gebhart/patrepeval huggingface dataset:
Memory-efficient inference in dynamic graphical models using multiple cores (2012)

We introduce the archipelagos algorithm for memory-efficient multi-core inference in dynamic graphical models. By making use of several processors running in parallel, the archipelagos algorithm uses exponentially less memory compared to basic forward-backward message passing algorithms (O(log T ) compared to O(T ) on sequences of length T ) and, under oftensatisfied assumptions on the relative speed of passing forward and backward messages, runs no slower. We also describe a simple variant of the algorithm that achieves a factor of two speedup over forward-backward on a single core. Experiments with our implementation of archipelagos for the computation of posterior marginal probabilities in an HMM validate the space/time complexity analysis: using four cores, the required memory on our test problem was reduced from 8 GB to 319 KB (a factor of 25000) relative to forwardbackward, but completed in essentially the same time. The archipelagos algorithm applies to any dynamic graphical model, including dynamic Bayesian networks, conditional random fields, and hidden conditional random fields.
Figure S6 from A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors (2023)

&lt;p&gt;Figure S6. Differential abundance analysis of antibiotic resistance genes and virulence factors between R and NR for WGS datasets.&lt;/p&gt;
Cloning of the netropsin resistance genes fromStreptomyces flavopersicus NRRL 2820 (2005)

Streptomyces flavopersicus NRRL 2820 (synonym: Streptomyces netropsis DSM40093) is resistant to the N-methylpyrrole-containing oligopeptide antibiotic netropsin. A 9.38 kb DNA-fragment was isolated from a genomic library of Streptomyces flavopersicus using an Escherichia coli-Streptomyces lividans shuttle vector which enables S. lividans to grow on netropsin-containing agar plates. By subcloning, the resistance was conferred to a 5.9 kb Eco RV fragment. DNA sequence analysis of this Eco RV fragment revealed two open reading frames (netP1 , 1556 bp and netP2 , 1773 bp). The deduced proteins share significant similarity to each other (27% identity) and to the large family to ABC-type multidrug resistance proteins. In each protein a conserved transmembrane and ATP binding domain was identified. Deletion analysis showed that both proteins are necessary for netropsin resistance indicating that the proteins form a heterodimeric ABC-transporter exporting netropsin.
Isolation and characterisation of mouse intestinal mesoangioblasts (2018)

This proof-of-principle study lays the foundation for further characterization of MABs as a possible cell source for intestinal smooth muscle regeneration and TE.
Grouping video shots into scenes based on 1D mosaic descriptors (2005)

This paper describes an original approach for structuring video documents into scenes by grouping video shots. The method is based on the construction of 1D mosaics. 1D mosaics are built based on X-ray projections of color video frames representing integration along vertical and horizontal axes. The mosaicing is realized by motion compensation in a 1D domain. Grouping of shots in a scene is done by local and global matching of mosaics, based on piecewise linear approximation and hierarchical clustering. The results obtained on feature documentaries are promising.
Research on Color Adaptation of Automobile Head-up Display Interface (2021)

The purpose of this paper is to study the color display problem of the car head-up display interface. The color recognition effect of the existing car head-up display interface differs greatly in different environments, and it cannot guarantee that the driver will always make a clear recognition. Based on the color coding theory and color adaptation theory of the digital interface, this paper redesigned the color coding method of the car's head-up display interface to ensure that its colors can adapt to different background colors and ensure the efficiency of reading. Through the overall simplification algorithm and the selective simplification algorithm, the main colors of the background environment are extracted, and the corresponding head-up display interface colors are matched according to the color coding theory to establish experimental materials. Then, using reaction time as a performance indicator, the participants' subjective feelings were tested and the driver's ability to recognize interface information in different driving environments was evaluated. The experimental conclusions show that the cognitive effect of the HUD interface optimized by the color adaptive theory is better than the existing interface, and it has made a positive contribution to improving the design of the automobile head-up display interface interface.
Effect of gas heating on the spatial structure of a traveling wave sustained Ar discharge (2001)

