gebhart/patrepeval huggingface dataset:
Role of non-coding RNAs and exosomal non-coding RNAs in retinoblastoma progression (2022)

Retinoblastoma (RB) is a rare aggressive intraocular malignancy of childhood that has the potential to affect vision, and can even be fatal in some children. While the tumor can be controlled efficiently at early stages, metastatic tumors lead to high mortality. Non-coding RNAs (ncRNAs) are implicated in a number of physiological cellular process, including differentiation, proliferation, migration, and invasion, The deregulation of ncRNAs is correlated with several diseases, particularly cancer. ncRNAs are categorized into two main groups based on their length, i.e. short and long ncRNAs. Moreover, ncRNA deregulation has been demonstrated to play a role in the pathogenesis and development of RB. Several ncRNAs, such as miR-491-3p, miR-613,and SUSD2 have been found to act as tumor suppressor genes in RB, but other ncRNAs, such as circ-E2F3, NEAT1, and TUG1 act as tumor promoter genes. Understanding the regulatory mechanisms of ncRNAs can provide new opportunities for RB therapy. In the present review, we discuss the functional roles of the most important ncRNAs in RB, their interaction with the genes responsible for RB initiation and progression, and possible future clinical applications as diagnostic and prognostic tools or as therapeutic targets.
Rapid identification of minor histocompatibility antigen HA‐1 subtypes H and R using fluorescence‐labeled oligonucleotides (2000)

Donor-recipient disparitiy of the minor histocompatibility antigen HA-1 is relevant for the development of graft-versus-host disease after HLA-matched sibling allogeneic bone marrow transplantation in HLA-A*0201-positive individuals. Two different alleles of HA-1 with a single amino acid polymorphism have been identified. Here we describe a time- and cost-efficient method for HA-1 typing of genomic DNA, using site-specific hybridization probes with the LightCycler. This method was compared with standard techniques as sequencing or allele-specific polymerase chain reaction (PCR) and proved to be specific, reliable and reproducible. We conclude that HA-1-subtyping using fluorescent-labeled oligonucleotides represents a attractive method for the screening of samples before allogeneic transplantation in HLA-A*0201-positive individuals.
Preliminary assessment of one-dimensional MR elastography for use in monitoring focused ultrasound therapy (2007)

The purpose of this work is to assess a fast technique that measures tissue stiffness and temperature during focused ultrasound thermal therapy (FUS). A one-dimensional (1D) MR elastography (MRE) pulse sequence was evaluated for the purpose of obtaining rapid measurements of thermally induced changes in tissue stiffness and temperature for monitoring FUS treatments. The accuracy of the 1D measurement was studied by comparing tissue displacements measured by 1D MRE with those measured by the well-established 2D MRE pulse sequence. The reproducibility of the 1D MRE measurement was assessed, in gel phantoms and ex vivo porcine tissue, for varied FUS intensity levels (31.5-199.9 W cm(-2)) and over a range of displacements at the focus (0.1-1 microm). Temperature elevations in agarose gel phantoms were measured using 1D MRE and calibrated using fiberoptic-thermometer-based measurements. The 1D MRE displacement measurements are highly correlated with those obtained with the 2D technique (R(2) = 0.88-0.93), indicating that 1D MRE can successfully measure tissue displacement. Ten repeated trials at each FUS power level yielded a minimum detectable displacement change of 0.2 microm in phantoms and 0.4 microm in tissue (at 95% confidence level). The 1D MRE temperature measurements correlated well with temperature changes measured simultaneously with fiberoptic thermometers (R(2) = 0.97). The 1D MRE technique is capable of detecting tissue displacements as low as 0.4 microm, which is an order of magnitude smaller than 5 microm displacements expected during FUS therapy (Le et al 2005 AIP Conf. Proc.: Ther. Ultrasound 829 186-90). Additionally, 1D MRE was shown to provide adequate measurements of temperature elevations in tissue. These findings indicate that 1D MRE may be an effective tool for monitoring FUS treatments.
Equivalent mutations in the two repeats of yeast TATA-binding protein confer distinct TATA recognition specificities. (1994)

