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opencc-by-4.0Mar 2024View details →

Supporting datasets for the article Using rare event algorithms to understand the statistics and dynamics of extreme heatwave seasons in South Asia

<h3>Supporting datasets for the article Using rare event algorithms to understand the statistics and dynamics of extreme heatwave seasons in South Asia, submitted to Environmental Research: Climate</h3>   The dataset contains all intermediate data used for the article. The raw outputs of the model may be available upon reasonable request to clement.lpr@gmail.com The climate model Plasim can be downloaded, together with its documentation, from the webpage of  the « Theoretische Meteorologie » group at the University of Hamburg: <a href="https://www.mi.uni-hamburg.de/en/arbeitsgruppen/theoretische-meteorologie/modelle/plasim.html">https://www.mi.uni-hamburg.de/en/arbeitsgruppen/theoretische-meteorologie/modelle/plasim.html</a> The three jupyter notebooks <a href="../api/records/10888194/draft/files/Figures_article_archive.ipynb/content" target="_blank" rel="noopener noreferrer">Figures_article_archive.ipynb</a>, <a href="../api/records/10888194/draft/files/Zg500_maps_article_archive.ipynb/content" target="_blank" rel="noopener noreferrer">Zg500_maps_article_archive.ipynb</a>, <a href="../api/records/10888194/draft/files/Correlation_maps_3days_ERA5_Plasim_archive.ipynb/content" target="_blank" rel="noopener noreferrer">Correlation_maps_3days_ERA5_Plasim_archive.ipynb</a> contain the analysis and code used to produce the figures in the article. <a href="../api/records/10888194/draft/files/pyscripts.tar/content" target="_blank" rel="noopener noreferrer">pyscripts.tar</a> contains 4 python utilities, data_proceeding_module.py, plot_routines.py, subseasonal_stats_utilities.py, utilities_REA_analysis.py that are imported by the notebooks.

opencc-by-4.0Apr 2024View details →

Codes for "Summer westerly wind intensification weakens Southern Ocean seasonal cycle under global warming" - submitted to Geophysical Research Letters

<pre>This repository contains the NCAR Command Language (NCL) codes (*.ncl files) used to produce the related contents of Zhang et al. (2024). For queries about this repository and its contents, please contact me (zhangyiwen2024@gmail.com). Figure 1.ncl: For plotting main Fig.1. Figure 2.ncl: For plotting main Fig.2. Figure 3.ncl: For plotting main Fig.3. Figure 4.ncl: For plotting main Fig.4. Figure 5.ncl: For plotting main Fig.5. References: Zhang et al. Summer westerly wind intensification weakens Southern Ocean seasonal cycle under global warming. Geophysical Research Letters. (2024).</pre>