In this work we report a theoretical and experimental study of the influence of gas heating on the spatial structure of a microwave Ar discharge sustained by a traveling surface wave. The theoretical analysis is based on a discharge model which couples in a self-consistent way electron and heavy particle kinetics, discharge electrodynamics, and gas thermal balance. The set of coupled equations used includes the electron Boltzmann equation, the rate balance equations for the most important excited species and charged particles, the gas thermal balance equation, and the equations describing wave propagation and power dissipation. The principal collisional and radiative processes which determine the populations in the Ar(3p54s) and Ar(3p54p) levels are accounted for. The field strength necessary for steady-state discharge operation is obtained from the balance between total rates of ionization (including direct and step-wise ionization and energy pooling reactions) and of electron loss due to the diffusion to the wall and bulk recombination. The gas thermal balance equation is solved using the experimentally obtained wall temperature as a boundary value. The model determines the axial discharge structure, i.e., the axial variation of the main discharge quantities. An experimental validation of the model predictions is achieved using probe techniques, emission spectroscopy, and radiophysics methods. In particular, spatially resolved measurements of the electron energy distribution function, gas temperature, wave electric field components, and wave attenuation have been carried out. As a result of the nonuniform wave power absorption along the wave path the gas temperature varies along the column. This variation induces axial changes in the neutral density and the reduced electric field which strongly affects the particle kinetics and the discharge electrodynamics, as demonstrated here.
Progress of small molecular inhibitors in the development of anti-influenza virus agents (2017)

The influenza pandemic is a major threat to human health, and highly aggressive strains such as H1N1, H5N1 and H7N9 have emphasized the need for therapeutic strategies to combat these pathogens. Influenza anti-viral agents, especially active small molecular inhibitors play important roles in controlling pandemics while vaccines are developed. Currently, only a few drugs, which function as influenza neuraminidase (NA) inhibitors and M2 ion channel protein inhibitors, are approved in clinical. However, the acquired resistance against current anti-influenza drugs and the emerging mutations of influenza virus itself remain the major challenging unmet medical needs for influenza treatment. It is highly desirable to identify novel anti-influenza agents. This paper reviews the progress of small molecular inhibitors act as antiviral agents, which include hemagglutinin (HA) inhibitors, RNA-dependent RNA polymerase (RdRp) inhibitors, NA inhibitors and M2 ion channel protein inhibitors etc. Moreover, we also summarize new, recently reported potential targets and discuss strategies for the development of new anti-influenza virus drugs.
Automatic control process analysis of gas pressure in electrostatic discharge measurement system (2015)

Based on requirement of new invented ESD measurement system, the automatic control system of pressure was designed to automatically control the pressure of experimental box. The proposed system uses STM32 MCU as its core. MCU, after received feedback signal of sensor, controls on-off state of solenoid valve with applying PID algorithm to output PWM impulse. Pressure of experimental box can set desire value and keep it stable. The design provides compensation to remove deficiency in original pressure control process, runs faster, more accurate and convenient operation than that before. The design provides accurate pressure environment in the experimental box of the new ESD measurement system.
Visualising the immune repertoire (2007)

Antibodies play a central role in the adaptive immunedefense of all vertebrates. Thereby, the specific recognitionof antigen structures by antibody molecules determinesthe success of the immune response. Therefore, the reper-toire of antigen binding sites within the immune systemof an individuum, but also, within a population, has beena mean focus of immunological research within the last 3decades. The first tool to analyse the DNA sequence of theantigen binding site of an antibody was DNAPLOT http://www.dnaplot.de. Associated with the Vbase database[1],the DNAPLOT search page was the first of its kind whichallowed the analysis of the modular composition of ofthese binding sites, the immunoglobulin gene rearrange-ments. The focus of this site was to identify and mark thegenetics elements that are used for these rearrangements.In the meantime, several similar tools are available,including the current DNAPLOT version at the VBASE2database [2]http://www.vbase2.org.
ChemInform Abstract: GOLD CARBENE COMPLEXES, PREPARATION, OXIDATION, AND LIGAND DISPLACEMENT (1974)

