular physiology of this state has not been as intensely studied as other parts of the life cycle, despite documented changes in behavior and metabolism. To study the effects of sperm depletion and aging of <i>C. elegans</i> during the first 6 d of adulthood, we measured the transcriptomes of first-day adult hermaphrodites and sixth-day sperm-depleted adults, and, at the same time points, mutant <i>fog-2(lf)</i> worms that have a feminized germline phenotype. We found that we could separate the effects of biological aging from sperm depletion. For a large subset of genes, young adult <i>fog-2(lf)</i> animals had the same gene expression changes as sperm-depleted sixth-day wild-type hermaphrodites, and these genes did not change expression when <i>fog-2(lf)</i> females reached the sixth day of adulthood. Taken together, this indicates that changing sperm status causes a change in the internal state of the worm, which we call the female-like state. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.
Solar-powered electrochemical energy storage: an alternative to solar fuels (2015)

The solar-powered electrochemical energy storage strategy integrates the solar energy conversion, storage and distribution functions into a single device.
Touching Art -- A Method for Visualizing Tactile Experience (2021)

It is human to want to touch artworks, to feel their surface curvature and texture, their shapes and structures, and to feel the hand of the artist. Museum guards need to be constantly vigilant to protect art objects from adoring and exploring touches by visitors. This paper introduces a novel technique for capturing where and how art objects are touched. In this method, the users' touch either adds, or subtracts, microscopic fluorescent particles from a three-dimensional art object. Viewing the object under ultraviolet light reveals their touch traces and gestures. We present human touch behavior for a three-dimensional stylized landscape, and for two abstract and two representational art objects. We also present the results of video recordings of real-time behavior and user interviews. The resulting data show the kinds of touches, and where they are directed, and also reveal important individual differences. We feel this method opens the door to studying art perception through touch, and also enables new kinds of studies into touch behavior in other applications, including visualization, embodied cognition, and design.
Asian Ethnic Group Classification Model Using Data Mining (2017)

In addition to identifying genetic differences between target populations, it is also important to determine the impact of genetic differences with regard to the respective target populations. In recent years, there has been an increasing number of cases where this approach is needed, and thus various statistical methods must be considered. In this study, genetic data from populations of Southeast and Southwest Asia were collected, and several statistical approaches were evaluated on the Y-chromosome short tandem repeat data. In order to develop a more accurate and practical classification model, we applied gradient boosting and ensemble techniques. To infer between the Southeast and Southwest Asian populations, the overall performance of the classification models was better than that of the decision trees and regression models used in the past. In conclusion, this study suggests that additional statistical approaches, such as data mining techniques, could provide more useful interpretations for forensic analyses. These trials are expected to be the basis for further studies extending from target regions to the entire continent of Asia as well as the use of additional genes such as mitochondrial genes.
Speech recognition in scale space (2005)

Scale-space filtering, proposed by Witkin (ICASSP 84) for describing natural structure in one-dimensional signals, has been extended for application to segmentation and description of vector-valued functions of time, such as speech spectrograms. By analyzing the rate of change of a vector trajectory at many different scales of time-smoothing, a tree of natural segments can be constructed. At various levels in the tree (i.e., at various scales), these segments are found to agree well with the kind of linguistically and perceptually important segments that spectrogram readers use to describe sound patterns of speech. Scale-space segmentations of cochleagrams (spectrograms based on a computational model of the peripheral auditory system) have been experimentally applied to word recognition. Recognition using fixed-scale segmentations with finite-state word models and a Viterbi search has led to speaker-independent digit recognition accuracies of greater than 97%, about the same as in tests with non-segmented cochleagrams. More complex recognition algorithms that use the segmentation tree are being developed, and scale-space experiments with connected digits and sentences are also underway.
<title>Novel coding technique for the implementation of an electro-optic analog-to-digital converter</title> (1993)

