Visible Spikes Research Articles

Towards Automated Analysis of Grain Spikes in Greenhouse Images Using Neural Network Approaches: A Comparative Investigation of Six Methods.

Automated analysis of small and optically variable plant organs, such as grain spikes, is highly demanded in quantitative plant science and breeding. Previous works primarily focused on the detection of prominently visible spikes emerging on the top of the grain plants growing in field conditions. However, accurate and automated analysis of all fully and partially visible spikes in greenhouse images renders a more challenging task, which was rarely addressed in the past. A particular difficulty for image analysis is represented by leaf-covered, occluded but also matured spikes of bushy crop cultivars that can hardly be differentiated from the remaining plant biomass. To address the challenge of automated analysis of arbitrary spike phenotypes in different grain crops and optical setups, here, we performed a comparative investigation of six neural network methods for pattern detection and segmentation in RGB images, including five deep and one shallow neural network. Our experimental results demonstrate that advanced deep learning methods show superior performance, achieving over 90% accuracy by detection and segmentation of spikes in wheat, barley and rye images. However, spike detection in new crop phenotypes can be performed more accurately than segmentation. Furthermore, the detection and segmentation of matured, partially visible and occluded spikes, for which phenotypes substantially deviate from the training set of regular spikes, still represent a challenge to neural network models trained on a limited set of a few hundreds of manually labeled ground truth images. Limitations and further potential improvements of the presented algorithmic frameworks for spike image analysis are discussed. Besides theoretical and experimental investigations, we provide a GUI-based tool (SpikeApp), which shows the application of pre-trained neural networks to fully automate spike detection, segmentation and phenotyping in images of greenhouse-grown plants.

Detection of epileptic activity in presumably normal EEG.

Monitoring epileptic activity in the absence of interictal discharges is a major need given the well-established lack of reliability of patients’ reports of their seizures. Up to now, there are no other tools than reviewing the seizure diary; however, seizures may not be remembered or dismissed voluntarily. In the present study, we set out to determine if EEG voltage maps of epileptogenic activity in individual patients can help to identify disease activity, even if their scalp EEG appears normal. Twenty-five patients with pharmacoresistant focal epilepsy were included. For each patient, 6 min of EEG with spikes (yes-spike) and without visually detectable epileptogenic discharges (no-spike) were selected from long-term monitoring recordings (EEG 31–37 channels). For each patient, we identified typical discharges, calculated their average and the corresponding scalp voltage map (‘spike-map’). We then fitted the spike-map for each patient on their (i) EEG epochs with visible spikes, (ii) epochs without any visible spike and (iii) EEGs of 48 controls. The global explained variance was used to estimate the presence of the spike-maps. The individual spike-map occurred more often in the spike-free EEGs of patients compared to EEGs of healthy controls (P = 0.001). Not surprisingly, this difference was higher if the EEGs contained spikes (P < 0.001). In patients, spike-maps were more frequent per second (P < 0.001) but with a shorter mean duration (P < 0.001) than in controls, for both no-spike and yes-spike EEGs. The amount of spike-maps was unrelated to clinical variables, like epilepsy severity, drug load or vigilance state. Voltage maps of spike activity are present very frequently in the scalp EEG of patients, even in presumably normal EEG. We conclude that spike-maps are a robust and potentially powerful marker to monitor subtle epileptogenic activity.

T144. EEG resting states are altered in focal epilepsy

Resting states represent the basic “atoms of thought” in the resting EEG but were found to be altered in a number of psychiatric and dementia conditions. In most studies, 4 basic maps are described (A = auditory, B = visual, C = salience, D = attention). In the present study we wanted to determine if EEG resting states are also altered in patients with chronic epilepsy 25 patients with chronic unifocal epilepsy were included. All patients underwent 37 channel EEGs. Three minutes of wake EEG without any detectable spikes were selected. We fitted the 4 EEG microstates to the: (i) EEG of patient without any visible spike and (ii) resting-state EEGs of 48 healthy-controls (HC). Global Explained Variance (GEV), Mean duration (MD) and Time Coverage (TC) were used to characterize the map amount. We found a significant GEV increase of map-D (p < 0.001), and decrease of map-C (p < 0.001). For map-C there was also a decrease of MD (p < 0.001) and TC (p < 0.01). These results did not change when fitting included the patient’s individual spike map. Physiologic resting state networks are significantly altered in patients with chronic epilepsy, which affects mainly the so-called salience (map-C) and attention states (map-D). Saliency networks include the anterior insula and dorsal anterior cingulate and play a crucial role in identifying relevant events to guide and adapt behavior. The increase of the attention map (parietal cortex, anterior cingulate, thalamus) probably reflects compensation of impaired salience functions. Further studies will determine if these changes could become an EEG biomarker of epilepsy, e.g. for patients with spike-negative EEG.

