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opencc-by-4.0Jun 2023View details →

Sluggish basal mantle structures support their long-lived stability

Dataset and script for "Sluggish basal mantle structures support their long-lived stability"

opencc-by-4.0Jun 2023View details →

Replication Package for ESEC/FSE 2023 Paper "How Early Participation Determines Long-Term Sustained Activity in GitHub Projects?"

This replication package can be used for replicating results in the paper. It contains 1) a dataset of 290,255 repositories; and 2) Python scripts for training and interpreting models. The GitHub repository of the paper is available at <a href="https://github.com/mcxwx123/Sustainable_projects">https://github.com/mcxwx123/Sustainable_projects</a>. We recommend manually setup the required environment in a commodity Linux machine with at least 1 CPU Core, 8GB Memory and 100GB empty storage space. We conduct development and execute all our experiments on a Ubuntu 20.04 server with two Intel Xeon Gold CPUs, 320GB memory, and 36TB RAID 5 Storage. We use GHTorrent to restore historical states of 290,255 repositories with more than 57 commits, 4 PRs, 1 issue, 1 fork and 2 stars. The raw data of repositories (collected in their first 1,3,5 months(s)) are stored in `Replication Package/data/prodata_1.pkl`, `Replication Package/data/prodata_3.pkl`, and `Replication Package/data/prodata_5.pkl`. The contribution of features resulting from LIME model is stored in `Replication Package/data/limeres_m3_t2_k1.pkl`. `Replication Package/data/X_test_m3_t2_k1.pkl` and `Replication Package/data/y_test_m3_t2_k1.pkl` store the test dataset for the LIME model. You can run `Replication Package/fitdata.py` to get the results in Table 3 and 4, run `Replication Package/draw_compare_variable.py` to get Figure 2 and run `Replication Package/allvari_statistics.py` to get Table 5. In `Replication Package/Variable_comparison_with_different_parameter.pdf`, we show the LIME results under different parameters. In `Replication Package/sample_pros.csv`, we also provide the list of randomly selected repositories in Section 3.1.   The explanations for collecting the variables, the examples of variable effects on project sustainability, and the hyperparameter setting of the machine learning models are provided in the README.md file.

Fig. 2 in Nematodes of the order Dorylaimida from Andalucía Oriental, Spain. The genus Enchodelus Thorne, 1939. 2. Description of three known species with rounded tail and long odontostyle

Fig. 2. Enchodelus groenlandicus (Ditlevsen, 1927) Thorne, 1939 (female). A: Variability of anterior region; B: Neck showing location of dorsal gland nucleus (large arrow) and one of subventral gland nuclei (small arrow); C: Anterior genital branch, with location of sphincter between uterus and oviduct marked by arrow; D: Detail of uterus-oviduct junction showing sphincter, distal pars dilatata uteri and cluster of hyaline cells surrounding intermediate narrow region of uterus; E: Entire body of female with four eggs; F: Variability of vulval region; G: Variability of tail. (Scale bars: A, D, F, G = 20 µm; B, C = 100 µm; E = 200 µm.)

Fig. 6. Enchodelus saxifragae Popovici, 1995 in Nematodes of the order Dorylaimida from Andalucía Oriental, Spain. The genus Enchodelus Thorne, 1939. 2. Description of three known species with rounded tail and long odontostyle

Fig. 6. Enchodelus saxifragae Popovici, 1995 (female). A: Variability of anterior region; B: Neck showing dorsal gland nucleus (large arrow) and one of subventral gland nuclei (small arrow); C: Variability of vulval region; D: Entire body; E: Detail of uterus-oviduct junction, showing sphincter, pars dilatata uteri and intermediate region of uterus surrounded by a cluster of hyaline cells; F: Anterior genital branch with location of sphincter between uterus and oviduct marked by arrow; G: Variability of tail. (Scale bars: A, C, E, G = 20 µm; B, F = 100 µm; D = 500 µm.)

Fig. 1 in Nematodes of the order Dorylaimida from Andalucía Oriental, Spain. The genus Enchodelus Thorne, 1939. 2. Description of three known species with rounded tail and long odontostyle

Fig. 1. Enchodelus groenlandicus (Ditlevsen, 1927) Thorne, 1939 (female). A: Entire body; B: Neck; C: Anterior region; D: Reconstruction of superficial appearance of anterior region, lateral view; E: Anterior genital branch; F: Tail; G: Vulval region. (Scale bars: A = 500 µm; B, E = 100 µm; C, D, F, G = 50 µm.)

Fig. 3 in Nematodes of the order Dorylaimida from Romania. The genus Enchodelus Thorne, 1939. 3. Species with rounded tail and long odontostyle

Fig. 3. Enchodelus macrodorus (de Man, 1880) Thorne, 1939. A: Female, entire; B, C, E: Anterior region in median, lateral view; D: Lip region in surface, lateral view; F: Pharyngeal expansion; G, H: Female genital system; I: Vagina; J, K: Female caudal region. (Scale bars: A = 200 µm; B, F-H = 20 µm; C-E, I-K = 10 µm.)

