gebhart/patrepeval huggingface dataset:
Cleavage of Double-Crossover Molecules by T4 Endonuclease VII (1994)

DNA double-crossover molecules containing two Holliday junctions have been prepared and treated with endonuclease VII, the resolvase from bacteriophage T4. One molecule contains antiparallel double-helical domains, and the other molecule contains parallel domains. The parallel double-crossover model system has been made tractable by closing the free ends of the molecule, to convert it to a catenane. The products resulting from the two substrates differ substantially. The molecule containing antiparallel helical domains is cleaved three nucleotides 3' to the crossover points, in a fashion similar to single Holliday junction analogs. The molecule containing parallel helical domains is cleaved, but the major points of scission are five nucleotides 5' to a branch point on the crossover strands and six nucleotides 3' to the same branch point on the non-crossover strands. The major sites of scission reflect features of molecular symmetry in each case, suggesting that the resolvase recognizes structural features. The cleavage results suggest that the antiparallel structure is the natural substrate, if the Holliday junction is unconstrained within the cell. It is straightforward to reconcile antiparallel Holliday junctions with the conventional parallel paradigm of recombination. Nevertheless, the cleavage of the parallel molecule shows that a parallel substrate could also be cleaved symmetrically by endonuclease VII (but with different products) if the molecule were constrained to assume that conformation within the cell.
Participatory Cultural Mapping Based on Collective Behavior Data in Location-Based Social Networks (2016)

Culture has been recognized as a driving impetus for human development. It co-evolves with both human belief and behavior. When studying culture, Cultural Mapping is a crucial tool to visualize different aspects of culture (e.g., religions and languages) from the perspectives of indigenous and local people. Existing cultural mapping approaches usually rely on large-scale survey data with respect to human beliefs, such as moral values. However, such a data collection method not only incurs a significant cost of both human resources and time, but also fails to capture human behavior, which massively reflects cultural information. In addition, it is practically difficult to collect large-scale human behavior data. Fortunately, with the recent boom in Location-Based Social Networks (LBSNs), a considerable number of users report their activities in LBSNs in a participatory manner, which provides us with an unprecedented opportunity to study large-scale user behavioral data. In this article, we propose a participatory cultural mapping approach based on collective behavior in LBSNs. First, we collect the participatory sensed user behavioral data from LBSNs. Second, since only local users are eligible for cultural mapping, we propose a progressive “home” location identification method to filter out ineligible users. Third, by extracting three key cultural features from daily activity, mobility, and linguistic perspectives, respectively, we propose a cultural clustering method to discover cultural clusters. Finally, we visualize the cultural clusters on the world map. Based on a real-world LBSN dataset, we experimentally validate our approach by conducting both qualitative and quantitative analysis on the generated cultural maps. The results show that our approach can subtly capture cultural features and generate representative cultural maps that correspond well with traditional cultural maps based on survey data.
Protein kinase activity of Tel1p and Mec1p, two <i>Saccharomyces cerevisiae</i> proteins related to the human ATM protein kinase (2000)

The Saccharomyces cerevisiae proteins Tel1p and Mec1p are involved in telomere length regulation and cellular responses to DNA damage. The closest relative of these proteins is the human Ataxia Telangiectasia Mutated (ATM) protein, a wortmannin-sensitive protein kinase that primarily phosphorylates serines in an SQ motif. We constructed yeast strains containing functional epitope-tagged versions of Tel1p and Mec1p. We showed that immunoprecipitated Tel1p and Mec1p were capable of in vitro phosphorylation of the mammalian protein PHAS-I (Phosphorylated Heat and Acid Stable protein). These activities are sensitive to wortmannin. Tel1p phosphorylates serine in an SQ motif in PHAS-I. Mutations in the kinase domains of Tel1p and Mec1p result in loss of in vitro kinase activity and the in vivo phenotypes associated with the null tel1 and mec1 mutations.
<title>Random graph representation for 3-D object models</title> (1992)

