gebhart/patrepeval huggingface dataset:
Antimicrobial activity of MHC class I-restricted CD8+ T cells in human tuberculosis (2000)

Studies of mouse models of tuberculosis (TB) infection have indicated a central role for MHC class I-restricted CD8+ T cells in protective immunity. To define antigens and epitopes of Mycobacterium tuberculosis (MTB) proteins that are presented by infected cells to CD8+ T cells, we screened 40 MTB proteins for HLA class I A*0201-binding motifs. Peptides that bound with high affinity to purified HLA molecules were subsequently analyzed for recognition by CD8+ cytotoxic T lymphocytes. We identified three epitopes recognized by CD8+ T cells from patients recovering from TB infection. Those three epitopes were derived from three different antigens: thymidylate synthase (ThyA(30-38)), RNA polymerase beta-subunit (RpoB(127-135)), and a putative phosphate transport system permease protein A-1 (PstA1(75-83)). In addition, CD8+ T cell lines specific for three peptides (ThyA(30-38), PstA1(75-83), and 85B(15-23)) were generated from peripheral blood mononuclear cells of normal HLA-A*0201 donors. These CD8+ T cell lines specifically recognized MTB-infected macrophages, as demonstrated by production of IFN-gamma and lysis of the infected target cells. Finally, CD8+ cytotoxic T lymphocytes reduced the viability of the intracellular MTB, providing evidence that CD8+ T cell recognition of MHC class I-restricted epitopes of these MTB antigens can contribute to effective immunity against the pathogen.
Assessing Breast Cancer Margins Ex Vivo Using Aqueous Quantum-Dot-Molecular Probes (2012)

Positive margins have been a critical issue that hinders the success of breast- conserving surgery. The incidence of positive margins is estimated to range from 20% to as high as 60%. Currently, there is no effective intraoperative method for margin assessment. It would be desirable if there is a rapid and reliable breast cancer margin assessment tool in the operating room so that further surgery can be continued if necessary to reduce re-excision rate. In this study, we seek to develop a sensitive and specific molecular probe to help surgeons assess if the surgical margin is clean. The molecular probe consists of the unique aqueous quantum dots developed in our laboratory conjugated with antibodies specific to breast cancer markers such as Tn-antigen. Excised tumors from tumor-bearing nude mice were used to demonstrate the method. AQD-Tn mAb probe proved to be sensitive and specific to identify cancer area quantitatively without being affected by the heterogeneity of the tissue. The integrity of the surgical specimen was not affected by the AQD treatment. Furthermore, AQD-Tn mAb method could determine margin status within 30 minutes of tumor excision, indicating its potential as an accurate intraoperative margin assessment method.
Dehydroxylation and Silanization of the Surfaces of β-Cristobalite Silica:  An ab Initio Simulation (2001)

Dehydroxylation and silanization processes on the silica surface are studied by ab initio molecular dynamics. The (100) and (111) surfaces of β-cristobalite are used as two possible models of the hydroxylated amorphous surface. The activation energy and latent heat for the dehydroxylation reactions of the (100) surface computed by constrained ab initio molecular dynamics are in reasonable agreement with experimental data on the amorphous surface. Adhesion reactions of silanes are simulated aiming at elucidating the binding mechanism of organosilanes used for instance as silica−polymer coupling agents. The simulation have provided insights on the occurrence of multiple silica−silane bonds and on the role of hydrolization of silane by physisorbed water in the adhesion on the wet surface.
MIXTURES OF EXPONENTIAL DISTRIBUTIONS TO DESCRIBE THE DISTRIBUTION OF POISSON MEANS IN ESTIMATING THE NUMBER OF UNOBSERVED CLASSES (2006)

In many fields of study scientists are interested in estimating the number of unobserved classes. A biologist may want to find the number of rare species of an animal population in order to conserve, manage, and monitor biodiversity; a library manager may want to know how many non-circulating items are present in a library system; or a clinical investigator may want to determine the number of unseen disease occurrences. A traditional way of estimating an unknown number of classes is by using a negative binomial model (Fisher, Corbet, and Williams 1943). The negative binomial model is based on assuming that the numbers of individuals from each class are independent Poisson samples, and that the means of these Poisson random variables follow a Gamma distribution. This thesis proposes a parametric model where the law of the mean frequency of classes is a finite mixture of exponential distributions. The proposed model has the following advantages: model simplicity, efficient computation using the EM algorithm, and a straightforward interpretation of the fitted model. Also,
First direct proof of internal conversion between bound states (2000)

