gebhart/patrepeval huggingface dataset:
A particle filter motion prediction algorithm based on an autoregressive model for real-time MRI-guided radiotherapy of lung cancer (2017)

This work introduces a 2D motion prediction algorithm for lung tumors applied to dynamic MR images that combines intrafractional tumor deformations. It is developed in the context of MR-linac treatments and evaluates uniform and patient-specific margins about the gross tumor volume to optimize the tumor coverage. Seven early stage non-small cell lung cancer patients were imaged in treatment position with a 1.5 T magnetic resonance using a balanced steady-state free precession sequence for one minute at a rate of four images per second and were instructed to breathe normally. The particle filter, in combination with the autoregressive model, is used to sequentially track and predict the tumor position 250 ms in the future from the current image. In addition, the autocontour extracted from a previous study (Bourque et al 2016 Med. Phys. 43 5161–9) is projected to the predicted position and various margins are evaluated. Averaged over all patients, the root mean square errors are (1.3 ± 0.5) mm and (2.0 ± 0.8) mm with and without prediction, respectively, and the difference in centroid position is (1.1 ± 0.4) mm with the prediction. The addition of the prediction algorithm leads to inferior errors for all cases. With such predictor, enlarging the propagated contour by a uniform 2 mm margin leads to a minimum recall of 97% over the entire patient population. Considering patient-specific margins based on of the Gaussian distribution around the mean error, the margins vary from 0.8 to 3.0 mm in anterior–posterior direction and from 1.2 to 3.2 mm in the superior–inferior direction. This study concludes that the advantage of such prediction algorithm highly depends on the tumor motion characteristics. For both uniform and patient-specific margins evaluation, smaller treatment margins could be used when combined to an accurate tracking and motion prediction algorithm. These results could offer guidance for future MR-guided lung tumor treatments.
The oxidized phospholipids linked to human apolipoprotein(a) do not derive from circulating low‐density lipoproteins and are probably of cellular origin (2008)

Lipoprotein (a) [Lp(a)], a cardiovascular risk factor, is a low-density lipoprotein (LDL) variant shown to bind to oxidized phospholipids (oxPLs); however, its binding mode and origin have not been clearly established. We isolated both LDL and Lp(a) from the plasma of a population of high-Lp(a) subjects and in each Lp(a) particle separated apolipoprotein(a) [apo(a)], from the LDL component, Lp(a(-)). These products were assayed by an ELISA using monoclonal antibody T15 with a known specificity for oxPLs. In each subject, the T15 reactivity was confined to apo(a). Moreover, the amount of oxPL bound to apo(a) was unaffected by plasma Lp(a) levels and apo(a) size polymorphism. We have previously shown that kringle V (KV) is the site of oxPL linkage in human apo(a). In this work, we expressed in human embryonic kidney cells a KV-containing recombinant that, when purified from the medium, contained oxPLs. In summary, in human plasma Lp(a), the oxPLs are located in apo(a) and not in the circulating LDLs, suggesting a cellular origin. This latter concept is supported by the studies in which an expressed KV-containing apo(a) microdomain exhibited oxPL reactivity. Thus, apo(a) can undergo potentially pathogenic posttranslational modifications in a cellular environment able to generate oxPL.
Predicting Visual Exemplars of Unseen Classes for Zero-Shot Learning (2017)

Leveraging class semantic descriptions and examples of known objects, zero-shot learning makes it possible to train a recognition model for an object class whose examples are not available. In this paper, we propose a novel zero-shot learning model that takes advantage of clustering structures in the semantic embedding space. The key idea is to impose the structural constraint that semantic representations must be predictive of the locations of their corresponding visual exemplars. To this end, this reduces to training multiple kernel-based regressors from semantic representation-exemplar pairs from labeled data of the seen object categories. Despite its simplicity, our approach significantly outperforms existing zero-shot learning methods on standard benchmark datasets, including the ImageNet dataset with more than 20,000 unseen categories.
Echinococcus granulosus: Epidemiology and state-of-the-art of diagnostics in animals (2015)

