Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation

Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mechanism of sclerotia formation is important for crop disease control. To identify the genes involved in this process for the development of disease control targets, the transcriptomes of this species were determined at three important developmental stages (mycelium, sclerotial initiation, and sclerotial maturation) using an RNA-sequencing approach. A total of 5,016, 6,433, and 5,004 differentially expressed genes (DEGs) were identified in the sclerotial initiation vs. mycelial, sclerotial maturation vs. mycelial, and sclerotial maturation vs. sclerotial initiation stages, respectively. Moreover, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses showed that these DEGs were enriched in diverse categories, including oxidoreductase activity, carbohydrate metabolic process, and oxidation-reduction processes. A total of 12 DEGs were further verified using reverse transcription quantitative PCR. Among the genes examined, NADPH oxidase 1 (NOX1) and superoxide dismutase (SOD) were highly induced in the stages of sclerotial initiation and maturation. In addition, the highest reactive oxygen species (ROS) production levels were detected during sclerotial initiation, and enzyme activities of NOX1, SOD, and catalase (CAT) matched with the gene expression profiles. To further evaluate the role of ROS in sclerotial formation, R. solani AG1 IA was treated with the CAT inhibitor aminotriazole and H2O2, resulting in the early differentiation of sclerotia. Taken together, this study provides useful information toward understanding the molecular basis of R. solani AG1 IA sclerotial formation and maturation, and identified the important role of ROS in these processes.
XIAP at the crossroads of cell death and inflammation

Accurate regulation of cell death is crucial for proper development and homeostasis of organisms. Consequently, deregulated cell death can lead to developmental defects, neuropathies, infections, inflammatory diseases and cancer. Many cell death regulators have additional functions, including important roles in cell division, metabolism, inflammatory signaling pathways and tumor biology. Inhibitor of apoptosis (IAP) proteins were initially identified as inhibitors of cell death during viral infection, but are no exception to that paradigm [1, 2]. Several IAP proteins, including XIAP (X chromosomelinked IAP), are ubiquitin E3 ligases with seminal roles in diverse signaling pathways [3]. The most prominent IAP ubiquitination substrates, RIP1 and RIP2 proteins, are modified by c-IAPs (cellular IAPs) and XIAP E3 activity in TNF and NOD2 signaling, respectively [3]. XIAP also influences RIP1 ubiquitination and RIP3 dependent cell death and IL-1β secretion in response to TNF [4]. XIAP is the only endogenous mammalian inhibitor of caspases, which function as executioner proteases in cell death pathways [2]. It uses its BIR2 domain and the linker region between the BIR1 and BIR2 domains to bind the substrate-binding groove of active caspases 3 and 7, and its BIR3 domain to bind the conserved four aminoterminal amino acids of the p12 small subunit of processed caspase-9 (Figure 1). Thus, not surprisingly, initial efforts at targeting IAP proteins in cancer were focused on antagonizing XIAP binding to and inhibition of caspases. However, although XIAP was the main target, most IAP antagonists had pan-IAP activity with no significant selectivity for XIAP [2]. Discovery and characterization of c-IAP1/2 selective and, more recently, XIAP selective antagonists confirmed that XIAP selective antagonism is not sufficient to promote cell death in cancer cells [2, 5]. Interestingly, the main effect of pan-IAP antagonists was the activation of c-IAP1/2 E3 activity leading to their auto-ubiquitination, proteasomal degradation and subsequent activation of canonical and noncanonical NFkB signaling and production of inflammatory cytokines [2]. The most important cytokine produced was TNF, Editorial: Autophagy and Cell Death
Reaching a consensus on research priorities for supporting women with autoimmune rheumatic diseases during pre-conception, pregnancy and early parenting: A Nominal Group Technique exercise with lay and professional stakeholders

