gebhart/patrepeval huggingface dataset:
Position specific variation in the rate of evolution in transcription factor binding sites (2003)

Background: The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results: Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion: As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA.
Angiographic outcomes following stenting or coronary artery bypass surgery of the left main coronary artery: fifteen-month outcomes from the synergy between PCI with TAXUS express and cardiac surgery left main angiographic substudy (SYNTAX-LE MANS) (2011)

At 15 months, 15.6% (41/263) of grafts were at least 50% obstructed but this was not significantly associated with MACCE; 92.4% (134/145) of patients had stents that remained patent at 15 months, and stent restenosis was significantly associated with MACCE, predominantly due to revascularisation.
Drug-Coated Balloons: Drugs Beyond Paclitaxel? (2022)

Despite the proven antiproliferative and/or anti-inflammatory effect of the drugs, none of the coatings significantly reduced LLL compared to uncoated balloons and thus, based on the results presented here, none of the tested coatings may be considered a substitute for the paclitaxel-based coatings currently in clinical use.
Efficient beam-correcting holographic collimator for laser diodes (1992)

We describe a method for recording a beam-correcting holographic collimator for laser diodes in the presence of recording-to-readout wavelength shift. An astigmatism-correcting, beam-shaping hologram recorded with this method at 488 nm displays a high-efficiency, near-diffraction-limited collimation of a diode beam at 820 nm.
Meta‐analysis: reduction in hepatic events following interferon‐alfa therapy of chronic hepatitis B (2010)

Interferon-alfa treatment reduces the risk of hepatic events particularly among responders to treatment.
Microhardness of Sputter‐Deposited Zirconia Films on Silicon Wafers (1997)

Calcia‐stabilized zirconia films were deposited on the surface of silicon 111 wafers using radio frequency (rf) magnetron sputter deposition. Deposition was conducted at substrate temperatures that varied in the range of 80°–900°C. X‐ray diffractometry results showed that all the films consisted of cubic zirconia. The fracture surface morphology and etched surfaces of the films were studied using scanning electron microscopy (SEM). Depending on the deposition temperature, the structure of the film was either columnar or equiaxed. The transition temperature from the columnar structure to the equiaxed structure was at a ratio of deposition temperature to melting temperature of } 0.42. The microhardness of the films was evaluated using a developed model that is based on the plastic zone analysis below a diamond (Vickers) indentor. From this model, the microhardness was found to increase as the deposition temperature increased, which was probably because the hardness of ceramic materials decreases as the defect concentration increases.
The diabetes-atrial fibrillation paradox (2019)

To the Editor We appreciate the editorial by Burden and Timpson1 highlighting collider bias as a potential explanation for our findings of a differential association between diabetes and atrial fibrillation (AF) by ethnicity as well as by heart failure (HF) type.2 Collider bias applies in aetiologic research where causal associations between two independent variables are spuriously created due to stratification by a causally related health outcome. First we point out that ours was not aetiologic research, and we specifically acknowledged that our observational study design does not allow ascertainment of causality. We nonetheless agree that the diabetes–AF paradox was one of our most intriguing observations, raising questions that, while not answered by …
Co2+ and Ni2+ resistance in Saccharomyces cerevisiae associated with a reduction in the accumulation of Mg2+. (1991)

A mutant strain of Saccharomyces cerevisiae (NR 6), which can be associated with a reduction in the accumulation of Mg2+ has been isolated. This mutant strain displays resistance to both Ni2+ and Co2+, but not, however, towards Cu2+, Cd2+, Mn2+, Zn2+ and Cr2O7(2-). Both Co2+ and Ni2+ uptake by the mutant strain is less than by the wild type (CMR-50). The inhibitory effects of Ni2+ and Co2+ on the growth of both strains NR-6 and CMR-50 can be cancelled by increasing the concentrations of Mg2+ in the medium and to a lower extent by the addition of Ca2+ which results in a decreased uptake of these metals. It therefore appears that the resistant mechanisms of this mutant strain NR-6 is due to a reduction in the uptake of Co2+ and Ni2+ via a Mg2+ transport system.
Novel extended modified twin test based sensing for cooperative communication under noise uncertainty (2016)

