gebhart/patrepeval huggingface dataset:
Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift (2018)

Single-cell RNA sequencing allows defining molecularly distinct cell subpopulations. However, the identification of specific sets of transcription factors (TFs) that define the identity of these subpopulations remains a challenge. Here we propose that subpopulation identity emerges from the synergistic activity of multiple TFs. Based on this concept, we develop a computational platform (TransSyn) for identifying synergistic transcriptional cores that determine cell subpopulation identities. TransSyn leverages single-cell RNA-seq data, and performs a dynamic search for an optimal synergistic transcriptional core using an information theoretic measure of synergy. A large-scale TransSyn analysis identifies transcriptional cores for 186 subpopulations, and predicts identity conversion TFs between 3786 pairs of cell subpopulations. Finally, TransSyn predictions enable experimental conversion of human hindbrain neuroepithelial cells into medial floor plate midbrain progenitors, capable of rapidly differentiating into dopaminergic neurons. Thus, TransSyn can facilitate designing strategies for conversion of cell subpopulation identities with potential applications in regenerative medicine.
Effect of CX516, an AMPA-Modulating Compound, on Cognition and Behavior in Fragile X Syndrome: AControlled Trial (2006)

A Phase II, 4-week randomized, double-blind, placebo-controlled clinical trial was conducted to evaluate the safety and efficacy of the Ampakine compound CX516 as a potential treatment for the underlying disorder in fragile X syndrome (FXS). After baseline screening, subjects with FXS (n = 49) underwent a 1-week placebo lead-in and then were randomized to study drug or placebo for a 4-week period. Cognitive and behavioral outcome measures were administered prior to treatment, at the end of treatment, and 2 weeks posttreatment. There were minimal side effects, no significant changes in safety parameters, and no serious adverse events. There was a 12.5% frequency of allergic rash in the CX516 group and 1 subject developed a substantial rash. There was also no significant improvement in memory, the primary outcome measure, or in secondary measures of language, attention/executive function, behavior, and overall functioning in CX516-treated subjects compared to placebo. This study did demonstrate that many outcome measures were reproducible in this test-retest setting for the FXS population, yet some were too difficult or variable. Adult subjects with FXS were able to complete an intensive clinical trial, and some valid outcome measures were identified for future FXS trial design. Problems with potency of CX516 in other studies have suggested dosing may have been inadequate for therapeutic effect and thus it remains unclear whether modulation of AMPA-mediated neurotransmission is a viable therapeutic strategy for the treatment of FXS.
An alternative extrinsic pathway of human blood coagulation (1982)

To study the interrelationships of the major human coagulation pathways, factor X activation in normal and various deficient human plasmas was evaluated when clotting was triggered by dilute rabbit or human thromboplastin. Various dilutions of thromboplastin were added to plasma samples containing 3H-labeled factor X, and the time course of factor X activation was determined. At a 1/250 dilution of rabbit brain thromboplastin the rate of factor X activation in factor VIII or factor IX deficient plasma was only 10% of the activation rate seen for normal or factor XI deficient plasma. Reconstitution of the deficient plasmas with factors VIII or IX, respectively, restored normal factor X activation. Similar results were obtained when various dilutions of human thromboplastin replaced the rabbit thromboplastin. From these experiments, it is inferred that normal activation of factor X in plasma due to dilute thromboplastin requires factors VII, IX and VIII. An alternative extrinsic pathway that involves factors VII, IX, and VIII may be a major physiologic extrinsic pathway, and this pathway may help to explain the clinical observations of bleeding diatheses in patients deficient in factors IX or VIII.
Automated Explanations as a Component of a Computer-Aided Design System (1982)

