gebhart/patrepeval huggingface dataset:
Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal (2015)

To date, no discrete genetic signature has been defined for isolated Dclk1+ tuft cells within the small intestine. Furthermore, recent reports on the functional significance of Dclk1+ cells in the small intestine have been inconsistent. These cells have been proposed to be fully differentiated cells, reserve stem cells, and tumor stem cells. In order to elucidate the potential function of Dclk1+ cells, we FACS-sorted Dclk1+ cells from mouse small intestinal epithelium using transgenic mice expressing YFP under the control of the Dclk1 promoter (Dclk1-CreER;Rosa26-YFP). Analysis of sorted YFP+ cells demonstrated marked enrichment (~6000 fold) for Dclk1 mRNA compared with YFP- cells. Dclk1+ population display ~6 fold enrichment for the putative quiescent stem cell marker Bmi1. We observed significantly greater expression of pluripotency genes, pro-survival genes, and quiescence markers in the Dclk1+ population. A significant increase in self-renewal capability (14-fold) was observed in in vitro isolated Dclk1+ cells. The unique genetic report presented in this manuscript suggests that Dclk1+ cells may maintain quiescence, pluripotency, and metabolic activity for survival/longevity. Functionally, these reserve characteristics manifest in vitro, with Dclk1+ cells exhibiting greater ability to self-renew. These findings indicate that quiescent stem-like functionality is a feature of Dclk1-expressing tuft cells.
Towards Software Evolution for Embedded Systems Based on MAPE Loop Encapsulation (2014)

Software evolution is an essential activity that adapts existing software to changes in requirements. Because of recent rapid requirements changes, systems are strongly required to evolve even if the target systems are embedded systems, whose implementation code is generally hard to be changed. This paper discusses the feasibility of applying self-adaptation mechanism for software evolution. We use the MAPE loop mechanism to evolve embedded systems without changing code inside the existing systems. This paper also reports preliminary results that we experimentally evolved a cleaning robot by following our approach. Our demonstrations show a part of additional behaviors as the results of software evolution that makes the cleaning robot possible to move obstacles. We also discuss the future directions of software evolution for embedded systems with the self-adaptive mechanism.
Fez1/Lzts1-deficient mice are more susceptible to N-butyl-N-(4-hydroxybutil) nitrosamine (BBN) carcinogenesis (2008)

FEZ1/LZTS1 is a tumor suppressor gene that is frequently altered in human cancers of different histotypes. We have reported previously that LZTS1 is downregulated in high-grade bladder cancer and that its restoration suppresses tumorigenicity in urothelial carcinoma cells. To further investigate the role of LZTS1 in the development of bladder cancer, we utilized heterozygous and nullizygous Lzts1 mice in a chemically induced carcinogenesis model. Fifty-eight mice consisting of 25 Lzts1(+/+), 17 Lzts1(+/-) and 16 Lzts1(-/-) were treated with N-butyl-N-(4-hydroxybutil) nitrosamine (BBN). Results showed that there was a significant increase in neoplastic lesions in the Lzts1(+/-) (82.3%) and Lzts1(-/-) (93.8%) versus Lzts1(+/+) (8.0%) mice after BBN treatment. No difference in cancer incidence between Lzts1(+/-) and Lzts1(-/-) was observed. Collectively, these findings indicate that loss of one or both LZTS1 alleles hampers the normal defenses of urothelial cells against carcinogens, favoring bladder cancer development. Therefore, LZTS1 may become an excellent target for gene therapy in advanced bladder carcinoma.
Cross‐layer design of outage optimum routing metric for wireless ad hoc networks (2011)

ABSTRACT A new routing metric for multihop wireless ad hoc networks is presented. The proposed metric is based on the computation of signal‐to‐noise ratio and path minimization of wireless ad hoc network outage probability in a fading environment. This metric improves the quality of service by reducing the number of dropped packets. Further, by modeling the network with a Trellis diagram and then using Viterbi algorithm to select the best routing path, we reduce the routing complexity of our approach. The performance of the proposed metric is compared with other commonly used routing metrics such as minimum hop count, expected transmission count, and two other signal‐to‐noise ratio‐based metrics in both mobile and stationary networks. Simulation results demonstrate the improvement achieved by this new metric. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Deep Neural Networks with Multi-Branch Architectures Are Less Non-Convex (2018)

