gebhart/patrepeval huggingface dataset:
Reconstructing 3D Lung Shape from a Single 2D Image during the Deaeration Deformation Process using Model-based Data Augmentation (2019)

Three-dimensional (3D) shape reconstruction is particularly important for computer assisted medical systems, especially in the case of lung surgeries, where large deaeration deformation occurs. Recently, 3D reconstruction methods based on machine learning techniques have achieved considerable success in computer vision. However, it is difficult to apply these approaches to the medical field, because the collection of a massive amount of clinic data for training is impractical. To solve this problem, this paper proposes a novel 3D shape reconstruction method that adopts both data augmentation techniques and convolutional neural networks. In the proposed method, a deformable statistical model of the 3D lungs is designed to augment various training data. As the experimental results demonstrate, even with a small database, the proposed method can realize 3D shape reconstruction for lungs during a deaeration deformation process from only one captured 2D image. Moreover, the proposed data augmentation technique can also be used in other fields where the training data are insufficient.
Reactivity of organosilicon precursors in remote hydrogen microwave plasma chemical vapor deposition of silicon carbide and silicon carbonitride thin‐film coatings (2009)

Abstract A number of organosilicon precursors for silicon carbide and silicon carbonitride thin‐film coatings, such as silanes, carbosilanes, aminosilanes, and disilazane, respectively, were characterized in terms of their reactivity in a remote microwave plasma chemical vapor deposition process, which was induced using hydrogen as plasma generating gas. The process displayed high selectivity with respect to the activating species and the chemical bonds in the molecular structure of the precursors. In view of very short life times of excited hydrogen plasma species the activation step takes place with an exclusive contribution of ground‐state hydrogen atoms. The CH, CC, SiC, SiN, CN and NH bonds present in the molecules of the precursors are non‐reactive and only the SiH or SiSi bonds play a key role in the activation step. The reactivity of the precursors was characterized in a quantitative way by the yield of the film growth parameter. The yield parameter expressing the mass of film per unit mass of the precursor fed to the reactor was calculated from the slopes of linear plots of time dependencies of film mass and precursor mass, which were determined for each investigated precursor. The reactivity of the precursors was found to be strongly dependent on the number of the SiH units present in their molecules and those containing two SiH units appeared to be most reactive. Copyright © 2009 John Wiley & Sons, Ltd.
Differentiation between Human Coronaviruses NL63 and 229E Using a Novel Double-Antibody Sandwich Enzyme-Linked Immunosorbent Assay Based on Specific Monoclonal Antibodies (2010)

Human coronaviruses (HCoVs) are responsible for respiratory tract infections ranging from common colds to severe acute respiratory syndrome. HCoV-NL63 and HCoV-229E are two of the four HCoVs that circulate worldwide and are close phylogenetic relatives. HCoV infections can lead to hospitalization of children, elderly individuals, and immunocompromised patients. Globally, approximately 5% of all upper and lower respiratory tract infections in hospitalized children are caused by HCoV-229E and HCoV-NL63. The latter virus has recently been associated with the childhood disease croup. Thus, differentiation between the two viruses is relevant for epidemiology studies. The aim of this study was to develop a double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) as a potential tool for identification and differentiation between HCoV-NL63 and HCoV-229E. The nucleocapsid (N) proteins of HCoV-NL63 and HCoV-229E were expressed in an Escherichia coli system and used to immunize mice in order to obtain monoclonal antibodies (MAbs) specific for each virus. Three specific MAbs to HCoV-NL63, one MAb specific to HCoV-229E, and four MAbs that recognized both viruses were obtained. After their characterization, three MAbs were selected in order to develop a differential DAS-ELISA. The described assay could detect up to 3 ng/ml of N protein and 50 50% tissue culture infective doses/ml of virus stock. No cross-reactivity with other human coronaviruses or closely related animal coronaviruses was found. The newly developed DAS-ELISA was species specific, and therefore, it could be considered a potential tool for detection and differentiation of HCoV-NL63 and HCoV-229E infections.
Hydrolytic Properties and Substrate Specificity of the Foot-and-Mouth Disease Leader Protease (2009)

