Miracle-dz/UniFAR-FTUs huggingface dataset:
Density- and resource-dependent movement characteristics in a rotifer

Summary Theory predicts that consumers can increase their energy intake by spending more time within resource-rich areas and/or by avoiding areas where local competitor densities are high. A consumer whose movements are described by a simple random walk can achieve these objectives by adjusting its turn frequency and/or speed. We recorded movements, as series of steps, by 180 individual rotifers (Brachionus calyciflorus) in glass capillary tubes to test the influence of resource density, competitor density and their statistical interaction on movement parameters. Four treatments contrasted opposing levels of algae (resource) and conspecific density in a 2 × 2 factorial design. Our results indicate that density- and resource-dependent behaviours act through different mechanisms to shape patterns of rotifer movement. Turn frequency increased up to twofold in resource-rich treatments, depending on the presence or absence of competitors. In contrast, swimming speed was 50% greater in the presence of competitors under all treatments, but was only slightly depressed by the presence of resources alone. We show how these two different movement mechanisms may be integrated into predictions of consumer population spread as resource and competitor densities vary. We discuss implications of the contrasting and complementary nature of these different movement mechanisms and their possible adaptations to different environmental stimuli.
Curative and Preventive Measures for Edema in Juvenile Japanese Char Salvelinus leucomaenis

Mortality associated with edema occurred in juvenile Japanese char Salvelinus leucomaenis. Scanning electron microscopy of gil surfaces and histological observations of the gils and kidneys of diseased juveniles indicated that the present pathological changes of the edema disease in juvenile Japanese char (EJJC) were similar to those of the previous study. We conducted three experiments to investigate curative and preventive measures for EJJC: a bath treatment with 1.0% salt water for a curative efect in the early stage of the disease, supplementation of ascorbic acid to the commercial diet (10,000 mg/kg diet) for prevention of the disease, and the supplementation of ascorbic acid along with increased water flow to improve the water quality also for the disease prevention. Results confirmed the curative efect of a 1.0% salt water bath treatment on the early stage of an EJJC outbreak, and the preventive efect on the dietary supplement of ascorbic acid with increasing water quantity before an outbreak.
Motivation to Learning Mathematics and Gender as Correlates of Senior Secondary School Students’ Performance in Mathematics

This study investigated senior secondary school students’ motivation to learning mathematics and gender as correlates of performance in mathematics. The sample consisted of 315 students from two government senior secondary schools in Lagos State, Nigeria using the quantitative research method within the blueprint of the descriptive survey research design. Data collected were analysed using percentages, means, standard deviation, independent samples t-test, Pearson Product Moment Correlation Coefficient (PPMCC) and standard and stepwise multiple linear regression analysis. Findings from the study revealed that there was a very high level of motivation to learn mathematics among senior secondary schools’ students in Nigeria. There was a significant influence of gender on students’ performance in mathematics but not on motivation to learn mathematics. It was also revealed that self-efficacy, gender and intrinsic motivation were the major significant predictors of performance in mathematics among the sample studied. Based on these findings, future studies in Nigeria should attempt to investigate the psychometric properties of the motivation to learn mathematics scale.
Predicting in situ soil N2O emission using NOE algorithm and soil database

This paper presents a new algorithm, Nitrous Oxide Emission (NOE) for simulating the emission of the greenhouse gas N2O from agricultural soils. N2O fluxes are calculated as the result of production through denitrification and nitrification and reduction through the last step of denitrification. Actual denitrification and nitrification rates are calculated from biological parameters and soil water‐filled pore space, temperature and mineral nitrogen contents. New suggestions in NOE consisted in introducing (1) biological site‐specific parameters of soil N2O reduction and (2) reduction of the N2O produced through nitrification to N2 through denitrification. This paper includes a database of 64 N2O fluxes measured on the field scale with corresponding environmental parameters collected from five agricultural situations in France. This database was used to test the validity of this algorithm. Site per site comparison of simulated N2O fluxes against observed data leads to mixed results. For 80% of the tested points, measured and simulated fluxes are in accordance whereas the others resulted in an important discrepancy. The origin of this discrepancy is discussed. On the other hand, mean annual fluxes measured on each site were strongly correlated to mean simulated annual fluxes. The biological site‐specific parameter of soil N2O reduction introduced into NOE appeared particularly useful to discriminate the general level of N2O emissions from site to site. Furthermore, the relevance of NOE was confirmed by comparing measured and simulated N2O fluxes using some data from the US TRAGNET database. We suggest the use of NOE on a regional scale in order to predict mean annual N2O emissions.
Multi-criteria decision-making for the life cycle of sustainable high pressure die casting products