Several recently proposed architectures of neural networks such as ResNeXt, Inception, Xception, SqueezeNet and Wide ResNet are based on the designing idea of having multiple branches and have demonstrated improved performance in many applications. We show that one cause for such success is due to the fact that the multi-branch architecture is less non-convex in terms of duality gap. The duality gap measures the degree of intrinsic non-convexity of an optimization problem: smaller gap in relative value implies lower degree of intrinsic non-convexity. The challenge is to quantitatively measure the duality gap of highly non-convex problems such as deep neural networks. In this work, we provide strong guarantees of this quantity for two classes of network architectures. For the neural networks with arbitrary activation functions, multi-branch architecture and a variant of hinge loss, we show that the duality gap of both population and empirical risks shrinks to zero as the number of branches increases. This result sheds light on better understanding the power of over-parametrization where increasing the network width tends to make the loss surface less non-convex. For the neural networks with linear activation function and $\ell_2$ loss, we show that the duality gap of empirical risk is zero. Our two results work for arbitrary depths and adversarial data, while the analytical techniques might be of independent interest to non-convex optimization more broadly. Experiments on both synthetic and real-world datasets validate our results.
A Study on the Ray Based Broad Band Modeling for Shallow Water Acoustic Wave Propagations (2006)

This paper proposes a ray-based forward modeling scheme which is suitable for the shallow water acoustic wave propagation simulations. The proposed model comprises of ray tracings for the layered media of which sound speed profiles are interpolated linearly. considerations of plane and spherical wave reflection coefficients. and calculations of the phases and the amplitudes of eigen rays. The main characteristic of the scheme is fast simulation time due to direct calculation of the broad-band time signals in the time-domain, i.e. without transformation of the frequency-domain solutions to the time si 밍 131s. Finally, we applied the model to 4-types of test environments and compared the resulting signals with those of ORCA and Ram in order to validate the proposed model.
Molecular and cellular mechanisms of profile changes of charged blood plasma free oligosaccharides in myeloproliferative disorders (2016)

Free oligosaccharides (FOS) are unbound to proteins or lipids structural analogs of their glycans. FOS appear as by-products of endoplasmic reticulum synthesis, cell control folding with endoplastic reticulum-associated degradation and lysosomal/endosomal breakdown of glycoconjugates. They may be either neutral or negatively charged depending on the way of their formation. Charged FOS appear during degradation of glycoconjugates in the lysosomal/endosomal system and are natural substrates for lysosomal sialidase-1. FOS are formed inside the cell but some of them can get into the extracellular space, and then into the blood and urine, where both neutral and charged structures were found. Secretion of charged FOS outside of the cell is most likely to be caused by the lysosomal exocytosis. The activity of neuraminidase-1 is known to be connected with the intensity of the lysosomal exocytosis. In our previous studies, it was found that HPLC-profiles of charged FOS were specifically changed in acute and chronic myeloproliferative blood disorders. The objective of this work was to analyze the molecular and cellular mechanisms of these changes and to test the hypothesis of their association with the activity change of lysosomal neuraminidase-1. Plasma samples of patients with acute and chronic leukaemia – polycytaemia vera, chronic idiopathic myelofibrosis, hypoplastic anaemia, myelodysplastic syndrome with transformation, acute lymphatic and acute myelomonocytic leukaemia – were collected for investigation. Plasma samples of practically healthy volunteers were obtained and used for comparison. After plasma deproteinization and FOS purification the oligosaccharides were labelled with anthranilic acid (2-AA), separated into the neutral and charged fractions with QAE Sephadex (Q25-120) chromatography and analysed using high-performance liquid chromatography (HPLC). Glucose unit values were determined following comparison with a 2-AA-labelled glucose oligomer ladder derived from a partial hydrolysate of dextran as an external standard. The data were collected and processed using Empower software. The charged FOS were digested with the sialidase from Arthrobacter ureafaciens. 2-AA – labelled free oligosaccharides from transferrin were used as an external standard for the structure decoding. In this paper, the changes in neraminidase-1 activity was first demonstrated on natural substrates, free oligosaccharides, in vivo. Chromatographic profiles of charged plasma FOS of patients with acute and chronic hematological malignancies revealed decreasing of neuraminidase-1 activity and increasing of the lysosomal exocytosis. Thus, chromatographic profiles of charged plasma FOS appeared to be a sensitive parameter of the lysosomal/endosomal status in normal or pathological states and to open up new prospects for their applications to the development of anti-cancer drugs designed to block the work of the lysosomal/endosomal system and monitoring of their action.
Solid State Gas Sensor Design Using Foreign Receptors (1999)