Foot-and-mouth disease virus, a global animal pathogen, possesses a single-stranded RNA genome that, on release into the infected cell, is immediately translated into a single polyprotein. This polyprotein product is cleaved during synthesis by proteinases contained within it into the mature viral proteins. The first cleavage is performed by the leader protease (Lb(pro)) between its own C-terminus and the N-terminus of VP4. Lb(pro) also specifically cleaves the two homologues of cellular eukaryotic initiation factor (eIF) 4G, preventing translation of capped mRNA. Viral protein synthesis is initiated internally and is thus unaffected. We used a panel of specifically designed FRET peptides to examine the effects of pH and ionic strength on Lb(pro) activity and investigate the size of the substrate binding site and substrate specificity. Compared to the class prototypes, papain and the cathepsins, Lb(pro) possesses several unusual characteristics, including a high sensitivity to salt and a very specific substrate binding site extending up to P(7). Indeed, almost all substitutions investigated were detrimental to Lb(pro) activity. Analysis of structural data showed that Lb(pro) binds residues P(1)-P(3) in an extended conformation, whereas residues P(4)-P(7) are bound in a short 3(10) helix. The specificity of Lb(pro) as revealed by the substituted peptides could be explained for all positions except P(5). Strikingly, Lb(pro) residues L178 and L143 contribute to the architecture of more than one substrate binding pocket. The diverse functions of these two Lb(pro) residues explain why Lb(pro) is one of the smallest, but simultaneously most specific, papain-like enzymes.
NIST Critically Selected Stability Constants of Metal Complexes Database (2004)

ed ligand possesses a structural formula for quick identification. Therefore the program is very easy to use. The data are critically selected, so that the values chosen are the most reliable. The Version 8.0 of the database is now a Windows application. It should be easier to use for most Users. Yet, an effort was made to maintain the efficient look and feel and color schemes of the original Versions 1.0 5.0, so the previous users would not be distracted by having to learn a new interface.
Two differing presentations of periocular dermatitis as a side effect of dupilumab for atopic dermatitis (2019)

Dupilumab is a monoclonal antibody used to treat atopic dermatitis. Worsening of atopic dermatitis and conjunctivitis following dupilumab use are reported adverse effects; however, there is little reported on the nature and mechanism of these complications. Here, we describe two patients with chronic atopic dermatitis who developed new or severely worsened periocular dermatitis, believed to be a side effect of dupilumab injections, and resolution after its discontinuation. We explore the possibility of dupilumab-induced suppression of Th2 mediated inflammation and upregulation of Th1 and IFNγ mediated inflammation as a possible mechanism.
EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom (2014)

Plant essential oils are complex mixtures of volatile organic compounds, which play indispensable roles in the environment, for the plant itself, as well as for humans. The potential biological information stored in essential oil composition data can provide an insight into the silent language of plants, and the roles of these chemical emissions in defense, communication and pollinator attraction. In order to decipher volatile profile patterns from a global perspective, we have developed the ESSential OIL DataBase (EssOilDB), a continually updated, freely available electronic database designed to provide knowledge resource for plant essential oils, that enables one to address a multitude of queries on volatile profiles of native, invasive, normal or stressed plants, across taxonomic clades, geographical locations and several other biotic and abiotic influences. To our knowledge, EssOilDB is the only database in the public domain providing an opportunity for context based scientific research on volatile patterns in plants. EssOilDB presently contains 123 041 essential oil records spanning a century of published reports on volatile profiles, with data from 92 plant taxonomic families, spread across diverse geographical locations all over the globe. We hope that this huge repository of VOCs will facilitate unraveling of the true significance of volatiles in plants, along with creating potential avenues for industrial applications of essential oils. We also illustrate the use of this database in terpene biology and show how EssOilDB can be used to complement data from computational genomics to gain insights into the diversity and variability of terpenoids in the plant kingdom. EssOilDB would serve as a valuable information resource, for students and researchers in plant biology, in the design and discovery of new odor profiles, as well as for entrepreneurs--the potential for generating consumer specific scents being one of the most attractive and interesting topics in the cosmetic industry. Database URL: http://nipgr.res.in/Essoildb/
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data (2008)

