gebhart/patrepeval huggingface dataset:
Review of fast monte carlo codes for dose calculation in radiation therapy treatment planning. (2011)

An important requirement in radiation therapy is a fast and accurate treatment planning system. This system, using computed tomography (CT) data, direction, and characteristics of the beam, calculates the dose at all points of the patient's volume. The two main factors in treatment planning system are accuracy and speed. According to these factors, various generations of treatment planning systems are developed. This article is a review of the Fast Monte Carlo treatment planning algorithms, which are accurate and fast at the same time. The Monte Carlo techniques are based on the transport of each individual particle (e.g., photon or electron) in the tissue. The transport of the particle is done using the physics of the interaction of the particles with matter. Other techniques transport the particles as a group. For a typical dose calculation in radiation therapy the code has to transport several millions particles, which take a few hours, therefore, the Monte Carlo techniques are accurate, but slow for clinical use. In recent years, with the development of the 'fast' Monte Carlo systems, one is able to perform dose calculation in a reasonable time for clinical use. The acceptable time for dose calculation is in the range of one minute. There is currently a growing interest in the fast Monte Carlo treatment planning systems and there are many commercial treatment planning systems that perform dose calculation in radiation therapy based on the Monte Carlo technique.
Cloning and expression of cyclosporin A- and FK506-sensitive nuclear factor of activated T-cells: NF45 and NF90. (1994)

Nuclear Factor of Activated T-cells (NF-AT) is a crucial transcription factor required for T-cell expression of interleukin 2. Purified NF-AT contains 45-kDa and 90-kDa subunits (Corthésy, B., and Kao, P. N. (1994) J. Biol. Chem. 269, 20682-20690). Partial internal amino acid sequences derived from each subunit indicate that these proteins are novel. The amino acid sequences were used to clone the cDNAs encoding each subunit. The cDNAs predict proteins of novel structures: NF45 has limited similarity to prokaryotic transcription factor sigma-54 and to human DNA topoisomerase II; NF90 has limited similarity to Drosophila Staufen in a domain predicted to bind double-stranded RNA. RNA encoding NF45 and NF90 exists in nonstimulated Jurkat T-cells and in all other cell types examined (HeLa, HepG2, K562). Immunofluorescence microscopy was used to demonstrate that both proteins are located in the nucleus of Jurkat T-cells. Clones NF45 and NF90 with a polyhistidine fusion tag were transiently expressed and processed in the native environment of Jurkat T-cells. Histidine-tagged NF45 and NF90 proteins, affinity-purified on nickel chelate columns, encode a NF-AT DNA-binding activity that is enhanced following T-cell stimulation, and this enhancement is blocked when T-cells are stimulated in the presence of cyclosporin A or FK506.
Cubic illumination (1997)

Cubic illumination specifies the spatial distribution of illumination about a point in terms of the illuminances on six faces of a small cube centred at the point. This form of specification is proposed as the basis of a system of applied photometry. Its advantage is that once the cubic illumination has been determined, whether by measurement or calculation, a range of indices of lighting may be derived quite readily. Analysis of the cubic illumination specification comprises defining two components of the illumination solid; the vector component defined by the illumination vector, and the symmetric component, which remains after subtraction of the vector component. The planar illuminance for any orientation, and the average illuminances of regular solids, such as a cylinder or sphere, are calculated by summing the contributions of these two components. By specifying a direction of view towards the point, indices which relate to how lighting might affect the appearance of a three-dimensional object located at the point may be calculated, and by specifying a direction of view from the point, the eye illuminance, or the illuminance of a plane normal to the direction of view, may be derived. The paper gives procedures for calculating, measuring and analysing cubic illumination, and reviews applications for the derived illumination metrics.
Dose-Dependent Effects of the Renin Inhibitor Zankiren HCl After a Single Oral Dose in Mildly Sodium-Depleted Normotensive Subjects (1995)

