Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript

Resonance Raman Spectroscopy For In-Situ Monitoring Of Radiation Damage

Radiation induced damage of metal centres in proteins is a severe problem in X-ray structure determination. Photoreduction can lead to erroneous structural implications, and in the worst cases cause structure solution to fail. Resonance Raman (RR) spectroscopy is well suited in-situ monitoring of X-ray induced photoreduction. However the laser excitation needed for RR can itself cause photoreduction of the metal centres. In the present study myoglobin and rubredoxin crystals were used as model systems to assess the feasibility of using RR for this application. It is shown that at least 10-15 RR spectra per crystal can be recorded at low laser power before severe photoreduction occurs.Furthermore it is possible to collect good quality RR spectra from cryocooled protein crystals with exposure times of only a few seconds. Following extended laser illumination photoreduction is observed through the formation and decay of spectral bands as a function of dose. The experimental setup planned for integration into the SLS protein crystallography beamlines is also described. This setup should also prove to be very useful for other experimental techniques at synchrotrons where X-ray photoreduction is a problem e.g. X-ray absorption spectroscopy.Fil: Meents, A.. Swiss Light Source; SuizaFil: Owen, R. L.. Swiss Light Source; SuizaFil: Murgida, Daniel Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Hildebrandt, P.. Swiss Light Source; SuizaFil: Schneider, R.. Swiss Light Source; SuizaFil: Pradervand, C.. Swiss Light Source; SuizaFil: Bohler, P.. Swiss Light Source; SuizaFil: Schulze Briese, C.. Swiss Light Source; Suiz

Alimentación de cerdos con suero de queso fresco en combinación con subproductos de molinería o grano de maíz

En el primer ensayo se midieron los rendimientos zootécnicos de cerdos durante los períodos de crecimiento y acabado (17 a 90 kg) alimentados con 7 raciones: 2 sin suero de queso fresco (SQF) basadas en maíz más torta de soya (M más TS) y maíz más torta de algodón (M más TA) o dietas controles, y las otras 5 con SQF en combinación con maíz-grano molido (MGM), o uno de los 4 subproductos de molinería siguientes: harina de arroz (HA), mogolla de trigo (MT), salvado de trigo (ST) y salvado de maíz (SM). En el segundo ensayo se midió el efecto de la alimentación con SQF, únicamente durante el período de acabado (43 a 92 kg) en combinación con los mismos subproductos de molinería del primer ensayo. Para los ensayos se emplearon 84 cerdos, mitad hembras y mitad machos castrados, de las razas Duroc (D), Landrace (L) y Yorkshire (Y), y cruces D x Y L x D, los cuales se asignaron al azar a cada ración. Los resultados del primer ensayo fueron: aumento de peso diario (APD) para el grupo SQF más HA: 600 gr; para el grupo SQF más MT: 580 gr y para el grupo SQF más MGM: 620 gr, aumentos que fueron inferiores a los obtenidos con las dietas controles (M más TS y M más TA), pero superiores significativamente a los obtenidos por los grupos SQF más SM: 490 gr y SQF más ST: 520 gr. El consumo promedio diario (CPD) de SQF fue de 15.3 y 21 L para los períodos de crecimiento y acabado, respectivamente. El CPD de subproductos de molinería y/o el MGM para los períodos mencionados fueron 1.1 y 1.5 kg, respectivamente. Los resultados del segundo ensayo tuvieron las mismas respuestas que en el primer estudio, pero con un menor CPD de SQF igual a 17 L y un mayor CPD de subproducto de molinería o MGM igual a 2 kg, lo cual sugiere falta de adaptación de su capacidad gastrointestinal. Estos resultados permitieron concluir que el SQF puede reemplazar en un 33 por ciento al concentrado balanceado convencional y no debe ser combinado con subproductos cuyo contenido final de fibra sea igual o exceda al 10 por ciento, vale decir, como SM o ST.In the first study, animal performance was measured on growing and finishing pigs (17 to 90 kg) feed seven diets: two with out whey, corn-soy bean meal (CSM) and corn-cotton seed oil meal (CCM); and the other five, with whole fresh whey (WFW) in combination with ground corn grain (GC), or one of the following four grain milling by-products: Rice bran (RB), wheat middlings (WM), wheat bran (WB) and corn bran (CB). In a second trial the effects of feeding WFW was studied by feedings pigs in the finishing fase (43 to 92 kg), that is, pigs that had not been expossed to whey in their diets during the growth period; WFW in combination with the milling by products: RB, WM, WB and CB. Duroc (D), Landrace (L) and Yorkshire (Y), and Duroc cross bred pigs (D x V and L x D), were used in this study. Employing a total of 84 pigs, 12 (six castrates and six females) were randomly alloted to each diet. Results of the first trial were: average daily gain (ADG) for the WFW-RB troup, 600 g; WFW-WM group, 580 g and the WFW-GC group, 620 g. These ADG were inferior to those abtained with the pigs on the control diets CSM and CCM, but superior to those groups of pigs on the WFW-CB (490 g) and WFW-WB (520 g) diets (P< 0.05). WFW daily average intake during the growth period was 15.3 liters and during the finishing period, 21.0 liters; average daily grain milling by-product intake for the two periods were: 1.1 and 1.5 kg, respectively. Results of the second study for those animals that received no WFW during the growth period, showed the same results as those of the first study, but with a lower WFW daily intake (17 liters/day), and a higher grain milling by-product intake: 2.0 kg/day. This fact suggests an adaptation of the gastro-intestinal tract in terms of liquid volume capacity of pigs fed WFW during the growth period. It is concluded that WFW can replace 33% of a conventional balanced diet, and should not be combined in rations whose total crude fiber content is equal to or exceeds 10%, such that will readly accur when wheat bran and corn bran are used.Maíz-zea maysPorcicultur

