1,027 research outputs found
Learning Shape Priors for Single-View 3D Completion and Reconstruction
The problem of single-view 3D shape completion or reconstruction is
challenging, because among the many possible shapes that explain an
observation, most are implausible and do not correspond to natural objects.
Recent research in the field has tackled this problem by exploiting the
expressiveness of deep convolutional networks. In fact, there is another level
of ambiguity that is often overlooked: among plausible shapes, there are still
multiple shapes that fit the 2D image equally well; i.e., the ground truth
shape is non-deterministic given a single-view input. Existing fully supervised
approaches fail to address this issue, and often produce blurry mean shapes
with smooth surfaces but no fine details.
In this paper, we propose ShapeHD, pushing the limit of single-view shape
completion and reconstruction by integrating deep generative models with
adversarially learned shape priors. The learned priors serve as a regularizer,
penalizing the model only if its output is unrealistic, not if it deviates from
the ground truth. Our design thus overcomes both levels of ambiguity
aforementioned. Experiments demonstrate that ShapeHD outperforms state of the
art by a large margin in both shape completion and shape reconstruction on
multiple real datasets.Comment: ECCV 2018. The first two authors contributed equally to this work.
Project page: http://shapehd.csail.mit.edu
TimelineQA: A Benchmark for Question Answering over Timelines
Lifelogs are descriptions of experiences that a person had during their life.
Lifelogs are created by fusing data from the multitude of digital services,
such as online photos, maps, shopping and content streaming services. Question
answering over lifelogs can offer personal assistants a critical resource when
they try to provide advice in context. However, obtaining answers to questions
over lifelogs is beyond the current state of the art of question answering
techniques for a variety of reasons, the most pronounced of which is that
lifelogs combine free text with some degree of structure such as temporal and
geographical information.
We create and publicly release TimelineQA1, a benchmark for accelerating
progress on querying lifelogs. TimelineQA generates lifelogs of imaginary
people. The episodes in the lifelog range from major life episodes such as high
school graduation to those that occur on a daily basis such as going for a run.
We describe a set of experiments on TimelineQA with several state-of-the-art QA
models. Our experiments reveal that for atomic queries, an extractive QA system
significantly out-performs a state-of-the-art retrieval-augmented QA system.
For multi-hop queries involving aggregates, we show that the best result is
obtained with a state-of-the-art table QA technique, assuming the ground truth
set of episodes for deriving the answer is available
Deep-Learning-based Fast and Accurate 3D CT Deformable Image Registration in Lung Cancer
Purpose: In some proton therapy facilities, patient alignment relies on two
2D orthogonal kV images, taken at fixed, oblique angles, as no 3D on-the-bed
imaging is available. The visibility of the tumor in kV images is limited since
the patient's 3D anatomy is projected onto a 2D plane, especially when the
tumor is behind high-density structures such as bones. This can lead to large
patient setup errors. A solution is to reconstruct the 3D CT image from the kV
images obtained at the treatment isocenter in the treatment position.
Methods: An asymmetric autoencoder-like network built with vision-transformer
blocks was developed. The data was collected from 1 head and neck patient: 2
orthogonal kV images (1024x1024 voxels), 1 3D CT with padding (512x512x512)
acquired from the in-room CT-on-rails before kVs were taken and 2
digitally-reconstructed-radiograph (DRR) images (512x512) based on the CT. We
resampled kV images every 8 voxels and DRR and CT every 4 voxels, thus formed a
dataset consisting of 262,144 samples, in which the images have a dimension of
128 for each direction. In training, both kV and DRR images were utilized, and
the encoder was encouraged to learn the jointed feature map from both kV and
DRR images. In testing, only independent kV images were used. The full-size
synthetic CT (sCT) was achieved by concatenating the sCTs generated by the
model according to their spatial information. The image quality of the
synthetic CT (sCT) was evaluated using mean absolute error (MAE) and
per-voxel-absolute-CT-number-difference volume histogram (CDVH).
Results: The model achieved a speed of 2.1s and a MAE of <40HU. The CDVH
showed that <5% of the voxels had a per-voxel-absolute-CT-number-difference
larger than 185 HU.
