gebhart/patrepeval huggingface dataset:
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists (2010)

High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser.
An Integrated Microfluidic Chip System for Single-Cell Secretion Profiling of Rare Circulating Tumor Cells (2014)

Genetic and transcriptional profiling, as well as surface marker identification of single circulating tumor cells (CTCs) have been demonstrated. However, quantitatively profiling of functional proteins at single CTC resolution has not yet been achieved, owing to the limited purity of the isolated CTC populations and a lack of single-cell proteomic approaches to handle and analyze rare CTCs. Here, we develop an integrated microfluidic system specifically designed for streamlining isolation, purification and single-cell secretomic profiling of CTCs from whole blood. Key to this platform is the use of photocleavable ssDNA-encoded antibody conjugates to enable a highly purified CTC population with <75 'contaminated' blood cells. An enhanced poly-L-lysine barcode pattern is created on the single-cell barcode chip for efficient capture rare CTC cells in microchambers for subsequent secreted protein profiling. This system was extensively evaluated and optimized with EpCAM-positive HCT116 cells seeded into whole blood. Patient blood samples were employed to assess the utility of the system for isolation, purification and single-cell secretion profiling of CTCs. The CTCs present in patient blood samples exhibit highly heterogeneous secretion profile of IL-8 and VEGF. The numbers of secreting CTCs are found not in accordance with CTC enumeration based on immunostaining in the parallel experiments.
Neutrophils and COVID-19: Nots, NETs, and knots (2020)

The pace of the COVID-19 pandemic makes it timely to take stock of evidence for the involvement of neutrophils and NETs, to weigh the implications, and to increase efficiency in clinical trials.
On-Orbit Servicing Missions: Challenges and Solutions for Spacecraft Operations (2010)

The DLR German Space Operations Center (GSOC) is currently involved in
the preparation of two On-Orbit Servicing missions, DEOS and OLEV. Due to the many
new challenges within those missions the ground segment design requires new concepts.
Accordingly, the paper presents the challenges and solutions regarding the communication
architecture including teleoperation and extended contact time. Additionally, we discuss a
method of vision based navigation which bridges the gap between absolute and purely
geometric navigation. Finally, an integrated system test including GSOC’s new EPOS facility is described.
Histogenesis of the nuclei griseum pontis, corporis pontobulbaris and reticularis tegmenti pontis (Bechterew) in the mouse an autoradiographic study (1966)

Abstract By means of autoradiography the time, site of origin and migration pathways of neuroblasts destined for three nuclei in the hindbrain of the mouse have been determined. The cells of the nuclei griseum pontis and corporis pontobulbaris arise on gestation days 12 through 16 in the rhombic lip from the obex to the lateral recess. Most cells migrate within 48 hours via the pontobulbar body to the base of the pons to form the nucleus griseum pontis; some migrate only a short distance along the pathway and collectively form the nucleus corporis pontobulbaris. Most cells of the nucleus reticularis tegmenti pontis (Bechterew) arise in the primitive basal ependymal plate of the pons on gestation days 12 and 13 and migrate ventrally into the tegmentum. Some probably arise at the rhombic lip and migrate via the pontobulbar body to the base of the pontine flexure where they turn dorsally into the tegmentum.
BRS-3: a novel bombesin receptor subtype selectively expressed in testis and lung carcinoma cells. (1993)

The bombesin (BN)-like peptides mediate a diverse spectrum of biological activities and have been implicated as autocrine growth factors in the pathogenesis and progression of some human small cell lung carcinoma tumors. Previously, two mammalian BN-like peptide receptor subtypes, gastrin-releasing peptide receptor and neuromedin-B receptor, have been cloned and characterized. In this study, we have isolated and characterized human genomic and complementary DNA (cDNA) clones encoding a new BN-like peptide receptor subtype, BN receptor subtype 3 (BRS-3). Expression of BRS-3 cDNA in Xenopus oocytes encodes a functional receptor that is specifically activated by BN-like peptides. Chromosome mapping studies indicate that the BRS-3 gene is located on human chromosome X. BRS-3 mRNA expression in rat tissues is limited to secondary spermatocytes in testis. In contrast, BRS-3 mRNA is widely expressed in a panel of human cell lines from all histological types of lung carcinoma. These results suggest a role for BN-like peptides and their receptors in mammalian reproductive physiology and also indicate that BRS-3 could serve as a potential therapeutic target for human lung carcinoma.
Pyramid Embedded Generative Adversarial Network for Automated Font Generation (2018)

