gebhart/patrepeval huggingface dataset:
A measure of the similarity of sets of sequences not requiring sequence alignment. (1986)

Determination of first- and second-order Markov chain homogeneity of sets of nuclear eukaryotic DNA sequences, both coding and noncoding, finds similarities imperceptible to the standard Needleman-Wunsch base matching or dot-matrix algorithms. These measures of the similarities of the distributions of adjacent pairs or triplets are in agreement with accepted evolutionary-tree topologies. Hierarchical clustering of the distributions of doublets of 30 miscellaneous coding sequences gives clusters in reasonable agreement with accepted biological classifications. In addition to similarity by homology, there is also observed similarity of disparate genes in the same organism--for example, all three disparate yeast genes (two enzymes and actin) form a well-distinguished cluster.
The G Glycoprotein of Respiratory Syncytial Virus Depresses Respiratory Rates through the CX3C Motif and Substance P (2003)

Respiratory syncytial virus (RSV) infection in the neonate can alter respiratory rates, i.e., lead to episodes of apnea. We show that RSV G glycoprotein reduces respiratory rates associated with the induction of substance P (SP) and G glycoprotein-CX3CR1 interaction, an effect that is inhibited by treatment with anti-G glycoprotein, anti-SP, or anti-CX3CR1 monoclonal antibodies. These data suggest new approaches for treating some aspects of RSV disease.
IL-25 drives remodelling in allergic airways disease induced by house dust mite (2012)

In addition to modulating acute inflammation, we now demonstrate a role for IL-25 in orchestrating airway remodelling. IL-25 also drives IL-33 and TSLP production in the lung. These data delineate a wider role for IL-25 in mediating structural changes to the lung following allergen exposure and implicate IL-25 as a novel therapeutic target for the treatment of airway remodelling in asthma.
The role of myeloperoxidase (MPO) for prognostic evaluation in sensitive cardiac troponin I negative chest pain patients in the emergency department (2013)

MPO has an independent prognostic value overall and most notably in patients tested negative with a higher sensitive cardiac troponin I assay. MPO could be a promising biomarker for the initial evaluation of patients in chest pain units and is worth further investigation.
Mutant of <i>Arabidopsis</i> Deficient in Xylem Loading of Phosphate (1991)

A mutant of Arabidopsis thaliana deficient in the accumulation of inorganic phosphate has been isolated by screening directly for plants with altered quantities of total leaf phosphate. The mutant plants accumulate approximately 5% as much inorganic phosphate, and 24 to 44% as much total phosphate, as wild-type plants in aerial portions of the plant. Growth of the mutant is reduced, relative to wild type, and it exhibits other symptoms normally associated with phosphate deficiency. The phosphate deficiency is caused by a single nuclear recessive mutation at a locus designated pho1. The rate of phosphate uptake into the roots was similar between mutant and wild-type plants over a wide range of external phosphate concentrations. In contrast, when plants were grown in media containing 200 micromolar phosphate or less, phosphate transfer to the shoots of the mutant was reduced to 3 to 10% of the wild-type levels. The defect in phosphate transfer to the shoots could be overcome by providing higher levels of phosphate. Transfer of sulfate to the shoots was essentially normal in the mutant, indicating that the pho1 lesion was not a general defect in anion transport. Movement of phosphate through the xylem of the shoots was not impaired. The results suggest that the mutant is deficient in activity of a protein required to load phosphate into the xylem.
Low-Power Distributed Data Flow Anomaly-Monitoring Technology for Industrial Internet of Things (2019)