Diagnosis and detection of Echinococcus granulosus (sensu lato) infection in animals is a prerequisite for epidemiological studies and surveillance of echinococcosis in endemic, re-emergent or emergent transmission zones. Advances in diagnostic approaches for definitive hosts and livestock, however, have not progressed equally over the last 20 years. Development of laboratory based diagnostics for canids using coproantigen ELISA and also coproPCR, have had a huge impact on epidemiological studies and more recently on surveillance during hydatid control programmes. In contrast, diagnosis of cystic echinococcosis (CE) in livestock still relies largely on conventional post-mortem inspection, despite a relatively low diagnostic sensitivity especially in early infections, as current serodiagnostics do not provide a sufficiently specific and sensitive practical pre-mortem alternative. As a result, testing of dog faecal samples by coproantigen ELISA, often combined with mass ultrasound screening programmes for human CE, has been the preferred approach for monitoring and surveillance in resource-poor endemic areas and during control schemes. In this article we review the current options and approaches for diagnosis of E. granulosus infection in definitive and animal intermediate hosts (including applications in non-domesticated species) and make conclusions and recommendations for further improvements in diagnosis for use in epidemiological studies and surveillance schemes.
Sequence analysis and modular organization of threonyl‐tRNA synthetase from <i>Thermus thermophilus</i> and its interrelation with threonyl‐tRNA synthetases of other origins (2000)

The gene encoding threonyl-tRNA synthetase (Thr-tRNA synthetase) from the extreme thermophilic eubacterium Thermus thermophilus HB8 has been cloned and sequenced. The ORF encodes a polypeptide chain of 659 amino acids (Mr 75 550) that shares strong similarities with other Thr-tRNA synthetases. Comparative analysis with the three-dimensional structure of other subclass IIa synthetases shows it to be organized into four structural modules: two N-terminal modules specific to Thr-tRNA synthetases, a catalytic core and a C-terminal anticodon-binding module. Comparison with the three-dimensional structure of Escherichia coli Thr-tRNA synthetase in complex with tRNAThr enabled identification of the residues involved in substrate binding and catalytic activity. Analysis by atomic absorption spectrometry of the enzyme overexpressed in E. coli revealed the presence in each monomer of one tightly bound zinc atom, which is essential for activity. Despite strong similarites in modular organization, Thr-tRNA synthetases diverge from other subclass IIa synthetases on the basis of their N-terminal extensions. The eubacterial and eukaryotic enzymes possess a large extension folded into two structural domains, N1 and N2, that are not significantly similar to the shorter extension of the archaebacterial enzymes. Investigation of a truncated Thr-tRNA synthetase demonstrated that domain N1 is not essential for tRNA charging. Thr-tRNA synthetase from T. thermophilus is of the eubacterial type, in contrast to other synthetases from this organism, which exhibit archaebacterial characteristics. Alignments show conservation of part of domain N2 in the C-terminal moiety of Ala-tRNA synthetases. Analysis of the nucleotide sequence upstream from the ORF showed the absence of both any anticodon-like stem-loop structure and a loop containing sequences complementary to the anticodon and the CCA end of tRNAThr. This means that the expression of Thr-tRNA synthetase in T. thermophilus is not regulated by the translational and trancriptional mechanisms described for E. coli thrS and Bacillus subtilis thrS and thrZ. Here we discuss our results in the context of evolution of the threonylation systems and of the position of T. thermophilus in the phylogenic tree.
Tumors of the Cervix, Vagina, and Vulva (2010)