Results from this study demonstrate for the first time that oral administration of a renin inhibitor can dose-dependently decrease blood pressure and circulating components of the RAS in normotensive volunteers as a result of documented absorption.
Multifunction InGaAs detector with on-chip signal processing (2013)

Advanced electro-optical systems are designed towards a more compact, low power, and low cost solution with respect to traditional systems. Integration of several components or functionalities, such as infrared imager, laser designator, laser range finder (LRF), into one multi-function detector serves this trend. SNIR Read-Out Integrated Circuit (ROIC) incorporates this high level of signal processing and with relatively low power consumption. In this paper we present measurement results from a Focal Plane Array (FPA) where the SNIR ROIC is Flip-Chip bonded to a 15µm pitch VGA InGaAs detector array. The FPA is integrated into a metallic vacuum sealed package. We present InGaAs arrays with dark current density below 1.5 nA/cm<sup>2</sup> at 280K (typically 1fA), Quantum Efficiency higher than 80% at 1550 nm and operability better than 99.5%. The metallic package is integrated with a low power proximity electronics which delivers Camera Link output. The overall power dissipation is less than 1W, not including Thermal-Electric Cooling (TEC), which is required in some applications. The various active and passive operation modes of this detector will be reviewed. Specifically, we concentrate on the "high gain" mode with low readout noise for Low Light Level imaging application. Another promising feature is the Asynchronous Laser Pulse Detection (ALPD) with remarkably low detection thresholds.
The T‐cell response to myelin basic protein in familial multiple sclerosis: Diversity of fine specificity, restricting elements, and T‐cell receptor usage (1993)

Indirect evidence suggests that an autoimmune response to myelin basic protein (MBP) may be involved in the pathogenesis of multiple sclerosis (MS). In MS, several reports have suggested that restricted T-cell populations respond to MPB, as in inbred rodents with the MS disease model experimental allergic encephalomyelitis. In experimental allergic encephalomyelitis, the T-cell repertoire to MBP varies between strains, and in MS it is likely that the response to MBP is also best defined under conditions where genetic differences between subjects are controlled. In this report, the fine specificity of the T-cell response to MBP was assessed in three families, each with multiple individuals affected with MS. We found that (1) comparable frequencies of MBP-reactive T-cell lines were obtained from peripheral blood of MS patients and their healthy siblings. Human leukocyte antigen (HLA) identical sibling pairs discordant for MS had similar frequencies of MBP-reactive T-cell lines. (2) A broad spectrum of MBP epitopes was recognized by T-cell lines from all individuals studied. Within a family, the fine specificity of MBP recognition showed little or no overlap between individuals, even between HLA identical siblings. (3) Recognition of MBP epitopes occurred in the context of different HLA class II alleles. At least four DR alleles each served as restricting elements for recognition of P82-101 or the carboxy terminal region of MBP, two regions thought to be important in the human T-cell response to the molecule. No relationship between the use of a particular DR allele and a response to a particular region of MBP could be established.(ABSTRACT TRUNCATED AT 250 WORDS)
Introduction to the Cell Broadband Engine Architecture (2007)

This paper provides an overview of the Cell Broadband Engine™ Architecture (CBEA). The CBEA defines a revolutionary extension to a more conventional processor organization and serves as the basis for the development of microprocessors targeted at the computer entertainment, multimedia, and real-time market segments. In this paper, the organization of the architecture is described, as well as the instruction set, commands, and facilities defined in the architecture. In many cases, the motivation for these facilities is explained and examples are provided to illustrate their intended use. In addition, this paper introduces the Software Development Kit and the software standards for a CBEA-compliant processor.
RoboLeader for reconnaissance by a team of robotic vehicles (2010)

