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opencc-zeroApr 2022View details →

Path-finding algorithm as a dispersal assessment method for invasive species with human-vectored long-distance dispersal event

Aim: An assessment method that can precisely represent human-vectored long-distance dispersals (HVLDD) is currently in need for effective management of invasive species. Here, we focused on HVLDD happening along roads and proposed a path-finding algorithm as a more precise dispersal assessment tool than the most widely used Euclidean distance method by using pine wilt disease (PWD) as a case study. Location: Busan Metropolitan City, Republic of Korea Methods: A path-finding algorithm, which calculates distances by considering spatial distribution of road networks, was tested for its effectiveness in estimating dispersal distances of HVLDD events. To this end, annual HVLDD cases were classified from entire PWD occurrence data from 2016 to 2019 and their dispersal distances were calculated using the path-finding algorithm and the Euclidean distance method. We constructed potential dispersal ranges based on the occurrence points in 2016, 2017, and 2018 using the respective year's mean dispersal distance for both methods, and their performances in accounting for each subsequent year's HVLDD cases were compared to determine which method calculated more precise distances. The information on which road class contributed more to dispersal occurrences and distances was analysed as well using the proposed algorithm. Results: The potential dispersal ranges of the path-finding algorithm accounted for more future anthropogenic infection cases than the ones that used the Euclidean distance method, validating its higher functionality. It also revealed that most HVLDDs started and ended on small roads, and large roads constituted the majority of the total dispersal length. Main Conclusions: The path-finding algorithm has proven to be a more effective dispersal assessment method for HVLDD events. It can help design effective control strategies. Thus, we encourage using the path-finding algorithm for dispersal assessment of invasive species that move along road networks, as well as for the development of more powerful HVLDD prediction models.a

opencc-by-4.0Jun 2022View details →

Enzymatic digestion method development for long-term stored chitinaceous planktonic samples - Data

<table> <tbody> <tr> <td>Data for  Carrillo-Barragán, Priscilla, Heather Sugden, Catherine Scott, and Clare Fitzsimmons. 2022.  “Enzymatic Digestion Method Development for Long-Term Stored Chitinaceous Planktonic Samples.”  Marine Pollution Bulletin. </td> </tr> </tbody> </table>

opencc-by-4.0Feb 2022View details →

Data set from long-term wind and acceleration monitoring of the Gjemnessund Bridge

The Gjemnessund Bridge has been monitored by accelerometers and anemometers for almost ten years. The data collected between 2013 and 2018 are now available in this open-access research entry, for free access and download. The data is collected in two h5-files (hierachical data format), with sampling rates 2 Hz and 10 Hz, downsampled from the raw sampling rate of 200 Hz. Some minimal signal processing is applied to the data in line with that applied to the Hardanger Bridge data described in Fenerci et al. (2021) and the Bergsøysund Bridge data described in Kvåle et al. (2022). The structure of the data is identical to that of the latter reference, which is described in a preprint appended to that research entry. The Python package opyndata available on GitHub contains useful tools compatible with the format of the dataset, for data import, processing and visualization.

opencc-zeroApr 2022View details →

Negative temporal autocorrelation in mast seeding dynamics positively influences both the long and short-term dynamics of a wild boar population

Temporal autocorrelation in environmental conditions influences population dynamics through its effects on vital rates. However, a comprehensive understanding of how and to what extent temporal autocorrelation shapes population dynamics is still lacking because most empirical studies have unrealistically assumed that environmental conditions are temporally independent. Mast seeding is a biological event characterized by highly fluctuating and synchronized seed production at the tree population scale, as well as a marked negative temporal autocorrelation. In the current context of global change, mast seeding events are expected to become more frequent, leading to strengthened negative temporal autocorrelations and thereby amplified cyclicality in mast seeding dynamics with cycles of length 2 years. Theory predicts that population growth rates are maximized when the environmental cyclicality of consumer resources and their generation times are closely matched. To test this prediction, we took advantage of the long-term monitoring of a wild boar population, a widespread seed consumer species characterized by a short generation time (ca. 2 years). As expected, simulations indicated that its stochastic population growth rate increased as mast seeding dynamics became more negatively autocorrelated. Our findings demonstrate that accounting for temporal autocorrelations in environmental conditions relative to generation time of the focal population is required, especially under global warming where the cyclicality in resource dynamics is likely to change.

