Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Digital Work Platforms in Negotiating New Power Dynamics: Experiences from a Social Digital Skills Platform in South Africa

Digital work platforms can serve as trust-mediating agents between workers and employers who are previously unknown to each other. The design decisions made by digital work platform developers have an impact on the power dynamics between workers and employers. We report on our experience with piloting a social digital platform, VASTBlu, designed to enable workers from township communities in South Africa to access work opportunities in the mainstream economy. We also discuss ways in which factors like symmetry of review or the frequency of review between parties could be consciously chosen to change the power dynamics between parties in a digital work platform, reducing unfair practices and bringing increased power and dignity to workers.
Associations of exercise and social support with mental health during quarantine and social-distancing measures during the COVID-19 pandemic: A cross-sectional survey in Germany

Introduction: Social distancing and quarantine measures applied during the COVID-19 pandemic might result in mental health problems. In this cross-sectional study we examined if perceived social support, exercise in minutes per week and change in exercise are protective factors regarding symptoms of depression, anxiety, and sleeping disorders. Method: In April 2020, n = 4271 German adults completed an online survey including mental health questionnaires regarding depression (PHQ-D), anxiety (PHQ-D) and sleep (PSQI), as well as questionnaires related to protective factors such as exercise (BSA-F), physical activity-related health competence (PAHCO) and social support (F-SozU). Results: Complete case analysis (n = 3700; mean age 33.13 {+/-} 11.73 years, 78.6 % females) resulted in elevated prevalence of depressive disorder (31.4%), panic disorder (5.7%) and other anxiety disorders (7.4%). 58.3% reported symptoms of insomnia. Three separate models of multiple regression were conducted. Perceived social support was associated with lower values of anxiety (beta = -0.10; t(19) = -6.46; p >0.001), lower values of depressive symptoms (beta = -0.22; t(19) = -15.71; p < . 001) and lower values of sleeping disorder symptoms (beta = -0.15; t(19) = -9.55; p < . 001). Change towards less exercise compared to the time before Covid-19 was associated with and higher values of anxiety (beta = -0.05; t(19) = -2.85; p= . 004), higher values of depressive symptoms (beta = -0.08; t(19) = -5.69; p < . 001), and higher values of sleeping disorder symptoms (beta = -0.07; t(19) = -4.54; p < . 000). Post-hoc analysis (ANOVAs) revealed that a change towards less exercise was significantly associated with more depressive, anxiety and sleeping disorder symptoms whereas a positive change was not. No significant association was found for exercise in minutes per week for all outcomes. Conclusion: The COVID-19 pandemic seems to have a negative impact on mental health in the German population. Social Support and a stable amount of exercise might attenuate these negative mental health consequences. Ongoing monitoring of the impact of the pandemic on mental health and possible protective factors is needed in order to create a basis for the development of appropriate prevention and intervention measures.
Germination of Psittacanthus schiedeanus (mistletoe) seeds after passage through the gut of Cedar Waxwings and Grey Silky-flycatchers1

Abstract Spatial patterns of mistletoe seed deposition are behaviorally determined by frugivorous birds but the effects of gut passage on mistletoe seed germination has received little attention. Here we investigate the effects of several predictors and passage through the digestive tube of two bird species, Grey Silky-flycatcher (GSF, Ptilogonys cinereus) and Cedar Waxwings (CW, Bombycilla cedrorum) on seed germination of Psittacanthus schiedeanus (Loranthaceae). Fruits were collected from mistletoe plants growing on three host tree species, Liquidambar styraciflua, Acacia pennatula, and Rapanea myricoides. More mistletoe seeds from Liquidambar trees germinated than those from Acacia and Rapanea trees, regardless of fruit treatment. Fewer seeds defecated by GSFs germinated compared to those defecated by CWs or manually extracted. However, analyzed within a generalized linear modeling framework, host source and seed weight were the best predictors for the occurrence of germination. Seeds were retained longer in the guts of GSFs than seeds in those of CWs, and increased retention time reduced significantly mistletoe seed germination. This study demonstrated that gut passage affected seed germination responses of mistletoes of P. schiedeanus, and additional studies should examine this relationship for other mistletoe-bird interactions.
Simulation of Urban Expansion in Estonia for 2046 Using Cellular Automata Model Based on the CORINE Land Cover Database

This research modelled "urban expansion" in the Harju County in Estonia, which includes the capital of the country, using remote sensing data of CORINE land cover database. Urban land use changes were detected by applying Markov model. Then, Markov transition probability maps were produced. Using MCE (Non_ Boolean Standardization and Weighted Linear Combination (WLC), suitability maps were extracted and these inputs used in the process of CA-Markov in IDRISI software to simulate the future scenario for the year 2046.
Glyphosate-resistant Horseweed (Conyza Canadensis) Emergence, Survival, and Fecundity in No-till Soybean

