Miracle-dz/UniFAR-FTUs huggingface dataset:
Vegetative traits predict grass species' invasiveness and the invasibility of restored grassland

Understanding how grass species' traits relate to their invasiveness and the invasibility of their monocultures can inform restoration of diverse grassland. We measured vegetative traits for 18 bunch grass species local to Pietermaritzburg (KwaZulu-Natal, South Africa) and measured their competitive effect on a phytometer. Using 3 m × 3 m plots planted as monocultures 12 years earlier, we related principal components of these traits to how species had invaded other species' plots (invasiveness), and how their monocultures had been invaded (invasibility). Species with high total leaf mass, many tillers and low specific leaf area (SLA) were most invasive and most resistant to invasion by other grasses. Short, slow-growing grasses were most invasible by forbs. This was partly explained by linking traits to invasion through competitive effect: grasses with high total leaf mass, many tillers and low SLA showed the strongest competitive effect, which appears to be necessary but not sufficient for invasiveness. Thus, traits can predict species' ecological performance and provide insight into the processes structuring plant communities. Restoring grasses with short stature, slow growth, low leaf mass, few tillers, and high SLA may facilitate invasion by other native species, thereby increasing species richness.
Effects of Inorganic Arsenic on Human Prostate Stem-Progenitor Cell Transformation, Autophagic Flux Blockade, and NRF2 Pathway Activation

Background: Inorganic arsenic (iAs) is an environmental toxicant associated with an increased risk of prostate cancer in chronically exposed populations worldwide. However, the biological mechanisms underlying iAs-induced prostate carcinogenesis remain unclear. Objectives: We studied how iAs affects normal human prostate stem-progenitor cells (PrSPCs) and drives transformation and interrogated the molecular mechanisms involved. Methods: PrSPCs were enriched by spheroid culture from normal human primary or immortalized prostate epithelial cells, and their differentiation capability was evaluated by organoid culture. Microarray analysis was conducted to identify iAs-dysregulated genes, and lentiviral infection was used for stable manipulation of identified genes. Soft agar colony growth assays were applied to examine iAs-induced transformation. For in vivo study, PrSPCs mixed with rat urogenital sinus mesenchyme were grafted under the renal capsule of nude mice to generate prostatelike tissues, and mice were exposed to 5 ppm (∼65μM) iAs in drinking water for 3 months. Results: Low-dose iAs (1μM) disturbed PrSPC homeostasis in vitro, leading to increased self-renewal and suppressed differentiation. Transcriptomic analysis indicated that iAs activated oncogenic pathways in PrSPCs, including the KEAP1-NRF2 pathway. Further, iAs-exposed proliferative progenitor cells exhibited NRF2 pathway activation that was sustained in their progeny cells. Knockdown of NRF2 inhibited spheroid formation by driving PrSPC differentiation, whereas its activation enhanced spheroid growth. Importantly, iAs-induced transformation was suppressed by NRF2 knockdown. Mechanistically, iAs suppressed Vacuolar ATPase subunit VMA5 expression, impairing lysosome acidification and inhibiting autophagic protein degradation including p62, which further activated NRF2. In vivo, chronic iAs exposure activated NRF2 in both epithelial and stroma cells of chimeric human prostate grafts and induced premalignant events. Conclusions: Low-dose iAs increased self-renewal and decreased differentiation of human PrSPCs by activating the p62-NRF2 axis, resulting in epithelial cell transformation. NRF2 is activated by iAs through specific autophagic flux blockade in progenitor cells, which may have potential therapeutic implications. https://doi.org/10.1289/EHP6471
The efficiency of two new formulated biofungicides in the control of damping-off and root rot of cucumber and improving the plant defence system

