gebhart/patrepeval huggingface dataset:
Serotonergic reinforcement of intestinal barrier function is impaired in irritable bowel syndrome (2014)

Oral 5-HTP induced alterations in mucosal 5-HT metabolism. In healthy controls, a reinforcement of the intestinal barrier was seen whereas such reaction was absent in IBS patients. This could indicate the presence of a serotonin-mediated mechanism aimed to reinforce intestinal barrier function, which seems to dysfunction in IBS patients.
Impact of flow control on quality of service driven packet scheduling disciplines (2003)

In this paper we investigate the interaction between window based flow control and a recently proposed packet scheduling discipline designed for real-time services. The scheduling discipline, called the dual queue discipline, has been shown to provide greater flexibility than other scheduling disciplines such as fair queueing. However, its performance on non real-time services has not been previously investigated. We show that the dual queue's performance for non real-time services is again better than that of alternative approaches, which indicates that it will perform well in an environment of mixed real-time and non real-time traffic, such as the current Internet.
SSD-6D: Making RGB-Based 3D Detection and 6D Pose Estimation Great Again (2017)

We present a novel method for detecting 3D model instances and estimating their 6D poses from RGB data in a single shot. To this end, we extend the popular SSD paradigm to cover the full 6D pose space and train on synthetic model data only. Our approach competes or surpasses current state-of-the-art methods that leverage RGBD data on multiple challenging datasets. Furthermore, our method produces these results at around 10Hz, which is many times faster than the related methods. For the sake of reproducibility, we make our trained networks and detection code publicly available.
Discovery of an Orally Active and Liver-Targeted Prodrug of 5-Fluoro-2′-Deoxyuridine for the Treatment of Hepatocellular Carcinoma (2016)

We report a series of novel O-(substituted benzyl) phosphoramidate prodrugs of 5-fluoro-2'-deoxyuridine for the treatment of hepatocellular carcinoma. Through structure optimization, the o-methylbenzyl analog (1t) was identified as an orally bioavailable and liver-targeted lead compound. This lead prodrug is well-tolerated at a dose up to 3 g/kg in Kuming mice via oral administration. An efficacy study demonstrated that it possesses good inhibitory effect (61.67% and 72.50%, respectively) on tumor growth in a mouse xenograft model. A metabolism study in Sprague-Dawley rats suggested that 1t can release the desired 5'-monophosphate in the liver with high liver-targeting index.
Th2 Response of Human Peripheral Monocytes Involves Isoform-Specific Induction of Monoamine Oxidase-A (2004)

Monocyte/macrophage function is critically regulated by specific cytokines and growth factors that they are exposed to at inflammatory sites. IL-4 and IL-13 are multifunctional cytokines generated mainly by Th2 lymphocytes that have important biological activities in allergy and inflammation. The Th2 response of human peripheral monocytes is characterized by complex alterations in the gene expression pattern, which involves dominant expression of CD23 cell surface Ag and lipid-peroxidizing 15-lipoxygenase-1 (15-LOX1). In this study, we report that the classical Th2 cytokines IL-4 and IL-13 strongly up-regulate expression of monoamine oxidase A (MAO-A) with no induction of the closely related isozyme, MAO-B. Real-time PCR indicated a >2000-fold up-regulation of the MAO-A transcripts, and immunohistochemistry revealed coexpression of the enzyme with 15-LOX1 in a major subpopulation of monocytes. MAO-A was also induced in lung carcinoma A549 cells by IL-4 in parallel with 15-LOX1. In promyelomonocytic U937 cells, which neither express 15-LOX1 nor MAO-A in response to IL-4 stimulation, expression of MAO-A was up-regulated following transfection with 15-LOX1. This is the first report indicating expression of MAO-A in human monocytes. Its isoform-specific up-regulation in response to Th2 cytokines suggests involvement of the enzyme in modulation of innate and/or acquired immune system.
Nondestructive measurement of the roughness of the inner surface of hollow core-photonic bandgap fibers (2016)