The ability to explain something, e.g., the operation of a complex machine or program, is an important, but poorly understood, component of intelligent behavior. We discuss an artificial intelligence approach to the modeling of the explanation process within the framework of a graphics-based CAD system currently under development, which can describe its own use, including the common ways to make and recover from errors. With a coordinated textual and pictorial display, the system, CADHELP, simulates an expert demonstrating the operation of the graphical features of the CAD subsystem. It consults a knowledge base of feature scripts to explain a feature, generate prompts as the feature is being operated, and to give certain types of help when a feature is misused. CADHELP provides these services by summarizing a feature script in different ways depending upon what it has told the user previously. The summarization process is based upon a theory of natural-language generation, in which a concept to be expressed is replaced in a short-term memory by words spanning part of its meaning interspersed with subconcepts still to be expressed. The generation process is mediated by a series of "sketchification" strategies, which prescribe which parts of a knowledge structure, a causal chain, or a single concept need not be expressed, since the listener should be able to infer them.
Enzyme-linked immunosorbent assay for detection of serum antibody in children vaccinated with Japanese encephalitis vaccine. (1986)

Serum antibodies in children who had been vaccinated with Japanese encephalitis (JE) vaccine were measured by enzyme-linked immunosorbent assay (ELISA) and neutralization (N) and hemagglutination-inhibition (HI) tests. Of 20 serum samples obtained after two shots of JE vaccine in the first year, all but one showed positive titers in the ELISA and N test, but five showed negative titers in the HI test. All 12 serum samples obtained after booster immunization with JE vaccine in the second year showed positive and considerably higher titers in all three tests. Moreover, a high correlation was found between the ELISA, N and HI titers. These results indicate that the ELISA is useful for detecting antibodies in subjects immunized with JE vaccine.
Prefrontal space ratio: comparison between trisomy 21 and euploid fetuses in the second trimester (2012)

The PFSR appears to be a highly sensitive and specific marker of trisomy 21 in the second trimester of pregnancy.
Human Eosinophils - Potential Pharmacological Model Applied in Human Histamine H<sub>4</sub> Receptor Research (2015)

Histamine and histamine receptors are well known for their immunomodulatory role in inflammation. In this review we describe the role of histamine and histamine H4 receptor on human eosinophils. In the first part of article we provide short summary of histamine and histamine receptors role in physiology and histamine related therapeutics used in clinics. We briefly describe the human histamine receptor H4 and its ligands, as well as human eosinophils. In the second part of the review we provide detailed description of known histamine effects on eosinophils including: intracellular calcium concentration flux, actin polymerization, cellular shape change, upregulation of adhesion proteins and cellular chemotaxis. We provide proofs that these effects are mainly connected with the activation of histamine H4 receptor. When examining experimental data we discuss the controversial results and limitations of the studies performed on isolated eosinophils. In conclusion we believe that studies on histamine H4 receptor on human eosinophils can provide interesting new biomarkers that can be used in clinical studies of histamine receptors, that in future might result in the development of new strategies in the treatment of chronic inflammatory conditions like asthma or allergy, in which eosinophils are involved.
Photoluminescence Investigation of the Effects of Barrier Thickness and Monolayer Coverage on Properties of Bilayer InAs/GaAs Quantum Dots (2008)

The optical properties of InAs/GaAs bi-layer quantum dots were investigated by photoluminescence (PL) measurements. We have studied the effects of the GaAs spacer thickness in between the dot layers and the monolayer coverage of the top quantum dot (QD) layer on the PL wavelengths and emission line-widths of the bi-layer QD samples grown at a low growth rate (0.028 ML/s). The samples showed multiple excited states for the top layer QDs suggesting the formation of large sized defect free islands in the top layer of the bilayer samples due to reduced growth rate. Also the samples were tuned to give peak emission close to similar to 1.3 mu m at room temperature and yielded an extremely narrow line-width of 16.8 meV at 25 K for lambda = 1.23 mu m.
PROTEIN STRUCTURE PREDICTION IN BIOLOGY AND MEDICINE (1999)