Background:Women with autoimmune rheumatic diseases (ARDs) find it difficult to get information and support with family planning, pregnancy, and early parenting. A systematic approach to prioritising research is required to accelerate development and evaluation of interventions to meet the complex needs of this population. Methods:A Nominal Group Technique (NGT) exercise was carried out with lay and professional stakeholders (n=29). Stakeholders were prepared for debate through presentation of available evidence. Stakeholders completed three tasks to develop, individually rank, and reach consensus on research priorities: Task 1 – mapping challenges and services using visual timelines; Task 2 - identifying research topics; Task 3 - individually ranking research topics in priority order. Results of the ranking exercise were fed back to the group for comment. Results:The main themes emerging from Task 1 were the need for provision of information, multi-disciplinary care, and social and peer support. In Task 2, 15 research topics and 58 sub-topics were identified around addressing the challenges and gaps in care identified during Task 1. In Task 3, a consensus was reached on the ten research topics that should be given the highest priority. These were individually ranked, resulting in the following order of priorities (from 1 – highest to 10 – lowest): 1. Shared decision-making early in the care pathway; 2. Pre-conception counseling; 3. Information about medication use during pregnancy/breastfeeding; 4. Personalised care planning; 5. Support for partners/family members; 6. Information about local support/disease specific issues; 7. Shared decision-making across the care pathway; 8. Peer-support; 9. Social inequalities in care, and; 10. Guidance on holistic/alternative therapies. Conclusions:This systematic approach to identification of research priorities from a multi-disciplinary and lay perspective indicated that activities should focus on development and evaluation of interventions that increase patient involvement in clinical decision-making, multi-disciplinary models of care, and timely provision of information.
Effects of Feeding Extruded Soybean, Ground Canola Seed and Whole Cottonseed on Ruminal Fermentation, Performance and Milk Fatty Acid Profile in Early Lactation Dairy Cows

Four ruminally cannulated Holstein cows averaging 43 days in milk (DIM) were used in a 4x4 Latin square to determine the effect of feeding extruded soybean, ground canola seed and whole cottonseed on ruminal fermentation and milk fatty acid profile. One hundred and twenty lactating Holstein cows, 58 (±31) DIM, were assigned to four treatments in a completely randomized block design to study the effects of the three types of oilseeds on production parameters and milk fatty acid profile. The four diets were a control diet (CON) and three diets in which 10% extruded soybean (ESB), 5% ground canola seed (GCS) and 10% whole cottonseed (WCS) were included, respectively. Diets consisted of concentrate mix, corn silage and Chinese wild rye and were balanced to similar concentrations of CP, NDF and ADF. Ruminal fermentation results showed that ruminal fermentation parameters, dry matter intake and milk yield were not significantly affected by treatments. However, compared with the control, feeding cows with the three oilseed diets reduced C14:0 and C16:0 and elevated C18:0 and C18:1 concentrations in milk, and feeding ESB increased C18:2 and cis9, transll conjugated linoleic acid (CLA). Production results showed that feeding ESB tended to increase actual milk yield (30.85 kg/d vs. 29.29 kg/d) and significantly decreased milk fat percentage (3.53% vs. 4.06%) compared with CON. Milk protein (3.41%) and solid non-fat (13.27%) from cows fed WCS were significantly higher than from cows fed CON (3.24% and 12.63%, respectively). Milk urea N concentrations from cows fed the ESB (164.12 mg/L) and GCS (169.91 mg/L) were higher than cows fed CON (132.31 mg/L). However, intake of DM, 4% fat corrected milk, energy corrected milk, milk fat and protein yields, milk lactose percentage and yield, somatic cell count and body condition score were not affected by different treatments. The proportion of medium-chain fatty acid with 14 to 16 C units in milk was greatly decreased in cows fed ESB, GCS and WCS. Feeding ESB increased the concentration in milk of C18:1, C18:2, C18:3 and cis9, transll-CLA content by 16.67%, 37.36%, 95.24%, 72.22%, respectively, feeding GCS improved C18:0 and C18:1 by 17.41% and 33.28%, respectively, and feeding WCS increased C18:0 by 31.01% compared with feeding CON. Both ruminal fermentation and production trial results indicated that supplementation of extruded soybean, ground canola seed and whole cottonseed could elevate the desirable poly- and monounsaturated fatty acid and decrease the medium chain fatty acid and saturated fatty acid content of milk fat without negative effects on ruminal fermentation and lactation performance.
Effects of increased temperature on plant communities depend on landscape location and precipitation