Sensory detection of gases has become increasingly important especially for emission control and environmental monitoring. This article reviews how well a design concept using foreign receptors works for developing three types of solid state gas sensors. For oxide-semiconductor gas sensors, noble metals, metal oxides or even metal carbonates can works as an effective receptor material to recognize reducing gases when finely dispersed on the base oxide grains. Alkaline metal salts of oxyacids can work as indispensable receptors to oxidic gases like CO2, NO2 and SO2 for potentiometric solid electrolyte gas sensors, while semiconducting oxides provide useful receptors to reducing or oxidizing gases when used as a sensing electrode for mixed potential type solid electrolyte gas sensors. Several gas sensors thus developed are demonstrated together with brief discussion.
Expression of the human histocompatibility leukocyte antigen DR3 transgene reduces the severity of demyelination in a murine model of multiple sclerosis. (1998)

The role of various MHC genes in determining the progression of multiple sclerosis (MS) remains controversial. The HLA-DR3 gene has been associated with benign relapsing MS in some genetic epidemiologic studies, but with disease progression in others. We induced demyelination in highly susceptible B10.M and B10.Q mice expressing the DR3 (HLA-DRB1*0301) transgene to determine directly the effects of a human transgene by infecting them with Theiler's murine encephalomyelitis virus (TMEV). DR3+ mice experienced a dramatic reduction in the extent and severity of demyelination compared with DR3- littermate controls, whereas anti-TMEV antibody titers, delayed-type hypersensitivity responses, and levels of infectious virus, virus antigen, and virus RNA were similar in both groups. To address a possible mechanism of how the human transgene is reducing virus-induced demyelination, we analyzed cytokine expression in the lesions and also determined whether B10.M mice can respond to peptides derived from the DR3 molecule. Intense staining for IFN-gamma and IL-4, T helper (TH) 1 and TH2 cytokines, respectively, was found in the lesions of TMEV-infected DR3- mice but not in the DR3+ transgenic mice at day 21 after infection. DR3 peptides elicited strong proliferative responses in B10.M mice but not in B10.M (DR3+) mice. These experiments are the first to demonstrate that a human class II DR gene can alter the severity of demyelination in an animal model of MS without influencing viral load. These experiments are consistent with a mechanism by which DR3 reduces demyelination by altering the cytokine expression in the lesions, possibly by deleting T cells involved in virus-induced pathology.
Orthotopic Replacement of Aortic Heart Valves with Tissue-Engineered Grafts (2013)

Tissue-engineered AV based on decellularized valve allografts satisfy short-term requirements of the systemic circulation in sheep. Although results of long-term experiments are pending, the lack of degenerative traits thus far, makes these grafts a promising alternative for future aortic heart valve surgery.
A MEMS-based programmable diffraction grating for optical holography in the spectral domain (2002)

A MEMS-based programmable diffraction grating has been developed that can generate arbitrary spatial grating profiles on a sub-millisecond time scale. Such profiles redirect wavelengths in a polychromatic light beam. These devices can synthesize the spectra of molecules and manipulate signals in a wavelength-division-multiplexed optical telecommunications system.
Harmonic Limited Test Waveform for Fast AWIS Dielectric Studies (2011)

