gebhart/patrepeval huggingface dataset:
Terahertz Dynamics in Human Cells and Their Chromatin (2014)

The terahertz dynamics of human cells of the U937 line and their chromatin has been investigated by high-resolution inelastic X-ray scattering. To highlight its dynamical features in situ, nuclear DNA has been stained by uranyl-acetate salt. The general behavior of the collective dynamics of the whole cell is quite similar to that of bulk water, with a nearly wavevector-independent branch located at about 5 meV and a propagating mode with a linear trend corresponding to a speed of sound of 2900 ± 100 m/s. We provide the first experimental evidence for the existence of two branches also in the dispersion curves of chromatin. The high-energy mode displays an acoustic-like behavior with a sound velocity similar to unstained cells, but in this case the branch likely originates from the superposition of intramolecular DNA optic modes. A low-energy optic-like branch, distinctive of the chromatin moiety, is found at about 2.5 meV.
Contextualized Spatio-Temporal Contrastive Learning with Self-Supervision (2021)

Modern self-supervised learning algorithms typically enforce persistency of instance representations across views. While being very effective on learning holistic image and video representations, such an objective becomes sub-optimal for learning spatio-temporally fine-grained features in videos, where scenes and instances evolve through space and time. In this paper, we present Contextualized Spatio-Temporal Contrastive Learning (ConST-CL) to effectively learn spatio-temporally fine-grained video representations via self-supervision. We first design a region-based pretext task which requires the model to transform in-stance representations from one view to another, guided by context features. Further, we introduce a simple network design that successfully reconciles the simultaneous learning process of both holistic and local representations. We evaluate our learned representations on a variety of downstream tasks and show that ConST-CL achieves competitive results on 6 datasets, including Kinetics, UCF, HMDB, AVA-Kinetics, AVA and OTB.
CFTR Localization in Native Airway Cells and Cell Lines Expressing Wild-type or F508del-CFTR by a Panel of Different Antibodies (2004)

The intracellular localization of cystic fibrosis transmembrane conductance regulator (CFTR) in native tissues is a major issue in the study of mutation, processing, and trafficking effects in CFTR and in the evaluation of therapeutic strategies in cystic fibrosis (CF). This work evaluated the applicability of ten different antibodies (Abs) under various fixation techniques for CFTR localization in fresh-brushed nasal epithelial cells collected from CF patients homozygous for F508del and control individuals. In parallel, the same Ab panel was also tested on BHK cell lines overexpressing wild-type or F508del CFTR. The Abs MATG1061, 169, Lis1, MP-CT1, CC24-R, MAB25031, and MAB1660 gave the best detection of CFTR in the apical region (AR) of nasal tall columnar epithelial (TCE) cells. The labeling pattern of these Abs was consistent with the postulated processing defect of F508del CFTR because only a minority of CF TCE cells present CFTR in the AR. In contrast, M3A7, MM13-4, and L12B4 weakly react with the AR and stain almost exclusively a cis-Golgi-like structure in the majority of CF and non-CF airway cells. In BHK cells, all the Abs enabled distinction between wild-type CFTR localization in cell membrane from F508del CFTR, which in these cells is exclusively located in the endoplasmic reticulum.
Resistance to Tobacco mosaic virus and Botrytis cinerea in tobacco transformed with complementary DNA encoding an inhibitor of viral replication‐like protein (2005)