We present optical and atomic force microscopy measurements of the roughness of the core wall surface within a hollow core photonic bandgap fiber (HC-PBGF) over the [3×10<sup>-2</sup> μm<sup>-1</sup>-30 μm<sup>-1</sup>] spatial frequency range. A recently developed immersion optical profilometry technique with picometer-scale sensitivity was used to measure the roughness of air-glass surfaces inside the fiber at unprecedentedly low spatial frequencies, which are known to have the highest impact on HC-PBGF scattering loss and, thus, determine their loss limit. Optical access to the inner surface of the core was obtained by the selective filling of the cladding holes with index matching liquid using techniques borrowed from micro-fluidics. Both measurement techniques reveal ultralow roughness levels exhibiting a 1/f spectral power density dependency characteristic of frozen surface capillary waves over a broad spatial frequency range. However, a deviation from this behavior at low spatial frequencies was observed for the first time, to the best of our knowledge.
RefSeq database growth influences the accuracy of <i>k</i> -mer-based species identification (2018)

ABSTRACT Accurate species-level taxonomic classification and profiling of complex microbial communities remains a challenge due to homologous regions shared among closely related species and a sparse representation of non-human associated microbes in the database. Although the database undoubtedly has a strong influence on the sensitivity of taxonomic classifiers and profilers, to date, no study has carefully explored this topic on historical RefSeq releases and explored its impact on accuracy. In this study, we examined the influence of the database, over time, on k -mer based sequence classification and profiling. We present three major findings: ( i ) database growth over time resulted in more classified reads, but fewer species-level classifications and more species-level misclassifications; ( ii ) Bayesian re-estimation of abundance helped to recover species-level classifications when the exact target strain was present; and ( iii ) Bayesian reestimation struggled when the database lacked the target strain, resulting in a notable decrease in accuracy. In summary, our findings suggest that the growth of RefSeq over time has strongly influenced the accuracy of k -mer based classification and profiling methods, resulting in different classification results depending on the particular database used. These results suggest a need for new algorithms specially adapted for large genome collections and better measures of classification uncertainty.
A new 4c–2e bond in B<sub>6</sub>H<sub>7</sub><sup>−</sup> (2007)

For N(C(4)H(9))(4)B(6)H(7) a proton is shown to be localised above one of the faces of the distorted octahedron, and rhomboid rings are formed as shown by topological analysis of charge densities.
A Blind Source Separation Framework for Monitoring Heart Beat Rate Using Nanofiber-Based Strain Sensors (2015)

A recently developed novel nanofiber-based strain sensor is introduced as a potential alternative to the conventional measurement tools for heart beat rate monitoring. Since the measured signals in real life are often contaminated by certain artifacts, in this paper, to overcome limitations of currently available empirical mode decomposing (EMD) and blind source separation-based methods and recover the buried heart beat signal accurately, we propose a novel blind source separation framework by combining noise-assisted multivariate EMD (NAMEMD) and multiset canonical correlation analysis (MCCA). The proposed method takes advantage of the multivariate data-adaptive nature of the NAMEMD and MCCA, which contributes to accurate extraction of the desired signal. The absolute correlation coefficients (ACCs) between the extracted signal and the original source signal are adopted to evaluate the performance of the proposed method in the simulation study. The average of the ACC yielded by the proposed method is 0.902, which is significantly higher than that by the state-of-the-art approaches. We also examine the proposed method on the nano-sensor data collected when the subject performs 11 tasks. It is shown that the proposed method can achieve better performance, especially for preserving the shape of the heart beat signal.
Enabling Semantic Queries Across Federated Bioinformatics Databases (2019)

Motivation Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. Results We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: 1) Bgee, a gene expression relational database; 2) OMA, a Hierarchical Data Format 5 (HDF5) orthology data store, and 3) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialised RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface. Project URL http://biosoda.expasy.org , https://github.com/biosoda/bioquery
Community annotation and remix (2006)

We present a platform for community-supported media annotation and remix, including a pilot deployment with a major film festival. The platform was well received by users as fun and easy to use. An analysis of the resulting data yielded insights into user behavior. Completed remixes exhibited a range of genres, with over a third showing thematic unity and a quarter showing some attempt at narrative. Remixes were often complex, using many short segments taken from various source media. Reuse of spoken and written language in source media, and the use of written language in user-defined overlay text segments proved to be essential for most users. We describe how community remix statistics can be leveraged for media summarization, browsing, and editing support. Further, the platform as a whole provides a solid base for a range of ongoing research into community annotation and remix including analysis of remix syntax, identification of reusable segments, media and segment tagging, structured annotation of media, collaborative media production, and hybrid content-based and community-in-the-loop approaches to understanding media semantics.
The observation of spectral variation indicative of porphyrin biomarkers in reflectance spectra of source rock - The application of remote sensing technology to petroleum geochemistry (1990)