Protein function prediction is a central problem in bioinformatics, increasing in importance recently due to the rapid accumulation of biological data awaiting interpretation. Sequence data represents the bulk of this new stock and is the obvious target for consideration as input, as newly sequenced organisms often lack any other type of biological characterization. We have previously introduced PFP (Protein Function Prediction) as our sequence-based predictor of Gene Ontology (GO) functional terms. PFP interprets the results of a PSI-BLAST search by extracting and scoring individual functional attributes, searching a wide range of E-value sequence matches, and utilizing conventional data mining techniques to fill in missing information. We have shown it to be effective in predicting both specific and low-resolution functional attributes when sufficient data is unavailable. Here we describe (1) significant improvements to the PFP infrastructure, including the addition of prediction significance and confidence scores, (2) a thorough benchmark of performance and comparisons to other related prediction methods, and (3) applications of PFP predictions to genome-scale data. We applied PFP predictions to uncharacterized protein sequences from 15 organisms. Among these sequences, 60-90% could be annotated with a GO molecular function term at high confidence (>or=80%). We also applied our predictions to the protein-protein interaction network of the Malaria plasmodium (Plasmodium falciparum). High confidence GO biological process predictions (>or=90%) from PFP increased the number of fully enriched interactions in this dataset from 23% of interactions to 94%. Our benchmark comparison shows significant performance improvement of PFP relative to GOtcha, InterProScan, and PSI-BLAST predictions. This is consistent with the performance of PFP as the overall best predictor in both the AFP-SIG '05 and CASP7 function (FN) assessments. PFP is available as a web service at http://dragon.bio.purdue.edu/pfp/.
Structure and Evolution of Human Apolipoprotein Genes: Identification of Regulatory Elements of the Human Apolipoprotein E Gene (2007)

The structures of the major human apolipoprotein genes have been determined. The genes for apoE, apoC-I, apoC-II, apoC-III, apoA-I, apoA-II and apoA-IV have similar structures, consisting of four exons and three introns, which suggests that they evolved from a common ancestral gene. The third and fourth exons of the ancestral gene appear to have evolved from the duplication of a 66-nucleotide repeat unit that encodes a 22-residue alpha-helical peptide element of amphipathic character. The apoA-I, apoC-III and apoA-IV genes are linked closely within a 20-kilobase (kb) span of chromosome 11. The apoE and apoC-I genes, together with an apoC-I' pseudogene, are linked closely within a 25-kb span of chromosome 19. To characterize potential functional relationships among the apolipoprotein genes, initial studies have been done to identify the molecular elements involved in the regulation of the human apoE gene. Fragments of the 5'-flanking portion of this gene were inserted into appropriate plasmid vectors, which contained the bacterial chloramphenicol acetyl transferase gene, and were examined for promoter activity and potential enhancer activity after transfection into cultured mammalian cells. Deletion mapping of the promoter region has identified multiple functional elements, including an enhancer, two G-C boxes (Sp 1 transcription factor binding sites) and an upstream control element. In addition, there is an enhancer located in the first intron. Interactions among these various control elements are likely to determine the ways in which the expression of the apoE gene is regulated.
Glass transition effect in liquation silicate–borate–phosphate glasses (2019)