Arbitrary Waveform Impedance Spectroscopy (AWIS) has been designed as a versatile tool for dielectric material studies. Among diverse features, it is capable of determining an entire dielectric spectrum from one measurement, provided the test voltage is rich enough in harmonics. However, extremely harmonic-rich test signals limit the measurement accuracy due to aliasing. Aliasing is caused by the data acquisition if there are harmonics above the Nyquist frequency. However, anti-alias filters, the customary solution, are preferably avoided when using AWIS due to high precision requirements. A remaining possibility is to control the aliasing by limiting the test signal harmonic content. In this paper we present an optimized waveform, which can be applied in situations where the test voltage waveform is not dictated by other requirements. In such cases it enables the use of AWIS for fast dielectric studies under rapidly changing environmental conditions.
HLA-CLASS II ANTIGEN EXPRESSION IN HUMAN HEART-LUNG ALLOGRAFTS (1990)

Long-term survival in heart-lung transplantation has ben hindered by the development of bronchiolitis obliterans (OB), which is believed to be a manifestation of chronic rejection of the lung. Since HLA-class II antigens are involved in the rejection response, the distribution of the class II products HLA-DR, HLA-DQ, and HLA-DP were studied in normal lung, and in transplanted lung with and without OB, utilizing frozen-section immunohistochemical techniques. All three allelic products are usually expressed on the epithelial, endothelial, and mesenchymal components of the lung. Sequential transbronchial biopsies from 4 recipients before and concurrent with the diagnosis of OB were stained with serial dilutions of monoclonal antibodies to assess the level of expression of the above class II products. Increased levels of HLA-DR and HLA-DP antigens may be seen on the bronchial and bronchiolar epithelium during OB, but the changes are subtle and complicated by many other variables. Additional studies are needed to confirm these preliminary results.
Design Criteria for Transparent Single-Wall Carbon Nanotube Thin-Film Transistors (2006)

A study based on two-dimensional percolation theory yielding quantitative parameters for optimum connectivity of transparent single-wall carbon nanotube (SWNT) thin films is reported. Optimum SWNT concentration in the filtrated solution was found to be 0.1 mg/L with a volume of 30 mL. Such parameters lead to SWNT fractions in the films of approximately Phi = 1.8 x 10(-3), much below the metallic percolation threshold, which is found to be approximately PhiC = 5.5 x 10(-3). Therefore, the performance of transparent carbon nanotube thin-film transistors is limited by the metallic SWNTs, even below their percolation threshold. We show how this effect is related to hopping or tunneling between neighboring metallic tubes.
Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of VIS649 (Sibeprenlimab), an APRIL-Neutralizing IgG2 Monoclonal Antibody, in Healthy Volunteers (2022)

VIS649 was safe, well tolerated, and reversibly suppressed APRIL and various immunoglobulins, without loss of antigen-specific vaccination response. Further clinical development of VIS649 for IgAN is warranted. Trial registration: ClinicalTrials.gov: NCT03719443.
A new complementary bipolar transistor structure (1972)

A novel complementary monolithic bipolar transistor structure has been developed. By adding one extra diffusion to the standard monolithic bipolar transistor process, a complementary pair of high current gain and very low saturation resistance n-p-n and p-n-p transistors can be fabricated on the same chip. High sheet resistances are also present in this structure. Novel low-voltage (1.3 V) complementary digital circuits have been fabricated by this new process.
Supplementary Figures 1-4 from GP369, an FGFR2-IIIb–Specific Antibody, Exhibits Potent Antitumor Activity against Human Cancers Driven by Activated FGFR2 Signaling (2023)

Supplementary Figures 1-4 from GP369, an FGFR2-IIIb–Specific Antibody, Exhibits Potent Antitumor Activity against Human Cancers Driven by Activated FGFR2 Signaling
Intercellular communication in cell‐mediated cytotoxicity. Fluorescein transfer between H‐2d target cells and H‐2b lymphocytes in vitro (1971)