. In recent years, the industrial use of the internet of things (IoT) has been constantly growing and is now widespread. Wireless sensor networks (WSNs) are a fundamental technology that has enabled such prevalent adoption of IoT in industry. WSNs can connect IoT sensors and monitor the working conditions of such sensors and of the overall environment, as well as detect unexpected system events in a timely and accurate manner. Monitoring large amounts of unstructured data generated by IoT devices and collected by the big-data analytics systems is a challenging task. Furthermore, detecting anomalies within the vast amount of data collected in real time by a centralized monitoring system is an even bigger challenge. In the context of the industrial use of the IoT, solutions for monitoring anomalies in distributed data flow need to be explored. In this paper, a low-power distributed data flow anomaly-monitoring model (LP-DDAM) is proposed to mitigate the communication overhead problem. As the data flow monitoring system is only interested in anomalies, which are rare, and the relationship among objects in terms of the size of their attribute values remains stable within any specific period of time, LP-DDAM integrates multiple objects as a complete set for processing, makes full use of the relationship among the objects, selects only one "representative" object for continuous monitoring, establishes certain constraints to ensure correctness, and reduces communication overheads by maintaining the overheads of constraints in exchange for a reduction in the number of monitored objects. Experiments on real data sets show that LP-DDAM can reduce communication overheads by approximately 70% when compared to an equivalent method that continuously monitors all objects under the same conditions.
Efficient electro-optic sampling detection of terahertz radiation via Cherenkov phase matching (2011)

We experimentally demonstrate an efficient electro-optic sampling scheme based on Cherenkov phase matching of broadband terahertz radiation with 800-nm femtosecond probe beam in a 0.5 mm-thick LiNbO3 crystal coupled to a Si prism. The electro-optic signal from a Cherenkov-phase-matched LiNbO3 crystal is found to be comparable to that with a 4 mm-thick ZnTe crystal using a collinear phase matching. The Cherenkov phase matching technique can be achieved with any probe wavelength and hence has an advantage over the collinear phase matching method.
Determining optimal configuration of video encoding parameters using numerical search algorithms (2008)

We introduce a systematic approach to configuring the video encoding parameters for optimal video encoding in this paper. The determination of optimal video encoding parameters is formulated as an optimization problem of maximizing the expected video encoding quality under a set of constraints that may include a video quality measure, a target bitrate, computation, memory bandwidth, etc. We use the Video Quality Metric, a measurement paradigm of video quality that is based on algorithms for objective measurement of video quality, to measure the expected video encoding performance. The optimization problem can be solved through an efficient multidimensional numerical search method, direct simplex search method, with encoding of various sequences with different encoding parameter settings. We illustrate the approach to determine parameters to enable optimal MB level quantization parameter adaptation in H.264 / AVC.
Inhibitory effects of benzyl isothiocyanate administered shortly before diethylnitrosamine or benzo[<i>a</i>]pyrene on pulmonary and forestomach neoplasia in A/J mice (1987)

The inhibitory effects of benzyl isothiocyanate, a naturally-occurring constituent of cruciferous vegetables, on carcinogenesis of the forestomach and lungs of female A/J mice given dimethylnitrosamine (DEN) or benzo[a]pyrene (BP) was investigated. When administered by gavage 15 min prior to p.o. carcinogen challenge, benzyl isothiocyanate almost completely inhibited forestomach tumor formation resulting from DEN but had no effect on pulmonary tumor formation. With BP as the carcinogen, benzyl isothiocyanate had inhibitory effects on carcinogenesis of both the forestomach and lungs, the latter being greater. The implications for epidemiology studies and for chemopreventive strategies of compounds that inhibit when administered shortly before carcinogen challenge are discussed.
Transgenerational CRISPR-Cas9 Activity Facilitates Multiplex Gene Editing in Allopolyploid Wheat (2018)

The CRISPR-Cas9-based multiplexed gene editing (MGE) provides a powerful method to modify multiple genomic regions simultaneously controlling different agronomic traits in crops. We applied the MGE construct built by combining the tandemly arrayed tRNA-gRNA units to generate heritable mutations in the <i>TaGW2</i>, <i>TaLpx-1</i>, and <i>TaMLO</i> genes of hexaploid wheat. The knockout mutations generated by this construct in all three homoeologous copies of one of the target genes, <i>TaGW2</i>, resulted in a substantial increase in seed size and thousand grain weight. We showed that the non-modified gRNA targets in the early generation plants can be edited by CRISPR-Cas9 in the following generations. Our results demonstrate that transgenerational gene editing activity can serve as the source of novel variation in the progeny of CRISPR-Cas9-expressing plants and suggest that the Cas9-inducible trait transfer for crop improvement can be achieved by crossing the plants expressing the gene editing constructs with the lines of interest.
Development and performance evaluation of bioenzyme-responsive temporary plugging materials (2023)