A key capability for an intelligent machine vision system is the ability to autonomously acquire new information about an environment. This is especially true in model-based 3-D object recognition, where a bottleneck exists in the generation of geometric models and the selection of suitable sets of features for recognizing each model. We describe a new model representation, based on the random graph, for use in 3-D object recognition. The random graph is a probabilistic representation of an ensemble of attributed graphs which can describe variations in both the structure and attribute values of structural patterns. The random graph is well-suited to accommodate the uncertain and incomplete nature of real-world data and is able to meet the information requirements for object recognition through the representation of feature visibility, detectability, and variability. In the random graph object model, vertices represent geometric features, such as points, edges, and planar surfaces, and arcs represent topological relations. Uncertainty in geometric feature attributes and in model structure is described by attaching probability distributions to model vertex and arc attribute values. A specific example, the point feature random graph model, has been implemented and is described in greater detail.
Predicting Breast Cancer Treatment Response using Diffuse Optical Tomography and Ultrasound (2020)

This clinical study validates an early treatment window for predicting complete or near-complete pathological response of breast cancer patients based on pretreatment total-hemoglobin level (THb), early changes of THb and ultrasound measurements following neoadjuvant chemotherapy.
Virology & Antiviral Research 2020 Editorial Note (2020)

The Journal of Virology &Antiviral Research, Scitechnol publication, is an international journal which published articles globally in the prime field of Virology, Microbiology, Viral Immunological and its applied fieldsand research advancements in the discipline. Its is an open access and peer reviewed journal handled by eminent Editorial Board and the manuscripts are peer-reviewed by potential reviewers according to their research interest.
Compensation for Nonuniform Resolution Using Penalized-Likelihood Reconstruction in Space-Variant Imaging Systems (2004)

Imaging systems that form estimates using a statistical approach generally yield images with nonuniform resolution properties. That is, the reconstructed images possess resolution properties marked by space-variant and/or anisotropic responses. We have previously developed a space-variant penalty for penalized-likelihood (PL) reconstruction that yields nearly uniform resolution properties. We demonstrated how to calculate this penalty efficiently and apply it to an idealized positron emission tomography (PET) system whose geometric response is space-invariant. In this paper, we demonstrate the efficient calculation and application of this penalty to space-variant systems. (The method is most appropriate when the system matrix has been precalculated.) We apply the penalty to a large field of view PET system where crystal penetration effects make the geometric response space-variant, and to a two-dimensional single photon emission computed tomography system whose detector responses are modeled by a depth-dependent Gaussian with linearly varying full-width at half-maximum. We perform a simulation study comparing reconstructions using our proposed PL approach with other reconstruction methods and demonstrate the relative resolution uniformity, and discuss tradeoffs among estimators that yield nearly uniform resolution. We observe similar noise performance for the PL and post-smoothed maximum-likelihood (ML) approaches with carefully matched resolution, so choosing one estimator over another should be made on other factors like computational complexity and convergence rates of the iterative reconstruction. Additionally, because the postsmoothed ML and the proposed PL approach can outperform one another in terms of resolution uniformity depending on the desired reconstruction resolution, we present and discuss a hybrid approach adopting both a penalty and post-smoothing.
839 (2012)