Abstract Horseweed has generally been considered a winter annual weed species, but efforts to control horseweed as a winter annual weed in no-till soybean production with glyphosate have routinely failed in southeast Indiana. The objective of this study was to determine emergence timing, plant survival, and fecundity of a glyphosate-resistant (GR) horseweed biotype in the presence or absence of other winter annual weeds or soybean. A field study was conducted from October 2003 to October 2004 and repeated from October 2004 to October 2005 in fields following no-till soybean production. Horseweed emergence was not observed in the fall of 2003. Winter survival of plants that emerged in the fall of 2004 was 20% by late April 2005 and was inversely related to fall rosette size. Horseweed population densities were the highest in mid-May of both years, and over 90% of the plants observed at this time emerged in the spring. Plant survival from mid-May to mid-October was 3% and 21% in 2004 and 2005, respectively. Horseweed with flower heads above the soybean canopy by early August had greater late-season survival and produced more seed than plants growing below the canopy. Horseweed with flower heads above the soybean canopy produced an average of 27,200 and 58,320 seeds plant−1 in 2004 and 2005, respectively. Our research indicates that this southeast Indiana horseweed biotype behaves primarily as a summer annual weed and produces significant amounts of seed when uncontrolled in no-till soybean production. Nomenclature: Glyphosate; horseweed, Conyza canadensis (L.) Cronq. ERICA; soybean, Glycine max (L.) Merr
Evaluation of antibacterial activity of Aspergillus and Penicillium spp.

Bacteria have known as one of the main important limitation factors of many agricultural products. The purpose of the present study was to evaluate the antibacterial activities of different species of Penicillium and Aspergillus on some important bacteria. For this intention 12 and 21 species of Aspergillus and Penicillium, were applied, respectively. Gram-negative bacteria conducted in this research were Pseudomonas viridiflava, Xanthomonas campestrispv. Campestris and Escherichia coli and the only gram-positive bacterium was Rhatayibacter iranicus. Fungal and bacterial isolates were dual cultured simultaneously on Potato Dextrose Broth (PDB) and were shaked with 120 rpm. The samples were investigated after a week. The results of this study demonstrated that none of fungal species could inhibit E. coli and the most of the studied species couldn’t suppress the growth of P. viridiflava except isolates of (5033, 5037, and 5071) from P. crysogenum. On the other hand, A. awamori, A. ferreus, A. ostiatus, A. niger, A. foetidus, P. mali, P. crustaseum and P. citrinumcould lead to inhibition of X. campestris pv. campestris Gram positive bacterium, Rhatayibacter iranicus, was not able to grow in the presence of all species of Aspergillus. On the contrary, species of P. piscarium, P. corylophilum, P. griseofulvum and P.chrysogenum couldn’t prevent its growth.
Structures of alfalfa polysaccharides and their antioxidative activities in mice

Four kinds of alfalfa-derived polysaccharides, API, APII, APIII and APIV, were extracted using Sephadex A-25 cellulose column chromatography. The most plentiful components, APII and APIII, were screened using Sephadex G-200 column chromatography. Data from HPLC, infrared spectroscopy, and NMR analysis showed that APII contained D-glucopyranosyl, D-fructose and APIII-b contained D-fructose, D-rhamnose, and D-glucopyranosyl, this last of which has a role in regulating animal immune systems, improving their ability to resist oxidative damage and tumors. In the present study, high doses of APII-a and APIII-b and medium doses of APIII-b were found to improve SOD and GSH-PX activity and reduce MDA levels in mice (P<0.05). The antioxidative functions of these polysaccharides took place in a dose-dependent manner.
Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding in vivo

Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements. Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we advance Single Molecule Footprinting to detect individual molecular interactions of transcription factors and nucleosomes with DNA at mouse cis-regulatory elements. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that for most types of transcription factors high DNA co-occupancy can occur in absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy for binding cooperativity. These findings elucidate the binding cooperativity mechanism used by transcription factors in absence of strict organisation of their binding motifs, a characteristic feature of most of enhancers.
The silencing factor Sir3 is a molecular bridge that sticks together distant loci

Physical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here we investigate the well conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3-5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing complex SIR composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long range contacts between distant regions, including the rDNA, telomeres, and internal Sir3 bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, and Sir4), Sir2 activity or chromosome context. Altogether these data suggest that Sir3 represents an uncommon example of protein able to bridge directly distant loci.
CoExp Web, a web tool for the exploitation of co-expression networks

