Miracle-dz/UniFAR-FTUs huggingface dataset:
The Application of The Skin Virome for Human Identification

The use of skin virome for human identification purposes offers a unique approach to instances where a viable and statistically relevant human DNA profile is unavailable. The human skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human virome metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collections periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches were employed, along with a database-based assessment, which resulted in three sets of stable putative viral markers. In total, with the three sets combined, 59 viral species and uncharacterized viral genome assemblies were identified as being significantly stable (P=5.3×10-15). Viral diversity, based on presence or absence, is significantly different across subjects (P<0.001). Here we demonstrate that not only is the human virome applicable to be used for human identification, but we have identified many viral signatures that can be used for forensic applications, thus providing a foundation to the novel field of forensic virology. Highlights Here we provide the largest human skin virome study, to date. Our study revealed novel diversity findings of high abundance for certain viral taxa, for example, the Cress-like DNA phages, that have not previously been characterized in human skin viral ecology studies. There were 59 putative human skin viral biomarkers suitable for human identification from the core stable human skin virome of 42 subjects. The putative markers we identified were significantly stable over a 6-month period of time within individuals and across three autosomal locations of left hand, right hand, and scalp. Diversity of profiles, based on the presence and absence of our putative marker data set, were significantly different across test subjects.
MurA escape mutations uncouple peptidoglycan biosynthesis from PrkA signaling

Gram-positive bacteria are protected by a thick mesh of peptidoglycan (PG) completely engulfing their cells. This PG network is the main component of the bacterial cell wall, it provides rigidity and acts as foundation for the attachment of other surface molecules. Biosynthesis of PG consumes a high amount of cellular resources and therefore requires careful adjustments to environmental conditions. An important switch in the control of PG biosynthesis of Listeria monocytogenes, a Gram-positive pathogen with a high infection fatality rate, is the serine/threonine protein kinase PrkA. A key substrate of this kinase is the small cytosolic protein ReoM. We have shown previously that ReoM phosphorylation regulates PG formation through control of MurA stability. MurA catalyzes the first step in PG biosynthesis and the current model suggests that phosphorylated ReoM prevents MurA degradation by the ClpCP protease. In contrast, conditions leading to ReoM dephosphorylation stimulate MurA degradation. How ReoM controls degradation of MurA and potential other substrates is not understood. Also, the individual contribution of the ~20 other known PrkA targets to PG biosynthesis regulation is unknown. We here present murA mutants which escape proteolytic degradation. The release of MurA from ClpCP-dependent proteolysis was able to activate PG biosynthesis and further enhanced the intrinsic cephalosporin resistance of L. monocytogenes. This latter effect required the RodA3/PBP B3 transglycosylase/transpeptidase pair. One murA escape mutation not only fully rescued an otherwise non-viable prkA mutant during growth in batch culture and inside macrophages but also overcompensated cephalosporin hypersensitivity. Our data collectively indicate that the main purpose of PrkA-mediated signaling in L. monocytogenes is control of MurA stability during standard laboratory growth conditions and intracellular growth in macrophages. These findings have important implications for the understanding of PG biosynthesis regulation and β-lactam resistance of L. monocytogenes and related Gram-positive bacteria.
A unique form of collective epithelial migration is crucial for tissue fusion in the secondary palate and can overcome loss of epithelial apoptosis

Tissue fusion is an oft-employed process in morphogenesis which often requires the removal of the epithelia intervening multiple distinct primordia to form one continuous structure. In the mammalian secondary palate, a midline epithelial seam (MES) forms between two palatal shelves and must be removed to allow mesenchymal confluence. Abundant apoptosis and cell extrusion in this epithelial seam support their importance in its removal. However, by genetically disrupting the intrinsic apoptotic regulators BAX and BAK within the MES, we find a complete loss of cell death and cell extrusion, but successful removal of the MES, indicating that developmental compensation enables fusion. Novel static and live imaging approaches reveal that the MES is removed through a unique form of collective epithelial cell migration in which epithelial trails and islands stream through the mesenchyme to reach the oral and nasal epithelial surfaces. These epithelial trails and islands begin to express periderm markers while retaining expression of the basal epithelial marker ΔNp63, suggesting their migration to the oral and nasal surface is concomitant with their differentiation to an epithelial intermediate. Live imaging reveals anisotropic actomyosin contractility within epithelial trails that drives their peristaltic movement, and genetic loss of non-muscle myosin IIA-mediated actomyosin contractility results in dispersion of epithelial collectives and dramatic failure of normal MES migration. These findings demonstrate redundancy between cellular mechanisms of morphogenesis and reveal a crucial role for a unique form of collective epithelial migration during tissue fusion.
Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits. Significance statement Understanding the genetic basis of important phenotypes is a central goal of genetics. However, the highly polygenic architectures of complex traits inferred by large-scale genome-wide association studies (GWAS) in humans stand in contrast to the results of quantitative trait locus (QTL) mapping studies in model organisms. Here, we use a barcoding approach to conduct QTL mapping in budding yeast at a scale two orders of magnitude larger than the previous state of the art. The resulting increase in power reveals the polygenic nature of complex traits in yeast, and offers insight into widespread patterns of pleiotropy and epistasis. Our data and analysis methods offer opportunities for future work in systems biology, and have implications for large-scale GWAS in human populations.
Physicochemical properties of modified trifoliate yam starches

Physicochemical properties of modified trifoliate yam starches were determined. Trifoliate yam starches were harvested and the starch was extracted. The extracted starch was modified using four methods (acid and alkali treatment, oxidation and acetylation). Colour and physicochemical properties of the modified starches were determined. Colour of pre-gelatinized trifoliate yam starch was significantly different (p<0.05) from other starches. The colour was yellowish/reddish while other starches were lighter in colour. The structures of untreated, oxidized, pre-gelatinized and acetylated starches were polygonal in shape. Granule sizes of native and modified trifoliate yam starches ranged from 2.53 to 3.86 μm. Amylose content of trifoliate yam starches ranged from 10.01 to 16.17%. