Miracle-dz/UniFAR-FTUs huggingface dataset:
Potential Pathway of Nitrous Oxide Formation in Plants

Plants can produce and emit nitrous oxide (N2O), a potent greenhouse gas, into the atmosphere, and several field-based studies have concluded that this gas is emitted at substantial amounts. However, the exact mechanisms of N2O production in plant cells are unknown. Several studies have hypothesised that plants might act as a medium to transport N2O produced by soil-inhabiting microorganisms. Contrarily, aseptically grown plants and axenic algal cells supplied with nitrate (NO3) are reported to emit N2O, indicating that it is produced inside plant cells by some unknown physiological phenomena. In this study, the possible sites, mechanisms, and enzymes involved in N2O production in plant cells are discussed. Based on the experimental evidence from various studies, we determined that N2O can be produced from nitric oxide (NO) in the mitochondria of plants. NO, a signaling molecule, is produced through oxidative and reductive pathways in eukaryotic cells. During hypoxia and anoxia, NO3 in the cytosol is metabolised to produce nitrite (NO2), which is reduced to form NO via the reductive pathway in the mitochondria. Under low oxygen condition, NO formed in the mitochondria is further reduced to N2O by the reduced form of cytochrome c oxidase (CcO). This pathway is active only when cells experience hypoxia or anoxia, and it may be involved in N2O formation in plants and soil-dwelling animals, as reported previously by several studies. NO can be toxic at a high concentration. Therefore, the reduction of NO to N2O in the mitochondria might protect the integrity of the mitochondria, and thus, protect the cell from the toxicity of NO accumulation under hypoxia and anoxia. As NO3 is a major source of nitrogen for plants and all plants may experience hypoxic and anoxic conditions owing to soil environmental factors, a significant global biogenic source of N2O may be its formation in plants via the proposed pathway.
Predictors and Mortality of Rapidly Progressive Interstitial Lung Disease in Patients With Idiopathic Inflammatory Myopathy: A Series of 474 Patients

Objective: This study was conducted to identify the characteristics and prognosis of rapidly progressive interstitial lung disease (RP-ILD) in idiopathic inflammatory myopathy (IIM) and to assess the predictors for poor survival of RP-ILD in IIM. Methods: A total of 474 patients with IIM were enrolled retrospectively according to medical records from Peking University People's Hospital. Clinical and laboratory characteristics recorded at the diagnosis of patients with RP-ILD and chronic ILD (C-ILD) were compared. The Kaplan–Meier estimator and univariate and multivariate analyses were used for data analysis. Results: ILD was identified in 65% (308/474) of patients with IIM. Patients with ILD were classified into two groups based on lung features: RP-ILD (38%, 117/308) and C-ILD (62%, 191/308). RP-ILD resulted in significantly higher mortality in IIM compared with C-ILD (27.4 vs. 7.9%, P < 0.05). In this study, by comparing IIM patients with and without RP-ILD, a list of initial predictors for RP-ILD development were identified, which included older age at onset, decreased peripheral lymphocytes, skin involvement (periungual erythema, skin ulceration, and subcutaneous/mediastinal emphysema), presence of anti-MDA5 antibody, serum tumor markers, etc. Further multivariate Cox proportional hazards model analysis identified that anti-MDA5 positivity was an independent risk factor for mortality due to RP-ILD (P < 0.05), and lymphocytes <30% in BALF might also be associated with poor survival of myositis-associated RP-ILD (P < 0.05). Conclusion: Our study shows that RP-ILD results in increased mortality in IIM. Anti-MDA5 positivity and a lower lymphocyte ratio in BALF might be the predictive factor of mortality due to RP-ILD.
NEURAL ENCODING OF FELT AND IMAGINED TOUCH WITHIN HUMAN POSTERIOR PARIETAL CORTEX

