gebhart/patrepeval huggingface dataset:
High-Level Expression of Plasmodium vivax Apical Membrane Antigen 1 (AMA-1) in Pichia pastoris : Strong Immunogenicity in Macaca mulatta Immunized with P. vivax AMA-1 and Adjuvant SBAS2 (1999)

The apical membrane antigen 1 (AMA-1) family is a promising family of malaria blood-stage vaccine candidates that have induced protection in rodent and nonhuman primate models of malaria. Correct conformation of the protein appears to be essential for the induction of parasite-inhibitory responses, and these responses appear to be primarily antibody mediated. Here we describe for the first time high-level secreted expression (over 50 mg/liter) of the Plasmodium vivax AMA-1 (PV66/AMA-1) ectodomain by using the methylotrophic yeast Pichia pastoris. To prevent nonnative glycosylation, a conservatively mutagenized PV66/AMA-1 gene (PV66Deltaglyc) lacking N-glycosylation sites was also developed. Expression of the PV66Deltaglyc ectodomain yielded similar levels of a homogeneous product that was nonglycosylated and was readily purified by ion-exchange and gel filtration chromatographies. Recombinant PV66Deltaglyc43-487 was reactive with conformation-dependent monoclonal antibodies. With the SBAS2 adjuvant, Pichia-expressed PV66Deltaglyc43-487 was highly immunogenic in five rhesus monkeys, inducing immunoglobulin G enzyme-linked immunosorbent assay titers in excess of 1:200,000. This group of monkeys had a weak trend showing lower cumulative parasite loads following a Plasmodium cynomolgi infection than in the control group.
Blue sensitizing dyes: synthesis, spectroscopy, and performance in photographic emulsions (1995)

The synthesis is given of 12 mostly unsymmetrical monomethine cyanine dyes containing the pyridine and/or the benzothiazole moiety. Dye structures were determined from mass spectrometric and nuclear magnetic resonance (NMR) data. In addition to providing structure information, fast atom bombardment mass spectrometry also proved an efficient method to test ionic homogeneity, and the NMR spectra provided additional information about the electron distribution in the dyes. The compounds were further characterized by elemental analysis, high-pressure liquid chromatography, and UV-visible spectroscopy. Finally, we tested the performance of the dyes as blue sensitizers in photographic T-grain emulsions (sensitivity increase and contrast).
Stack configurations for tubular solid oxide fuel cells (2023)

A fuel cell unit includes an array of solid oxide fuel cell tubes having porous metallic exterior surfaces, interior fuel cell layers, and interior surfaces, each of the tubes having at least one open end; and, at least one header in operable communication with the array of solid oxide fuel cell tubes for directing a first reactive gas into contact with the porous metallic exterior surfaces and for directing a second reactive gas into contact with the interior surfaces, the header further including at least one busbar disposed in electrical contact with at least one surface selected from the group consisting of the porous metallic exterior surfaces and the interior surfaces.
교통과 토지이용 정보를 결합한 서울 인구분포의 시공간적 분석: 4차원 시각화 방법을 토대로 (2018)

도시공간에서 인구분포는 하루의 시간축을 따라 통행흐름의 변화와 함께 변동성을 보인다. 통행흐름은 도시민들이 하루 일과가 진행되면서 그들의 활동과 관련된 시설물이 입지한 지점으로 이동한 결과물이므로 도시민의 활동과 관련 시설물의 분포에 직접적인 영향을 받는다. 따라서 도시 인구분포의 시공간적 특성은 도시민의 일상생활과 관련된 활동공간의 분포와 그것을 방문하는 통행흐름을 결합하여 분석할 필요가 있다. 본 연구에서는 토지이용과 통행흐름에 대한 정보가 풍부한 서울시를 대상으로 건축물데이터베이스와 교통카드데이터베이스를 활용하여 하루 및 일주일 시간축을 따라 변동성을 보이는 도시공간의 인구분포를 분석한다. 일반적인 통계적 기법으로는 파악하기 어려운 시공간적 분석을 위하여 자바프로그램을 이용하여 시간과 공간을 결합한 4차원 시각화 방법을 고안한다. 이러한 4차원 시공간에서 역동적 시각화를 이용하면 직관적인 분석이 가능할 뿐만 아니라 인구분포의 시공간적 특성을 보다 효과적으로 파악할 수 있다. 이를 위하여 먼저 각 지점에 위치한 건축물을 용도에 따라 주거, 업무, 상업 활동으로 구분하고, 일주일분 교통카드데이터베이스에서 1분 단위로 각 지점의 버스와 지하철로 오가는 승객수를 산출하고, 이를 4차원으로 시각화하여 교통과 토지이용을 결합해서 서울시 인구분포의 시공간적 특성을 분석한다. 그 결과로 서울의 인구분포는 토지이용에 따라 뚜렷한 시공간적 특성을 보임을 파악할 수 있으며, 특히 업무활동, 상업활동, 주거활동의 혼합 양상에 따라 하루 시간축을 따라 인구분포 양상에 뚜렷한 차이가 있음을 확인하였다. 이러한 연구결과는 도시 시설의 입지계획과 교통계획 수립에 매우 유용하게 활용될 수 있다.
Transformation Based Learning for Specialization of Generic Event Extractions (2002)