We report a new coding technique for the implementation of an electro-optic analog-to-digital (A/D) converter. This coding and A/D conversion can be implemented with an array of tunable, high finesse, channel waveguide Fabry-Perot etalons. Preconfigured dc biases have been shown, on a proton exchanged device on x-cut LiNbO<SUB>3</SUB>, to shift the quantized etalon transmission peaks with respect to the applied rf signal voltage necessary for converting analog voltages to digital optical transmissions. Some design considerations for the implementation of the device are discussed.
WE‐D‐L100F‐02: Parallel Magnetic Resonance Imaging (or, Scanners, Cell Phones, and the Surprising Guises of Modern Tomography) (2007)

Today, parallel data acquisition approaches are used widely in MRI, both for clinical diagnostic imaging and for research applications. Whereas in a traditional sequential MRI scan, data are collected one point and one line at a time in the presence of varying magnetic field gradients, parallel MRI uses spatial information from arrays of radiofrequency detector coils to acquire multiple data points simultaneously, thereby circumventing basic limits on imaging speed and efficiency associated with traditional sequential approaches. The use of RF coil information in combination with the traditional Fourier information available from field gradients increases the complexity of image reconstruction. In fact, parallel MR image reconstruction may be represented as a generalized linear inverse problem. This formulation highlights connections with other modalities as well as shedding light on both the potential and the limitations of parallel imaging. In this talk, the fundamentals of parallel MR image acquisition and reconstruction will be reviewed. Analogies with X‐ray computed tomography, MIMO wireless communication, and magnetoencephalography will be explored, and some future directions in parallel MR reconstruction algorithms, hardware design, and clinical applications will be surveyed. Educational Objectives: 1. Understand the basic physical principles of parallel MR data acquisition and the basic mathematical principles of parallel MR image reconstruction. 2. Recognize analogies with other imaging modalities and communication technologies. 3. Identify fundamental physical (electrodynamic) limits of performance of parallel MRI systems. 4. Appreciate some of the most common current and the most promising future clinical applications of parallel MRI.
Phylogenetic analysis of Pacific salmon (genus Oncorhynchus) using nuclear and mitochondrial DNA sequences (1997)

Recent phylogenetic analyses of Pacific salmon of genus Oncorhynchus based on sequences from mitochondrial DNA and one nuclear growth hormone intron supported two subgroups:one with chinook (O. tshawytscha) and coho (O. kisutch) salmon and the other with pink (O. gorbuscha), sockeye (O. nerka), and chum (O. keta) salmon. In the latter group, a sister relationship was indicated between pink and chum salmon. Previous studies based on morphological and allozyme data had suggested a closer relationship between pink and sockeye salmon. In this paper we present a combined analysis of 4365 base pairs aligned sequence from nuclear and mitochondrial genes including new sequence data from the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal DNA, the sequences of three growth hormone introns (GH1C, GH2C, GH2D) and the sequences of the ATPase6 and ND3 genes of the mtDNA. Phylogenetic analysis of the combined data set gives strong support to a close relationship between pink and chum salmon and between coho and chinook salmon.
New Low power Digital Sub-band Predistorter for OFDM Signals (2019)

The adaptive digital predistorter (DPD) offers an effective technique for compensating for nonlinear distortion and improving the efficiency of high power amplifiers (HPAs). However, in small cell environments, the power consumed by the DPD is no longer negligible and significantly affects the overall efficiency of the DPD+HPA cascade. In this paper, we present new architecture for the baseband DPD that has very low power consumption. The proposed DPD comprises a cascade sub-band filters block and a memoryless adaptive predistorter. The sub-band filtering technique is used to compensate for the orthogonal frequency-division multiplexing (OFDM) signal in-band distortions caused by the HPA memory effect, and the memoryless predistorter compensates for both the in-band and out-of-band transmitting (Tx) signal distortions. The sampling rate of the sub-band filters is only 1/(N · L) of the sampling rate of the Tx OFDM signal (N is IFFT size, L is the Tx signal oversampling ratio). Therefore, the power consumption of the proposed subband DPD is significantly less than that of the typical memory-polynomial (M-P) DPD operating at a rate of N · L. The simulation result for a 20-MHz LTE system shows that the power consumed by the proposed sub-band DPD is reduced by a factor of five compared to that consumed by the M-P DPD and provides similar linearization quality.
Data Supplement from GPER-Targeted, <sup>99m</sup>Tc-Labeled, Nonsteroidal Ligands Demonstrate Selective Tumor Imaging and <i>In Vivo</i> Estrogen Binding (2023)