Protein structure prediction from sequence has made rapid advances in the last few years, gaining increased attention after the success of the CASP meetings. Specifically, threading predictions were shown to work for many cases previously thought to be outside of the scope of prediction methods. The papers in this session address a wide scope of topics, ranging from techniques for validation of prediction methods and further improvements of threading algorithms, to specific applications of protein structure predictions in biology.
Characterization of a new drug-resistant human myeloma cell line that expresses P-glycoprotein. (1986)

Multiple myeloma is a disease with a high initial chemotherapeutic response but virtually no cures due to emergence of drug resistance. A doxorubicin-resistant human myeloma cell line (8226/Dox) has been selected from the myeloma cell line RPMI8226 by continuously exposing cells to gradually increasing doses of doxorubicin. The resistant phenotype has been retained for over 2 months despite growth in drug-free medium. The resistant subline was cross-resistant to mitoxantrone, acronycine, etoposide, and vincristine. The 8226/Dox cell line remained sensitive to melphalan but acquired collateral sensitivity to dexamethasone. Intracellular doxorubicin accumulation, as measured by [14C]doxorubicin and high-performance liquid chromatography, was decreased by 54% at 1 h for 8226/Dox compared to the sensitive line. Efflux of doxorubicin was significantly greater in the resistant subline as compared to the sensitive parent cell line. Membrane analysis using immunoblotting techniques detected increased expression of the integral membrane protein P-glycoprotein (Mr 170,000) in the resistant subline. Cytogenetic analysis of 8226/Dox revealed a 7q-anomaly not seen in the parent cell line. No double minutes or homogeneously staining regions were observed. The drug sensitivity/resistance pattern of the resistant cell line correlates well with clinical observations indicating the potential of this cell line as a model for resistance in multiple myeloma.
Expression of claudins 1, 2, 3, 4, 5 and 7 in various types of tumours (2005)

The results show that claudins 1, 2, 3, 4, 5 and 7 can be used as markers for epithelial differentiation and to distinguish epithelial neoplasms from lymphomas and selectively also from soft tissue and naevocytic lesions. Since these claudins show type-specific differential expression in epithelial tumours, they may also be of some value in distinguishing different epithelial tumours from each other. Additionally, claudin 5 shows promise as a marker for endothelial lesions compared with other soft tissue lesions.
Multiwavelength absorbance detection for solute recognition in liquid chromatography (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultiwavelength absorbance detection for solute recognition in liquid chromatographyAnton C. J. H. Drouen, Hugo A. H. Billiet, and Leo. De GalanCite this: Anal. Chem. 1985, 57, 6, 962–968Publication Date (Print):May 1, 1985Publication History Published online1 May 2002Published inissue 1 May 1985https://pubs.acs.org/doi/10.1021/ac00283a003https://doi.org/10.1021/ac00283a003research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cell-density-dependent changes in cell-surface glycopeptides and in adhesion of cultured intestinal epithelial cells (1982)

We studied mannose-containing glycopeptides and glycoproteins of subconfluent and confluent intestinal epithelial cells in culture. Cells were labelled with d-[2-(3)H]mannose for 24h and treated with Pronase or trypsin to release cell-surface components. The cell-surface and cell-residue fractions were then exhaustively digested with Pronase and the resulting glycopeptides were fractionated on Bio-Gel P-6, before and after treatment with endo-beta-N-acetylglucosaminidase H to distinguish between high-mannose and complex oligosaccharides. The cell-surface glycopeptides were enriched in complex oligosaccharides as compared with residue glycopeptides, which contained predominantly high-mannose oligosaccharides. Cell-surface glycopeptides of confluent cells contained a much higher proportion of complex oligosaccharides than did glycopeptides from subconfluent cells. The ability of the cells to bind [(3)H]concanavalin A decreased linearly with increasing cell density up to 5 days in culture and then remained constant. When growth of the cells was completely inhibited by either retinoic acid or cortisol, no significant difference was observed in the ratio of complex to high-mannose oligosaccharides in the cell-surface glycopeptides of subconfluent cells. Only minor differences were found in total mannose-labelled glycoproteins between subconfluent and confluent cells by two-dimensional gel analysis. The adhesion of the cells to the substratum was measured at different stages of growth and cell density. Subconfluent cells displayed a relatively weak adhesion, which markedly increased with increased cell density up to 6 days in culture. It is suggested that alterations in the structure of the carbohydrates of the cell-surface glycoproteins are dependent on cell density rather than on cell growth. These changes in the glycopeptides are correlated with the changes in adhesion of the cells to the substratum.
Making Core Decompression Work (1990)