As part of our Evidence Extraction and Link Discovery (EELD) project, we proposed to use Transformation Based Learning (TBL) to learn domain-specific specializations for generic event extractions. The primary goal of our learning task was to reduce the amount of human effort required for specializing generic event extractions to domains that are new and specific. Three initial annotation cycles and one annotation review and correction cycle involving a total of 70 documents were completed, with slightly over 32 hours required for the entire annotation effort; where possible, the annotation cycles started with bootstrapped files resulting from the application of TBL rules learned after the prior annotation cycle. A five-fold evaluation was completed using the annotated files as the gold standard for evaluation purposes. When our analysis was limited to specialized event types with 10 or more examples available for training, we achieved 67.93% Coverage, 88.93% Accuracy, and an F-score of 77.02%. Several conclusions can be drawn from our study: (1) the use of TBL to learn specializations of generic extractions to specific domains is possible, (2) the use of TBL leads to a significant reduction in the human effort involved in specializing to a new domain, (3) sparsity of training data has a large impact on the results of learning, and (4) with more training instances, coverage and accuracy would improve. Motivation: In the early days of Information Extraction (IE), IE systems extracted a limited amount of information in order to fill in the blanks in a predefined domain-specific template. Today&amp;apos;s IE systems increasingly rely on a much broader model of generic event, entity and relation extraction in order to capture a wide variety of useful information in various domains....
Karyotype and nucleic acid content in Zantedeschia aethiopica Spr. and Zantedeschia elliottiana Engl. (2012)

Analysis of karyotype, nucleic deoxyribonucleic acid (DNA) content and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were performed in Zantedeschia aethiopica and Zantedeschia elliottiana. Mitotic metaphase in both species showed 2n=32. The chromosomes of both species were quite similar with medium length ranging from 1.55 ± 0.04 to 3.85 ± 0.12 µM in Z. aethiopica and 2.15 ± 0.04 to 3.90 ± 0.12 µM in Z. elliottiana. However, some differences were found in morphology and centromeric position among the chromosomes. Identification of individual chromosomes was carried out using chromosomes length, and centromeric positions. The karyotype of Z. aethiopica was determined to be 2n = 32 = 14 m + 18 sm and of Z. elliottiana to be 2n = 32 = 10 m + 22 sm. The 2C nuclear DNA content was found to be 3.72 ± 0.10 picograms (equivalent to 3638.16 mega base pairs) for Z. aethiopica and 1144.26 ± 0.05 picograms (equivalent to 1144.26 mega base pairs) for Z. elliottiana. Leaf protein analysis showed 11 and 9 bands for Z. aethiopica and Z. elliottiana, respectively, among which some were species specific. These results may provide useful information regarding Zantedeschia for the study of taxonomic relationships, genetics and breeding.
Modeling human road crossing decisions as reward maximization with visual perception limitations (2023)

Understanding the interaction between different road users is critical for road safety and automated vehicles (AVs). Existing mathematical models on this topic have been proposed based mostly on either cognitive or machine learning (ML) approaches. However, current cognitive models are incapable of simulating road user trajectories in general scenarios, and ML models lack a focus on the mechanisms generating the behavior and take a high-level perspective which can cause failures to capture important human-like behaviors. Here, we develop a model of human pedestrian crossing decisions based on computational rationality, an approach using deep reinforcement learning (RL) to learn boundedly optimal behavior policies given human constraints, in our case a model of the limited human visual system. We show that the proposed combined cognitive-RL model captures human-like patterns of gap acceptance and crossing initiation time. Interestingly, our model's decisions are sensitive to not only the time gap, but also the speed of the approaching vehicle, something which has been described as a "bias" in human gap acceptance behavior. However, our results suggest that this is instead a rational adaption to human perceptual limitations. Moreover, we demonstrate an approach to accounting for individual differences in computational rationality models, by conditioning the RL policy on the parameters of the human constraints. Our results demonstrate the feasibility of generating more human-like road user behavior by combining RL with cognitive models.
Bubble mesh (1995)