Conclusion: A patient-specific vision-transformer-based network was developed
and shown to be accurate and efficient to reconstruct 3D CT images from kV
images.Comment: 9 figure
Circulating microRNAs Reveal Time Course of Organ Injury in a Porcine Model of Acetaminophen-Induced Acute Liver Failure
Acute liver failure is a rare but catastrophic condition which can progress rapidly to multi-organ failure. Studies investigating the onset of individual organ injury such as the liver, kidneys and brain during the evolution of acute liver failure, are lacking. MicroRNAs are short, non-coding strands of RNA that are released into the circulation following tissue injury. In this study, we have characterised the release of both global microRNA and specific microRNA species into the plasma using a porcine model of acetaminophen-induced acute liver failure. Pigs were induced to acute liver failure with oral acetaminophen over 19h±2h and death occurred 13h±3h thereafter. Global microRNA concentrations increased 4h prior to acute liver failure in plasma (P<0.0001) but not in isolated exosomes, and were associated with increasing plasma levels of the damage-associated molecular pattern molecule, genomic DNA (P<0.0001). MiR122 increased around the time of onset of acute liver failure (P<0.0001) and was associated with increasing international normalised ratio (P<0.0001). MiR192 increased 8h after acute liver failure (P<0.0001) and was associated with increasing creatinine (P<0.0001). The increase in miR124-1 occurred concurrent with the pre-terminal increase in intracranial pressure (P<0.0001) and was associated with decreasing cerebral perfusion pressure (P<0.002)
Beam mask and sliding window-facilitated deep learning-based accurate and efficient dose prediction for pencil beam scanning proton therapy
Purpose: To develop a DL-based PBSPT dose prediction workflow with high
accuracy and balanced complexity to support on-line adaptive proton therapy
clinical decision and subsequent replanning.
Methods: PBSPT plans of 103 prostate cancer patients and 83 lung cancer
patients previously treated at our institution were included in the study, each
with CTs, structure sets, and plan doses calculated by the in-house developed
Monte-Carlo dose engine. For the ablation study, we designed three experiments
corresponding to the following three methods: 1) Experiment 1, the conventional
region of interest (ROI) method. 2) Experiment 2, the beam mask (generated by
raytracing of proton beams) method to improve proton dose prediction. 3)
Experiment 3, the sliding window method for the model to focus on local details
to further improve proton dose prediction. A fully connected 3D-Unet was
adopted as the backbone. Dose volume histogram (DVH) indices, 3D Gamma passing
rates, and dice coefficients for the structures enclosed by the iso-dose lines
between the predicted and the ground truth doses were used as the evaluation
metrics. The calculation time for each proton dose prediction was recorded to
evaluate the method's efficiency.
Results: Compared to the conventional ROI method, the beam mask method
improved the agreement of DVH indices for both targets and OARs and the sliding
window method further improved the agreement of the DVH indices. For the 3D
Gamma passing rates in the target, OARs, and BODY (outside target and OARs),
the beam mask method can improve the passing rates in these regions and the
sliding window method further improved them. A similar trend was also observed
for the dice coefficients. In fact, this trend was especially remarkable for
relatively low prescription isodose lines. The dose predictions for all the
testing cases were completed within 0.25s
Expression and Differential Responsiveness of Central Nervous System Glial Cell Populations to the Acute Phase Protein Serum Amyloid A
Acute-phase response is a systemic reaction to environmental/inflammatory insults and involves hepatic production of acute-phase proteins, including serum amyloid A (SAA). Extrahepatically, SAA immunoreactivity is found in axonal myelin sheaths of cortex in Alzheimer's disease and multiple sclerosis (MS), although its cellular origin is unclear. We examined the responses of cultured rat cortical astrocytes, microglia and oligodendrocyte precursor cells (OPCs) to master pro-inflammatory cytokine tumour necrosis factor (TNF)-\u3b1 and lipopolysaccaride (LPS). TNF-\u3b1 time-dependently increased Saa1 (but not Saa3) mRNA expression in purified microglia, enriched astrocytes, and OPCs (as did LPS for microglia and astrocytes). Astrocytes depleted of microglia were markedly less responsive to TNF-\u3b1 and LPS, even after re-addition of microglia. Microglia and enriched astrocytes showed complementary Saa1 expression profiles following TNF-\u3b1 or LPS challenge, being higher in microglia with TNF-\u3b1 and higher in astrocytes with LPS. Recombinant human apo-SAA stimulated production of both inflammatory mediators and its own mRNA in microglia and enriched, but not microglia-depleted astrocytes. Co-ultramicronized palmitoylethanolamide/luteolin, an established anti-inflammatory/neuroprotective agent, reduced Saa1 expression in OPCs subjected to TNF-\u3b1 treatment. These last data, together with past findings suggest that co-ultramicronized palmitoylethanolamide/luteolin may be a novel approach in the treatment of inflammatory demyelinating disorders like MS