To investigate the process of TATA box recognition by the TATA box-binding protein (TBP), we have performed a detailed genetic and biochemical analysis of two Saccharomyces cerevisiae TBP mutants with altered DNA-binding specificity. The mutant proteins have amino acid substitutions (Leu-205 to Phe and Leu-114 to Phe) at equivalent positions within the two repeats of TBP that are involved in TATA element binding. In an in vivo assay that employs a nearly complete set of single point mutations of the consensus TATAAA sequence, one of the TBP mutants (TBP-L114F) recognizes the sequence TATAAG, while the other TBP mutant (TBP-L205F) recognizes one substitution at the first position of the TATA element, CATAAA, and three substitutions at the 3' end of the TATA box. Specificity patterns determined from in vitro transcription experiments with purified recombinant wild-type TBP and TBP-L205F agree closely with those observed in vivo, indicating that altered TATA utilization in the mutant strains is a direct consequence of altered TATA recognition by the mutant TBPs. The distinct TATA recognition patterns exhibited by TBP-L114F and TBP-L205F strongly suggest that in vivo, TBP binds to the TATA element in a specific orientation. The orientation predicted from these studies is further supported by the identification of intragenic suppressors that correct the defect of TBP-L205F. This orientation is consistent with that observed in vitro by crystallographic analyses of TBP-TATA box complexes. Finally, the importance of altered DNA-binding specificity in transcriptional regulation at the S. cerevisiae his4-912 delta promoter was addressed for TBP-L205F. A mutational analysis of this promoter region demonstrates that the nonconsensus TATA element CATAAA is required for a transcriptional effect of TBP-L205F in vivo. This finding suggests that the interaction of TBP with nonconsensus TATA elements may play an important regulatory role in transcription initiation.
A novel semiconductor compatible path for nano-graphene synthesis using CBr4 precursor and Ga catalyst (2014)

We propose a novel semiconductor compatible path for nano-graphene synthesis using precursors containing C-Br bonding and liquid catalyst. The unique combination of CBr4 as precursor and Ga as catalyst leads to efficient C precipitation at a synthesis temperature of 200°C or lower. The non-wetting nature of liquid Ga on tested substrates limits nano-scale graphene to form on Ga droplets and substrate surfaces at low synthesis temperatures of T ≤ 450°C and at droplet/substrate interfaces by C diffusion via droplet edges when T ≥ 400°C. Good quality interface nano-graphene is demonstrated and the quality can be further improved by optimization of synthesis conditions and proper selection of substrate type and orientation. The proposed method provides a scalable and transfer-free route to synthesize graphene/semiconductor heterostructures, graphene quantum dots as well as patterned graphene nano-structures at a medium temperature range of 400–700°C suitable for most important elementary and compound semiconductors.
Bifunctional Carbon Dots—Magnetic and Fluorescent Hybrid Nanoparticles for Diagnostic Applications (2020)

There is a huge demand for materials capable of simple detection or separation after conjugation with specific biologic substances when applied as a diagnostic tools. Taking into account the photoluminescence properties of C-dots and the highly magnetic properties of Fe(0), a new hybrid composite of these components was synthesized via ultrasound irradiation. The material was fully characterized by various physicochemical techniques. The main goal of the current study was to obtain a highly magnetic and intense fluorescent hybrid material. The goal was achieved. In addition, magnetic particles tended to agglomerate. The new hybrid can be suspended in ethanol, which is an additional feature of the current research. The dispersion of the hybrid nanoparticles in ethanol was achieved by utilizing the interaction of iron particles with C-dots which were decorated with functional groups on their surface. The newly formed hybrid material has potential applications in diagnostic by conjugating with specific antibodies or with any other biologic compounds. Such application may be useful in detection of various diseases such as: cancer, tuberculosis, etc.
Characterizing the UAV-to-Machine UWB Radio Channel in Smart Factories (2021)