Autonomous teams of robotic vehicles are gaining significant importance in military applications in the realm of reconnaissance and the execution of vital tasks. As teams of robotic vehicles grow in size and mission complexity, ever increasing burden is placed on the human operators charged with overseeing such operations. It is imperative that, in order to increase future mission complexity and success, a certain amount of work load be removed from the operator and a greater level of autonomy be given to the unmanned systems. A modular architecture has been developed which allows for components to be added on to the RoboLeader utility providing expanded capability of the design with little modification to existing architecture. Currently, the RoboLeader utility assesses intelligence on ground conditions and provides the human operator with alternate path plans for a series of situations which require difference path solutions.
Identifying and treating patients with suboptimal responses (2004)

Multiple sclerosis (MS) is an immune-mediated neurologic disease in which acute inflammatory events early in the disease course contribute to subsequent neurologic disability. The early relapsing inflammatory phase is followed by a progressive degenerative phase in which the frequency of acute inflammatory attacks diminishes but progressive loss of neurologic function continues. Current immune therapies are most effective in suppressing the acute inflammatory events that characterize the earlier stages of disease. Optimal suppression of these inflammatory events is likely to have the best potential for delaying or preventing loss of axons and decline in neurologic function. In view of these considerations, and because MS is a heterogeneous disease and response to disease-modifying agents (DMA) varies across individuals, it is important to identify suboptimal responders as early as possible to allow therapeutic modification while the opportunity to avert future loss of function remains. At present, no criteria for identifying suboptimal responders have been validated. In January 2004, a group of neurologists from 16 MS centers in the United States met to develop a consensus on criteria for defining suboptimal response for use in compelling clinical situations and to prompt clinical studies to validate the efficacy of these criteria. Consensus criteria included relapse rates of either 1/year or unchanged from pretreatment rates, incomplete recovery from multiple attacks, evolution of polyregional neurologic involvement, recurrent brainstem or spinal cord lesions, and cumulative loss of neurologic function sufficient to disrupt daily activities. The panel then considered the use of mitoxantrone for patients with worsening MS and a suboptimal response to DMA therapy.
Novel Biomedical Imaging Systems (2008)

The overall purpose of the dissertation is to design and develop novel optical imaging systems that require minimal or no mechanical scanning to reduce the acquisition time for extracting image data from biological tissue samples. Two imaging modalities have been focused upon: a parallel optical coherence tomography (POCT) system and a volume holographic imaging system (VHIS). Optical coherence tomography (OCT) is a coherent imaging technique, which shows great promise in biomedical applications. A POCT system is a novel technology that replaces mechanically transverse scanning in the lateral direction with electronic scanning. This will reduce the time required to acquire image data. In this system an array with multiple reduced diameter (15μm) single mode fibers (SMFs) is required to obtain an image in the transverse direction. Each fiber in the array is configured in an interferometer and is used to image one pixel in the transverse direction. A VHIS is based on volume holographic gratings acting as Bragg filters in conjunction with conventional optical imaging components to form a spatial-spectral imaging system. The high angular selectivity of the VHIS can be used to obtain two-dimensional image information from objects without the need for mechanical scanning. In addition, the high wavelength selectivity of the VHIS can provide spectral information of a specific area of the object that is being observed. Multiple sections of the object are projected using multiplexed holographic gratings in the same volume of the Phenanthrenquinone- (PQ-) doped Poly (methyl methacrylate) (PMMA) recording material.
Potential Antiviral and Antituberculous Compounds. II. N‐(2‐dibenzothiophenyl)‐N′‐alkyl and N′‐aryl thioureas, N‐(2‐dibenzothiophenyl) and N‐(2‐dibenzothiophenyl‐5‐dioxide) amidines (1967)

Abstract Seventeen new condensation products of 2‐amino dibenzothiophene with several alkyl and aryl isothiocyanates and eight new substituted amidines with 2‐dibenzothiophenyl and 2‐dibenzothiophenyl‐5‐dioxide substituents have been prepared with a view to study their antiviral and tuberculostatic activity.
Efficient collective swimming by harnessing vortices through deep reinforcement learning (2018)

