Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow

Methane is a potent greenhouse gas that contributes to global warming. However, under certain conditions, its release into the atmosphere can be mitigated by methane-oxidizing microorganisms. Typically, cultivated wetlands (i.e., paddy fields) are a major source of methane (CH4) while forests and meadow uplands are considered to be CH4 sinks. As the global need for rice production increases each year, more uplands are converted to inundated paddy fields. To investigate soils that may be converted into productive land for rice production, we investigated a paddy field and adjacent meadow in Northern Italy. Using a combination of 16S rRNA gene amplicon sequencing to analyze the bacterial community, and gas flux measurements to quantify CH4 emissions, we looked for differences between classically defined CH4 sinks (meadow soils) and CH4 sources (paddy fields). Analysis of the total bacterial community revealed that the family Fimbriimonadaceae, which belongs to the phylum Armatimonadetes, was significantly higher in paddy field soils driving the difference between paddy and meadow soils. Whereas, we found that the methylotrophic families Methyloligellaceae and Methylomirabilaceae were also present in higher relative abundance in the paddy field. Despite these major differences, CH4 fluxes were highly variable between the two sites with no significant differences observed. Furthermore, we found the Methylomonaceae family to be more abundant at the center of a neighboring paddy field compared to the edge of the paddy field from the current study, hinting at methanotrophic variation based on location. Taking these results into account, we propose a conceptual model to explain possible scenarios that may result in paddy and meadow fields not exhibiting classical source/sink properties. These findings call for caution when including paddy and meadow areas separately into global CH4 flux calculations, and urge further research to discern drivers of CH4 cycling under a range of environmental conditions rather than relying on assumptions.
Importance of the Implementation of Processes Derived from Strategic Management. a Case Study

Companies are in need of developing business assessments that allow them to identify whether their activities meet the criteria required by the market. The objective of the research is to establish the strategic factors that promote the competitiveness of companies in the plastics sector in the city of Bogota. This is presented through the application of a diagnosis to 21 companies belonging to the plastics sector, using the MIGSA diagnosis tool (Sustainable Management and Partnership Indicators Model) and the use of Principal Component Analysis (PCA) to establish strategic factors by grouping study variables
Six new species of the brine shrimp Parartemia Sayce 1903 (Crustacea: Anostraca: Artemiina) in Western Australia

The Australian anostracan fauna is generically depauperate, but species-rich due to radiation within Branchinella and also Parartemia. Most Parartemia, including the six new species, occur in Western Australia, with P. boomeranga sp. nov. in the inner Wheatbelt, P. mouritzi sp. nov. in the eastern Wheatbelt, P. purpurea sp. nov. in the Esperance hinterland, P. veronicae sp. nov. in the Goldfields, P. bicorna sp. nov. in Lake Carey in the northern Goldfields and P. laticaudata sp. nov. in the far north and the Northern Territory. All species use lock and key amplexus meaning that the second antennae of males are highly differentiated and in females the last few thoracomeres are variously modified and the 10th, and especially 11th, thoracopods much reduced. Although many of the new species occur in remote salinas, some are endangered due to anthropogenic salinisation.
Which Selective Logging Intensity is Most Suitable for the Maintenance of Soil Properties and the Promotion of Natural Regeneration in Highly Continental Scots Pine Forests?–Results 19 Years after Harvest Operations in Mongolia

Scots pine (Pinus sylvestris L.) forests are one of the main vegetation types in the Asian forest-steppe zone. However, over-harvesting currently threatens the natural regeneration and sustainability of these forests. In this study, we examine the long-term effects of different logging intensities on soil properties and natural regeneration in a natural Scots pine forest in the West Khentii Mountains (Mongolia), 19 years after selective logging. Our experimental design included five treatments: clear cut (CC), treatments with high (HI), medium (MI), low (LI) intensities, and a reference parcel with no logging impact at all (RE). We described and quantified the harvest events and applied ANOVA and LMM modeling to analyze and explain the long-term impacts of the logging intensities on soil properties and natural regeneration. We found that logging has a significant negative influence on the physical and chemical properties of the soil because it increases soil compaction and reduces soil nutrients. The most critical impacts of logging were on soil bulk density, total porosity, organic matter, and total nitrogen and phosphorus. The LMM modeling showed that organic matter (OgM), total nitrogen (TN), available K (AK) and pH values are especially impacted by logging. Our study revealed that the values for all of these variables show a linear decrease with increasing selective logging intensity and have a level of significance of p < 0.05. Another finding of this study is that selective logging with low and medium intensities can promote natural regeneration of Scots pine to numbers above those of the reference site (RE). High intensity logging and clear-cuts, however, limit the regeneration of Scots pine, reduce overall seedling numbers (p < 0.05), and create conditions that are suitable only for the regeneration of deciduous tree species. This underlines the risk of Scots pine forest degradation, either by replacement by broad-leaf trees or by conversion into non-forest ecosystems.
Applications and Recruitment Performance of Web-Based Respondent-Driven Sampling: Scoping Review

