julilili42/papers huggingface dataset:
A pel-based Volume Rendering Accelerator
2013-09-21

We discuss the underlying algorithms, design principles and implementation issues of an extremely compact and cost-efficient volume rendering accelerator for PCI-based systems. It operates on classified and shaded data sets which have been coded and compressed usingRedundant Block Compression (RBC), a tech nique originating from 2D-imaging and extended to 3D. This specific encoding scheme reduces drastically the required data traffic between the volume memory and the processing units. Thus, the volume data set can be placed into the main memory of the host, eliminating the need of a separate volume memory. Fur thermore, the tri-Iinear interpolation needed for perspective raycasting is very much simpli fied for RBC-transformed data sets.All in all, these techniques allow a volume ren dering accelerator to be implemented as a sin gle-chip coprocessor, or as an FPGA-based prototype for monochrome data sets as pre sented in this work. Although using a lossy compression scheme, image quality is still high, and expected frame rates are between 2 and 5Hz for typical data sets of 2563 voxels.
TheWavelet Stream: Interactive Multi Resolution Light Field Rendering
2013-09-21

One of the most general image based object representations is the Light Field. Unfortunately, a large amount of data is required to reconstruct high quality views from a Light Field. In this paper, we present the wavelet stream which employs non-standard four-dimensional wavelet decomposition for Light Field compression. It allows for progressive transmission, storage, and rendering of compressed Light Field data. Our results show that 0.8% of the original coefficients or 0.3 bits per pixel, respectively are sufficient to obtain visually pleasing new views. Additionally, the wavelet stream allows for an adaptive multi-resolution representation of the Light Field data. Furthermore, a silhouetteencoding scheme helps to reduce the number of coefficients required. Our data structure allows to store arbitrary vector-valued data like RGB- or YUV-data. The Light Field data stored in the wavelet stream can be decompressed in real time for interactive rendering. For this, the reconstruction algorithm uses supplementary caching schemes.
A Scalable Architecture for Volume Rendering
2013-09-21

We describe the operational principles of a scalable hardware accelerator for volume rendering. The basic philosophy is to provide an atomic unit which already provides sophisticated volume graphics at interactive rendering speed. Realtime speed can then be achieved by operating multiple units in par allel. The basic unit consists of just four VLSI chips and the volume memory and thus meets the requirements of a small size and low costs. Never theless it provides arbitrary perspective projections (e.g., for walk-throughs), Phong shading, a freely moveable light source, depth-cueing and interac tive, non-binary classification (semi-transparent display) at a frame rate of about 2.5Hz for 256 3 data sets.
Efficient Space Leaping for Ray casting Architectures
2013-09-21

One of the most severe problems for ray casting architectures is the waste of computation cycles and I/O bandwidth, due to redundant sampling of empty space. While several techniques exist for software implementations to skip these empty regions, few are suitable for hardware implementation. The few which have been presented either require a tremendous amount of logic or are not feasible for high frequency designs (i.e. running at 100 MHz) where latency is the one of the biggest issues. In this paper, we present an efficient space leaping mechanism which requires only a small amount of SRAM (4 Kbit for a 256&lt;sup&gt;3&lt;/sup&gt; volume) and can be easily integrated into ray casting architectures. For each sub-cube of the volume, a bit is stored in an occupancy map, which can be generated in real-time, using the VIZARD II architecture. Hence, space leaping can be classification dependent achieving yet another significant speed-up over skipping only the empty space (voxel
Translucent and Opaque Direct Volume Rendering for Virtual Endoscopy Applications
2013-09-21

Virtual endoscopy applications frequently require the visual representation of several material interfaces to show the relevant data feature to the user. This requires the specification of complex transfer function which classify the various materials and color them appropriately. In this paper, we explore the use of the direct volume rendering for virtual endoscopy. We specifically look into the visual representation of different anatomical features of various volume datasets, which are located below the inner surface of the organ of interest. Furthermore, we present how interactivity can be accomplished with the VIZARD II ray casting accelerator board.
A VLSI Design for Fast Vector Normalization
2013-09-21