opencc-zeroApr 2022View details →

Coordination of care by breeders and helpers in the cooperatively breeding long-tailed tit, Aegithalos caudatus

In species with biparental and cooperative brood care, multiple carers cooperate by contributing costly investment to raise a shared brood. However, shared benefits and individual costs also give rise to conflict among carers over investment. Coordination of provisioning visits has been hypothesized to facilitate the resolution of this conflict, preventing exploitation, and ensuring collective investment in the shared brood. We used a 26-year study of long-tailed tits, Aegithalos caudatus, a facultative cooperative breeder, to investigate whether care by parents and helpers is coordinated, whether there are consistent differences in coordination between individuals and reproductive roles, and whether coordination varies with helper relatedness to breeders. Coordination takes the form of turn-taking (alternation) or feeding within a short time interval of another carer (synchrony), and both behaviors were observed to occur more than expected by chance, i.e. 'active' coordination. First, we found that active alternation decreased with group size while active synchrony occurred at all group sizes. Secondly, we show that alternation was repeatable between observations at the same nest, while synchrony was repeatable between observations of the same individual. Active synchrony varied with reproductive status, with helpers synchronizing visits more than breeders, although active alternation did not vary with reproductive status. Finally, we found no significant effect of relatedness on either alternation or synchrony exhibited by helpers. In conclusion, we demonstrate active coordination of provisioning by carers and conclude that coordination is a socially plastic behavior depending on reproductive status and the number of carers raising the brood.

opencc-by-4.0Jun 2022View details →

Long read proteogenomics to characterize protein isoform diversity in human umbilical vein endothelial cells (HUVECs)

Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system and their phenotypes can be modulated by protein isoforms. To characterize the isoform landscape within EC, we applied a long read proteogenomics approach to analyze human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream MS analysis to infer protein isoform expression. We detected 53,836 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signaling pathways. Finally, we identified novel protein isoforms arising from a diversity of splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.

opencc-by-4.0May 2022View details →

Designing of Fiber Bragg Gratings for Long-distance Optical Fiber Sensing Networks

Research data of Modelling and Simulation in Engineering journal article “Designing of Fiber Bragg Gratings for Long-distance Optical Fiber Sensing Networks”. Most optical sensors on the market are optical fiber Bragg grating (FBG) sensors with low reflectivity (typically 7-40%) and low side-lobe suppression (SLS) ratio (typically SLS <15dB), which prevents these sensors from being effectively used for long-distance remote monitoring and sensor network solutions. This research is based on designing the optimal grating structure of FBG sensors and estimating their optimal apodization parameters necessary for sensor networks and long-distance monitoring solutions. Gaussian, sine and raised sine apodizations are studied to achieve the main requirements, which are - maximally high reflectivity (at least 90%) and side-lobe suppression (at least 20 dB), as well as maximally narrow bandwidth (FWHM<0.2 nm), FBGs with uniform (without apodization). Results gathered in this research propose high-efficiency FBG grating apodizations, which can be further physically realized for optical sensor networks and long-distance (at least 40 km) monitoring solutions.

opencc-by-4.0May 2022View details →

Nocturnal flight calls dataset: long-term acoustic monitoring of birds migrating at night