&lt;p&gt;Figure S1: HPLC radiochromatograms of labeled compounds 5,6 and 8. Figure S2. HPLC radiochromatograms of urine and plasma from mouse injected with labeled compound 5. Table S1. Time-dependent biodistribution of labeled compound 5.&lt;/p&gt;
Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome (2013)

Actinomycetes, filamentous actinobacteria from the soil, are the deepest natural source of useful medicinal compounds, including antibiotics, antifungals, and anticancer agents. There is great interest in developing new strategies that increase the diversity of metabolites secreted by actinomycetes in the laboratory. Here we used several metabolomic approaches to examine the chemicals made by these bacteria when grown in pairwise coculture. We found that these interspecies interactions stimulated production of numerous chemical compounds that were not made when they grew alone. Among these compounds were at least 12 different versions of a molecule called desferrioxamine, a siderophore used by the bacteria to gather iron. Many other compounds of unknown identity were also observed, and the pattern of compound production varied greatly among the interaction sets. These findings suggest that chemical interactions between actinomycetes are surprisingly complex and that coculture may be a promising strategy for finding new molecules from actinomycetes.
Im2depth: Scalable exemplar based depth transfer (2014)

The rapid increase in number of high quality mobile cameras have opened up an array of new problems in mobile vision. Mobile cameras are predominantly monocular and are devoid of any sense of depth, making them heavily reliant on 2D image processing. Understanding 3D structure of scenes being imaged can greatly improve the performance of existing vision/graphics techniques. In this regard, recent availability of large scale RGB-D datasets beg for more effective data driven strategies to leverage the scale of data. We propose a depth recovery mechanism “im2depth”, that is lightweight enough to run on mobile platforms, while leveraging the large scale nature of modern RGB-D datasets. Our key observation is to form a basis (dictionary) over the RGB and depth spaces, and represent depth maps by a sparse linear combination of weights over dictionary elements. Subsequently, a prediction function is estimated between weight vectors in RGB to depth space to recover depth maps from query images. A final superpixel post processor aligns depth maps with occlusion boundaries, creating physically plausible results. We conclude with thorough experimentation with four state of the art depth recovery algorithms, and observe an improvement of over 6.5 percent in shape recovery, and over 10cm reduction in average L1 error.
Supplementary Table S2 from E7090, a Novel Selective Inhibitor of Fibroblast Growth Factor Receptors, Displays Potent Antitumor Activity and Prolongs Survival in Preclinical Models (2023)

&lt;p&gt;IC&lt;sub&gt;50&lt;/sub&gt; values for growth inhibition of various cancer cell lines by E7090.&lt;/p&gt;
Assimilation of excess ammonium into amino acids and nitrogen translocation in Arabidopsis thaliana– roles of glutamate synthases and carbamoylphosphate synthetase in leaves (2009)