Abstract Global climate change is affecting and will continue to affect ecosystems worldwide. Specifically, temperature and precipitation are both expected to shift globally, and their separate and interactive effects will likely affect ecosystems differentially depending on current temperature, precipitation regimes, and other biotic and environmental factors. It is not currently understood how the effects of increasing temperature on plant communities may depend on either precipitation or where communities lie on soil moisture gradients. Such knowledge would play a crucial role in increasing our predictive ability for future effects of climate change in different systems. To this end, we conducted a multi‐factor global change experiment at two locations, differing in temperature, moisture, aspect, and plant community composition, on the same slope in the northern Mongolian steppe. The natural differences in temperature and moisture between locations served as a point of comparison for the experimental manipulations of temperature and precipitation. We conducted two separate experiments, one examining the effect of climate manipulation via open‐top chambers (OTCs) across the two different slope locations, the other a factorial OTC by watering experiment at one of the two locations. By combining these experiments, we were able to assess how OTCs impact plant productivity and diversity across a natural and manipulated range of soil moisture. We found that warming effects were context dependent, with the greatest negative impacts of warming on diversity in the warmer, drier upper slope location and in the unwatered plots. Our study is an important step in understanding how global change will affect ecosystems across multiple scales and locations.
Polygonum multiflorum water extract protects against nitric oxide by LPSinduced in RAW 264.7 macrophages

The purpose of this study was to investigate the effects of Polygonum multiflorum Water Extract (PMWE) on the production of inflammatory mediators in RAW 264.7 mouse macrophages induced by Lipopolysaccharide (LPS). We examined effect of PMWE on the cell viability of RAW 264.7 macrophages cells and investigated anti-inflammatory effect of PMWE by the production of proinflammatory cytokines such as Nitric Oxide (NO). No significant changes have been found in the mouse macrophage cell viability by the PMWE at the concentration of 0.1, 0.5 and 1 mg/ml. Furthermore, PMWE significantly inhibited the production of NO in the LPS-induced macrophages at the concentration of 0.1, 0.5 and 1 mg/ml. In addition, The PMWE inhibited the production of NO more strongly than 2, 3, 5, 4’-Tetrahydroxystilbene-2-O-β-D-Glucoside (THSG), which is well-known as a strong antioxidant agent. These results suggest that PMWE has anti-inflammatory effect through the regulating the production of NO in the LPS-induced macrophages.
NEURONAL CELL COUNT AND MORPHOMETRIC STUDY OF HIPPOCAMPAL CA1 PYRAMIDAL NEURONS AFTER CHRONIC NIGELLA SATIVA ADMINISTRATION

Nigella sativa, a commonly consumed natural supplement, is known for its antioxidant and neuroprotective effects. Following the previous studies which showed its positive effects on spatial memory performance, the current study focused on the neurohistological effect of Nigella sativa on hippocampal cornu ammonis 1 (CA1) pyramidal neurons. The hippocampus is important for memory formation; thus, it is essential to elucidate the characteristics of its constituent neurons. Male Sprague Dawley rats were chronically force-fed for five days a week for 20 consecutive weeks (100 days) with Nigella sativa oil (NSO) (6.0 µl/100 g body weight) and corn oil (CO) (0.1 ml/100 g body weight) as control. Dorsal hippocampal transverse sections (10 µm thick) from both groups were visualized under the light microscope and morphometric analysis was conducted using the Image-Pro Premier 9.1 64-bit software. Only cresyl-violet stained neuronal somas with each having whole visible nucleus and nucleolus were included in the morphometric analysis. Mean number of neuronal cell count in NSO group was found to be higher than the controls. Significant differences in somatic area/SA, somatic perimeter/SP, somatic aspect ratio/SAR, somatic circularity index/SCI, and somatic roundness/SRo were observed between the groups. Values of two parameters (SA and SP) of NSO group indicated significantly larger sized CA1 neurons, whereas values of the other three parameters (SAR, SCI and SRo) significantly indicated less round in shape CA1 neurons. These distinct effects on the morphological characteristics could be due to NSO various biochemical constituents.
Assessing Composition in Sentence Vector Representations