With the evolution of 5G wireless communication systems, we have witnessed an increase in the demand for wireless broadband applications and services. However, fixed allocation of the frequency spectrum has led to an under-utilization of the spectral resources, making it hard to find unoccupied bands to deploy new services. To address the spectrum scarcity problem, a new and promising technology has emerged, namely cognitive radio. In particular, centralized cooperative spectrum sensing (CSS) is becoming an effective strategy to discover unused frequency bands, since it allows to overcome issues related to shadowing and noise uncertainty. Here, we propose an extension of the modified twin test based on a double test that takes into account correlated observations in a real communication scenario, considering different noise uncertainty values. In particular, our test employs two fusion rules together (i.e. OR and Majority), salvaging those detection cases that would otherwise go undetected due to the noise uncertainty. The obtained results show that the proposed method outperforms the conventional CSS and modified twin test, highlighting its robustness in the presence of noise uncertainty.
Newly-Discovered Neural Features Expand the Pathobiological Knowledge of Blastic Plasmacytoid Dendritic Cell Neoplasm (2021)

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and highly aggressive hematologic malignancy originating from plasmacytoid dendritic cells (pDCs). The microRNA expression profile of BPDCN was compared to that of normal pDCs and the impact of miRNA dysregulation on the BPDCN transcriptional program was assessed. MiRNA and gene expression profiling data were integrated to obtain the BPDCN miRNA-regulatory network. The biological process mainly dysregulated by this network was predicted to be neurogenesis, a phenomenon raising growing interest in solid tumors. Neurogenesis was explored in BPDCN by querying different molecular sources (RNA sequencing, Chromatin immunoprecipitation-sequencing, and immunohistochemistry). It was shown that BPDCN cells upregulated neural mitogen genes possibly critical for tumor dissemination, expressed neuronal progenitor markers involved in cell migration, exchanged acetylcholine neurotransmitter, and overexpressed multiple neural receptors that may stimulate tumor proliferation, migration and cross-talk with the nervous system. Most neural genes upregulated in BPDCN are currently investigated as therapeutic targets.
Interference Cancellation Using Power Minimization and Self-coherence Properties of GPS Signals (2004)

This paper presents the performance analysis of two digital beam forming techniques used in conjunction with a software GPS receiver to mitigate interference to GPS signals in interference environment. The first method is the constrained minimum power (MOP) method. The second method is the so-called self-coherence restoral (SCORE) method. Both experimental and simulation data are used in the study. The study was performed using experiment data collected in an anechoic chamber to obtain GPS and interference signals. A two by two GPS antenna array and a four channel radio frequency front end were used to collect simulated GPS data generated using hardwarebased simulator in controlled interference environment. Three types of interference signals are deployed in the experiments: FM chirp, binary phase shift key, and broadband. The interference power levels used were +20, +30, and +40 dB above GPS signal power. A software GPS receiver was used to perform acquisition of GPS signals to evaluate the performance of the beam forming algorithms. The preliminary result showed that the MOP method can effectively mitigate all three types of interference at all power levels if a single interference source is present. Experiments using multiple broadband interference sources were also analyzed and our results shown that the effectiveness of the MOP method diminishes as the interference signal power increases and ceases to function at the +40 dB level. The SCORE method does not exhibit consistent performance for the experimental data. This is consistent with our simulation results which show that for the SCORE algorithm to generate satisfactory results, sufficient number of antenna elements is necessary even if there is no interference source present. The number of antenna element is determined by the number of satellites available, as well as the number of interference sources. The experimental and simulation results are discussed in this paper.
Interplay Between V-ATPase G1 and Small EV-miRNAs Modulates ERK1/2 Activation in GBM Stem Cells and Nonneoplastic Milieu (2020)