Summary This paper presents the CoExp Web tool. CoExp is a software tool and a Web resource that fosters research on co-expression network models by providing a highly usable means to exploit and share multiple network models. Availability and Implementation the Web resource is accessible at https://snca.atica. um.es/coexp/. The software at the front and back-ends is accessible at https://github.com/SoniaRuiz/CoExp_Web. Contact skgtsg0@ucl.ac. uk (Sonia García-Ruíz)
Fuel Treatment Longevity in Ponderosa Pine-Dominated Forest 24 Years After Cutting and Prescribed Burning

Fuels reduction treatments to mitigate fire behavior are common in ponderosa pine ecosystems of the western United States. While initial impacts of fuel treatments have been reported, less is known about treatment longevity as live and dead fuels change with time. We analyzed fuel dynamics in ponderosa pine–Douglas-fir forests 21–23 years following experimental fuel reduction designed as two independent studies of cutting combined with burning: one tested a commercial thinning strategy, while a second tested a retention shelterwood strategy to reduce fuels while also restoring ponderosa pine forests. Treated units were harvested in 1992 and half of the units were prescribed burned 1 to 2 years later. After 22 to 23 years post-treatment, few differences in fuel load persist and all treatments have increased ladder fuels in the form of live saplings and seedlings. Canopy fuel loads were lower in treated units compared to untreated control units; however, no other canopy fuel metric differed between treatments. The only persistent difference in surface fuels was in the retention shelterwood, where 1 h fuels were lower in the treated units compared to control units. Crown fire hazard varied greatly, but means were similar between treatments. The increased hazard was driven by increases in live surface fuels from seedlings and saplings in the retention shelterwood, which increased canopy bulk density and reduced canopy base height. The overstory was still dominated by ponderosa pine 22–23 years later for all treatments, but the smaller size classes were primarily Douglas-fir, suggesting that without future disturbance, dominance will shift from pine to Douglas-fir dominated forests. The exception to this was the cut+fall burn treatment in the commercial thinning, where ponderosa pine outnumbered Douglas-fir trees across all size classes. The treatments that included a broadcast prescribed burn killed many existing seedlings and saplings. Our findings support other studies showing fuel reduction and restoration treatments are most successful with a combination of cutting and burning strategies, but also show that fuel treatments in low-elevation dry forests will likely not remain effective for much longer than historical mean fire return intervals.
Metal contamination and oxidative stress biomarkers in estuarine fish following a mine tailing disaster

The Rio Doce estuary in Brazil was impacted by the deposition of mine tailings caused by the collapse of a mining dam in 2015. Since the disaster, the estuary is experiencing chronic trace metal contamination effects, but potential trace metal accumulation in fishes has not been reported. Trace metals in aquatic ecosystems pose severe threats to the aquatic biota, so we hypothesized that the accumulation of trace metals in estuarine sediments nearly two years after the disaster would cause contaminant bioaccumulation, resulting in the biosynthesis of metal-responsive proteins in fishes. We determined trace metal concentrations in sediment samples, metal concentrations, and quantified stress protein concentrations in the liver and muscle tissue of five different fish species in the estuary. Our results revealed high concentrations of trace metals in estuarine sediments when compared to published baseline values for this estuary. The demersal fish species Cathorops spixii and Genidens genidens had the highest Hg, As, Se, Cr, and Mn concentrations in both hepatic and muscle tissues. Metal bioaccumulation in fish was statistically correlated with the biosynthesis of metallothionein and reduced glutathione in both fish liver and muscle tissue. The trace metals detected in fish tissues resemble those in the contaminated sediments present at the estuary at the time of this study and were also significantly correlated to protein levels. Trace metals in fish muscle were above the maximum permissible limits for human consumption, suggesting potential human health risks that require further determination. Our study supports the high biogeochemical mobility of trace metals between contaminated sediments and local biota in estuarine ecosystems.
Use of Biochemical Genetic Variants for Identification of Sockeye Salmon (Oncorhynchus nerka) Stocks in Cook Inlet, Alaska

We used the geographic distributions of biochemical genetic variants in sockeye salmon (Oncorhynchus nerka) to describe features of its population structure and to identify stocks in commercial catches from the central fishing district of Cook Inlet, Alaska. Allelic frequencies for 6 polymorphic loci were determined for samples of 13 spawning areas using starch gel electrophoresis and were used as the basis of stock classification. The level of genetic variation, estimated by average heterozygosity, was 4.6%. Likelihood ratio tests for heterogeneity among allelic frequencies indicated a significant degree of heterogeneity among spawning areas within the Susitna and Kenai rivers, but not among the spawning areas within the Kasilof River. These tests also indicated that for the Kasilof River, where multi-year samples were taken, allelic frequencies were not significantly different for two consecutive years. Cluster analysis of genetic similarities between samples indicated that the samples from the Kasilof .
Heart Rate Variability as an Index of Differential Brain Dynamics at Rest and After Acute Stress Induction