We present direct evidence for the process of internal conversion between bound atomic states (BIC) when the binding energy of the converted electron becomes larger than the nuclear transition energy. This process has been proposed as an explanation of the measured, unexpectedly short lifetime of the first excited state of ${}^{125}\mathrm{Te}$ with charge state larger than ${44}^{+}.$ We have detected the ${K}_{\ensuremath{\alpha}}$ x rays emitted in flight which follow the filling of the K-shell vacancy created by the bound internal conversion process, together with $\ensuremath{\gamma}$ rays from Te ions in charge states ranging between ${44}^{+}$ and ${48}^{+}.$ For ${\mathrm{Te}}^{45+}$ and ${\mathrm{Te}}^{46+},$ the comparison of the x-ray to $\ensuremath{\gamma}$-ray ratios with the theoretical calculations of the internal conversion coefficients including decay to bound atomic states, assuming Te ions in their ground electronic state, show poor agreement. The agreement becomes good if account is taken of BIC decay of excited initial states with different occupancies of the ${2p}_{1/2}$ and ${2p}_{3/2}$ subshells. In this situation, the half-life becomes sensitive to the precise initial state and simple specification of the charge state alone is no longer appropriate.
Polycationic Sulfonamides for the Sequestration of Endotoxin (2007)

Lipopolysaccharides (LPS) play a key role in the pathogenesis of septic shock, a major cause of mortality in the critically ill patient. We had previously shown that monoacylated polyamine compounds specifically bind to and neutralize the activity of LPS with high in vitro potency and afford complete protection in a murine model of endotoxic shock. Fatty acid amides of polyamines may be rapidly cleared from systemic circulation due to their susceptibility to nonspecific serum amidases and, thus, would be predicted to have a short duration of action. In a systematic effort to increase the likelihood of better bioavailability properties together with structural modifications that may result in gains in activity, we now report structure-activity relationships pertaining to endotoxin-binding and -neutralizing activities of homologated polyamine sulfonamides.
Collision detection of cylindrical rigid bodies for motion planning (2006)

This paper presents a novel methodology for detecting collisions of cylindrically shaped rigid bodies moving in three dimensions. This algorithm uses line geometry and dual number algebra to exploit the geometry of right circular cylindrical objects to facilitate the detection of collisions. First, the rigid bodies are modelled with infinite cylinders and an efficient necessary condition for collision is evaluated. If the necessary condition is not satisfied then the two bodies do not collide. If the necessary condition is satisfied then a collision between the bodies may occur and we proceed to the next stage of the algorithm. In the second stage the bodies are modelled with finite cylinders and a definitive necessary and sufficient collision detection algorithm is employed. The result is a straight-forward and efficient means of detecting collisions of cylindrically shaped bodies moving in three dimensions. This methodology has applications in robot motion planning, spatial mechanism design, and workspace analysis of parallel kinematic machines such as Stewart-Gough platforms. A case study of motion planning for an industrial robot is included
Metamaterial absorbers for 24-GHz automotive radar applications (2017)

Absorbers for automotive radar applications must satisfy some requirements such as a wide incident angle, polarization insensitivity, flexibility, low-profile structure, and low cost. To satisfy these requirements, we propose two types of metamaterial absorber for a 24-GHz automotive radar system. The first absorber is composed of 60 × 60 equally spaced unit cells with an electric LC resonator, a substrate, and a ground sheet. It has a peak absorptivity of 99.7% at 24.1 GHz and total full-width at half-maximum (FWHM) of 1.0 GHz. To increase the FWHM, a bandwidth-enhanced absorber was designed by arranging the unit cells into an optimized offset sub-array structure. The proposed absorber exhibited peaks at 24.1 and 25.2 GHz with absorptivities of 97.8 and 74.5%, respectively. The FWHM improved by 900 MHz compared with that of an equally spaced absorber. The measured results of the fabricated absorbers agreed well with the simulated ones.
Studies on Production of Lipids in Fungi. II. (1981)

The lipid productivities of six species (11 strains) of fungi of the order Mucorales in the class Zygomycetes obtained from Institute for Fermentation, Osaka, were investigated. The total lipid extracts of fungus cells grown by stationary culture method were separated to neutral lipid and polar lipid fractions by silicic acid column chromatography, and the amounts of both fractions were determined. Fatty acid compositions of the lipids were analyzed by gas liquid chromatography. Futhermore, the compositions of both lipid fraction were quantitatively determined by thin layer chromatographic analysis. The total lipid amount of Mortierella isabellina IFO No. 7884 was 86.1% of the dry fungus cells cultivated at 20°C.
Chiral Ammonium Aryloxides: Efficient Multipurpose Basic Organocatalysts (2015)

Abstract This review summarizes the recent developments in chiral quaternary ammonium aryloxides as flexible organocatalysts that are able to act as both a Brønsted and Lewis base. A particular class of ammonium aryloxides, namely betaines, has emerged as an efficient class of catalysts. The performance of betaines stems mainly from the intramolecular nature of these ammonium ion pairs, leading to highly reactive catalytic species with a high level of organization. The above‐mentioned catalysts have been successfully applied to a wide range of asymmetric chemical transformations, including Mukaiyama aldol reactions, tandem Michael addition/lactonization sequences, trifluoromethylation reactions, aza‐Henry reactions, silyl enolates protonation reactions, and Steglich‐type rearrangements, with a high level of enantioselectivity.
Making It all Better?: 'Sicko' (2007)

In his series of increasingly successful films over the past decade, director Mike Moore has brought moral indignation at social injustice into the mainstream, taking simply phrased potshots at various problems. 'Sicko' represents a new type of documentary which is more opinion piece than academic analysis.
3D steady‐state diffusion‐weighted imaging with trajectory using radially batched internal navigator echoes (TURBINE) (2009)

While most diffusion-weighted imaging (DWI) is acquired using single-shot diffusion-weighted spin-echo echo-planar imaging, steady-state DWI is an alternative method with the potential to achieve higher-resolution images with less distortion. Steady-state DWI is, however, best suited to a segmented three-dimensional acquisition and thus requires three-dimensional navigation to fully correct for motion artifacts. In this paper, a method for three-dimensional motion-corrected steady-state DWI is presented. The method uses a unique acquisition and reconstruction scheme named trajectory using radially batched internal navigator echoes (TURBINE). Steady-state DWI with TURBINE uses slab-selection and a short echo-planar imaging (EPI) readout each pulse repetition time. Successive EPI readouts are rotated about the phase-encode axis. For image reconstruction, batches of cardiac-synchronized readouts are used to form three-dimensional navigators from a fully sampled central k-space cylinder. In vivo steady-state DWI with TURBINE is demonstrated in human brain. Motion artifacts are corrected using refocusing reconstruction and TURBINE images prove less distorted compared to two-dimensional single-shot diffusion-weighted-spin-EPI.
High-throughput realization of an infrared selective absorber/emitter by DUV microsphere projection lithography (2015)

In this paper, we present a low-cost and high-throughput nanofabrication method to realize metasurfaces that have selective absorption/emission in the mid-infrared region of the electromagnetic spectrum. We have developed DUV projection lithography to produce arbitrary patterns with sub-80 nm feature sizes. As examples of practical applications, we experimentally demonstrate structures with single and double spectral absorption/emission features, and in close agreement with numerical simulation. The fundamental mechanism of perfect absorption is discussed as well. Selective infrared absorbers/emitters are critical elements in realizing efficient thermophotovoltaic cells and high-performance biosensors.
A Study of Three-Dimensional Reconstruction Using High Overlap Aerial Photograph Sequence (2011)