The ATP6V1G1 subunit (V1G1) of the vacuolar proton ATPase (V-ATPase) pump is crucial for glioma stem cells (GSC) maintenance and <i>in vivo</i> tumorigenicity. Moreover, V-ATPase reprograms the tumor microenvironment through acidification and release of extracellular vesicles (EV). Therefore, we investigated the role of V1G1 in GSC small EVs and their effects on primary brain cultures. To this end, small EVs were isolated from patients-derived GSCs grown as neurospheres (NS) with high (V1G1<sup>HIGH</sup>-NS) or low (V1G1<sup>LOW</sup>-NS) V1G1 expression and analyzed for V-ATPase subunits presence, miRNA contents, and cellular responses in recipient cultures. Our results show that NS-derived small EVs stimulate proliferation and motility of recipient cells, with small EV derived from V1G1<sup>HIGH</sup>-NS showing the most pronounced activity. This involved activation of ERK1/2 signaling, in a response reversed by V-ATPase inhibition in NS-producing small EV. The miRNA profile of V1G1<sup>HIGH</sup>-NS-derived small EVs differed significantly from that of V1G1<sup>LOW</sup>-NS, which included miRNAs predicted to target MAPK/ERK signaling. Mechanistically, forced expression of a MAPK-targeting pool of miRNAs in recipient cells suppressed MAPK/ERK pathway activation and blunted the prooncogenic effects of V1G1<sup>HIGH</sup> small EV. These findings propose that the GSC influences the brain milieu through a V1G1-coordinated EVs release of MAPK/ERK-targeting miRNAs. Interfering with V-ATPase activity could prevent ERK-dependent oncogenic reprogramming of the microenvironment, potentially hampering local GBM infiltration. IMPLICATIONS: Our data identify a novel molecular mechanism of gliomagenesis specific of the GBM stem cell niche, which coordinates a V-ATPase-dependent reprogramming of the brain microenvironment through the release of specialized EVs.
Evaluation of Time-of-Flight Secondary Ion Mass Spectrometry for Metal Contamination Monitoring on Si Wafer Surfaces (2000)

Due to stringent IC‐production requirements, the metallic contamination of silicon surfaces decreases to very low concentration levels (below ). Therefore new alternatives to measure the presence of these contaminants and to quantify their amounts are investigated. This study focuses on the capabilities of time of flight secondary ion mass spectrometry (TOF‐SIMS). It compares and combines TOF‐SIMS results with those of the standard technique direct total reflectance X‐ray fluorescence spectroscopy (TXRF). Next, it investigates the influence of the surface oxidation state (i.e., bare silicon, native and thermal oxide) on the TOF‐SIMS signal response. Then, TOF‐SIMS surface spectra are quantified using relative sensitivity factors, according to two different approaches (experimentally vs. theoretically derived). Finally, the influence of oxidation ambient on Fe redistribution in the thermal oxide layer is studied using the TOF‐SIMS dual beam option to perform depth profiling. A good general agreement is obtained between the quantified TOF‐SIMS surface spectra and the TXRF values. For the Fe distribution in the oxide layer, TOFSIMS reaches qualitatively the same conclusions as vapor‐phase decomposition‐droplet collection TXRF. For 5 nm oxide samples no difference between both furnace ambients can be observed. For 15 nm oxides, however, more Fe is trapped in the oxide when oxygen is added to the ambient. © 2000 The Electrochemical Society. All rights reserved.
Androgen Receptor Upregulation Mediates Radioresistance after Ionizing Radiation (2015)

Clinical trials have established the benefit of androgen deprivation therapy (ADT) combined with radiotherapy in prostate cancer. ADT sensitizes prostate cancer to radiotherapy-induced death at least in part through inhibition of DNA repair machinery, but for unknown reasons, adjuvant ADT provides further survival benefits. Here, we show that androgen receptor (AR) expression and activity are durably upregulated following radiotherapy in multiple human prostate cancer models in vitro and in vivo. Moreover, the degree of AR upregulation correlates with survival in vitro and time to tumor progression in animal models. We also provide evidence of AR pathway upregulation, measured by a rise in serum levels of AR-regulated hK2 protein, in nearly 20% of patients after radiotherapy. Furthermore, these men were three-fold more likely to experience subsequent biochemical failure. Collectively, these data demonstrate that radiotherapy can upregulate AR signaling after therapy to an extent that negatively affects disease progression and/or survival.
ChemInform Abstract: Total Synthesis of ( +)‐Latrunculin B. (1986)

Abstract Total Synthesis of ( +)‐Latrunculin B. ‐ The carboxylate (I) is converted to the ke‐ tonc (III) in 4 steps.
An Animal Model of Inhaled Vitamin E Acetate and EVALI-like Lung Injury (2020)

An Animal Model of EVALI In this study, investigators developed a mouse model of e-cigarette, or vaping, product use–associated lung injury. They showed that in these mice, vitamin E acetate induce...
The role of the neu oncogene product in cell transformation and normal development. (1988)

p185neu, the protein product of the neu gene, is a tyrosine kinase receptor with structural similarity to the epidermal growth factor (EGF) receptor. The cognate ligand for the p185neu receptor remains unknown. We have defined: 1) stage and tissue-specific expression patterns of the neu gene product in developing tissues; 2) p185neu phosphorylation and the regulation of p185neu tyrosine kinase activity by EGF. 3) Synergistic interactions of cellular rat p185neu and EGF receptor leading to cell transformation; 4) structural and functional differences of normal and oncogenic p185neu. These observations explain some features of how p185neu is involved in normal development and neoplastic transformation.
Local Severe Storm Tracking and Warning in Pre-Convection Stage from the New Generation Geostationary Weather Satellite Measurements (2019)

Accurate and prior identification of local severe storm systems in pre-convection environments using geostationary satellite imagery measurements is a challenging task. Methodologies for “convective initiation” identification have already been developed and explored for operational nowcasting applications; however, warning of such convective systems using the new generation of geostationary satellite imagery measurements in pre-convection environments is still not well studied. In this investigation, the Random Forest (RF) machine learning algorithm is used to develop a predictive statistical model for tracking and identifying three different types of convective storm systems (weak, medium, and severe) over East Asia by combining spatially-temporally collocated Himawari-8 (H08) measurements and Numerical Weather Prediction (NWP) forecast data. The Global Precipitation Measurement (GPM) gridded product is used as a benchmark to train the predictive models based on a sample-balance technique which can adjust or balance the samples of three different convection types to avoid over-fitting any type of dataset. Variables such as brightness temperatures (BTs) from H08 water vapor absorption bands (6.2 μm, 6.9 μm and 7.3 μm) and Total Precipitable Water (TPW) from NWP show relatively high ranks in the predictive model training. These sensitive variables are closely associated with convectively dominated precipitation areas, indicating the importance of predictors from both H08 and NWP data. The final optimal RF model is achieved with an accuracy of 0.79 for classification of all convective storm systems, while the Probability of Detection (POD) of this model for severe and medium convections can reach 0.66 and 0.70, respectively. Two typical sudden convective storm cases in the warm season of 2018 tracked by this algorithm are described, and results indicate that the H08 and NWP based statistical model using the RF algorithm is capable of capturing local burst convective storm systems about 1–2 h earlier than the outbreak of heavy rainfall.
Protective Effect of Phloroglucinol on Oxidative Stress-Induced DNA Damage and Apoptosis through Activation of the Nrf2/HO-1 Signaling Pathway in HaCaT Human Keratinocytes (2019)

