gebhart/patrepeval huggingface dataset:
Report on the Third International Workshop on XQuery Implementation, Experience and Perspectives (XIME-P 2006) (2007)

On June 30, 2006, XIME-P 2006 , the International Workshop on XQuery Implementation, Experience and Perspectives was held. This workshop marks the third event in a workshop series whose primary aim is to shed light on XQuery systems, specification aspects, foundations of the language, and the many perceivable shapes it may take on in the future. Like the two previous workshops of 2004 (Paris) and 2005 (Baltimore), XIME-P 2006 was held as a co-located workshop of the ACM SIGMOD Conference, which this year was held in Chicago, IL, USA. The 2006 edition was co-chaired by Michael Carey and Torsten Grust. The workshop web site can be found at www.ximep-2006.org.
Structure of a biological oxygen sensor: A new mechanism for heme-driven signal transduction (1998)

The FixL proteins are biological oxygen sensors that restrict the expression of specific genes to hypoxic conditions. FixL's oxygen-detecting domain is a heme binding region that controls the activity of an attached histidine kinase. The FixL switch is regulated by binding of oxygen and other strong-field ligands. In the absence of bound ligand, the heme domain permits kinase activity. In the presence of bound ligand, this domain turns off kinase activity. Comparison of the structures of two forms of the Bradyrhizobium japonicum FixL heme domain, one in the "on" state without bound ligand and one in the "off" state with bound cyanide, reveals a mechanism of regulation by a heme that is distinct from the classical hemoglobin models. The close structural resemblance of the FixL heme domain to the photoactive yellow protein confirms the existence of a PAS structural motif but reveals the presence of an alternative regulatory gateway.
The Artificial Evolution of an Enzyme by Random Mutagenesis: The Development of Formaldehyde Dehydrogenase (2004)

A unique variant of glutathione independent formaldehyde dehydrogenase of Pseudomonas putida was obtained by random mutagenesis using the PCR-reaction. This YM042 mutant, S318G, was a cold-adapted formaldehyde dehyrogenase. The activity at 29 degrees C of the variant was 1.7-fold higher than that of the wild type. The K(m) values of the mutant at 37 degrees C were 0.40 mM for NAD(+) and 2.5 mM for formaldehyde, while those of the wild-type were 0.18 mM for NAD(+) and 2.1 mM for formaldehyde. The catalytic efficiency for formaldehyde was about 1.5-fold greater in the mutant than in the wild-type enzyme. The optimum pHs and temperatures of the mutant and the wild-type enzyme were 7.5, and 8.0 and 37 degrees C, and 47 degrees C, respectively. The thermal stability of the mutant was lower than that of the wild type.
Pharmacological activation of the p53 pathway in haematological malignancies (2009)

p53 gene mutations are rarely detected at diagnosis in common haematological cancers such as multiple myeloma (MM), acute myeloid leukaemia (AML), chronic lymphocytic leukaemia (CLL) and Hodgkin's disease (HD), although their prevalence may increase with progression to more aggressive or advanced stages. Therapeutic induction of p53 might therefore be particularly suitable for the treatment of haematological malignancies. Some of the anti-tumour activity of current chemotherapeutics has been derived from activation of p53. However, until recently it was unknown whether p53 signalling is functional in certain haematological cancers including MM and if p53 activity is sufficient to trigger an apoptotic response. With the recent discovery of nutlins, which represent the first highly selective small molecule inhibitors of the p53-MDM2 interaction, pharmacological tools are now available to induce p53 irrespective of upstream signalling defects, and to functionally analyse the downstream p53 pathway in primary leukaemia and lymphoma cells. Combination therapy is emerging as a key factor, and development of non-genotoxic combinations seems very promising for tackling the problems of toxicity and resistance. This review will highlight recent findings in the research into molecules capable of modulating p53 protein activities and mechanisms that activate the p53 pathway, restoring response to therapy in haematological malignancies.
RhoA-ROCK Pathway is Important for T-Cell Migration in a Mouse Stroke Model (2017)

International audience
Effects of Homology Length in the Repeat Region on Minus-Strand DNA Transfer and Retroviral Replication (2001)