opencc-by-4.0Apr 2024View details →

The Turone Sheep Seasonal Brain Dataset

<h1>Abstract</h1> To cope with seasonal modifications of the environmental resources, brain anticipates and changes both its structural organisation and functioning. However, the tempo and mode of these central changes have been poorly investigated in mammalians. Here we describe a longitudinal morphometric neuroimaging study in a well know animal model to study seasonality: sheep. Using new magnetic resonance imaging (MRI) resources comprising a high-resolution brain template, its associated tissue priors (500-µm isotropic resolution) and a corresponding sheep brain atlas (202 regions of interest) we investigate the impact of seasonal transitions between winter and summer season on brain microstructure using voxel-based morphometry. We observed significant modifications of grey matter concentration (GMC) in pivotal brain areas involved in circadian rhythms (pineal, hypothalamus) and light processing (suprageniculate nucleus) but also within regions related to sensory processing, learning, memory, behavior control, and social cognition. These findings provide new insights into mammalian brain functioning revealing its flexibility and its adaptability to cope to environmental changes. <h1>Material and methods</h1> <h2> Animals</h2> Seventeen adult, sexually mature multiparous ewes (Ovis aries) of 3.4 ± 0.3 years old (weight = 64.5 ± 5.5 kg) have been included in this protocol and have been scanned at the PIXANIM platform (INRAE, French National Research Institute for Agriculture, Food & Environment, Nouzilly, France). Females were ovariectomized and implanted with an oestradiol silastic implant (2 cm) at the end of october, two months before the first scan session. The ewes were kept permanently indoors and fed ad libitum with dehydrated lucerne, maize, straw, and a supplement of vitamins and minerals, and had free access to water. All the procedures were conducted in accordance with the European directive 2010/63/EU on the protection of animals used for scientific purposes and the experimental protocol was approved by the local ethical committee (comité d’éthique en expérimentation animale Val-de-Loire) under reference number 00510.02.   <h2>Surgical procedure</h2> First, ewes were fasted 24 h before surgery. Day of surgery, an i.v. injection of thiopental (14 mg/kg body weight, BW; Nesdonal, Merial, Villeurbanne, France) was done to induce analgesia, then animals were intubated and maintained under anesthesia by a mixture of 3 to 4% isoflurane (Vetflurane, Virbac, Carros, France) vaporized in 100% oxygen. Ovariectomy were conducted under sterile surgical conditions. Local anaesthesia with lidocaine (4%, Lurocaïne, Vétoquinol, Luré, France) was given prior laparotomy. Ovaries were surgically extracted, and the tissues were sutured. The entire procedure was performed within 20 min. Postoperative ventilation with oxygen was maintained until the first signs of awakening appeared. Animals were then housed individually for 6 h in a padded stall before being put back with congeners. They received an anti-inflammatory drug for 2 days (2 mg/kg, flunixin meglumine, Finadyne®, Intervet, Beaucouzé, France) to relief pain and an antiedema medication: (1 mg/kg BW of furosemide, Dimazon®, Intervet, Beaucouzé, France) at the end of surgery. Animals were treated with a diuretic medication associating 3 mg/kg of hydrochlorothiazide with 0.03 mg/kg dexamethasone (Diurizone®, Vétoquinol, Luré, France) for 2 days.   <h2>Photoperiodic conditions</h2> Two scanning sessions were performed for each animal at opposite moment of the circannual cycle: a first session was performed between mid-January/February (from 13/01/2014 to 17/02/2014), during the sexual season and a second session was performed between mid-June and mid-July (from 16/06/2014 to 22/07/2014) during the season of sexual rest. As 4-5 weeks were necessary to scan the entire group, animals were housed two weeks before and during each scan session (2-3 weeks) in photoperiodic facilities to ensure similar light duration for each subject and to avoid a photoperiodic shift over the scanning sessions (winter scanning session: mean daylight 556.1 min ± 22.26 min; summer scanning session: daylight 943.3 min ± 13.90 min). Therefore, ewes were housed under a 9h light/15h dark photoperiod (light on at 8AM, daylight duration 540 min) during the winter scan session and under a 15h light/9h dark photoperiod (lights on at 6h AM, daylight duration 960 min) during the summer scan session.   <h2>Melatonin response to photoperiodic exposure</h2> To ensure that animals were responsive to the photoperiodic treatment, one week before the start of each MRI scan session, serial blood samplings were performed overnight to measure the pattern of blood melatonin secretion. This was done following previous procedures used in our laboratory (Tricoire et al., 2002). Briefly, animals were housed individually 24h hours and implanted with a catheter into the jugular before blood sampling to limit potential stressful response of the animals. Blood sampling was performed under dim red light once per hour from one hour before the lights turn off until 2 hours after they turn on. Blood samples were then centrifugated and plasma stored at -80°c until assay. Melatonin assay was performed as previously documented in our laboratory (Tricoire et al., 2002).   <h2>In vivo MRI acquisitions</h2> Animal preparation for MRI data acquisitions were performed as previously described (Ella et al., 2015, 2017). Briefly, animals were anesthetized with an intramuscular injection of ketamine just before the scan, intubated, maintained during the scan on 3% isoflurane vaporized in oxygen and continuously monitored by a MR-compatible Aestiva®/5 systems (Madison, USA). Three MR acquisitions were performed (see Ella et al., 2015 for the details of each acquisition) on each animal secured in a prone position in 3 Tesla VERIO Siemens systems (Erlangen, Germany), front legs apart and bent towards the abdomen, using a flexible coil (Siemens FLEX Large 4 elements) tied around the head. The sequences have been optimized to be perform in time compatible with anaesthesia (≤1h), to reduce artefact (folding, truncation, etc.) and to optimize SNR. For each acquisition parameters have been set as previously describe in Ella and Keller (2015): - Three dimensional SPC-IR acquired in the sagittal plane (Echo Time/Repetition Time = 413 ms/4000 ms, Flip Angle = 120°, Inversion Time = 380 ms, Number of Excitation = 10, Partial Fourier = 1, Slice Thickness = 0.35 mm, Slice Number = 208, Field of View = 179.2x179.2 mm, matrix = 512x512, final resolution 0.35 mm3). - Three dimensional T1 MPRAGE acquired in the sagittal plane (Echo Time/Repetition Time = 3.18 ms/2500 ms, Flip Angle = 12°, Inversion Time = 900 ms, Number of Excitation = 8, Partial Fourier = 1, Slice Thickness = 0.5 mm, Slice Number = 288, Field of View = 192x192 mm, matrix = 384x384, final resolution 0.5mm3). - Three dimensional T2 MEDIC acquired in the sagittal plane (Echo Time/Repetition Time = 2.1 ms/38 ms, Flip Angle = 8°, Number of Excitation = 6, Partial Fourier = 0.75, Slice Thickness = 0.4 mm, Slice Number = 256, Field of View = 179.2x179.2 mm, matrix = 448x448, final resolution 0.4 mm3).   <h2>Additional feature: Computed Tomography (CT) sheep template.</h2> Tomographic data of nine ewes’ skulls have been acquired on our CT-scan (Siemens Somatom Definition AS, Siemens Corp., Germany). The X-ray source was set at 100 kV and 120 mA/s. A total of 800 slices were acquired using the following parameters: Thickness = 0.4 mm, Slice Number = 800, Field of View = 204,8x 204,8 mm, matrix = 512x512, final resolution 0.4 mm3) reconstructed using a filter Safire I26. DICOM data were converted to NIFTI format and organized as a standardized data sets that accordingly to the Brain Imaging Data Structure (BIDS) using BIDScoin and are downloadable on Zenodo.