The publication of this edition marks the transition in diagnosis of lower genital tract lesions from a largely morphologic activity to one based upon integrated assessment using microscopy and molecular biology. Furthermore, the ability to integrate these diagnostic approaches with clinical data for patient management has been heightened. The introduction of prophylactic vaccines for preventing human papillomavirus (HPV) infections and cervical cancer precursors also thrusts pathology into a new unprecedented public health role with regard to disease monitoring, which will likely expand over time. Finally, the realisation that cervical cancer is becoming increasingly preventable carries with it both a sense of accomplishment and the recognition that this must now be translated into an achievable goal of cancer prevention in underdeveloped nations. Although the text has remained concise in order to maintain the primary function of the book as an atlas rather than a comprehensive textbook, it has been substantially updated to reflect the changes in the field since the previous edition was published in 1992. In this regard, the number of illustrations, all of which are in colourr, has almost doubled. Both the text and the photomicrographs emphasise the importance of immunohistochemistry and molecular in situ hybridisation as adjuncts to morphology in routine clinical diagnosis. A binary (low-grade and high-grade squamous intraepithelial lesion) classification for histology, analogous to TBS for cytology, replaces the four-tiered dysplasia/CIS system and the three-tiered CIN system. This Atlas will be a useful reference for pathologists, residents, and students for years to come.
ANALYSIS OF SOUND PATTERNS THROUGH WAVELET TRANSFORMS (1987)

This paper starts with a brief discussion of so-called wavelet transforms, i.e., decompositions of arbitrary signals into localized contributions labelled by a scale parameter. The main features of the method are first illustrated through simple mathematical examples. Then we present the first applications of the method to the recognition and visualisation of characteristic features of speech and of musical sounds.
The Effects of Variable Time Window Width and Signal Position Within FFT Bin on WISPR Performance. (1996)

Abstract : The effect of variable width of the time window in time frequency analysis on WISPR performance is investigated, along with the effect of signal position within the signal bin. The results demonstrate that variable width of the time window in FFT/DFT calculations has only a small effect on WISPR performance, as long as the full signal energy is contained within the signal bin. But the loss of even a small portion of the signal energy from the signal bin has a dramatic effect on the WISPR level, and causes deterioration in WISPR performance by several decibels. The average power level is only slightly affected by such changes. The sensitivity of the WISPR level to the signal position within the signal bin provides a means to determine the signal frequency more precisely, avoiding the necessity to carry out calculations using much larger data sets.
HPHT growth and x-ray characterization of high-quality type IIa diamond (2009)

The trend in synchrotron radiation (x-rays) is towards higher brilliance. This may lead to a very high power density, of the order of hundreds of watts per square millimetre at the x-ray optical elements. These elements are, typically, windows, polarizers, filters and monochromators. The preferred material for Bragg diffracting optical elements at present is silicon, which can be grown to a very high crystal perfection and workable size as well as rather easily processed to the required surface quality. This allows x-ray optical elements to be built with a sufficient degree of lattice perfection and crystal processing that they may preserve transversal coherence in the x-ray beam. This is important for the new techniques which include phase-sensitive imaging experiments like holo-tomography, x-ray photon correlation spectroscopy, coherent diffraction imaging and nanofocusing. Diamond has a lower absorption coefficient than silicon, a better thermal conductivity and lower thermal expansion coefficient which would make it the preferred material if the crystal perfection (bulk and surface) could be improved. Synthetic HPHT-grown (high pressure, high temperature) type Ib material can readily be produced in the necessary sizes of 4-8 mm square and with a nitrogen content of typically a few hundred parts per million. This material has applications in the less demanding roles such as phase plates: however, in a coherence-preserving beamline, where all elements must be of the same high quality, its quality is far from sufficient. Advances in HPHT synthesis methods have allowed the growth of type IIa diamond crystals of the same size as type Ib, but with substantially lower nitrogen content. Characterization of this high purity type IIa material has been carried out with the result that the crystalline (bulk) perfection of some of the HPHT-grown materials is approaching the quality required for the more demanding applications such as imaging applications and imaging applications with coherence preservation. The targets for further development of the type IIa diamond are size, crystal perfection, as measured by the techniques of white beam and monochromatic x-ray diffraction imaging (historically called x-ray topography), and also surface quality. Diamond plates extracted from the cubic growth sector furthest from the seed of the new low strain material produces no measurable broadening of the x-ray rocking curve width. One measures essentially the crystal reflectivity as defined by the intrinsic reflectivity curve (Darwin curve) width of a perfect crystal. In these cases the more sensitive technique of plane wave topography has been used to establish a local upper limit of the strain at the level of an 'effective misorientation' of 10(-7) rad.
[Antigenic polysaccharides of bacteria. 32. The structure of O-specific polysaccharide chains of Pseudomonas cepacia serotype B and E lipopolysaccharides containing D-fucose]. (1988)