Homology between the two repeat (R) regions in the retroviral genome mediates minus-strand DNA transfer during reverse transcription. We sought to define the effects of R homology lengths on minus-strand DNA transfer. We generated five murine leukemia virus (MLV)-based vectors that contained identical sequences but different lengths of the 3' R (3, 6, 12, 24 and 69 nucleotides [nt]); 69 nt is the full-length MLV R. After one round of replication, viral titers from the vector with a full-length downstream R were compared with viral titers generated from the other four vectors with reduced R lengths. Viral titers generated from vectors with R lengths reduced to one-third (24 nt) or one-sixth (12 nt) that of the wild type were not significantly affected; however, viral titers generated from vectors with only 3- or 6-nt homology in the R region were significantly lower. Because expression and packaging of the RNA were similar among all the vectors, the differences in the viral titers most likely reflected the impact of the homology lengths on the efficiency of minus-strand DNA transfer. The molecular nature of minus-strand DNA transfer was characterized in 63 proviruses. Precise R-to-R transfer was observed in most proviruses generated from vectors with 12-, 24-, or 69-nt homology in R, whereas aberrant transfers were predominantly used to generate proviruses from vectors with 3- or 6-nt homology. Reverse transcription using RNA transcribed from an upstream promoter, termed read-in RNA transcripts, resulted in most of the aberrant transfers. These data demonstrate that minus-strand DNA transfer is homology driven and a minimum homology length is required for accurate and efficient minus-strand DNA transfer.
Signal-dependent film grain noise generation using homomorphic adaptive filtering (2000)

A technique for the generation of signal-dependent film grain noise is presented. It finds applications in television and motion picture productions where artificial film grain noise is added to computer-generated synthetic images to give them a realistic appearance. After decoupling the signal from the noise, using the generalised homomorphic transformation, the noise is removed from the noisy image using the proposed adaptive filtering scheme. The noise parameter is then estimated using the higher-order statistics (skewness or kurtosis) of the observed image and the filtered image statistics, and it is used to generate film grain noise. Computer simulation results demonstrate the effectiveness of the proposed method.
Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing (2022)

Abstract Polycomb group (PcG) proteins modulate higher-order genome folding and play a critical role in silencing transcription during development. It is commonly proposed that PcG dependent changes in genome folding, which compact chromatin, contribute directly to repression by blocking binding of activating complexes and demixing repressed targets from non-repressed chromatin. To test this model we utilized Optical Reconstruction of Chromatin Architecture (ORCA) to trace the 3-dimensional folding of the Hoxa gene cluster, a canonical Polycomb target, allowing us to analyze thousands of DNA traces in single cells. In cell types ranging from embryonic stem cells to brain tissue, we find that PcG-bound chromatin frequently explores decompact states and partial mixing with neighboring chromatin, while remaining uniformly repressed, challenging the repression-by-compaction model. Using polymer physics simulations, we show that the flexible ensembles we observe can be explained by dynamic contacts mediated by multivalent interactions that are too weak to induce phase separation. Instead, these transient contacts contribute to accurate propagation of the epigenetic state without ectopic spreading or gradual erosion. We propose that the distinctive 3D organization of Polycomb chromatin, reflects a mechanism of “spatial feedback” required for stable repression.
Techniques for Structuring Database Records (1983)

Structuring database records by considering data item usage can yield substantial efficiencies in the operating cost of database systems. However, since the number of possible physical record structures for database of practical significance is enormous, and their evaluation is extremely complex, determining efficient record structures by full enumeration is generally infeasible. This paper discusses the techniques of mathematical clustering, iterative grouping refinement, mathematical programming, and hierarchic aggregation, which can be used to quickly determine efficient record structures for large, shared databases.
Detection and monitoring of changes in metallic structures using multimode acoustic signals (2023)

Methods for detecting and monitoring changes in mechanical structures and in walls of pipes, vessels and storage tanks, using muitimode acoustic signal propagation and detection, are described. Acoustic signals having chosen amplitude-time-frequency characteristics excite multiple modes in the structure under investigation, are generated and received at a small number of accessible locations, such as the ends of pipes and the tops and bottoms of vessels and storage tanks, with the inspection region between transmit and receive transducers. Small mechanical changes lead to acoustic scattering and attenuation among the various modes, which are detectable as changes in received signal intensity. Such changes may include material loss, material conversion and material addition. Once the structure is characterized in a known condition, the present method may be used to monitor the structure at a later time to determine whether changes have taken place. Methods for effective temperature compensation are also described. In addition, various pipe geometries and complex pipe geometries involving elbows, flanges, and the like can be monitored.
Sox6 cell-autonomously stimulates erythroid cell survival, proliferation, and terminal maturation and is thereby an important enhancer of definitive erythropoiesis during mouse development (2006)