Phloroglucinol (PG) is a component of phlorotannins, which are abundant in marine brown alga species. Recent studies have shown that PG is beneficial in protecting cells from oxidative stress. In this study, we evaluated the protective efficacy of PG in HaCaT human skin keratinocytes stimulated with oxidative stress (hydrogen peroxide, H<sub>2</sub>O<sub>2</sub>). The results showed that PG significantly inhibited the H<sub>2</sub>O<sub>2</sub>-induced growth inhibition in HaCaT cells, which was associated with increased expression of heme oxygenase-1 (HO-1) by the activation of nuclear factor erythroid 2-related factor-2 (Nrf2). PG remarkably reversed H<sub>2</sub>O<sub>2</sub>-induced excessive ROS production, DNA damage, and apoptosis. Additionally, H<sub>2</sub>O<sub>2</sub>-induced mitochondrial dysfunction was related to a decrease in ATP levels, and in the presence of PG, these changes were significantly impaired. Furthermore, the increases of cytosolic release of cytochrome <i>c</i> and ratio of Bax to Bcl-2, and the activation of caspase-9 and caspase-3 by the H<sub>2</sub>O<sub>2</sub> were markedly abolished under the condition of PG pretreatment. However, the inhibition of HO-1 function using zinc protoporphyrin, a HO-1 inhibitor, markedly attenuated these protective effects of PG against H<sub>2</sub>O<sub>2</sub>. Overall, our results suggest that PG is able to protect HaCaT keratinocytes against oxidative stress-induced DNA damage and apoptosis through activating the Nrf2/HO-1 signaling pathway.
Evoked potentials generated by deep brain stimulation for Parkinson's disease (2022)

We describe the current scientific landscape of evoked potentials to facilitate and stimulate further investigation.
Benefits of Ultra-Fast-Track Anesthesia in Left Ventricular Assist Device Implantation: Propensity Score Matched Analysis (2017)

Objectives: The use of left ventricular assist devices (LVADs) has gained significant importance for treatment of end-stage heart failure. Fast-track procedures are well established in cardiac surgery, whereas knowledge of their benefits after LVAD implantation is sparse. We hypothesized that ultra-fast-track anesthesia (UFTA) with in-theater extubation or at a maximum of 4 hour after surgery is feasible in INTERMACS level 3 and 4 patients and might prevent postoperative complications.
Roles of CpcF and CpcG1 in Peroxiredoxin-Mediated Oxidative Stress Responses and Cellular Fitness in the Cyanobacterium Synechocystis sp. PCC 6803 (2019)

As a component of the photosynthetic apparatus in cyanobacteria, the phycobilisome (PBS) plays an important role in harvesting and transferring light energy to the core photosynthetic reaction centers. The size, composition (phycobiliprotein and chromophore), and assembly of PBSs can be dynamic to cope with tuning photosynthesis and associated cellular fitness in variable light environments. Here, we explore the role of PBS-related stress responses by analyzing deletion mutants of <i>cpcF</i> or <i>cpcG1</i> genes in <i>Synechocystis</i> sp. PCC 6803. The <i>cpcF</i> gene encodes a lyase that links the phycocyanobilin (PCB) chromophore to the alpha subunit of phycocyanin (PC), a central phycobiliprotein (PBP) in PBSs. Deletion of <i>cpcF</i> (i.e., Δ<i>cpcF</i> strain) resulted in slow growth, reduced greening, elevated reactive oxygen species (ROS) levels, together with an elevated accumulation of a stress-related Peroxiredoxin protein (Sll1621). Additionally, Δ<i>cpcF</i> exhibited reduced sensitivity to a photosynthesis-related stress inducer, methyl viologen (MV), which disrupts electron transfer. The <i>cpcG1</i> gene encodes a linker protein that serves to connect PC to the core PBP allophycocyanin. A deletion mutant of <i>cpcG1</i> (i.e.,Δ<i>cpcG1</i>) exhibited delayed growth, a defect in pigmentation, reduced accumulation of ROS, and insensitivity to MV treatment. By comparison, Δ<i>cpcF</i> and Δ<i>cpcG1</i> exhibited similarity in growth, pigmentation, and stress responses; yet, these strains showed distinct phenotypes for ROS accumulation, sensitivity to MV and Sll1621 accumulation. Our data emphasize an importance of the regulation of PBS structure in ROS-mediated stress responses that impact successful growth and development in cyanobacteria.