In the scientific literature there is a scarcity of comprehensive and organic studies on performance indicators encompassing sustainability and their influence on decision-making. This work aims at selecting the most suitable material to manufacture an automotive component using a high pressure die casting (HPDC) process according to four classes of metrics: cost, time, quality and sustainability. The performance of three different alloys (aluminium-A380, magnesium-AZ91D and zinc-ZA8) was evaluated considering overall product life cycle aspects and process characteristics through a deterministic technique for order of preference by similarity to ideal solution (TOPSIS). Results show that the zinc alloy should be chosen on a unit mass-basis mainly thanks to its significantly superior quality and sustainability performance. This study demonstrates that the inclusion of the sustainability dimension in a multi-criteria decision analysis context challenges well-established material selection trends in the automotive industry developed during the past decades.
Evolution of the number of communicative civilizations in the Galaxy: implications on Fermi paradox

Abstract It has been recently proposed DeVito [(2019) On the meaning of Fermi's paradox. Futures, 389–414] that a minimal number of contacts with alien radio-communicative civilizations could be justified by their logarithmically slow rate of growth in the Galaxy. Here we further develop this approach to the Fermi paradox, with the purpose of expanding the ensemble of the possible styles of growth that are consistent with the hypothesis of a minimal number of contacts. Generalizing the approach in DeVito (2019), we show that a logarithmic style of growth is still found. We also find that a style of growth following a power law would be admissible, however characterized by an exponent less than one, hence describing a sublinear increase in the number of communicative civilizations, still qualitatively in agreement with DeVito (2019). No solutions are found indicating a superlinear increase in the number of communicative civilizations, following for example an exponentially diverging law, which would cause, in the long run, an unsustainable proliferation. Although largely speculative, our findings corroborate the idea that a sublinear rate of increase in the number of communicative civilizations in the Galaxy could constitute a further resolution of Fermi paradox, implying a constant and minimal – but not zero – number of contacts.
The group selection–inclusive fitness equivalence claim: not true and not relevant

Abstract Abstract The debate on (cultural) group selection regularly suffers from an inclusive fitness overdose. The classical view is that all group selection is kin selection, and that Hamilton's rule works for all models. I claim that not all group selection is kin selection, and that Hamilton's rule does not always get the direction of selection right. More importantly, I will argue that the paper by Smith (2020; Cultural group selection and human cooperation: a conceptual and empirical review. Evolutionary Human Sciences, 2) shows that inclusive fitness is not particularly relevant for much of the empirical evidence relating to the question whether or not cultural group selection shaped human behaviour.
Isolation and identification of cellulolytic bacteria at fibric, hemic and sapric peat in Teluk Bakung Peatland, Kubu Raya District, Indonesia