Upstream and downstream wind-stress forcing of seasonal variability of Luzon Strait Deep Overflow transport

This is the dataset used for figures in paper "Upstream and downstream wind-stress forcing of seasonal variability of Luzon Strait Deep Overflow transport".

Vitellogenins level as a biomarker of the honey bee colony seasonal dynamics

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Seasonal tree height dataset from 2018 to 2023 in Shenzhen

We utilized LiDAR and satellite data to extract features of spectral, vegetation, texture, polarization, terrain, and season. By integrating these features with machine, deep learning, and optimization methods, we dynamically estimated tree heights in Shenzhen during the summer and winter from 2018 to 2023 and validate seasonal and regional scalability. Model's R2 was 0.799 and MAE was 1.581 m. Model also has a strong generalizability to estimate tree height across seasons and regions.

The response of nitrogen transformation to hydrological regime at sediment-water interface of seasonal lakes in floodplain: Insights from the Three Gorges Dam-Poyang Lake system

This study establishes a coupled model integrating hydrodynamics and nitrogen transformation to elucidate the impacts of the hydrological regime of the Yangtze River after the operation of Three Gorges Dam.

opencc-by-4.0Jun 2024View details →

Dissolved Mn(III) is a key redox intermediate in sediments of a seasonally euxinic coastal basin

Dataset and computer model used in the article "Dissolved Mn(III) is a key redox intermediate in sediments of a seasonally euxinic coastal basin"  in Biogeosciences.

