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opennotspecifiedJan 2022View details →

FIGURE 2 in Changminia gen. nov., a new genus of daddy-long-leg spiders (Araneae: Pholcidae) from karst caves in Southeast Asia

FIGURE 2. Changminia huangdi comb. nov., paratype male (IZCAS-Ar 21439). A–B. Pedipalp (A. Prolateral view; B. Retrolateral view); C–D. Distal part of procursus (C. Prolateral view, arrow indicates short, pointed prolatero-subdistal apophysis; D. Dorsal view, arrow indicates pointed dorsal apophysis). b = bulb, e = embolus, pr = procursus. Scale bars: 0.20 (A–B), 0.05 (C–D).

Experimental manipulation of photoperiod influences migration timing in a wild, long-distance migratory songbird

Previous laboratory studies have demonstrated the role of photoperiod in cueing the migration timing of small land birds; however, how migration timing of young birds in wild environments develops in relation to these cues have rarely been investigated. Such investigations can make important contributions to our developing understanding of the phenotypic plasticity of migration timing to new conditions with climate change, where changes in the timing of nesting may expose juvenile birds to different photoperiods. We investigated the impact of manipulating photoperiod during nestling development in a long-distance migratory songbird on the timing of post-breeding movements in the wild. Using programmable lighting installed in the nest-boxes of purple martins (Progne subis), we exposed developing nestlings, from hatch to fledge date, to an extended photoperiod that matched the day length of the summer solstice in Manitoba, Canada. We found that birds with a simulated, earlier photoperiod had a longer nesting period and later fledge and autumn departure dates than control group birds. This study demonstrates the phenotypic plasticity of first-year birds to the ontogenetic effect of their hatch date in the formation of the timing of their first post-breeding movements. Further, we discuss how these results have implications for the potential use of assisted evolution approaches to alter migration timing to match new conditions with climate change.

Does salinization impact long-term Daphnia assemblage dynamics? Evidence from the sediment egg bank in a small hard-water lake

Salinization of freshwater ecosystems threatens global aquatic biodiversity. There is a need for studies that follow populations in situ during salinization to understand the effects on species and ecosystems. We follow 170 years of Daphnia dynamics in the sediment ephippia archive of a small urban lake near St. Paul, Minnesota, to characterize effects of severe recent salinization on lake Daphnia. We found modest changes in the flux of ephippia in this lake; all three key Daphnia functional groups remained in the assemblage throughout the period of salinization. Reconstruction of the size distribution of D. pulicaria demonstrated that predation pressure by fish may not have increased for the largest and most susceptible member of the assemblage despite cultural meromixis. Our findings highlight that in hardwater lakes, the effects of salinization are nuanced and require further investigation to better understand overall impacts of salinization on lake Daphnia assemblages.

Long-term effect of regular physical activity and exercise habits in patients with early parkinson disease