Energy transport during 3D small-scale reconnection driven by anisotropic plasma turbulence

Energy dissipation in collisionless plasmas is a longstanding fundamental physics problem. Although it is well known that magnetic reconnection and turbulence are coupled and transport energy from system-size scales to sub-proton scales, the details of the energy distribution and energy dissipation channels remain poorly understood. Especially, the energy transfer and transport associated with three dimensional (3D) small-scale reconnection that occurs as a consequence of a turbulent cascade is unknown. We use an explicit fully kinetic particle-in-cell code to simulate 3D small scale magnetic reconnection events forming in anisotropic and Alfv\'enic decaying turbulence. We identify a highly dynamic and asymmetric reconnection event that involves two reconnecting flux ropes. We use a two-fluid approach based on the Boltzmann equation to study the spatial energy transfer associated with the reconnection event and compare the power density terms in the two-fluid energy equations with standard energy-based damping, heating and dissipation proxies. Our findings suggest that the electron bulk flow transports thermal energy density more efficiently than kinetic energy density. Moreover, in our turbulent reconnection event, the energy-density transfer is dominated by plasma compression. This is consistent with turbulent current sheets and turbulent reconnection events, but not with laminar reconnection.Comment: Accepted for publication in Ap

The Fate of Sub-micron Circumplanetary Dust Grains II: Multipolar Fields

We study the radial and vertical stability of dust grains launched with all charge-to-mass ratios at arbitrary distances from rotating planets with complex magnetic fields. We show that the aligned dipole magnetic field model analyzed by Jontof-Hutter and Hamilton (2012) is an excellent approximation in most cases, but that fundamentally new physics arises with the inclusion of non-axisymmetric magnetic field terms. In particular, large numbers of distant negatively-charged dust grains, stable in a magnetic dipole, can be driven to escape by a more complex field. We trace the origin of the instability to overlapping Lorentz resonances which are extremely powerful when the gravitational and electromagnetic forces on a dust grain are comparable. These resonances enable a dust grain to tap the spin energy of the planet to power its escape. We also explore the relatively minor influence of different launch speeds and the far more important effects of variable grain charge. Only the latter are capable of significantly affecting the micron-sized grains that dominate visible and infrared images of faint dust rings. Finally, we present full stability maps for Earth, Jupiter, Saturn, Uranus, and Neptune with magnetic fields modeled out to octupole order. Not surprisingly, dust in the tortured magnetic fields of Uranus and Neptune show the greatest instability.Comment: 60 pages in manuscript format, 17 figures, 1 tabl

Wet scavenging of soluble gases in DC3 deep convective storms using WRF-Chem simulations and aircraft observations

We examine wet scavenging of soluble trace gases in storms observed during the Deep Convective Clouds and Chemistry (DC3) field campaign. We conduct high-resolution simulations with the Weather Research and Forecasting model with Chemistry (WRF-Chem) of a severe storm in Oklahoma. The model represents well the storm location, size, and structure as compared with Next Generation Weather Radar reflectivity, and simulated CO transport is consistent with aircraft observations. Scavenging efficiencies (SEs) between inflow and outflow of soluble species are calculated from aircraft measurements and model simulations. Using a simple wet scavenging scheme, we simulate the SE of each soluble species within the error bars of the observations. The simulated SEs of all species except nitric acid (HNO_3) are highly sensitive to the values specified for the fractions retained in ice when cloud water freezes. To reproduce the observations, we must assume zero ice retention for formaldehyde (CH_2O) and hydrogen peroxide (H_2O_2) and complete retention for methyl hydrogen peroxide (CH_3OOH) and sulfur dioxide (SO_2), likely to compensate for the lack of aqueous chemistry in the model. We then compare scavenging efficiencies among storms that formed in Alabama and northeast Colorado and the Oklahoma storm. Significant differences in SEs are seen among storms and species. More scavenging of HNO_3 and less removal of CH_3OOH are seen in storms with higher maximum flash rates, an indication of more graupel mass. Graupel is associated with mixed-phase scavenging and lightning production of nitrogen oxides (NO_x), processes that may explain the observed differences in HNO_3 and CH_3OOH scavenging

