gebhart/patrepeval huggingface dataset:
Lassa Fever Virus Peptides Predicted by Computational Analysis Induce Epitope-Specific Cytotoxic-T-Lymphocyte Responses in HLA-A2.1 Transgenic Mice (2005)

Lassa fever is a hemorrhagic disease caused by Lassa fever virus (LV). Although the precise host defense mechanism(s) that affords protection against LV is not completely understood, cellular immunity mediated by cytotoxic T lymphocytes (CTLs) plays a pivotal role in controlling viral replication and LV infection. To date, there have been no reports mapping major histocompatibility complex (MHC) class I-binding CTL epitopes for LV. Using computer-assisted algorithms, we identified five HLA-A2.1-binding peptides of LV glycoprotein (GP) and two peptides from LV nucleoprotein (NP). Synthesized peptides were examined for their ability to bind to MHC class I molecules using a flow cytometric assay that measures peptide stabilization of class I. Three of the LV-GP peptides tested (LLGTFTWTL, SLYKGVYEL, and YLISIFLHL) stabilized HLA-A2. The LV-NP peptides tested failed to stabilize this HLA-A2. We then investigated the ability of the HLA-A2-binding LV-GP peptides to generate peptide-specific CTLs in HLA-A2.1 transgenic mice. Functional assays used to confirm CTL activation included gamma interferon enzyme-linked immunospot (ELISPOT) assays and intracellular cytokine staining of CD8+ T cells from peptide-primed mice. CTL assays were also performed to verify the cytolytic activity of peptide-pulsed target cells. Each of the LV-GP peptides induced CTL responses in HLA-A2-transgenic mice. MHC class I tetramers prepared using one LV-GP peptide that showed the highest cytolytic index (LLGTFTWTL) confirmed that peptide-binding CD8+ T cells were present in pooled lymphocytes harvested from peptide-primed mice. These findings provide direct evidence for the existence of LV-derived GP epitopes that may be useful in the development of protective immunogens for this hemorrhagic virus.
Design rules for non-Manhattan shapes (2000)

An approach to MEMS Computer Aided Design tools has been to make use of Integrated Circuits CAD suites with specific enhancements for MEMS designs. Extending the IC Design Rule Checkers to non-Manhattan shapes is one of these needed enhancements. IF anecdotally used in IC designs, non-manhattan shapes are intensively used in todays state of the art MEMS products. High performance gyroscopes and yaw rate sensors made in surface micromachining processes feature spiral springs and torsional combdrives made of toroidal fingers. Applying classical DRCs to these layouts generate thousands of false errors. The errors are false because they do not affect the manufacturability of the device. But because of their number, they prevent the designers from detecting real errors in their layout. Most false errors are generated by rounding floating point vertices' coordinates, translating different data types and snapping points to a grid. This paper presents a new methodology to eliminate false errors generated by the DRC of non-manhattan shapes. This methodology includes adding a tolerance factor to Microsystem design rules with respect to the geometric properties of non-manhattan shapes and the manufacturing grid parameters, closely controlling the vertices coordinates when automatically generating the non manhattan shapes and controlling the snapping on the grid. This methodology has been implemented in MEMSCAP Microsystem engineering kits and has been validated for three foundry design rules: BOSCH, SensoNor, and AMS
Multiplication by two integers using the minimum number of adders (2005)

The two-coefficient minimum-adder graph (MAG2) algorithm is described and shown to be optimal. A partial implementation, optimal for pairs of integers up to 8 bits, outperforms the best existing algorithms.
Utilization of Polyethylene and Paraffin Waxes as Controlled Delivery Systems for Different Fertilizers (1999)