In this paper, we investigate the Chinese font synthesis problem and propose a Pyramid Embedded Generative Adversarial Network (PEGAN) to automatically generate Chinese character images. The PEGAN consists of one generator and one discriminator. The generator is built using one encoder-decoder structure with cascaded refinement connections and mirror skip connections. The cascaded refinement connections embed a multiscale pyramid of downsampled original input into the encoder feature maps of different layers, and multi-scale feature maps from the encoder are connected to the corresponding feature maps in the decoder to make the mirror skip connections. Through combining the generative adversarial loss, pixel-wise loss, category loss and perceptual loss, the generator and discriminator can be trained alternately to synthesize character images. In order to verify the effectiveness of our proposed PEGAN, we first build one evaluation set, in which the characters are selected according to their stroke number and frequency of use, and then use both qualitative and quantitative metrics to measure the performance of our model comparing with the baseline method. The experimental results demonstrate the effectiveness of our proposed model, it shows the potential to automatically extend small font banks into complete ones.
BPF‐1, a pathogen‐induced DNA‐binding protein involved in the plant defense response (1993)

The mechanisms by which plants restrict the growth of pathogens include transient activation of numerous defense-related genes. Box P is a putative cis-acting element of a distinct group of such genes, including those encoding the enzyme phenylalanine ammonialyase (PAL). A DNA-binding activity to Box P was identified in nuclear extracts from cultured parsley cells and a cDNA encoding the protein BPF-1 (Box P-binding Factor) partially characterized. BPF-1 binds to this element with specificity similar to that of the binding activity in nuclear extracts. BPF-1 mRNA accumulates rapidly in elicitor-treated parsley cells and around fungal infection sites on parsley leaves. This accumulation is, at least partly, due to a rapid and transient increase in the transcription rate of BPF-1. Moreover, tight correlation between the relative amounts of BPF-1 and PAL mRNAs was observed in different organs of a parsley plant. These results are consistent with the hypothesis that BPF-1 is involved in disease resistance by modulating plant defense gene expression.
Comparison of surfactants for dynamic surface modification of poly(dimethylsiloxane) microchips (2005)

In the present report, the use of negatively charged surfactants as modifiers of the background electrolyte is reported using poly(dimethylsiloxane) (PDMS) microchips. In particular, the use of anionic surfactants, such as sodium dodecyl sulfate, phosphatidic acid, and deoxycholate, was studied. When surfactants were present in the run buffer, an increase in the electroosmotic flow (EOF) was observed. Two additional effects were also observed: (i) stabilization of the run-to-run EOF, (ii) an improvement in the electrochemical response for several biomolecules. In order to characterize the analysis conditions, the effects of different surfactant, electrolyte, and pH were studied. EOF measurements were performed using either the current monitoring method or by detection of a neutral molecule. The first adsorption/desorption kinetics studies are also reported for different surfactants onto PDMS. The separation of biologically important analytes (glucose, penicillin, phenol, and homovanillic acid) was improved decreasing the analysis time from 200 to 125 s. However, no significant changes in the number of theoretical plates were observed.
Clomipramine and Sexual Function in Men with Premature Ejaculation and Controls (1996)

Clomipramine (25 mg. as needed) effectively increases ejaculatory latency in men with primary premature ejaculation, while treatment is not effective in those with premature ejaculation and erectile dysfunction.
Unsupervised clustering of multivariate circular data (2012)