Ultrastructure of duck Tembusu virus observed by electron microscopy with negative staining.

Duck Tembusu virus (DTMUV) is a newly emerging enveloped flavivirus. This study shows the ultrastructure of DTMUV using viral purification, negative staining and electron microscopy. Electron microscopic examinations revealed mature DTMUV particles with 50 to 75 nm in diameter and typical enveloped flavivirus structure that consists of the internal nucleocapsid, an inner layer of lipid bilayer and an external layer of E glycoprotein ectodomain. Particles appear to be mostly spherical. In particular, RNA core is deep colored and dense, both capsid and lipid bilayer are clearly visible, the capsid forms regular hexagon, and E glycoprotein ectodomain forms a fringe instead of visible spikes. Thus, this report about the clear ultrastructure of the DTMUV particles will be the major driving forces behind structural biology of DTMUV.

P358 EEG resting states are altered in focal epilepsy

Introduction Resting states represent the basic “atoms of thought” in the resting EEG but were found to be altered in a number of psychiatric and dementia conditions. In most studies, 4 basic maps are described (A = auditory, B = visual, C = salience, D = attention). In the present study we wanted to determine if EEG resting states are also altered in patients with chronic epilepsy Methods 25 patients with chronic unifocal epilepsy were included. All patients underwent 37 channel EEGs. Three minutes of wake EEG without any detectable spikes were selected. We fitted the 4 EEG microstates to the: (i) EEG of patient without any visible spike and (ii) resting-state EEGs of 48 healthy-controls (HC). Global Explained Variance (GEV), Mean duration (MD) and Time Coverage (TC) were used to characterize the map amount. Results We found a significant GEV increase of map-D (p Conclusion Physiologic resting state networks are significantly altered in patients with chronic epilepsy, which affects mainly the so-called salience (map-C) and attention states (map-D). Saliency networks include the anterior insula and dorsal anterior cingulate and play a crucial role in identifying relevant events to guide and adapt behavior. The increase of the attention map (parietal cortex, anterior cingulate, thalamus) probably reflects compensation of impaired salience functions. Further studies will determine if these changes could become an EEG biomarker of epilepsy, e.g. for patients with spike-negative EEG.

Power attack defense

Battery systems are crucial components for mission-critical data centers. Without secure energy backup, existing under-provisioned data centers are largely unguarded targets for cyber criminals. Particularly for today's scale-out servers, power oversubscription unavoidably taxes a data center's backup energy resources, leaving very little room for dealing with emergency. Besides, the emerging trend towards deploying distributed energy storage architecture causes the associated energy backup of each rack to shrink, making servers vulnerable to power anomalies. As a result, an attacker can generate power peaks to easily crash or disrupt a power-constrained system. This study aims at securing data centers from malicious loads that seek to drain their precious energy storage and overload server racks without prior detection. We term such load as Power Virus (PV) and demonstrate its basic two-phase attacking model and characterize its behaviors on real systems. The PV can learn the victim rack's battery characteristics by disguising as benign loads. Once gaining enough information, the PV can be mutated to generate hidden power spikes that have a high chance to overload the system. To defend against PV, we propose power attack defense (PAD), a novel energy management patch built on lightweight software and hardware mechanisms. PAD not only increases the attacking cost considerably by hiding vulnerable racks from visible spikes, it also strengthens the last line of defense against hidden spikes. Using Google cluster traces we show that PAD can effectively raise the bar of a successful power attack: compared to prior arts, it increases the data center survival time by 1.6~11X and provides better performance guarantee. It enables modern data centers to safely exploit the benefits that power oversubscription may provide, with the slightest cost overhead.

Morphology and Molecular Composition of Purified Bovine Viral Diarrhea Virus Envelope.

