gebhart/patrepeval huggingface dataset:
Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer (2021)

Squamous cell carcinomas (SCCs) comprise one of the most common histologic types of human cancer. Transcriptional dysregulation of SCC cells is orchestrated by tumor protein p63 (TP63), a master transcription factor (TF) and a well-researched SCC-specific oncogene. In the present study, both Gene Set Enrichment Analysis (GSEA) of SCC patient samples and in vitro loss-of-function assays establish fatty-acid metabolism as a key pathway downstream of TP63. Further studies identify sterol regulatory element binding transcription factor 1 (SREBF1) as a central mediator linking TP63 with fatty-acid metabolism, which regulates the biosynthesis of fatty-acids, sphingolipids (SL), and glycerophospholipids (GPL), as revealed by liquid chromatography tandem mass spectrometry (LC-MS/MS)-based lipidomics. Moreover, a feedback co-regulatory loop consisting of SREBF1/TP63/Kruppel like factor 5 (KLF5) is identified, which promotes overexpression of all three TFs in SCCs. Downstream of SREBF1, a non-canonical, SCC-specific function is elucidated: SREBF1 cooperates with TP63/KLF5 to regulate hundreds of cis-regulatory elements across the SCC epigenome, which converge on activating cancer-promoting pathways. Indeed, SREBF1 is essential for SCC viability and migration, and its overexpression is associated with poor survival in SCC patients. Taken together, these data shed light on mechanisms of transcriptional dysregulation in cancer, identify specific epigenetic regulators of lipid metabolism, and uncover SREBF1 as a potential therapeutic target and prognostic marker in SCC.
THE EFFECT OF CONVECTION ON AXISYMMETRIC PARABOLIC DENDRITES (1988)

Abstract Moving boundary solutions of the Navier Stokes and energy equations are obtained for shape-preserving isothermal paraboloids of revolution by using the Oseen viscous flow approximation. The theoretical results are in good agreement with the precise data of Glicksman et al. on succinonitrilc. The intensity of thermal convection as indicated by the Grashof number is shown to increase approximately as the inverse of the square of the super-cooling which may have important implications in microgravity experiments.
A Case of Xanthinuria: A Study on the Metabolism of Pyrazinamide and Allopurinol. (1991)

A 74-year-old female was diagnosed as having xanthinuria by measurement of the uric acid level in plasma, purine bases in urine and activity of xanthine oxidase in the duodenal mucosa. The determination of the urinary excretion of purine bases in her family demonstrated a slightly increased urinary excretion of oxypurines in her younger brother, suggesting that he was a heterozygote. The pyrazinamide-loading test and allopurinol-loading test demonstrated that she could neither metabolize pyrazinoic acid into 5-hydroxypyrazinoic acid nor allopurinol into oxypurinol, although there was a slight metabolizing of prazinamide into 5-hydroxypyrazinamide. This suggested that she belonged to the subgroup which can neither metabolize pyrazinamide into 5-hydroxypyrazinamide, pyrazinoic acid into 5-hydroxypyrazinoic acid nor allopurinol into oxypurinol.
Detection and Quantification of Hydrogen Peroxide in Aqueous Solutions Using Chemical Exchange Saturation Transfer (2017)

The development of new analytical methods to accurately quantify hydrogen peroxide is of great interest. In the current study, we developed a new magnetic resonance (MR) method for noninvasively quantifying hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) in aqueous solutions based on chemical exchange saturation transfer (CEST), an emerging MRI contrast mechanism. Our method can detect H<sub>2</sub>O<sub>2</sub> by its specific CEST signal at ∼6.2 ppm downfield from water resonance, with more than 1000 times signal amplification compared to the direct NMR detection. To improve the accuracy of quantification, we comprehensively investigated the effects of sample properties on CEST detection, including pH, temperature, and relaxation times. To accelerate the NMR measurement, we implemented an ultrafast Z-spectroscopic (UFZ) CEST method to boost the acquisition speed to 2 s per CEST spectrum. To accurately quantify H<sub>2</sub>O<sub>2</sub> in unknown samples, we also implemented a standard addition method, which eliminated the need for predetermined calibration curves. Our results clearly demonstrate that the presented CEST-based technique is a simple, noninvasive, quick, and accurate method for quantifying H<sub>2</sub>O<sub>2</sub> in aqueous solutions.
Strained silicon photonics for Pockels effect based modulation (2017)