Fig. 4. Enchodelus saxifragae Popovici, 1995. A in Nematodes of the order Dorylaimida from Romania. The genus Enchodelus Thorne, 1939. 3. Species with rounded tail and long odontostyle

Fig. 4. Enchodelus saxifragae Popovici, 1995. A: Female, entire; B-D: Anterior region in median, lateral view; E: Vagina; F: Pharyngeal expansion; G, H: Female genital system; I: Male posterior region; J, K: Female caudal region; L, M: Spicule. (Scale bars: A = 200 µm; B, C, F-I = 20 µm; D, E, J-M = 10 µm.)

Fig. 2 in Nematodes of the order Dorylaimida from Romania. The genus Enchodelus Thorne, 1939. 3. Species with rounded tail and long odontostyle

Fig. 2. Enchodelus carpaticus sp. n. A: Female, entire; B, C: Anterior region in median, lateral view; D: Pharyngeal expansion; E: Neck region; F-H: Arrows point at cell mass located in dorsal position between cardia level and proximal end of anterior ovary; I: Female genital system; J: Female posterior region; K, L: Vagina (arrow indicates advulval cells); M: Female caudal region. (Scale bars: A = 200 µm; B-D, F-H = 20 µm; E, I, J = 50 µm; K-M = 10 µm.)

Fig. 1 in Nematodes of the order Dorylaimida from Romania. The genus Enchodelus Thorne, 1939. 3. Species with rounded tail and long odontostyle

Fig. 1. Enchodelus carpaticus sp. n. A: Female, entire; B: Anterior region in median, lateral view; C: Lip region in surface, lateral view; D: Neck region; E: Female posterior region; F: Pharyngeal expansion; G: Vagina; H: Female genital system; I, J: Cell mass located in dorsal position between cardia level and proximal end of anterior ovary; K: Female caudal region.

Fig. 3. SEM micrographs. A-C in Nematodes of the order Dorylaimida from Andalucía Oriental, Spain. The genus Enchodelus Thorne, 1939. 2. Description of three known species with rounded tail and long odontostyle

Fig. 3. SEM micrographs. A-C: Enchodelus groenlandicus (Ditlevsen, 1927) Thorne, 1939, anterior end. A: Semi en face view; B: Lateral view; C: En face view. D-F: Enchodelus macrodorus (de Man, 1880) Thorne, 1939, anterior end. D: Semi en face view; E: Lateral view; F: En face view. G-I: Enchodelus saxifragae Popovici, 1995, anterior end. G: Semi en face view; H: Lateral view; I: En face view. J-L: Vulval region, J: Enchodelus groenlandicus; K: Enchodelus macrodorus; L: Enchodelus saxifragae. (Scale bars: A, B, E, G, H, J-L = 20 µm; C, D, F, I = 10 µm.)

opencc-by-4.0Jul 2023View details →

A novel immune-related prognostic signature based on Chemoradiotherapy sensitivity predicts long-term survival in patients with esophageal squamous cell carcinoma.

Raw Data for PeerJ

dryad32/100

Data from: Long term monitoring reveals the importance of large, long unburnt areas and smaller fires in moderating mammal declines in fire-prone savanna of northern Australia

Biodiversity loss is often attributable to multiple interacting pressures that are moderated across environmental gradients. These processes contribute to complex responses that are challenging to interpret and understand. Well-designed and well-implemented monitoring can play a vital role in this but is rarely undertaken. Mounting evidence suggests that current fire regimes across savanna ecosystems have contributed to the decline of a range of biota. Hence, contemporary fire regimes are at odds with conservation goals. Using an extensive spatio-temporal monitoring dataset from three large National Parks in northern Australia, we applied generalised linear mixed models to examine: 1) trends in mammal richness and abundance through time and how these vary across environmental gradients such as productivity or landscape position (e.g., terrain ruggedness); and 2) how fire, a potential driver, is moderated by environmental gradients. Across 24-years, major declines in mammal richness and abundance were observed with greater reductions in less rugged and less mesic habitats. Patterns of decline were related to multiple aspects of fire regimes, but not changes in vegetation structure and composition, or the arrival of Cane Toads Rhinella marina and concomitant poisoning of predatory animals during consumption. More pronounced declines occurred in sites that were exposed to larger fires, had less long unburnt (5 years without fire) vegetation, and were more distant from large, long unburnt patches. Relationships between mammal persistence and fire varied among vegetation communities, with the strongest fire effects observed in lowland woodland – relatively drier with few barriers to fire spread – where the availability of long unburnt areas moderated declines more than in other vegetation communities. Synthesis and applications. Current fire regimes are contributing to mammal declines in northern Australian savanna. Collectively, our results highlight: 1) the value of long term monitoring, and importance of considering landscape position when assessing faunal responses to landscape-level perturbations like fire; 2) that significant improvements in fire regimes are required to ameliorate mammal declines; and 3) the need to shift management focus from retaining small, short-lived unburnt patches towards preserving relatively large contiguous areas of long unburnt habitat, particularly in less rugged lowland and sandstone woodlands.

