gebhart/patrepeval huggingface dataset:
New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites (2009)

MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5'-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5'-UTR motifs, implying both miRNA and 5'-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3'-end interaction sites in the 5'-UTRs turn out to simultaneously contain 5'-end interaction sites in the 3'-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3'-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5'-UTR and keep it from reaching the start-codon, preventing 60S association.
RBM4 Interacts with an Intronic Element and Stimulates Tau Exon 10 Inclusion (2006)

Tau protein, which binds to and stabilizes microtubules, is critical for neuronal survival and function. In the human brain, tau pre-mRNA splicing is regulated to maintain a delicate balance of exon 10-containing and exon 10-skipping isoforms. Splicing mutations affecting tau exon 10 alternative splicing lead to tauopathies, a group of neurodegenerative disorders including dementia. Molecular mechanisms regulating tau alternative splicing remain to be elucidated. In this study, we have developed an expression cloning strategy to identify splicing factors that stimulate tau exon 10 inclusion. Using this expression cloning approach, we have identified a previously unknown tau exon 10 splicing regulator, RBM4 (RNA binding motif protein 4). In cells transfected with a tau minigene, RBM4 overexpression leads to an increased inclusion of exon 10, whereas RBM4 down-regulation decreases exon 10 inclusion. The activity of RBM4 in stimulating tau exon 10 inclusion is abolished by mutations in its RNA-binding domain. A putative intronic splicing enhancer located in intron 10 of the tau gene is required for the splicing stimulatory activity of RBM4. Immunohistological analyses reveal that RBM4 is expressed in the human brain regions affected in tauopathy, including the hippocampus and frontal cortex. Our study demonstrates that RBM4 is involved in tau exon 10 alternative splicing. Our work also suggests that down-regulating tau exon 10 splicing activators, such as RBM4, may be of therapeutic potential in tauopathies involving excessive tau exon 10 inclusion.
Quantum Approximate Optimization Algorithm: Performance, Mechanism, and Implementation on Near-Term Devices (2018)

The Quantum Approximate Optimization Algorithm (QAOA) is a hybrid quantum-classical variational algorithm designed to tackle combinatorial optimization problems. Despite its promise for near-term quantum applications, not much is currently understood about QAOA's performance beyond its lowest-depth variant. An essential but missing ingredient for understanding and deploying QAOA is a constructive approach to carry out the outer-loop classical optimization. We provide an in-depth study of the performance of QAOA on MaxCut problems by developing an efficient parameter-optimization procedure and revealing its ability to exploit non-adiabatic operations. Building on observed patterns in optimal parameters, we propose heuristic strategies for initializing optimizations to find quasi-optimal $p$-level QAOA parameters in $O(\text{poly}(p))$ time, whereas the standard strategy of random initialization requires $2^{O(p)}$ optimization runs to achieve similar performance. We then benchmark QAOA and compare it with quantum annealing, especially on difficult instances where adiabatic quantum annealing fails due to small spectral gaps. The comparison reveals that QAOA can learn via optimization to utilize non-adiabatic mechanisms to circumvent the challenges associated with vanishing spectral gaps. Finally, we provide a realistic resource analysis on the experimental implementation of QAOA. When quantum fluctuations in measurements are accounted for, we illustrate that optimization will be important only for problem sizes beyond numerical simulations, but accessible on near-term devices. We propose a feasible implementation of large MaxCut problems with a few hundred vertices in a system of 2D neutral atoms, reaching the regime to challenge the best classical algorithms.
Direct laser interference technology and potential applications (2014)

Development of direct laser interference technology (DLIT) is reviewed in this paper. With the merits of being independent on the pretreatment, mask and pattern transfer processes, DLIT is demonstrated a facile and efficient method of producing sub-micro structures on various material surfaces. From a representative perspective, a number of past achievements, containing theoretical and practice aspects, attained by the nanosecond, picosecond, and femtosecond laser interference techniques are introduced. Advantages and limitations in comparison to one another are also addressed. With the progress of the emerging subwavelength structures (e.g. metasurfaces, plasmonic structures) offering the fascinating possibility of controlling the behaviour of light in an unprecedented way, the perspectives of potential applications benefited from DLIT are finally given.
NTRUReEncrypt (2015)