The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains

The ATP-dependent chromatin-remodelling enzyme Chd1 is a 168-kDa protein consisting of a double chromodomain, Snf2-related ATPase domain, and a C-terminal DNA-binding domain. Here, we show the DNA-binding domain is required for Saccharomyces cerevisiae Chd1 to bind and remodel nucleosomes. The crystal structure of this domain reveals the presence of structural homology to SANT and SLIDE domains previously identified in ISWI remodelling enzymes. The presence of these domains in ISWI and Chd1 chromatin-remodelling enzymes may provide a means of efficiently harnessing the action of the Snf2-related ATPase domain for the purpose of nucleosome spacing and provide an explanation for partial redundancy between these proteins. Site directed mutagenesis was used to identify residues important for DNA binding and generate a model describing the interaction of this domain with DNA. Through inclusion of Chd1 sequences in homology searches SLIDE domains were identified in CHD6–9 proteins. Point mutations to conserved amino acids within the human CHD7 SLIDE domain have been identified in patients with CHARGE syndrome

C5 Palsy After Cervical Spine Surgery: A Multicenter Retrospective Review of 59 Cases.

STUDY DESIGN: A multicenter, retrospective review of C5 palsy after cervical spine surgery. OBJECTIVE: Postoperative C5 palsy is a known complication of cervical decompressive spinal surgery. The goal of this study was to review the incidence, patient characteristics, and outcome of C5 palsy in patients undergoing cervical spine surgery. METHODS: We conducted a multicenter, retrospective review of 13 946 patients across 21 centers who received cervical spine surgery (levels C2 to C7) between January 1, 2005, and December 31, 2011, inclusive. P values were calculated using 2-sample t test for continuous variables and χ(2) tests or Fisher exact tests for categorical variables. RESULTS: Of the 13 946 cases reviewed, 59 patients experienced a postoperative C5 palsy. The incidence rate across the 21 sites ranged from 0% to 2.5%. At most recent follow-up, 32 patients reported complete resolution of symptoms (54.2%), 15 had symptoms resolve with residual effects (25.4%), 10 patients did not recover (17.0%), and 2 were lost to follow-up (3.4%). CONCLUSION: C5 palsy occurred in all surgical approaches and across a variety of diagnoses. The majority of patients had full recovery or recovery with residual effects. This study represents the largest series of North American patients reviewed to date

Epidural Hematoma Following Cervical Spine Surgery.

STUDY DESIGN: A multicentered retrospective case series. OBJECTIVE: To determine the incidence and circumstances surrounding the development of a symptomatic postoperative epidural hematoma in the cervical spine. METHODS: Patients who underwent cervical spine surgery between January 1, 2005, and December 31, 2011, at 23 institutions were reviewed, and all patients who developed an epidural hematoma were identified. RESULTS: A total of 16 582 cervical spine surgeries were identified, and 15 patients developed a postoperative epidural hematoma, for a total incidence of 0.090%. Substantial variation between institutions was noted, with 11 sites reporting no epidural hematomas, and 1 site reporting an incidence of 0.76%. All patients initially presented with a neurologic deficit. Nine patients had complete resolution of the neurologic deficit after hematoma evacuation; however 2 of the 3 patients (66%) who had a delay in the diagnosis of the epidural hematoma had residual neurologic deficits compared to only 4 of the 12 patients (33%) who had no delay in the diagnosis or treatment (P = .53). Additionally, the patients who experienced a postoperative epidural hematoma did not experience any significant improvement in health-related quality-of-life metrics as a result of the index procedure at final follow-up evaluation. CONCLUSION: This is the largest series to date to analyze the incidence of an epidural hematoma following cervical spine surgery, and this study suggest that an epidural hematoma occurs in approximately 1 out of 1000 cervical spine surgeries. Prompt diagnosis and treatment may improve the chance of making a complete neurologic recovery, but patients who develop this complication do not show improvements in the health-related quality-of-life measurements