Seasonal and interannual variability of soil heterotrophic respiration and autotrophic respiration in typical grassland of Inner Mongolia

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opencc-zeroOct 2021View details →

Supplementary material 2 from: Armijos-Ojeda D, Székely D, Székely P, Cogălniceanu D, Cisneros-Heredia DF, Ordóñez-Delgado L, Escudero A, Espinosa CI (2021) Amphibians of the equatorial seasonally dry forests of Ecuador and Peru. ZooKeys 1063: 23-48. https://doi.org/10.3897/zookeys.1063.69580

Appendix 1. Reference list for life-history characteristics of amphibians of the Equatorial Seasonally Dry Forest (Table 1)

opencc-zeroOct 2021View details →

Seasonal particle responses to near-bed shear stress in a shallow, wave- and current-driven environment

Novel analysis of in-situ acoustic and optical data collected in a shallow, wave- and current-driven environment enabled determination of: (1) particle characteristics that were most affected by near-bed physical forcing over seasonal scales, and (2) characteristic shear stress, tchar, at which the rate of change to particle characteristics was most pronounced. Near-bed forcing and particle responses varied by season. Results indicated that moderate tchar values of 0.125 Pa drove changes in particle composition during summer. In winter, particle concentration effects were most affected at tchar of 0.05 Pa, suggesting dominance of fluff layer resuspension. Changes to particle size were most relevant during a biologically productive springtime period, with initiation of particle disaggregation occurring most commonly at tchar of 0.25 Pa. These results suggest that it may be more important to parameterize tchar, as opposed to critical shear stress for erosion, for sediment transport models.

Daily abundance of Dall's sheep peaks during late summer in a seasonal habitat of high-management interest

Informing conservation and management decisions for habitats frequented by species of high management interest often face the challenge of limited resources for conducting wildlife surveys. When surveys are focused on local areas or sparsely distributed species, it may also be difficult to obtain counts sufficient for implementing abundance models that account for imperfect detection. With replicated aerial surveys collected within a 70.25 km2 portion of the Eastern Alaska Range, Alaska, USA during the summers of 2013–2015, we estimated daily abundance of Dall's sheep using two different estimation methods: Bayesian N-mixture models and Poisson regression models. We then compared estimates of relative abundance from both model types while paying special attention to the assumption of closure within individual survey units. With abundance estimates obtained from individual survey days, we then estimated the average number of Dall's sheep within the survey area for the period 1 July–1 October. Daily ewe abundance followed a quadratic pattern, with 10–20 ewes being within our survey area in early July and late September, and approximately 90 ewes within the survey area in mid-August. Lamb to ewe ratios averaged 0.2 from July–September, while ram to ewe ratios averaged 0.4 from July until mid-August before increasing to about 1.0 by the end of September. These results indicate that our survey area is an important habitat to local Dall's sheep populations when lambs are vulnerable to predators. Accordingly, human recreation and military training within the survey area should be minimized 1.5–3.0 months after parturition to minimize disturbance. We also found that N-mixture models displayed a pattern of abundance estimates that increased in magnitude as model complexity increased. We thus recommend an a priori approach to N-mixture model construction that balances the risk of overfitting models to modest data against the risk of fitting models that do not explain heterogeneity in abundance and detection probability. Lastly, we suggest simple improvements to replicated, aerial surveys for species like Dall's sheep focused on reducing violations of the closure assumption within individual survey units, which can reduce bias of density estimates obtained with N-mixture models.