The ability of Rhizoleen-T and Rhizoleen-B to suppress the roots’ diseases of cucumber caused by Fusarium oxysporum and Rhizoctonia solani and induction of the plant defence system was evaluated. The results showed a significant suppression in damping-off and root rot of cucumber when the two biofungicides were applied. They increased the surviving percentage of the treated plants to 98.0% and reduced the mean disease rating to 1.0. The biofungicides significantly enhanced the plant’s morphology and physiology when compared with either infected or non-infected control. The mechanism of action of the biofungicides is could be through the enhancement of the plant defences, in addition to their antifungal effect. They stimulated the defence of the plants by increasing the content of proline and phenols and induction the defensin genes. Biofungicides induced defence genes in the 50-day-old treated plants. The biofungicides are effective, cost effective and applicable in the control of root diseases of cucumber.
Comparison of real time and malachite-green based loop-mediated isothermal amplification assays for the detection of Plasmodium vivax and P. falciparum

The current context of malaria elimination requires urgent development and implementation of highly sensitive and specific methods for prompt detection and treatment of malaria parasites. Such methods should overcome current delays in diagnosis, allow the detection of low-density infections and address the difficulties in accessing remote endemic communities. In this study, we assessed the performance of the RealAmp and malachite-green loop mediated isothermal amplification (MG-LAMP) methodologies, using microscopy and conventional nested-PCR as reference techniques. Both LAMP techniques were performed for Plasmodium genus, P. falciparum, and P. vivax identification using 136 whole blood samples collected from three communities located in the Peruvian Amazon basin. Turnaround time and costs of performing the LAMP assays were estimated and compared to that of microscopy and nested-PCR. Using nested-PCR as reference standard, we calculated the sensitivity, specificity and 95% confidence interval (CI) for all methods. RealAmp had a sensitivity of 92% (95% CI: 85–96.5%) and specificity of 100% (95% CI: 89.1–100%) for species detection; sensitivity and specificity of MG-LAMP were 94% (95% CI: 87.5–97.8%) and 100% (89.1–100%), respectively. Whereas microscopy showed 88.1% sensitivity (95% CI: 80.2–93.7%) and 100% specificity (95%: 89.1–100%). The turnaround time and costs of performing the LAMP assays were lower compared to those associated with nested-PCR but higher than those associated with microscopy. The two LAMP assays were shown to be more sensitive and simple to implement than microscopy. Both LAMP methodologies could be used as large-scale screening tests, but the MG-LAMP assay uses a simple, portable heat-block while the RealAmp requires a RealAmp machine or a real-time PCR machine. This makes the MG-LAMP an appropriate choice for malaria surveillance studies in endemic sites. Use of LAMP tests in active case detection of Plasmodium parasites could help to detect positive malaria cases early.
Responses of seed-hoarding behaviour to conspecific audiences in scatter- and/or larder-hoarding rodents

In rodents, the presence of conspecifics may trigger changes in food-hoarding behaviour when the risk of pilferage is perceived to be high. It is not clear how hoarding intensity and hoarding patterns (scatter- or larder-hoarding) of rodents change in the presence of conspecific audiences or if the nature of the change is different between sexes, or influenced by body size. We investigated these questions in Korean field mice (Apodemus peninsulae) (KFM, showing both scatter- and larder-hoarding behaviours) and Chinese white-bellied rats (Niviventer confucianus) (CWBR, showing larder-hoarding behaviours only) through carefully controlled experiments in outdoor enclosures. We observed the seed-hoarding behaviour of focal females and males of each species in the presence of a conspecific audience of the opposite sex, same sex, and alone (control treatment). We found both rodent species increased hoarding efforts when faced with an increased pilferage risk (presence of audiences), supporting the pilferage tolerance hypotheses or forage competition hypotheses. In contrast with previous studies, we found potential pilferage risk can result in a KFM shift from scatterhoarding to larder-hoarding, supporting the larder defence hypotheses, not the catastrophic avoidance hypotheses. However, the relationship between hoarding patterns, and body size or sex, is rather complex and requires further investigation.
Investigation of the effects of probiotic, Bacillus subtilis on stress reactions in laying hens using infrared thermography