In this paper, we study an unsupervised clustering problem. The originality of this problem lies in the data, which consist of the positions of five separate X-ray beams on a circle. Radiation therapists positioned the five X-ray beam 'projectors' around each patient on a predefined circle. However, similarities exist in positioning for certain groups of patients, and we aim to describe these similarities with the goal of creating pre-adjustment settings that could help save time during X-ray positioning. We therefore performed unsupervised clustering of observed X-ray positions. Because the data for each patient consist of five angle measurements, Euclidean distances are not appropriated. Furthermore, we cannot perform k-means algorithm, usually used for minimizing corresponding distortion because we cannot calculate centers of clusters. We present here solutions to these problems. First, we define a suitable distance on the circle. Then, we adapt an algorithm based on simulated annealing to minimize distortion. This algorithm is shown to be theoretically convergent. Finally, we present simulations on simulated and real data.
Full-field birefringence imaging by thermal-light polarization-sensitive optical coherence tomography II Instrument and results (2003)

We describe an instrument for measuring the magnitude of birefringence of tomographic images and the principal directions of axes that use thermal-light polarization-sensitive optical coherence tomography. The instrument permits full-field measurements with an axial resolution of 1.5 microm and a transverse resolution limited by diffraction. We obtained a sensitivity of 84 dB, limited by shot noise, when we integrated the signal for 1 s. We verified the validity of the measurement by measuring the birefringence of a variable phase shifter. We present typical results obtained with optical samples.
Intrinsic Human Immunodeficiency Virus Type 1 Resistance of Hematopoietic Stem Cells Despite Coreceptor Expression (1999)

ABSTRACT Interactions of human immunodeficiency virus type 1 (HIV-1) with hematopoietic stem cells may define restrictions on immune reconstitution following effective antiretroviral therapy and affect stem cell gene therapy strategies for AIDS. In the present study, we demonstrated mRNA and cell surface expression of HIV-1 receptors CD4 and the chemokine receptors CCR-5 and CXCR-4 in fractionated cells representing multiple stages of hematopoietic development. Chemokine receptor function was documented in subsets of cells by calcium flux in response to a cognate ligand. Productive infection by HIV-1 via these receptors was observed with the notable exception of stem cells, in which case the presence of CD4, CXCR-4, and CCR-5, as documented by single-cell analysis for expression and function, was insufficient for infection. Neither productive infection, transgene expression, nor virus entry was detectable following exposure of stem cells to either wild-type HIV-1 or lentivirus constructs pseudotyped in HIV-1 envelopes of macrophage-tropic, T-cell-tropic, or dualtropic specificity. Successful entry into stem cells of a vesicular stomatitis virus G protein-pseudotyped HIV-1 construct demonstrated that the resistance to HIV-1 was mediated at the level of virus-cell membrane fusion and entry. These data define the hematopoietic stem cell as a sanctuary cell which is resistant to HIV-1 infection by a mechanism independent of receptor and coreceptor expression that suggests a novel means of cellular protection from HIV-1.
8T SRAM Cell as a Multibit Dot-Product Engine for Beyond Von Neumann Computing (2019)