Erythropoiesis, the essential process of hematopoietic stem cell development into erythrocytes, is controlled by lineage-specific transcription factors that determine cell fate and differentiation and by the hormone erythropoietin that stimulates cell survival and proliferation. Here we identify the Sry-related high-mobility-group (HMG) box transcription factor Sox6 as an important enhancer of definitive erythropoiesis. Sox6 is highly expressed in proerythroblasts and erythroblasts in the fetal liver, neonatal spleen, and bone marrow. Mouse fetuses and pups lacking Sox6 develop erythroid cells slowly and feature misshapen, short-lived erythrocytes. They compensate for anemia by elevating the serum level of erythropoietin and progressively enlarging their erythropoietic tissues. Erythroid-specific inactivation of Sox6 causes the same phenotype, demonstrating cell-autonomous roles for Sox6 in erythroid cells. Sox6 potentiates the ability of erythropoietin signaling to promote proerythroblast survival and has an effect additive to that of erythropoietin in stimulating proerythroblast and erythroblast proliferation. Sox6 also critically facilitates erythroblast and reticulocyte maturation, including hemoglobinization, cell condensation, and enucleation, and ensures erythrocyte cytoskeleton long-term stability. It does not control adult globin and erythrocyte cytoskeleton genes but acts by stabilizing filamentous actin (F-actin) levels. Sox6 thus enhances erythroid cell development at multiple levels and thereby ensures adequate production and quality of red blood cells.
Verursacht die Infusion oder Inhalation von Prostaglandin-Trägerlösungen (Äthanol, Glycin-Puffer) pulmonalvaskuläre oder respiratorische Effekte? (2007)

The effect of inhaled or intravenously infused PGE1 and PGI2 is not influenced by their preparations containing ethanol or glycine buffer.
Using a deformable surface model to obtain a shape representation of the cortex (1996)

This paper examines the problem of obtaining a mathematical representation of the outer cortex of the human brain, which is a key problem in several applications, including morphological analysis of the brain, and spatial normalization and registration of brain images. A parameterization of the outer cortex is first obtained using a deformable surface algorithm which, motivated by the structure of the cortex, is constructed to find the central layer of thick surfaces. Based on this parameterization, a hierarchical representation of the outer cortical structure is proposed through its depth map and its curvature maps at various scales. Various experiments on magnetic resonance data are presented.
FEM analysis on the losses characteristic and temperature distribution of laminated core in MCR (2019)

The loss and temperature characteristics of magnetic valve type controllable reactor (MCR) lays great influence on its performance and safe operation. Abnormal magnetic field and hot spots can be caused by the laminated joint sheets distributed in magnetic valves. In this paper, a three-dimensional (3-D) finite element simulation model of MCR with distributed magnetic valves is established in COMSOL 5.3a firstly. Secondly, the loss and temperature of laminated joint sheets embedded in iron-cores are simulated using magneto-thermal coupling method. Finally, the joint building factor (JBF) is presented to compute and evaluate the relationship between loss characteristics and structure of magnetic valves. The results show that abnormal high-temperature of laminated core occurs in the magnetic valves. Both the maximum temperature and the JBF increases rapidly with the increase of magnetic flux intensity or the number of layers of silicon steel sheets. The simulation results are in accordance with practical operated MCR and provide guidance for its thermal safety.
Effects of vehicle vibrations on mm-wave channel: Doppler spread and correlative channel sounding (2016)

This paper deals with evaluating the effect of vehicle vibrations on the mm-wave intra-vehicular channel. As some of the vehicles' vibration amplitude may reach the order of millimeters, i.e., the amplitude is comparable with the mm-wave wavelength (≈5 mm), it can produce severe Doppler spreads. This paper evaluates Doppler spreads utilizing a mm-wave time-domain correlative channel sounder built into a vehicle which has been driven at different speeds on a variety of roads with a broad spectrum of surface quality.
Associations between dietary inflammatory scores and biomarkers of inflammation in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (2023)

Our results suggest that the four dietary inflammatory scores were associated with some biomarkers of inflammation and could be used to assess the inflammatory potential of diet in European adults but are not sufficient to capture the inflammatory status of an individual. These findings can help to better understand the inflammatory potential of diet, but they need to be replicated in studies with repeated dietary measurements.
A method of human-robot collaboration for grinding of workpieces (2015)

This paper presents a strategy of human-robot collaboration in grinding system. A collision-avoidance region, which ensures an operator should not be collision with a robot arm, is firstly detected by tracking the operator motion. Then, a path planning method, which uses control points of NURBS (Non-Uniform Rational B-Splines) to modify the path of the robot, is presented. Hence, whenever a possible collision with the robot and operator is predicted, the robot trajectory could be changed accordingly. Finally, a human-robot collaboration grinding system is built to enable a robot to perform safe grinding operations with the aid of humans.
Mean heart dose-based normal tissue complication probability model for pericardial effusion: a study in oesophageal cancer patients (2021)