The design of a vector normalizer is described. It is an integral part of our graphics subsystemfor scientific visualization, but will be of great use for speeding up any computer graphics architecture.In the actual design, the circuitry handles 3D-vectors with 33 bit two's complement components.The components of the normalized vectors are computed as 16 bit two's complementfixed-point numbers. Due to the overall pipeline architecture, the chip accepts one 3D-vectorand produces one normalized vector each clock.To normalize a 3D-vector, three square operations, two additions, one square root operationand three divisions must be performed. The target clock frequency is 50 MHz, by which theperformance of the chip rates at 450 MOPS.A single-chip VLSI implementation is currently in work, simulation results will be available bythe end of the third quarter '93. We use Mentor 8.2 tools on HP 700 workstations and Toshiba'sTC160G Gate Array technology.
Hardware for Superior Texture Performance
2013-09-21

Mapping textures onto suIfaces of computer-gener ated objects is a technique which greatly improves the realism of their appearance. Unfortunately, this imposes high computational demands and, even worse, tremendous memory bandwidth require ments on the graphics system. Tight cost frames in the industry in conjunction with ever increasing user expectations make the design of a powerful texture mapping unit a difficult task.To meet these requirements we follow two different approaches. On the technology side, we observe a rapidly emerging technology which offers the com bination of enormous transfer rates and computing power: logic-embedded memories.On the algorithmic side, a common way to reduce data traffic is image compression. Its application to texture mapping, however, is difficult since the decompression must be done at pixel frequency.In this work we will focus on the latter approach, describing the use of a specific compression scheme for texture mapping. It allows the use of a very sim ple and fast decompression hardware, bringing high performance texture mapping to low-cost systems.
Cube-4 Implementations on the Teramac Custom Computing Machine
2013-09-21

We present two implementations of the Cube-4 volume rendering architecture on the Teramac custom computing machine. Cube-4 uses a slice parallel ray-casting algorithm that allows for a paral lel and pipelined implementation of ray-casting with tri-linear interpolation and surface normal estimation from interpolated samples. Shading, classification and compositing are part of rendering pipeline. With the partitioning schemes introduced in this paper, Cube-4 is capable of rendering large datasets with a limited number of pipelines. The Teramac hardware simulator at the Hewlett-Packard research laboratories, Palo Alto, CA, on which Cube-4 was implemented, belongs to the new class of custom computing machines. Teramac combines the speed of special-purpose hardware with the flexibility of general-purpose computel's. With Teramac as a development tool we were able to implement in just five weeks working Cube-4 prototypes, capable of rendering for example datasets of 1283 voxels in 0.65 seconds at 0,96 MHz processing frequency. The performance results from these implementations indicate real-time performance for high-resolution data-sets.
Parallelization and Hardware Support for Ray Tracing
2013-09-21

Even on the latest workstations ray tracing is still a very time-consuming algorithm.This paper makes a thorough analysis of previous attempts to accelerate raytracing by means of parallelization with general purpose processors and by means of designing special purpose processors. Since much work has been done concurrently by many researchers, only the most important milestones are mentioned. The conclusionsdrawn are quite different from those in many other papers.
CYP2D6 Genotype and Adjuvant Tamoxifen: Meta-Analysis of Heterogeneous Study Populations
2013-09-23

The International Tamoxifen Pharmacogenomics Consortium was established to address the controversy regarding cytochrome P450 2D6 (CYP2D6) status and clinical outcomes in tamoxifen therapy. We performed a meta-analysis on data from 4,973 tamoxifen-treated patients (12 globally distributed sites). Using strict eligibility requirements (postmenopausal women with estrogen receptor-positive breast cancer, receiving 20 mg/day tamoxifen for 5 years, criterion 1); CYP2D6 poor metabolizer status was associated with poorer invasive disease-free survival (IDFS: hazard ratio = 1.25; 95% confidence interval = 1.06, 1.47; P = 0.009). However, CYP2D6 status was not statistically significant when tamoxifen duration, menopausal status, and annual follow-up were not specified (criterion 2, n = 2,443; P = 0.25) or when no exclusions were applied (criterion 3, n = 4,935; P = 0.38). Although CYP2D6 is a strong predictor of IDFS using strict inclusion criteria, because the results are not robust to inclusion criteria (these were not defined a priori), prospective studies are necessary to fully establish the value of CYP2D6 genotyping in tamoxifen therapy.
A spastic paraplegia mouse model reveals REEP1-dependent ER shaping
2013-09-23