Paraffin and polyethylene waxes were found to be efficient as controlled delivery systems for six different commercial-grade fertilizers. These fertilizers are monoammonium phosphate, diammonium phosphate, NP, NPK-4, and NPK-14 grades, and granular triple superphosphate fertilizers. Dissolution tests were performed for matrix-type formulations in order to determine the influence of waxes on the fertilizers release rate. Three different diffusion release formulas were tested for describing the release rate of the different fertilizers. The release times were at least doubled for all of the fertilizers while using either paraffin wax or polyethylene wax. The polyethylene wax gives longer release times than the paraffin wax.
Clinical results and complications in mobile-bearing total knee arthroplasty. (2005)

The low-contact stress mobile-bearing implant has the longest continuous follow-up, with over 25 years of data compiled in the designers' original study. In several peer-reviewed publications, the long-term outcome and clinical performance of the femorotibial articulation, patellar resurfacing, and various issues of surgical technique, such as cruciate retention or sacrifice, tibial axis alignment method of bone resection, cemented versus cementless implants, and the use of the lateral approach for patients with valgus deformed knees are analyzed. These results are compared with those of outcome studies of total knee arthroplasty in general. Results from a recent multicenter outcome study evaluate the survivorship results from surgeons around the world who have extensive experience with the low-contact stress implant.
Phasor analysis of multiphoton spectral images distinguishes autofluorescence components of <i>in vivo</i> human skin (2013)

Skin contains many autofluorescent components that can be studied using spectral imaging. We employed a spectral phasor method to analyse two photon excited autofluorescence and second harmonic generation images of in vivo human skin. This method allows segmentation of images based on spectral features. Various structures in the skin could be distinguished, including Stratum Corneum, epidermal cells and dermis. The spectral phasor analysis allowed investigation of their fluorescence composition and identification of signals from NADH, keratin, FAD, melanin, collagen and elastin. Interestingly, two populations of epidermal cells could be distinguished with different melanin content.
Digital Bispectral Analysis and Its Applications to Nonlinear Wave Interactions (1979)

The bispectrum, which is an ensemble average of a product of three spectral components, is shown to be a very useful diagnostic tool in experimental studies of nonlinear wave interactions in random media. In particular, it is shown that the bicoherence spectrum may be used to discriminate between nonlinearly coupled waves and spontaneously excited waves and to measure the fraction of wave power due to the quadratic wave coupling in a self-excited fluctuation spectrum. Practical aspects of digital bispectral analysis techniques, such as estimation and statistical variability of the estimator, are also discussed. Finally, applications of bispectral analysis techniques in the analysis and interpretation of plasma fluctuation data are described.
Resolution and adrenergic activities of the optical isomers of 4‐[1‐(1‐Naphthyl)ethyl]‐1<i>H</i>‐imidazole (1992)

Recently we synthesized a naphthalene analog of medetomidine, 4-[1-(1-naphthyl)ethyl]-1H-imidazole hydrochloride (1), and found it to be highly potent in adrenergic systems. The separation of optical isomers of this naphthalene analog was achieved by using the isomers of tartaric acid. The optical purities of the isomers were determined by HPLC using a chiral column. Using X-ray analysis the (+)-isomer was determined to have the S absolute configuration. It has been reported that the (+)-isomer of medetomidine (2) is the most potent enantiomer on alpha 2-adrenergic receptors. There were both qualitative and quantitative differences in biological activities of the optical isomers of 1 in alpha 1- and alpha 2-adrenergic receptor systems of guinea pig ileum and human platelets. (+)-(S)-1, but not (-)-(R)-1 was a selective agonist of alpha 2-mediated responses in ileum whereas (-)-(R)-1 was more potent than (+)-(S)-1 as an inhibitor of alpha 2-mediated platelet aggregation.
A Review of Technical Advances in Virtual Colonoscopy (2001)

Early detection of polyps has proven to lead to a decrease in incidence of colon cancer. In the past few years, virtual colonoscopy has been developed as a patient-friendly screening technique. The procedure comprises the following steps. First, the patient&apos;s colon is cleansed and transanally inflated with air. Subsequently, a 3D image volume is acquired of the abdomen by CT or MRI. Finally, the bowel surface is extracted and visualized, after which the physician virtually navigates through the colon and examines the surface for abnormalities. This paper describes the progress in research for virtual colonoscopy.
Laser speckle contrast analysis (LASCA): a nonscanning, full-field technique for monitoring capillary blood flow (1996)