Ocean gas hydrate is a potentially efficient and clean oil and gas alternative energy resource. Wells with complex structure, such as horizontal wells, can improve the extraction efficiency; however, drilling operations face challenges such as wellbore instability and reservoir damage due to the complex interaction between drilling fluids and hydrate reservoirs. This work presents a ceramsite temporary plugging microcapsule that uses ceramsite modified by 3-aminopropyltriethoxysilane as the core material and chitosan and sodium alginate as shell materials. It exhibits high strength during drilling and excellent plugging effects. After the action of bioenzymes, it can easily be dissolved, leading to high permeability post-drilling. The analysis and performance evaluation of ceramsite microcapsules show that their particle size is generally 40 μm, which can match the pore size of the hydrate reservoir depending on the number of encapsulation layers. Bioenzyme optimization at 15 ◦C yields the best permeability recovery of 74.5% for the low-temperature composite enzyme. As the temperature rises, the permeability recovery rate of ceramic microcapsules gradually increases and the difference in permeability recovery rate between 5 and 25 ◦C becomes more significant. With a longer degradation time, the permeability recovery rate of ceramsite microcapsules gradually enhances and the difference in permeability recovery rate becomes smaller after 12 h. The microcapsules exhibit a specific inhibitory effect on the decomposition of hydrates. Utilizing bioenzyme- responsive ceramsite microcapsules as temporary plugging materials can establish an “isolation barrier” around the wellbore, effectively sealing off the interaction between the wellbore and the gas hydrate reservoir during the drilling process. Re-opening the flow path around the well by bio-enzymatic unblocking at the end of drilling proves to be effective in solving the problem of balancing the stability of the well wall and protecting the reservoir. Document Type: Original article Cited as: Sun, J., Li, Y., Liao, B., Bai, Y., Li, W., Wang, J. Development and performance evaluation of bioenzyme-responsive temporary plugging materials. Advances in Geo-Energy Research, 2024, 11(1): 20-28. https://doi.org/10.46690/ager.2024.01.03
Membrane-binding and activation mechanism of PTEN (2003)

PTEN is a tumor suppressor that reverses the action of phosphoinositide 3-kinase by catalyzing the removal of the 3' phosphate of phosphoinositides. Despite the critical role of PTEN in cell signaling and regulation, the mechanisms of its membrane recruitment and activation is still poorly understood. PTEN is composed of an N-terminal phosphatase domain, a C2 domain, and a C-terminal tail region that contains the PSD-95/Dlg/ZO-1 homology (PDZ) domain-binding sequence and multiple phosphorylation sites. Our in vitro surface plasmon resonance measurements using immobilized vesicles showed that both the phosphatase domain and the C2 domain, but not the C-terminal tail, are involved in electrostatic membrane binding of PTEN. Furthermore, the phosphorylation-mimicking mutation on the C-terminal tail of PTEN caused an approximately 80-fold reduction in its membrane affinity, mainly by slowing the membrane-association step. Subcellular localization studies of PTEN transfected into HEK293T and HeLa cells indicated that targeting of PTEN to the plasma membrane is coupled with rapid degradation and that the phosphatase domain and the C2 domain are both necessary and sufficient for its membrane recruitment. Results also indicated that the phosphorylation regulates the targeting of PTEN to the plasma membrane not by blocking the PDZ domain-binding site but by interfering with electrostatic membrane binding of PTEN. On the basis of these results, we propose a membrane-binding and activation mechanism for PTEN, in which the phosphorylation/dephosphorylation of the C-terminal region serves as an electrostatic switch that controls the membrane translocation of the protein.
Role of spiro-OMeTAD in performance deterioration of perovskite solar cells at high temperature and reuse of the perovskite films to avoid Pb-waste (2018)

Undertaken this study to understand the performance degradation of perovskite solar cells at high temperature and under a humid environment, and then tried to reuse the perovskite films from the degraded cells to recover the cell efficiency so as to avoid Pb-waste.
Increased frequency of circulating IL-21 producing Th-cells in patients with granulomatosis with polyangiitis (GPA) (2013)

