gebhart/patrepeval huggingface dataset:
Potent stimulation of fibroblast growth factor 19 expression in the human ileum by bile acids (2013)

Fibroblast growth factor 19 (FGF19) is proposed to be a negative feedback regulator of hepatic bile acid (BA) synthesis. We aimed to clarify the distribution of FGF19 expression in human intestine and to investigate induction in a novel explant system. Ileal and colonic mucosal biopsies were obtained at endoscopy and analyzed for FGF19 transcript expression. Primary explants were incubated with physiological concentrations of various BA for up to 6 h, and expression of FGF19 and other genes was determined. FGF19 transcripts were detected in ileum but were unquantifiable in colon. No loss of FGF19 mRNA occurred as a consequence of the explant system. Ileal FGF19 transcript expression was induced 350-fold by 50 μM chenodeoxycholate (CDCA, n = 24, P < 0.0001) and 161-fold by 50 μM glycochenodeoxycholate (GCDCA, n = 12, P = 0.0005). The responses of other genes to CDCA or GCDCA (50 μM) were smaller: median increases of ileal bile acid binding protein, organic solute transporter-α and -β, and short heterodimer partner were 2.4- to 4.0-fold; apical membrane sodium bile acid transporter and farnesoid X receptor (FXR) showed little change. The EC50 for FGF19 transcript induction by CDCA was 20 μM. FGF19 protein concentrations were significantly higher in the culture fluid from BA-stimulated explants. FGF19 induction with cholate was 81% of that found with CDCA, but deoxycholate (40%) and lithocholate (4%) were significantly less potent. The synthetic FXR agonist obeticholic acid was much more potent than CDCA with a 70-fold FGF19 stimulation at 1 μM. We concluded that FGF19 expression in human ileum is very highly responsive to BA. Changes in FGF19 induction are a potential mechanism involved in disorders of BA homeostasis.
Single-shot slightly-off-axis interferometry based Hilbert phase microscopy of red blood cells (2011)

A slightly-off-axis interferometry based Hilbert phase microscopy (HPM) method is developed to quantitatively obtain the phase distribution. Owing to its single-shot nature and details detection ability, HPM can be used to investigate rapid phenomena that take place in transparent structures such as biological cells. Moreover, the slightly-off-axis interferometry owns higher effective bandwidth and more sensitivity than traditional off-axis interferometry. The proposed method takes advantages of the above techniques to obtain the phase image of the red blood cells and compared with the traditional off-axis interferometry and phase retrieval algorithm based on the FFT. The experimental results show that the proposed method owns fine spatial details and real-time imaging ability. We are sure that the proposed method provides a breakthrough for real-time observing and quantitative analyzing of cells in vivo.
Syntax is from Mars while Semantics from Venus! Insights from Spectral Analysis of Distributional Similarity Networks (2009)

We study the global topology of the syntactic and semantic distributional similarity networks for English through the technique of spectral analysis. We observe that while the syntactic network has a hierarchical structure with strong communities and their mixtures, the semantic network has several tightly knit communities along with a large core without any such well-defined community structure.
Calibration of Dynamic Building Energy Models with Multiple Responses Using Bayesian Inference and Linear Regression Models (2015)

This paper proposes a lightweight Bayesian calibration of dynamic models that accounts for model parameter uncertainties. A regression model was built to represent the dynamic model using parameter screening and multiple linear regression. Given this regression model and prior probability distributions of its input parameters, a Bayesian calibration method is developed to provide their posterior distributions. A case study is presented and the result shows considerable alignment between model prediction and measurement after calibration. This indicates its capability to perform fast risk-conscious calibration for most current retrofit practice where only monthly consumption and demand data are available.
Enrichment in tumor-reactive CD8+ T-lymphocytes by positive selection from the blood and lymph nodes of patients with head and neck cancer. (1991)