The family Flaviviridae includes viruses that have different virion structures and morphogenesis mechanisms. Most cellular and molecular studies have been so far performed with viruses of the Hepacivirus and Flavivirus genera. Here, we studied bovine viral diarrhea virus (BVDV), a member of the Pestivirus genus. We set up a method to purify BVDV virions and analyzed their morphology by electron microscopy and their protein and lipid composition by mass spectrometry. Cryo-electron microscopy showed near spherical viral particles displaying an electron-dense capsid surrounded by a phospholipid bilayer with no visible spikes. Most particles had a diameter of 50 nm and about 2% were larger with a diameter of up to 65 nm, suggesting some size flexibility during BVDV morphogenesis. Morphological and biochemical data suggested a low envelope glycoprotein content of BVDV particles, E1 and E2 being apparently less abundant than Erns. Lipid content of BVDV particles displayed a ~2.3 to 3.5-fold enrichment in cholesterol, sphingomyelin and hexosyl-ceramide, concomitant with a 1.5 to 5-fold reduction of all glycerophospholipid classes, as compared to lipid content of MDBK cells. Although BVDV buds in the endoplasmic reticulum, its lipid content differs from a typical endoplasmic reticulum membrane composition. This suggests that BVDV morphogenesis includes a mechanism of lipid sorting. Functional analyses confirmed the importance of cholesterol and sphingomyelin for BVDV entry. Surprisingly, despite a high cholesterol and sphingolipid content of BVDV envelope, E2 was not found in detergent-resistant membranes. Our results indicate that there are differences between the structure and molecular composition of viral particles of Flaviviruses, Pestiviruses and Hepaciviruses within the Flaviviridae family.

Detection of epileptic activity in absence of EEG interictal epileptic discharges

To assess if the EEGs of epileptic patients without any detectable spikes contain the voltage specific epileptic map. Fifteen patients with pharmaco-resistant focal epilepsy were included. Six minutes of resting state EEG with and without any detectable spikes were selected from long-term recording (31-channels, ref:FCz). Resting-state EEGs from 48 healthy control-subjects were also recorded. For each patient EEG, we calculated the averaged spike and its voltage map. We fitted the spike map on (i) EEG of patient with visible spikes (ii) EEG of the same patient without any visible spike and (iii) EEGs of the 48 controls. The presence of the voltage epileptic map was characterized by: mean-correlation and Global Explained Variance (GEV). For these criteria statistical differences between (1) controls and EEG with spikes, and (2) controls and EEG without spikes were evaluated. The patient-specific epileptic voltage map was significantly more represented in the spike-free EEGs of patients than in EEGs of healthy controls (GEV p = 0.029; mean-correlation p = 0.032). This difference was more accentuated for patient-EEGs containing spikes (GEV p = 0.001, mean-correlation p < 0.001). Scalp EEGs of pharmaco-resistant epilepsy patients contains the epileptic voltage map (index of epileptic activity), even in absence of any detectable interictal epileptic discharges.

Temporal trends of perfluoroalkyl substances in limed biosolids from a large municipal water resource recovery facility

While the recycling of wastewater biosolids via land-application is a sustainable practice for nutrient recovery and soil reclamation that has become increasingly common worldwide, concerns remain that this practice may become a source of toxic, persistent organic pollutants to the environment. This study concentrates on assessing the presence and the temporal trends of 12 perfluoroalkyl substances (PFASs), pollutants of global consequence, in limed Class B biosolids from a municipal water resource recovery facility (WRRF), also know as a wastewater treatment plant. PFASs are of significant concern due to their extensive presence and persistence in environmental and biotic samples worldwide, most notably human blood samples. Class B biosolids were collected from the WRRF, prior to land-application, approximately every two to three months, from 2005 to 2013. Overall, this study found that concentrations of the 7 detectable PFAS compounds remained unchanged over the 8-year period, a result that is consistent with other temporal studies of these compounds in sewage sludges. From these analyzed compounds, the highest mean concentrations observed over the study period were 25.1 ng/g dw, 23.5 ng/g dw, and 22.5 ng/g dw for perfluorononanoic acid (PFNA), perfluorooctanoic acid (PFOA), and perfluorooctanesulfonic acid (PFOS), respectively, and these compounds were detected at concentrations 2.5–5 times higher than the remaining, detectable PFASs. Furthermore, it was observed that PFOS, while demonstrating no overall change during the study, exhibited a visible spike in concentration from late 2006 to early 2007. This study indicates that concentrations of PFASs in WRRFs have been stagnant over time, despite regulation.This study also demonstrates that the use of glass jars with polytetrafluoroethylene-lined lids, a common storage method for environmental samples, will not influence PFOA and PFNA concentrations in archived biosolids samples.