This study was aimed at investigating the physiological role of ferredoxin-glutamate synthases (EC 1.4.1.7), NADH-glutamate synthase (EC 1.4.1.14) and carbamoylphosphate synthetase (EC 6.3.5.5) in Arabidopsis. Phenotypic analysis revealed a high level of photorespiratory ammonium, glutamine/glutamate and asparagine/aspartate in the GLU1 mutant lacking the major ferredoxin-glutamate synthase, indicating that excess photorespiratory ammonium was detoxified into amino acids for transport out of the veins. Consistent with these results, promoter analysis and in situ hybridization demonstrated that GLU1 and GLU2 were expressed in the mesophyll and phloem companion cell-sieve element complex. However, these phenotypic changes were not detected in the GLU2 mutant defective in the second ferredoxin-glutamate synthase gene. The impairment in primary ammonium assimilation in the GLT mutant under nonphotorespiratory high-CO(2) conditions underlined the importance of NADH-glutamate synthase for amino acid trafficking, given that this gene only accounted for 3% of total glutamate synthase activity. The excess ammonium from either endogenous photorespiration or the exogenous medium was shifted to arginine. The promoter analysis and slight effects on overall arginine synthesis in the T-DNA insertion mutant in the single carbamoylphosphate synthetase large subunit gene indicated that carbamoylphosphate synthetase located in the chloroplasts was not limiting for ammonium assimilation into arginine. The data provided evidence that ferredoxin-glutamate synthases, NADH-glutamate synthase and carbamoylphosphate synthetase play specific physiological roles in ammonium assimilation in the mesophyll and phloem for the synthesis and transport of glutamine, glutamate, arginine, and derived amino acids.
Relations Entre les Potentiels de Demi‐Vague et la Constitution Chimique de Composes Azoiques Determination de la Structure Chimique de Deux Colorants (1957)

Abstract Through polarographic measurements the authors prove the correct chemical structure of two dyestuffs, obtained by chromogenic development with colourcouplers of the indazolontype, and for which a mesoionic structure as well as an orthosubstituted azostructure was considered possible.
FAST IMAGE MATCHING BASED ON FOURIER-MELLIN PHASE CORRELATION FOR TAG-LESS IDENTIFICATION OF MASS-PRODUCED PARTS (2018)

This paper proposes a fast technique for matching a query image to numerous database images under geometric variations in rotation, scale, and translation. Our proposed method extracts the Fourier-Mellin phase features from the images for invariant matching. The online matching process in our method is fast because it directly determines identification based on the correlation value between those features without the geometric alignment. Our method also proposes selecting only the low frequency bands of those features to be matched for improving identification accuracies, as the high frequency bands tend to be inaccurate in Fourier-Mellin transform. The benefits of our method were verified in our experiments to match the "fingerprint" images of 1,210 metal shafts. The processing time of the 1-vs.-1,210 matching was only 0.136 seconds on a standard desktop computer, and all individuals were identified with no errors.
Protein kinases in human leukemic cells (1985)

Protein kinase activities and cyclic AMP binding capacity were investigated in human peripheral blood cells from leukemic patients and normal controls. Using [gamma 32P] ATP as phosphoryldonor, the phosphorylating activities were not found to be significantly different in either normal or leukemic cells when measured on both artificial basic and acidic substrates. In contrast, the GTP-dependent casein kinase activity, CK2, which is almost undetectable in normal granulocytes, was markedly increased in highly proliferating myeloblastic cells from patients with acute myelogenous leukemia (AML) or with chronic myelogenous leukemia in blastic crisis (BC-CML). Levels of endogenous phosphotyrosine were not higher in leukemic cells than in normal peripheral lymphocytes or granulocytes. Finally, cAMP binding capacity was found to be increased in several types of proliferating leukemic cells, due to a higher amount of the R1-type regulatory subunit of the cAMP-dependent protein kinases. Specific patterns of cAMP binding proteins observed in the different types of normal blood cells were rather blurred in leukemic cells. In conclusion, modifications observed in human leukemic cells seem to be more related to proliferation or blockage in normal differentiation than to their cellular origin.
Expression of the T Cell Gamma Gene by a Functionally Defined Human T Cell Clone Characterization at DNA, RNA, and Cell Membrane Level (1988)