Large-scale digital computing almost exclusively relies on the von Neumann architecture, which comprises separate units for storage and computations. The energy-expensive transfer of data from the memory units to the computing cores results in the well-known von Neumann bottleneck. Various approaches aimed toward bypassing the von Neumann bottleneck are being extensively explored in the literature. These include in-memory computing based on CMOS and beyond CMOS technologies, wherein by making modifications to the memory array, vector computations can be carried out as close to the memory units as possible. Interestingly, in-memory techniques based on CMOS technology are of special importance due to the ubiquitous presence of field-effect transistors and the resultant ease of large-scale manufacturing and commercialization. On the other hand, perhaps the most important computation required for applications such as machine learning, etc., comprises the dot-product operation. Emerging nonvolatile memristive technologies have been shown to be very efficient in computing analog dot products in an in situ fashion. The memristive analog computation of the dot product results in much faster operation as opposed to digital vector in-memory bitwise Boolean computations. However, challenges with respect to large-scale manufacturing coupled with the limited endurance of memristors have hindered rapid commercialization of memristive-based computing solutions. In this paper, we show that the standard 8 transistor (8T) digital SRAM array can be configured as an analoglike in-memory multibit dot-product engine (DPE). By applying appropriate analog voltages to the read ports of the 8T SRAM array and sensing the output current, an approximate analog-digital DPE can be implemented. We present two different configurations for enabling multibit dot-product computations in the 8T SRAM cell array, without modifying the standard bit-cell structure. We also demonstrate the robustness of the present proposal in presence of nonidealities such as the effect of line resistances and transistor threshold voltage variations. Since our proposal preserves the standard 8T-SRAM array structure, it can be used as a storage element with standard read-write instructions and also as an on-demand analoglike dot-product accelerator.
Learning Robust Color Name Models from Web Images (2012)

We use images that have been collected using an Internet search engine to train color name models for color naming and recognition tasks. Considering color histogram bands as being words of an image and the color names as classes, we use the supervised latent Dirichlet allocation to train our model. To pre-process the training data, we use state-of-the art salient object detection and a Kullback–Leibler divergence based outlier detection. In summary, we achieve state-of-the-art performance on the eBay data set and improve the similarity between labels assigned by our model and human observers by approximately 14%. 1
Ureteral Access: Innovations in Guidewire and Balloon Catheter Systems (1987)

No AccessJournal of Urology1 Jun 1987Ureteral Access: Innovations in Guidewire and Balloon Catheter Systems Jerry D. Giesy, Matthew W. Hoskins, George D. Hermann, and Thomas J. Fogarty Jerry D. GiesyJerry D. Giesy More articles by this author , Matthew W. HoskinsMatthew W. Hoskins More articles by this author , George D. HermannGeorge D. Hermann More articles by this author , and Thomas J. FogartyThomas J. Fogarty More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)75674-1AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Ureteral Access: Innovations in Guidewire and Balloon Catheter Systems." The Journal of Urology, 137(6), p. 234A © 1987 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 137Issue 6June 1987Page: 234A Advertisement Copyright & Permissions© 1987 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Jerry D. Giesy More articles by this author Matthew W. Hoskins More articles by this author George D. Hermann More articles by this author Thomas J. Fogarty More articles by this author Expand All Advertisement PDF DownloadLoading ...
Efficient Computation of the Tree Edit Distance (2015)

We consider the classical tree edit distance between ordered labelled trees, which is defined as the minimum-cost sequence of node edit operations that transform one tree into another. The state-of-the-art solutions for the tree edit distance are not satisfactory. The main competitors in the field either have optimal worst-case complexity but the worst case happens frequently, or they are very efficient for some tree shapes but degenerate for others. This leads to unpredictable and often infeasible runtimes. There is no obvious way to choose between the algorithms. In this article we present RTED, a robust tree edit distance algorithm. The asymptotic complexity of our algorithm is smaller than or equal to the complexity of the best competitors for any input instance, that is, our algorithm is both efficient and worst-case optimal. This is achieved by computing a dynamic decomposition strategy that depends on the input trees. RTED is shown optimal among all algorithms that use LRH ( left-right-heavy ) strategies, which include RTED and the fastest tree edit distance algorithms presented in literature. In our experiments on synthetic and real-world data we empirically evaluate our solution and compare it to the state-of-the-art.
Quantitative Phase Imaging Using Hard X Rays (1996)

The quantitative imaging of a phase object using 16 keV x rays is reported. The theoretical basis of the techniques is presented along with its implementation using a synchrotron x-ray source. We find that our phase image is in quantitative agreement with independent measurements of the object.
Annealing-Free High-Mobility Diketopyrrolopyrrole−Quaterthiophene Copolymer for Solution-Processed Organic Thin Film Transistors (2011)