We investigated the normal tissue complication probability (NTCP) of the incidence of pericardial effusion (PCE) based on the mean heart dose (MHD) in patients with oesophageal cancer treated with definitive chemoradiotherapy. The incidences of PCE in any grade (A-PCE) and symptomatic PCE (S-PCE) were evaluated separately. To identify predictors for PCE, several clinical and dose-volume parameters were analysed using a receiver operating characteristic (ROC) curve and multivariate regression analysis. To validate its clinical applicability, the generated NTCP model was compared to the Lyman-Kutcher-Burman (LKB) model. Among 229 eligible patients, A-PCE and S-PCE were observed in 100 (43.7%) and 18 (7.9%) patients, respectively. MHD showed a preferable area under the curve (AUC) value for S-PCE (AUC = 0.821) and A-PCE (AUC = 0.734). MHD was the only significant predictor for A-PCE; MHD and hypertension were selected as significant factors for S-PCE. The estimated NTCP, using the MHD-based model, showed excellent correspondence to the LKB model in A-PCE and S-PCE. The NTCP curve of A-PCE was gentler than that of S-PCE and had no threshold. The MHD-based NTCP model was simple but comparable to the LKB model for both A-PCE and S-PCE. Therefore, the estimated NTCP may provide clinically useful parameters for predicting PCE.
Machine learning-enabled real-time detection of cloud and aerosol layers using airborne lidar (2023)

Lidar profiling of the atmosphere provides information on existence of cloud and aerosol layers and the height and structure of those layers. Knowledge of feature boundaries is a key input to assimilation models. Moreover, identifying feature boundaries with minimal latency is essential to impact operational assimilation and real-time decision making. Using advanced convolution neural network algorithms, we demonstrate real-time determination of atmospheric feature boundaries using an airborne backscatter lidar. Results are shown to agree well with traditional processing methods and are produced with higher horizontal resolution than the traditional method. Demonstrated using airborne lidar, the algorithms and process are extendable to real-time generation of data products from a future spaceborne sensor.
Real-Time Dense Mapping for Self-driving Vehicles using Fisheye Cameras (2018)

We present a real-time dense geometric mapping algorithm for large-scale environments. Unlike existing methods which use pinhole cameras, our implementation is based on fisheye cameras which have larger field of view and benefit some other tasks including Visual-Inertial Odometry, localization and object detection around vehicles. Our algorithm runs on in-vehicle PCs at 15 Hz approximately, enabling vision-only 3D scene perception for self-driving vehicles. For each synchronized set of images captured by multiple cameras, we first compute a depth map for a reference camera using plane-sweeping stereo. To maintain both accuracy and efficiency, while accounting for the fact that fisheye images have a rather low resolution, we recover the depths using multiple image resolutions. We adopt the fast object detection framework YOLOv3 to remove potentially dynamic objects. At the end of the pipeline, we fuse the fisheye depth images into the truncated signed distance function (TSDF) volume to obtain a 3D map. We evaluate our method on large-scale urban datasets, and results show that our method works well even in complex environments.
UWB Baby Monitor (2010)

A successful case for UWB technology application to Vital Signs Monitoring Systems created by authors is presented in this paper. Baby Monitor for remote contactless monitoring of respiratory and heart rate is designed both for consumer and medical infant monitoring applications. Unlike conventional sound- and video-based baby monitors, which do not provide any useful information at infant sleep time (no sounds or static picture) the devices allow permanent parental control and effectively prevent Sudden Infant Death Syndrome (SIDS) from occurring. SIDS is reported to be leading death cause of healthy infants after one month age.
ChemInform Abstract: Electrochemical Oxidation of Pyrrole Derivatives in Alcoholic Medium. (1989)

Abstract Whereas the electrochemical methoxylation of unsubstituted pyrrole affords only a polymer, the derivatives (II), (V) and (VIII) give the products shown in the scheme.
A gene for nonspecific mental retardation is localized to Xp22.2-p21.2 in a Belgian family (1994)

The selection of an instrument partially depends on the goal of the study. In many situations however, the PDQ-39 will probably be the most appropriate HRQoL instrument. The PDQL may be considered as an alternative, whereas the PLQ may be considered in studies involving German speaking patients with Parkinson's disease. Use of the PIMS should be considered only as a means of identifying areas of potential problems.
Sandwich Construction in the Elastic Range (1952)

A brief survey is made of a selected group of problems concerned with the elastic behavior of sandwich construction. These include the wrinkling of the facings under compressive load and the effect of shear deformation in the core on the deflection of uniformly loaded panels and on the buckling loads of panels subjected to edgewise compression or shear. In most of the investigations made at the Forest Products Laboratory in cooperation with the Air Force-Navy-Civil Subcommittee on Aircraft Design Criteria, the materials of the facings and core have been taken to be orthotropic. In this paper, in order to show the characteristic features of the behavior of sandwich construction in as simple form as possible, the formulas and curves are presented for constructions with isotropic facings and cores. These results are obtained directly from those for orthotropic materials. Reference is made to reports containing the corresponding more general results.
Hierarchical clustering (2008)

Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced undergraduates and graduate students in computer science. Based on feedback from extensive classroom experience, the book has been carefully structured in order to make teaching more natural and effective. Slides and additional exercises (with solutions for lecturers) are also available through the book's supporting website to help course instructors prepare their lectures.