The increased frequency of circulating IL-21 producing Th-cells in ANCA-positive GPA patients and the stimulating capacity of IL-21 on ANCA-production suggest a role for these cells in the immunopathogenesis of GPA. Blockade of IL-21 could constitute a new therapeutic strategy for GPA.
Retinoids and Apoptosis: Implications for Cancer Chemoprevention and Therapy (1995)

Lung cancer in the United States leads other cancers in both incidence and mortality (1). The severe morbidity of lung cancer and the discouraging 15% overall 5-year survival rate have not improved despite advancements in treatment modalities. Furthermore, the incidence of lung cancer among women is increasing. Therefore, novel approaches to control this dreadful disease are urgently needed. Biological agents such as differentiati oninducing agents are being evaluated in clinical trials for their potential use for therapy and prevention of a variety of malignancies, including lung cancer (2,5). Among these novel agents are vitamin A analogues (retinoids) that modulate the growth and differentiation of a variety of normal and malignant celjs in vitro and in vivo (4). All-fra/w-retinoic acid (ATRA) was found to be effective in the treatment of patients with acute promyelocytic leukemia by inducing granulocytic differentiation of the leukemia cells in vivo (5). 13-c/s-Retinoic acid (13CRA) has demonstrated efficacy in suppressing premalignant oral lesions and in preventing the development of second primary cancers in the upper aerodigestive tract in patients with head and neck cancer (6). Likewise, retinyl palmitate was found
TexMesh: Reconstructing Detailed Human Texture and Geometry from RGB-D Video (2020)

We present TexMesh, a novel approach to reconstruct detailed human meshes with high-resolution full-body texture from RGB-D video. TexMesh enables high quality free-viewpoint rendering of humans. Given the RGB frames, the captured environment map, and the coarse per-frame human mesh from RGB-D tracking, our method reconstructs spatiotemporally consistent and detailed per-frame meshes along with a high-resolution albedo texture. By using the incident illumination we are able to accurately estimate local surface geometry and albedo, which allows us to further use photometric constraints to adapt a synthetically trained model to real-world sequences in a self-supervised manner for detailed surface geometry and high-resolution texture estimation. In practice, we train our models on a short example sequence for self-adaptation and the model runs at interactive framerate afterwards. We validate TexMesh on synthetic and real-world data, and show it outperforms the state of art quantitatively and qualitatively.
Cerebral blood flow, arteriovenous oxygen difference, and outcome in head injured patients. (1992)

Cerebral blood flow (CBF) and other physiological variables were measured repeatedly for up to 10 days after severe head injury in 102 patients, and CBF levels were related to outcome. Twenty five of the patients had a reduced CBF [mean (SD) 0.29 (0.05) ml/g/min]; 47 had a normal CBF, (0.41 (0.10) ml/g/min); and 30 had a raised CBF (0.62 (0.14) ml/g/min). Cerebral arteriovenous oxygen differences were inversely related to CBF and averaged 2.1 (0.7) mumol/ml in the group with reduced CBF, 1.9 (0.5) mumol/ml in the group with normal CBF, and 1.6 (0.4) mumol/ml in the group with raised CBF. Patients with a reduced CBF had a poorer outcome than patients with a normal or raised CBF. Mortality was highest in patients with a reduced CBF, and was 32% at three months after injury, whereas only 21% of the patients with a normal CBF and 20% of the patients with a raised CBF died. There were no differences in the type of injury, initial score on the Glasgow Coma Scale, mean intracranial pressure (ICP), highest ICP, or the amount of medical treatment required to keep the ICP less than 20 mm Hg in each group. Systemic factors did not significantly contribute to the differences in CBF among the three groups. A logistic regression model of the effect of CBF on neurological outcome was developed. When adjusted for variables which were found to be significant confounders, including age, initial Glasgow Coma Score, haemoglobin concentration, cerebral perfusion pressure and cerebral metabolic rate of oxygen, a reduced CBF remained significantly associated with an unfavourable neurological outcome.
Using a Charging Coordinate in Studies of Ionization Induced Partial Unfolding (2006)

