Alloreactive cytotoxic T lymphocytes generated in the presence of viral- derived peptides show exquisite peptide and MHC specificity

The nature of alloreactivity to MHC molecules has been enigmatic, primarily because of the observation that allogeneic responses are considerably stronger than syngeneic responses. To better determine the specificity potential of allogeneic responses, we have generated alloreactive CTL specific for exogenous, viral-derived peptide ligands. This approach allowed us to critically evaluate both the peptide- and MHC-specificity of these alloreactive T cells. Exploiting the accessibility of the H-2Ld class I molecule for exogenous peptide ligands, alloreactive CTL were generated that are specific for either murine cytomegalovirus (MCMV) or lymphocytic choriomeningitis virus (LCMV) peptides bound by Ld alloantigens. Peptide specificity was initially observed in bulk cultures of alloreactive CTL only when tested on peptide-sensitized T2.Ld target cells that have defective presentation of endogenous peptides. Subsequent cloning of bulk alloreactive CTL lines generated to MCMV yielded CTL clones that had exquisitely specific MCMV peptide recognition requirement. All of the MCMV/Ld alloreactive CTL clones were also exquisitely MHC-specific in that none of the CTL clones lysed targets expressing MCMV/Lq complexes, even though Lq differs from Ld by only six amino acid residues and Lq also binds the MCMV peptide. This observation clearly demonstrates that alloreactive CTL are capable of the same degree of specificity for target cell recognition as are syngeneic CTL in MHC-restricted responses

Astronomy in the Cloud: Using MapReduce for Image Coaddition

In the coming decade, astronomical surveys of the sky will generate tens of terabytes of images and detect hundreds of millions of sources every night. The study of these sources will involve computation challenges such as anomaly detection and classification, and moving object tracking. Since such studies benefit from the highest quality data, methods such as image coaddition (stacking) will be a critical preprocessing step prior to scientific investigation. With a requirement that these images be analyzed on a nightly basis to identify moving sources or transient objects, these data streams present many computational challenges. Given the quantity of data involved, the computational load of these problems can only be addressed by distributing the workload over a large number of nodes. However, the high data throughput demanded by these applications may present scalability challenges for certain storage architectures. One scalable data-processing method that has emerged in recent years is MapReduce, and in this paper we focus on its popular open-source implementation called Hadoop. In the Hadoop framework, the data is partitioned among storage attached directly to worker nodes, and the processing workload is scheduled in parallel on the nodes that contain the required input data. A further motivation for using Hadoop is that it allows us to exploit cloud computing resources, e.g., Amazon's EC2. We report on our experience implementing a scalable image-processing pipeline for the SDSS imaging database using Hadoop. This multi-terabyte imaging dataset provides a good testbed for algorithm development since its scope and structure approximate future surveys. First, we describe MapReduce and how we adapted image coaddition to the MapReduce framework. Then we describe a number of optimizations to our basic approach and report experimental results comparing their performance.Comment: 31 pages, 11 figures, 2 table

The EMAIL test – measurement of integrated saccade latency and visual processing times without eye-tracking

INTRODUCTION: The acquisition and processing of visual information often involve eye-movements and motor responses. Visual processing times and oculomotor parameters are of interest since fatigue as well as temporary changes in alertness caused by common drugs can also affect task completion times and overall accuracy in visual search. Eye-trackers are useful in such studies, but expensive equipment is needed and accurate measurements require careful calibration. We propose a new method to measure integrated oculomotor response parameters that is simple to carry out and does not require eye-tracking equipment. The EMAIL (Eye Movement and Intrinsic Latency) test captures parameters that describe both the time course of eye-movement generation as well as the time needed to detect and process specific object attributes at the end of each saccade. METHODS: The test relies on measuring the time needed to detect peripheral targets, carry out an appropriate eyemovement and process some feature of the stimulus (such as colour, coherent motion, rapid flicker, spatial orientation or acuity). In this round of experiments, the stimulus was a Landolt ring flanked by distractors and presented at a randomly selected location on either side of fixation, 8o in the periphery. The measurement variable is the target presentation time, δT, needed to achieve ~ 73% correct response. The subject’s task is to saccade to the peripheral target, to register the gap in the central ring and to press one of four response buttons to indicate its correct orientation. Eye -tracking was added to this initial research study to separate the cortical processing time needed to detect the orientation of the gap in the Landolt ring from the integrated task completion time. RESULTS: The results obtained so far show a significant effect of age and fatigue. Under normal conditions, measured times are in the range 160 to 270 ms. In general, δT values are longer when vertical eye-movements are involved. The greatest changes are observed in saccade latency and the cortical processing times. DISCUSSION: The new EMAIL test provides a simple method to investigate how fatigue and other factors affect visual processing times. When combined with eye-tracking, the test makes it possible to measure changes in cortical processing times for specific stimulus attributes and may also turn out to be a useful tool to assess the severity of loss in traumatic brain injury studies