Abstract We have previously cloned a 1016‐bp‐long complementary DNA (cDNA) clone (named NC330) encoding an inhibitor of virus replication (IVR)‐like protein from induced‐resistant leaves of Nicotiana tabacum cv. Samsun NN. In the present work, NC330 cDNA was cloned in an Agrobacterium binary vector and introduced into the genome of N. tabacum cv. Samsun nn that is susceptible to Tobacco mosaic virus (TMV). Eight R 0 were highly resistant, with TMV titres less than 2% of the controls. The progeny of these primary transformants resulted in four TMV‐resistant and four susceptible lines. The progeny of the plant with highest resistance for TMV was selfed during four generations. In the R 2 generation, out of 112 plants tested, 3 plants showed excellent resistance and 5 a lesser degree of resistance. NC330 transcripts were detected in these R 2 plants as well as in their R 1 and R 0 parents. Two R 2 plants were self‐pollinated to obtain the R 3 generation. All the 25 R 3 progeny plants of one line contained PCR‐amplifiable NC330, compared with only 6 of the 23 progeny plants from the other line. Following TMV inoculation, virus was undetectable in seven of the eight tested R 3 progeny of the first line and five of the six R 3 progeny plants of the second line. NC330 transcripts were detected in the TMV‐resistant transgenic plants but also in some susceptible plants. TMV resistance was suppressed when the plants were kept at higher temperatures (32–34°C), whereas returning the plants to lower temperatures (24–26°C) restored resistance. Transgenic plants resistant to TMV were also resistant to B. cinerea following inoculation of seedlings or of whole plants. The presence of the NC330 DNA was correlated with changes in the physiology of the transgenic plant. Seed germination was inhibited at high temperatures and in the dark. Rootlets of germinating seeds of the transgenic plants grew significantly faster than those of control seeds. These observations were correlated with a significantly higher concentration of abscisic acid in the seeds and seedlings of the transgenic plants. In silico analysis suggests that the NC330 protein translated from the NC330 cDNA is a tetratricopeptide repeats protein and that it may be involved in protein–protein interaction as part of the pathogen resistance mechanism.
AXL-dependent infection of human fetal endothelial cells distinguishes Zika virus from other pathogenic flaviviruses (2017)

Although a causal relationship between Zika virus (ZIKV) and microcephaly has been established, it remains unclear why ZIKV, but not other pathogenic flaviviruses, causes congenital defects. Here we show that when viruses are produced in mammalian cells, ZIKV, but not the closely related dengue virus (DENV) or West Nile virus (WNV), can efficiently infect key placental barrier cells that directly contact the fetal bloodstream. We show that AXL, a receptor tyrosine kinase, is the primary ZIKV entry cofactor on human umbilical vein endothelial cells (HUVECs), and that ZIKV uses AXL with much greater efficiency than does DENV or WNV. Consistent with this observation, only ZIKV, but not WNV or DENV, bound the AXL ligand Gas6. In comparison, when DENV and WNV were produced in insect cells, they also infected HUVECs in an AXL-dependent manner. Our data suggest that ZIKV, when produced from mammalian cells, infects fetal endothelial cells much more efficiently than other pathogenic flaviviruses because it binds Gas6 more avidly, which in turn facilitates its interaction with AXL.
Simulation of bipolar transistors degradation at various dose rates and electrical modes for high dose conditions (2013)

Radiation response of bipolar devices irradiated under various electrical modes and dose rates at high doses are experimentally investigated. Nonlinear numerical model including ELDRS effects and electric field reduction at high doses has been developed and validated. Dose degradation of a bipolar transistor's gain factor at different dose rates and electrical modes has been simulated and explained in a unified way, based on dependence of the charge yield in isolation oxides on dose rates and electric fields. It has been shown that at high doses one needs to use a nonlinear, self-consisted numerical approach, accounting simultaneous suppression of the oxide electric field induced by trapped charge. Correspondingly, two types of degradation saturation have been revealed: (i) due to simultaneous thermal annealing, and (ii) due to total dose dependent electric field reduction in oxides. The former implies proportionality of the saturation dose and degradation level to dose rate, the latter permits dose rate independent saturation levels of degradation.
P-185) Ex vivo inhibition by flutoprazepam of 3H-flunitrazepam binding to mouse brain homogenate. (1983)