The unmanned aerial vehicle (UAV), as a low-cost airborne instrument platform, enjoys a lot of advantages such as flexible, high resolution and so on. Currently, UAV is widely used in resource management and environmental surveillance as it can obtain a sequence of high overlap images by continuously shooting on specified areas, of which the overlap is up to 60% along the heading, and is up to 30% in the side. Stereo pair refers to the same area in two different images which are taken from different angles. Actually, the overlap area obtained from aerial photograph sequence contains a lot of stereo pairs, which can be used to the 3D reconstruction. In this paper, three-dimensional reconstruction using intersection of the overlap area obtained by UAV image sequence is systematically studied in theory. First, pixel-level matching algorithm of overlap area is carried. Second, coordinates of pixels in overlap area is calculated with condition equations. Third, applying the separation over point cloud constituted by matched pixels; in the end, the three dimensional algorithm of terrain and its features is studied.
Distributed Location Databases for Tracking Highly Mobile Objects (2001)

In current distributed systems, the notion of mobility is emerging in many forms and applications. Increasingly many users are not tied to a fixed access point but instead use wireless communications or dial-up services to access data independent of their physical location. Furthermore, mobile software, a popular example being mobile agents, is frequently used as a new form of building distributed network-centric applications. Tracking mobile objects, i.e. identifying their current location, is central to such settings. In this paper, we exploit the use of hierarchical distributed location databases, where each database site covers a specific geographical region and contains location information about all objects residing in it. For highly mobile objects, a scheme based on forwarding pointers enhanced with auxiliary caching techniques is presented, to reduce the cost of the overall network and database traffic generated by frequent location updates. The scheme is extended to support concurrency and failure recovery. Performance is demonstrated through a number of simulation experiments for a range of call to mobility ratios and for a variety of moving and calling behaviors.
<i>Glycine soja</i> PI 468916 SCN Resistance Loci's Associated Effects on Soybean Seed Yield and Other Agronomic Traits (2006)

The soybean cyst nematode (SCN, Heterodera glycines Riggs and Niblack) is the most important soybean [ Glycine max (L.) Merr.] pathogen in the USA and its control relies on genetic resistance. When resistance genes from exotic sources are transferred into elite cultivars, deleterious alleles are frequently transferred with resistance through genetic linkages. Two SCN resistance loci have been identified in G. soja Sieb. and Zucc. PI 468916, and the effect these loci have on yield and other agronomic traits is not known. The objective of this study was to determine the effect of each G. soja SCN resistance gene on yield and other agronomic traits in elite soybean backgrounds. These effects were tested in two populations each segregating for SCN resistance derived from G. soja , with one population also segregating for the SCN resistance loci, rhg 1, derived from G. max PI 88788. Each population was analyzed for genetic markers linked to the SCN resistance loci and field tested in multiple environments with low to high SCN infestations. The G. soja and rhg1 SCN resistance alleles either had no effect or significantly ( P < 0.05) enhanced yield compared with the susceptible alleles. The SCN resistance alleles were also associated with increasing days to maturity, plant height, and lodging scores. Deployment of the G. soja SCN resistance loci will increase the genetic diversity for SCN resistance and will provide breeders with an alternative source of SCN resistance that is not associated with reduced yield.
Growth and Sporulation of <i>Bacillus subtilis</i> Mutants Blocked in the Pyruvate Dehydrogenase Complex (1969)

Two "ACE" mutants of Bacillus subtilis which require acetate for growth on glucose minimal medium have been isolated. They do not grow with acetoin, 2,3-butanediol, fatty acids, isoleucine, lipoic acid, malic acid, pyruvic acid, succinic acid, thiamine, or valine, but respond somewhat to glutamate or citrate. The mutants lack the activity of the pyruvate dehydrogenase complex; they excrete pyruvate and later acetoin. They grow in nutrient sporulation medium (NSMP) to one-half the normal turbidity and do not sporulate subsequently. When acetate is added to NSMP (at the optimal concentration of 0.07 m), the ACE mutants grow to the normal turbidity and then sporulate normally. Growth but not sporulation is restored in NSMP upon addition of 2,3-butanediol, citrate, glucose, glutamate, glycerol, or ribose, but not upon addition of acetoin, malate, oxaloacetate, pyruvate, and several other compounds. After growth in NSMP has stopped, the mutants incorporate uracil only at a very low rate, which can be increased by the addition of acetate, citrate, or glutamate. Furthermore, the metabolism of acetoin is prevented after growth has stopped but can be restored by the addition of acetate. All these results can be explained by a lack of reduced nicotinamide adenine dinucleotide (NADH) resulting from the deficiency in acetylcoenzyme A. In fact, after growth of the ACE mutants had stopped, the NADH concentration was at the borderline of measurability, whereas it increased significantly upon addition of glucose. The growing standard strain contains, at the same bacterial turbidity, at least 20 times more NADH (230 pmole/optical density unit at 600 nm) than the nongrowing ACE mutants. The isolated spores, obtained after growth in NSMP plus acetate, can be initiated to germinate in the presence of either l-alanine or the combination of l-asparagine, fructose, glucose, and potassium; addition of acetate is not required and has no effect.
Serum Advanced Glycosylation End Products: A New Class of Uremic Toxins? (1994)