The ionization of groups in proteins may sometimes involve a partial unfolding and/or water penetration. Unfortunately the corresponding structural changes might not be captured by microscopic free energy perturbation (FEP) approaches due to activation barriers that are not surmounted in nanosecond FEP simulations. This problem is apparent, for example, from mutation experiments that introduced ionizable groups in protein interiors and from the difficulties to reproduce the corresponding pKa changes by microscopic approaches. Here we develop a new general approach for treating such challenging cases. Our approach drives the protein structural change by increasing the charge of the ionized group beyond its physical value and thus overcoming the barriers for the partial unfolding by a physically consistent process. The potential of our approach is illustrated by the evaluation of the pKa of the Val66Glu mutant of staphylococcal nuclease. In this case it is first demonstrated that standard FEP approaches give extremely disappointing results for this pKa. On the other hand, our "overcharging" approach gives a much more realistic result. We believe that the present approach represents a breakthrough in FEP studies of ionizable residues in proteins, and expect this strategy to be useful in studies of a wide range of challenging problems including simulations of hydrogen exchange processes.
Bilateral guided upsampling (2016)

We present an algorithm to accelerate a large class of image processing operators. Given a low-resolution reference input and output pair, we model the operator by fitting local curves that map the input to the output. We can then produce a full-resolution output by evaluating these low-resolution curves on the full-resolution input. We demonstrate that this faithfully models state-of-the-art operators for tone mapping, style transfer, and recoloring. The curves are computed by lifting the input into a bilateral grid and then solving for the 3D array of affine matrices that best maps input color to output color per x, y , intensity bin. We enforce a smoothness term on the matrices which prevents false edges and noise amplification. We can either globally optimize this energy, or quickly approximate a solution by locally fitting matrices and then enforcing smoothness by blurring in grid space. This latter option reduces to joint bilateral upsampling [Kopf et al. 2007] or the guided filter [He et al. 2013], depending on the choice of parameters. The cost of running the algorithm is reduced to the cost of running the original algorithm at greatly reduced resolution, as fitting the curves takes about 10 ms on mobile devices, and 1--2 ms on desktop CPUs, and evaluating the curves can be done with a simple GPU shader.
Collaborative augmented reality for better standards (2007)

Concurrent engineering depends on clear communication between all members of the development process. As that communication becomes more and more complex, the quality of the standards used to move and understand that information likewise becomes more and more important. If the standard is incomplete, redundant, or ambiguous, most of the expected benefits are lost. In order to improve data exchange standards, explicit data models are required. However, creating those data models is a process that requires collaboration between domain experts. What is needed is a solution that encourages interaction without requiring a high level of data modeling expertise. Focus is a software tool designed to provide such an environment. It is a distributed design and conferencing application which uses augmented reality to allow domain experts to come together in real time for data modeling. By developing Focus, we hope to allow domain experts to create data models without first having to learn complex UML modeling programs. Because of the networked nature of Focus, it is easier to ensure the participation of the best domain experts regardless of location. This paper details the development, features, and expected benefits of Focus in a collaborative engineering environment.
Fuzzy logic vs traditional approaches to the design of microcontroller-based systems (2002)

The use of fuzzy logic for closed loop control is compared to the more traditional approaches of zero-pole placement in the z-plane and the choice of PID (proportional, integral, differential) parameters. A common type of positioning system is used as an example to illustrate these different approaches and to allow practical comparisons. Results of a simulation study of the model system, using specific implementations of the three control techniques, show that fuzzy logic can be used to achieve a degree of compensation that is nearly as good as that achieved by more conventional techniques. The fuzzy logic approach requires more code, hence, more power on the part of the microcontroller, but it does not require that the designer have a knowledge of feedback control theory. Because fuzzy logic is a straightforward approach, based upon practical knowledge of the system to be controlled, its use has some advantages over the other approaches if an analytic model of the system is difficult to construct. Certain demands are placed upon the microcontroller in all three cases, and these are discussed here in some detail. Two popular microcontrollers, the MC68HC16 and MC68332, are examined to explore their individually unique features that make them particularly suitable for one or the other of the control schemes studied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>