Flutoprazepam (FPZ), a new antianxiety drug of benzodiazepine class, was found to be more active in preventing pentetrazole induced convulsion than predicted from the Ki value obtained from binding studies in vitro. Several benzodiazepines are extensively biotransformed in vivo, giving rise to active metabolites. This complicates any attempt to correlate pharmacological effects with in vitro potencies, taking into account that benzodiazepines are metabolized differently in various animal species. Therefore, we studied the ability of FPZ and its metabolites, N-desalkyl-FPZ and N-desalkyl-3-OH-FPZ, to inhibit 3H-flunitrazepam (FNZ) binding to mouse brain ex vivo and compared it with the potencies for anti-pentetrazole activity. FPZ and its metabolites inhibited the specific 3H-FNZ binding dose-dependently as diazepam (DZP), prazepam (PZP), nitrazepam (NZP) and chlordiazepoxide (CZP) did. With regard to ID50 (mg/kg, p.o.), the potency of FPZ was about 3-6 times higher than those of DZP, NZP and PZP and was about 80 times higher than that of CZP. Two metabolites of FPZ were 1-2 times as active as FPZ. The correlation between the ED50 values for anti-pentetrazole activity and the ID50 values was statistically significant (r=0.929). These results suggest that the two metabolites of FPZ participate partly in the pharmacological effect of FPZ.
Data from The Activation of the WNT Signaling Pathway Is a Hallmark in Neurofibromatosis Type 1 Tumorigenesis (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The hallmark of neurofibromatosis type 1 (NF1) is the onset of dermal or plexiform neurofibromas, mainly composed of Schwann cells. Plexiform neurofibromas can transform into malignant peripheral nerve sheath tumors (MPNST) that are resistant to therapies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The aim of this study was to identify an additional pathway in the NF1 tumorigenesis. We focused our work on Wnt signaling that is highly implicated in cancer, mainly in regulating the proliferation of cancer stem cells. We quantified mRNAs of 89 Wnt pathway genes in 57 NF1-associated tumors including dermal and plexiform neurofibromas and MPNSTs. Expression of two major stem cell marker genes and five major epithelial–mesenchymal transition marker genes was also assessed. The expression of significantly deregulated Wnt genes was then studied in normal human Schwann cells, fibroblasts, endothelial cells, and mast cells and in seven MPNST cell lines.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The expression of nine Wnt genes was significantly deregulated in plexiform neurofibromas in comparison with dermal neurofibromas. Twenty Wnt genes showed altered expression in MPNST biopsies and cell lines. Immunohistochemical studies confirmed the Wnt pathway activation in NF1-associated MPNSTs. We then confirmed that the knockdown of &lt;i&gt;NF1&lt;/i&gt; in Schwann cells but not in epithelial cells provoked the activation of Wnt pathway by functional transfection assays. Furthermore, we showed that the protein expression of active β-catenin was increased in &lt;i&gt;NF1&lt;/i&gt;-silenced cell lines. Wnt pathway activation was strongly associated to both cancer stem cell reservoir and Schwann–mesenchymal transition.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; We highlighted the implication of Wnt pathway in NF1-associated tumorigenesis. &lt;i&gt;Clin Cancer Res; 20(2); 358–71. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Dynamic textures for human movement recognition (2010)

Human motion can be seen as a type of texture pattern. In this paper, we adopt the ideas of spatiotemporal analysis and the use of local features for motion description. We describe human movements with dynamic texture features. The proposed method is computationally simple and suitable for various applications such as action and gait recognition. We use Gentle AdaBoost to perform feature selection and build strong models from weak classifiers. We verify the performance of our methods on the challenging KTH and USF datasets, achieving high accuracy.
Predicting discomfort glare from outdoor lighting installations (2008)

In addition to sky glow and light trespass, discomfort glare from outdoor lighting installations is a growing concern to the public. A series of experimental investigations was performed to assess the relative impacts of light source photometric characteristics on subjective ratings of discomfort glare. The results converge, demonstrating the influence of light source illuminance, surround illuminance and ambient illuminance on subjective judgements of discomfort glare. A simple model relating these photometric quantities is proposed for making predictions of discomfort glare from outdoor lighting installations. This model can be readily incorporated into existing frameworks for evaluating light pollution as well as into lighting calculation software.
Squirrel search algorithm based intelligent controller for interconnected power system (2023)

In this paper, a novel controller, namely fractional order fuzzy proportional-integral-derivative (FOFPID) has been proposed for the dual area power system of hydro-thermal-gas units (DAHTG). The squirrel search algorithm (SSA) is implemented to achieve the optimal values of the controller tuning parameters. Further, various non-linearity constraints, such as governor dead band (GDB), generation rate constraint (GRC) and communication time delays (CTDs) have also been considered to test the effectiveness of the proposed controller in a real-time environment. The step load of 10% is provided as the disturbance under the regulation. In addition, the coordinated strategy of a static synchronous series compensator (SSSC) device and superconducting magnetic energy storage (SMES) is employed in the proposed system to enhance the system’s performance. Further, the accuracy, effectiveness and robustness of the proposed controller are revealed through the comparative analysis with classical PID and traditional fuzzy PID controllers. Furthermore, presented controller efficacy is revealed with the other recently reported control techniques by implementing it on the two-area thermal system with GDB. The comparative analysis shows the better performance of the proposed controller than these two. Finally, the sensitivity analysis is performed to check the controller robustness.
Motorcycle Helmet Noise and Active Noise Reduction (2011)

