Miracle-dz/UniFAR-FTUs huggingface dataset:
The cospecification of the shape and material properties of light permeable materials

Significance One of the longest-standing problems in vision science is understanding how images carry information about the shape and material of surfaces. Previous work has treated shape and material perception as computationally ill posed: It is thought that either material needs to be known to infer shape or shape needs to be known to infer material. Here, we offer an explanation of how the human visual system simultaneously recovers 3D shape and material. We show that there are intersecting physical constraints caused by surface curvature on different “kinds” of image structure—subsurface scattering, specular reflections, and self-occluding contours. The intersecting constraints cause specific patterns of covariation that are characteristic of translucent materials and are also potent cues to 3D shape. The problem of extracting the three-dimensional (3D) shape and material properties of surfaces from images is considered to be inherently ill posed. It is thought that a priori knowledge about either 3D shape is needed to infer material properties, or knowledge about material properties are needed to derive 3D shape. Here, we show that there is information in images that cospecify both the material composition and 3D shape of light permeable (translucent) materials. Specifically, we show that the intensity gradients generated by subsurface scattering, the shape of self-occluding contours, and the distribution of specular reflections covary in systematic ways that are diagnostic of both the surface’s 3D shape and its material properties. These sources of image covariation emerge from being causally linked to a common environmental source: 3D surface curvature. We show that these sources of covariation take the form of “photogeometric constraints,” which link variations in intensity (photometric constraints) to the sign and direction of 3D surface curvature (geometric constraints). We experimentally demonstrate that this covariation generates emergent cues that the visual system exploits to derive the 3D shape and material properties of translucent surfaces and demonstrate the potency of these cues by constructing counterfeit images that evoke vivid percepts of 3D shape and translucency. The concepts of covariation and cospecification articulated herein suggest a principled conceptual path forward for identifying emergent cues that can be used to solve problems in vision that have historically been assumed to be ill posed.
B-Cell Memory Responses to Variant Viral Antigens

A central feature of vertebrate immune systems is the ability to form antigen-specific immune memory in response to microbial challenge and so provide protection against future infection. In conflict with this process is the ability that many viruses have to mutate their antigens to escape infection- or vaccine-induced antibody memory responses. Mutable viruses such as dengue virus, influenza virus and of course coronavirus have a major global health impact, exacerbated by this ability to evade immune responses through mutation. There have been several outstanding recent studies on B-cell memory that also shed light on the potential and limitations of antibody memory to protect against viral antigen variation, and so promise to inform new strategies for vaccine design. For the purposes of this review, the current understanding of the different memory B-cell (MBC) populations, and their potential to recognize mutant antigens, will be described prior to some examples from antibody responses against the highly mutable RNA based flaviviruses, influenza virus and SARS-CoV-2.
An Overview of Current Knowledge of Deadly CoVs and Their Interface with Innate Immunity

Coronaviruses are a large family of zoonotic RNA viruses, whose infection can lead to mild or lethal respiratory tract disease. Severe Acute Respiratory Syndrome-Coronavirus-1 (SARS-CoV-1) first emerged in Guangdong, China in 2002 and spread to 29 countries, infecting 8089 individuals and causing 774 deaths. In 2012, Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) emerged in Saudi Arabia and has spread to 27 countries, with a mortality rate of ~34%. In 2019, SARS-CoV-2 emerged and has spread to 220 countries, infecting over 100,000,000 people and causing more than 2,000,000 deaths to date. These three human coronaviruses cause diseases of varying severity. Most people develop mild, common cold-like symptoms, while some develop acute respiratory distress syndrome (ARDS). The success of all viruses, including coronaviruses, relies on their evolved abilities to evade and modulate the host anti-viral and pro-inflammatory immune responses. However, we still do not fully understand the transmission, phylogeny, epidemiology, and pathogenesis of MERS-CoV and SARS-CoV-1 and -2. Despite the rapid application of a range of therapies for SARS-CoV-2, such as convalescent plasma, remdesivir, hydroxychloroquine and type I interferon, no fully effective treatment has been determined. Remarkably, COVID-19 vaccine research and development have produced several offerings that are now been administered worldwide. Here, we summarise an up-to-date understanding of epidemiology, immunomodulation and ongoing anti-viral and immunosuppressive treatment strategies. Indeed, understanding the interplay between coronaviruses and the anti-viral immune response is crucial to identifying novel targets for therapeutic intervention, which may even prove invaluable for the control of future emerging coronavirus.
E‐selectin negatively regulates polymorphonuclear neutrophil transmigration through altered endothelial junction integrity