opencc-zeroJul 2023View details →

dryad32/100

Data for: Lack of intergenerational reproductive conflict, rather than lack of inclusive fitness benefits, likely explains absence of post-reproductive lifespan in long-finned pilot whales

Life history theory suggests that individuals should reproduce until death, yet females of a small number of mammals live for a significant period after ceasing reproduction, a phenomenon known as post-reproductive lifespan. It is thought that the evolution of this trait is facilitated by increasing local relatedness throughout a female's lifetime. This allows older females to gain inclusive fitness through helping their offspring (known as a mother effect) and/or grandoffspring (known as a grandmother effect), rather than gaining direct fitness through reproducing. However, older females may only benefit from stopping reproducing when their direct offspring compete with those of their daughters. Here, we investigate whether a lack of post-reproductive lifespan in long-finned pilot whales (Globicephala melas) results from minimal benefits incurred from the presence of older females, or from a lack of costs resulting from mother-daughter co-reproduction. Using microsatellite data, we conducted parentage analysis on individuals from 25 pods and find that younger females were more likely to have offspring if their mother was present in their pod, indicating that mothers may assist inexperienced daughters to reproduce. However, we found no evidence of reproductive conflict between co-reproducing mothers and daughters, indicating that females may be able to reproduce into old age whilst simultaneously aiding their daughters in reproduction. This highlights the importance of reproductive conflict in the evolution of a post-reproductive lifespan and demonstrates that mother and grandmother effects alone do not result in the evolution of a post-reproductive lifespan.

opencc-zeroJul 2023View details →

opencc-by-4.0Feb 2023View details →

Thermal adaptation of microbial respiration persists throughout long-term soil carbon decomposition

The microbial respiration data supporting the main findings of the study titled 'Thermal adaptation of microbial respiration persists throughout long-term soil carbon decomposition'. Mass-specific microbial respiration was consistently lower under higher long-term incubation temperatures, suggesting the occurrence and persistence of microbial thermal adaptation in long-term soil carbon decomposition.

opencc-by-4.0Mar 2023View details →

The data used in correspondence on the article entitled "Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation'."

The data used in correspondence on the article entitled “Reply: Correspondence on NanoVar’s performance outlined by Jiang T. et al. in ‘Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation’.”. It contains the benchmarking results evaluated by Truvari. The running log files of NanoVar are also included in this repository.

Fig. 4 in Survey of the allelopathic potential of Mediterranean macroalgae: production of long-chain polyunsaturated aldehydes (PUAs)

Fig. 4. Relative abundance (%) of aldehydes in macroalgae sampled in July 2017 (A) and April 2018 (B).

Fig. 3 in Survey of the allelopathic potential of Mediterranean macroalgae: production of long-chain polyunsaturated aldehydes (PUAs)

Fig. 3. Representative chromatograms (m/z 181) of standard compounds and algal extracts: (A) standards; (B) Ulva cf. rigida; (C) Dictyopteris polypodioides. The numbers 1–13 correspond to the oxime derivates of the putatively identified substances: (1) hexadienal; (2) benzaldehyde; (3) 2,4-heptadienal; (4) 2,4- octadienal; (5) 2,4-decadienal; (6) nonatetraenal; (7) nonatrienal; (8) decatetraenal; (9) hexadecadienal; (10) pentadecanal/hexadecaheptaenal; (11) tetradecapentaenal; (12) hexadecatrienal; (13) hexadecatetraenal.

Fig. 2 in Survey of the allelopathic potential of Mediterranean macroalgae: production of long-chain polyunsaturated aldehydes (PUAs)

Fig. 2. Total aldehydes production (nmol g 1) in Mediterranean macroalgae (data are mean ± st. dev. of 3 replicates).

Fig. 5 in Survey of the allelopathic potential of Mediterranean macroalgae: production of long-chain polyunsaturated aldehydes (PUAs)

Fig. 5. Aldehydes production (nmol g 1) by Dictyopteris polypodioides at the different sampling times (data are mean ± st. dev. of 3 replicates).

Fig. 2 in Long-chain alkenes and alkadienes of eight lichen species collected in Japan

Fig. 2. Mass spectra of 1,8-heptadecadiene (1), 6,9-heptadecadiene (2), 8-heptadecene (3), 7-heptadecene (4), 1-heptadecene (5), 3-heptadecene (6), 1-octadecene (7), 4-octadecene (8), 5-nonadecene (9), and 6-eicosene (10) from lichens and mass spectra of their DMDS adducts.