To study antitumor functions of T-lymphocyte subpopulations in the blood [peripheral blood lymphocytes (PBLs)] and tumor-draining lymph nodes (LNs) of patients (n = 26) with squamous cell carcinoma of the head and neck (SCCHN), antibody-coated devices were used to positively select CD8+ or CD4+ cells. The mean percentage of CD8+ cells captured on antibody-coated flasks from PBLs was 92% and that captured from lymph node lymphocytes (LNLs) was 98%. The initial enrichment in CD4+ T-cells was comparable. CD8+ T-lymphocytes captured from PBLs proliferated as well as unseparated lymphocytes in both patients with SCCHN and normal donors, while captured CD4+ PBLs of the patients showed significantly lower expansion than those of normal volunteers. Unseparated LNLs proliferated as well as PBLs, but captured CD4+ or CD8+ LNLs failed to proliferate in the presence of interleukin 2 (100 units/ml) and phytohemagglutinin (5 micrograms/ml). The addition to captured LNL cultures of irradiated autologous or allogeneic feeder cells significantly improved expansion of CD8+ LNLs but not CD4+ LNLs. During 15-day culture of captured CD8+ PBLs or CD8+ LNLs in the presence of feeder cells, a significant (P less than 0.05) enrichment in CD8+ T-cells was maintained [94 +/- 5% (mean +/- SEM) or 99.5 +/- 0.1%, respectively, on day 15]. Capture of CD8+ LNLs and their expansion resulted in the outgrowth of CD8+CD11b- effectors which had no or little cytotoxicity against Daudi, low cytotoxicity against K562, and very high levels of cytotoxicity against 4 different natural killer cell-resistant SCCHN targets, as measured in 4-h 51Cr release assays. Such significant enrichment in SCCHN-restricted cytotoxicity could be obtained with LNLs from tumor-uninvolved LNs but not from tumor-involved LNs. Captured and cultured CD4+ LNLs had no preferential anti-SCCHN cytotoxicity. The addition of irradiated autologous tumor cells to captured CD8+ PBLs did not result in improved proliferation or antitumor function of the effector cells. Positive selection on antibody-coated flasks of CD8+ T-lymphocytes from tumor-uninvolved LNs of patients with SCCHN led to the enrichment in SCCHN-restricted but the major histocompatibility complex-unrestricted effector cells in 15-day cultures. Thus, CD8+ lymphocytes separated from tumor-draining LNs in patients with head and neck cancer contained cytolytic T-cell precursors capable of developing into effectors with preferential activity against SCCHN targets.
Accelerated Sparse Neural Training: A Provable and Efficient Method to Find N:M Transposable Masks (2021)

Unstructured pruning reduces the memory footprint in deep neural networks (DNNs). Recently, researchers proposed different types of structural pruning intending to reduce also the computation complexity. In this work, we first suggest a new measure called mask-diversity which correlates with the expected accuracy of the different types of structural pruning. We focus on the recently suggested N:M fine-grained block sparsity mask, in which for each block of M weights, we have at least N zeros. While N:M fine-grained block sparsity allows acceleration in actual modern hardware, it can be used only to accelerate the inference phase. In order to allow for similar accelerations in the training phase, we suggest a novel transposable fine-grained sparsity mask, where the same mask can be used for both forward and backward passes. Our transposable mask guarantees that both the weight matrix and its transpose follow the same sparsity pattern; thus, the matrix multiplication required for passing the error backward can also be accelerated. We formulate the problem of finding the optimal transposable-mask as a minimum-cost flow problem. Additionally, to speed up the minimum-cost flow computation, we also introduce a fast linear-time approximation that can be used when the masks dynamically change during training. Our experiments suggest a 2x speed-up in the matrix multiplications with no accuracy degradation over vision and language models. Finally, to solve the problem of switching between different structure constraints, we suggest a method to convert a pre-trained model with unstructured sparsity to an N:M fine-grained block sparsity model with little to no training. A reference implementation can be found at https://github.com/papers-submission/structured_transposable_masks.
"Stem cell candidates" purified by liquid culture in the presence of Steel factor, IL-3, and 5FU are strictly stroma-dependent and have myeloid, lymphoid, and megakaryocytic potential. (1997)