V2. Detection of epileptic activity in absence of EEG interictal epileptic discharges

Rationale Aim: to assess if the EEGs of epileptic patients with any detectable spikes contain the voltage epileptic map, specific of the individual patient. Methods Fifteen patients with pharmaco-resistant focal epilepsy were included. Six minutes of EEG with spikes and six minutes without any detectable spikes were selected from long-term monitoring recording during wakeful resting state (EEG 31-channels, ref: FCz). Resting-state EEG from 48 healthy control subjects were also recorded and corrected for artifacts. For the EEG of each patient, we calculated the averaged spike and its voltage map. We fitted the spike map on (i) EEG of patient with visible spikes (ii) EEG of the same patient without any visible spike and (iii) EEGs of the 48 controls. The amount of presence of the voltage epileptic map was characterized using two criteria: mean correlation and Global Explained Variance (GEV). For these criteria statistical differences between (1) controls and EEG with spikes, and (2) controls and EEG without spikes were evaluated using z-scores. Results The patient-specific epileptic voltage map was significantly more represented in the spike-free EEGs of patients than in EEGs of healthy controls (GEV p = 0.029; mean correlation p = 0.032). This difference was more accentuated for the patient EEGs containing spikes (GEV p = 0.001, mean correlation (p Discussion Scalp EEGs of patients with pharmaco-resistant epilepsy contains the epileptic voltage map (index of epileptic activity), even in absence of any detectable interictal epileptic discharges. This finding suggests that epileptic voltage map could be a new epileptic bio-marker (SPUM grant 140332 and 141165).

Effect of radiation induced current on the quality of MR images in an integrated linac‐MR system

In integrated linac-MRI systems, the RF coils are exposed to the linac's pulsed radiation, leading to a measurable radiation induced current (RIC). This work (1) visualizes the RIC in MRI raw data and determines its effect on the MR image signal-to-noise ratio (SNR) (b) examines the effect of linac dose rate on SNR degradations, (c) examines the RIC effect on different MRI sequences, (d) examines the effect of altering the MRI sequence timing on the RIC, and (e) uses a postprocessing method to reduce the RIC signal from the MR raw data. MR images were acquired on the linac-MR prototype system using various imaging sequences (gradient echo, spin echo, and bSSFP), dose rates (0, 50, 100, 150, 200, and 250 MU∕min) and repetition times (TR) with the gradient echo sequence. The images were acquired with the radiation beam either directly incident or blocked from the RF coils. The SNR was calculated for each of these scenarios, showing a loss in SNR due to RIC. Finally, a postprocessing method was applied to the image k-space data in order to remove partially the RIC signal and recover some of the lost SNR. The RIC produces visible spikes in the k-space data acquired with the linac's radiation incident on the RF coils. This RIC leads to a loss in imaging SNR that increases with increasing linac dose rate (15%-18% loss at 250 MU∕min). The SNR loss seen with increasing linac dose rate appears to be largely independent of the MR sequence used. Changing the imaging TR had interesting visual effects on the appearance of RIC in k-space due to the timing between the linac's pulsing and the MR sequence, but did not change the SNR loss for a given linac dose rate. The use of a postprocessing algorithm was able to remove much of the RIC noise spikes from the MR image k-space data, resulting in the recovery of a significant portion, up to 81% (Table II), of the lost image SNR. The presence of RIC in MR RF coils leads to a loss of SNR which is directly related to the linac dose rate. The RIC related loss in SNR is likely to increase for systems that are able to provide larger than 250 MU∕min dose. Some of this SNR loss can be recovered through the use of a postprocessing algorithm, which removes the RIC artefact from the image k-space.

Computed tomography in patients with cardiac pacemakers: difficulties and solutions

The presence of cardiac pacemaker systems may significantly limit interpretation of multi-slice computed tomography (MSCT) images. In 80 patients (45 men; aged 69.5 ± 13.4) with previously implanted anti-arrhythmic devices, a 64-slice CT (Aquilion-64) was performed. In 61 patients (76.3%), ECG gating was used (coronaries visualization) and in 19 patients (23.7%) without ECG gating (not coronaries visualization). In all 19 patients without ECG gating MSCT images were diagnostic. In 37 (60.6%) patients of 61, there was no problem with gating process and image quality was diagnostic. In 24 (39.4%) with visible spikes in the ECG-gating group, there were difficulties in differentiating the R spike from an artificial spike (unipolar pacing) by MSCT software. In 15 patients (24.6%) after reprogramming, it was possible to obtain good quality images. In nine (14.7%) patients, it was not possible to reprogram devices due to old unipolar leads, but in two cases (3.3%), ECG gating was corrected manually and good image quality was obtained. In seven (11.5%) patients, it was not possible to perform ECG gating. The ECG gating process was identified as the main cause of the imaging problems. Bipolar leads working as bipolar pacing seem to be necessary to perform MSCT with ECG gating. A unipolar system lead may cause serious problems with reconstructions.

Immunoelectron microscopy of influenza A virus neuraminidase glycoprotein topography.

