Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking Darwin’s naturalisation hypothesis and Elton’s diversity–invasibility hypothesis in experimental grassland communities

Darwin’s naturalisation hypothesis posing that phylogenetic distance of alien species to native residents predicts invasion success, and Elton’s diversity–invasibility hypothesis posing that diversity of native communities confers resistance to invasion, are both rooted in ideas of species coexistence. Because the two hypotheses are inherently linked, the mechanisms underlying them may interact in driving the invasion success. Even so, these links and interactions have not been explicitly disentangled in one experimental study before. To disentangle the links between the two hypotheses, we used 36 native grassland herbs to create greenhouse mesocosms with 90 grassland communities of different diversities, and introduced each of five herbaceous alien species as seeds and seedlings. We used phylogeny and four functional traits (plant height, specific leaf area, leaf size, and seed mass) to calculate different measures of phylogenetic and functional distance and diversity. Specifically, we tested how the alien–native distance (phylogenetic or functional) and the native diversity (phylogenetic or functional) affected each other in their effects on germination, seedling survival, growth, and reproduction of the aliens. Overall, our results supported both hypotheses. Multivariate functional distance based on four traits jointly had stronger positive effects than phylogenetic distance and the univariate ones based on each trait separately. Moreover, the aliens were more successful if they were more competitive by being taller and having larger leaves with a lower SLA than the native residents. Univariate functional diversity based on each trait separately had stronger negative effects than phylogenetic and multivariate functional diversity. Most importantly, we found that the effects of alien–native phylogenetic and multivariate functional distance became stronger as diversity increased. Our analyses with single traits also showed that the strength of the effects of both alien–native hierarchical functional distances (indicative of competitive inequalities) and absolute functional distances (indicative of niche differences) increased at higher diversities, where competition is more severe. Synthesis. Our study explicitly demonstrates for the first time how the mechanisms underlying the two classical invasion hypotheses interact in driving invasion success in grassland communities. This may help to explain some of the puzzling results of studies testing either of the two hypotheses.
Characterization of the role of several COPI complex isoforms during the early acceptance of compatible pollen grains in Arabidopsis thaliana

COPI is a seven subunit coatomer complex, consisting of α, β, β′, γ, δ, ε, and ξ; in A. thaliana, COPI is necessary for retrograde transport from the Golgi to the Endoplasmic Reticulum, Golgi maintenance, and cell-plate formation in plant cells. Vesicle recruitment to the pollen contact point is required for pollen hydration and pollen tube penetration. To determine what other aspects of trafficking may be involved in the stigmatic papillae acceptance of compatible pollen, knock-out lines of several isoforms of the COPI complex were characterized in their roles during compatible pollination. Isoforms that were studied included α1-COPI, β-COPI, β′-COPI, γ-COPI and ε-COPI. Each mutant line was characterized in regards to pollen grain adherence, pollen tube penetration, and seed set. Of the mutant lines examined, α1-copi had the strongest phenotype with issues with compatible pollen grain adherence, tube germination and reduction in seed set while other lines had milder but visible retardation in compatible pollen acceptance. The data presented here are the first study of the role of the COPI complex in compatible pollinations and that certain subunit isoforms are required for compatible pollen acceptance.
HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine

Machine learning (ML) is emerging as an essential tool in the molecular modeling community. The most mature applications are in batch learning with data generated from molecular modeling calculations. For example, one can run a molecular dynamics (MD) or density functional theory (DFT) simulation to completion, from which the trajectory is then used as input data to train a deep neural network that reproduces the energetics at a fraction of the computational cost. Some recent examples include an energy-conserving force-field learned with a custom gradient-domain model (Chmiela et al., 2017), DFT-based neural network force-fields (J. S. Smith et al., 2017a), and a neural network coarse-grained potential (Wang et al., 2019). Other applications include the use of ML methods for collective variable (CV) calculation (Trapl et al., 2019) and enhanced sampling (Wang, Lamim Ribeiro, & Tiwary, 2020) for MD simulations. A limitation of these methods is that they treat the molecular modeling calculations as a static dataset, whereas molecular modeling calculations can be treated as interrogative functions, opening the door to methods like reinforcement learning or active learning. Thus there is a clear limitation of existing implementations due to their sequential nature of going from calculation to ML. Another practical issue is that neural network force-field implementations often duplicate standard ML frameworks, preventing them from keeping progress with state-of-the art methods. For example Rupp, Tkatchenko, Müller, & Anatole Von Lilienfeld (2012) and Botu & Ramprasad (2015) are benchmark works in this field and custom implementations. This limits the scope and speed of translating ML advances to the molecular modeling community.
Effects of a fall rye cover crop on weeds and productivity of Phaseolus beans

Abstract: Fall-seeded rye (Secale cereale) is known to suppress weeds through physical and allelopathic properties. This study examined the effects of fall rye cover crops on weed and dry bean (Phaseolus vulgaris) productivity over four site–years in Manitoba. In addition to rye, we tested early versus late spring rye termination times as well as herbicide use in a factorial experiment with four replicates. In the absence of herbicides, rye reduced early-season broadleaf and grassy weed plant populations by 44%–72% and 43%–88%, respectively. Terminating rye at the four-leaf stage (∼1100 kg dry matter ha-1) provided the same level of weed suppression as termination at booting (∼3100 kg dry matter ha-1). Early rye termination increased bean plant populations (significant at three out of four sites), bean development (four out of four sites), bean biomass (two out of four sites), and bean yield (three out of four sites) compared with later termination. Lower bean yield with rye at one site–year was attributed to dry early season conditions, where rye reduced soil water content. While the rye cover crop provided multiple benefits to bean production, early termination resulted in the best agronomic outcome. Rye was beneficial to weed control even when herbicides were used.
Nutritional Evaluation of Soybean Hulls with or without β-Mannanase Supplement on Performance, Intestinal Morphometric and Carcass Yield of Broilers Chickens

The objective was to evaluate the performance, intestinal morphology and carcass yield of broilers fed corn-soybean meal (SBM) diet or cornSBM-soybean hull (SH) with or without β-mannanase supplementation. Thousand four hundred and forty Cobb Slow-malechicks were housed design following a factorial scheme 2 x 2 (corn-SBM diet and corn-SBMSH diet vs with and without β-mannanase), composing 4 treatments and 9 replicates each treatment, with 40 birds each replicate. At 21 days, corn-SBM diet supplemented with β-mannanase resulted in better (p<0.05) feed conversion. At 42 days, the weight gain (p<0.05) and feed intake (p<0.05) of the birds fed diets containing SH was 2.6% and 2.9% higher than that of birds fed corn-SBM diets, respectively, independent of β-mannanase supplementation. Birds supplemented with β-mannanase had a lower length of villi (p<0.05) and absorption area (p<0.05) of jejunum mucosa, and higher (p<0.05) relative liver weight. Diets with SH and without addition of β-mannanase resulted in higher relative liver weight (p<0.05) and lower percentage of fat in the carcass. It was not found statistical differences (p>0.05) in the quality of the poultry litter with the inclusion of the enzyme in the diet. The use of β-mannanase in diets with higher concentration of fiber improves the feed conversion of broilers from 1 to 21 days and can be an important nutritional and economic strategy in situations of unavailability of raw material of better quality. Corn-SBM-SH diet resulted in greater weight gain at 42 days than corn-SBM diet.
Someone else’s problem? The IFRS enforcement field in Europe