Berardi et al. (Science 1995; 267:105) reported recently that combined cytokine stimulation and antimetabolite treatment were able to isolate cells with characteristics of hemopoietic stem cells. Bone marrow (BM) low-density cells were cultured for 1 week in the presence of Steel factor (SF), IL-3, and the antimetabolite 5-FU. Following this approach one in 10(5) BM cells were purified. These cells showed no clonogenic potential in soft gel assays but presented a striking myeloid-lymphoid potential as long-term culture-initiating cells (LTC-ICs). We investigated this new "stem cell candidate." following a similar approach we purified one in 55,000/130,000 cells from cord blood and peripheral blood in mobilized cancer patients. These cells displayed no clonogenic potential in methylcellulose assays in the presence of different cytokine combinations and generated very few or no clonogenic progenitors in liquid cultures in the presence of cytokines. When seeded on layers derived from the murine BM stromal cell line M2-10B4, 38-86% of the cells purified using this approach generated multilineage progenitors acting as LTC-lCs. In a different series of studies, after 5-week culture on human BM stromal cell line L87/4 layers, cells were forced to selected lineage differentiation by culture in the presence of low concentrations of SF and high concentrations of lineage-specific cytokines such as Flt3-ligand (myeloid and pre-B cell differentiation), Tpo (megakaryocytic differentiation). IL-7, and IL-2 (pre-B and NK differentiation). After 12-day culture under these conditions, generation of myeloid, pre-B, megakaryocytic, and NK progenitors was assessed by immunohistochemistry, flow cytometry, and mRNA expression of CD7, 14, 19, 41b, S6, and 61. We conclude that this procedure for multilineage progenitor cell purification is simple and effective and could have major implications for gene transfer and stem cell transplantation.
Image-Based Mechanical Analysis of Stent Deformation: Concept and Exemplary Implementation for Aortic Valve Stents (2013)

An approach for extracting the radial force load on an implanted stent from medical images is proposed. To exemplify the approach, a system is presented which computes a radial force estimation from computer tomography images acquired from patients who underwent transcatheter aortic valve implantation (TAVI). The deformed shape of the implanted valve prosthesis' Nitinol frame is extracted from the images. A set of displacement vectors is computed that parameterizes the observed deformation. An iterative relaxation algorithm is employed to adapt the information extracted from the images to a finite-element model of the stent, and the radial components of the interaction forces between the stent and the tissue are extracted. For the evaluation of the method, tests were run using the clinical data from 21 patients. Stent modeling and extraction of the radial forces were successful in 18 cases. Synthetic test cases were generated, in addition, for assessing the sensitivity to the measurement errors. In a sensitivity analysis, the geometric error of the stent reconstruction was below 0.3 mm, which is below the image resolution. The distribution of the radial forces was qualitatively and quantitatively reasonable. An uncertainty remains in the quantitative evaluation of the radial forces due to the uncertainty in defining a radial direction on the deformed stent. With our approach, the mechanical situation of TAVI stents after the implantation can be studied in vivo, which may help to understand the mechanisms that lead to the complications and improve stent design.
Switchable multi-wavelength fiber ring laser based on a compact in-fiber Mach-Zehnder interferometer with photonic crystal fiber (2009)

Switchable multi-wavelength fiber ring laser with an in-fiber Mach-Zehnder interferometer incorporated into the ring cavity serving as wavelength-selective filter at room temperature is demonstrated. The filter is formed by splicing a section of few-mode photonic crystal fiber (PCF) and two segments of single mode fiber (SMF) with the air-holes on the both sides of PCF intentionally collapsed in the vicinity of the splices. By adjusting the states of the polarization controller (PC) appropriately, the laser can be switched among the stable single-, dual- and triple-wavelength lasing operations by exploiting polarization hole burning (PHB) effect.
The study of blue organic light emitting diodes with a CuPc electron transporting layer (2004)