In this work, the results of Ultra-Wideband air-to-ground measurements carried out in a real-world factory environment are presented and discussed. With intelligent industrial deployments in mind, we envision a scenario where the Unmanned Aerial Vehicle can be used as a supplementary tool for factory operation, optimization and control. Measurements address narrow band and wide band characterization of the wireless radio channel, and can be used for link budget calculation, interference studies and time dispersion assessment in real factories, without the usual limitation for both radio terminals to be close to ground. The measurements are performed at different locations and different heights over the 3.1-5.3 GHz band. Some fundamental propagation parameters values are determined vs. distance, height and propagation conditions. The measurements are complemented with, and compared to, conventional ground-to-ground measurements with the same setup. The conducted measurement campaign gives an insight for realizing wireless applications in smart connected factories, including UAV-assisted applications.
Refinement and Validation of the Thermal Stratification Analysis: A post-processing methodology for determining temperature distributions in an experimental HCCI engine (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Refinements were made to a post-processing technique, termed the Thermal Stratification Analysis (TSA), that couples the mass fraction burned data to ignition timing predictions from the autoignition integral to calculate an apparent temperature distribution from an experimental HCCI data point. Specifically, the analysis is expanded to include all of the mass in the cylinder by fitting the unburned mass with an exponential function, characteristic of the wall-affected region.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The analysis-derived temperature distributions are then validated in two ways. First, the output data from CFD simulations are processed with the Thermal Stratification Analysis and the calculated temperature distributions are compared to the known CFD distributions. The results show very good agreement between the calculated TSA and known CFD distributions, except at the leading (hottest) edge where the CFD distributions exhibit a discrete step change and the calculated TSA distributions show a smooth progression. Next, the analysis-derived temperature distributions are compared to optically measured distributions calculated from PLIF images. The calculated distributions agree very well with the optically measured distributions at TDC and around the phasing of the combustion event.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Finally, an intake temperature (or combustion phasing) sweep is processed with the TSA and the results show that the higher intake temperature (and earlier phased) conditions have a much wider distribution due to the increasing difference between the gas temperature and the wall temperature and possibly the increasing in-cylinder turbulence as combustion phasing advances toward TDC.&lt;/div&gt;&lt;/div&gt;
Ambient laser ablation sampling for capillary electrophoresis mass spectrometry (2013)

A novel interface for ambient sampling to CE/MS was developed. The interface is generally applicable and has potential utility for mass spectrometry imaging as well as the loading of microfluidic devices from untreated ambient samples.
Vapor transport deposition and epitaxy of orthorhombic SnS on glass and NaCl substrates (2013)

Polycrystalline SnS, Sn2S3, and SnS2 were deposited onto glass substrates by vapor transport deposition, with the stoichiometry controlled by deposition temperature. In addition, epitaxial growth of orthorhombic SnS(010) films on NaCl(100) with thicknesses up to 600 nm was demonstrated. The in-plane [100] directions of SnS and NaCl are oriented approximately 45° apart, and the translational relationship between SnS and NaCl was predicted by density functional theory. The epitaxial SnS is p-type with carrier concentration on the order of 1017 cm−3 and Hall hole mobility of 385 cm2 V−1 s−1 in-plane. It has indirect and direct bandgaps of 1.0 and 2.3 eV, respectively.
RiceUndeveloped Tapetum1Is a Major Regulator of Early Tapetum Development (2005)

The tapetum, the innermost of four sporophytic layers in the anther wall, comes in direct contact with the developing male gametophyte and is thought to play a crucial role in the development and maturation of microspores. Here, we report the identification of rice (Oryza sativa) Undeveloped Tapetum1 (Udt1), which is required for the differentiation of secondary parietal cells to mature tapetal cells. T-DNA or retrotransposon Tos17 insertions in the Udt1 gene caused male sterility. The anther walls and meiocytes of the mutants were normal during the early premeiosis stage, but their tapeta failed to differentiate and became vacuolated during the meiotic stage. In addition, meiocytes did not develop to microspores, and middle layer degeneration was inhibited. Consequently, the anther locules contained no pollen. The UDT1:green fluorescent protein fusion protein was localized to the nucleus. This, together with its homology with other basic helix-loop-helix proteins, suggests that UDT1 is a transcription factor. DNA microarray analysis identified 958 downregulated and 267 upregulated genes in the udt1-1 anthers, suggesting that Udt1 plays a major role in maintaining tapetum development, starting in early meiosis.
Acousto-optical modulation of thin film lithium niobate waveguide devices (2019)