Transendothelial migration (TEM) of neutrophils under blood flow is critical in the inflammatory cascade. However, the role of endothelial plasticity in this process is not fully understood. Therefore, we used an in vitro model to test the dynamics of human polymorphonuclear neutrophil (PMN) TEM across lipopolysaccharide‐treated human umbilical vein endothelial cell (HUVEC) monolayers. Interestingly, shRNA‐E‐selectin knockdown in HUVECs destabilized endothelial junctional integrity by reducing actin branching and increasing stress fiber at cell–cell junctions. This process is accomplished by downregulating the activation of cortactin and Arp2/3, which in turn alters the adhesive function of VE‐cadherin, enhancing PMN transmigration. Meanwhile, redundant P‐selectins possess overlapping functions in E‐selectin‐mediated neutrophil adhesion, and transmigration. These results demonstrate, to our knowledge, for the first time, that E‐selectins negatively regulate neutrophil transmigration through alterations in endothelial plasticity. Furthermore, it improves our understanding of the mechanisms underlying actin remodeling, and junctional integrity, in endothelial cells mediating leukocyte TEM.
Assessment of Motor Dysfunction with Virtual Reality in Patients Undergoing [123I]FP-CIT SPECT/CT Brain Imaging

[123I]FP-CIT SPECT has been valuable for distinguishing Parkinson disease (PD) from essential tremor. However, its performance for quantitative assessment of motor dysfunction has not been established. A virtual reality (VR) application was developed and compared with [123I]FP-CIT SPECT/CT for detection of severity of motor dysfunction. Forty-four patients (21 males, 23 females, age 64.5 ± 12.4) with abnormal [123I]FP-CIT SPECT/CT underwent assessment of bradykinesia, activities of daily living, and tremor with VR. Support vector machines (SVM) machine learning models were applied to VR and SPECT data. Receiver operating characteristic (ROC) analysis demonstrated greater area under the curve (AUC) for VR (0.8418, 95% CI 0.6071–0.9617) compared with brain SPECT (0.5357, 95% CI 0.3373–0.7357, p = 0.029) for detection of motor dysfunction. Logistic regression identified VR as an independent predictor of motor dysfunction (Odds Ratio 326.4, SE 2.17, p = 0.008). SVM for prediction of the Unified Parkinson’s Disease Rating Scale Part III (UPDRS-III) demonstrated greater R-squared of 0.713 (p = 0.008) for VR, compared with 0.0764 (p = 0.361) for brain SPECT. This study demonstrates that VR can be safely used in patients prior to [123I]FP-CIT SPECT imaging and may improve prediction of motor dysfunction. This test has the potential to provide a simple, objective, quantitative analysis of motor symptoms in PD patients.
Morphological integration of the human brain across adolescence and adulthood

Significance Attaining correct anatomical proportions is an important developmental goal. Although the patterning of individual deviations from such proportions has been well-studied in nonhuman animals and various human body measurements, this theoretical framework has not been applied to human brain morphology. We analyze individual deviations from proportionality norms (“anatomical imbalance”) in a collection of over 20,000 brain MRI scans to reveal that individuals grow closer to proportionality norms in development and further from proportionality norms in aging. This effect is greatest in brain networks that support higher-order cognition and least in brain networks that support sensorimotor functions. We demonstrate that deviation from proportionality norms—a measure of neurodevelopmental coordination—is associated with cognitive function and sensitive to variation in prenatal stress. Brain structural covariance norms capture the coordination of neurodevelopmental programs between different brain regions. We develop and apply anatomical imbalance mapping (AIM), a method to measure and model individual deviations from these norms, to provide a lifespan map of morphological integration in the human cortex. In cross-sectional and longitudinal data, analysis of whole-brain average anatomical imbalance reveals a reproducible tightening of structural covariance by age 25 y, which loosens after the seventh decade of life. Anatomical imbalance change in development and in aging is greatest in the association cortex and least in the sensorimotor cortex. Finally, we show that interindividual variation in whole-brain average anatomical imbalance is positively correlated with a marker of human prenatal stress (birthweight disparity between monozygotic twins) and negatively correlated with general cognitive ability. This work provides methods and empirical insights to advance our understanding of coordinated anatomical organization of the human brain and its interindividual variation.
Intracellular Redox-Modulated Pathways as Targets for Effective Approaches in the Treatment of Viral Infection