Abstract Fluorescein permeable junctions occur infrequently between unsensitized C57BL/6 lymphocytes (H‐2 b ) and DBA/2 mastocytoma cells (H‐2 d ), but the incidence of such junctions increases significantly with lymphocytes from animals sensitized against the mastocytes. The mastocytoma cells were labeled intracellularly with fluorescein using permeant (non‐fluorescent) fluorescein dipropionate which is hydrolyzed to free fluorescein within the cells; they were additionally stained with neutral red. As an in vitro model of cell‐mediated cytotoxicity the Brunner system was used in which close contact is a prerequisite of cell lysis. With contacts of aggressor cells to targets fluorescein permeable junctions were found in 17 out of 23 experiments, or 168 times, when sensitized spleen cells from female C57BL mice took part in the reaction. This incidence is significantly greater than in control experiments with normal spleen cells, when fluorescein permeable junctions were observed only 28 times and in only 9 out of 23 experiments.
A new constitutively activating mutation of the Gs protein alpha subunit-gsp oncogene is found in human pituitary tumours. (1990)

A new 227 Gln----Lys oncogenic mutation of the Gs alpha subunit (the GTP-binding protein that stimulates adenylyl cyclase) has been found in three out of eight human growth hormone-secreting pituitary tumours of the group 2, characterized by high cAMP and constitutively activated adenylyl cyclase. The additional five group 2 tumours expressed another, previously described mutation, 201 Arg----Cys, while the tumours of group 1, characterized by normal cAMP and adenylyl cyclase activity, expressed neither these nor the two other mutations of the same sites previously described in group 2. The Gln 227 site of alpha s corresponds to the Gln 61 site in the low Mw G protein, p21 ras, where the Leu substitution had already been shown to be oncogenic. The oncogenic potential (gsp oncogene) of the mutations so far observed depends on the reduced GTPase activity intrinsic to alpha s, with constitutive activation of the protein and marked elevation of cAMP. The latter is the intracellular messenger that stimulates growth of pituitary growth hormone-secreting cells and other cell types.
MOZ is essential for maintenance of hematopoietic stem cells (2006)

Monocytic leukemia zinc-finger protein (MOZ), a MYST family histone acetyltransferase, is involved in the chromosome translocations associated with acute myeloid leukemia. MOZ acts as a transcriptional coactivator for AML1, which is essential for establishment of definitive hematopoiesis. To investigate the roles of MOZ in normal hematopoiesis, we generated MOZ-null mice. MOZ-/- mice died around embryonic day 15 (E15). In MOZ-/- E14.5 embryos, hematopoietic stem cells, lineage-committed progenitors, and B lineage cells were severely reduced. On the other hand, arrest of erythroid maturation and elevated myeloid lineage populations were observed. MOZ-deficient fetal liver cells could not reconstitute hematopoiesis of recipients after transplantation. Analysis using microarray and flow cytometry revealed that expression of thrombopoietin receptor (c-Mpl), HoxA9, and c-Kit was down-regulated. These results show that MOZ is required for maintenance of hematopoietic stem cells, and that it plays a role in differentiation of erythroid and myeloid cells. Some aspects of the MOZ-/- phenotype are similar to that observed in PU.1-deficient mice. MOZ was able to interact with PU.1 and activate PU.1-dependent transcription, thus suggesting a physical and functional link between PU.1 and MOZ.
Generation of Digital Brain Phantom for Machine Learning Application of Dopamine Transporter Radionuclide Imaging (2022)

While machine learning (ML) methods may significantly improve image quality for SPECT imaging for the diagnosis and monitoring of Parkinson's disease (PD), they require a large amount of data for training. It is often difficult to collect a large population of patient data to support the ML research, and the ground truth of lesion is also unknown. This paper leverages a generative adversarial network (GAN) to generate digital brain phantoms for training ML-based PD SPECT algorithms. A total of 594 PET 3D brain models from 155 patients (113 male and 42 female) were reviewed and 1597 2D slices containing the full or a portion of the striatum were selected. Corresponding attenuation maps were also generated based on these images. The data were then used to develop a GAN for generating 2D brain phantoms, where each phantom consisted of a radioactivity image and the corresponding attenuation map. Statistical methods including histogram, Fréchet distance, and structural similarity were used to evaluate the generator based on 10,000 generated phantoms. When the generated phantoms and training dataset were both passed to the discriminator, similar normal distributions were obtained, which indicated the discriminator was unable to distinguish the generated phantoms from the training datasets. The generated digital phantoms can be used for 2D SPECT simulation and serve as the ground truth to develop ML-based reconstruction algorithms. The cumulated experience from this work also laid the foundation for building a 3D GAN for the same application.