The use of alternative foundations for constructing more secure and efficient cryptographic schemes is a topic worth exploring. In the case of proxy re-encryption, the vast majority of schemes are based on number theoretic problems such as the discrete logarithm. In this paper we present NTRUReEncrypt, a new bidirectional and multihop proxy re-encryption scheme based on NTRU, a widely known lattice-based cryptosystem. We provide two versions of our scheme: the first one is based on the conventional NTRU encryption scheme and, although it lacks a security proof, remains as efficient as its predecessor; the second one is based on a variant of NTRU proposed by Stehlé and Steinfeld, which is proven CPA-secure under the hardness of the Ring-LWE problem. To the best of our knowledge, our proposals are the first proxy re-encryption schemes to be based on the NTRU primitive. In addition, we provide experimental results to show the efficiency of our proposal, as well as a comparison with previous proxy re-encryption schemes, which confirms that our first scheme outperforms the rest by an order of magnitude.
The anti-viral dynamin family member MxB participates in mitochondrial integrity (2020)

The membrane deforming dynamin family members MxA and MxB are large GTPases that convey resistance to a variety of infectious viruses. During viral infection, Mx proteins are known to show markedly increased expression via an interferon-responsive promoter to associate with nuclear pores. In this study we report that MxB is an inner mitochondrial membrane GTPase that plays an important role in the morphology and function of this organelle. Expression of mutant MxB or siRNA knockdown of MxB leads to fragmented mitochondria with disrupted inner membranes that are unable to maintain a proton gradient, while expelling their nucleoid-based genome into the cytoplasm. These findings implicate a dynamin family member in mitochondrial-based changes frequently observed during an interferon-based, anti-viral response.
Adverse events in health care: Setting priorities based on economic evaluation (1999)

Adverse events arising from health-care management, rather than a disease process, may place as great a burden on society as all other forms of injury put together. By analysing data from the Quality in Australian Health Care Study (a retrospective review of 14 179 medical records representative of admissions to Australian acute care hospitals in 1992), and applying costing techniques based on Diagnosis Related Group (DRG) cost weights, it is possible to compare the economic impacts of different kinds of adverse events. This can assist in determining priorities for interventions. However, due to limitations inherent in DRG cost weights, there is a need to employ further techniques to refine the costing base of adverse events so that it more closely reflects their resource use. Decisions to invest resources in strategies that reduce the risk of adverse events can then be properly informed by economic data.
Hydrogen-Fueled Combustion Turbine Cycles (1996)

As part of its World Energy Network (WE-NET) Program, the Japanese New Energy and Industrial Technology Development Organization (NEDO) is funding a Westinghouse-led team to develop conceptual designs of hydrogen-fueled combustion turbine power plants capable of greater than 60% high heating value (HHV) thermal efficiency. The conceptual design task is taking place in the second year of the 28-year program, which has the goal of developing a hydrogen-based renewable energy economy. Due to the requirement that the power plant must be environmentally benign, special closed cycles are being investigated which will meet the requirements of the program while allowing for pilot plant testing in the near future. This paper investigates a variety of possible cycle configurations and working fluids and describes the selection methodology used to identify the best candidate. Optimization of the selected cycle is then described, which results in the basis for the conceptual design.
Mechanosensing by the α6-integrin confers an invasive fibroblast phenotype and mediates lung fibrosis (2016)