A new noninvasive technique for monitoring capillary blood flow has been developed. Based on the phenomenon of time-varying laser speckle, it is a digital version of single-exposure speckle photography. It provides a velocity map of the area of interest in real time without the need for scanning. The results of some initial experiments on volunteers are presented.
Document recommendation in social tagging services (2010)

Social tagging services allow users to annotate various online resources with freely chosen keywords (tags). They not only facilitate the users in finding and organizing online resources, but also provide meaningful collaborative semantic data which can potentially be exploited by recommender systems. Traditional studies on recommender systems focused on user rating data, while recently social tagging data is becoming more and more prevalent. How to perform resource recommendation based on tagging data is an emerging research topic. In this paper we consider the problem of document (e.g. Web pages, research papers) recommendation using purely tagging data. That is, we only have data containing users, tags, documents and the relationships among them. We propose a novel graph-based representation learning algorithm for this purpose. The users, tags and documents are represented in the same semantic space in which two related objects are close to each other. For a given user, we recommend those documents that are sufficiently close to him/her. Experimental results on two data sets crawled from Del.icio.us and CiteULike show that our algorithm can generate promising recommendations and outperforms traditional recommendation algorithms.
Isolation of enhanced eicosapentaenoic acid producing mutants of <i>Nannochloropsis oculata</i> ST‐6 using ethyl methane sulfonate induced mutagenesis techniques and their characterization at mRNA transcript level (2006)

SUMMARY Ethyl methane sulfonate‐induced mutagenesis techniques were used to obtain cerulenin and erythromycin resistant mutant strains, which show a marked increase of 29 and 12%, respectively, in eicosapentaenoic acid content compared to the wild type (WT) strain. The increase in eicosapentaenoic acid content in both strains correlated well with a concomitant increase in 14:0, 16:0, 16:1, 18:0 and 20:4 n − 6 content of fatty acids. However, the linoleic acid content increased only in the cerulenin resistant strain, whereas the erythromycin resistant strain was completely devoid of this fatty acid, providing a contrasting feature for further study. Partial characterization of the mutant strains based on whole cell ultrastructure, growth patterns with or without selection pressure as well as at different temperatures revealed that the mutants were more thermotolerant, and maintained their morphological and genomic fidelity, although minor changes in band patterns were noted with random amplified polymorphic DNA techniques compared to the WT strain. Therefore, the developed new strains could have wider applications as planktonic feed for the mariculture industry. Further characterization of the mutants at the molecular level revealed that steady‐state mRNA transcript levels of chloroplast‐localized Δ12 desaturase and stearoyl‐ACP desaturase genes showed a contrasting transcript profile. However, the level of endoplasmic reticulum‐localized Δ12 desaturase mRNA transcript in either of the mutant strains was almost equal to that of the WT strain. Based on this observation, we postulate that the complete loss of 18:2 fatty acid content in the erythromycin resistant strain might be a result of mutation in the chloroplast‐localized Δ12 desaturase gene and that the increased content of very long chain‐polyunsaturated fatty acids might result from extrachloroplastic lipid desaturase activity, a phenomenon similar to that in the majority of angiosperms.
Application of molecular genetics to prenatal diagnosis and carrier detection in the hemophilias: some limitations (1985)