Glass transformation effect of liquation glasses from the SiO2–B2O3–P2O5–K2O–MgO–CaO system was studied by DSC, SEM–EDS and 31P, 29Si and 11B MAS NMR spectroscopy methods. The relation between the B2O3 content in the analysed glasses and phase separation phenomenon, structure and glass transition effects was discussed. It was shown that increasing content of B2O3 causes the formation of P–O–BIII, P–O–BIV and Si–O–BIII and Si–O–BIV bonds which results in the appearance of liquation in analysed glasses. Simultaneously, double glass transition effect was observed with gradual decrease of Tg and Ea values. The observed relations were explained using crystalochemical parameters (iG, L) of chemical bonds present in the structure of analysed glasses.
Transcellular biosynthesis of cysteinyl leukotrienes in rat neuronal and glial cells (2007)

Leukotrienes are mediators of inflammation that belong to a family of lipids derived from arachidonic acid by the action of 5-lipoxygenase. Leukotrienes have been detected in the central nervous system in association with different pathological events, but little is known about their biosynthesis or function in the brain. When rat neurons and glial cells in primary culture were stimulated with the calcium ionophore, no significant biosynthesis of leukotrienes was detected using liquid chromatography/mass spectrometry (LC/MS) techniques. However, when exogenous LTA(4) was added to these cultured cells, both neurons and glia were able to synthesize LTC(4). Activated neutrophils are known to supply LTA(4) to other cells for transcellular biosynthesis of cysteinyl-leukotrienes. Since neutrophils can infiltrate brain tissue after stroke or traumatic brain injury, we examined whether neutrophils play a similar role in the central nervous system. When peripheral blood neutrophils were co-cultured with rat neurons, glia cells, and then stimulated with calcium ionophore, a robust production of LTC(4), LTD(4), and LTE(4) was observed, revealing that neurons and glia can participate in the transcellular mechanism of leukotriene biosynthesis. The formation of LTC(4) through this mechanism may be relevant in the genesis and progression of the inflammatory response as a result of brain injury.
A real-time rear view camera based obstacle detection (2009)

This paper presents a robust real-time rear-view camera based object detection algorithm for backup aid and parking assist applications. The system is capable of handling the challenges of stationary as well as moving objects in rear view of the host vehicle, utilizing a single car-mounted rear-view fish-eye camera. A motion-based and edge-based object detection algorithm was developed in order to detect near distance objects and distant objects respectively. Furthermore, a free-space detection algorithm was developed which is used to detect areas where no objects appeared in front of the vehicle path. A tracker-based fusion algorithm was used to track and fuse detection results of individual detection algorithms. Experiments have been carried out by applying the proposed algorithm on prerecorded sequences as well as within a test vehicle and thus in a closed loop environment. The experimental results indicate promising detection performance.
Foetal Protection against Bovine Virus Diarrhoea Virus after Two‐step Vaccination (2002)

In order to assess the efficacy of a two-step vaccination protocol with respect to foetal protection against transplacental infections with bovine virus diarrhoea virus (BVDV) with special attention to BVDV-2 seronegative heifers were vaccinated with an inactivated BVDV-1 vaccine and boostered with a modified live BVDV-1 vaccine after 4 weeks. A second group was left unvaccinated as control. Between days 30 and 120 of pregnancy the heifers of both groups were intranasally challenged with a mixture of BVDV-1 and -2. All heifers of the vaccinated group gave birth to nine clinically healthy, seronegative (precolostral) and BVDV-free calves. In contrast in the control group four BVDV viraemic underdeveloped calves were born. Additionally, one calf was stillborn and another viraemic calf was not viable and died 2 days after birth. All six calves of the control group were viraemic with BVDV-2. This study demonstrated for the first time that two-step vaccination of breeding cattle with a modified live BVDV vaccine 4 weeks after application of an inactivated BVDV vaccine was capable of providing a foetal protection against transplacental infection with BVDV-2.
Automated regression test generation (1998)