This paper presents a new computational method for fully automated triangular mesh generation, consistently applicable to wire-frame, surface, solid, and nonmanifold geometries.
Overview of the ICRP/ICRU adult reference computational phantoms and dose conversion coefficients for external idealised exposures (2013)

This paper reviews the ICRP Publications 110 and 116 describing the reference computational phantoms and dose conversion coefficients for external exposures. The International Commission on Radiological Protection (ICRP) in its 2007 Recommendations made several revisions to the methods of calculation of the protection quantities. In order to implement these recommendations, the DOCAL task group of the ICRP developed computational phantoms representing the reference adult male and female and then calculated a set of dose conversion coefficients for various types of idealised external exposures. This paper focuses on the dose conversion coefficients for neutrons and investigates their relationship with the conversion coefficients of the protection and operational quantities of ICRP Publication 74. Contributing factors to the differences between these sets of conversion coefficients are discussed in terms of the changes in phantoms employed and the radiation and tissue weighting factors.
Interactive and Deterministic Data Cleaning (2016)

We present Falcon, an interactive, deterministic, and declarative data cleaning system, which uses SQL update queries as the language to repair data. Falcon does not rely on the existence of a set of pre-defined data quality rules. On the contrary, it encourages users to explore the data, identify possible problems, and make updates to fix them. Bootstrapped by one user update, Falcon guesses a set of possible sql update queries that can be used to repair the data. The main technical challenge addressed in this paper consists in finding a set of sql update queries that is minimal in size and at the same time fixes the largest number of errors in the data. We formalize this problem as a search in a lattice-shaped space. To guarantee that the chosen updates are semantically correct, Falcon navigates the lattice by interacting with users to gradually validate the set of sql update queries. Besides using traditional one-hop based traverse algorithms (e.g., BFS or DFS), we describe novel multi-hop search algorithms such that Falcon can dive over the lattice and conduct the search efficiently. Our novel search strategy is coupled with a number of optimization techniques to further prune the search space and efficiently maintain the lattice. We have conducted extensive experiments using both real-world and synthetic datasets to show that Falcon can effectively communicate with users in data repairing.
[Neurological manifestations in patients with sera positive for Borrelia burgdorferi]. (1997)

Eight years of case histories of patients with positive serum tests for Borrelia burgdorferi (Bb) are reviewed with the aims of analyzing the neurological manifestations involved and of assessing the value of serology in the diagnosis of neuroborreliosis (NB) in our clinical setting. Of the 105 cases with neurological manifestations that could be examined, 25 patients (24%) with other infections, neoplasms or other diseases had false positive serologies. Forty-one patients (39%) met the criteria for NB diagnosis: 26 had lymphocytic meningitis, 13 had polyradiculitis and 20 had cranial neuropathy. Spinal fluid cultures were positive in 43% of the patients on whom the test was performed, and all patients in this group who were treated with antibiotics improved. The other 39 patients (37%) had only neurological manifestations, which were not typical of NB (peripheral neuropathy, stroke, demyelinating disease, dementia or myelopathy), but for which no other etiology could be demonstrated. Spinal fluid serology was positive in 16% of those cases studied and none of those treated only with antibiotics improved. Among patients with both neurological manifestations and Bb positive serology, there were many false positives and cases with signs that were of dubious relation to infection by Bb; therefore, the prevalence of cases consistent with NB is low [corrected].
The effect of the cytochrome P‐450 system inducers on the development of drosophila melanogaster (1993)

D. melanogaster development was markedly retarded and its survival decreased by larvae treatment with compounds being strong inducers of the cytochrome P-450 2B in mammals--phenobarbital (PB*), perfluorodecaline (PFD), transtilbene oxide (TSO), and triphenyldioxane (TPD). At the same time, the weak inducer hexobarbital or the selective cytochrome P-450 inducer in mice but not in rats 1,4-bis[2-(dichloropyridyl-oxy)]-benzene (DPB) did not affect the larvae development. The cytochrome P-450 1A1 inducers benzo(a)anthracene (BA) and beta-naphtoflavone (BNF) were also not effective. The toxicity of phenobarbital was shown to be decreased by the cytochrome P-450 inhibitor piperonyl butoxide by adding 20-hydroxyecdysone or by treatment with aminophylline--the indirect enhancer of ecdysone production in the larval prothoracic gland. The hypothesis of the moulting hormone degradation as the cause of elevated larvae mortality resulting from the induced high mixed function oxidase activity has been discussed.
Evaluation of Textile Fiber Evidence: A Review (1987)