Integrated saccade latency as a measure of fatigue

INTRODUCTION: High workload, long working hours and inadequate sleep patterns can have deleterious effects on an individual’s performance. Fatigue is often linked with compromised cognitive and motor function. Our information processing system becomes overloaded and unable to monitor and suppress irrelevant information. Subsequent changes in oculomotor parameters and cortical processing times may therefore provide useful biomarkers to assess one’s state of fatigue. We propose a new non-invasive method to quantify fatigue by measuring Eye Movement And Intrinsic Latencies (EMAIL) without the use of any eye-tracking equipment. METHODS: The test is easy to perform and employs a Landolt C flanked by ring distractors. The test is presented at an eccentricity of 8°, randomly on either side of fixation point within ±5° elevation. The measurement variable is the time of presentation, δT. The subject’s task is to saccade to the peripheral target, register the orientation of the gap and respond by pressing one of four buttons. The EMAIL test measures the presentation time, δT, the subject needs to detect the peripheral target, generate an appropriate eye-movement and register the orientation of the gap. RESULTS: The EMAIL test was used to measure the stimulus presentation times needed to achieve 73% correct responses (using a one up, two down staircase). These times were subject specific and ranged from 165 to 200ms in the absence of fatigue. We investigated how, δT, is affected by exposure to other visually demanding tasks and levels of controlled fatigue. Measured integrated oculomotor responses such as latencies and visual processing times were found to increase significantly following demanding visual tasks by as much as 20ms, but only when fatigued. Preliminary findings using the EMAIL test also show that this technique can be used to investigate the effect of stimulants such as caffeine and depressants, such as alcohol. CONCLUSIONS: The EMAIL test provides a simple method to measure oculomotor parameters and to investigate how these are affected by fatigue. This method can be incorporated in the overall safety management system that is often needed in a number of work areas that involve visually-demanding and safety-critical tasks. The measured parameters provide information about an individual’s level of alertness and may also be of relevance in other industries in order to evaluate drugs developed to control fatigue

Superclustering at Redshift Z=0.54

We present strong evidence for the existence of a supercluster at a redshift of z=0.54 in the direction of Selected Area 68. From the distribution of galaxies with spectroscopic redshifts we find that there is a large over-density of galaxies (a factor of four over the number expected in an unclustered universe) within the redshift range 0.530 < z < 0.555. By considering the spatial distribution of galaxies within this redshift range (using spectroscopic and photometric redshifts) we show that the galaxies in SA68 form a linear structure passing from the South-West of the survey field through to the North-East (with a position angle of approximately 35 deg East of North). This position angle is coincident with the positions of the X-ray clusters CL0016+16, RX J0018.3+1618 and a new X-ray cluster, RX J0018.8+1602, centered near the radio source 54W084. All three of these sources are at a redshift of approximately z=0.54 and have position angles, derived from their X-ray photon distributions, consistent with that measured for the supercluster. Assuming a redshift of 0.54 for the distribution of galaxies and a FWHM dispersion in redshift of 0.020 this represents a coherent structure with a radial extent of 31 Mpc, transverse dimension of 12 Mpc, and a thickness of approximately 4 Mpc. The detection of this possible supercluster demonstrates the power of using X-ray observations, combined with multicolor observations, to map the large scale distribution of galaxies at intermediate redshifts.Comment: 12 pages, 3 figures, Latex, aaspp4.sty, accepted for publication in Ap J Letters. Figure 3 and followup observations can be found at http://tarkus.pha.jhu.edu/~ajc/papers/supercluster

Anatomy of Cirrus Clouds: Results from the Emerald Airborne Campaigns

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Imaging ballistic carrier trajectories in graphene using scanning gate microscopy

We use scanning gate microscopy to map out the trajectories of ballistic carriers in high-mobility graphene encapsulated by hexagonal boron nitride and subject to a weak magnetic field. We employ a magnetic focusing geometry to image carriers that emerge ballistically from an injector, follow a cyclotron path due to the Lorentz force from an applied magnetic field, and land on an adjacent collector probe. The local electric field generated by the scanning tip in the vicinity of the carriers deflects their trajectories, modifying the proportion of carriers focused into the collector. By measuring the voltage at the collector while scanning the tip, we are able to obtain images with arcs that are consistent with the expected cyclotron motion. We also demonstrate that the tip can be used to redirect misaligned carriers back to the collector.This work was partly supported by the EPSRC; a Grant-in-Aid for Scientific Research on Innovative Areas “Science of Atomic Layers” from the Ministry of Education, Culture, Sports, Science and Technology (MEXT); the Project for Developing Innovation Systems of MEXT; the Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS); and the CREST, Japan Science and Technology Agency.This is the author accepted manuscript. The final version is available from AIP via http://dx.doi.org/10.1063/1.493747

The Effect of Agricultural Practices on a Dairy Farm on Nitrate Leaching to 1m

Dairy farms, in Ireland, carry the highest stock densities and use the highest rates of fertiliser nitrogen (N). They constitute the highest risk of nitrate leaching, especially where soils are thin or free-draining. The effect of 4 grass managements on leaching was studied on a dairy farm having free-draining soils overlying Karst limestone. This was a new, farm-comprehensive approach to nitrate leaching which had not been carried out previously