Castela senticosa (Simaroubaceae: Sapindales), a new species from the Caribbean clade endemic to seasonally dry tropical forest on Hispaniola

Recent fieldwork in the Sierra Martín García in southwestern Dominican Republic has yielded a new species of the American clade Castela (Simaroubaceae), Castela senticosa sp. nov., from seasonally dry tropical forest. This species has been collected from two separate localities, including Môle St. Nicolas in northwestern Haiti in 1929, but until now fertile material with both flowers and fruit was unknown. We provide a photographic plate and illustration, place it phylogenetically using plastome data, and compare it morphologically with close relatives. This increases the number of known species of Castela on Hispaniola from one to two, both of which are endemic but from different clades, and yields another species for the Greater Antilles, a known biodiversity hotspot and clear center of diversification for this group of arid-adapted, thorny shrubs. This work emphasizes that seasonally dry tropical forest, although often understudied, house as yet undiscovered biodiversity and deserve far more comprehensive studies.

Data from: Seasonal variation in resource selection by subadult golden eagles in the Great Basin Desert

Golden eagles (Aquila chrysaetos) are a long-lived and wide-ranging species believed to be stable or in slight decline across North America. Golden eagles have an extended subadult stage (4–5 years) that is critical to maintaining recruitment into the breeding population and population viability. We investigated patterns of resource selection for subadults in the Great Basin Desert of the western United States during summer and winter, 2013–2019. We monitored 46 subadults with GPS transmitters and related locations (n = 99,037) with predictors hypothesized to influence seasonal patterns of space use with mixed-effects logistic regression.

opencc-by-4.0Nov 2021View details →

Spatio-temporal variation in dry season determines the Amazonian fire calendar

Spatio-temporal variation in dry season determines the Amazonian fire calendar Contact: nsc.nathaliacarvalho@gmail.com Data repository for the paper: Carvalho et al. Spatio-temporal variation in dry season determines the Amazonian fire calendar. Environmental Research Letters (2021). Background: Fire is one of the main anthropogenic drivers that threatens the Amazon. Despite the clear link between rainfall and fire, the spatial and temporal relationship between these variables is still poorly understood in the Amazon. We stratified the Amazon basin according to the dry season onset/end and investigated its relationship with the spatio-temporal variation of fire. We found well-defined seasonal fire patterns related to variation of the dry season end.  Fire Amazonian Calendar: Our results and maps are also available in a user-friendly interface (<a href="http://amazonianfirecalendar.shinyapps.io/fire_amazon/">amazonianfirecalendar.shinyapps.io/fire_amazon/</a>).  Dataset: Rasters files of the dry season (onset, end, length) and fire dynamics (Monthly percentage of fire in the peak month, Fire peak month and Critical Fire Period). Coverage: Amazon basin Spatial resolution: 10km Coordinate reference system: South America Albers Equal Area Conic with Datum SAD69 For the use of this dataset, please cite: Carvalho, N. S.; Anderson L. O.; Nunes C. A.; Pessôa, A. C.M.; Silva Junior, C. H. L., Reis, J.B.C.; Shimabukuro, Y. E.; Berenguer E.; Barlow J. and Aragão, L. E. O. C. Spatio-temporal variation in dry season determines the Amazonian fire calendar. Environmental Research Letters (2021). <a href="https://doi.org/10.1088/1748-9326/ac3aa3">https://doi.org/10.1088/1748-9326/ac3aa3</a>

opennotspecifiedMar 2013View details →

Subspecies and Distribution. S. n. mgricollis Spix, 1823 — Brazilian Amazon, N Peru, and possibly SE Colombia, between the Rio Ica—Putumayo and the rios Solimoes-Amazonas and Napo, W as far the seasonally flooded forest varzea along the Tamboryacu. S. n. graellsiJiménez de la Espada, 1870 — S Colombia, NE Ecuador, and N Peru, S of the upper Rio Caqueta (W from the mouth of the Rio Yari) in Colombia, S to both sides of the upper Putumayo as far as the N (left) bank of the Rio Napo, extending E between the Napo and Putumayo as far as the seasonally flooded forest along the Tamboryacu. S. mn. hernandezi Hershkovitz, 1982 — S Colombia, Meta Department, between the rios Caqueta, Caguan, and Orteguaza and the base of the Cordillera Oriental to the Rio Guayabero. in Callitrichiade