Background Web-based respondent-driven sampling is a novel sampling method for the recruitment of participants for generating population estimates, studying social network characteristics, and delivering health interventions. However, the application, barriers and facilitators, and recruitment performance of web-based respondent-driven sampling have not yet been systematically investigated. Objective Our objectives were to provide an overview of published research using web-based respondent-driven sampling and to investigate factors related to the recruitment performance of web-based respondent-driven sampling. Methods We conducted a scoping review on web-based respondent-driven sampling studies published between 2000 and 2019. We used the process evaluation of complex interventions framework to gain insights into how web-based respondent-driven sampling was implemented, what mechanisms of impact drove recruitment, what the role of context was in the study, and how these components together influenced the recruitment performance of web-based respondent-driven sampling. Results We included 18 studies from 8 countries (high- and low-middle income countries), in which web-based respondent-driven sampling was used for making population estimates (n=12), studying social network characteristics (n=3), and delivering health-related interventions (n=3). Studies used web-based respondent-driven sampling to recruit between 19 and 3448 participants from a variety of target populations. Studies differed greatly in the number of seeds recruited, the proportion of successfully recruiting participants, the number of recruitment waves, the type of incentives offered to participants, and the duration of data collection. Studies that recruited relatively more seeds, through online platforms, and with less rigorous selection procedures reported relatively low percentages of successfully recruiting seeds. Studies that did not offer at least one guaranteed material incentive reported relatively fewer waves and lower percentages of successfully recruiting participants. The time of data collection was shortest in studies with university students. Conclusions Web-based respondent-driven sampling can be successfully applied to recruit individuals for making population estimates, studying social network characteristics, and delivering health interventions. In general, seed and peer recruitment may be enhanced by rigorously selecting and motivating seeds, offering at least one guaranteed material incentive, and facilitating adequate recruitment options regarding the target population’s online connectedness and communication behavior. Potential trade-offs should be taken into account when implementing web-based respondent-driven sampling, such as having less opportunities to implement rigorous seed selection procedures when recruiting many seeds, as well as issues around online rather than physical participation, such as the risk of cheaters participating repeatedly.
The impact of alternative land and yield assumptions in herbaceous biomass supply modeling: one‐size‐fits‐all resource assessment?

The Billion‐ton Reports series has addressed the technical economic potential of supplying additional biomass from farmland and forests. Underlying each of the reports and supporting scenarios is a series of assumptions that drive the modeled output. The assumptions have developed over time with the support of technical experts from industry, academia, and government. Energy crops have not yet reached commodity scale, and only exist in commercial production in a limited number of regions, so many of the key assumptions of biomass potential are not supported by commercial demonstrations across multiple regions. This report examines the biomass potential of herbaceous energy crops from US farmland when alternative assumptions concerning production are modeled. In particular, the assumption of energy grasses, both perennial and annual, is modified with respect to land eligibility, annual rotations, and yield growth. The results of these changes are presented in six scenarios – three of which are modifications to the base‐case scenario and three to the high‐yield scenario. The impact on land enrolled and biomass supply are discussed with respect to the most recent 2016 Billion‐ton Report results. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd
Perancangan Stasiun Kerja pada Praktikum Perancangan Teknik Industri 3 dengan Konsep Learning Factory untuk Menerapkan OBE

Penelitian ini bertujuan untuk merancang stasiun kerja operator untuk lintasan perakitan manual di Praktikum Perancangan Teknik Industri (PTI) 3 berdasarkan konsep learning factory untuk menerapkan pendekatan Outcome-based Education (OBE). Penerapan OBE bertujuan untuk meningkatkan pemahaman siswa terhadap materi pembelajaran perancangan sistem kerja dan sistem produksi. Latar belakang dari penelitian ini adalah kurangnya dukungan fasilitas dalam praktikum PTI 3. Pendekatan OBE digunakan untuk mengidentifikasi kebutuhan desain alat peraga stasiun kerja untuk meningkatkan pemahaman siswa dalam proses pembelajaran. 8 stasiun kerja dirancang di jalur perakitan. Efisiensi jalur perakitan meningkat 17% dan pemahaman siswa hingga 155% setelah proses perakitan dilakukan menggunakan alat peraga.
Effect of diets containing graded levels of low glucosinolate rapeseed press cake on reproductive organs and hormonal status in gilts and their female piglets