On the basis of acid hydrolysis, methylation, 1H and 13C NMR analysis, and calculation of specific optical rotation, the following structures were established for O-specific polysaccharides of Pseudomonas cepacia serotypes B and E: ----3)-beta-D-Galf-(1----3)-alpha-D-Fucp-(1----serotype B ----3)-beta-D-GlcpNAc-(1----3)-alpha-D-Fucp-(1----serotype E A characteristic feature of the polysaccharides is the presence of D-fucose, rather rare for bacterial antigens.
SLOW-RELEASE NITROGEN FERTILIZERS AND NITROGEN ADDITIVES FOR FIELD CROPS (2010)

Nitrogen management continues to be difficult due to transformations of nitrogen fertilizers that are possible when applied to soil and the uncertainties of weather (Cabrera et al., 2008). Nitrogen fertilizer in the form of urea is subject to ammonia volatilization through the activity of the urease enzyme found ubiquitously in soil (Kissel et al., 2008). Nitrate fertilizer is subject to leaching (Randall et al., 2008) or denitrification (Coyne, 2008) depending on the water content of the soil and water movement through the soil. Ammonium forms of N can be fixed (Kissel et al., 2008), or can be transformed to nitrate through the activities of specific soil bacteria (Norton, 2008). Because of these and other processes, nitrogen use efficiency is low.
Intrahepatic delivery of α-galactosylceramide-pulsed dendritic cells suppresses liver tumor (2006)

These results demonstrate that alphaGCDC injection into the liver can efficiently activate NK cells that in turn reject liver tumors to establish potent acquired immunity against the original tumor.
Characterization of a newly established human gastric cancer cell line HGT-1 bearing histamine H2-receptors. (1982)

A human gastric adenocarcinoma cell line, HGT-1, was established in vitro from the primary tumor of a 60-year-old patient. Histological examination of the tumor revealed a poorly differentiated adenocarcinoma. Primary tumor cells were cloned in soft agarose and gave rise to tumor colonies. The procedures enabling us to form a continuous cell line from the agarose colonies are described. The cultured cells grew as monolayers of closely apposed polygonal cells with a population-doubling time of 19.48 +/- 1.20 (S.E.) hr during exponential growth at passage 59. They had an epithelial morphology. Ultrastructural studies revealed the presence of microvilli and tight junctions. The HGT-1 cell line is tumorigenic in nude mice and has a hyperdiploid karyotype with a modal number of 57 chromosomes. It exhibits numerous marker chromosomes. These human gastric epithelial cells do not secrete mucus or carcinoembryonic antigen. They exhibit functional histamine H2-receptors mediating cellular cyclic adenosine 3':5'-monophosphate production and adenylate cyclase activation. In conclusion, the use of a soft-agarose clonogenic assay permitted us to develop a cancer cell line without the problems of fibroblastic cell contamination. The existence of histamine H2-receptors on gastric HGT-1 cells stresses the importance of this line as a model for studies of regulatory mechanisms involved in gastric secretion.
Modeling of Low Inductive Busbar Connections (1996)

The high power levels required by many power electronic applications well as the very low switching times encountered in new semiconductor devices have created a need for low wiring inductances. The busbar technology is an effective industrial way to reduce the interconnection inductance between (for instance) the feeding source and the converter. It consists of a stacking of several copper sheets, each separated from the other by a dielectric. The connections between these sheets and the different devices are made with screws. The authors present a way of modeling a busbar. Using a simulation tool, InCa, dedicated to inductance and resistance calculations, it is possible to obtain the L, R equivalent circuit of a busbar. Moreover, it allows the determination of the current density in any cross section of any busbar sheet. In order to validate the modeling, a chopper structure using this kind of connection has been realized and measurements have been made.
Characterization of tumor infiltrating Natural Killer cell subset (2015)