Fish in schooling formations navigate complex flow-fields replete with mechanical energy in the vortex wakes of their companions. Their schooling behaviour has been associated with evolutionary advantages including collective energy savings. How fish harvest energy from their complex fluid environment and the underlying physical mechanisms governing energy-extraction during collective swimming, is still unknown. Here we show that fish can improve their sustained propulsive efficiency by actively following, and judiciously intercepting, vortices in the wake of other swimmers. This swimming strategy leads to collective energy-savings and is revealed through the first ever combination of deep reinforcement learning with high-fidelity flow simulations. We find that a `smart-swimmer' can adapt its position and body deformation to synchronise with the momentum of the oncoming vortices, improving its average swimming-efficiency at no cost to the leader. The results show that fish may harvest energy deposited in vortices produced by their peers, and support the conjecture that swimming in formation is energetically advantageous. Moreover, this study demonstrates that deep reinforcement learning can produce navigation algorithms for complex flow-fields, with promising implications for energy savings in autonomous robotic swarms.
Bio‐Orthogonal Polymer Coatings for Co‐Presentation of Biomolecules (2012)

Controlled presentation of biomolecules on synthetic substrates is an important aspect for biomaterials development. If the immobilization of multiple biomolecules is required, highly efficient orthogonal surface chemistries are needed to ensure the precision of the immobilization. In this communication, chemical vapor deposition (CVD) copolymerization is used to fabricate polymer coatings with controlled ratio of alkyne and pentafluorophenyl ester (Pfp-ester) groups. Cyclic argine-glycine-aspartic acid (cRGD) adhesion peptide and epidermal growth factor (EGF) are immobilized through alkyne-azide cycloaddtion ("click" chemistry) and active ester-amine reaction, respectively. Cell studies with human umbilical vein endothelial cells (HUVEC) and A431 cell lines demonstrate the biological activity of the coimmobilized biomolecules.
Driver mutations (2010)

Commentary to: Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM)Hannah Carter, Josue Samayoa, Ralph H. Hruban and Rachel Karchin
ChemInform Abstract: 4‐(INDOLYL‐3)‐1‐(BENZIMIDAZOLONYLALKYL)PIPERIDINES, A NOVEL GROUP OF POTENTIAL ANTIALLERGY COMPOUNDS (1985)

A group of indolyl-benzimidazolone-piperidines is described and the structure-activity with reference to the passive cutaneous anaphylaxis (PCA) in rats is discussed. Compound 7b, 4-(indolyl-3)-1-(benzimidazolonyl-propyl)-piperidine, which has the highest potency in this test, was studied in more detail with regard to antihistaminic and secretory cell stabilization properties.
Importance-Driven Feature Enhancement in Volume Visualization (2005)

This paper presents importance-driven feature enhancement as a technique for the automatic generation of cut-away and ghosted views out of volumetric data. The presented focus+context approach removes or suppresses less important parts of a scene to reveal more important underlying information. However, less important parts are fully visible in those regions, where important visual information is not lost, i.e., more relevant features are not occluded. Features within the volumetric data are first classified according to a new dimension, denoted as object importance. This property determines which structures should be readily discernible and which structures are less important. Next, for each feature, various representations (levels of sparseness) from a dense to a sparse depiction are defined. Levels of sparseness define a spectrum of optical properties or rendering styles. The resulting image is generated by ray-casting and combining the intersected features proportional to their importance (importance compositing). The paper includes an extended discussion on several possible schemes for levels of sparseness specification. Furthermore, different approaches to importance compositing are treated.
Targeting Inflammatory Cytokines and Extracellular Matrix Composition to Promote Wound Regeneration (2013)