Introduction: Diffuse alveolar hemorrhage (DAH) is a clinical syndrome that can manifest as a complication in cancer patients and carries a substantial mortality. Minimal data exists regarding effective treatment options. Retrospective studies have cited high-dose steroids as primary therapy with fibrinolytic agents used adjunctively may reduce mortality. Practices at our institution have changed to include the use of fibrinolytic agents in addition to steroids for the acute treatment of DAH. Hypothesis: This study was conducted to characterize current prescribing practices at a comprehensive cancer center for the acute treatment of DAH in critically ill cancer patients and to determine the impact of steroid dosing on mortality in patients receiving methylprednisolone (MP) with aminocaproic acid (ACA) infusions. Methods: Medical intensive care unit patients > 18 years of age with a diagnosis of DAH treated with MP and ACA were retrospectively analyzed over 48 consecutive months. Diagnosis was based on clinical presentation consistent with DAH or available bronchoscopic and autopsy findings. Data collection included patient demographics, pharmacological treatment, ventilator days, ICU length of stay, thrombotic complications, bronchoscopic and autopsy findings, and mortality. Low, medium, and high-dose MP was defined as less than 250 mg, 250 to less than 1000mg, or greater than or equal to 1000 mg, respectively. Results: 206 cancer patients were identified who received MP at a mean dose of 502 mg/day and ACA infusion at 1 g/hour. There were no differences in baseline characteristics including age, platelet count, oxygen requirements, or APACHE II and SOFA scores. 55 patients received low-dose MP, 105 medium-dose MP, and 46 high-dose MP. Amongst the 3 groups, there were no differences in 100-day mortality (85.5%, 78.1%, 91.3%, p=0.12). There were also no differences in ventilator days (p=0.12), ICU length of stay (p=0.79), or hospital length of stay (p=0.82). Conclusions: DAH is a significant contributor to mortality in the cancer population. In patients treated with MP and ACA, escalation of MP dose may have no improvement on outcomes and survival in this patient population.
Cut5 Is Required for the Binding of Atr and DNA Polymerase α to Genotoxin-damaged Chromatin (2003)

DNA damage triggers the assembly of checkpoint signaling proteins on chromatin that activate the Chk1 signaling pathway and block S-phase progression. Here we show that genotoxin-induced Chk1 activation requires Cut5 (Mus101/TopBP1) in a process that is independent of the role of Cut5 in DNA replication. Analysis of the role of Cut5 in checkpoint activation revealed that it associated with chromatin following DNA damage in a process that required RPA. Additionally, Cut5 was required for the recruitment of Atr, DNA polymerase alpha, and Rad1 but not RPA to chromatin following DNA damage. Taken together, these results demonstrate that Cut5 plays an integral role in the recruitment and assembly of the Chk1 signaling cascade components following DNA damage.
Suramin inhibits initiation of defense signaling by systemin, chitosan, and a β-glucan elicitor in suspension-cultured <i>Lycopersicon peruvianum</i> cells (2000)

Systemin-mediated defense signaling in tomato (Lycopersicon esculentum) plants is analogous to the cytokine-mediated inflammatory response in animals. Herein, we report that the initiation of defense signaling in suspension-cultured cells of Lycopersicon peruvianum by the peptide systemin, as well as by chitosan and beta-glucan elicitor from Phytophtora megasperma, is inhibited by the polysulfonated naphtylurea compound suramin, a known inhibitor of cytokine and growth factor receptor interactions in animal cells. Using a radioreceptor assay, we show that suramin interfered with the binding of the systemin analog (125)I-Tyr-2, Ala-15-systemin to the systemin receptor with an IC(50) of 160 microM. Additionally, labeling of the systemin receptor with a photoaffinity analog of systemin was inhibited in the presence of suramin. Receptor-mediated tyrosine phosphorylation of a 48-kDa mitogen-activated protein kinase and alkalinization of the medium of suspension-cultured cells in response to systemin and carbohydrate elicitors were also inhibited by suramin. The inhibition of medium alkalinization by suramin was reversible in the presence of high concentrations of systemin and carbohydrate elicitors. Calyculin A and erythrosin B, intracellular inhibitors of phosphatases and plasma membrane proton ATPases, respectively, both induce medium alkalinization, but neither response was inhibited by suramin. The polysulfonated compound heparin did not inhibit systemin-induced medium alkalinization. NF 007, a suramin derivative, induced medium alkalinization, indicating that neither NF 007 nor heparin interact with elicitor receptors like suramin. The data indicate that cell-surface receptors in plants show some common structural features with animal cytokine and growth factor receptors that can interact with suramin to interfere with ligand binding.
ChemInform Abstract: TRANSFORMATION STRENGTHENING OF β“‐ALUMINA WITH TETRAGONAL ZIRCONIA (1983)

Abstract Die im spannungsfreien Zustand oberhalb ca. 1200°C stabile tetragonale Phase von ZrO 2 [ZrO2 (t)] kann durch Legierung mit Y,O3 auf Raumtemp. gebracht werden.
CWMBRAN'S COMING SUPERSTORE ‐ And how it may affect shopping patterns (1975)