Abstract The problem of establishing whether or not a certain fibrous textile is the source of a particular single fiber collected from a crime scene is discussed in this paper. A single evidential fiber present at a crime scene can be associated with four major events. These are fiber transfer, persistence after transfer, evidence collection, and fiber analysis. These events are reviewed by drawing on both published research and general scientific principles.
Blind hyperspectral denoising (2015)

In this work we propose a new formulation for hyperspectral denoising based on the Blind Compressed Sensing (BCS) framework. BCS learns the sparsifying basis during signal recovery combining the advantages of standard sparse recovery with dictionary learning. We show that our proposed formulation yields better results than a state-of-the- art technique hyperspectral denoising both in terms of PSNR (more than 1dB improvement) and visual quality.
Which Asymmetric Tibial Component Is Optimally Designed for Calipered Kinematically Aligned Total Knee Arthroplasty? (2021)

Calipered kinematically aligned (KA) total knee arthroplasty (TKA) restores the patient's prearthritic joint lines and sets internal-external rotation of the tibial component parallel to the flexion-extension (FE) plane, which is not a mechanical alignment (MA) target. Two asymmetric tibial components designed for MA set the tibial component to either a femoral component (FC) target or a tibial tubercle (TT) target. The study determined the optimal asymmetric tibial component to use with KA as the one with smaller IE deviation from the MA target, greater coverage of tibial resection, and lower incidence of cortical overhang. The study included 40 patients treated with bilateral calipered KA TKA with different asymmetric tibial components in opposite knees. A best-fit of a kinematic tibial template to the tibial resection set the template's slot parallel to the knee's FE plane. Each asymmetric tibial component's anterior-posterior (AP) axis was set parallel to the slot. Computer tomography analysis determined the IE deviation (-internal/+ external) of each tibial component from its MA target, tibial resection coverage by the baseplate and insert, and incidence of cortical overhang. The patient-reported Forgotten Joint Score (FJS) and Oxford Knee Score (OKS) determined outcomes. The mean IE deviation from the MA target was 2 degrees external for the FC-target asymmetric tibial component and -8 degrees internal for the TT-target asymmetric tibial component (<i>p</i> < 0.001). Tibial resection coverage by the baseplate (insert) was 88% (84%) for the FC target and 84% (79%) for the TT target (<i>p</i> < 0.001 for baseplate and insert). The FC target insert covered 3 mm more of the posterolateral resection (<i>p</i> < 0.001). Posteromedial coverage was comparable. The incidence of cortical overhang was 2.5% for each baseplate. There was no difference in FJS and OKS. When performing calipered KA, the more optimal design was the asymmetric tibial component with the FC target because of the smaller deviation from its MA target and the greater coverage of the tibial resection by the baseplate and insert.
On models, bounds, and estimation algorithms for time-varying phase noise (2011)

In this paper, a new discrete-time model of phase noise for digital communication systems, based on a continuous-time representation of time-varying phase noise is derived and its statistical characteristics are presented. The proposed phase noise model is shown to be more accurate than the classical Wiener model. Next, using the this model, non-data-aided (NDA) and decision-directed (DD) maximum-likelihood (ML) estimators of time-varying phase noise are derived. To evaluate the performance of the proposed estimators, the Cramér-Rao lower bound (CRLB) for each estimation approach is derived and by using Monte-Carlo simulations it is shown that the mean-square error (MSE) of the proposed estimators converges to the CRLB at moderate signal-to-noise ratios (SNR). Finally, simulation results show that the proposed estimators outperform existing estimation methods as the variance of the phase noise process increases.
[Preliminary application of an improved Demons deformable registration algorithm in tumor radiotherapy]. (2012)

Due to the influence of different scanning conditions in fractionated radiation, the density range of the treatment image and the planning image may be different. The improved Demons algorithm can achieve faster and more accurate radiotherapy.
P2-006　　Profiles of Receptors for Specialized Lipid Mediators on Synoviocyte from Osteoarthritis (2014)