The goal of the study was to assess whether tonic immobility (TI)-induced stress reactions in laying hens can be reduced by probiotic supplementation and if the changes in body surface temperature, as a stress indicator, are genetically dependent and can be detected using infrared thermography (IRT). Seventy-one white and 70 brown hens were used. Hens were randomly assigned to three treatments at 1-day-old: beak trimmed and fed a regular diet; non-beak trimmed and fed a regular diet; and non-beak trimmed and fed a diet supplemented with probiotics, Bacillus subtilis. At 40 weeks of age, hens were tested for TI reactions. Eye and face temperatures were measured with IRT immediately before and after TI testing. Results revealed that the probiotic supplementation did not affect hens’ stress responses to TI testing; the left and right eye temperatures increased by 0.26s°C and 0.15°C, respectively, while right face temperature tended to increase following TI testing. However, the right eye (32.60°C for white, and 32.35°C for brown) and face (39.51°C for white, and 39.36°C for brown) temperatures differed significantly among genetic lines. There was a positive correlation between TI duration and the changes of the left and right eye temperatures after TI testing in white hens. Based on these results, hens experienced TI-induced surface temperature changes that were detectable using IRT. White hens experienced greater stress reactions in response to TI than brown hens. However, supplementation with Bacillus subtilis did not attenuate hens’ reaction to TI testing.
Structure and function of a flavin-dependent S-monooxygenase from garlic (Allium sativum)

Allicin is a component of the characteristic smell and flavor of garlic (Allium sativum). A flavin-containing monooxygenase (FMO) produced by A. sativum (AsFMO) was previously proposed to oxidize S-allyl-l-cysteine (SAC) to alliin, an allicin precursor. Here, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC; however, the enzyme was highly active with l-cysteine, N-acetyl-l-cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly (KD of ∼2 μm) to AsFMO and that the hydride transfer occurs with pro-R stereospecificity. We detected the formation of a long-wavelength band when AsFMO was reduced by NADPH, probably representing the formation of a charge-transfer complex. In the absence of substrate, the reduced enzyme, in complex with NADP+, reacted with oxygen and formed an intermediate with a spectrum characteristic of C4a-hydroperoxyflavin, which decays several orders of magnitude more slowly than the kcat. The presence of substrate enhanced C4a-hydroperoxyflavin formation and, upon hydroxylation, oxidation occurred with a rate constant similar to the kcat. The structure of AsFMO complexed with FAD at 2.08-Å resolution features two domains for binding of FAD and NADPH, representative of class B flavin monooxygenases. These biochemical and structural results are consistent with AsFMO being an S-monooxygenase involved in allicin biosynthesis through direct formation of sulfenic acid and not SAC oxidation.
The Politicization of Risk: Party Cues, Polarization, and Public Perceptions of Climate Change Risk

Previous research shows that public perceptions of climate change risk are strongly related to the individual willingness to support climate mitigation and adaptation policy. In this article, I investigate how public perceptions of climate change risk are affected by communications from political parties and the degree of polarization among them. Specifically, using survey data from Sweden, Norway, Australia, and New Zealand, I study the relationship between party source cues, perceived polarization, and public perceptions of climate change risk. The results reveal a positive relationship between party cues and perceptions of climate change risk, indicating that individuals adjust their risk perceptions to align with their party preference. Furthermore, a negative relationship between perceived polarization and individual risk perceptions is also discovered, showing that individuals tend to be less concerned with climate change the more polarization they perceive. However, the effect of perceived polarization is found to be limited to more abstract perceptions of risk, while being unrelated to perceptions of concrete risks. Even with some contextual variance, the results generally hold up well across the four countries.
Analysis of the Hosts and Transmission Paths of SARS-CoV-2 in the COVID-19 Outbreak