Axonopathies are a group of clinically diverse disorders characterized by the progressive degeneration of the axons of specific neurons. In hereditary spastic paraplegia (HSP), the axons of cortical motor neurons degenerate and cause a spastic movement disorder. HSP is linked to mutations in several loci known collectively as the spastic paraplegia genes (SPGs). We identified a heterozygous receptor accessory protein 1 (REEP1) exon 2 deletion in a patient suffering from the autosomal dominantly inherited HSP variant SPG31. We generated the corresponding mouse model to study the underlying cellular pathology. Mice with heterozygous deletion of exon 2 in Reep1 displayed a gait disorder closely resembling SPG31 in humans. Homozygous exon 2 deletion resulted in the complete loss of REEP1 and a more severe phenotype with earlier onset. At the molecular level, we demonstrated that REEP1 is a neuron-specific, membrane-binding, and membrane curvature-inducing protein that resides in the ER. We further show that Reep1 expression was prominent in cortical motor neurons. In REEP1-deficient mice, these neurons showed reduced complexity of the peripheral ER upon ultrastructural analysis. Our study connects proper neuronal ER architecture to long-term axon survival.
Correction: Oxidative Burst of Circulating Neutrophils Following Traumatic Brain Injury in Human
2013-09-23

Besides secondary injury at the lesional site, Traumatic brain injury (TBI) can cause a systemic inflammatory response, which may cause damage to initially unaffected organs and potentially further exacerbate the original injury.Here we investigated plasma levels of important inflammatory mediators, oxidative activity of circulating leukocytes, particularly focusing on neutrophils, from TBI subjects and control subjects with general trauma from 6 hours to 2 weeks following injury, comparing with values from uninjured subjects.We observed increased plasma level of inflammatory cytokines/molecules TNF-a, IL-6 and CRP, dramatically increased circulating leukocyte counts and elevated expression of TNF-a and iNOS in circulating leukocytes from TBI patients, which suggests a systemic inflammatory response following TBI.Our data further showed increased free radical production in leukocyte homogenates and elevated expression of key oxidative enzymes iNOS, COX-2 and NADPH oxidase (gp91 phox ) in circulating leukocytes, indicating an intense induction of oxidative burst following TBI, which is significantly greater than that in control subjects with general trauma.Furthermore, flow cytometry assay proved neutrophils as the largest population in circulation after TBI and showed significantly up-regulated oxidative activity and suppressed phagocytosis rate for circulating neutrophils following brain trauma.It suggests that the highly activated neutrophils might play an important role in the secondary damage, even outside the injured brain.Taken together, the potent systemic inflammatory response induced by TBI, especially the intensively increase oxidative activity of circulating leukocytes, mainly neutrophils, may lead to a systemic damage, dysfunction/damage of bystander tissues/organs and even further exacerbate secondary local damage.Controlling these pathophysiological processes may be a promising therapeutic strategy and will protect unaffected organs and the injured brain from the secondary damage.
Identification of Autoantigens in Body Fluids by Combining Pull-Downs and Organic Precipitations of Intact Immune Complexes with Quantitative Label-Free Mass Spectrometry
2013-09-23