We present on experimental results of strain-induced Pockels effect in silicon based on Mach-Zehnder interferometer modulators. We theoretically studied both Pockels effect and carrier parasitic effect in silicon under an electric field. We demonstrated high speed Pockels-based optical modulation up to 25 GHz.
Activation sensitizes human memory B cells to B‐cell receptor‐induced apoptosis (1999)

The outcome of antigen receptor (B-cell receptor; BCR) ligation on B-cell survival can be influenced by multiple parameters. They are linked to the physical properties of the antigen itself, the maturational stage of the cells and the costimuli provided by different components of the innate and acquired immunity. Here we report that apoptosis prevails over stimulation when a BCR agonist is applied to human memory B cells which have been preactivated by CD40 ligand or anti-immunoglobulin antibodies. The susceptibility of activated memory B cells to BCR-induced killing is correlated with their enhanced expression of the transcripts encoding the pro-apoptotic molecules Bax, c-Myc and p53. The BCR-mediated apoptosis of activated memory B cells does not require extensive cross-linking of the antigen receptors and relies neither on engagement of the FcgammaRII nor on the Fas/Fas ligand (Fas-L) system. Our findings suggest that activation stimuli open the BCR-induced apoptotic pathway in memory B cells. Therefore we propose that the concept of activation-induced cell death (AICD), originally described for T cells, also applies to mature B lymphocytes. The functions fulfilled by the AICD of mature B cells in the regulation of B-cell responses are discussed.
Relaxant effect of brain natriuretic peptide in nonsensitized and passively sensitized isolated human bronchi (2009)

Brain natriuretic peptide (BNP) relaxes guinea pig tracheal smooth muscle in vitro and is effective in preventing ovalbumin-induced bronchoconstriction and microvascular leakage in guinea pigs in vivo. Nonetheless, published studies on BNP in human airways in vitro are still lacking in the literature. The aim of this study was to investigate the effect of BNP in isolated human bronchi. The relaxant effect of BNP (1 nM to 10 microM) was assessed in nonsensitized and in passively sensitized human bronchial airways pre-contracted with submaximal concentration (EC(70)) of carbachol or histamine. At the end of the experiment, papaverine (500 microM) was then added. BNP induced a weak relaxant activity on carbachol-contracted bronchi in nonsensitized (relaxation: 4.23+/-0.51%) and passively sensitized bronchi (relaxation: 11.31+/-2.22%). On the other hand, BNP induced a relaxant activity on His-contracted bronchi in nonsensitized (relaxation: 42.52+/-9.03%) and in passively sensitized (relaxation: 60.57+/-9.58%). All these findings are a clear documentation of the modest relaxant role of BNP in asthma and, likely, COPD.
Functional heterogeneity of CD4+ T lymphocytes: two subpopulations with counteracting immunoregulatory functions identified with the monoclonal antibodies WR16 and WR19. (1987)

Monoclonal antibodies (MoAbs) WR16 and WR19 bound to 47% and 43% of CD4+ tonsil T lymphocytes, respectively. WR16 immunoprecipitated a 220,000 molecular weight (MW) component that was also expressed on CD8+ lymphocytes and on B lymphocytes, whereas binding of WR19 was restricted to CD4+ lymphocytes. Binding of these two MoAbs on freshly prepared tonsil CD4+ T lymphocytes was mutually exclusive, and they were used to prepare reciprocal CD4+ subpopulations by negative depletion using the panning technique. Recombination of subsets isolated in this way with autologous B lymphocytes activated with pokeweed mitogen demonstrated that WR16+/OKT4+ lymphocytes suppressed B lymphocyte Ig secretion, whereas WR19+/OKT4+ lymphocytes helped B lymphocyte Ig secretion. Removal of WR16+ cells from a CD4+ helper cell population enhanced B lymphocyte Ig secretion rate, whilst the re-addition of WR16+ cells to WR19+ helper cells reduced B lymphocyte Ig secretion rates to that seen with non-fractionated CD4+ helper cells. The overall level of helper activity induced by a given CD4+ population was thus a consequence of an interaction between WR19+ helper cells and WR16+ suppressor cells. The WR16+ subset of CD4+ cells exhibited a greater proliferation rate than WR19+/CD4+ cells in response to mitogen. Proliferation of negatively selected WR16+/CD4+ lymphocytes was inhibited by pretreatment with WR16, which also induced a concomitant increase in the level of suppressor activity of these cells. Expression of the antigens identified by these two MoAbs was not constant as phytohaemagglutinin activation of T lymphocytes induced a loss of WR16 binding with a simultaneous increase in the level of WR19 bound/cell and in the proportion of WR19+ cells. T lymphocyte clones selected from a normal population were composed of a disproportionately high number positive for WR19 and negative for WR16. These data indicated that the absence of the WR19 antigen on WR16+ cells may be transient as the antigen was acquired by the majority of CD4+ T lymphocytes after activation. These two MoAbs may therefore be used to predict the functional status of a heterogeneous population of CD4+ lymphocytes and may also prove to be of use in the study of CD4+ T lymphocyte activation.
Neutrophils Promote Liver Metastasis via Mac-1–Mediated Interactions with Circulating Tumor Cells (2012)