Using immunoelectron microscopy, the distribution of influenza A virus neuraminidase (NA) glycoproteins was examined, after performing immunoreactions to virions on the grid. With polyclonal antibody, the immunolabels of the glycoproteins were found to be homogeneously distributed, whereas with monoclonal antibody they were found to be distributed in clusters. After destruction of haemagglutinin (HA) but not of NA activity with a high concentration of trypsin, the remaining visible spikes were evenly distributed. This finding was consistent with the absence of immunolabelling with anti-HA antibody, and the homogeneous pattern of immunolabels with anti-NA polyclonal antibody, but not with the clustered labelling with the anti-NA monoclonal antibody. Thus, the immunolabelling image with anti-NA polyclonal antibody was considered to reflect the true one.

Comparisons of Belmont Virus, a Possible Bunyavirus Unique to Australia, with Bunyamwera Virus

Belmont virus is an arbovirus isolated from mosquitoes and has a preference for marsupial hosts. The diameter of virions by negative staining (122 nm before fixation and 91 nm after fixation) was greater than that of Bunyamwera virus (94 nm and 79 nm respectively). However, the particles of both viruses appeared morphologically identical and sedimented at the same rate in sucrose density gradients. Belmont virus had a tripartite segmented RNA genome (28S, 24S and 11S) similar to Bunyamwera virus RNA (33S, 26S and 16S). The mol. wt. of these RNA species of Belmont virus measured by gel electrophoresis was 3.2 x 10(6), 2.4 x 10(6) and 0.3 x 10(6) compared to 2.9 x 10(6), 1.8 x 10(6) and 0.3 x 10(6) for the L, M and S species of Bunyamwera virus RNA. Both viruses comprised four structural proteins of the same relative proportions and corresponding mol. wt. For Bunyamwera virus, these were 145 x 10(3) (L), 104 x 10(3) (G1), 32 x 10(3) (G2) and 22 x 10(3) (N). The equivalent proteins of Belmont virus had mol. wt. of 147 x 10(3) (P147), 107 x 10(3) (G107), 28 x 10(3) (P28) and 25 x 10(3) (P25). Under conditions in which the envelope glycoproteins G1 and G2 of Bunyamwera virus were labelled in glucosamine, only G107 of Belmont virus was labelled. However, both G107 and P28 of Belmont virus were solubilized by non-ionic detergent and were then separable from the nucleocapsid containing all the RNA and P25. Chymotrypsin treatment of Belmont virus digested only G107, leaving a residue of P25 and P28, and of visible spikes. Similarly, G2 and the spikes of Bunyamwera virus resisted digestion with chymotrypsin. It was concluded that P28 is an envelope protein, equivalent to G2. Belmont virus thus appears to be a typical member of the Bunyaviridae but is unique in that it lacks carbohydrate in the small envelope protein (P28).

Is a cortical focus driving a cortico-thalamic circuit in human absence epilepsy?

Event Abstract Back to Event Is a cortical focus driving a cortico-thalamic circuit in human absence epilepsy? Pauly Ossenblok1*, Bert Kornips1, Disha Gupta1, 2, Petra Van Houdt1 and Gilles Van Luijtelaar2 1 SLU, Division of Biometry and Systems Analysis, Sweden 2 Radboud University, Netherlands Aim: To describe the cortical cortico-thalamic circuit involvement during the evolvement of MEG spike-and-wave discharges (SWDs) in order to identify a focal cortical onset zone in human absence epilepsy. Methods: MEG recordings were performed for 20 patients (6-15 years of age) with absence seizures, ranging from patients with typical childhood absence epilepsy, who can be treated quite successfully with anti-epileptics, to more complex atypical forms and children who had absences and complex partial clinical features. For each seizure of these children non-linear association analysis was performed for time windows moving through the SWDs present in the MEG. Next, the cluster coefficients were calculated for all significant associations (>0.95) for each MEG sensor based on the graph theory (1). Results: Studying in detail the changes in time and space of the cluster values revealed cortical node activity preceding the first visible spike of the SWDs and in the "build up" period towards the generalized 3 Hz SWDs. The latter showed, like in the study of Westmijse et al. (2), a recurrent pattern of focal regional activity during the spikes alternated by generalized activity during the slow-wave phase of the SWDs, indicating most likely the involvement of a cortico-thalamic network. The results indicate a focal cortical onset zone that differs for the clinically distinct patient populations, whereas the activity underlying the generalized SWDs seems to share a common network during the evolvement of these discharges for all patients studied. Conclusion: The cluster analysis method enables the study of the distinct phases of the SWDs in time and space, which is helpful in identifying the driving cortical node of these discharges. This information can be very helpful for diagnoses and successful treatment of children with absence epilepsy. Acknowledgments: Funded by the Dutch Organization for Scientific Research (NWO).