Crossbred gilts were offered rapeseed press cake (RSP) as follows: control (no RSP in diet during growth/ pregnancy/lactation), M-RSP (medium RSP levels: 100/50/100 g/kg RSP) and H-RSP (high RSP levels: 150/80/ 150 g/kg RSP). Plasma concentrations of free thyroxine (FT 4 ), tri-iodothyronine (T 3 ), luteinizing hormone (LH), prolactin (PRL), progesterone (P 4 ) and androstenedione (A 4 ), weights of thyroid gland, ovaries and uterus, length of uterine horns, and number of corpora lutea (CL) were measured in gilts during the mid-luteal phase of their first oestrous cycle. Serum concentrations of FT 4 , T 3 , LH and PRL, weights of thyroids, ovaries, uteri, adrenals, kidneys, liver and spleen were measured in female piglets on 2nd and 28th day of lactation. RSP diets, affected thyroid weights, number of CL, uterine horn length, mean concentrations of plasma FT 4 , T 3 , PRL, and P 4 in gilts. Changes of weights of ovaries in 2-day-old piglets and weights of uterus, adrenal gland and kidneys in 28-day-old piglets from RSP groups were observed.
Could Nodding Syndrome (NS) in Northern Uganda be an environmentally induced alteration of ancestral microbiota?

Hippocrates stated in 460-C.370 BC that, “All diseases begin in the Gut. ” This statement may be beginning to have meanings in the advent of new diseases such as Nodding Syndrome (NS) and Autism Spectrum Disorder (ASD). Interestingly, a recent publication from China in the journal of microbiology in 2017 suggests that high grain diet had dynamically shifted the composition of mucosa-associated microbiota and induced mucosal Injuries in the colon of Sheep. NS is a devastating childhood neurological disorder characterized by atonic seizure, cognitive impairment, head nodding, wasting and stunted growth. In addition, NS in Northern Uganda is clustered in time (those who were in IDPs), in space (discretely observed on either sides of the two rivers of Aswa and Pager) and in person (onset mainly between the ages of 5-15 years) and therefore exhibits spatial temporality. The first case of NS was noticed in Kitgum district in 1997, one year after the reported displacement of that community into IDP. Prior to that internal displacement, there were no reported cases of NS. The same scenario occurred in the IDPs of Odek, Gulu district where the population was displaced into IDPs in 2001 and approximately a year later in 2002, cases of NS began to appear. In the IDPs, children that eventually developed NS fed nearly exclusively on food ration provided by relief agencies and roughly a year later, cases of NS began to appear. In the other East African countries, there were no reported cases of NS prior to internal displacement and dependence on food ration. The observed common factors in the three East African regions where NS occurs at endemic proportion are perhaps: Internal displacement and feeding on relief food. These researchers suggest that NS may have perhaps resulted from dietary and environmental factors during IDPs which may have been foreign to their GIT and links this observation to the concept of microbiota-gut-brain axis.
Food Science of Animal Resources

A pig-specific real-time PCR assay based on the mitochondrial ND5 gene was developed to detect porcine material in food and other products. To optimize the performance of assay, seven commercial TaqMan master mixes and two real-time PCR platforms (Applied Biosystems StepOnePlus and Bio-rad CFX Connect) were used to evaluate the limit of detection (LOD) as well as the PCR efficiency and specificity. The LODs and PCR efficiencies for the seven master mixes on two platforms were 0.5–5 pg/reaction and 84.96%–108.80%, respectively. Additionally, non-specific amplifications of DNA from other animal samples (human, dog, cow, and chicken) were observed for four master mixes. These results imply that the sensitivity and specificity of a real-time PCR assay may vary depending on master mix and platform used. The best combination of master mix and real-time PCR platform can accurately detect 0.5 pg porcine DNA, with a PCR efficiency of 100.49%.
Critical dynamics are a homeostatic set point of cortical networks in vivo

The brain is constantly challenged by severely destabilizing forces: proteins turn over rapidly, Hebbian modifications alter and introduce positive feedback into networks, and environments change over many timescales. Homeostatic plasticity mechanisms, which operate via negative feedback, are believed to compensate for these changes and constrain neuronal activity to a firing rate (FR) set point1,2,3. For decades, it has been widely assumed that activity in neural networks is robust as a direct result of the widespread expression of FR homeostasis1,4. Here we reveal that network dynamics are stabilized independent of excitatory FR homeostasis and that cortical networks actively self-organize around an ideal computational regime. We continuously tracked network spiking activity in the visual cortex (V1) of freely behaving rats for nine days. We found that, under baseline conditions, networks of excitatory neurons are robustly organized around criticality, a regime known to maximize information capacity and dynamic range. Monocular deprivation (MD) revealed a dissociation of excitatory FRs and network dynamics. MD immediately and severely disrupted network organization, which returned precisely to criticality over 48h. In contrast, both the excitatory FR drop and the subsequent FR recovery trailed the timecourse of network changes by more than 30h. Model investigations suggest a role for inhibitory neurons in maintaining critical dynamics. Collectively, these results show that complex activity in cortical circuits is actively maintained near criticality and that this organization is not explained by previously identified mechanisms of pyramidal neuron FR homeostasis.
Role of Dietary Carotenoids in Different Etiologies of Chronic Liver Diseases