A donor-acceptor polymer semiconductor, PDQT, comprising diketopyrrolopyrrole (DPP) and β-unsubstituted quaterthiophene (QT) for organic thin film transistors (OTFTs) is reported. This polymer forms ordered layer-by-layer lamellar packing with an edge-on orientation in thin films even without thermal annealing. The strong intermolecular interactions arising from the fused aromatic DPP moiety and the DPP-QT donor-acceptor interaction facilitate the spontaneous self-assembly of the polymer chains into close proximity and form a large π-π overlap, which are favorable for intermolecular charge hopping. The well-interconnected crystalline grains form efficient intergranular charge transport pathways. The desirable chemical, electronic, and morphological structures of PDQT bring about high hole mobility of up to 0.97 cm(2)/(V·s) in OTFTs with polymer thin films annealed at a mild temperature of 100 °C and similarly high mobility of 0.89 cm(2)/(V·s) for polymer thin films even without thermal annealing.
Real-time algorithm for retinal tracking (1993)

Conventional retinal laser photocoagulation is presently performed by an ophthalmologist manually aiming a low-power laser beam at a desired site and firing a high-power laser for a preselected interval of time. To automate this process a retinal tracker must acquire a target, track small saccades, and identify loss of track during a large saccade. The authors successfully implemented a real-time algorithm that used a simple computer, video digitizing card, low light video camera, and fundus camera to perform rudimentary tracking on a photograph of a retina undergoing smooth circular motion. The algorithm tracked speeds up to 5 Hz, or 27 degrees/s, which equated to the retina moving in a 525 microns diameter circle.
Continuous-wave supercontinuum laser based on an erbium-doped fiber ring cavity incorporating a highly nonlinear optical fiber (2005)

We experimentally demonstrate a novel erbium-doped fiber based continuous-wave (cw) supercontinuum laser. The laser has a simple ring-cavity structure incorporating an erbium-doped fiber and a highly nonlinear dispersion-shifted fiber (HNL-DSF). Differently from previously demonstrated cw supercontinuum sources based on single propagation of a strong Raman pump laser beam through a highly nonlinear fiber, erbium gain inside the cavity generates a seed light oscillation, and the oscillated light subsequently evolves into a supercontinuum by nonlinear effects such as modulation instability and stimulated Raman scattering in the HNL-DSF. High quality of the depolarized supercontinuum laser output with a spectral bandwidth larger than 250 nm is readily achieved.
Rescue of vector-expressed fowl plague virus hemagglutinin in biologically active form by acidotropic agents and coexpressed M2 protein (1994)

The hemagglutinin of the Rostock strain of fowl plague virus was expressed in CV-1 cells by a simian virus 40 vector, and its stability in the exocytotic transport process was examined by a fusion assay. A 50-fold increase in the fusion activity of the hemagglutinin was observed when expression occurred in the presence of ammonium chloride, Tris-HCl, or high doses of amantadine. When chloroquine, another acidotropic agent, was used, the hemagglutinin exposed at the cell surface had to be activated by trypsin, because intracellular cleavage was inhibited by this compound. Hemagglutinin mutants resistant to intracellular cleavage did not require acidotropic agents for full expression of fusion activity, when treated with trypsin after arrival at the cell surface. These results indicate that fowl plague virus hemagglutinin expressed by a simian virus 40 vector is denatured in the acidic milieu of the exocytotic pathway and that cleavage is a major factor responsible for the pH instability. Coexpression with the M2 protein also markedly enhanced the fusion activity of the hemagglutinin, and this effect was inhibited by low doses of amantadine. These results support the concept that M2, known to have ion channel function, protects the hemagglutinin from denaturation by raising the pH in the exocytotic transport system. The data also stress the importance of acidotropic agents or coexpressed M2 for the structural and functional integrity of vector-expressed hemagglutinin.