Although circulating neutrophils are associated with distant metastasis and poor outcome in a number of epithelial malignancies, it remains unclear whether neutrophils play an active causal role in the metastatic cascade. Using in vivo models of metastasis, we found that neutrophils promote cancer cell adhesion within liver sinusoids and, thereby, influence metastasis. Neutrophil depletion before cancer cell inoculation resulted in a decreased number of gross metastases in an intrasplenic model of liver metastasis. This effect was reversed when inflamed neutrophils were co-inoculated with cancer cells. In addition, early adhesion within liver sinusoids was inhibited in the absence of neutrophils and partially restored with a short perfusion of isolated activated neutrophils. Intravital microscopy showed that cancer cells adhered directly on top of arrested neutrophils, indicating that neutrophils may act as a bridge to facilitate interactions between cancer cells and the liver parenchyma. The adhesion of lipopolysaccharide-activated neutrophils to cancer cells was mediated by neutrophil Mac-1/ICAM-1. Our findings, therefore, show a novel role for neutrophils in the early adhesive steps of liver metastasis.
Synthesis and Photoluminescence Properties of Sm<sup>3+</sup>-Doped Ca<sub>10</sub>(PO<sub>4</sub>)<sub>6</sub>(OH)<sub>2</sub> Nanowire (2011)

The Sm 3+ -doped Ca 10 (PO 4 ) 6 (OH) 2 nanowires are synthesized by hydrothermal method. X-ray diffraction confirmed that the nanowires are made of the hexagonal Ca 10 (PO 4 ) 6 (OH) 2 . Scanning electron microscope and transmission electron microscope analysis show that the lengths of the nanowires are approximately 5μm, and their diameters are around 100 nm, and the aspect (length/diameter) ratio is about 50. The room temperature photoluminescence (PL) spectra of Sm 3+ -doped Ca 10 (PO 4 ) 6 (OH) 2 nanowires doped with different Sm 3+ concentration under 405 nm excitation has been investigated. It is found that there are three main sharp emissions peaks at near 569, 604, and 649 nm. The three emissions are due to the f-f forbidden transitions of the 4f electrons of Sm 3+ , corresponding to 4 G 5/2 → 6 H 5/2 (569 nm), 6 H 7/2 (604 nm), and 6 H 9/2 (649 nm), respectively. In addition, concentration quenching is also observed. It is found that the Sm 3+ 4 G 5/2 → 6 H 7/2 (604 nm) emission intensity of Sm 3+ -doped Ca 10 (PO 4 ) 6 (OH) 2 nanowires significantly increases with the increase of Sm 3+ concentration, and shows a maximum when Sm 3+ doping content is 0.5%. If Sm 3+ concentration continues to increase, namely more than 0.5%, the Sm 3+ 4 G 5/2 → 6 H 7/2 emission intensity decreases.
The fragile‐X syndrome: a growing gene causing familial intellectual disability (1994)

The fragile-X syndrome is the most common cause of familial intellectual disability. Recently, the gene related to the fragile-X syndrome [the 'fragile-X mental retardation'-1 (FMR-1) gene] has been isolated. In this review, clinical and molecular aspects of the fragile-X syndrome, current benefits and future prospects are discussed.
Scl isoforms act downstream of etsrp to specify angioblasts and definitive hematopoietic stem cells (2010)