Objective: Owing to the lack of long-term observations and/or comprehensive adjustment for confounding factors, reliable conclusions regarding long-term effects of exercise and regular physical activity in Parkinson's disease (PD) have yet to be drawn. Here, using data from the Parkinson's Progression Markers Initiative study that includes longitudinal and comprehensive evaluations of many clinical parameters, we examined the long-term effects of regular physical activity and exercise habits on the course of PD. Methods: In this observational cohort study, we primarily used the multivariate linear mixed-effects models to analyze the interaction effects of their regular physical activity and moderate-to-vigorous exercise levels, measured through the Physical Activity Scale for the Elderly questionnaire, on the progression of clinical parameters, after adjusting for age, sex, levodopa-equivalent dose, and disease duration. We also calculated bootstrapping 95% confidence intervals (CIs), and conducted sensitivity analyses using the multiple imputation method and subgroup analyses using the propensity score matching to match for all baseline background factors. Results: 237 early PD patients [median (interquartile range); age, 63.0 (56.0–70.0) years; Male, 69.2%; follow-up duration, 5.0 (4.0–6.0) years] were included. Regular physical activity and moderate-to-vigorous exercise levels at the baseline did not significantly affect the subsequent clinical progression of PD. However, average regular overall physical activity levels over time were significantly associated with slower deterioration of postural and gait stability [standardized fixed-effects coefficients of the interaction term (βinteraction) = -0.10 (95% CI, -0.14 to -0.06)], activities of daily living [βinteraction = 0.08 (95% CI, 0.04 to 0.12)], and processing speed [βinteraction = 0.05 (95% CI, 0.03 to 0.08)] in PD patients. Moderate-to-vigorous exercise levels were preferentially associated with slower decline of postural and gait stability [βinteraction = -0.09 (95% CI, -0.13 to -0.05)] and work-related activity levels were primarily associated with slower deterioration of processing speed [βinteraction = 0.07 (95% CI, 0.04 to 0.09)]. Multiple imputation and propensity score matching confirmed the robustness of our results. Conclusions: In the long-term, the maintenance of high regular physical activity levels and exercise habits was robustly associated with better clinical course of PD, with each type of physical activity having different effects.

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long-distance dispersal

Aim: Digitization of herbarium specimens and DNA sequencing efforts in the past decade have enabled integrative analyses of patterns of diversity and endemism in a phylogenetic context. Here, we compare the best available floristic databases to a comprehensive specimen database to examine spatial patterns of moss phylogenetic assembly. We test the hypotheses that 1) mosses exhibit phylogenetic regionalization, 2) islands contain significantly high phylogenetic diversity, and 3) that moss phylogenetic endemism is low on a global scale. Location: Global Taxon: Mosses Methods: We developed a phylogeny of 3,654 moss species using 25 markers and compiled a global specimen database from online repositories. We calculated floristic and phylogenetic measures of diversity and endemism and performed randomizations to test for significant deviations from expectations. We use rarefaction and extrapolation to alleviate substantial differences in sampling effort across the globe. We used both phylogenetic and floristic methods to test for spatial regionalization. We compare our specimen-based results to those obtained using a floristic dataset. Results: Phylogenetic diversity is more robust to missing data than species richness. Mean phylogenetic distance was significantly higher than expected in areas with high species richness, indicating that reported richness in these areas is likely a product of repeated colonization. Phylogenetic endemism is low globally. Phylogenetic regionalizations cluster into a Holarctic/Holantarctic temperate region, a pantropical region, and a region composed of Australia, New Zealand, and South Africa. Main Conclusions: Future efforts for collecting, sequencing, and databasing moss species should focus on the tropics, particularly Africa and Southeast Asia. We provide further evidence to support several important theories developed in moss biogeography, including the role of long-distance dispersal in shaping floristic patterns, the dominance of anagenesis in driving patterns of island diversity, and the role of climatic instability in driving patterns of assembly in the Holarctic.

opencc-by-4.0Jan 2022View details →

Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability

This repository includes the code and the processed climate data used to examine the long-term change in atmospheric CO2 growth rate. The code will generate the main figures (Figure 1, 2 and 3) in the paper - Luo, X. & Keenan, T. F. (2022) Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability. Nature Communications, doi: 10.1038/s41467-022-28824-5. Please refer to the "Data Availability Statement" in the paper and cite the original sources if you need to use one or more datasets published here. There are three files in the repository: 1) CGR_analysis_input.mat is the processed data in matlab format to support the study; 2) master_figures_CGR_publish_v1.m is the main matlab routine that used to generate figures; 3) supporting code is a folder that contains third-party routines to support the main routine.

opennotspecifiedJan 2022View details →

◂Fig. 9 Scanning electron microscopy images of branches of Ramisyllis kingghidorahi n. sp. A–F Midbody branching regions with segments of different morphologies, as long as wide with long dorsal cirri in A–C, much longer with short dorsal cirri in D, E and F Details of cirri alternation in length. A, C, E–F In dorsal view; B and D in ventral view. Scale bars: 200 µm A, C, 100 µm B, F, 400 µm D, and 500 µm E in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan

◂Fig. 9 Scanning electron microscopy images of branches of Ramisyllis kingghidorahi n. sp. A–F Midbody branching regions with segments of different morphologies, as long as wide with long dorsal cirri in A–C, much longer with short dorsal cirri in D, E and F Details of cirri alternation in length. A, C, E–F In dorsal view; B and D in ventral view. Scale bars: 200 µm A, C, 100 µm B, F, 400 µm D, and 500 µm E

opennotspecifiedJan 2022View details →

◂Fig. 8 Light microscope images of living specimens of Ramisyllis kingghidorahi n. sp. A Branching point. B, E–G Posterior ends showing pygidia. C, D, H, I Midbody segments in regions of long dorsal cirri. Arrows point to the ventral blood vessel in H and the digestive tract in I.A, D, E, and I in dorsal view. B, C, F and H in ventral view. G In lateral view. Scale bars: 500 µm A, E, 200 µm B, C, D, 100 µm F, H, I, and 50 µm G in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan

◂Fig. 8 Light microscope images of living specimens of Ramisyllis kingghidorahi n. sp. A Branching point. B, E–G Posterior ends showing pygidia. C, D, H, I Midbody segments in regions of long dorsal cirri. Arrows point to the ventral blood vessel in H and the digestive tract in I.A, D, E, and I in dorsal view. B, C, F and H in ventral view. G In lateral view. Scale bars: 500 µm A, E, 200 µm B, C, D, 100 µm F, H, I, and 50 µm G

opencc-by-4.0Dec 2021View details →

Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection

The datasets uploaded in this Zenodo entry were generated in the single cell RNA sequencing part of the project. For the scRNAseq analysis, cells from ten patients and the same time point were pooled together, generating four individual sample sets in total: (1) patients CoV2_T001- CoV2_T010, acute; (2) patients CoV2_T001- CoV2_T010, six months post-infection; (3) patients CoV2_T011- CoV2_T020, acute; (4) patients CoV2_T011- CoV2_T011-20, six months post-infection. We additionally generated two more sample sets: using 5000 unsorted PBMCs from each patient’s sample: (5) patients CoV2_T001- CoV2_T010, six months post-infection unsorted; (6) patients CoV2_T011- CoV2_T020, six months post-infection unsorted. The cells in these two sample sets were hashed. Finally, using PBMCs from four healthy donors, we generated sample set (7) by sorting and pooling 2000 CD8+ T cells from each healthy donor sample. We are here providing the pre-processed sets for each sample set (1-7), i.e. : - "filtered feature bc matrix" files, as output from the ‘cellranger multi’ pipeline (Cell Ranger version 5.0.0), containing cell-RNA count matrices and cell-ADT matrices. ADTs comprise counts for TotalSeq antibodies and dCODE Dextramers. - "filtered_contig_annotations.csv" files, as output from the ‘cellranger multi’ pipeline (Cell Ranger version 5.0.0), containing High-level annotations of each high-confidence, cellular contig for TCR clonal analysis. This file is not present for sets 5 and 6, because we did not perform TCR profiling for these samples. - "clusters.tsv" files, as output from the souporcell SNP analysis (version 2). To cluster cells based on their patient specific genetic variants, we merged sample sets 1, 2  and 5 (comprising sorted cells from both time points of patients CoV2_T001- CoV2_T010 and unsorted cells of the same patients) and sets 3, 4 and 6 (comprising cells from both time points of patients CoV2_T011- CoV2_T020 and unsorted cells of the same patients). Then, we executed the souporcell pipeline with option k=10 (number of clusters to be determined) for each of the two merged sample sets. Together, these files allow to reproduce the analysis as reported in the paper. Additionally, we provide the Seurat Objects "Integrated.h5seurat"  and "Integrated_NA_filtered.h5seurat" which can be used to skip the pre-processing steps of the data analysis. See the code provided on https://github.com/Moors-Code/SARS-CoV-2-Tcell-Boyman-collaboration for details.