Matrix stiffening is a prominent feature of pulmonary fibrosis. In this study, we demonstrate that matrix stiffness regulates the ability of fibrotic lung myofibroblasts to invade the basement membrane (BM). We identify α6-integrin as a mechanosensing integrin subunit that mediates matrix stiffness-regulated myofibroblast invasion. Increasing α6-expression, specifically the B isoform (α6B), couples β1-integrin to mediate MMP-2-dependent pericellular proteolysis of BM collagen IV, leading to myofibroblast invasion. Human idiopathic pulmonary fibrosis lung myofibroblasts express high levels of α6-integrin in vitro and in vivo. Genetic ablation of α6 in collagen-expressing mesenchymal cells or pharmacological blockade of matrix stiffness-regulated α6-expression protects mice against bleomycin injury-induced experimental lung fibrosis. These findings suggest that α6-integrin is a matrix stiffness-regulated mechanosensitive molecule which confers an invasive fibroblast phenotype and mediates experimental lung fibrosis. Targeting this mechanosensing α6(β1)-integrin offers a novel anti-fibrotic strategy against lung fibrosis.
Sustainable Bio-Derived Synthetic Paraffinic Kerosene (Bio-SPK) Jet Fuel Flights and Engine Tests Program Results (2009)

This paper describes the results of an industry effo rt to test Bio-derived Synthetic Paraffinic Kerosene (Bio-SPK) from natural plant oils. The program included the identification and sourcing of sustainable feedstocks, the use of a new fuel processing method, nu merous fuel tests, engine operability, performance and emissions tests, and flight testing in three Boeing aircraft models. The Bio-SPK blended fuels have potential to reduce life cycle CO2 emissions and be compatible with current aircraft, systems, and infrastructure.
Correlation between Specific Immunosuppression and Polyclonal B Cell Activation Induced by a Protein Secreted by <i>Streptococcus mutans</i> (1988)

The relationship between polyclonal B cell activation and immunosuppressor effects induced by F5'EP-Sm, a non-cytotoxic protein secreted by Streptococcus mutans, was studied in C57BL/6 mice. Mice treated with F5'EP-Sm exhibited a considerable increase in splenic nonspecific Ig plaque-forming cells (PFC) compared with untreated mice. The isotypic pattern of non-specific PFC responses favours IgG2a approximately equal to IgG2b greater than IgG3 greater than IgG1 approximately equal to IgM, when taken as a ratio between treated and untreated animals. When F5'EP-Sm was administered 2 days before immunization with sheep red blood cells (SRBC), the non-specific PFC production was accompanied by an ephemeral increase in specific PFC against SRBC 1 day after immunization, which was quickly replaced by a strong immunosuppression. In contrast, when F5'EP-Sm was injected after priming, there was little or no demonstrable suppression of specific PFC, and the increase of non-specific PFC was much less evident. The kinetic curves representing increase or decrease in relation to controls of specific and non-specific PFC are almost mirror images in each of the isotypes. The in vivo suppressor effect was abrogated in thymectomized mice, although the involvement of the T cell compartment is probably secondary to the B cell mitogen effect, since T-depleted spleen cells proliferate and synthesize non-specific Ig when stimulated in vitro with F5'EP-Sm.
A net practice for software project management (1999)

Technical and managerial complexity increasingly overwhelm project managers. To rein in that complexity, the authors propose PM-Net, a model that captures the concurrent, iterative, and evolutionary nature of software development. It adopts the basic concepts of Petri nets, graphical models of information flow, with extensions to represent both decisions and artifacts.
Gain optimization of germanosilicate fiber Raman amplifier and its applications in the compensation of Raman-induced crosstalk among wavelength division multiplexing channels (2001)

Spectral characteristics of the stimulated Raman scattering (SRS) process were theoretically investigated for step-index silica optical fibers with various GeO/sub 2/ concentrations. Optimal-fiber lengths and germanium concentration, where the first Stokes power reaches maximum, were calculated at various pump power levels for application in Raman amplifiers. Based on this analysis, we proposed and experimentally demonstrated a new channel-equalizing technique to simultaneously compensate Raman-induced crosstalk and amplify wavelength-division-multiplexing (WDM) signals using a discrete Raman amplifier in the 1.5-/spl mu/m range. As a further application of SRS in germanosilicate glass fibers, we introduce an all-optical variable attenuator for channel equalization that could be used in dynamic optical power tilt control in WDM systems.
Radiation injury in surgical pathology (1981)