Due to its strong piezoelectric effect and photo-elastic property, lithium niobate is widely used for acousto-optical applications. However, conventional bulk lithium niobate waveguide devices exhibit a large footprint and limited light–sound interaction resulting from the weak guiding of light. Here, we report the first acousto-optical modulators with surface acoustic wave generation, phononic cavity, and low-loss photonic waveguide devices monolithically integrated on a 500 nm thick film of lithium niobate on an insulator. Modulation efficiency was optimized by properly arranging the propagation directions of surface acoustic waves and optical guided modes. The effective photo-elastic coefficient extracted by comparing the first and third harmonic modulation signals from an on-chip Mach–Zehnder interferometer indicates the excellent acousto-optical properties of lithium niobate are preserved in the thin film implementation. Such material property finding is of crucial importance in designing various types of acousto-optical devices. Much stronger amplitude modulation was achieved in a high Q (>300,000) optical resonator due to the higher optical sensitivity. Our results pave the path for developing novel acousto-optical devices using thin film lithium niobate.
Interleukin 18 stimulates HIV type 1 in monocytic cells (1998)

The cytokine interleukin (IL) 18 (formerly interferon gamma-inducing factor) induces the T helper type 1 response. In the present studies, IL-18 increased HIV type 1 (HIV-1) production from 5- to 30-fold in the chronically infected U1 monocytic cell line. Inhibition of tumor necrosis factor (TNF) activity by the addition of TNF-binding protein reduced IL-18-stimulated HIV-1 production by 48%. In the same cultures, IL-18-induced IL-8 was inhibited by 96%. Also, a neutralizing anti-IL-6 mAb reduced IL-18-induced HIV-1 by 63%. Stimulation of U1 cells with IL-18 resulted in increased production of IL-6, and exogenous IL-6 added to U1 cells increased HIV-1 production 4-fold over control. A specific inhibitor of the p38 mitogen-activated protein kinase reduced IL-18-induced HIV-1 by 73%, and a 50% inhibition was observed at 0.05 microM. In the same cultures, IL-8 was inhibited by 87%. By gel-shift and supershift analyses, increased binding activity of the transcription factor NF-kappaB was measured in nuclear extracts from U1 cells 1 h after exposure to IL-18. These results demonstrate induction of HIV-1 by IL-18 in a monocyte target associated with an intermediate role for TNF and IL-6, activation of p38 mitogen-activated protein kinase, and nuclear translocation of NF-kappaB.
Modeling of dynamic trap density increase for aging simulation of any MOSFET circuits (2017)

A compact aging model for circuit simulation has been developed by considering all possible trapped carriers within MOSFETs. The hot carrier effect and the N(P)BTI effect are modeled by integrating the substrate current as well as the oxide field change due to the trapped carriers. Additionally, the carriers trapped within the highly resistive drift region are included for high-voltage (HV)-MOSFET modeling. The aging model considers the dynamic trap-density increase as a function of circuit-operation time with dynamically varying stress conditions for each individual MOSFET. A self-consistent solution is obtained by iteratively solving the Poisson equation including the trap density. The model is verified to be applicable for any type of MOSFETs covering advanced technologies as well as HV-MOSFETs.
Robustness of Deep Equilibrium Architectures to Changes in the Measurement Model (2022)

Deep model-based architectures (DMBAs) are widely used in imaging inverse problems to integrate physical measurement models and learned image priors. Plug-and-play priors (PnP) and deep equilibrium models (DEQ) are two DMBA frameworks that have received significant attention. The key difference between the two is that the image prior in DEQ is trained by using a specific measurement model, while that in PnP is trained as a general image denoiser. This difference is behind a common assumption that PnP is more robust to changes in the measurement models compared to DEQ. This paper investigates the robustness of DEQ priors to changes in the measurement models. Our results on two imaging inverse problems suggest that DEQ priors trained under mismatched measurement models outperform image denoisers.
Rheology and Oxidative Stability of Whey Protein Isolate‐Stabilized Menhaden Oil‐in‐Water Emulsions as a Function of Heat Treatment (2009)