opencc-by-4.0Feb 2022View details →

GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads

C.elegans, O.sativa and Human assemblies produced by GALA software

opencc-zeroFeb 2022View details →

Automated bird sound classifications of long-duration recordings produce occupancy model outputs similar to manually annotated data

Occupancy modeling is used to evaluate avian distributions and habitat associations, yet it typically requires extensive survey effort because a minimum of three repeat samples are required for accurate parameter estimation. Autonomous recording units (ARUs) can reduce the need for surveyors on site, yet ARUs utility were limited by hardware costs and the time required to manually annotate recordings. Software that identifies bird vocalizations may reduce expert time needed, if classification is sufficiently accurate. We assessed the performance of BirdNET – an automated classifier capable of identifying vocalizations from >900 North American and European bird species – by comparing automated to manual annotations of recordings of 13 breeding bird species collected in northwestern California. We compared the parameter estimates of occupancy models evaluating habitat associations supplied with manually annotated data (9 min recording segments) to output from models supplied with BirdNET detections. We used three sets of BirdNET output to evaluate the duration of automatic annotation needed to approach manually annotated model parameter estimates: 9-min, 87-min, and 87-min of high-confidence detections. We incorporated 100 3-sec manually validated BirdNET detections per species to estimate true and false positive rates within an occupancy model. BirdNET correctly identified 90% and 65% of the bird species a human detected when data were restricted to detections exceeding a low or high confidence score threshold, respectively. Occupancy estimates, including habitat associations, were similar regardless of method. Precision (proportion of true positives to all detections) was >0.70 for 9 of 13 species, and a low of 0.29. However, processing of longer recordings was needed to rival manually annotated data. We conclude that BirdNET is suitable for annotating multispecies recordings for occupancy modeling when extended recording durations are used. Together, ARUs and BirdNET may benefit monitoring and, ultimately, conservation of bird populations by greatly increasing monitoring opportunities.

opencc-zeroFeb 2022View details →

Data from: A shift from phenol to silica-based leaf defenses during long-term soil and ecosystem development

The resource availability hypothesis predicts that plants adapted to infertile soils have high levels of anti-herbivore leaf defenses. This hypothesis has been mostly explored for secondary metabolites such as phenolics, while it remains underexplored for silica-based defenses. We determined leaf concentrations of total phenols and silicon (Si) in plants growing along the 2-million-year Jurien Bay chronosequence, exhibiting an extreme gradient of soil fertility. We found that nitrogen (N) limitation on young soils led to a greater expression of phenol-based defenses, whereas old, phosphorus (P)-impoverished soils favored silica-based defenses. Both defense types were negatively correlated at the community and individual species level. Our results suggest a tradeoff among these two leaf defense strategies based on the strength and type of nutrient limitation, thereby opening up new perspectives for the resource availability hypothesis and plant defense research. This study also highlights the importance of silica-based defenses under low P supply.

opencc-zeroFeb 2022View details →

Supplementary material 1 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431

Table S1. List of specimens used for this study, including their voucher information, plate location, indexing, amplicon concentration and sequencing results, both as an output from SMRT tools (CCSs) and as an output from DADA2 (sequence variants). Table S2. List of the 64 barcode sequences used to index the samples. Used barcode pairs are listed in Table S1

FIGURE 98 in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURE 98. Distribution of Psechrus in continental South East Asia. Symbols (unicoloured): species belonging to the himalayanus-group. Symbols (black, filled with light colour): species belonging to the ancoralis-group. Distribution of Psechrus in northern Vietnam, see Fig. 96. The distribution of P. demiror sp. nov. is unclear (see corresponding species description), hence the violet, unicoloured trapezes are depicted with question mark each.