In the human posterior parietal cortex (PPC), single units encode high-dimensional information with partially mixed representations that enable small populations of neurons to encode many variables relevant to movement planning, execution, cognition, and perception. Here we test whether a PPC neuronal population previously demonstrated to encode visual and motor information is similarly selective in the somatosensory domain. We recorded from 1423 neurons within the PPC of a human clinical trial participant during objective touch presentation and during tactile imagery. Neurons encoded experienced touch with bilateral receptive fields, organized by body part, and covered all tested regions. Tactile imagery evoked body part specific responses that shared a neural substrate with experienced touch. Our results are the first neuron level evidence of touch encoding in human PPC and its cognitive engagement during tactile imagery which may reflect semantic processing, sensory anticipation, and imagined touch.
Toward a Dynamic Metacommunity Approach to Marine Reserve Theory

Abstract Coastal habitats have recently received much attention from policymakers, but marine reserve theory still needs to integrate across scales, from local dynamics of communities to biogeographic patterns of species distribution, recognizing coastal ecosystems as complex adaptive systems in which local processes and anthropogenic disturbances can result in large-scale biological changes. We present a theoretical framework that provides a new perspective on the science underlying the design of marine reserve networks. Coastal marine systems may be usefully considered as metacommunities in which propagules are exchanged among components, and in which the persistence of one species depends on that of others. Our results suggest that the large-scale distribution of marine species can be dynamic and can result from local ecological processes. We discuss the potential implications of these findings for marine reserve design and the need for long-term monitoring programs to validate predictions from metacommunity models. Only through an integrated and dynamic global perspective can scientists and managers achieve the underlying goals of marine conservation.
Variation in relaxation of non-photochemical quenching in a soybean nested association mapping panel as a potential source for breeding improved photosynthesis

Improving the efficiency of crop photosynthesis has the potential to increase yields. Genetic manipulation showed photosynthesis can be improved in Tobacco by speeding up relaxation of photoprotective mechanisms, known as non-photochemical quenching (NPQ), during high to low light transitions. However, it is unclear if natural variation in NPQ relaxation can be exploited in crop breeding programs. To address this issue, we measured NPQ relaxation in the 41 parents of a soybean NAM population in field experiments in Illinois during 2018 and 2019. There was significant variation in amount and rate of fast, energy dependent quenching (qE) between genotypes. However, strong environmental effects led to a lack of correlation between values measured over the two growing season, and low broad-sense heritability estimates (< 0.3). These data suggest that either improvements in screening techniques, or transgenic manipulation, will be required to unlock the potential for improving the efficiency of NPQ relaxation in soybean. Table of Abbreviations
Pyronaridine and artesunate are potential antiviral drugs against COVID-19 and influenza

Since the first human case was reported in Wuhan Province, China in December 2019, SARS-CoV-2 has caused millions of human infections in more than 200 countries worldwide with an approximately 4.01% case-fatality rate (as of 27 July, 2020; based on a WHO situation report), and COVID-19 pandemic has paralyzed our global community. Even though a few candidate drugs, such as remdesivir (a broad antiviral prodrug) and hydroxychloroquine, have been investigated in human clinical trials, their therapeutic efficacy needs to be clarified further to be used to treat COVID-19 patients. Here we show that pyronaridine and artesunate, which are the chemical components of anti-malarial drug Pyramax®, exhibit antiviral activity against SARS-CoV-2 and influenza viruses. In human lung epithelial (Calu-3) cells, pyronaridine and artesunate were highly effective against SARS-CoV-2 while hydroxychloroquine did not show any effect at concentrations of less than 100 μM. In viral growth kinetics, both pyronaridine and artesunate inhibited the growth of SARS-CoV-2 and seasonal influenza A virus in Calu-3 cells. Taken together, we suggest that artesunate and pyronaridine might be effective drug candidates for use in human patients with COVID-19 and/or influenza, which may co-circulate during this coming winter season.
Developmental PCB Exposure Disrupts Synaptic Transmission and Connectivity in the Rat Auditory Cortex, Independent of Its Effects on Peripheral Hearing Threshold