Abstract Die Isocyanide (I) reagieren mit Natriumtetrachloraurat (II) in Gegenwart von NH 4 PF 5 zu den Gold‐Komplexen (III).
Strain Sensing Using Multiwalled Carbon Nanotube Film Subjected to Temperature Variation (2010)

In this study, the real time strain response of the Multiwalled Carbon Nanotube (MWCNT) film is studied at macroscale experimentally. The response of the MWCNT film to temperature changes is also presented in the study. The MWCNT film is attached to a brass specimen using vacuum bonding, and the brass specimen is subjected to tensile load and voltage output from MWCNT film is obtained using four-point probe and a sensitive voltage measurement device. Experimental results demonstrate a linear relationship between change in voltage across the film and change in strain in the brass specimen when subjected to tensile load. The MWCNT film also exhibited excellent reversible electromechanical characteristics when the specimen was unloaded. The response of the MWCNT film to temperature is also studied and it is observed that the resistance of the MWCNT film decreased upon heating. The MWCNT film exhibited a stable and linear voltage response to changes in temperature. The experimental results demonstrate the effectiveness of Multiwalled carbon nanotubes in strain sensing as well as the effect of temperature on the MWCNT film.
Preparation of Biologically Active Fluorescent Heparin Composed of Fluorescein-Labeled Species and Its Behavior to Antithrombin III1 (1981)

A hog-mucosal heparin purified gel-chromatographically (total sulfate, 2.20; N-sulfate, 0.82; N-acetyl, 0.15 (mol/mol HexN); activity, 184 USP units/mg) was partially N-desulfated to give a product (total sulfate, 2.12; N-sulfate, 0.71 (mol/mol HexN); activity, 159 USP units/mg). The free amino groups in the product was extensively labeled with fluoresceinylthiocarbamoyl (FTC) groups, and the labeled product was chromatographed on Octyl-Sepharose CL-4B to give a heparin preparation of fluorescein-labeled species (total sulfate, 2.04; N-sulfate, 0.72; degree of substitution, 0.059 (mol/mol HexN); activity, 155 USP units/mg). The fluorescent heparin thus obtained was indicated from its analytical data to have one FTC group pr heparin molecule irrespective of the molecular weight. The fluorescent heparin was separated into the low-affinity (56.6%) and high-affinity (43.4%) fractions for antithrombin III, and the anticoagulant activities of the two types of fluorescent heparin were compared with those of the starting heparin and the partially N-desulfated heparin, suggesting that FTC-substitution in heparin molecules had no effect on the known biological interaction with mobilized or immobilized antithrombin III.
Secondary metabolites by chemical screening. 7. I. Elaiophylin derivatives and their biological activities. (1990)

The synthesis and the biological activity of 34 acyl derivatives of elaiophylin (1) and 6 deglycosidation products were described. Especially the unsymmetric deglycosidation products 33, 38 and 40 and dimethyloctahydroelaiophylin (21) exhibited an activity against nematodes.
Monitoring the itinerary of lysosomal cholesterol in Niemann-Pick Type C1-deficient cells after cyclodextrin treatment (2020)