Control and Characterization of Individual Grains and Grain Boundaries in Graphene Grown by Chemical Vapor Deposition
The strong interest in graphene has motivated the scalable production of high
quality graphene and graphene devices. Since large-scale graphene films
synthesized to date are typically polycrystalline, it is important to
characterize and control grain boundaries, generally believed to degrade
graphene quality. Here we study single-crystal graphene grains synthesized by
ambient CVD on polycrystalline Cu, and show how individual boundaries between
coalescing grains affect graphene's electronic properties. The graphene grains
show no definite epitaxial relationship with the Cu substrate, and can cross Cu
grain boundaries. The edges of these grains are found to be predominantly
parallel to zigzag directions. We show that grain boundaries give a significant
Raman "D" peak, impede electrical transport, and induce prominent weak
localization indicative of intervalley scattering in graphene. Finally, we
demonstrate an approach using pre-patterned growth seeds to control graphene
nucleation, opening a route towards scalable fabrication of single-crystal
graphene devices without grain boundaries.Comment: New version with additional data. Accepted by Nature Material
Human neutrophil clearance of bacterial pathogens triggers anti-microbial gamma delta T cell responses in early infection
Human blood Vc9/Vd2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vc9/Vd2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vc9/Vd2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-c and tumor necrosis factor (TNF)-a. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vc9/Vd2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-a dependent proliferation of Vc9/Vd2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting cd T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vc9/Vd2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The cd T celldriven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of cd T cells and TNF-a and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive cd T cells in early infection and suggest novel diagnostic and therapeutic approaches.Martin S. Davey, Chan-Yu Lin, Gareth W. Roberts, Sinéad Heuston, Amanda C. Brown, James A. Chess, Mark A. Toleman, Cormac G.M. Gahan, Colin Hill, Tanya Parish, John D. Williams, Simon J. Davies, David W. Johnson, Nicholas Topley, Bernhard Moser and Matthias Eber
High efficient electrical stimulation of hippocampal slices with vertically aligned carbon nanofiber microbrush array
Long-term neuroprostheses for functional electrical stimulation must efficiently stimulate tissue without electrolyzing water and raising the extracellular pH to toxic levels. Comparison of the stimulation efficiency of tungsten wire electrodes (W wires), platinum microelectrode arrays (PtMEA), as-grown vertically aligned carbon nanofiber microbrush arrays (VACNF MBAs), and polypyrrole coated (PPy-coated) VACNF MBAs in eliciting field potentials in the hippocampus slice indicates that, at low stimulating voltages that preclude the electrolysis of water, only the PPy-coated VACNF MBA is able to stimulate the CA3 to CA1 pathway. Unlike the W wires, PtMEA, as-grown VACNF MBA, and the PPy-coated VACNF MBA elicit only excitatory postsynaptic potentials (EPSPs). Furthermore, the PPy-coated VACNF MBA evokes somatic action potentials in addition to EPSPs. These results highlight the PPy-coated VACNF’s advantages in lower electrode impedance, ability to stimulate tissue through a biocompatible chloride flux, and stable vertical alignment in liquid that enables access to spatially confined regions of neuronal cells
Resolution of LPS-induced airway inflammation and goblet cell hyperplasia is independent of IL-18
BACKGROUND: The resolution of inflammatory responses in the lung has not been described in detail and the role of specific cytokines influencing the resolution process is largely unknown. METHODS: The present study was designed to describe the resolution of inflammation from 3 h through 90 d following an acute injury by a single intratracheal instillation of F344/N rats with LPS. We documented the inflammatory cell types and cytokines found in the bronchoalveolar lavage fluid (BALF), and epithelial changes in the axial airway and investigated whether IL-18 may play a role in the resolution process by reducing its levels with anti-IL-18 antibodies. RESULTS: Three major stages of inflammation and resolution were observed in the BALF during the resolution. The first stage was characterized by PMNs that increased over 3 h to 1 d and decreased to background levels by d 6–8. The second stage of inflammation was characterized by macrophage influx reaching maximum numbers at d 6 and decreasing to background levels by d 40. A third stage of inflammation was observed for lymphocytes which were elevated over d 3–6. Interestingly, IL-18 and IL-9 levels in the BALF showed a cyclic pattern with peak levels at d 4, 8, and 16 while decreasing to background levels at d 1–2, 6, and 12. Depletion of IL-18 caused decreased PMN numbers at d 2, but no changes in inflammatory cell number or type at later time points. CONCLUSION: These data suggest that IL-18 plays a role in enhancing the LPS-induced neutrophilic inflammation of the lung, but does not affect the resolution of inflammation
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