Abstract Polychlorinated biphenyls (PCBs) are enduring environmental toxicants and exposure is associated with neurodevelopmental deficits. The auditory system appears particularly sensitive, as previous work has shown that developmental PCB exposure causes both hearing loss and gross disruptions in the organization of the rat auditory cortex. However, the mechanisms underlying PCB-induced changes are not known, nor is it known whether the central effects of PCBs are a consequence of peripheral hearing loss. Here, we study changes in both peripheral and central auditory function in rats with developmental PCB exposure using a combination of optical and electrophysiological approaches. Female rats were exposed to an environmental PCB mixture in utero and until weaning. At adulthood, auditory brainstem responses (ABRs) were measured, and synaptic currents were recorded in slices from auditory cortex layer 2/3 neurons. Spontaneous IPSCs (sIPSCs) and miniature IPSCs (mIPSCs) were more frequent in PCB-exposed rats compared with controls and the normal relationship between IPSC parameters and peripheral hearing was eliminated in PCB-exposed rats. No changes in spontaneous EPSCs were found. Conversely, when synaptic currents were evoked by laser photostimulation of caged-glutamate, PCB exposure did not affect evoked inhibitory transmission, but increased the total excitatory charge, the number and distance of sites that evoke a significant response. Together, these findings indicate that early developmental exposure to PCBs causes long-lasting changes in both inhibitory and excitatory neurotransmission in the auditory cortex that are independent of peripheral hearing changes, suggesting the effects are because of the direct impact of PCBs on the developing auditory cortex.
Influence of membrane-cortex linkers on the extrusion of membrane tubes

The cell membrane is an inhomogeneous system composed of phospholipids, sterols and proteins that can be directly attached to underlying cytoskeleton. The linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations we find that the force for tube extrusion has a non-linear dependence on the density of membrane-cortex attachments: at a wide range of low and intermediate densities of linkers the force is not significantly influenced by the presence of membrane linking proteins and resembles that of the bare membrane. For large concentrations of linkers however the force substantially increases compared to the bare membrane. In both cases the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical-tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had negligible effect on the force. Our results shed new light on the importance of local effects in membrane reshaping at the nanoscopic scales.
Faster Cryptococcus Melanization Increases Virulence in Experimental and Human Cryptococcosis

Cryptococcus spp. are important human pathogens responsible for about 180,000 deaths per year. Studying their virulence attributes can lead to better cryptococcosis prevention and treatment. In this work, we systematically investigated virulence attributes of Cryptococcus spp. clinical isolates and correlated them with patient data. We collected 66 C. neoformans and 19 C. gattii isolates from Brazilian patients and analyzed multiple phenotypes related with their capsule, production of laccase, melanin and extracellular vesicles. We also tested their virulence in Galleria mellonella and ability to evade macrophage LC3-associated phagocytosis (LAP). All phenotypes analyzed varied widely among the isolates, but C. neoformans isolates tended to melanize faster and more intensely and produce thinner capsules in comparison with C. gattii. We also observed correlations that match previous studies, such as that between secreted laccase – but not total melanin production – and disease outcome in patients. The most striking results, though, came from our measurements of Cryptococcus colony melanization kinetics, which followed a sigmoidal curve for most isolates. Faster melanization correlated positively with LAP evasion, virulence in G. mellonella and worse prognosis in humans. These results suggest that the speed of melanization, more than the total amount of melanin Cryptococcus spp. produces, is crucial for virulence. Graphical abstract
Confirmation bias is adaptive when coupled with efficient metacognition