In the present study we describe one CD2+CD3+ clone termed DS6 which expressed neither CD4 nor CD8 differentiation antigens and failed to react with WT31, a monoclonal antibody directed against the T cell antigen receptor alpha/beta heterodimer. This clone was isolated from peripheral blood T lymphocytes of a patient with a prolonged immunodeficiency after allogeneic bone marrow transplantation. Normal-sized T cell gamma gene transcripts were detected in DS6 by northern analysis, whereas no mature beta or alpha chain mRNA were found. The rearrangement of TCR beta chain genes and T cell gamma genes was analysed. While in DS6, TCR beta chain genes remain in germinal configuration, and a unique pattern of monoallelic T cell gamma gene rearrangement was observed. The rearrangement involves the recently described V gamma 5 segment and the J gamma 1 joining segment, which is located upstream of the C gamma 1 constant region. To determine the molecular structure present on DS6, an immunoprecipitation was performed with monoclonal anti-CD3 antibody and a rabbit antiserum raised against gamma protein. We have observed, in association with the CD3 complex, a 90 kDa structure which under reducing conditions resolves into three subunits of 45, 40 and 37 kDa. We demonstrated that the rabbit anti-gamma serum only immunoprecipitates the two lower bands. The upper band corresponds to a presently undefined T cell receptor chain. Next, we showed the non major histocompatibility complex (MHC)-restricted cytolytic activity exhibited by these CD3+CD4-CD8- cloned T cells and inhibition of the natural killer (NK)-like activity by the anti-CD3 monoclonal antibody. The triggering of CD2 or CD3 molecules increased IL-2 receptor expression on DS6 but failed to induce cell proliferation. This contrasts with recent results obtained with gamma-expressing T cell clones and illustrates the functional heterogeneity of the cells bearing the second T cell receptor.
Infrared properties and mechanism of Al-doped ZnO thin films (2005)

Al-doped zinc oxide (ZAO) thin films were prepared by middle-frequency alternative magnetron sputtering with ZAO (ZnO+2%Al2O3) ceramic target. IR (infrared reflection) spectrom-etry was used to examine infrared reflection properties. The influences of film thickness, substrate temperature and argon gas pressure on the performances of ZAO thin films were investigated. The technical parameters for depositing ZAO films with high infrared reflection were determined.
A single‐nucleotide polymorphism in the TP53 and MDM‐2 gene modifies breast cancer risk in an ethnic Arab population (2011)

Breast cancer is the most common oncological disease in women worldwide. Genetic predisposition to breast cancer can be associated with single-nucleotide polymorphisms (SNPs), which are observed in many women. Such gene polymorphisms, in combination with nutritional and environmental factors, can affect breast cancer development. The tumor suppressor TP53 and its negative regulator MDM2 play crucial roles in carcinogenesis. Previous case-control studies have revealed that TP53 72Arg > Pro and MDM2 309T > G polymorphisms contribute to the risk of common cancers. However, the relationship between these two functional polymorphisms and breast cancer susceptibility in the Saudi population has not been explored. In this study, we performed a case-control study of patients with breast cancer and healthy controls in a Saudi population using TaqMan-based real-time PCR. We found an increased breast cancer risk associated with the MDM2 GG [odds ratio (OR) = 2.79, 95% confidence interval (CI) = 2.04-3.92] and TG [OR = 1.43, 95% CI = 1.12-2.02] genotypes. An increased risk was also associated with the TP53 Pro/Pro genotype (OR = 2.19, 95% CI = 1.54-3.06) compared with the Arg/Arg genotype. The gene-gene interaction of MDM2 and TP53 polymorphisms increased breast cancer risk in a multiplicative manner (OR for the presence of both MDM2 GG and TP53 Pro/Pro genotypes = 7.71, 95% CI = 3.49-17.54). These findings suggest that polymorphisms of MDM2 and TP53 genes may be a genetic modifier for developing breast cancer in this ethnic population in the Arab world.