1From the Department of Pathology, University of Colorado School of Medicine and Penrose Hospital, Colorado Springs, Colorado 2From the Stanford University School of Medicine and Veterans Administration Medical Center, Palo Alto, California
Therapeutic Advances and Challenges in the Management of HER2-Positive Gastroesophageal Cancers (2022)

Gastroesophageal cancer is one of the most common cancers in the world, with a high rate of mortality. While there has been significant progress over the past decade, particularly with the addition of anti-HER2 therapies to platinum-based chemotherapy agents in the advanced setting, the prognosis remains poor and the treatment options for this disease entity remain limited. In this review, we discuss the current therapeutic landscape for HER2-positive gastroesphageal cancer and the seminal clinical trials that have shaped our approach to this disease entity. In addition, we highlight some of the challenges to the understanding and management of this disease, specifically discussing the breadth of molecular diversity and intratumoral heterogeneity of HER2 expression that impact the clinical efficacy and prognosis. Furthermore, we discuss the potential role of next-generation sequencing (NGS) and circulating-tumor DNA (ctDNA) as complementary tools to immunohistochemistry (IHC) and fluorescent in-situ hybridization (FISH) to guiding clinical decision making. Finally, we highlight promising clinical trials of new treatment regimens that will likely reshape the therapeutic approach to this disease entity.
Accuracy of the advanced trauma life support guidelines for predicting systolic blood pressure using carotid, femoral, and radial pulses: observational study (2000)

that in the regions we have studied the direct effect of the moderate warming predicted in the next 50 years would be to reduce, at least briefly, both winter mortality and total mortality. This could be continued into a large, sustained reduction in overall mortality if additional action is taken to prevent relaxation of protective measures against outdoor and indoor cold stress as winters become milder. These findings should not, of course, diminish concerns about possible indirect effects of prolonged global warming, such as flooding of low lying areas due to a rise in sea level or about direct effects of heat stress in hotter regions.
Design of arbitrary waveform generator based on FPGA and Wi-Fi for miniature mass spectrometer (2017)

Mass Spectrometer is an important tool to analyze biological macromolecules. With the development of technology, miniature mass spectrometer is emerging to meet the increasing demands of on-site and personalized applications. Electronics system is an important part of the instrument, which is required to generate various waveform signals to accomplish ion isolation, excitation and ejection. Based on FPGA and Wi-Fi, a design of an arbitrary waveform generator system is presented. In this system, two DC and two analog signals of the mass spectrometers scan function can be generated with 40MSPS DAC controlled by FPGA. The hardware and software design is introduced in detail. The result shows that a scan function for mass analysis is accomplished based on the system.
Ultrasound-mediated optical tomography: a review of current methods (2011)

Ultrasound-mediated optical tomography (UOT) is a hybrid technique that is able to combine the high penetration depth and high spatial resolution of ultrasound imaging to overcome the limits imposed by optical scattering for deep tissue optical sensing and imaging. It has been proposed as a method to detect blood concentrations, oxygenation and metabolism at depth in tissue for the detection of vascularized tumours or the presence of absorbing or scattering contrast agents. In this paper, the basic principles of the method are outlined and methods for simulating the UOT signal are described. The main detection methods are then summarized with a discussion of the advantages and disadvantages of each. The recent focus on increasing the weak UOT signal through the use of the acoustic radiation force is explained, together with a summary of our results showing sensitivity to the mechanical shear stiffness and optical absorption properties of tissue-mimicking phantoms.
Mode Locked Fiber Lasers (2013)