The south Wales region is increasingly taking on a test‐tube character for assessing shopping patterns throughout the country as a whole. Cwmbran New Town, situated some five miles south of Pontypool and 16 miles north‐east of Cardiff, has been described as being “likely to be regarded as Britain's most successful out‐of‐town shopping centre.” Some 88% of planned retail floorspace is located in the town centre, the remainder being in eight neighbourhood shopping centres. In addition, the town is within the catchment area of the UK's first‐ever Carrefour, at Caerphilly; and an Asda unit at Rogerstone (Newport). A further major development is to be the arrival of a Woolco superstore of 100,000 sq ft, to be opened in the centre in the autumn; in addition there is likely to be a Marks & Spencer next year, plus a 50,000 sq ft supermarket for J.Sainsbury. Everybody, it seems, is coming to Cwmbran. This article sets out to examine patterns of shopping behaviour before these developments take place, and specifically consumer attitudes to the Woolco superstore. The authors conclude from their survey that neighbourhood centres will suffer a reduction in sales volume, and that in the town centre, blight may extend.
A novel AOI system for OLED panel inspection (2005)

Organic light emitting diode (OLED) technology uses substances that emit red, green, blue or white light. An OLED panel consists of stacks of several thin layers of different materials, as such it is not easy to inspect the common OLED defects. In this paper, an autooptical inspection (AOI) system which can detect such defects effectively and robustly was proposed and developed. The proposed system can also identify, in which layer the defect occurred. Meanwhile, a moving mechanism coupled with a lighting mechanism was proposed and implemented for grabbing clear images. The proposed AOI system would provide great help in improving the OLED production process and the quality control process.
High Velocity Interparticle Collisions Driven by Ultrasound (2004)

Ultrasonic irradiation of slurries produces high velocity impacts between solid metal particles that are sufficient to cause interparticle melting. Sonication of 5 mum Zn powder as a slurry in alkanes, for example, produces dense agglomerates 50 mum in diameter consisting of approximately 1000 fused particles. Particle size was found to be the most influential parameter in inducing local melting during interparticle collisions. Ultrasonic irradiation of mixed powders resulted in formation of agglomerates with larger Zn particles "soldered" by the smaller ones. A simple kinematic model of the ultrasound-driven interparticle fusion predicts a melting criterion that is nonmonotonically dependent on particle size and is shown to be in agreement with experiment.
A Real-Time Thermal Self-Elimination Method for Static Mode Operated Freestanding Piezoresistive Microcantilever-Based Biosensors (2018)

Here, we provide a method and apparatus for real-time compensation of the thermal effect of single free-standing piezoresistive microcantilever-based biosensors. The sensor chip contained an on-chip fixed piezoresistor that served as a temperature sensor, and a multilayer microcantilever with an embedded piezoresistor served as a biomolecular sensor. This method employed the calibrated relationship between the resistance and the temperature of piezoresistors to eliminate the thermal effect on the sensor, including the temperature coefficient of resistance (TCR) and bimorph effect. From experimental results, the method was verified to reduce the signal of thermal effect from 25.6 μV/°C to 0.3 μV/°C, which was approximately two orders of magnitude less than that before the processing of the thermal elimination method. Furthermore, the proposed approach and system successfully demonstrated its effective real-time thermal self-elimination on biomolecular detection without any thermostat device to control the environmental temperature. This method realizes the miniaturization of an overall measurement system of the sensor, which can be used to develop portable medical devices and microarray analysis platforms.
Breast cancer metastasis to bone: evolving models and research challenges. (2003)

. Thus, improve-ments in long-term survival will be most helped by betterunderstanding of the metastatic process.Skeletal metastases are common, particularly from breast,prostate and myeloma tumors. In many cases, the frequencyof metastasis to bone is greater than metastases elsewhere.Whereas 73% of women develop bone metastases, only 33%develop lung and/or liver metastases. While patients can sur-vive a relatively long time with bone lesions, their quality oflife is miserable due to intractable pain, fractures, spinalcord compression and metabolic complications
Production of brain-derived neurotrophic factor by mononuclear cells of patients with multiple sclerosis treated with glatiramer acetate, interferon-β 1a, and high doses of immunoglobulins (2007)