Recent lineage studies suggest that hematopoietic stem cells (HSCs) may be derived from endothelial cells. However, the genetic hierarchy governing the emergence of HSCs remains elusive. We report here that zebrafish ets1-related protein (etsrp), which is essential for vascular endothelial development, also plays a critical role in the initiation of definitive hematopoiesis by controlling the expression of 2 stem cell leukemia (scl) isoforms (scl-alpha and scl-beta) in angioblasts. In etsrp morphants, which are deficient in endothelial and HSC development, scl-alpha alone partially rescues angioblast specification, arterial-venous differentiation, and the expression of HSC markers, runx1 and c-myb, whereas scl-beta requires angioblast rescue by fli1a to restore runx1 expression. Interestingly, when vascular endothelial growth factor (Vegf) signaling is inhibited, HSC marker expression can still be restored by scl-alpha in etsrp morphants, whereas the rescue of arterial ephrinb2a expression is blocked. Furthermore, both scl isoforms partially rescue runx1 but not ephrinb2a expression in embryos deficient in Vegf signaling. Our data suggest that downstream of etsrp, scl-alpha and fli1a specify the angioblasts, whereas scl-beta further initiates HSC specification from this angioblast population, and that Vegf signaling acts upstream of scl-beta during definitive hematopoiesis.
Evaluation of the impact of severity of itching symptoms on the level of depression in patients with allergic contact eczema (preliminary study) Ocena wpływu nasilenia świądu na poziom objawów depresji u pacjentów z alergicznym wypryskiem kontaktowym (badania wstępne) (2014)

Introduction: Allergic contact dermatitis is one of the most frequent skin disorders in the general population as well as among people who work professionally. Allergic contact allergens are simple chemical compounds. The most common are nickel and fragrance substances. Aim of the research: To estimate if and how the degree of itching in allergic contact dermatitis influences the development of depression. Material and methods: The treatment was conducted on a group of 17 people with allergic contact dermatitis. Each person was treated in order to estimate the level of depression using Becks scale and the level of itching. Next, it was estimated if the level of itching had any influence on the development of depression. Results: All skin diseases, including allergic contact eczema affect the biological and psychosocial functioning, and the qual ity of human. Five patients out of 17 showed features of depression: 3 mild (2 men and 1 woman), which is the most common state of transition, and 2 (women) moderately-severe depressive symptoms. Both patients with moderately-severe depressive symptoms had a significant degree of severity of pruritus. Conclusions: It was stated that the level of itching has no influence on the development of depression.
Ultrafast Dynamics of Flavins in Five Redox States (2008)

We report here our systematic studies of excited-state dynamics of two common flavin molecules, FMN and FAD, in five redox states--oxidized form, neutral and anionic semiquinones, and neutral and anionic fully reduced hydroquinones--in solution and in inert protein environments with femtosecond resolution. Using protein environments, we were able to stabilize two semiquinone radicals and thus observed their weak emission spectra. Significantly, we observed a strong correlation between their excited-state dynamics and the planarity of their flavin isoalloxazine ring. For a bent ring structure, we observed ultrafast dynamics from a few to hundreds of picoseconds and strong excitation-wavelength dependence of emission spectra, indicating deactivation during relaxation. A butterfly bending motion is invoked to get access to conical intersection(s) to facilitate deactivation. These states include the anionic semiquinone radical and fully reduced neutral and anionic hydroquinones in solution. In a planar configuration, flavins have a long lifetime of nanoseconds, except for the stacked conformation of FAD, where intramolecular electron transfer between the ring and the adenine moiety in 5-9 ps as well as subsequent charge recombination in 30-40 ps were observed. These observed distinct dynamics, controlled by the flavin ring flexibility, are fundamental to flavoenzyme's functions, as observed in photolyase with a planar structure to lengthen the lifetime to maximize DNA repair efficiency and in insect type 1 cryptochrome with a flexible structure to vary the excited-state deactivation to modulate the functional channel.
On the Tradeoffs between Static and Dynamic Adaptive Optimization for an Automotive Application (2017)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Government regulations for fuel economy and emission standards have driven the development of technologies that improve engine performance and efficiency. These technologies are enabled by an increased number of actuators and increasingly sophisticated control algorithms. As a consequence, engine control calibration time, which entails sweeping all actuators at each speed-load point to determine the actuator combination that meets constraints and delivers ideal performance, has increased significantly. In this work we present two adaptive optimization methods, both based on an indirect adaptive control framework, which improve calibration efficiency by searching for the optimal process inputs without visiting all input combinations explicitly. The difference between the methods is implementation of the algorithm in steady-state vs dynamic operating conditions. The goal of this work is to study the optimization performance tradeoffs between robustness to sensor noise and required optimization time. We demonstrate both methods on an engine installed in a dynamometer where multiple actuators were calibrated to minimize Break Specific Fuel Consumption (BSFC), while satisfying input and output constraints.&lt;/div&gt;&lt;/div&gt;
YOLO9000: Better, Faster, Stronger (2016)