Regression testing involves testing the modified program in order to establish the confidence in the modifications. Existing regression testing methods generate test cases to satisfy selected testing criteria in the hope that this process may reveal faults in the modified program. In this paper we present a novel approach of automated regression test generation in which all generated test cases uncover an error(s). This approach is used to test the common functionality of the original program and its modified version, i.e., it is used for programs whose functionality is unchanged after modifications. The goal in this approach is to identify test cases for which the original program and the modified program produce different outputs. If such a test is found, then this test uncovers an error. The problem of finding such a test case may be reduced to the problem of finding program input on which a selected statement is executed. As a result, existing methods of automated test data generation for white-box testing may be used to generate these tests. Our experiments have shown that our approach may improve the chances of finding software errors as compared to the existing methods of regression testing. The advantage of our approach is that it is fully automated and that all generated test cases reveal an error(s).
Using an external gating signal to estimate noise in PET with an emphasis on tracer avid tumors (2010)

The purpose of this study is to establish and validate a methodology for estimating the standard deviation of voxels with large activity concentrations within a PET image using replicate imaging that is immediately available for use in the clinic. To do this, ensembles of voxels in the averaged replicate images were compared to the corresponding ensembles in images derived from summed sinograms. In addition, the replicate imaging noise estimate was compared to a noise estimate based on an ensemble of voxels within a region. To make this comparison two phantoms were used. The first phantom was a seven-chamber phantom constructed of 1 liter plastic bottles. Each chamber of this phantom was filled with a different activity concentration relative to the lowest activity concentration with ratios of 1:1, 1:1, 2:1, 2:1, 4:1, 8:1 and 16:1. The second phantom was a GE Well-Counter phantom. These phantoms were imaged and reconstructed on a GE DSTE PET/CT scanner with 2D and 3D reprojection filtered backprojection (FBP), and with 2D- and 3D-ordered subset expectation maximization (OSEM). A series of tests were applied to the resulting images that showed that the region and replicate imaging methods for estimating standard deviation were equivalent for backprojection reconstructions. Furthermore, the noise properties of the FBP algorithms allowed scaling the replicate estimates of the standard deviation by a factor of 1/square root N, where N is the number of replicate images, to obtain the standard deviation of the full data image. This was not the case for OSEM image reconstruction. Due to nonlinearity of the OSEM algorithm, the noise is shown to be both position and activity concentration dependent in such a way that no simple scaling factor can be used to extrapolate noise as a function of counts. The use of the Well-Counter phantom contributed to the development of a heuristic extrapolation of the noise as a function of radius in FBP. In addition, the signal-to-noise ratio for high uptake objects was confirmed to be higher with backprojection image reconstruction methods. These techniques were applied to several patient data sets acquired in either 2D or 3D mode, with (18)F (FLT and FDG). Images of the standard deviation and signal-to-noise ratios were constructed and the standard deviations of the tumors' uptake were determined. Finally, a radial noise extrapolation relationship deduced in this paper was applied to patient data.
Stable fluorescent gold nanoparticles for detection of Cu<sup>2+</sup>with good sensitivity and selectivity (2011)

A simple and one-pot method for the synthesis of water-soluble, red-emitting, highly fluorescent gold nanoparticles has been reported using 11-mercaptoundecanoic acid (11-MUA) as the protecting group. We found that the fluorescent gold nanoparticles could selectively detect copper ions in aqueous solution, with a limit of detection of about 87 nM.
Commercial Nanoparticles for Stem Cell Labeling and Tracking (2013)

Stem cell therapy provides promising solutions for diseases and injuries that conventional medicines and therapies cannot effectively treat. To achieve its full therapeutic potentials, the homing process, survival, differentiation, and engraftment of stem cells post transplantation must be clearly understood. To address this need, non-invasive imaging technologies based on nanoparticles (NPs) have been developed to track transplanted stem cells. Here we summarize existing commercial NPs which can act as contrast agents of three commonly used imaging modalities, including fluorescence imaging, magnetic resonance imaging and photoacoustic imaging, for stem cell labeling and tracking. Specifically, we go through their technologies, industry distributors, applications and existing concerns in stem cell research. Finally, we provide an industry perspective on the potential challenges and future for the development of new NP products.