Sixty, relapsing remitting (RR) multiple sclerosis (MS) patients, who underwent treatment with glatiramer acetate (GA), interferon (IFN)-beta 1a, and immunoglobulins (Igs) (20 per treatment group), were assessed for levels of brain-derived neurotrophic factor (BDNF) in the supernatants of unstimulated and stimulated peripheral blood mononuclear cells (PBMCs) in the first year of treatment. Phytohemagglutinin (PHA), anti-OKT3 antibody, myelin basic protein (MPB) and GA were used as stimuli. Cytokine responses by ELISPOT and lymphoproliferative responses were also assessed. The GA-treated MS patient group showed a progressive increase in BDNF levels, from baseline to month three; thereafter, the levels remained stable and significantly greater compared with baseline and controls (ANOVA=P<0.001). IFN-beta 1a had no effect on BDNF production, whereas Igs induced a slight decrease (ANOVA=P<0.04). ELISPOT analysis revealed a significant decrease of IFN-gamma, an increase of interleukin (IL)-4 and IL-5 in GA-treated MS patients, and an increase of IL-10 in patients treated with IFN-beta 1a and GA. No significant correlation was found between BDNF secretion in the supernatants of PBMCs and cytokine response, lesional load, and measures of atrophy. Increased BDNF production related to GA treatment can have implications for understanding the mechanism of action of this immunomodulatory agent, in light of evidence suggesting its effects in promoting neuroprotective immunity in MS patients; however, a clinically measurable effect, especially in terms of an impact on actual disease progression, remains to be established.
Tactile programming: a unified manipulation paradigm supporting program comprehension, composition and sharing (2002)

Although visual programming techniques have been used to lower the threshold of programming for end users, they are not sufficient for creating end user programming environments that are both easy to use and powerful. To achieve this, an environment must support the definition of programs that are not just static representations of behavior, but are instead dynamic collections of program objects which can be applied in a number of contexts rather than just a program editor. We describe an approach to end user programming called tactile programming which extends visual techniques with a unified program manipulation paradigm that makes programs easy to comprehend, compose and, most importantly, share over the World Wide Web. Tactile programming's inherent ability to support the social context in which programming takes place along with its ability to ease program comprehension and composition is what differentiates this approach from others. In the context of the Agentsheets programming substrate, we have created an instance of a tactile programming environment called Visual AgenTalk which is used to create interactive simulations.
Universal signal processing method for multimode reflective sensors (1988)

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Eye-to-Eye Calibration - Extrinsic Calibration of Multi-Camera Systems Using Hand-Eye Calibration Methods (2015)

The problem addressed in this thesis is the extrinsic calibration of embedded multi-camera systems without overlapping views, i.e., to determine the positions and orientations of rigidly coupled cameras with respect to a common coordinate frame from captured images. Such camera systems are of increasing interest for computer vision applications due to their large combined field of view, providing practical use for visual navigation and 3d scene reconstruction. However, in order to propagate observations from one camera to another, the parameters of the coordinate transformation between both cameras have to be determined accurately. Classical methods for extrinsic camera calibration relying on spatial correspondences between images cannot be applied here. The central topic of this work is an analysis of methods based on hand-eye calibration that exploit constraints of rigidly coupled motions to solve this problem from visual camera ego-motion estimation only, without need for additional sensors for pose tracking such as inertial measurement units or vehicle odometry. The resulting extrinsic calibration methods are referred to as "eye-to-eye calibration". We provide solutions based on pose measurements (geometric eye-to-eye calibration), decoupling the actual pose estimation from the extrinsic calibration, and solutions based on images measurements (visual eye-to-eye calibration), integrating both steps within a general Structure from Motion framework. Specific solutions are also proposed for critical motion configurations such as planar motion which often occurs in vehicle-based applications.