Organic light emitting diodes using copper phthalocyanine (CuPc), instead of tris-(8-hydroxguinoline) aluminum (AIq), as an electron transporting layer are fabricated. The outcome of this structure significantly facilitates electron transporting through the organic materials, thus resulting in the reduction of operating voltages. The emitted light exhibits a peak at 410 nm and the CIE coordinates are (0.15,0.07).
Trapped pulse generation by femtosecond soliton pulse in birefringent optical fibers (2002)

A novel phenomenon of trapped pulse generation by orthogonally polarized femtosecond soliton pulse is discovered in low birefringent optical fiber. As pulse propagation, wavelengths of soliton pulse and trapped pulse are shifted toward longer wavelength side due to effects of soliton selffrequency shift and pulse trapping. The energy of trapped pulse is increased exponentially through Raman gain of soliton pulse and orthogonally polarized and temporally overlapped two colored femtosecond twin pulses are generated. The spectrogram of output pulses is observed using crosscorrelation frequency resolved optical gating technique. The characteristics of this phenomenon are also analyzed numerically and numerical results are almost in agreement with experimental ones.
Li+ and H+ Conducting Polyelectrolytes with Covalently Bonded Anions (2009)

New single-ion conducting methacrylate-based polyelectrolytes were prepared by radical copolymerization of methacrylic acid (MA) or lithium methacrylate (LiMA), 2-ethoxyethyl methacrylate (EOEMA) and 2-methoxyethyl methacrylate (EGMEMA) as purely cation-conducting (Li+ or H+) polyelectrolytes with covalently bonded carboxylic groups. For conductivity improvement, a series of polyelectrolytes with an embedded aprotic solvent, propylene carbonate (PC) or dimethylformamide (DMF) were prepared. After optimisation of the polyelectrolyte composition, the highest conductivity values were found for poly(MA–EOEMA)–PC (2.2?10–6 S cm–1) and poly(LiMA–EGMEMA)–DMF (1.9.10–4 S cm–1). The polyelectrolytes were also characterized by voltammetry and thermogravimetry. The accessible potential window on gold electrode is ca. 1.75–2 V for H+ polyelectrolytes and over 3.5 V for Li+ polyelectrolytes. The polyelectrolytes without aprotic solvents are stable up to 185 °C and those containing the solvents up to 105–115 °C.
Extensions of MADM (Mosaic Analysis with Double Markers) in Mice (2012)

Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM.
Optimizing word alignment combination for phrase table training (2009)

Combining word alignments trained in two translation directions has mostly relied on heuristics that are not directly motivated by intended applications. We propose a novel method that performs combination as an optimization process. Our algorithm explicitly maximizes the effectiveness function with greedy search for phrase table training or synchronized grammar extraction. Experimental results show that the proposed method leads to significantly better translation quality than existing methods. Analysis suggests that this simple approach is able to maintain accuracy while maximizing coverage.
Microbial production of <scp>D</scp>‐mannitol and <scp>D</scp>‐fructose from glycerol (1970)

Abstract In view of the recent development that some petrochemical products are efficiently available as substrates for the fermentation industry, glycerol manufactured from propylene by chemical synthesis would also be hoped for the purpose. This paper describes some of the factors influencing mannitol production from glycerol by Torulopsis yeasts and a microbial conversion of glycerol to D ‐fructose via mannitol, in which two sequential steps of yeast and Acetobacter fermentation are involved. Torulopsis mannitofaciens CBS 5981 and Torulopsis vcrsatilis CBS 1752, exceptionally good mannitol producers, were selected for the study. High concentrations of nitrogen sources and KH 2 PO 4 in the medium markedly decreased mannitol yield in spite of good utilization of the substrate. T. mannitofaciens produced mannitol in yield of 31% of the glycerol consumed at optimal condition. The fermentation by washed yeast cells gave much higher mannitol yield of more than 50%. A sequential fermentation process was carried out without isolation and purification of the intermediate and yielded.51.7%. D ‐fructose from the glycerol.
Role of Vitamin D Glucosiduronate in Calcium Homeostasis (1980)