Biases in the consideration of evidence can reduce the chances of consensus between people with different viewpoints. While such altered information processing typically leads to detrimental performance in laboratory tasks, the ubiquitous nature of confirmation bias makes it unlikely that selective information processing is universally harmful. Here we suggest that confirmation bias is adaptive to the extent that agents have good metacognition, allowing them to downweight contradictory information when correct but still able to seek new information when they realise they are wrong. Using simulation-based modelling, we explore how the adaptiveness of holding a confirmation bias depends on such metacognitive insight. We find that the behavioural consequences of selective information processing are systematically affected by agents’ introspective abilities. Strikingly, we find that selective information processing can even improve decision-making when compared to unbiased evidence accumulation, as long as it is accompanied by good metacognition. These results further suggest that interventions which boost people’s metacognition might be efficient in alleviating the negative effects of selective information processing on issues such as political polarisation.
α(1,3)-Fucosyltransferase VII and α(2,3)-Sialyltransferase IV Are Up-Regulated in Activated CD4 T Cells and Maintained After Their Differentiation into Th1 and Migration into Inflammatory Sites

Activated Th1 CD4 T cells bind to P-selectin and migrate into inflamed tissue, whereas Th2 cells do not. We show that α(1,3)-fucosyltransferase VII (FucT-VII) and α(2,3)-sialyltransferase IV (ST3GalIV), which are crucial for the biosynthesis of functional P-selectin ligands, are absent in naive CD4 T cells, but are rapidly up-regulated upon activation. Th1 or Th2 differentiation in the presence of polarizing cytokines leads to down-regulation of FucT-VII mRNA selectively in Th2 but not in Th1 cells. Influencing the differentiation by varying the priming dose of antigenic peptide results in similar FucT-VII down-regulation only in Ag-specific Th2 cells. ST3GalIV levels remain elevated. FucT-VII and ST3GalIV mRNAs are also up-regulated by Th1 cells primed in vivo and recruited into the lymph nodes draining delayed-type hypersensitivity sites. We identify FucT-VII gene expression as a principal difference between Th1 and Th2 cells, and underscore the importance of FucT-VII and ST3GalIV expression for the biosynthesis of functional selectin ligands.
Mechanisms involved in the production of differently colored feathers in the structurally-colored Swallow Tanager (Tersina viridis; Aves: Thraupidae)

Non-iridescent, structurally-based coloration in birds originates from the feather’s internal nanostructure (the keratin spongy matrix), but the presence of melanin and the characteristics of the barb’s cortex can affect the resulting color. Here we investigate how this nanostructure is regulated and combined with other elements in differently-colored plumage patches. To do so, we investigated the association between light reflectance and the morphology of feathers from the back and belly plumage patches of male Swallow Tanagers (Tersina viridis), which look greenish-blue and white, respectively. Both plumage patches have a reflectance peak around 550 nm, but the reflectance spectrum is much less saturated in the belly. The barbs of both types of feathers have similar spongy matrices at their tips which produce similar reflectance spectra. However, the color of the belly feather barbs changes from light green at the tip to white closer to the rachis. These barbs lack pigments and their morphology changes considerably: the spongy matrix is reduced, being almost hollow, and has a different shape towards the rachis. Instead, we observed deposition of melanin underneath the spongy matrix in the back feathers which had a much saturated coloration that was consistent along the barbs’ length. Overall, our results suggest that the color differences between the white and greenish-blue plumage are mostly due to the differential deposition of melanin and a reduction of the spongy matrix in some parts of the belly feather barbs, and not a result of changes in the periodicity of the spongy matrix.
Invited review: Development and expression of dairy calf feeding behaviour