Nowadays, to satisfy the increase of internet demands and requirement, two multiplexing techniques are used: WDM (Wavelength Division Multiplex) and TDM (Time Division Mul‐ tiplex). WDM still more used than TDM. However, for practical system applications, such as optical CDMA (Code Division Multiplex Access) and OTDM (Optical Time Division Multi‐ plex) systems, high speed optical communications require light sources with a repetition rate control. In this area, pulsed fiber lasers have become very attractive.
Erratum: Orientational Coupling Amplification in Ferroelectric Nematic Colloids [Phys. Rev. Lett.<b>97</b>, 147801 (2006)] (2007)

In a recent Letter Phys. Rev. Lett. 97, 147801 (2006), we reported significant amplification of orientational coupling in a BaTiO 3 ferroelectric nanocolloids liquid crystal. We found that the nematic orientation coupling in nematic mixture MLC-6609 increased by 10% for particle concentrations of 0.2%. A manifestation of the increased orientational order was that the nematic-isotropic transition temperature T NI increased from 90.2 to 128:9 C when nanoparticles were added to a host. The same formulation of liquid crystal, surfactant, and solvent, but omitting the particles, was tested after heating and vacuuming, and no change in T NI was observed. We regarded this as evidence that the increase in T NI was a result of the added particles. An order of magnitude calculation indicated that the cause of the gain in the orientational order could be the strong electric field produced by the permanently polarized particles.
Cell shape for microcellular systems in residential and commercial environments (1994)

Personal communication services (PCS) will make use of low antennas and low radiated power to achieve base station coverage over microcells having radius of about 500 m. For such small cells the configuration of buildings surrounding the base station will have a major influence on the propagation in different directions, and hence on cell shape. This paper presents a theoretical approach to determining cell shape for residential and commercial regions, where the buildings are of a relatively uniform height, and are closely spaced in rows along the streets. Because it is based in theory, the model treats base station antenna height and location, and frequency as input parameters, in addition to area specific descriptors of the buildings, such as average height, location with respect to the streets, and street geometry. As an example, contour plots of signal level have been computed for an area having two story town houses located on a rectangular street grid, and for base station antennas located mid-block, at a street intersection, and in the backyards of the buildings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Use of Intralipid for kinetic analysis of HDL apoC-III: evidence for a homogeneous kinetic pool of apoC-III in plasma (2006)

Apolipoprotein C-III (apoC-III) is an important regulator of lipoprotein metabolism. Radioisotope and stable isotope kinetic studies show differing results in relation to the kinetics of apoC-III in HDL. Kinetic analysis of HDL apoC-III may be difficult because of its low concentration, as well as the presence of other apoproteins at higher concentration, in the HDL fraction. We used Intralipid(R) (IL), known to preferentially extract apoC proteins from plasma, as a means of extracting apoC-III from HDL before apoprotein separation by isoelectric focusing gel electrophoresis for the measurement of tracer enrichment. Protein purity was assessed by an isoleucine-to-leucine (Ile/Leu) ratio, as apoC-III contains no isoleucine. We compared apoC-III kinetics in 14 men using a bolus infusion of deuterated leucine. The Ile/Leu ratio for IL-extracted HDL (IL-HDL) apoC-III (3.0 +/- 0.7%) was not different from that of VLDL apoC-III (2.6 +/- 0.6%) but was significantly lower than that of untreated HDL apoC-III (9.0 +/- 2.9%) (P < 0.001). The isotopic enrichment curves and fractional catabolic rates (FCRs) for IL-HDL apoC-III were not different from those of VLDL apoC-III. In contrast, HDL apoC-III had significantly lower isotopic enrichments and FCRs than IL-HDL apoC-III (P < 0.001). In conclusion, this simple IL method can be used to isolate apoC-III from HDL with minimal interference from other HDL apoproteins, and it demonstrates that the kinetics of apoC-III in VLDL and HDL are similar, supporting the concept of a single kinetically homogeneous pool of apoC-III in plasma.