<b>Significance:</b> Delayed wound healing is one of the most challenging complications of several diseases, including diabetes. There is a vast interest in finding efficient treatments that promote scarless wound healing. The ability of the fetus to regenerate skin wounds after injury has generated much interest in the fetus as a model of regeneration. In this review, we evaluate the role and differential regulation of inflammation, extracellular matrix (ECM) composition, and mechanical stress in determining wound phenotype after injury. <b>Recent Advances:</b> Comparisons between postnatal and fetal wounds have revealed many differences in the healing process. Fetal skin wound healing is characterized by a reduced inflammatory response, an ECM rich in type III collagen and high-molecular-weight hyaluronic acid (HMW-HA), and minimal mechanical stress. In contrast, adult wounds have a sustained inflammatory response, an ECM with increased type I collagen, and low-molecular-weight (LMW-HA) and are subject to significant mechanical load. <b>Critical Issues:</b> The differential regulation of these processes in the fetus compared with the adult plays a critical role in promoting regeneration in the fetus while resulting in scar formation in the adult. <b>Future Directions:</b> Understanding the significance of inflammation and biomechanical forces in wound healing may help in designing therapeutic strategies for the management of chronic nonhealing wounds.
Distance and Cable Length Measurement System (2009)

A simple, economic and successful design for distance and cable length detection is presented. The measurement system is based on the continuous repetition of a pulse that endlessly travels along the distance to be detected. There is a pulse repeater at both ends of the distance or cable to be measured. The endless repetition of the pulse generates a frequency that varies almost inversely with the distance to be measured. The resolution and distance or cable length range could be adjusted by varying the repetition time delay introduced at both ends and the measurement time. With this design a distance can be measured with centimeter resolution using electronic system with microsecond resolution, simplifying classical time of flight designs which require electronics with picosecond resolution. This design was also applied to position measurement.
Red Cell Suspensions in SAGM Medium (1983)

Red cells depleted of buffy coat and more than 90% of the plasma were suspended and stored in a medium composed of sodium chloride, adenine, glucose and mannitol (SAGM). The 24-hour posttransfusion survival of 51Cr-labeled red cells was 83.5±5.3% (n = 4) after storage for 35 days and 77.4±4.7% (n = 6) after 42 days. No abnormal in vivo hemolysis occurred as judged from posttransfusion haptoglobin consumption studies. No abnormal body temperature elevation was found at continuous pertransfusion recordings. The frequency of febrile or urticarial transfusion reactions was 0.19% as compared to 0.68% during a whole-blood transfusion period. Since a mean of 280 ml of plasma can be collected from each blood unit the plasma-saving effects of the system are considerable. Favorable large-scale clinical experience is reported.
Metabolic activation of the nucleoside analog 9-[( 2-hydroxy-1-(hydroxymethyl)ethoxy]methyl)guanine in human diploid fibroblasts infected with human cytomegalovirus. (1985)

9-[( 2-Hydroxy-1-(hydroxymethyl)ethoxy]-methyl)guanine (BW B759U) is a more potent inhibitor of human cytomegalovirus (HCMV) in vitro than is the related nucleoside analog acyclovir (ACV). BW B759U was selectively activated to the 5'-triphosphate (BW B759U-triphosphate) in cells infected with HCMV to levels at least 10-fold higher than those measured for ACV-triphosphate and up to as much as 100-fold higher than the levels found in uninfected cells. BW B759U-triphosphate accumulated in HCMV-infected cells with time; the rate of this increase was dependent upon the drug dose and virus multiplicity of infection. Enzyme activities that catalyzed the phosphorylation of thymidine and 2'-deoxycytidine increased 3- to 7-fold in extracts of cells early after HCMV infection but thereafter declined. No concomitant increase in the rate of BW B759U phosphorylation was detected under these assay conditions. Maximal rate of accumulation of both BW B759U-triphosphate and ACV-triphosphate after a short exposure to drug occurred in the late phase of the infective cycle, as the titer of extracellular virus reached a peak in untreated cultures, but after the decline of stimulated host deoxypyrimidine kinase activities. Once formed, the BW B759U-triphosphate pool decreased very slowly and thus it persisted for several days in both HCMV-infected and uninfected cells.