The incidence of collisions between motorcyclists and other vehicles may be significantly reduced by research that improves the acoustic awareness of cyclists, and thus heightens the ability of cyclists to respond to unexpected incursions from the surrounding traffic. We use our hearing as an early warning system, and hearing swiftly redirects our vision and attention. This shift in gaze is critical to our capacity to assess the location, direction of travel, and velocity of approaching vehicles. The present study was composed of two experiments. In the first experiment a Neumann KU-100 dummy head with embedded binaural microphones was used to measure noise levels in a motorcycle helmet as a function of velocity. Noise levels were measured in two helmets, one with active noise reduction technology, and one without. The results showed that noise levels exceeded 100 dB (A) at highway speeds in the absence of noise reduction technology. The helmet with active noise control ear muffs was able to attenuate helmet noise by up to 26 dB. Active noise control technology shows great promise for noise reduction for the motorcycle helmet industry, and the development of "quiet" helmets is important for both hearing conservation and highway safety. The second experiment surveyed subjective perceptions of helmet noise by motorcyclists. The results from the present sample showed that 92.1% of the respondents objected to the high noise levels associated with cycling, 63.5 % wore earplugs, 46.8% reported tinnitus, and 95.2% wanted a quieter helmet.
Tetrahymena RIB72A and RIB72B are microtubule inner proteins in the ciliary doublet microtubules (2018)

Doublet and triplet microtubules are essential and highly stable core structures of centrioles, basal bodies, cilia, and flagella. In contrast to dynamic cytoplasmic micro-tubules, their luminal surface is coated with regularly arranged microtubule inner proteins (MIPs). However, the protein composition and biological function(s) of MIPs remain poorly understood. Using genetic, biochemical, and imaging techniques, we identified Tetrahymena RIB72A and RIB72B proteins as ciliary MIPs. Fluorescence imaging of tagged RIB72A and RIB72B showed that both proteins colocalize to Tetrahymena cilia and basal bodies but assemble independently. Cryoelectron tomography of RIB72A and/or RIB72B knockout strains revealed major structural defects in the ciliary A-tubule involving MIP1, MIP4, and MIP6 structures. The defects of individual mutants were complementary in the double mutant. All mutants had reduced swimming speed and ciliary beat frequencies, and high-speed video imaging revealed abnormal highly curved cilia during power stroke. Our results show that RIB72A and RIB72B are crucial for the structural assembly of ciliary A-tubule MIPs and are important for proper ciliary motility.
Phylogenetic Footprinting Based on Harmonic Clustering and Classification Algorithm (2009)

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regions from multiple species, and reliable proteins classification is necessary for the identification of orthologous regions. There are two major grouping methods, i.e. classification and clustering, and classification needs prior-knowledge, while clustering bases on the sequence similarity. In practice, the results of classification and clustering are often inconsistent. For this problem, this paper proposed harmonic clustering-classification algorithm, by this algorithm, the results of classification and clustering keep high consistency, then according to the classification, phylogenetic footprinting was implemented on Azospirillum species and its orthologous strains, and compared to the traditional methods, the results were more useful and reliable.
Toti-/Pluripotential Stem Cells and Epigenetic Modifications (2006)

