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opencc-by-4.0Dec 2021View details →

Experiences Implementing and Utilizing a Notional Machine in the Classroom

Notional Machine Specification for: Paul E. Dickson, Tim Richards, and Brett A. Becker. 2022. Experiences Implementing and Utilizing a Notional Machine in the Classroom. In Proceedings of the 53rd ACM Technical Symposium on Computer Science Education V. 1 (SIGCSE 2022), March 3–5, 2022, Providence, RI, USA. ACM, New York, NY, USA, 7 pages. https://doi.org/10.1145/3478431.3499320   When referring to this dataset, please cite the above article. That contains the DOI of this dataset. Please do not cite this dataset directly without citing the article.

opencc-by-4.0Sep 2021View details →

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Polysaccharide utilization loci (PULs) in the human gut microbiome have critical roles in shaping human health and ecological dynamics. We develop a CRISPR-FnCpf1-RecT genome-editing tool to study 23 PULs in the highly abundant species B. uniformis (BU). We identify the glycan-degrading functions of multiple PULs and elucidate transcriptional coordination between PULs that enables the population to adapt to the loss of PULs. Exploiting a pooled BU mutant barcoding strategy, we demonstrate that the in vitro fitness and the colonization ability of BU in the murine gut is enhanced by deletion of specific PULs and modulated by glycan availability. We show that BU PULs can mediate complex glycan-dependent interactions with butyrate producers that depend on the mechanism of degradation and the butyrate producer glycan utilizing ability. In sum, PULs are major determinants of community dynamics and butyrate production and can provide a selective advantage or disadvantage depending on the nutritional landscape.

opencc-by-4.0Jan 2022View details →

A Dataset for Utility Prediction in Computational Persuasion with Machine Learning Techniques

This dataset contains data for a new benchmark for the prediction of user's utilities with Machine Learning techniques for Computational Persuasion. This work has been accepted at AAAI-22, more information in the relative repository containing the source code: <a href="https://github.com/ivanDonadello/ML-Argument-Based-Computational-Persuasion">https://github.com/ivanDonadello/ML-Argument-Based-Computational-Persuasion</a>

opencc-by-4.0Feb 2022View details →

Response to COVID-19: Clients' perspectives on the utilization of reproductive, maternal and child health care services in Nigeria

This dataset was a part of a cross-sectional descriptive study in 320 rural communities in 32 Local Government Areas (LGAs) across the Federal Capital Territory (FCT), Abuja, and 9 out of the 36 Nigerian States in 2020. The dataset contains views of women who used primary health care centres in the selected LGAs for maternal and child health care, and family planning services before, during, and after the COVID-19 pandemic lockdown in Nigeria. The sample size was determined using the Yamane sample size formula. The estimated sample size per State was 384 (3,840 for nine States and FCT), with a 10% adjustment for non-response, the total sample size was 422 per State or location (4220 for the nine States and FCT). The data are stored in SPSS format.  The study was an initiative of UNFPA Nigeria. They coordinated it under the One UN Basket fund to respond to COVID-19 and implemented it under the supervision of three national NGOs: The Women’s Health and Action Research Centre (WHARC), Education as a Vaccine (EVA), and the Planned Parenthood Federation of Nigeria (PPFN).

opencc-by-4.0Jul 2022View details →

Intention to utilize telehealth service in Bangladesh

This data consists of information on participants' knowledge, perceived benefit, perceived concerns, and predispositions related to telehealth services in Bangladesh. In the data set, k1 to k5 indicted the items of knowledge. Similarly, pb1 to pb4 indicate perceived benefit, pc indicates the item of perceived concern, and pd1 to pd2 indicates the items of predisposition. This data set also includes information related to the demographic and perceived health status information.

opencc-by-4.0Sep 2022View details →

A Survey of Electron Conics at Jupiter Utilizing the JADE-E Data During Science Orbits 01, 03-30

This dataset provides Figure 1 from the AGU JGR: Space Physics article of the same name as a PNG image. It also includes text files with the data to reproduce Figures 2-13 in the same AGU JGR:Space Physics article. Key Points: <ol> <li>We surveyed the JADE-E data for science orbits 01, 03-30 and found upward, downward, and bidirectional electron conics 2.5% of the time</li> <li>We observed all electron conics to occur most often at altitudes of 0.3-0.4 RJ and local times of 15-16h</li> <li>We observed all electron conic types to have energies greater than 0.7 keV below an altitude of 0.5 RJ and over the main auroral region</li> </ol> Abstract We present a survey of electron conics over Jupiter’s high latitude regions utilizing 22.6 hours of data from the Jovian Auroral Distribution Experiment electron (JADE-E) instrument aboard NASA’s Juno spacecraft during science orbits 01 and 03-30. We observed electron conics for about 2.5% of this time and characterized them into three types based on their direction of motion along Jupiter’s magnetic field lines: upward, downward, and bidirectional. We observed the upward electron conics most often and at energies of 0.057-80.1 keV, while we observed the downward electron conics least often and at energies of 0.073-1.2 keV. We observed bidirectional electron conics mostly around the same times and places as the upward electron conics having energies of 0.081-49.6 keV. We observed all electron conic types to occur mostly at altitudes 0.3-0.4 RJ and local times 15-16h. Furthermore, we observed all electron conic types to have energies greater than 0.7 keV below an altitude of 0.5 RJ and over the main auroral region.