This study adopts an institutional lens to explore enforcement as a complex and nuanced phenomenon shaped by the dynamics of its social context. It examines an IFRS regulatory incident that fails to conclude with any decision or resolving action in the context of the European Union, and as such invites serious questioning of enforcement functions. From our analysis accounting enforcement emerges as an interacting issue-based field in which auditors and the national enforcement agency adhere narrowly to their tasks, ensuring formal but not substantive IFRS compliance. Field participants are seen to respond to institutional pressures strategically by avoiding public positions and delegating choices to other actors, substantially accepting earnings manipulation. Our study shows that the national enforcer increased its interactions with other regulatory actors (i.e. agencies concerned with the setting and interpretation of standards) in the case of controversial issues and their responses can heavily influence overall enforcement effectiveness. Furthermore, its findings contribute to debates on the need for a pan-European enforcement agency and shed light on the importance of IFRS interpretation for the enforceability of international accounting standards.
A nutritional evaluation of the berry of a new grape: 'Karaerik' (Vitis vinifera L.)

Grape berries are a good source of nutrients and nutraceuticals and have many benefits for human health. Growing interest in the export potential and consumption of a new grape (cv. Karaerik), cultivated as a table grape in Turkey, encouraged us to profile its major nutrient contents from six different locations. Due to its popularity, the nutritional value of this grape berry needs to be investigated to ascertain its potential economic and health benefits. The most abundant sugars in the grape berry were fructose and glucose (peel/whole fruit; averages 236.57 and 127.87, and 183.36 and 108.60 (g kg -1 fresh weight), respectively), while the major organic acids were tartaric and malic acids (7.17 and 2.81, and 2.61 and 1.76(g kg -1 fresh weight), respectively). Linoleic acid (peel/whole fruit/seed; 37.14, 33.12 and 57.83%, respectively) was the predominant fatty acid, while potassium (peel/whole fruit/seed; 9331.5, 10226.33 and 5354 mg/g dry weight, respectively) was the predominant mineral, followed by phosphorus (1592.8, 2672 and 3072.67) in the berry. Our results demonstrate that the nutrient components and physicochemical parameters varied significantly among the sampling locations. The grape berry contains considerable quantities of potentially beneficial healthy nutrients worthy of further evaluation.
Body and milk quality traits of purebred Holstein and three-generation crossbred cows from Viking Red, Montbéliarde, and Holstein sires

The objective of this study was to investigate the effects of 3-way rotational crossbreeding scheme of Holstein (HO) cows with Montbeliarde (MO), Viking Red (VR) and HO sires on body and milk quality traits. Cows were purebred HO; F1: (MO × HO; VR × HO); F2: [MO × (VR × HO); VR × (MO × HO)]; F3: {HO × [MO × (VR × HO)]}; HO × [VR x (MO × HO)]}. Data were collected on 745 cows kept in a commercial farm located in Northern Italy. Milk data were acquired from official milk recording and body condition score (BCS) and conformation traits were measured once by trained evaluator. Data were analyzed using a linear model including fixed effects of parity, DIM class and breed combinations. Average body traits: height at withers (HW), body length (BL) and heart girth (HG) of cows were 139,162 and 207 cm respectively. Crossbred cows had shorter HW, BL and HG than pure HO but greater BCS. Milk yield averaged 31.5 kg/d, with fat and protein content close to 3.8 and 3.75%, respectively. Purebred HO produced greater volume of milk than crossbreds but milk from HO had lower protein content. Different combinations of crossbred cows showed similar performance in terms of milk yield traits, but evidenced different body size. The trial is currently in progress to increase cow sample size and widen the number of herds involved.
Teaching methods shape neural tuning to visual words in beginning readers

The impact of global vs. phonics teaching methods for reading on the emergence of left hemisphere neural specialization for word recognition is unknown in children. We tested 42 first graders behaviorally and with electroencephalography with Fast Periodic Visual Stimulation to measure selective neural responses to letter strings. Letter strings were inserted periodically (1/5) in pseudofonts in 40sec sequences displayed at 6Hz and were either words globally taught at school, eliciting visual whole-word form recognition (global method), or control words/pseudowords eliciting grapheme-phoneme mappings (phonic method). Selective responses (F/5, 1.2Hz) were left lateralized for control stimuli but bilateral for globally taught words, especially in poor readers. These results show that global method instruction induces activation in the right hemisphere, involved in holistic processing and visual object recognition, rather than in the specialized left hemisphere for reading. Poor readers, given their difficulties in automatizing grapheme-phoneme mappings, mostly rely on this alternative inadequate strategy.
Lessons for the COVID-19 response from a multidrugresistant tuberculosis study in South Africa: How public health promotion can reach vulnerable young women