Prenatal diagnosis and carrier detection in the hemophilias have received much attention in recent years. The error rate in prenatal diagnosis by fetoscopy is less than 1%; fetoscopy is not possible, however, until the second trimester of pregnancy. Carrier detection based on bioassays of plasma has an irreducible error rate (approximately 5%?), because of the “lyonization” phenomenon in heterozygous women, and the final results are always probabilistic. New DNA methods promise to alleviate these difficulties. Prenatal diagnosis can be accomplished in the first trimester. “Lyonization” is bypassed in carrier detection, and the results may sometimes be essentially nonprobabilistic. But the DNA methods have certain limitations of their own which are not widely appreciated. Aside from cost and the necessity to adopt a new technology, there are inherent genetic problems: mothers must be heterozygous for both a disease gene and a marker gene, final results are probabilistic if the marker gene lies outside the disease gene, and multiple marker genes are often in linkage disequilibrium. We have concluded that a clinical unit planning to use the DNA methods must also maintain the conventional methods at a high level of performance.
The Influence of Platelet Collagen Receptor Polymorphisms in Hemostasis and Thrombotic Disease (2002)

Extracellular collagens modulate the rate of platelet activation and thereby markedly influence hemostasis and thrombosis. Platelet receptors for collagens, such as the integrin alpha(2)beta(1), platelet glycoprotein (GP) VI or, indirectly, the GPIb complex, are unexploited targets of pharmacological control, and polymorphisms of these receptors have recently become factored into the genetic risk for thrombosis. Seemingly contradictory findings already exist with regard to the contribution of GPIbalpha and integrin alpha(2) polymorphisms, but these discrepancies will be resolved once there is better standardization of clinical studies. There is already substantial evidence that GPIbalpha VNTR A or B alleles, the GPIbalpha-5C allele, and integrin alpha(2) allele 1 (T(807)) each contribute to increased risk for morbidity in thrombotic disease. However, larger, prospective genetic and epidemiological studies are needed to clarify the role of each of these polymorphisms, the contribution of other platelet receptor polymorphisms, and the synergistic effects of combinations of these factors. In addition, in vitro studies that establish the functional relevance of these polymorphisms will provide sound biological explanations for the results of clinical correlation studies.
The zebrafish : biology (1999)

This is the first in a two-volume, comprehensive treatment of the methodologies used in researching the zebrafish, an emerging vertebrate model system. The text includes discussions on development, genetic methodologies, and model applications.
Propiedades y aplicaciones de la fibra de algarroba (Prosopis pallida L.) (1999)

Mesquite (Prosopis pallida) is one of the main crops growing in arid and semi-arid zones in Latin America. The use of its fruit, mesquite pods, is rather limited in these regions, and it is mainly used as animal forage. However, it is possible to obtain fibre concentrates in a pilot plant process, with a content of insoluble dietary fibre of 50-80% depending on the extraction process applied. Also, seeds are very rich in a galactomannan gum similar to guam or locust bean gums, widely used in the food industry. Both dietary fibre concentrates and mesquite gum have properties (water holding capacity, glucose retardation index and fermentability) similar to those of other insoluble and soluble fibres. Therefore, they are susceptible of use as food ingredients, which would improve the global use of this crop and increase the economic profit derived from its culture.
Topical clonidine for orofacial pain: a pilot study. (1997)

An open-label trial of clonidine, an alpha 2-adrenergic agonist, was prescribed for patients with a clinical diagnosis of oral neuropathic pain or neuralgia involving the oral cavity. Clonidine (0.2 mg/g) was prepared in a cream base and applied four times daily to the site of pain. Seventeen patients were assessed: 10 were diagnosed with neuropathic pain, and 7 with neuralgia. Two of the 17 patients had complaints overlapping both neuropathic and neuralgic pain. In the patients with neuropathic pain, an overall mean reduction in severity of burning of 36% (on a 10-point visual analogue scale) was reported. Half of these patients reported clinical improvement; however, no patients reported complete resolution of symptoms. Of the patients with characteristics of neuralgia, 57% improved; and in those who reported improvement, a mean reduction of approximately 54% was reported. In the 4 patients with neuralgia who responded, a 94% reduction in pain was reported, with complete resolution of pain in 2 patients. This open-label clinical trial suggests that topical clonidine may be effective in the management of some patients with oral neuralgia-like pain, but may have a more limited effect in those patients with oral neuropathic pain. Besides type of pain, no other variables predicted which of the patients would achieve pain reduction with topical clonidine. Although confirmation of clinical efficacy requires double-blind clinical studies, this initial trial suggests that further study is warranted.
The man behind the syndrome. P. Beighton and G. Beighton. 275 × 195 mm. Pp. 240. Illustrated. 1986. London: Springer Verlag. £19.90 (1987)