Host-directed therapy using drugs that target cellular pathways required for virus lifecycle or its clearance might represent an effective approach for treating infectious diseases. Changes in redox homeostasis, including intracellular glutathione (GSH) depletion, are one of the key events that favor virus replication and contribute to the pathogenesis of virus-induced disease. Redox homeostasis has an important role in maintaining an appropriate Th1/Th2 balance, which is necessary to mount an effective immune response against viral infection and to avoid excessive inflammatory responses. It is known that excessive production of reactive oxygen species (ROS) induced by viral infection activates nuclear factor (NF)-kB, which orchestrates the expression of viral and host genes involved in the viral replication and inflammatory response. Moreover, redox-regulated protein disulfide isomerase (PDI) chaperones have an essential role in catalyzing formation of disulfide bonds in viral proteins. This review aims at describing the role of GSH in modulating redox sensitive pathways, in particular that mediated by NF-kB, and PDI activity. The second part of the review discusses the effectiveness of GSH-boosting molecules as broad-spectrum antivirals acting in a multifaceted way that includes the modulation of immune and inflammatory responses.
Relation between Mood and the Host-Microbiome Co-Metabolite 3-Indoxylsulfate: Results from the Observational Prospective NutriNet-Santé Study

Gut microbiota metabolizes tryptophan into indole, which can influence brain and behavior. Indeed, some oxidized derivatives of indole, formed in the liver, have neuroactive properties, and indole overproduction by the gut microbiota induces an anxio-depressive phenotype in rodents. The aim of this study was to investigate in humans whether there was a relationship between recurrent depressive symptoms and indole production by the gut microbiota. A case-control study was conducted in 45–65-year-old women, who were participants in the observational prospective NutriNet-Santé Study. Cases were defined as having two Center for Epidemiological Studies-Depression Scales (CES-D) scores ≥ 23 at a two-year interval (recurrent depressive symptoms, n = 87). Each case was matched with two controls (two CES-D <23; n = 174). Urinary excretion of 3-indoxylsulfate, the major final metabolite of indole, was used as a biomarker of indole production by the gut microbiota. Conditional logistic regression models for paired data showed a positive association between urinary 3-indoxylsulfate concentrations, grouped in tertiles, and recurrent depressive symptoms (odds ratio = 2.46, p for trend = 0.0264 in the final model adjusted for confounding factors). This association suggested that indole production by the gut microbiota may play a role in the onset of mood disorders in humans.
Rhizosphere Microbiomes in a Historical Maize-Soybean Rotation System Respond to Host Species and Nitrogen Fertilization at the Genus and Subgenus Levels

Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. ABSTRACT Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage.
Exploring Sports Nutrition Knowledge in Elite Gaelic Footballers

Nutrition intake plays a crucial role in improving athletic performance, enhancing adaptations to training, and augmenting recovery from exercise. However, research has reported that Gaelic footballers consistently fail to meet energy and carbohydrate recommendations. Sports nutrition knowledge (SNK) can influence the dietary intake of athletes, and therefore has the potential to have a significant impact on athletic performance. The aim of this study was to investigate the current level of SNK in elite Gaelic footballers (n = 100). An online version of the Nutrition for Sport Knowledge Questionnaire (NSKQ) was used to assess sports SNK. The overall mean SNK scores for Gaelic footballers and practitioners were 47.6 ± 12.3% and 78.1 ± 8.3%, respectively. There were no differences in knowledge between age groups, education level or divisional status. The top three sources of nutrition information identified by participants were team dietitian/nutritionists (84.0%), athletic trainers/strength and conditioning coaches (73%), and social media (37%). The results show that there is a major gap in the SNK of Gaelic footballers, while practitioners demonstrated a promising SNK, that could support Gaelic footballers. There is a need for development of interventions and knowledge transfer partnerships, including more effective methods of educating Gaelic footballers and translating sports nutrition principles to players. Developing appropriate nutritional education strategies using online resources and mobile applications could help to improve nutritional knowledge and practice of Gaelic footballers.
Controlled growth of nanocrystalline rods, hexagonal plates and spherical particles of the vaterite form of calcium carbonate