Background. As the world grapples with the COVID-19 pandemic, lessons from responding to diseases that are endemic to Africa, such as HIV/AIDS, malaria, yellow fever, Lassa fever and Ebola, can inform responses to the new challenge. Gaps in and successes of South Africa (SA)’s established tuberculosis (TB) management programme have potential to inform COVID-19 responses. Objectives. To present the findings of a 2019 study that assessed how communication can contribute to improving health outcomes among young women with multidrug-resistant TB (MDR-TB) in SA. Methods. Primary qualitative data were collected from 20 purposefully selected participants in eThekwini Metro, KwaZulu-Natal Province. Data were collected through focus group discussions with women with MDR-TB, and key informant interviews with their family members, health workers and KwaZulu-Natal health department personnel. Results. The study assessed how age, gender, socioeconomic status, geographic location and comorbidity converge to influence susceptibility to communicable diseases and risk of mortality, and proposes that vulnerabilty factors be incorporated into both MDR-TB and COVID-19 responses. Conclusion. In the early stages of the COVID-19 pandemic, much is unknown about the incubation period and infection transmission modes, and there have been suggestions that asymptomatic people may be infectious. In highly populated urban areas, television and radio (local soap operas, dramas and hard news programmes), social media (Facebook and WhatsApp) and information from children are the best mediums for reaching young women to provide integrated public health education about both MDR-TB and COVID-19.
Impact of Plow Timing on Simultaneous Nitrogen Losses in Potato Production Systems Using Conventional Tillage Practices

Improving plowing management of high nitrogen (N) containing crops is essential in reducing both environmental and economic losses. The timing of plowing may be an important soil and nutrient conservation practice. A field study on a 3 yr potato rotation was conducted in Prince Edward Island, Canada to examine the effects of plow time on corresponding N losses of nitrate-N (NO3--N) and nitrous oxide (N2O). The study site consisted of nine tile drained plots (12 m spacing) with three treatments of plow time; early fall (EF), late fall (LF) temperature based, and the following spring (S) plow. The cropping rotations consisted of barley under-seeded with red clover in yr 1, red clover in yr 2, and Russet Burbank potatoes in yr 3. Each tile drained plot fed into a sample collection station where 50 mL water samples were obtained during flow events and analyzed for NO3--N. Nitrous oxide samples were also simultaneously obtained from the soil surface throughout the monitoring period using a static chamber methodology. Cumulative NO3--N loads over the 3 yrs were found to be reduced at 14.3 and 19.9 kg ha-1 for LF and S respectively, when compared to the EF plow at 24.4 kg ha-1. Nitrous oxide losses were variable and low in magnitude throughout the study (0.04-1.2% of the N applied). Overall, findings from this research suggest that the timing of plowing could be considered when trying to minimize N losses via tile drainage effluent. When considering NO3--N total loads during the rotation period, LF had reduced losses compared to EF in all years of the study. Late fall reduced N2O losses in 1 year by 38.2% compared to S, likely due the incorporation of red clover legume crop. Yields were found to be similar throughout treatments and cropping years, although LF was found to have 2 and 3-fold significant increases in yield of 10 oz potatoes vs. EF and S, respectively. Findings generated from this study will provide nutrient management and environmental farm planners, as well as producers with useful information for improving current management strategies within agricultural drainage systems.
The role of microRNA-132/212 in molecular circadian clock regulation