General Description: This is a development set used in the experiments in the Ph.D. thesis: "Nowe metody akustycznej identyfikacji ptaków migrujących nocą" ("Novel methods of acoustic identification of birds migrating at night") by Hanna Pamula. The project focuses on the detection (and - partially - classification) of passerine birds' calls from long-term audio recordings collected during bird autumn migration between 2016 and 2019. The dataset consists of >56,5 hours of recordings with annotations of nocturnal flight calls of passerine birds migrating along the Baltic Sea coast, Poland.   Folder Structure Development_Set_3.1.zip |_Development_Set_3.1/     |__Training_Set/             |____*.wav             |____*.txt     |__Validation_Set/             |____*.wav             |____*.txt     |__Testing_Set/             |____*.wav             |____*.txt Training Set: 86 recordings Validation Set: 8 recordings Testing set: 18 recordings (BUT: uploaded 20 recordings, as in the previous version of the dataset - version 3, two additional recordings were used. Then, they were deleted in the final version of development set 3.1. Two additional recordings are: 'BUK5_20161101_002104a and BUK5_20161101_002104b) Names of waveforms and annotations are matching. Waveforms: The whole dataset consists of 114 recordings. One hundred thirteen recordings are about 30 minutes long (29min56s – 29min 59s), one recording is 1min20s. All data were recorded at 44,100 Hz sampling rate, one channel, with SM2 Wildlife Acoustics recorders + SMX-NFC microphone. The recording sessions were performed at night (starting time and date denoted in a file name) on the Baltic Sea coast in Poland (Dąbkowice, near Darłowo). Annotations: Transcriptions were produced using Audacity 2.4.1: https://www.audacityteam.org/ by an experienced birdwatcher, Hanna Pamula. While every effort has been made to ensure the quality and accuracy of the labels, some errors may occur, taking into account the difficulty of nocturnal call recognition and transcription tasks in general. Transcription format: [Starting time (sec)] [Ending time (sec)] [Label] Meaning of the labels: 1. Positive classes – migrating passerine birds: <ul> <li>'s' – song thrush call (Turdus philomelos)</li> <li>'k' – blackbird call (Turdus merula)</li> <li>'d' – redwing call (Turdus iliacus)</li> <li>'r' – robin call (Erithacus rubecula)</li> <li>‘kwiczol’ – fieldfare call (Turdus pilaris)</li> <li>‘skowronek’ – skylark call (Alauda arvensis)</li> <li>Each of the above labels could also have a question mark '?', e.g. 'r?', 'k?' – meaning that it's not a sure label. In a bird call detection task, they are regarded as positive chunks containing bird call(s).</li> <li>'ni' – non identified bird call (distant/quiet/not recognized)</li> </ul> Only the supposed calls of migrating passerine birds were labeled; other sounds of species were ignored (e.g., robin's tik-calling, which can be often heard at dusk, and may be regarded as warning sounds). 2. Negative classes – other marked sound events: <ul> <li>'g' – other bird calls/songs/sounds. Sounds that could confuse the model; for example, sounds of migrating geese, cranes, plovers calls, etc.</li> <li>'gh' – human voices</li> <li>'t' – cracks, clicks, raindrops, other noise</li> <li>‘puszczyk’ – tawny owl voice (Strix aluco)</li> <li>'czapla' – grey heron voice (Ardea cinerea)</li> </ul> Not all occurrences of the negative sounds were labeled – only some chosen examples to represent the possible noises/negative samples. Thus these annotations can't be used for entirely different detection / classification tasks than intended, e.g., detecting migrating cranes or human voices in long-term recordings. 3. Labels to be excluded from analysis: <ul> <li>'???', '??? mysz', '??? high freq' – unknown, not sure if the sound event is a birds' call or not. Uncertainty about belonging to a positive/negative class in the detection task.</li> </ul>

(10)-Strobl2022A-DS0008 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0008 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0004 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0004 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0001 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0001 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0003 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0003 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0002 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0002 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0007 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0007 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0009 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0009 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0006 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0006 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0005 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

opencc-by-4.0May 2022View details →

Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter

Data and code for mixed-model analysis for the article:  Mukhacheva S.V. (2022) Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter" // Russian Journal of Ecology. Vol. 5.  Data provided by S.V. Mukhacheva Code provided by A.N. Sozontov

opencc-zeroMay 2022View details →

Experimental data: Inferring strategies from observations in long iterated prisoner's dilemma experiments

While many theoretical studies have revealed the strategies that could lead to and maintain cooperation in the Iterated Prisoner's Dilemma, less is known about what human participants actually do in this game and how strategies change when being confronted with anonymous partners in each round. Previous attempts used short experiments, made different assumptions of possible strategies, and led to very different conclusions. We present here two long treatments that differ in the partner matching strategy used, i.e. fixed or shuffled partners. Here we use unsupervised methods to cluster the players based on their actions and then Hidden Markov Model to infer what are those strategies in each cluster. Analysis of the inferred strategies reveals that fixed partner interaction leads to a behavioral self-organization. Shuffled partners generate subgroups of strategies that remain entangled, apparently blocking the self-selection process that leads to fully cooperating participants in the fixed partner treatment. Analyzing the latter in more detail shows that AllC, AllD, TFT- and WSLS-like behavior can be observed. This study also reveals that long treatments are needed as experiments less than 25 rounds capture mostly the learning phase participants go through in these kinds of experiments.