Most autoimmune diseases are multifactorial diseases and are caused by the immunological reaction against a number of autoantigens. Key for understanding autoimmune pathologies is the knowledge of the targeted autoantigens, both initially and during disease progression. We present an approach for autoantigen identification based on isolation of intact autoantibody-antigen complexes from body fluids. After organic precipitation of high molecular weight proteins and free immunoglobulins, released autoantigens were identified by quantitative label-free liquid chromatography mass spectrometry. We confirmed feasibility of target enrichment and identification from highly complex body fluid proteomes by spiking of a predefined antibody-antigen complex at low level of abundance. As a proof of principle, we studied the blinding disease autoimmune uveitis, which is caused by autoreactive T-cells attacking the inner eye and is accompanied by autoantibodies. We identified three novel autoantigens in the spontaneous animal model equine recurrent uveitis (secreted acidic phosphoprotein osteopontin, extracellular matrix protein 1, and metalloproteinase inhibitor 2) and confirmed the presence of the corresponding autoantibodies in 15-25% of patient samples by enzyme-linked immunosorbent assay. Thus, this workflow led to the identification of novel autoantigens in autoimmune uveitis and may provide a versatile and useful tool to identify autoantigens in other autoimmune diseases in the future.
Uptake of phytodetritus by benthic foraminifera under oxygen depletion at the Indian Margin (Arabian Sea)
2013-09-23

Abstract. Benthic foraminifera in sediments on the Indian margin of the Arabian Sea where the oxygen minimum zone (OMZ) impinges on the continental slope are exposed to particularly severe levels of oxygen depletion. Food supply for the benthic community is high but delivered in distinct pulses during upwelling and water mixing events associated with summer and winter monsoon periods. In order to investigate the response by benthic foraminifera to such pulsed food delivery under oxygen concentrations of less than 0.1 mL L−1 (4.5 μmol L−1), an in situ isotope labeling experiment (13C, 15N) was performed at the western continental slope of India at 540 m water depth (OMZ core region). The assemblage of living foraminifera (&gt;125 μm) in the uppermost centimeter at this depth is characterized by an unexpectedly high population density of 3982 ind. 10 cm−2 and a strong dominance by few calcareous species. For the experiment, we concentrated on the nine most abundant taxa, which constitute 93% of the entire foraminifera population at 0–1 cm sediment depth. Increased concentrations of 13C and 15N in the cytoplasm indicate that all investigated taxa took up the labeled phytodetritus during the 4 day experimental phase. In total, these nine species had assimilated 113.8 mg C m−2 (17.5% of the total added carbon). The uptake of nitrogen by the three most abundant taxa (Bolivina aff. B. dilatata, Cassidulina sp., Bulimina gibba) was 2.7 mg N m−2 (2% of the total added nitrogen) and showed the successful application of 15N as tracer in foraminiferal studies. The short-term response to the offered phytodetritus varied largely among foraminiferal species with Uvigerina schwageri being by far the most important species in short-term processing whereas the most abundant taxa Bolivina aff. B. dilatata and Cassidulina sp. showed comparably low uptake of the offered food. We suggest that the observed species-specific differences are related to individual biomass of species and to specific feeding preferences. The high numbers of living foraminifera and their rapid response to deposited fresh phytodetritus demonstrate the importance of foraminifera in short-term carbon cycling under oxygen-depleted conditions. We propose that foraminifera at the studied site benefit from unique adaptations in their metabolisms to nearly anoxic conditions as well as from the exclusion of macrofauna and the resulting relaxation of competition for food and low predation pressure.
Synthesis and Skeletal Transformations of Trinuclear Palladium and Nickel Phosphido Complexes
2013-09-23