Meaningful assessment of a treatment modality for osteonecrosis (ON) must take into account a number of factors: (1) an accurate diagnosis, (2) consistent staging of the disease process, (3) understanding of the variability of the disease, (4) consistent application of the treatment modality (or the surgical technique), and (5) a clear understanding of the goal of the treatment used. This article reviews the important steps of a diagnostic algorithm that has been used to accurately diagnose and stage the disease process of ON. A consistent surgical technique with clearly defined goals is also outlined. The results of two clinical studies that were based on these diagnostic and therapeutic philosophies and that assess the role of core decompression in the treatment of ON are reviewed. The first study compared core decompression to conservative management in a prospective randomized study of 55 hips. Decompression provided more predictable pain relief and changed the indications for further surgical intervention more consistently than did conservative management. The second study represents a preliminary review of a ten-year study of the decompression procedure; it showed that core decompression was particularly useful in Stage I and Stage II ON. Roentgenographic stabilization was most predictable for Stage I hips. Core decompression can be a safe, effective, and predictable procedure in the treatment of Stage I and Stage II ON.
SCGAN: Saliency Map-Guided Colorization With Generative Adversarial Network (2020)

Given a grayscale photograph, the colorization system estimates a visually plausible colorful image. Conventional methods often use semantics to colorize grayscale images. However, in these methods, only classification semantic information is embedded, resulting in semantic confusion and color bleeding in the final colorized image. To address these issues, we propose a fully automatic Saliency Map-guided Colorization with Generative Adversarial Network (SCGAN) framework. It jointly predicts the colorization and saliency map to minimize semantic confusion and color bleeding in the colorized image. Since the global features from pre-trained VGG-16-Gray network are embedded to the colorization encoder, the proposed SCGAN can be trained with much less data than state-of-the-art methods to achieve perceptually reasonable colorization. In addition, we propose a novel saliency map-based guidance method. Branches of the colorization decoder are used to predict the saliency map as a proxy target. Moreover, two hierarchical discriminators are utilized for the generated colorization and saliency map, respectively, in order to strengthen visual perception performance. The proposed system is evaluated on ImageNet validation set. Experimental results show that SCGAN can generate more reasonable colorized images than state-of-the-art techniques.
Sound scattering and local heating from pulse-driven microbubbles (1999)

Using a bubble dynamical model based on the Rayleigh–Plesset equation, it is shown that the experimentally observed spectra of sound emitted from diagnostic microbubble contrast agents under the action of short, strong ultrasonic pulses can be understood from the interplay of enhanced sound emission due to nonlinear bubble oscillations and enhanced sound damping due to the occurrence of high frequencies in the emitted spectrum. The latter effect counteracts the pronounced increases in the scattering cross sections in the regime of nonlinear bubble response. Sound absorption furthermore leads to highly localized heating of the liquid (e.g., blood) over a distance of several μm near the collapsing bubble. This temperature rise is, however, too brief and the heated liquid volume too small to be hazardous to the patient’s health.
Erratum: Thermal Expansion of Platinum and Platinum-Rhodium ALloys (2014)

contains an error. It should read 100 (t, 0 C) = 8.79 10 -4 t + 0.805 10 -7 t 2 .
2D vs 3D integration: Architecture-technology co-design for future mobile MPSoC platforms (2014)