The mammalian central circadian clock is localized in the suprachiasmatic nucleus (SCN), and is responsible for orchestrating ~24-hour rhythms in behavior and physiology. An additional property of timekeeping in organisms is seasonal adaptation, or adaptation to seasonal variations in environmental conditions. Melatonin signaling has been studied for its role in adapting physiology to seasonal light/dark variations, yet the SCN is responsible for encoding and relaying daylength information by unknown mechanisms. MicroRNAs are small non-coding RNAs that regulate gene expression post-transcriptionally. MicroRNA-132 is part of a microRNA cluster, miR-132/212, that is often expressed in tandem, with well-characterized roles in neuronal plasticity. MiR-132 has been shown to modulate photic entrainment in acute paradigms; however, the role of miR-132/212 in acute and long-term circadian plasticity has not been explored. I aimed to do so in this study using a loss-of-function approach. I found that miR-132/212 ablation alters entrainment to non-24 hour cycles and seasonal photoperiods, and is accompanied by heightened clock protein rhythm amplitude and altered photoperiod-dependent clock protein expression patterns in the SCN. MiR-132/212-deficient SCN neurons show decreased dendritic spine density, which could potentially underlie the perturbed rhythmicity in clock gene expression and behavioral phenotypes. In the seasonal mammal Mesocricetus auratus, adaptation to winter-like photoperiods
Beyond forests in the Amazon: biogeography and floristic relationships of the Amazonian savannas

Open habitats such as grasslands occupy < 5% of the Amazon and are currently grouped under the broad term Amazonian savanna, covering an area of c. 267 000 km2, mostly in Brazil and Bolivia. These habitats are found isolated within an extensive rainforest matrix, having a distinct flora from the latter. The lower Amazon River is home to several patches of savanna that occupy both south and north banks of the river, in Santarém, Alenquer and Monte Alegre. Although having an abundance of herbaceous plants, most studies on these open areas focus only on tree species, ignoring the relevant non-woody component of the vegetation. Our objectives were to provide new surveys of seed plants for two Amazonian savanna sites and to take the opportunity to revisit the biogeographical links between Amazonian savanna, Amazonian canga vegetation and the central Brazilian cerrado (CBC) and caatinga, analysing woody and herbaceous plants. We created a floristic database that includes sites of Amazonian savannas, including campinarana, coastal scrub (restinga), CBC and Amazonian campos rupestres (on canga or other substrate). We compared those sites using multivariate analyses to find out the degree of floristic resemblance between sites. We prepared a new list of 406 species of seed plants [336 in Parque Estadual de Monte Alegre (PEMA) and 117 in Serra do Itauajuri (SI)], including 23 new records for the state of Pará and some putative new species for science. The Amazonian savannas form three loosely arranged groups, whereas the Amazonian canga formed a cohesive assemblage. Both groups were contrasted against cerrado and caatinga sites and had a distinctive flora from both. Sites from north-western Pará (Alter do Chão, PEMA and SI) were grouped with their northern counterparts in Roraima. An improved representation of the flora of these sites is provided, with more insight into the relationship between the Amazonian savanna sites and other vegetation types. It is worrying that recent changes of the Brazilian legislation place open environments, such as PEMA, in the path of vulnerability to disturbance and destruction.
Determination of dye biosorption capacity of lichens and reusability of wastes as antimicrobial agents

Abstract Determination of dye biosorption capacity by lichen biosorbent and reusability of the waste lichen biosorbent as an antimicrobial agent are the aims of this study. The study has three stages: 1. to carry out dye biosorption assays, 2. to scan antimicrobial activity of waste lichen biosorbent after dye loaded, 3. to examine the antimicrobial function of a fabric which absorbed waste lichen extract. The optimal conditions for the best dye biosorption were determined. After the biosorption experiments, the waste lichen biomass was harvested from the working solution and the extraction of dye-loaded waste biomass was done using methanol and ethanol. The extracts obtained from both dye-loaded and un-loaded biosorbents were scanned for antimicrobial activity potential by the disk diffusion method. The results of this study showed that the waste lichen biosorbent of biosorption processes can be reused as antimicrobial agents.