The severe respiratory disease COVID-19 was initially reported in Wuhan, China, in December 2019, and spread into many provinces from Wuhan. The corresponding pathogen was soon identified as a novel coronavirus named SARS-CoV-2 (formerly, 2019-nCoV). As of 2 May, 2020, over 3 million COVID-19 cases had been confirmed, and 235,290 deaths had been reported globally, and the numbers are still increasing. It is important to understand the phylogenetic relationship between SARS-CoV-2 and known coronaviruses, and to identify its hosts for preventing the next round of emergency outbreak. In this study, we employ an effective alignment-free approach, the Natural Vector method, to analyze the phylogeny and classify the coronaviruses based on genomic and protein data. Our results show that SARS-CoV-2 is closely related to, but distinct from the SARS-CoV branch. By analyzing the genetic distances from the SARS-CoV-2 strain to the coronaviruses residing in animal hosts, we establish that the most possible transmission path originates from bats to pangolins to humans.
Does enemy-free space for eggs contribute to a leaf beetle’s oviposition preference for a nutritionally inferior host plant?

Summary 1 Natural enemies are likely to influence the interactions between herbivorous insects and their host plants. In particular, selection exerted by natural enemies could favour host-plant switches and cause, or maintain, oviposition preference for a host species that is nutritionally inferior to another acceptable host. 2 In a previous study, it was shown that larvae of the leaf beetle Oreina elongata perform better on Adenostyles alliariae (Asteraceae) than on Cirsium spinosissimum (Asteraceae). Moreover, A. alliariae provides larval and adult beetles with sequestrable chemical defences. However, in the field, egg densities are much higher on C. spinosissimum than on adjacent A. alliariae. 3 In this study, it was investigated whether this oviposition pattern could be maintained by C. spinosissimum, providing the eggs of O. elongata with better protection from natural enemies. In a field experiment, the survival of eggs was quantified on plants of each of the two species, with and without enemy exclusion. 4 Egg survival was equal for both host species when enemies were excluded from the plants, but it was higher on C. spinosissimum than on A. alliariae when enemies were allowed to the plants. It was also experimentally tested whether the higher egg densities observed in the field on C. spinosissimum are actually due to oviposition preference by the beetle. In a no-choice test, females laid more eggs on C. spinosissimum than on A. alliariae. 5 It can thus be confirmed that C. spinosissimum is really preferred for oviposition and it is concluded that this preference is likely to be maintained, at least partly, by a higher egg survival on C. spinosissimum due to enemy-free space provided by this host plant.
Genetic Variability and Biochemical Systematics of Domestic and Wild Cat Populations (Felis silvestris: Felidae)

Genetic variability and phylogenetic relationships among domestic and wild populations of cats were studied by allozyme electrophoresis. Tissues were obtained from 67 specimens of European wild cats ( Felis silvestris silvestris ), African wild cats ( F. s. libyca ), and domestic cats from Italy; 54 presumptive loci were resolved. The average proportion of polymorphic loci and heterozygosity were P = 0.11, H = 0.042 in the wild cat, and P = 0.20, H = 0.066 in the domestic cat. Despite reduced genetic variability, local populations of wild cats were not inbred, as indicated by nonsignificant F IS values. Both F ST and Nei's genetic distances between domestic and wild populations were low ( F ST = 0.04; D = 0.0082). Dendrograms indicate that the domestic cat belongs to the African wild cat lineage, which supports current hypotheses on cat domestication. Based on the genetic evidence, we suggest that the European wild cat, the African wild cat, and the domestic cat belong to the same polytypic species ( Felis silvestris Schreber, 1777), and that the European and African wild cats diverged approximately 20,000 years ago.
Roles of Category, Shape, and Spatial Frequency in Shaping Animal and Tool Selectivity in the Occipitotemporal Cortex