The spectral signature of porphyrin compounds, considered to be biomarkers of depositional environment and thermal maturity, have been identified in reflectance spectra of oil shales. The key bands identified, in order of intensity, are the Soret (0.40 microns), alpha (0.57 microns), and beta (0.53 microns) bands. The observed bands represent the composite spectral signature of all porphyrin compounds present in the sample and, therefore, change position and intensity in accordance with changes in porphyrin chemistry.
Distribution-Aware Coordinate Representation for Human Pose Estimation (2019)

While being the de facto standard coordinate representation in human pose estimation, heatmap is never systematically investigated in the literature, to our best knowledge. This work fills this gap by studying the coordinate representation with a particular focus on the heatmap. Interestingly, we found that the process of decoding the predicted heatmaps into the final joint coordinates in the original image space is surprisingly significant for human pose estimation performance, which nevertheless was not recognised before. In light of the discovered importance, we further probe the design limitations of the standard coordinate decoding method widely used by existing methods, and propose a more principled distribution-aware decoding method. Meanwhile, we improve the standard coordinate encoding process (i.e. transforming ground-truth coordinates to heatmaps) by generating accurate heatmap distributions for unbiased model training. Taking the two together, we formulate a novel Distribution-Aware coordinate Representation of Keypoint (DARK) method. Serving as a model-agnostic plug-in, DARK significantly improves the performance of a variety of state-of-the-art human pose estimation models. Extensive experiments show that DARK yields the best results on two common benchmarks, MPII and COCO, consistently validating the usefulness and effectiveness of our novel coordinate representation idea.
Blockchain Oriented Software Testing - Challenges and Approaches (2018)

The distributed ledger technology presents a very innovative and secure way of managing transactions online. Hailed as one of the greatest inventions after the Internet, blockchain is set to pioneer changes in the way businesses are conducted today through its promise of secure, tamper-proof, peer-to-peer decentralized networks with distributed consensus. These fundamental features built into the very fabric bring in a host of additional dimensions and present greater challenges in their testing. Not only are the technological changes significant, but also significant are changes from a business standpoint. A new wave of blockchain oriented software development is emerging at an unprecedented rate. This places an additional responsibility on the Quality Assurance teams to deliver first-time quality while minimizing the impact of testing on the teams delivery. This paper highlights the challenges currently faced in testing such applications. It also acknowledges the need to devise specialized tools and techniques for blockchain oriented software testing in order to ensure high standards of quality.
Identification of a Novel Receptor Tyrosine Kinase Expressed in Acute Myeloid Leukemic Blasts (1995)

Using the polymerase chain reaction with degenerate oligonucleotides derived from conserved motifs within the catalytic kinase domain of protein tyrosine kinases, and RNA extracted from embryonic stem cells, sequences that encode a segment of the kinase domain of several potentially novel receptor tyrosine kinases (RTKs) have been identified. One of these was selected for further study because in Northern analysis it hybridized to RNA from multipotential hematopoietic cell lines, but not from lines representative of lineage-committed cells. A cDNA for this receptor, designated developmental tyrosine kinase (DTK), was isolated and encodes a protein with structural similarities to AXL. Together these receptors form a new class of RTK. DTK is expressed in a number of human leukemic cell lines, and in the blasts of 6 of 11 patients with acute myeloid leukemia (AML) analyzed. The structure of DTK suggests that it may function as a cell adhesion molecule, and mediate cell-to-cell or cell-matrix interactions between hematopoietic cells and their respective microenvironments.
Exploring context information for inter-camera multiple target tracking (2014)

In this paper, we present a new solution to inter-camera multiple target tracking with non-overlapping fields of view. The identities of people are maintained when they are moving from one camera to another. Instead of matching snapshots of people across cameras, we mainly explore what kind of context information from videos can be used for inter-camera tracking. We introduce two kinds of context information, spatio-temporal context and relative appearance context in this paper. The spatio-temporal context indicates a way of collecting samples for discriminative appearance learning where target-specific appearance models are learned to distinguish different people from each other. The relative appearance context models inter-object appearance similarities for people walking in proximity. The relative appearance model helps disambiguate individual appearance matching across cameras. We show improved performance with context information for inter-camera tracking. Our method achieves promising results in two crowded scenes compared with state-of-art methods.
Efficacy of SHP2 phosphatase inhibition in cancers with nucleotide-cycling oncogenic RAS, RAS-GTP dependent oncogenic BRAF and NF1 loss (2017)