Niemann-Pick disease type C (NPC) disease is a lipid-storage disorder that is caused by mutations in the genes encoding NPC proteins and results in lysosomal cholesterol accumulation. 2-Hydroxypropyl-β-cyclodextrin (CD) has been shown to reduce lysosomal cholesterol levels and enhance sterol homeostatic responses, but CD's mechanism of action remains unknown. Recent work provides evidence that CD stimulates lysosomal exocytosis, raising the possibility that lysosomal cholesterol is released in exosomes. However, therapeutic concentrations of CD do not alter total cellular cholesterol, and cholesterol homeostatic responses at the ER are most consistent with increased ER membrane cholesterol. To address these disparate findings, here we used stable isotope labeling to track the movement of lipoprotein cholesterol cargo in response to CD in NPC1-deficient U2OS cells. Although released cholesterol was detectable, it was not associated with extracellular vesicles. Rather, we demonstrate that lysosomal cholesterol trafficks to the plasma membrane (PM), where it exchanges with lipoprotein-bound cholesterol in a CD-dependent manner. We found that in the absence of suitable extracellular cholesterol acceptors, cholesterol exchange is abrogated, cholesterol accumulates in the PM, and reesterification at the ER is increased. These results support a model in which CD promotes intracellular redistribution of lysosomal cholesterol, but not cholesterol exocytosis or efflux, during the restoration of cholesterol homeostatic responses.
Key Components of Collaborative Research in the Context of Environmental Health: A Scoping Review (2017)

In a collaborative research process, the participation of interdisciplinary researchers and multi-sectoral stakeholders supports the co-creation, translation, and exchange of new knowledge. Following a scoping review methodology, we explored the collaborative research processes in the specific context of environment and human health research. Initially, our literature search strategy identified 1,328 publications. After several phases of reviewing and applying screening criteria to titles, abstracts, and full text, 45 publications were selected for final review. Data were charted by different topics and then collated, summarized, and analyzed thematically. From the different experiences and research approaches analyzed, we identified comprehensive details of the key components, facilitators, challenges, and best practices that impact the collaborative research process. Specifically, we identified the following seven emerging themes: (a) allocating time and resources, (b) addressing disciplinary and sectoral issues, (c) building relationships, (d) ensuring representation, (e) embedding participation in the research, (f) supporting ongoing collaboration, and (g) developing knowledge translation and exchange.
Diversity Guided Evolutionary Mining of Hierarchical Process Models (2015)

Easy-to-understand and up-to-date models of business processes are important for enterprises, as they aim to describe how work is executed in reality and provide a starting point for process analysis and optimization. With an increasing amount of event data logged by information systems today, the automatic discovery of process models from process logs has become possible. Whereas most existing techniques focus on the discovery of well-formalized models (e.g. Petri nets) which are popular among researchers, business analysts prefer business domain-specific models (such as Business Process Model Notation, BPMN) which are not well formally specified. We present and evaluate an approach for discovering the latter type of process models by formally specifying a hierarchical view on business process models and applying an evolution strategy on it. The evolution strategy efficiently finds process models which best represent a given event log by using fast methods for process model conformance checking, and is partly guided by the diversity of the process model population. The approach contributes to the field of evolutionary algorithms by showing that they can be successfully applied in the real-world use case of process discovery, and contributes to the process discovery domain by providing a promising alternative to existing methods.
Inhibition of glycogen synthesis in Saccharomyces cerevisiae by the mating pheromone alpha-factor. (1991)

Treatment of the yeast Saccharomyces cerevisiae with the pheromone alpha-factor caused an inhibition of glycogen synthesis in MATa haploid cells but not in MAT alpha cells or MATa/MAT alpha diploid cells. The concentration of alpha-factor required for a half-maximal inhibition was comparable to that required for the induction of the FUS1 gene. Strains containing a disruption in ste2 or ste12 or temperature-sensitive mutations in ste4, ste7, or ste11 continued to divide and to accumulate glycogen in the presence of alpha-factor. In contrast, inhibition of glycogen occurred upon exposure to mating pheromone of far1 mutants which, under this condition, fail to arrest in G1 and continue to divide while simultaneously undergoing the transcriptional induction and morphological changes typical of mating cells. The inhibition of glycogen accumulation by alpha-factor persisted in a strain lacking glycogen phosphorylase (EC 2.4.1.1), which ruled out the participation of this enzyme in the pheromone response. Glycogen synthase (EC 2.4.1.11) from a cells treated with alpha-factor was found primarily in the glucose 6-phosphate-dependent (inactive) form whereas the total activity was unaltered. This indicates that the action of mating pheromone is mainly to inhibit the interconversion of the inactive glucose 6-phosphate-dependent form to the active glucose 6-phosphate-independent form of glycogen synthase without affecting the concentration of the enzyme.
Spiral inertial waves emitted from geophysical vortices (2016)