Menhaden oil-in-water emulsions (20%, v/v) were stabilized by 2 wt% whey protein isolate (WPI) with 0.2 wt% xanthan gum (XG) in the presence of 10 mM CaCl(2) and 200 microM EDTA at pH 7. Droplet size, lipid oxidation, and rheological properties of the emulsions were investigated as a function of heating temperature and time. During heating, droplet size reached a maximum at 70 degrees C and then decreased at 90 degrees C, which can be attributed to both heating effect on increased hydrophobic attractions and the influence of CaCl(2) on decreased electrostatic repulsions. Combination of effects of EDTA and heat treatment contributed to oxidative stability of the heated emulsions. The rheological data indicate that the WPI/XG-stabilized emulsions undergo a state transition from being viscous like to an elastic like upon substantial thermal treatment. Heating below 70 degrees C or for less than 10 min at 70 degrees C favors droplet aggregation while heating at 90 degrees C or for 15 min or longer at 70 degrees C facilitates WPI adsorption and rearrangement. WPI adsorption leads to the formation of protein network around the droplet surface, which promotes oxidative stability of menhaden oil. Heating also aggravates thermodynamic incompatibility between XG and WPI, which contributes to droplet aggregation and the accumulation of more WPI around the droplet surfaces as well.
Bioresorbable Nanostructured Chemical Sensor for Monitoring of pH Level In Vivo (2022)

Here, the authors report on the manufacturing and in vivo assessment of a bioresorbable nanostructured pH sensor. The sensor consists of a micrometer-thick porous silica membrane conformably coated layer-by-layer with a nanometer-thick multilayer stack of two polyelectrolytes labeled with a pH-insensitive fluorophore. The sensor fluorescence changes linearly with the pH value in the range 4 to 7.5 upon swelling/shrinking of the polymer multilayer and enables performing real-time measurements of the pH level with high stability, reproducibility, and accuracy, over 100 h of continuous operation. In vivo studies carried out implanting the sensor in the subcutis on the back of mice confirm real-time monitoring of the local pH level through skin. Full degradation of the pH sensor occurs in one week from implant in the animal model, and its biocompatibility after 2 months is confirmed by histological and fluorescence analyses. The proposed approach can be extended to the detection of other (bio)markers in vivo by engineering the functionality of one (at least) of the polyelectrolytes with suitable receptors, thus paving the way to implantable bioresorbable chemical sensors.
Use of a Stringent Dimerizer-Regulated Gene Expression System for Controlled BMP2 Delivery (2006)

Gene therapy using constitutively active viral promoters to drive expression of bone morphogenetic proteins (BMPs) has been extensively evaluated as a strategy for inducing bone regeneration. However, this approach offers little control over the concentration, timing, or duration of BMP synthesis. To gain greater control over BMP kinetics, we developed a new inducible system for the controlled expression of BMP2 using a two-component transcription factor that is dimerized with rapamycin (Rap). This approach provided stringent control over BMP2 synthesis with no BMP expression detected in the uninduced state. Rapamycin or the less immunosuppressive analogue, AP21967, rapidly and reversibly induced BMP2 in a dose-dependent manner (range 0.1-10 nM). Subcutaneous implants of fibroblasts containing the Rap-inducible system in syngeneic C57BL/6 mice were highly responsive to ip Rap injection (0.1-1 mg/kg). Peak BMP2 levels were detected within 24 h of a single Rap injection and declined to undetectable levels after 8-10 days. Alternate-day Rap injections (1 mg/kg) for 6 weeks induced subcutaneous ectopic bone formation. Rap-dependent healing of a critical-sized cranial defect was also achieved using this system. This regulated BMP2 expression system will be extremely useful for examining the role of timing and sequence of BMP delivery on bone regeneration.
Multiple agent coordination for stochastic target interception using MILP (2011)

In this paper we present an approach to solving a stochastic multi-target interception problem. In the multi-target interception problem, a team of mobile sensors is tasked with intercepting a set of potential targets to reduce appropriately assigned damage cost. Our principal contribution is to express a stochastic version of the problem with a generalized cost as a mixed-integer linear program so that optimal sensor motion can be computed efficiently. Indeed, our optimization program for the stochastic problem has similar computational costs as the optimization program for the corresponding deterministic problem. Our solution presumes that the system can be approximated by linear dynamics and Gaussian noise, with Gaussian localization uncertainty.