Does the nature of representation in the category-selective regions in the occipitotemporal cortex reflect visual or conceptual properties? Previous research showed that natural variability in visual features across categories, quantified by image gist statistics, is highly correlated with the different neural responses observed in the occipitotemporal cortex. Using fMRI, we examined whether category selectivity for animals and tools would remain, when image gist statistics were comparable across categories. Critically, we investigated how category, shape, and spatial frequency may contribute to the category selectivity in the animal- and tool-selective regions. Female and male human observers viewed low- or high-passed images of round or elongated animals and tools that shared comparable gist statistics in the main experiment, and animal and tool images of naturally varied gist statistics in a separate localizer. Univariate analysis revealed robust category-selective responses for images with comparable gist statistics across categories. Successful classification for category (animals/tools), shape (round/elongated), and spatial frequency (low/high) was also observed, with highest classification accuracy for category. Representational similarity analyses further revealed that the activation patterns in the animal-selective regions were most correlated with a model that represents only animal information, whereas the activation patterns in the tool-selective regions were most correlated with a model that represents only tool information, suggesting that these regions selectively represent information of only animals or tools. Together, in addition to visual features, the distinction between animal and tool representations in the occipitotemporal cortex is likely shaped by higher-level conceptual influences such as categorization or interpretation of visual inputs. SIGNIFICANCE STATEMENT Since different categories often vary systematically in both visual and conceptual features, it remains unclear what kinds of information determine category-selective responses in the occipitotemporal cortex. To minimize the influences of low- and mid-level visual features, here we used a diverse image set of animals and tools that shared comparable gist statistics. We manipulated category (animals/tools), shape (round/elongated), and spatial frequency (low/high), and found that the representational content of the animal- and tool-selective regions is primarily determined by their preferred categories only, regardless of shape or spatial frequency. Our results show that category-selective responses in the occipitotemporal cortex are influenced by higher-level processing such as categorization or interpretation of visual inputs, and highlight the specificity in these category-selective regions.
Poor outcome and prolonged persistence of SARS‐CoV‐2 RNA in COVID‐19 patients with haematological malignancies; King's College Hospital experience

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), emerged at the end of 2019 and caused an infection named COVID-19 (Guan, Ni et al. 2020). Patients with compromised immune systems are at increased risk of complications but this risk is not precisely defined (Liang, Guan et al. 2020). Although age, gender, comorbidities and ethnicity are risk factors for adverse outcomes (Huang, Wang et al. 2020), various pre-existing conditions, including haematological cancers, have also been reported to correlate with poor outcomes (Aries, Davies et al. 2020, He, Chen et al. 2020, Malard, Genthon et al. 2020, Martin-Moro, Marquet et al. 2020, medRxiv 2020).
Malaria Vectors and Vector Surveillance in Limpopo Province (South Africa): 1927 to 2018

Despite the annual implementation of a robust and extensive indoor residual spraying programme against malaria vectors in Limpopo Province (South Africa), significant transmission continues and is a serious impediment to South Africa’s malaria elimination objectives. In order to gain a better understanding regarding possible causes of this residual malaria, we conducted a literature review of the historical species composition and abundance of malaria vector mosquitoes in the Limpopo River Valley region of the Vhembe District, northern Limpopo Province, the region with the highest remaining annual malaria cases in South Africa. In addition, mosquito surveys were carried out in the same region between October 2017 and October 2018. A total of 2225 adult mosquitoes were collected using CO2-baited tent and light traps, human landing catches and cow-baited traps. Of the 1443 Anopheles collected, 516 were members of the An. gambiae complex and 511 An. funestus group. In the malaria endemic rural areas outside the Kruger National Park, one specimen each of An. gambiae s.s. and An. funestus and only three of An. arabiensis were collected. The latter species was abundant at a remote hot spring in the neighboring Kruger National Park. Eighteen other species of Anopheles were collected. Our survey results support the historical findings that An. arabiensis, the species widely held to be the prime malaria vector in South Africa, is a rare species in the malaria endemic Limpopo River Valley. The implications of the mosquito surveys for malaria transmission, elimination and vector control in northern Limpopo Province and neighboring regions are discussed.