Abstract By numerically simulating an initially unstable geophysical vortex, we discover for the first time a special kind of inertial waves, which are emitted in a spiral manner from the vortices; we refer to these waves as spiral inertial waves (SIWs). SIWs appear at small Rossby numbers (0.01 ≤ Ro ≤ 1) according to our parameter sweep experiments; the amplitude, wavelength and frequency of SIWs are sensitive to Rossby numbers. We extend the Lighthill–Ford radiation into inertial waves, and propose an indicator for the emission of inertial waves; this indicator may be adopted into general circulation models to parameterize inertial waves. Additionally, in our tracer releasing experiments, SIWs organize tracers into spirals, and modify the tracer’s local rate of change by advecting tracers vertically. Further, the spirals of SIWs resembles some spiral features observed in the ocean and atmosphere, such as spiral ocean eddies and spiral hurricane rainbands; thus, SIWs may offer another mechanism to form spiral eddies and rainbands. Since no density anomaly is required to generate the spirals of SIWs, we infer that the density anomaly, hence the baroclinic or frontal instability, is unlikely to be the key factor in the formation of these spiral features.
Towards a usable stereoscopic augmented reality interface for the manipulation of virtual cursors (2003)

The combination of augmented reality (AR) systems and stereoscopic display devices has created a powerful tool with which to supplement our view. One application for such systems is for the augmented teleoperation of unmanned vehicles, deployed in remote or hazardous environments. Research in this area has highlighted the need for accurate 3D measurement techniques - such as through the use of virtual cursors. This paper describes our work in the development of an AR interface designed to assist the accurate selection of position in 3D space. We describe some preliminary experimental work using virtual cursors before discussing how we believe depth cues can be utilized to allow a user to make a more informed judgment of depth in unprepared environments. It is expected that the guidelines outlined in this report will be used as a benchmark for the development of further 3D ARA cursors.
Impact of APOE ε4 genotype on α4β2 nicotinic acetylcholine receptor availability in mild Alzheimer's dementia: a (-)-F-18-Flubatine PET study (2019)

Whether there is an influence of the APOE ε4 allele on α4β2 nicotinic acetylcholine receptor (α4β2-nAChR) availability in Alzheimer's dementia (AD) is under debate. To analyze the effect of APOE ε4 on α4β2-nAChR availability in mild AD in vivo, we investigated patients with mild AD (CDR = 1), positive for APOE ε4 (AD-APOE ε4+) and negative for APOE ε4 (AD-APOE ε4-) using the recently developed α4β2-nAChR-specific radioligand (-)-F-18-Flubatine and PET.
Guanidinium Chlorides with Triphenylene Moieties Displaying Columnar Mesophases (2008)

Novel guanidinium chlorides 6a−f which are tethered to a pentaalkyloxytriphenylene unit have been prepared by a five-step sequence from hexaalkyloxytriphenylenes 1a−f. The mesomorphic properties of 6a−f were studied by DSC, POM, and X-ray diffraction. Columnar rectangular mesophases were found for derivatives 6b−f with long alkyl chains. Detailed SAXS experiments revealed a change of the common Colr (C2/m) phase to Colr (P2m) phase with increasing chain length. Derivative 6a with pentyl side chain displayed only unidentified crystalline or plastic crystalline properties.
Evaluation of Polymer Degradation in Controlled Microbial Chemostats (1992)

We have developed protocols for the assessment of polymer degradation utilizing stable, well-controlled microbial chemostats (digesters) with easily measurable and quantifiable populations of microorganisms. This paper describes the use of three different chemostats [thermophilic (60°C) anaerobic, thermophilic (60°C) aerobic, and mesophilic (35°C) aerobic] to assess the degradation of a variety of commercially available polymer films.