FIGURE 94 in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURE 94. Distribution of Psechrus in southern India and Sri Lanka. Symbols: species belonging to the torvus-group. Arrow: Distribution of P. crepido sp. nov.

FIGURES 93a–b in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURES 93a–b. Psechrus spp., photos of mating behaviour (a) and female carrying egg sac (b). a ♀ (above) and ♂ (below) P. luangprabang from Laos, Vientiane Prov. b ♀ P. senoculatus from China, Sichuan Prov. Photos by Peter Jäger, Frankfurt am Main.

FIGURES 91a–o in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURES 91a–o. Psechrus spp., photos of vulva, dorsal view. a P. ancoralis. b P. rani. c P. laos sp. nov. d P. antraeus. e P. khammouan. f P. steineri. g P. inflatus sp. nov. h P. himalayanus. i P. marsyandi. j P. pakawini sp. nov. k P. ghecuanus. l P. demiror sp. nov. m P. luangprabang. n P. jaegeri sp. nov. o P. vivax sp. nov. a ♀ SB 324 from Laos, Luang Prabang Prov. b ♀ SB 818 from China, Hongkong. c ♀ paratype SB 374 from Laos, Bolikhamsay Prov. d ♀ SB 294 from Laos, Vientiane Prov. e ♀ SB 382 from Laos, Khammouan Prov. f ♀ holotype SB 65 from Laos, Khammouan Prov., Xe Bangfai cave system. g ♀ paratype SB 951 from China, Yunnan Prov. h ♀ SB 988 from India, Uttarakhand Prov. i ♀ paratype SB 227 from Nepal, Dhawalagiri Prov. j ♀ paratype SB 214 from Thailand, Chiang Mai Prov. k ♀ SB 39 from Laos, Luang Nam Tha Prov. l ♀ holotype SB 331 from "Indochina". m ♀ SB 424 from Laos, Vientiane Prov. n ♀ paratype SB 300 from Laos, Champasak Prov. o ♀ paratype SB 366 from Thailand, Trat Prov., Koh Chang.

FIGURES 90a–k in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURES 90a–k. Psechrus spp., photos of vulva, dorsal view. a P. argentatus. b P. libelti. c P. mulu. d P. borneo. e P. annulatus. f P. aluco sp. nov. g P. decollatus sp. nov. h P. singaporensis. i P. elachys sp. nov. j P. norops sp. nov. k P. arcuatus sp. nov. a ♀ SB 551 from Papua New Guinea, Morobe Prov. b ♀ SB 87 from Indonesia, Sumatra, Mentawei Islds. c ♀ SB 253 from Malaysia, Borneo, Sarawak Prov. d ♀ holotype SB 279 from Indonesia, Kalimantan Timur Prov. e ♀ lectotype SB 829 from Indonesia, Jawa Tengah Prov. f ♀ holotype SB 123 from Indonesia, Jawa Barat Prov. g ♀ holotype SB 501 from Indonesia, Jawa Timur Prov. h ♀ SB 220 from Singapore. i ♀ holotype SB 861 from Thailand, Satun Prov. j ♀ holotype SB 860 from Malaysia, Pahang Prov. k ♀ holotype SB 333 from Indonesia, Sumatera Barat Prov.

FIGURE 100 in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURE 100. Distribution of Psechrus in eastern Malaysia and central Indonesia. Symbols (unicoloured): species belonging to the annulatus-group. Symbols (black, filled with light colour): species belonging to the mulu-group. Arrows: species belonging to the argentatus-group.

FIGURE 96 in The lace-sheet-weavers—a long story (Araneae: Psechridae: Psechrus)

FIGURE 96. Distribution of Psechrus in China and northern Vietnam. All species belong to the sinensis-group except P. inflatus sp. nov. (himalayanus-group) and P. rani (ancoralis-group). Distribution of Psechrus in Taiwan, see Fig. 97. For the distribution of P. ghecuanus in China, see Fig. 98.