Subspecies and Distribution. S. n. mgricollis Spix, 1823 — Brazilian Amazon, N Peru, and possibly SE Colombia, between the Rio Ica—Putumayo and the rios Solimoes-Amazonas and Napo, W as far the seasonally flooded forest varzea along the Tamboryacu. S. n. graellsiJiménez de la Espada, 1870 — S Colombia, NE Ecuador, and N Peru, S of the upper Rio Caqueta (W from the mouth of the Rio Yari) in Colombia, S to both sides of the upper Putumayo as far as the N (left) bank of the Rio Napo, extending E between the Napo and Putumayo as far as the seasonally flooded forest along the Tamboryacu. S. mn. hernandezi Hershkovitz, 1982 — S Colombia, Meta Department, between the rios Caqueta, Caguan, and Orteguaza and the base of the Cordillera Oriental to the Rio Guayabero.

Data from: Season rather than habitat affects lynx survival and risk of mortality in the human-dominated landscape of southern Sweden

Landscapes are mosaics of habitat associated with different risks and resources, including human activities, which can affect individual survival in wildlife. Different relationships between habitat characteristics and human-caused and natural mortality can result in attractive sinks. We used individual-based data from 97 Eurasian lynx (Lynx lynx) monitored for 160 exposure years to link adult survival and the risk of mortality to home range habitat characteristics in the human-dominated landscape of southern Sweden. Human-caused mortality dominated mortality causes (24 out of 37 deaths). We did not detect any strong effects of habitat characteristics explaining the variation in mortality risk in lynx. Although the density of roe deer affects several aspects of lynx ecology, we could not detect any effects of roe deer density on lynx survival, probably because roe deer density was sufficiently high in our study area. Instead, there was a high seasonal variation in mortality lynx. Mortality was highest during the hunting season for lynx (February 16 – March 31), as well as during autumn and winter, probably because lynx poaching occurred opportunistically during the hunting season for moose and roe deer. We did not find any indication that human activity created attractive sinks for lynx, since there was no contrasting pattern between human-caused and natural mortality in terms of habitat characteristics. One explanation for the limited influence of the home range characteristics may be that lynx in our study died from multiple causes (natural causes 35%, legal hunting 27 %, poaching 22 % and vehicle collisions 16 %). Therefore, it is less likely that one or a few habitat characteristics could explain the risk of mortality at the home range scale. There is strong evidence that lynx can coexist with humans in multi-use and human-dominated landscapes, even without large protected areas, if the management regimes are favourable.

The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa

Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (He : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.

opencc-zeroDec 2021View details →

The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator

Anthropogenic linear features facilitate access and travel efficiency for predators, and can influence predator distribution and encounter rates with prey. We used GPS collar data from eight wolf packs and characteristics of seismic lines to investigate whether (1) ease-of-travel or (2) access to areas presumed to be preferred by prey best explained seasonal selection patterns of wolves near seismic lines, and whether the density of anthropogenic features led to functional responses in habitat selection. At a broad scale, wolves showed evidence of habitat-driven functional responses by exhibiting greater selection for areas near low-vegetation height seismic lines in areas with low densities of anthropogenic features. We highlight the importance of considering landscape heterogeneity and habitat characteristics, and the functional response in habitat selection when investigating seasonal behaviour-based selection patterns. Our results support behaviour in line with search for primary prey during summer and fall, and ease-of-travel during spring, while patterns of selection during winter aligned best with ease-of-travel for the less-industrialized foothills landscape, and with search for primary prey in the more-industrialized boreal landscape. These results highlight that time-sensitive restoration actions on anthropogenic features can affect the probability of overlap between predators and threatened prey within different landscapes.