3D stacked ICs (3D-SIC) are viable alternatives to overcome limitations faced by mobile MPSoC platforms in 2D designs. In this paper, we evaluate 2D-ICs and 3D-SICs (memory-on-logic) at system architecture level for a complex MPSoC platform instantiated for wireless PHY processing (WLAN, LTE). For a 10-core heterogeneous MPSoC instantiation, we compare its implementations as 2D-IC and 3D-SIC (based on Cu-Cu bonding), and for two different level-1 data memory organization and communication bus structure. We also analyse impact of system level choices (memory organization, communication structure) for both 2D and 3D interconnects.
Improved efficacy and safety of theophylline in the control of airways hyperreactivity. (1982)

Theophylline is a potent bronchodilator that can be effective as maintenance medication for preventing chronic symptoms of asthma. Benefit and risk of toxicity both relate directly to serum concentration, however, and large interpatient variability in rates of elimination require that dosage be individualized by measurement of serum concentration. Reliably absorbed slow-release formulations provide more stable blood levels for around-the-clock therapy and thus offer both convenience and major therapeutic advantage in stabilizing the hyperreactive airways that characterize chronic asthma.
Real-time band structure changes of GaAs during continuous dynamic compression to 5 GPa (2009)

Real time changes of the GaAs band structure were determined using time-resolved photoluminescence (PL) spectroscopy, with nanosecond resolution, in single-event continuous compression experiments. Continuous compression to 5 GPa over 150 ns was achieved by impacting fused silica buffers preceding the GaAs crystals. PL spectra and compression wave profiles were measured simultaneously for uniaxial strain compression along the [100] orientation. Below 3 GPa, PL peaks from Te donors and Zn acceptors showed a blueshift upon compression, consistent with a widening of the band gap. At 3 GPa, the PL intensity decreased abruptly, due to a direct-to-indirect transition.
Ursolic Acid Inhibits Cigarette Smoke Extract-Induced Human Bronchial Epithelial Cell Injury and Prevents Development of Lung Cancer (2012)

Cigarette smoking is the main cause of chronic obstructive pulmonary disease and lung cancer. The present study was aimed to explore the chemopreventive effect of ursolic acid (UA) on these diseases. In the CSE treated normal human bronchial epithelial cell model, UA alleviated cytotoxicity caused by CSE, recovered the intracellular redox balance, and relieved the stimulation of external deleterious factors as well. UA mitigated CSE-induced DNA damage through the Nrf2 (nuclear factor erythroid 2-related factor 2) pathway. Moreover, UA inhibited lung cancer development in the model established by A549 cells in nude mice in vivo. For the first time, our results indicate that UA could be developed as a potential lung cancer chemopreventive agent.
Homotopy Continuation for Sensor Networks Self-Calibration (2021)

Given a sensor network, TDOA self-calibration aims at simultaneously estimating the positions of receivers and transmitters, and transmitters time offsets. This can be formulated as a system of polynomial equations. Due to the elevated number of unknowns and the nonlinearity of the problem, obtaining an accurate solution efficiently is nontrivial. Previous work has shown that iterative algorithms are sensitive to initialization and little noise can lead to failure in convergence. Hence, research has focused on algebraic techniques. Stable and efficient algebraic solvers have been proposed for some network configurations, but they do not work for smaller networks. In this paper, we use homotopy continuation to solve four previously unsolved configurations in 2D TDOA self-calibration, including a minimal one. As a theoretical contribution, we investigate the number of solutions of the new minimal configuration, showing this is much lower than previous estimates. As a more practical contribution, we also present new subminimal solvers, which can be used to achieve unique accurate solutions in previously unsolvable configurations. We demonstrate our solvers are stable both with clean and noisy data, even without nonlinear refinement afterwards. Moreover, we demonstrate the suitability of homotopy continuation for sensor network calibration problems, opening prospects to new applications.