Fig. 3 in Occurrence of a Skin Parasite Argulus coregoni (Branchiura: Argulidae) on Salmonids in Mountain Streams, Central Japan, with Discussion on Its Longitudinal Distribution and Host Utilization in Rivers

Fig. 3. Mountain streams where the salmonids infected with Argulus coregoni were caught in Gifu Prefecture, central Japan. A, Main stream of the upper Maze River (locality 1 in Fig. 2); B, tributary of the Hida River (locality 2); C, tributary of the Tsukechi River (locality 3); D, tributary of the Yoshida River (locality 4); E, main stream of the Itoshiro River (locality 5); F, tributary of the Itoshiro River (locality 5); G, tributary of the Sho River (locality 6); H, main stream of the Gamada River (locality 7).

Fig. 2 in Occurrence of a Skin Parasite Argulus coregoni (Branchiura: Argulidae) on Salmonids in Mountain Streams, Central Japan, with Discussion on Its Longitudinal Distribution and Host Utilization in Rivers

Fig. 2. Map showing the collection localities of salmonids infect- ed with Argulus coregoni (closed circles 1–7) in rivers of Gifu Prefecture, central Japan. The collection localities of ayu, Plecoglossus altivelis altivelis, infected with A. coregoni, are also shown (open triangles 8–11). 1, Upper reaches of the Maze River; 2, tributary of the Hida River; 3, tributary of the Tsukechi River; 4, tributary of the Yoshida River; 5, the Itoshiro River; 6, tributary of the Sho River; 7, the Gamada River; 8, middle reaches of the Maze River; 9, middle reaches of the Shira River; 10. middle reaches of the Nagara River; 11, lower reaches of the Nagara River.

Fig. 1 in Occurrence of a Skin Parasite Argulus coregoni (Branchiura: Argulidae) on Salmonids in Mountain Streams, Central Japan, with Discussion on Its Longitudinal Distribution and Host Utilization in Rivers

Fig. 1. Argulus coregoni, male, NSMT-Cr 30777, from a white-spotted char, Salvelinus leucomaenis, from the Gamada River, Gifu Prefecture, ethanol-preserved specimen, A, Dorsal view; B, ventral view; C, two females infecting a white-spotted char (180 mm FL) near the left pectoral fin (from the Maze River); D, one female infecting a red-spotted masu salmon, Oncorhynchus masou ishikawae (103 mm FL), near the base of the dorsal fin (from a tributary of the Hida River); E, one female (left) and one male (right) infecting a masu salmon, O. m. masou (257 mm FL), near the left pectoral fin (from the Itoshiro River); F, one female infecting a hybrid between white-spotted char and masu salmon (165 mm FL) near the dorsal fin (from the Itoshiro River). Arrowheads indicate individuals of A. coregoni. See Fig. 2 for the locations of the rivers. Scale bars: A, B, 2 mm; C–F, 20 mm.

Fig. 4 in Occurrence of a Skin Parasite Argulus coregoni (Branchiura: Argulidae) on Salmonids in Mountain Streams, Central Japan, with Discussion on Its Longitudinal Distribution and Host Utilization in Rivers

Fig. 4. Distribution of 31 specimens of Argulus coregoni (closed circles) on the host's body surface. A total of 32 specimens of A. coregoni were collected, but the attachment site for one individual was not recorded.

APPENDIX 3 in Fungal/bacterial syntrophy of glycerol utilization

APPENDIX 3. — Growth of Escherichia coli T.Escherich on M0 medium supplemented with glycerol. Escherichia coli DH5α was inoculated at position indicated by the blue dots (except at the one on the center where Podospora anserina (Rabenh.) Niessl would be inoculated when the plates contain the fungus, e.g. see Fig. 7) on the indicated media and the plates were incubated for 20 days at 27°C under constant illumination at which point photographs were taken. In these conditions, the growth of the E. coli colonies is readily visible after one week of incubation and starts to mask the blue dots, except on M0 that does not permit the growth of E. coli.