Miller-Cushon, E. K. and DeVries, T. J. 2015. Invited review: Development and expression of dairy calf feeding behaviour. Can. J. Anim. Sci. 95: 341-350. Feeding and housing practices for dairy calves impact performance and growth early in life, as well as feeding behaviour. There is also increasing evidence that early exposure to different feeding and housing strategies influence the development of feeding behaviour. The dairy calf needs access to milk in sufficient quantities to maintain health and high-levels of growth. In addition, intake of solid feed, such as grain concentrate, is necessary early in life to establish fermentation and develop the rumen. In dairy calves, feeding behaviour patterns can have direct impact on nutrient consumption and, consequently, growth. Further, recent research has provided evidence that behaviour patterns that develop in response to management factors early in life may persist once learned, potentially having longer-term implications for health and welfare. Thus, there is potential for various nutritional, housing, and management factors to impact the learning of feeding behaviour early in the life of dairy calves. This review provides several examples of early management factors that influence feeding behaviour of dairy calves and, in turn, impact calf growth and welfare. For example, providing continuous, ad libitum access to milk results not only in greater growth, but also in meal patterns that more closely resemble the natural behaviour of a calf suckling its dam. Housing management also has the potential to influence when, and how much, a calf eats. Whereas social facilitation promotes intake, particularly at weaning, competition for feed in group-housed calves restricts feeding patterns and degree of feeding synchrony. With regards to provision of solid feed, recent data suggest that providing physically effective hay, in addition to grain concentrate, may be beneficial for the rumen environment and consequent growth and efficiency. However, the physical form and presentation of forage may also influence feeding behaviour of calves, in particular feed sorting, which can impact both immediate nutrient intakes as well as the development and persistence of that behaviour. For example, calves provided hay and concentrate as a mixture begin to sort their feed early in life, with the pattern of sorting depending on hay particle size. Feed sorting in young calves may reflect a motivation to consume a proportion of hay in the diet. In general, it appears to be beneficial for early growth and welfare to support milk and solid feed intake through unrestricted allowances and less-competitive feeding environments. Continued research in this area is needed to assess the longevity of learned behaviour patterns, and what factors may influence their persistence.
Crystal Structure Reveals the Full Ras–Raf Interface and Advances Mechanistic Understanding of Raf Activation

The interaction between Ras and Raf-kinase through the Ras-binding (RBD) and cysteine-rich domains (CRD) of Raf is essential for signaling through the mitogen-activated protein kinase (MAPK) pathway, yet the molecular mechanism leading to Raf activation has remained elusive. We present the 2.8 Å crystal structure of the HRas/CRaf-RBD_CRD complex showing the Ras/Raf interface as a continuous surface on Ras. In the Ras dimer, with helices roughly perpendicular to the membrane, the CRD is located between the two Ras protomers and far from the membrane, where its dynamic nature in the Ras binding pocket is expected to accommodate BRaf and CRaf heterodimers. Our structure and its analysis by MD simulations, combined with work in the literature, result in a molecular model in which Ras binding is involved in the release of Raf autoinhibition while the Ras/Raf complex dimerizes to promote a platform for signal amplification, with Raf-CRD poised to have direct and allosteric effects on both the Ras active site and the dimerization interface.
How Much Method-in-Use Matters? A Case Study of Agile and Waterfall Software Projects and their Design Routine Variation

Development methods are rarely followed to the letter, and, consequently, their effects are often in doubt. At the same time, information systems scholars know little about the extent to which a given method truly influences software design and its outcomes. In this paper, we approach this gap by adopting a routine lens and using a novel methodological approach. Theoretically, we treat methods as (organizational) ostensive routine specifications and deploy routine construct as a feasible unit of analysis to analyze the effects of a method on actual, “performed” design routines. We formulated a research framework that identifies method, situation fitness, agency, and random noise as main sources of software design routine variation. Empirically, we applied the framework to examine the extent to which waterfall and agile methods induce variation in software design routines. We trace-enacted design activities in three software projects in a large IT organization that followed an object-oriented waterfall method and three software projects that followed an agile method and then analyzed these traces using a mixed-methods approach involving gene sequencing methods, Markov models, and qualitative content analysis. Our analysis shows that, in both cases, method-induced variation using agile and waterfall methods accounts for about 40% of all activities, while the remaining 60% can be explained by a designer’s personal habits, the project’s fitness conditions, and environmental noise. Generally, the effect of method on software design activities is smaller than assumed and the impact of designer and project conditions on software processes and outcomes should thus not be understated.