Carotenoids are tetraterpenoid organic pigments synthesized by a variety of plants and microorganisms. Dietary carotenoids, taken by animals through food, play an essential role in cell differentiation, morphogenesis, vision, prevention of cancer, atherosclerosis, and age-related macular degeneration in humans due to their potential to suppress oxidative stress. As reactive oxygen species and oxidative damage to biomolecules have been found to be involved in the causation and progression of chronic liver diseases (CLDs), including hepatocellular carcinoma (HCC), which is one of the major causes of morbidity and mortality worldwide. Therefore, dietary antioxidants, which inactivate reactive oxygen species and obstruct oxidative damage, are considered as vital prophylactic strategic molecules. Data from various epidemiological studies and clinical trials strongly validate the observation that adequate carotenoid supplementation may significantly reduce the risk of several liver disorders. This chapter, thus, provides a comprehensive account of dietary carotenoids and includes the recent information with respect to their role in pre- vention of liver diseases.
Testing Operating Performance of Chinese Listed Firms before and after Cross-border M&As: The Role of Entrepreneurial Orientation

At a time when China encourages its firms to go overseas, especially to countries and regions involved in its “Belt and Road Initiative”, and sets up a favorable domestic environment for innovation and entrepreneurship, this paper is a first trial looking along both the two dimensions to test whether Chinese firms’ operating performance changes after cross-border merger and acquisition (CBM&A) activities, using entrepreneurial orientation (EO) as a moderating factor. The paper combines data from Chinese listed firms’ annual reports, Chinese stock market financial statements database and the Zephyr database from 2001 to 2015 to examine how acquirers’ operating performance changes after CBM&A activities using EO as a moderating factor. In order to test whether the results are affected by the stock market, this paper also defines abnormal return on equity (ROE) to detect abnormal operating performance. After these, the paper divides the sample into separate industry groups to see whether results will change. The results obtained for the whole sample show that the performance of Chinese listed firms is fluctuant after CBM&As within the sample years. It increases one year after the acquisition but drops two years later and then follows an increasing trend again. The moderating factor of EO is not significant for the sample as a whole. However, after dividing the sample into separate industry groups, it becomes clear that different industries have their own characteristics. EO helps Chinese listed firms to adjust to the post-acquisition situation and even to improve their performance to some extent in the metal mining industry and the business services industry. When ROE is substituted with abnormal ROE, the results do not change much.
A new Approximate Bayesian Computation framework to distinguish among complex evolutionary models using whole-genome data

Inferring past demographic histories is crucial in population genetics, and the amount of complete genomes now available for many species should in principle facilitate this inference. In practice, however, the available inferential methods suffer from severe limitations. Although hundreds complete genomes can be simultaneously analyzed, complex demographic processes can easily exceed computational constraints, and there are no standard procedures to make sure that the estimates obtained are reliable. Here we present ABC-SeS, a new Approximate Bayesian Computation (ABC) framework, based on the Random Forest algorithm, to infer complex past population processes using complete genomes. All possible pairs of populations are compared, and the data are summarized by the full genomic distribution of the four mutually exclusive categories of segregating sites, a set of statistics fast to compute even from unphased genome data. We constructed an efficient ABC pipeline and tested how accurately it allows one to recognize the true model among models of increasing complexity, using simulated data and taking into account different sampling strategies in terms of number of individuals analyzed, number and size of the genetic loci considered. Once assessed the power of ABC-SeS in the comparison of even complex models, we applied it to the analysis of real data, testing models on the dispersal of anatomically modern humans out of Africa and exploring the evolutionary relationships of the three species of Orangutan inhabiting Borneo and Sumatra. The flexibility of our ABC framework, combined with the power provided by the set of statistics proposed pave the way for reliable inference of past population processes for any species for which high coverage genomes are available. Authors’ summary We propose a new method for inferring demographic history from whole-genome data, ABC-SeS. The idea is to analyze the distributions of segregating sites within an Approximate Bayesian Computation framework, using a Random Forest approach. Extensive simulation shows that ABC-SeS can handle very large datasets and identify the model that generated the data, even when population relationships are complicated by factors such as admixture. We also provide guidelines concerning the sampling strategies leading to the most accurate inference. As examples of possible applications, we show: (1) that complex alternative models on human dispersal out of Africa can now be formally tested and compared by ABC-SeS; and (2) that the evolutionary relationships among three orangutan species can now be better assessed by ABC-SeS than by alternative methods.