Abstract Trinuclear phosphido complexes of palladium and nickel were synthesized and characterized. [M{(2‐Me 2 NC 6 H 4 )PPh}(OAc)] 3 [M = Pd ( 2 ), Ni ( 6 )] were obtained from the respective acetate, [Pd(OAc) 2 ] 3 or [Ni(OAc) 2 (H 2 O) 4 ], in reactions with the secondary aminophosphane (2‐Me 2 NC 6 H 4 )PHPh ( 1 ). The chloride derivative [Pd{(2‐Me 2 NC 6 H 4 )PPh}Cl] 3 ( 4a ) was generated from the reaction of the chelating ligand 1 with Na 2 PdCl 4 . The reaction of the acetate 2 with p ‐toluenesulfonic acid ( p TsOH) led to the formation of the tosylate analogue [Pd{(2‐Me 2 NC 6 H 4 )PPh}(OTs)] 3 ( 3 ). From the reaction of the tosylate trimer 3 with CsCl, CsBr or NaI, the substitution products [Pd{(2‐Me 2 NC 6 H 4 )PPh}X] 3 [X = Cl ( 4a ), Br ( 4b ), I ( 4c )] were isolated. From the reaction of the acetate 2 with HBF 4 or HClO 4 in acetonitrile, the solvent adduct [Pd(NP)(NCCH 3 )] 3 3+ was isolated as the BF 4 – ( 5a ) or ClO 4 – salt ( 5b ). The phosphido‐bridged complexes were characterized by single‐crystal structural analyses ( 2 , 4 , 5a and 6 ), solution NMR experiments, and in the case of 2 and 4a by solid‐state 31 P cross‐polarization magic‐angle spinning NMR spectroscopy. The crystal structures show the six‐membered (MP) 3 cores in twist‐boat or boat conformations that appear to be maintained in solution, according to NMR evidence. A search for (MP) 3 structures in the Cambridge Structural Database reveals that these two conformations are the most common ones (46 % twist‐boat, 21 % boat, 17 % chair).
Least Informative Dimensions
2013-09-23

We present a novel non-parametric method for finding a subspace of stimulus fea-tures that contains all information about the response of a system. Our method generalizes similar approaches to this problem such as spike triggered average, spike triggered covariance, or maximally informative dimensions. Instead of max-imizing the mutual information between features and responses directly, we use integral probability metrics in kernel Hilbert spaces to minimize the information between uninformative features and the combination of informative features and responses. Since estimators of these metrics access the data via kernels, are easy to compute, and exhibit good theoretical convergence properties, our method can easily be generalized to populations of neurons or spike patterns. By using a par-ticular expansion of the mutual information, we can show that the informative features must contain all information if we can make the uninformative features independent of the rest. 1
Overexpression of synphilin-1 promotes clearance of soluble and misfolded alpha-synuclein without restoring the motor phenotype in aged A30P transgenic mice
2013-09-24

Lewy bodies and neurites are the pathological hallmark of Parkinson's disease. These structures are composed of fibrillized and ubiquitinated alpha-synuclein suggesting that impaired protein clearance is an important event in aggregate formation. The A30P mutation is known for its fast oligomerization, but slow fibrillization rate. Despite its toxicity to neurons, mechanisms involved in either clearance or conversion of A30P alpha-synuclein from its soluble state into insoluble fibrils and their effects in vivo are poorly understood. Synphilin-1 is present in Lewy bodies, interacting with alpha-synuclein in vivo and in vitro and promotes its sequestration into aggresomes, which are thought to act as cytoprotective agents facilitating protein degradation. We therefore crossed animals overexpressing A30P alpha-synuclein with synphilin-1 transgenic mice to analyze its impact on aggregation, protein clearance and phenotype progression. We observed that co-expression of synphilin-1 mildly delayed the motor phenotype caused by A30P alpha-synuclein. Additionally, the presence of N- and C-terminal truncated alpha-synuclein species and fibrils were strongly reduced in double-transgenic mice when compared with single-transgenic A30P mice. Insolubility of mutant A30P and formation of aggresomes was still detectable in aged double-transgenic mice, paralleled by an increase of ubiquitinated proteins and high autophagic activity. Hence, this study supports the notion that co-expression of synphilin-1 promotes formation of autophagic-susceptible aggresomes and consecutively the degradation of human A30P alpha-synuclein. Notably, although synphilin-1 overexpression significantly reduced formation of fibrils and astrogliosis in aged animals, a similar phenotype is present in single- and double-transgenic mice suggesting additional neurotoxic processes in disease progression.