An important component of achieving language understanding is mastering the composition of sentence meaning, but an immediate challenge to solving this problem is the opacity of sentence vector representations produced by current neural sentence composition models. We present a method to address this challenge, developing tasks that directly target compositional meaning information in sentence vector representations with a high degree of precision and control. To enable the creation of these controlled tasks, we introduce a specialized sentence generation system that produces large, annotated sentence sets meeting specified syntactic, semantic and lexical constraints. We describe the details of the method and generation system, and then present results of experiments applying our method to probe for compositional information in embeddings from a number of existing sentence composition models. We find that the method is able to extract useful information about the differing capacities of these models, and we discuss the implications of our results with respect to these systems’ capturing of sentence information. We make available for public use the datasets used for these experiments, as well as the generation system.
Modeling CO2 emissions from Arctic lakes: Model development and site‐level study

Recent studies indicated that Arctic lakes play an important role in receiving, processing, and storing organic carbon exported from terrestrial ecosystems. To quantify the contribution of Arctic lakes to the global carbon cycle, we developed a one‐dimensional process‐based Arctic Lake Biogeochemistry Model (ALBM) that explicitly simulates the dynamics of organic and inorganic carbon in Arctic lakes. By realistically modeling water mixing, carbon biogeochemistry, and permafrost carbon loading, the model can reproduce the seasonal variability of CO2 fluxes from the study Arctic lakes. The simulated area‐weighted CO2 fluxes from yedoma thermokarst lakes, nonyedoma thermokarst lakes, and glacial lakes are 29.5, 13.0, and 21.4 g C m−2 yr−1, respectively, close to the observed values (31.2, 17.2, and 16.5 ± 7.7 g C m−2 yr−1, respectively). The simulations show that the high CO2 fluxes from yedoma thermokarst lakes are stimulated by the biomineralization of mobilized labile organic carbon from thawing yedoma permafrost. The simulations also imply that the relative contribution of glacial lakes to the global carbon cycle could be the largest because of their much larger surface area and high biomineralization and carbon loading. According to the model, sunlight‐induced organic carbon degradation is more important for shallow nonyedoma thermokarst lakes but its overall contribution to the global carbon cycle could be limited. Overall, the ALBM can simulate the whole‐lake carbon balance of Arctic lakes, a difficult task for field and laboratory experiments and other biogeochemistry models.
Cultural Engagement and the Economic Performance of the Cultural and Creative Industries: An Occupational Critique

This article presents a new critical engagement with the concept of Cultural and Creative Industries (CCIs), focusing on the rationale for grouping occupations and industries under this label. We show how the definition of ‘creativity’ used to demonstrate CCIs’ economic performance remains contested and variable, particularly with regard to the inclusion of specific parts of the IT sector. In demonstrating the importance of IT to the economic narrative regarding CCIs, we then unfold a related critique, exploring patterns in cultural consumption within CCI occupations. We demonstrate how some CCI workers have distinctively high cultural consumption, others reflect their broader social class, and some, including IT workers, show lower than expected consumption. Overall, we question the coherence of the prevailing CCI category, particularly in government policy, and suggest a new mode of ‘cultural’ occupational analysis for the sociology of CCIs.
Age and growth of some delphinids in south-eastern Brazil