FIG. 7 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 7. — Production of mycelium and perithecia in the presence of Escherichia coli T.Escherich by Podospora anserina (Rabenh.) Niessl wild-type and mutant strains. The plates were inoculated at the same time at the center by a mat+/mat- heterokaryon of the fungus with the indicated genotypes, alone or with E. coli DH5α at the position indicated by the blue dots on the right and left of the center (visible on the M0 plates). The plates were incubated for 20 days at 27°C and constant illumination, after which they were photographed.Escherichia coli promoted the growth of the mycelium (clearly visible on plates containing 0.1 M glycerol) for all strains, and development of perithecia (clearly visible as small black dots on plates containing 0.05 M glycerol) in all strains except for the PaGut2Δ mutant.

FIG. 4 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 4. — Phenotype of the G3P mutants. Growth and fertility on M2 were evaluated eight days after inoculation of mat+/mat- heterokaryons of the indicated strains. For M2, the top plates are cultures on the M2 medium; the bottom ones are the cover of the same plates onto which ascospores seen as tiny black dots were expelled. Growth on M0, M0 + 0.05 M glycerol, and M0 + 0.1 M glycerol was evaluated after four days of growth.

FIG. 2 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 2. — Growth and fertility of Podospora anserina (Rabenh.) Niessl on glycerol media. The plates were inoculated at the center with a mat+/mat- heterokaryon and incubated for three weeks at 27°C in the presence of constant light, at which time pictures were taken. Arrowheads point toward ascospore-containing perithecia. See also Figure 4 for a dark field picture of the wild-type strain growing on M0 and M0 + 0.05 M glycerol. Top, Petri plate (Ø= 8 cm). Scale bars: 200 µm.

FIG. 1 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 1. — Scheme of glycerol import and catabolism in Podospora anserina (Rabenh.) Niessl as transposed from pathways known in Saccharomyces cerevisiae Meyen ex E.C.Hansen, Schizosaccharomyces pombe Lindner, and Aspergillus nidulans G.Winter.

FIG. 6 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 6. — Production of perithecia by Podospora anserina (Rabenh.) Niessl in the presence of Paenibacillus validus (Nakamura) Ash et al. and Escherichia coli T.Escherich. The presence of large amounts of mature perithecia (the black dots) are seen around and farther away from the bacterial colony on media containing 0.02 M glycerol. The fungus formed a dense mycelium on a plate containing 0.1 glycerol and the bacteria. Note that at 0.1 M glycerol, P. anserina remained sterile even in the presence of bacteria. Scale bars: 250 µm.

FIG. 3 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 3. — Toxicity of glycerol. M2 and M0 Plates containing the indicated concentration of glycerol (gly) and sorbitol (sorb) were inoculated at the center with a mat+/mat- heterokaryon and incubated for two weeks at 27°C in the presence of constant light, at which time pictures were taken. Perithecia are visible as small black dots. On the M2 medium, the presence of 0.1 M of glycerol inhibited growth and abolished fertility; higher concentrations of glycerol resulted in no growth. On the contrary, Podospora anserina (Rabenh.) Niessl grew and was fertile even in M2 medium containing the highest concentration of sorbitol. Podospora anserina was also fertile on medium containing sorbitol as sole carbon source at all concentrations, while it produced no visible perithecia on a medium with the same glycerol concentrations after two weeks.

FIG. 5. — The PaGut1 in Fungal/bacterial syntrophy of glycerol utilization

FIG. 5. — The PaGut1Δ and PaGUT2Δ mutants are sterile on glycerol media. Small but mature perithecia can be seen at the periphery of the colony when the wild type is incubated for 20 days on media containing 0.02 M glycerol, while they cannot be seen in the PaGut1Δ, PaGUT2Δ, and PaGut1Δ PaGUT2Δ mutants. Bottom, enlargement of representative fruiting bodies. Scale bars: 250 µm.

APPENDIX 2 in Fungal/bacterial syntrophy of glycerol utilization

APPENDIX 2. — Phylogenetic analysis of NDGD. The tree was rooted with the divergent protein encoded by Pa_7_11100. The AN7193 protein defined as a NDGD is in red and the Podospora anserina (Rabenh.) Niessl proteins are in blue.

APPENDIX 1 in Fungal/bacterial syntrophy of glycerol utilization

APPENDIX 1. — Southern blot validation of the deletions. For each gene, on the left, schematic representation of the wild-type and deleted locus. Enzymes and probes (in yellow with *) used for Southern blots are indicated; on the right, corresponding autoradiograms. In both cases, the two tested candidates had the correct replacement; WT = wild type