We introduce YOLO9000, a state-of-the-art, real-time object detection system that can detect over 9000 object categories. First we propose various improvements to the YOLO detection method, both novel and drawn from prior work. The improved model, YOLOv2, is state-of-the-art on standard detection tasks like PASCAL VOC and COCO. At 67 FPS, YOLOv2 gets 76.8 mAP on VOC 2007. At 40 FPS, YOLOv2 gets 78.6 mAP, outperforming state-of-the-art methods like Faster RCNN with ResNet and SSD while still running significantly faster. Finally we propose a method to jointly train on object detection and classification. Using this method we train YOLO9000 simultaneously on the COCO detection dataset and the ImageNet classification dataset. Our joint training allows YOLO9000 to predict detections for object classes that don't have labelled detection data. We validate our approach on the ImageNet detection task. YOLO9000 gets 19.7 mAP on the ImageNet detection validation set despite only having detection data for 44 of the 200 classes. On the 156 classes not in COCO, YOLO9000 gets 16.0 mAP. But YOLO can detect more than just 200 classes; it predicts detections for more than 9000 different object categories. And it still runs in real-time.
Regulation of the erythropoietin receptor and involvement of JAK2 in differentiation of J2E erythroid cells. (1996)

In response to erythropoietin, J2E cells proliferate and differentiate into mature hemoglobin-producing erythroid cells. Here we show that following hormonal stimulation, between 10 and 17 proteins, including the erythropoietin receptor and JAK2, were tyrosine phosphorylated immediately after exposure to the hormone. Although the receptor was only phosphorylated to 15% of its maximum with 0.1 unit/ml erythropoietin, this was sufficient to induce peak hemoglobin synthesis. The importance of JAK2 to J2E cell maturation was demonstrated by inhibiting JAK2 protein synthesis with antisense oligonucleotides; not only was erythropoietin-stimulated mitogenesis inhibited by this procedure, but differentiation was also suppressed. In addition, the activation of STAT5 paralleled the kinetics of receptor phosphorylation. During differentiation, 94% decrease in surface erythropoietin receptors was detected 48 h after ligand binding, but transcription of the receptor gene, mRNA steady-state levels, protein content, and translation rates did not alter with hormonal stimulation. We concluded from these experiments that (a) sub-maximal receptor phosphorylation is sufficient for differentiation to proceed; (b) JAK2 is required for erythropoietin-induced cell division and maturation; and (c) post-translational processing, or translocation, play important roles in controlling surface erythropoietin receptor numbers.
CMOS luminescence lifetime sensor for white LED multi-spectral characterization (2017)

Time constants and luminescence lifetimes of an InGaN-based white LED at different wavelengths are characterized by a novel multi-cycle charge modulation based CMOS image sensor chip. To enable high sensitivity, we propose parasitic insensitive multi-cycle charge modulation scheme for low-light lifetime extraction. The designed in-pixel CTIA-based structure is able to capture the weak luminescence-induced voltage signal by accumulating photon-generated charges in 25 discrete gated time windows within 10ms, in which each time window has 10us pulse width. A pinned photodiode on chip with 1.04pA dark current is utilized for luminescence detection. The proposed circuitry can achieve 2.1mV/(nW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) responsivity and 4.38nW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> resolution at 630nm wavelength for intensity measurement and 45ns resolution for lifetime measurement.
Recurrent Batch Normalization (2016)

We propose a reparameterization of LSTM that brings the benefits of batch normalization to recurrent neural networks. Whereas previous works only apply batch normalization to the input-to-hidden transformation of RNNs, we demonstrate that it is both possible and beneficial to batch-normalize the hidden-to-hidden transition, thereby reducing internal covariate shift between time steps. We evaluate our proposal on various sequential problems such as sequence classification, language modeling and question answering. Our empirical results show that our batch-normalized LSTM consistently leads to faster convergence and improved generalization.