Khotimah S, Suharjono, Ardyati T, Nurani Y. 2020. Isolation and identification of cellulolytic bacteria at fibric, hemic, and sapric peat in Teluk Bakung Peatland, Kubu Raya District, Indonesia. Biodiversitas 21: 2103-2112. Cellulose degrading bacteria was one of the microbial removers of organic matter contained in the soil into simpler monomers so that it can be utilized by other organisms. The objective of the research was to obtain cellulose-degrading bacteria found on fibric, hemic, and sapric peat in forest and shrubs (oil palm). The bacteria were isolated by pour plate method on 1% CMC media. Selected isolates were assayed quantitatively based on the activity of cellulase enzyme, identified with 16S rDNA. The density of cellulolytic bacteria in the secondary forest peat of fibric, hemic, sapric were 2.1x10 cfu/g, 5.9x10 cfu/g, and 4.9x10 cfu/g whereas, in the area of shrubs/oil palm peat fibric, hemic and sapric 6.9x10 cfu/g, 8.4x10 cfu/g and 3.4x10 cfu/g respectively. There were 19 bacterial isolates that have clear zones around the colony as degradation of cellulose had highest ability to degrade cellulose with clear zones of 5-7 mm. The strain of SB1.1. 1 showed highest activity of cellulase enzyme 11.17 U/mL, followed by HH3.1. 1 strain and SB2.3 7.83 U/mL. Based on the phylogeny tree, strain SB1.1. 1 and HH3.1. 1 have the closest kinship relationship with Bacillus cereus with a kinship relationship of 100%, while SB2.3 has the closest kinship relationship with Bacillus stratosphericus with a relationship of 99.85 %.
P4HB modulates epithelial-mesenchymal transition and the β-catenin/Snail pathway influencing chemoresistance in liver cancer cells

The aim of the present study was to investigate the role of prolyl 4-hydroxylase beta polypeptide (P4HB) in the chemoresistance of liver cancer. Drug-resistant liver cancer cell lines, such as HepG2/adriamycin (ADR) cells, were treated and screened using adriamycin. Gene interference was used to silence the expression of P4HB in liver cancer cells. Cell viability, invasiveness and migration were assessed using CCK8, Transwell and wound healing assays, respectively. In addition, changes to key genes and proteins in the epithelial-mesenchymal transition (EMT) and β-catenin/Snail pathway were analyzed using reverse transcription-quantitative PCR and western blotting. Drug-resistant HepG2/ADR cells were successfully cultivated; the IC50 to ADR for HepG2/ADR and HepG2 cell lines was 4.85 and 0.61 µM, respectively. HepG2/ADR cells exhibited higher invasion and migration abilities compared with HepG2 cells (P<0.05). E-cadherin mRNA and protein expression levels in HepG2/ADR cells were decreased significantly, whereas P4HB, N-cadherin and vimentin mRNA and protein levels were significantly increased compared with HepG2 cells (all P<0.05). Knockdown of P4HB significantly decreased cell viability and the invasion and migration ability of HepG2/ADR cells. In addition, P4HB knockdown enhanced E-cadherin mRNA and protein expression levels, whereas N-cadherin, vimentin, total β-catenin, nuclear β-catenin and Snail mRNA and protein levels were significantly decreased (all P<0.05). Overall, the present study demonstrated that EMT and β-catenin/Snail pathway influence P4HB modulation in liver cancer chemoresistance.
Utilization of elite Korean japonica rice varieties for association mapping of heading time, culm length, and amylose and protein content.

Association mapping is widely used in rice and other crops to identify genes underlying important agronomic traits. Most association mapping studies use diversity panels comprising accessions with various geographical origins to exploit their wide genetic variation. While locally adapted breeding lines are rarely used in association mapping owing to limited genetic diversity, genes/alleles identified from elite germplasm are practically valuable as they can be directly utilized in breeding programs. In this study, we analyzed genetic diversity of 179 rice varieties (161 japonica and 18 Tongil-type) released in Korea from 1970 to 2006 using 192 microsatellite markers evenly distributed across the genome. The 161 japonica rice varieties were genetically very close to each other with limited diversity as they were developed mainly through elite-by-elite crosses to meet the specific local demands for high quality japonica rice in Korea. Despite the narrow genetic background, abundant phenotypic variation was observed in heading time, culm length, and amylose and protein content in the 161 japonica rice varieties. Using these varieties in association mapping, we identified six, seven, ten, and four loci significantly associated with heading time, culm length, and amylose and protein content, respectively. The sums of allelic effects of these loci showed highly significant positive correlation with the observed phenotypic values for each trait, indicating that the allelic variation at these loci can be useful when designing cross combinations and predicting progeny performance in local breeding programs.
Performance of tomato (solanum Lycopersicum L.) genotypes under naturally ventilated polyhouse in kumaon hills of Uttarakhand (India)