Evidence has been presented suggesting the presence of vitamin D(3) 3beta-glucosiduronate and 1,25-dihydroxyvitamin D(3) glucosiduronate in rat bile. To evaluate the role of vitamin D glucosiduronates in calcium and phosphorus homeostasis, we synthesized vitamin D(3) 3beta-glucosiduronate and tested its biological activity in calcium- and vitamin D-deficient rats. After the intravenous administration of vitamin D(3) 3beta-glucosiduronate to rats maintained on a low calcium diet, there was an increase in duodenal calcium transport and an increase in serum calcium. Vitamin D(3) 3beta-glucosiduronate, however, was less active than equimolar amounts of vitamin D(3). At doses of less than 0.65-1 nmol per rat, the conjugate exhibited no activity. When vitamin D(3) 3beta-glucosiduronate was administered to vitamin D-deficient rats, 25-hydroxyvitamin D was detected in the serum; the increase in serum 25-hydroxyvitamin D levels was less than that observed after the administration of an equimolar amount of vitamin D(3). Vitamin D(3) 3beta-glucosiduronate showed no detectable activity in the induction of calcium binding protein in chick embryonic duodena, a system in which no endogenous steroid beta-glucuronidase activity is detectable. These data demonstrate that vitamin D(3) 3beta-glucosiduronate is biologically active in vivo and that the observed activity is due to hydrolysis of the conjugate to vitamin D(3). As vitamin D(3) 3beta-glucosiduronate is excreted in the bile of rats, it is possible that this conjugate is reutilized in vivo after hydrolysis to free vitamin D(3). These results suggest the existence of a mechanism for reutilization of the biliary products of vitamin D(3).
Deep Learning-Based Channel Estimation for Massive MIMO Systems (2019)

In this letter, we propose a deep learning (DL)-based channel estimation scheme for the massive multiple-input multiple-output (MIMO) system. Unlike existing studies, we develop the channel estimation scheme for the case that the pilot length is smaller than the number of transmit antennas. The proposed scheme takes a two-stage estimation process: 1) a DL-based pilot-aided channel estimation and 2) a DL-based data-aided channel estimation. In the first stage, the pilot itself and the channel estimator are jointly designed by using both a two-layer neural network (TNN) and a deep neural network (DNN). In the second stage, the accuracy of channel estimation is further enhanced by using another DNN in an iterative manner. The simulation results demonstrate that the proposed channel estimation scheme has much better performance than the conventional channel estimation scheme. We also derive a useful insight into the optimal pilot length given the number of transmit antennas.
Auditory localization of nearby sources. II. Localization of a broadband source (1999)

Although many researchers have examined auditory localization for relatively distant sound sources, little is known about the spatial perception of nearby sources. In the region within 1 m of a listener's head, defined as the "proximal region," the interaural level difference increases dramatically as the source approaches the head, while the interaural time delay is roughly independent of distance. An experiment has been performed to evaluate proximal-region localization performance. An auditory point source was moved to a random position within 1 m of the subject's head, and the subject responded by pointing to the perceived location of the sound with an electromagnetic position sensor. The overall angular error (17 degrees) was roughly comparable to previously measured results in distal-region experiments. Azimuth error increased slightly as the sound source approached the head, but elevation performance was essentially independent of source distance. Distance localization performance was generally better than has been reported in distal-region experiments and was strongly dependent on azimuth, with the stimulus-response correlation ranging from 0.85 to the side of the head to less than 0.4 in the median plane. The results suggest that the enlarged binaural difference cues found in the head-related transfer function (HRTF) for nearby sources are important to auditory distance perception in the proximal region.
Interaction techniques for a highly interactive 3D geometric modeling system (1993)

No abstract available.