This study provides the first compilation on age and growth of some delphinids in south-eastern Brazil (18°25′S–25°45′S). A total of 154 delphinids were reported: 44 Atlantic spotted dolphin Stenella frontalis; 36 bottlenose dolphin Tursiops truncatus; 26 ‘Brazilian’ common dolphin Delphinus sp. ; 20 rough-toothed dolphin Steno bredanensis; 16 Fraser's dolphin Lagenodelphis hosei; 3 false killer whale Pseudorca crassidens; 3 unidentified Stenella sp. ; 2 pantropical spotted dolphin Stenella attenuata; 2 short-finned pilot whale Globicephala macrorhynchus; 1 spinner dolphin Stenella longirostris; and 1 striped dolphin Stenella coeruleoalba. Age was estimated by counting the number of growth layer groups present in the dentine in 74.5% of the sample. The growth of 92 individuals of the first five species was determined by the Gompertz model to length-at-age data. Stenella frontalis—the oldest specimen was 23 y and the asymptotic length of 224.4 cm predicted by growth curve occurred at about 20 y; T. truncatus—the oldest specimen was 26 y and the asymptotic length of 301.3 cm predicted by growth curve occurred at about 20 y; Delphinus sp. —the oldest dolphin was 18 y and the asymptotic length of 215.9 cm predicted by growth curve occurred at about 5–6 y; S. bredanensis—the oldest specimen was 24 y and the asymptotic length of 258.1 cm predicted by growth curve occurred at about 10 y; L. hosei—the oldest specimen was 19 y and the asymptotic length of 231.2 cm predicted by growth curve occurred at about 7–8 y. Only age was estimated for the other species. The age-at-length data for S. frontalis, Delphinus sp. , S. bredanensis and L. hosei were consistent, suggesting a good agreement with previous work on these species. For T. truncatus, the age at asymptotic length obtained in this study might be confirmed by increasing the sample size. The information currently presented will contribute to further life history research of delphinids on the western south Atlantic coast.
Combating deforestation: From satellite to intervention

Near–real-time monitoring and response are possible Tropical forests are critically important for human livelihoods, climate stability, and biodiversity conservation but remain threatened (1). Recent years have seen major strides in documenting historical and annual tropical forest loss with satellites (2). Now, a convergence of satellite technologies and analytical capabilities makes it increasingly possible to monitor deforestation in near real time, on the scale of days, weeks, or months, rather than years (3, 4). This advance creates greater potential for near–real-time action as well and could play a key role in achieving local, national, and international forest, biodiversity, and climate policy goals, as there is a global imperative to address deforestation. Challenges remain, however, to attaining effective policy action based on the new technology. On the basis of lessons learned from pioneering work in Brazil and Peru, we suggest at least two key factors for successfully linking the technical and policy realms. On the technical side, it is critical to capitalize on continually improving satellite technology to better detect, understand, and prioritize deforestation events. On the policy side, institution building, along with related civil-society engagement, is needed to facilitate effective action within complex government frameworks. We outline a five-step protocol for near–real-time tropical deforestation monitoring, with the goal of bridging the gap between technology and policy.
La gestión ambiental del turismo. El plan estratégico de turismo sustentable de Necochea, Argentina

Los destinos maduros del litoral, desde finales de los '80 vienen afrontando la necesidad de renovacion. En Necochea la emergencia de la agenda turistica, hizo necesario que se articulen nuevas politicas turisticas planteadas en el Plan estrategico de turismo sustentable. Se analizaron los criterios planificadores establecidos para la formulacion y proyeccion del plan, identificando el tipo de estrategias a adoptar para la consolidacion de Necochea como destino turistico sustentable. Se utiliza el metodo de investigacion-accion participativa desarrollado en cuatro instancias analizando la concepcion, la formulacion y la proyeccion del plan y la evaluacion los procesos politicos sociales. En los resultados se constata que el Plan facilito un proceso de internalizacion de la politica turistica, legitimado desde un enfoque participativo, validando la incidencia de la ciudadania en la politica publica de turismo. Se infiere un efecto positivo por la divulgacion de los resultados y el compromiso asumido por el gobierno local.