Journal Article The man behind the syndrome. P. Beighton and G. Beighton. 275 × 195 mm. Pp. 240. Illustrated. 1986. London: Springer Verlag. £19.90 Get access The Man Behind the Syndrome. P Beighton and G Beighton. 275 × 195 mm. Pp. 240. Illustrated. 1986. London: Springer Verlag. £19.90. A E Young A E Young Search for other works by this author on: Oxford Academic Google Scholar British Journal of Surgery, Volume 74, Issue 1, January 1987, Page 77, https://doi.org/10.1002/bjs.1800740143 Published: 08 December 2005
NMR Imaging of the Liver in Two Cases of Iron Overload (1984)

Two cases of iron overload in the liver are presented--one of hemochromatosis with associated hepatoma and one of hemosiderosis with probable androgen dependent multicentric hepatic adenomas. Nuclear magnetic resonance scans displayed the tumours as well as low liver parenchymal signal intensity on the saturation-recovery, inversion-recovery, and spin-echo pulse sequences probably as a result of decreased tissue T1 and T2.
New Theoretical Results on Channelized Hotelling Observer Performance Estimation With Known Difference of Class Means (2013)

Task-based assessments of image quality constitute a rigorous, principled approach to the evaluation of imaging system performance. To conduct such assessments, it has been recognized that mathematical model observers are very useful, particularly for purposes of imaging system development and optimization. One type of model observer that has been widely applied in the medical imaging community is the channelized Hotelling observer (CHO). Since estimates of CHO performance typically include statistical variability, it is important to control and limit this variability to maximize the statistical power of image-quality studies. In a previous paper, we demonstrated that by including prior knowledge of the image class means, a large decrease in the bias and variance of CHO performance estimates can be realized. The purpose of the present work is to present refinements and extensions of the estimation theory given in our previous paper, which was limited to point estimation with equal numbers of images from each class. Specifically, we present and characterize minimum-variance unbiased point estimators for observer signal-to-noise ratio (SNR) that allow for unequal numbers of lesion-absent and lesion-present images. Building on this SNR point estimation theory, we then show that confidence intervals with exactly-known coverage probabilities can be constructed for commonly-used CHO performance measures. Moreover, we propose simple, approximate confidence intervals for CHO performance, and we show that they are well-behaved in most scenarios of interest.
Misfit and threading dislocations in HgCdTe epitaxy (1986)

A new theory relating substrate, misfit, and threading dislocations is presented for abrupt and graded heterojunctions based on the assumption of complete local strain relief. We have for the first time been able to treat two- and three-dimensional misfit dislocation structures in a unified way and experimentally verify the distinction in epitaxial HgCdTe. We confirm earlier findings that the areal density of interfacial dislocations nA in a cross section of the interface is proportional to the lattice constant gradient. If the interface width w is narrower than a theoretically predicted critical value w0, the misfit structure becomes two-dimensional and a linear dislocation density nL applies. The maximum of nA (attained at w=w0) is equal to n2L. Another new result of the theory is that the average misfit segment length is inversely proportional to the substrate dislocation density. The threading dislocation density is predicted to be low when the average segment length is comparable to the substrate lateral dimensions. For cases of low epitaxial dislocation content, the calculated substrate densities corresponding to such segments compare favorably with measured values. Compositional profiles and misfit dislocation densities were obtained on the same angle lapped HgCdTe epilayers by visible reflection spectroscopy and preferential etching, respectively. The former monitored the E1 interband transition as a function of position with a microspectrophotometer while the latter employed a modified Polisar No. 2 etchant. Both linear and areal distributions were observed and their occurrence was correctly predicted by the theory.