This study was aimed to assess the performance of various tomato genotypes under ventilated poly-house conditions. The study was conducted in Kumaun hills of Uttarakhand (India) during summer 2017. The study revealed the presence of high genotypic and high heritability for most economic traits viz., number of fruits plant−1, yield plant−1, ascorbic acid content and total antioxidant activities. The variety ‘VL-4’ proved superior over other varieties with respect to fruit length (5.43 cm), fruit width (5.27 cm), number of fruits plant−1 (51.67), average fruit weight (85.34 g) and fruit yield plant−1 (4.42 kg). Highest luminous (L*= 49.96), TSS (6.03oB), reducing sugar (1.99%) and total sugar (3.39%) were estimated in genotype ‘H-86’; whereas highest red colour (a*= 42.43) and total antioxidant activity (28.06 mMTE L−1) were found in hybrid ‘Dev’ and maximum yellow colour (b*= 48.8) in hybrid ‘Badshah’. The chroma (C*= 57.16), ascorbic acid (40.22 mg 100 g−1), non-reducing sugar (1.62%) and lowest hue angle (ho=38.83) were found maximum in hybrid ‘Shahanshah’. The maximum heritability (broad sense) estimates were noted for total sugar (100%) and non-reducing sugar (100%). The study depicted the scope of further improvement of these traits through selection procedure and these genotypes could be considered for further heterosis breeding programme for future improvement.
Early survival and growth in populations of grayling with recent common ancestors—field experiments

Among eight populations of grayling Thymallus thymallus that shared common ancestors 8–28 generations earlier, mean egg mortality ranged between 1·2 and 59·8%; mortality during yolk sac absorption was low (0middot;0–8middot;0%) and mean survival to swim-up was high (90–97%), with two exceptions (20% and 50%). Survival probabilities differed significantly among populations, even after statistically adjusting for size at swim-up and water depth, water velocity, gravel size and temperature. Development time from fertilization to first observed swim-up was significantly different among populations, ranging between 27 to 40 days, or 264 to 280 degree-days. Mean specific growth rates during the first external feeding period varied between 1·2 and 2·0% day-1 among populations. Population-specific growth rates were independent of temperature. Rates of divergence were of the same order as in other salmonid studies showing rapid evolution. The phenotypic differences may be due partly to genetic differentiation among the populations.
Metabolic engineering of Arabidopsis to produce nutritionally important DHA in seed oil.

Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are nutritionally important long-chain (≥ C20) omega-3 polyunsaturated fatty acids (ω3 LC-PUFA) currently obtained mainly from marine sources. A set of genes encoding the fatty acid chain elongation and desaturation enzymes required for the synthesis of LC-PUFA from their C18 PUFA precursors was expressed seed-specifically in Arabidopsis thaliana. This resulted in the synthesis of DHA, the most nutritionally important ω3 LC-PUFA, for the first time in seed oils, along with its precursor EPA and the ω6 LC-PUFA arachidonic acid (ARA). The assembled pathway utilised Δ5 and Δ6 desaturases that operate on acyl-CoA substrates and led to higher levels of synthesis of LC-PUFA than previously reported with acyl-PC desaturases. This demonstrates the potential for development of land plants as alternative sources of DHA and other LC-PUFA to meet the growing demand for these nutrients.
Sphagnum macrostructure as an indicator of decay and compaction in peat cores from an ombrotrophic South Swedish peat-bog