Pure vaterite (hexagonal) phase of calcium carbonate has been obtained at room temperature (20 °C) using a microemulsion route. The process resulted in uniform micron-sized hexagonal plates (∼1 µm) of vaterite where 9.375 µmol of Ca2+ and CO32− ions was used while at lower concentration (0.625 μmol) cubes of calcite phase were obtained. High magnification TEM images of the hexagonal plates shows an assembly of spherical nanoparticles (∼50 nm). At an optimal concentration, rod-shaped vaterite particles were obtained at 40 °C. This is the first report of the rod-shaped morphology of the vaterite phase. The length and diameter of the rods have been found to be ∼250 and ∼30 nm, respectively. The surface charge of the vaterite phase (rod-shaped) was found to be +31 mV which is consistent with the high ionic concentration used in the synthesis.
Monalbidins A–E, Decalins with Potential Cytotoxic Activities from Marine Derived Fungus Monascus albidus BB3

Five new decalins, monalbidins A–E (1, 2 and 7–9), together with 16 known compounds (3–6 and 10–21), were isolated from the AcOEt extract of marine derived fungus Monascus albidus BB3 cultured in GPY medium. Among the known compounds, 1‐hydroxymonacolin L (11), dehydromonacolin J (15), 8‐O‐acetylmonacolin J (19) and O‐acetylmonacolin K (21) were separated from natural sources for the first time. Their structures were determined by comprehensive analysis on the 1D and 2D NMR, HR‐ESI‐MS, UV and IR data, and their absolute configurations were assigned by experimental and calculated ECD data, and X‐ray single‐crystal diffraction analysis. Monalbidins C and D (7 and 8), monacolin K methyl ester (13), dehydromonacolin L (14), dehydromonacolin K (16), monacolin K (20) and O‐acetylmonacolin K (21) showed moderate cytotoxicity against human cancer cell lines SUNE1, HepG2, QGY7701, HCT116 and MDA‐MB‐231.
Sulfur Amino Acid Status Controls Selenium Methylation in Pseudomonas tolaasii: Identification of a Novel Metabolite from Promiscuous Enzyme Reactions

Volatilization from soil to the atmosphere is a major driver for Se deficiency. “Bottom-up” models for atmospheric Se transport are based on laboratory experiments quantifying volatile Se compounds. The high Se and low S concentrations in such studies poorly represent the environment. ABSTRACT Selenium (Se) deficiency affects many millions of people worldwide, and the volatilization of methylated Se species to the atmosphere may prevent Se from entering the food chain. Despite the extent of Se deficiency, little is known about fluxes in volatile Se species and their temporal and spatial variation in the environment, giving rise to uncertainty in atmospheric transport models. To systematically determine fluxes, one can rely on laboratory microcosm experiments to quantify Se volatilization in different conditions. Here, it is demonstrated that the sulfur (S) status of bacteria crucially determines the amount of Se volatilized. Solid-phase microextraction gas chromatography mass spectrometry showed that Pseudomonas tolaasii efficiently and rapidly (92% in 18 h) volatilized Se to dimethyl diselenide and dimethyl selenyl sulfide through promiscuous enzymatic reactions with the S metabolism. However, when the cells were supplemented with cystine (but not methionine), a major proportion of the Se (∼48%) was channeled to thus-far-unknown, nonvolatile Se compounds at the expense of the previously formed dimethyl diselenide and dimethyl selenyl sulfide (accounting for <4% of total Se). Ion chromatography and solid-phase extraction were used to isolate unknowns, and electrospray ionization ion trap mass spectrometry, electrospray ionization quadrupole time-of-flight mass spectrometry, and microprobe nuclear magnetic resonance spectrometry were used to identify the major unknown as a novel Se metabolite, 2-hydroxy-3-(methylselanyl)propanoic acid. Environmental S concentrations often exceed Se concentrations by orders of magnitude. This suggests that in fact S status may be a major control of selenium fluxes to the atmosphere. IMPORTANCE Volatilization from soil to the atmosphere is a major driver for Se deficiency. “Bottom-up” models for atmospheric Se transport are based on laboratory experiments quantifying volatile Se compounds. The high Se and low S concentrations in such studies poorly represent the environment. Here, we show that S amino acid status has in fact a decisive effect on the production of volatile Se species in Pseudomonas tolaasii. When the strain was supplemented with S amino acids, a major proportion of the Se was channeled to thus-far-unknown, nonvolatile Se compounds at the expense of volatile compounds. This hierarchical control of the microbial S amino acid status on Se cycling has been thus far neglected. Understanding these interactions—if they occur in the environment—will help to improve atmospheric Se models and thus predict drivers of Se deficiency.