Abstract Oncogenic alterations in the RAS-RAF-MEK-ERK pathway, including mutant forms of KRAS, BRAF, and loss of the tumor suppressor and RAS GTPase-activating protein (GAP) NF1, drive the growth of a wide spectrum of human cancers. While BRAF and MEK inhibitors are effective in many patients with oncogenic BRAF V600E, there are no effective targeted therapies for individuals with cancers driven by other pathway alterations, including oncogenic KRAS, non-V600E BRAF, and NF1 loss. Here, we show that targeting the PTPN11/SHP2 phosphatase with a novel small molecule allosteric inhibitor is effective against cancers bearing nucleotide-cycling oncogenic RAS (e.g. KRAS G12C), RAS-GTP dependent oncogenic BRAF (e.g. class 3 BRAF mutants), or NF1 loss in multiple preclinical models in vitro and in vivo. SHP2 inhibition suppressed the levels of RAS-GTP and phosphorylated ERK in these models and induced growth inhibition. Expression of a constitutively active mutant of the RAS guanine nucleotide exchange factor (GEF) SOS1 rescued cells from the effects of SHP2 inhibition, suggesting that SHP2 blockade decreases oncogenic RAS-RAF-MEK-ERK signaling by disrupting SOS1-mediated RAS-GTP loading. Our findings illuminate a critical function for SHP2 in promoting oncogenic RAS activation and downstream signaling in cancers with nucleotide-cycling oncogenic RAS, RAS-GTP dependent oncogenic BRAF, and NF1 loss. SHP2 inhibition thus represents a rational, biomarker-driven therapeutic strategy to be tested in patients with cancers of diverse origins bearing these oncogenic drivers and for which current treatments are largely ineffective.
Chemically synthesized zinc finger molecules as nano-addressable probes for double-stranded DNAs (2005)

Our experiments describe an alternative method of dsDNA recognition using zinc finger (ZF) molecules which bind DNA specifically and with high affinity. Our aim was to develop zinc finger probes which are able to bind to dsDNA molecules at predetermined sites. In our basic approach we used pairs of complementary oligonucleotides to form dsDNAs, containing one of the three SP1-transcription factor motifs as a zinc finger recognition site. Two zinc finger probes of the SP1 motif were chemically synthesized and modified with a Dy-633 fluorophore. The SP1 peptides were folded into functional zinc fingers using zinc chloride. The addressable dsDNAs were immobilized on optical fibres, and the kinetics and binding rates of the artificial zinc finger probes were measured by a fluorescence detecting device (photomultiplying tube). The two zinc fingers and their corresponding DNA recognition sites served as specific probes and controls for the matching site and vice versa. Our experiments showed that a variety of dsDNA-binding probes may be created by modification of the amino acid sequence of natural zinc finger proteins. Our findings offer an alternative approach of addressing dsDNA molecules, for example for use in a nanoarray device.
Averaging scan patterns and what they can tell us (2006)

While fixation data and saccadic indices have been employed as individual measures, less frequent analysis has been attempted on the sequence or pattern data that these two indices together create. The patterns of fixations and saccades are rich and complex, and hence, they are typically studied as individual paths or parts of paths that are isolated. Analysis is usually a visual comparison, although more recently there have been studies that have compared scan patterns statistically [Josephson and Holmes 2002; Pan et al. 2002; Yarbus 1967]. In the current work we explore a method for deriving an "average" scan pattern aggregated from many users viewing the same visual stimulus (web site).
Enzymatic Removal of Carboxyl Protecting Groups. III. Fast Removal of Allyl and Chloroethyl Esters by <i>Bacillus subtilis</i> Esterase (BS2) (2007)

An esterase from Bacillus subtilis (BS2) allows the fast and selective removal of allyl, 2-chloroethyl, and 2,2,2-chloroethyl esters under mild conditions in high yields. In addition, BS2 easily hydrolyzes phenacyl esters, while the hydrolysis of sterically hindered diphenylmethyl esters is slow, requiring longer reaction time and higher enzyme/substrate ratio.