The brain continuously receives input from the internal and external environment. Using this information, the brain exerts its influence on both itself and the body to facilitate an appropriate response. The dynamic interplay between the brain and the heart and how external conditions modulate this relationship deserves attention. In high-stress situations, synchrony between various brain regions such as the prefrontal cortex and the heart may alter. This flexibility is believed to facilitate transitions between functional states related to cognitive, emotional, and especially autonomic activity. This study examined the dynamic temporal functional association of heart rate variability (HRV) with the interaction between three main canonical brain networks in 38 healthy male subjects at rest and directly after a psychosocial stress task. A sliding window approach was used to estimate the functional connectivity (FC) among the salience network (SN), central executive network (CEN), and default mode network (DMN) in 60-s windows on time series of blood-oxygen-level dependent (BOLD) signal. FC between brain networks was calculated by Pearson correlation. A multilevel linear mixed model was conducted to examine the window-by-window association between the root mean square of successive differences between normal heartbeats (RMSSD) and FC of network-pairs across sessions. Our findings showed that the minute-by-minute correlation between the FC and RMSSD was significantly stronger between DMN and CEN than for SN and CEN in the baseline session [b = 4.36, t(5025) = 3.20, p = 0.006]. Additionally, this differential relationship between network pairs and RMSSD disappeared after the stress task; FC between DMN and CEN showed a weaker correlation with RMSSD in comparison to baseline [b = −3.35, t(5025) = −3.47, p = 0.006]. These results suggest a dynamic functional interplay between HRV and the functional association between brain networks that varies depending on the needs created by changing conditions.
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools

Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to small library sizes and high sequence error, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore sequencing RNA-seq datasets with the goal of obtaining gene-level and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (“sequins”) as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator Smchd1 were analysed using a mix of long-read specific tools for preprocessing together with established short-read RNA-seq methods. We used limma-voom to perform differential gene expression analysis, and the novel FLAMES pipeline to perform isoform identification and quantification, followed by DRIMSeq and limma-diffSplice (with stageR) to perform differential transcript usage analysis. We compared results from the sequins dataset to the ground truth, and results of the mouse dataset to a previous short-read study on equivalent samples. Overall, our work shows that transcriptomic analysis of long-read nanopore data using short-read software and methods that are already in wide use can yield meaningful results.
A long 5' UTR of the rice OsMac1 mRNA enabling the sufficient translation of the downstream ORF

Untranslated regions (UTRs) of mRNA are involved in many posttranscriptional regulatory pathways. The rice OsMac1 mRNA had a 5′ UTR of more than 500 nucleotides (nt), containing a CU-rich region and three upstream open reading frames (uORFs) preceding the downstream ORF. The expected GFP-fusion protein was detected at the cell membrane, indicating the occurrence of translation of the downstream ORF. The 5′ UTR contained three splicing variants that were generated by alternative splicing. A reporter analysis using β-glucuronidase indicated that only the longest one, UTRc, showed a significant ability for the efficient translation of the downstream ORF, whereas other splicing variants showed low level of translational efficiency of the corresponding ORF. These results suggested that the additional 38-nt sequence unique to UTRc localized between the CU-rich region and the uORFs may be involved in the increased translational efficiency of the downstream ORF located after the long 5′ UTR.
Evidence of antimicrobial activity of date fruits in combination with high intensity ultrasound.

Although dates are highly nutritious materials that may support the growth of spoilage and pathogenic organisms, they are typically safe to store at ambient temperature in a warehouse for up to several months. The goal of this research was to better understand the apparent long-term microbial stability of dates and to investigate new means to further enhance their stability. To this purpose, several different extraction methods with different ultrasonic intensity, ratio of date fruit to water and temperature were first used to investigate their effects on microbial count. Secondly, "continuous high-intensity ultrasound waves irradiated date and water mixture" sterilized by cold manner and then used as a culture media for native micro flora of dates. Antimicrobial activity was evaluated using agar dilution assay. Results indicate the existence of anti-microbial and anti-fungal activity in date components. Furthermore, sonication of dates decreased microbial counts. Results suggest a synergistic effect between ultrasonication and the presence of antimicrobial substances in date syrup leading to an overall reduction in the initial microbial load of the product. On the whole, 85% decrease was observed in susceptible type of fungi known as Gilmaniella.