Nuclear reprogramming induces global changes of epigenetic profile and confers pluripotency on specialized somatic nuclei. Embryonic stem (ES) cells retain nuclear reprogramming activity as shown by cell fusion with adult somatic cells. The reprogrammed somatic nuclei resemble ES cell nuclei in pluripotential competence. Changes of histone tail modifications in somatic cell-derived genome by cell fusion demonstrate that the molecular process of nuclear reprogramming is separable at least in two steps: erasure of somatic epigenetic modification (genome-wide reprogramming) and establishment of pluripotential epigenetic modification (gene-specific reprogramming). In the latter step, the newly identified transcriptional factor Nanog functions in maintaining pluripotency in cooperation with other key gene Oct4. Somatic-derived Nanog is reactivated in the reprogrammed nuclei in hybrid cells and also in cloned blastocysts. It is unclear which key molecules are responsible for the nuclear reprogramming. It is, however, evident that adult somatic cell nuclei are capable of being reprogrammed in vitro by cell fusion with ES cells. A technological innovation for eliminating ES-derived chromosomes from the hybrid nuclei could make the production of personalized pluripotential stem cells without the need for therapeutic cloning possible.
Nordihydroguaiaretic Acid: From Herbal Medicine to Clinical Development for Cancer and Chronic Diseases (2020)

Nordihydroguaiaretic acid (NDGA) is a phenolic lignan obtained from <i>Larrea tridentata</i>, the creosote bush found in Mexico and USA deserts, that has been used in traditional medicine for the treatment of numerous diseases such as cancer, renal, cardiovascular, immunological, and neurological disorders, and even aging. NDGA presents two catechol rings that confer a very potent antioxidant activity by scavenging oxygen free radicals and this may explain part of its therapeutic action. Additional effects include inhibition of lipoxygenases (LOXs) and activation of signaling pathways that impinge on the transcription factor Nuclear Factor Erythroid 2-related Factor (NRF2). On the other hand, the oxidation of the catechols to the corresponding quinones my elicit alterations in proteins and DNA that raise safety concerns. This review describes the current knowledge on NDGA, its targets and side effects, and its synthetic analogs as promising therapeutic agents, highlighting their mechanism of action and clinical projection towards therapy of neurodegenerative, liver, and kidney disease, as well as cancer.
In Vitro Susceptibility of Clinical Staphylococcus aureus Small-Colony Variants to β-Lactam and Non-β-Lactam Antibiotics (2018)

The <i>Staphylococcus aureus</i> small-colony variant (SCV) phenotype has been associated with relapsing and antibiotic-refractory infections. However, little is known about the activities of antibiotics on clinical SCVs. Here, we demonstrated that SCVs without detectable auxotrophies were at least as susceptible to most β-lactam and non-β-lactam antibiotics <i>in vitro</i> as their corresponding clonally identical strains with a normal phenotype. After prolonged incubation, a regrowth phenomenon has been observed in gradient diffusion inhibition zones irrespective of the strains' phenotype.
Protein Phosphatase 2A and Cdc7 Kinase Regulate the DNA Unwinding Element-binding Protein in Replication Initiation (2014)

The DNA unwinding element (DUE)-binding protein (DUE-B) binds to replication origins coordinately with the minichromosome maintenance (MCM) helicase and the helicase activator Cdc45 in vivo, and loads Cdc45 onto chromatin in Xenopus egg extracts. Human DUE-B also retains the aminoacyl-tRNA proofreading function of its shorter orthologs in lower organisms. Here we report that phosphorylation of the DUE-B unstructured C-terminal domain unique to higher organisms regulates DUE-B intermolecular binding. Gel filtration analyses show that unphosphorylated DUE-B forms multiple high molecular weight (HMW) complexes. Several aminoacyl-tRNA synthetases and Mcm2-7 proteins were identified by mass spectrometry of the HMW complexes. Aminoacyl-tRNA synthetase binding is RNase A sensitive, whereas interaction with Mcm2-7 is nuclease resistant. Unphosphorylated DUE-B HMW complex formation is decreased by PP2A inhibition or direct DUE-B phosphorylation, and increased by inhibition of Cdc7. These results indicate that the state of DUE-B phosphorylation is maintained by the equilibrium between Cdc7-dependent phosphorylation and PP2A-dependent dephosphorylation, each previously shown to regulate replication initiation. Alanine mutation of the DUE-B C-terminal phosphorylation target sites increases MCM binding but blocks Cdc45 loading in vivo and inhibits cell division. In egg extracts alanine mutation of the DUE-B C-terminal phosphorylation sites blocks Cdc45 loading and inhibits DNA replication. The effects of DUE-B C-terminal phosphorylation reveal a novel S phase kinase regulatory mechanism for Cdc45 loading and MCM helicase activation.