【Background】 As specialized pro-resolving mediators (SPM) derived from fatty acids are detectable in synovial fluids in osteoarthritis (OA), they appear to take some roles for disease pathogenesis. Receptors for SPMs have been found, such as leukotriene B4 receptor (BLT1), formyl peptide receptor 2 (FPR2), and chemokine like receptor 1 (CMKLR1). 【Purpose】 To identify the significance of receptors for SPMs on the cells in synovial tissue from OA joints. 【Methods】 Expression of BLT1, FPR2 and CMKLR1 on synoviocytes from OA patients (45.5% women, mean age 69 years, mean BMI 27.9 kg/m(2)) and macrophage were analysed by flow cytometry and quantitative PCR. 【Results】 FPR2 and CMKLR1 are found on synoviocyte, in which mean expression by flow cytometry were 8.5% and 6.2%, respectively, but BLT1 was less than 2.0%, although all of them decreased by keeping incubation. LPS treatment increased rather FPR2, but not so much CMKLR1, on synoviocytes and macrophage. 【Conclusion】 There are FPR2 or CMKLR1 positive cells in synovial tissues, and especially FPR2 seems to have a certain function under inflammatory conditions.
Changes in Bone Mineral Density, Body Composition, and Lipid Metabolism during Growth Hormone (GH) Treatment in Children with GH Deficiency1 (1997)

Adults with childhood onset GH deficiency (GHD) have reduced bone mass, increased fat mass, and disorders of lipid metabolism. The aim of the present study was to evaluate bone mineral density (BMD), bone metabolism, body composition, and lipid metabolism in GHD children before and during 2-3 yr of GH treatment (GHRx). Forty children with GHD, mean age 7.9 yr, participated in the study of bone metabolism and body composition; and an additional group of 17 GHD children, in the study of lipid metabolism. Lumbar spine BMD, total body BMD, and body composition were measured with dual-energy x-ray absorptiometry. Volumetric BMD (bone mineral apparent density, BMAD) was calculated to correct for bone size. BMD, BMAD, lean tissue mass, bone mineral content, fat mass, and percentage body fat were expressed as SD scores (SDS), in comparison with normative data of the same population. Lumbar spine BMD and BMAD and total body BMD were all decreased at baseline. All BMD variables increased significantly during GHRx, lumbar spine BMD SDS, already after 6 months of treatment. Lean tissue mass SDS increased continuously. Bone mineral content SDS started to increase after 6 months GHRx. Fat mass SDS decreased during the first 6 months of GHRx and remained stable thereafter. Biochemical parameters of bone formation and bone resorption did not differ from normal at baseline and increased during the first 6 months of GHRx. Serum 1,25 dihydroxyvitamin D increased continuously during GHRx, whereas PTH and serum calcium remained stable. Lipid profile was normal at baseline: Atherogenic index had decreased and apolipoprotein A1(Apo-A1) had increased after 3 yr of treatment. In conclusion, children with GHD have decreased bone mass. BMD, together with height and lean tissue mass, increased during GHRx. GHRx had a beneficial effect on lipid metabolism.
Proteolytic Processing of Human Cytomegalovirus Glycoprotein B Is Dispensable for Viral Growth in Culture (2002)

Glycoprotein B (gB) of human cytomegalovirus (HCMV), which is considered essential for the viral life cycle, is proteolytically processed during maturation. Since gB homologues of several other herpesviruses remain uncleaved, the relevance of this property of HCMV gB for viral infectivity is unclear. Here we report on the construction of a viral mutant in which the recognition site of gB for the cellular endoprotease furin was destroyed. Because mutagenesis of essential proteins may result in a lethal phenotype, a replication-deficient HCMV gB-null genome encoding enhanced green fluorescent protein was constructed, and complementation by mutant gBs was initially evaluated in transient-cotransfection assays. Cotransfection of plasmids expressing authentic gB or gB with a mutated cleavage site (gB-DeltaFur) led to the formation of green fluorescent miniplaques which were considered to result from one cycle of phenotypic complementation of the gB-null genome. To verify these results, two recombinant HCMV genomes were constructed: HCMV-BAC-DeltaMhdI, with a deletion of hydrophobic domain 1 of gB that appeared to be essential for viral growth in the cotransfection experiments, and HCMV-BACDeltaFur, in which the gB cleavage site was mutated by amino acid substitution. Consistent with the results of the cotransfection assays, only the DeltaFur mutant replicated in human fibroblasts, showing growth kinetics comparable to that of wild-type virus. gB in mutant-infected cells was uncleaved, whereas glycosylation and transport to the cell surface were not impaired. Extracellular mutant virus contained exclusively uncleaved gB, indicating that proteolytic processing of gB is dispensable for viral replication in cell culture.