Irreversible advanced glycosylation end products (AGE) are shown to induce tissue damage by a variety of chemical and cellular mechanisms. When administered to normal animals, AGE-modified albumin reacts covalently with tissue proteins to produce complex vascular alterations closely resembling diabetic vasculopathy. In humans, the clearance of serum with renal insufficiency and is severely impaired in diabetic patients with end-stage renal disease (ESRD). The renal clearance of AGE-peptides was estimated at 0.72 +/- 0.23 ml/min for normal subjects, and 0.61 +/- 0.2 ml/min for diabetics with normal glomerular filtration rate (GFR) (p value NS). After comparing different modes of treatment of patients with ESRD, we noted that, although conventional hemodialysis is ineffective, high-flux dialysis (HF) markedly reduces AGE levels only to return to near-pretreatment levels within 3 h. In chronic ambulatory peritoneal dialysis (CAPD)-treated patients, serum AGE are similar to those achieved by hemodialysis. In contrast, AGE levels in diabetics with renal transplantation decreased 8 h after surgery and remained within the normal range over the long term. Human serum AGE peptides (M.W. between 2,000 and 6,000) are shown to retain strong cross-linking activity with collagen in vitro. AGE peptides in human circulation may represent a thus far unrecognized class of reactive and potentially toxic substances which can exacerbate extrarenal vascular pathology, through their covalent attachment onto matrix proteins.
Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils (2001)

The capacity of 12 soils to degrade atrazine was studied in laboratory incubations using radiolabelled atrazine. Eight soils showed enhanced degradation of this compound. Twenty-five bacterial strains able to degrade atrazine were isolated by an enrichment method from 10 of these soils. These soils were chosen for their wide range of physico-chemical characteristics. Their history of treatment with atrazine was also variable. The genetic diversity of atrazine degraders was determined by amplified ribosomal restriction analysis (ARDRA) of the 16S rDNA gene with three restriction endonucleases. The 25 bacterial strains were grouped into five ARDRA types. By sequencing and aligning the 16S rDNA genes, the isolates were shown to belong to the Gram-negative species Chelatobacter heintzii, Aminobacter aminovorans, Stenotrophomonas maltophilia and to the Gram-positive genus Arthrobacter crystallopoietes. These species were not described previously as being capable of atrazine degradation. Most Gram-negative bacteria could mineralise (14)C ring labelled atrazine and carried the atzA, atzB, atzC and trzD genes. Gram-positive strains could convert atrazine to cyanuric acid and carried only the atzB and atzC genes. In this study, we describe the atrazine degradation capacities and corresponding genes in bacterial species that were not known as atrazine degraders. We report for the first time the occurrence of the trzD gene in these atrazine-mineralising bacteria and we demonstrate the potential use of colony hybridisation to isolate bacteria involved in atrazine degradation.
Future Operating Concepts for Maritime Geospatial Forces and Defending Australia in the Australia Pacific Century (2009)

The key impact of the new Defense White Paper 2009 in Australia on future operating concepts for maritime geospatial forces and defending Australia in the Australia Pacific century is discussed. The Offshore Combatant Vessel (OCV) concept delivered through the Defense White Paper poses several challenges for the future Hydrographic Survey Force (HSF).