Decay and compaction can be determined from a quantified analysis of macrostructure of Sphagnum peat in short cores from ombrotrophic peat-bogs. Because stems of Sphagnum fuscum were intact to a depth of 30 cm, compaction of peat in the region can be determined from the increase in the cumulative length of S. fuscum stems per unit peat volume with depth (.)
Long Generation Time Delays the Genetic Response to Habitat Fragmentation in the Threatened Florida Sand Skink

Abstract A recent study showed that populations of the threatened Florida Sand Skink had limited loss of genetic diversity over the past 60 yr as a consequence of anthropogenic fragmentation. This study assumed that 60 yr represents 30–37 generations for the Florida Sand Skink, but a new evaluation of mark–recapture data shows that 60 yr represents only about 15 generations. This result suggests that too little time may have passed to observe the full genetic consequences of contemporary anthropogenic fragmentation in the Florida Sand Skink and reinforces similar results from other species. We suggest that snapshots of existing genetic variability in fragmented populations are limited in their ability to predict the evolutionary fate of a species unless life-history attributes of the organism are taken into account.
Description of Stenomitos kolaenensis and S. hiloensis sp. nov. (Leptolyngbyaceae, Cyanobacteria) with an emendation of the genus

Stenomitos is a recently established cyanobacterial genus, some species of which appear to be cryptic. Here we describe two new species in this genus, Stenomitos kolaensis sp. nov. isolated from the Al-Fe humic podzols of a boreal forest near Nikel town, Murmansk region, Russia and S. hiloensis sp. nov. isolated from a basaltic seep wall on Akeola Road, Hilo, Hawaii, USA. Phylogenetic analyses were conducted on the 16S and 16S-23S ITS rRNA gene regions using Bayesian Inference, and Maximum Likelihood. Phylogenetic analysis of the 16S-23S ITS rRNA region resulted in both S. kolaensis and S. hiloensis forming separate clades from other Stenomitos lineages. Antarctic strains of Stenomitos frigidus (previously reported as “Leptolyngbya frigida”) show that species to be polyphyletic and in need of revision. The structure of the conserved ITS regions (Box-B, D1-D1ʹ, V2 and V3 helices) provided support for separation of the species, and the p-distances among aligned ITS regions further confirmed that a number of species exist within the genus. S. kolaensis and S. hiloensis can be distinguished from other described Stenomitos species (S. rutilans and S. tremulus) by their geographical distribution, habitat preference, 16S rRNA phylogeny, and differences in the secondary structure of the 16S-23S ITS region.
Protein microarray generation by in situ protein expression from template DNA

Today, whole genomes are analyzed by Next‐Generation Sequencing systems, or displayed by DNA microarray in situ synthesis. However, genomic data are mainly static and do not exactly reveal the complexity of protein interaction networks of any organism or cell. To investigate protein interactions, the generation of protein microarrays, displaying whole proteomes is a prerequisite. But traditional protein microarray generation is time consuming, costly, and is restricted by a wide range of technical difficulties concerning cell culturing, protein purification, and transfer onto microarray. Some of these obstacles can be bypassed by application of cell‐free expression systems, enabling fast in situ synthesis of protein microarrays without need for cell culturing. This review provides a historical timeline of the different methods to generate protein microarrays by cell‐free expression, highlights differences and similarities, and reports the current state of the different approaches.
VARIANCE IN SPECIES RICHNESS, SPECIES ASSOCIATION, AND NICHE LIMITATION

A low variance in species richness, relative to a null model, has been proposed as evidence for niche limitation in ecologicaI communities. We demonstrate that niche limitation does not inevitably lead to low variance in species richness. Furthermore. low variance in species richness can be caused by physical limits to the number of individuals in a sample, and by spatial dependence. Two methods (the rotation/ reflection method and the random shifts method) for creating spatially-explicit null models are proposed to correct for spatial dependence in transect-based and grid-based sampling schemes. These methods can also be used to correct for measures of association between species. The rotation/reflection method is not as powerful as the random shifts method, but the latter requires some simplifying assumptions about the nature of spatial patterns. A new sampling design, the trainsect, is proposed to eliminate the need for spatial assumptions