The presence of tumor-infiltrating Natural Killer (NK) within a tumor bed may be indicative of an ongoing immune response toward the tumor. However, many studies have shown that an intense NK infiltration, is associated with advanced disease and may even facilitate cancer development. The exact role of the tumor infiltrating NK cells and the correlation between their presence and poor prognosis remains unclear. Interestingly, during pregnancy high numbers of a specific NK subset, CD56(bright)CD16(dim), are accumulated within first trimester deciduas. These decidual NK (dNK) cells are unique in their gene expression pattern secret angiogenic factors that induce vascular growth. In the present study we demonstrate a significant enrichment of a CD56(brigh)CD16(dim) NK cells within tumors. These NK cells express several dNK markers including VEGF. Hence, this study adds new insights into the identity of tumor residual NK cells, which has clear implications for the treatment of human cancer.
GENETIC ANALYSIS OF RESISTANCE TO BENZIMIDAZOLES IN PHYSARUM: DIFFERENTIAL EXPRESSION OF β-TUBULIN GENES (1984)

Physarum displays two vegetative cell types, uninucleate myxamoebae and multinucleate plasmodia. Mutant myxamoebae of Physarum resistant to the antitubulin drug methylbenzimidazole-2-yl-carbamate (MBC) were isolated. All mutants tested were cross-resistant to other benzimidazoles but not to cycloheximide or emetine. Genetic analysis showed that mutation to MBC resistance can occur at any one of four unlinked loci, benA, benB, benC or benD. MBC resistance of benB and benD mutants was expressed in plasmodia, but benA and benC mutant plasmodia were MBC sensitive, suggesting that benA and benC encode myxamoeba-specific products. Myxamoebae carrying the recessive benD210 mutation express a beta-tubulin with novel electrophoretic mobility, in addition to a beta-tubulin with wild-type mobility. This and other evidence indicates that benD is a structural gene for beta-tubulin, and that at least two beta-tubulin genes are expressed in myxamoebae. Comparisons of the beta-tubulins of wild-type and benD210 strains by gel electrophoresis revealed that, of the three (or more) beta-tubulin genes expressed in Physarum, one, benD, is expressed in both myxamoebae and plasmodia, one is expressed specifically in myxamoebae and one is expressed specifically in plasmodia. However, mutation in only one gene, benD, is sufficient to confer MBC resistance on both myxamoebae and plasmodia.
INTRANASALLY AND ORALLY EFFECTIVE ADJUVANTS FROM CHINESE AND JAPANESE MEDICINAL HERBS FOR NASAL INFLUENZA VACCINE (2005)

ISHS III WOCMAP Congress on Medicinal and Aromatic Plants - Volume 5: Quality, Efficacy, Safety, Processing and Trade in Medicinal and Aromatic Plants INTRANASALLY AND ORALLY EFFECTIVE ADJUVANTS FROM CHINESE AND JAPANESE MEDICINAL HERBS FOR NASAL INFLUENZA VACCINE
Constructing Role-Based Access Control and Delegation Based on Hierarchical IBS (2007)

Authentication and authorization are crucial for information and system security. Role-based delegation based on role-based access control (KBAC) can act as an efficient means of authorization management in distributed collaborative environment. In this paper, we present a scheme that integrates hierarchical identity-based signature (Hierarchical IBS) technique to perform role-based access control and role-based delegation. In our suggestion, original user-role assignment relation can be regarded as a particular form of one-depth delegation. We eliminate the use of digital certificates, and handle the multi- depth role-based delegation based on hierarchical identity-based signature scheme [8]. Our access control process can provide both aspects of user authentication and role-based authorization simultaneously, so the independent authentication procedure is eliminated. We also prove the security of our scheme in the random oracle model.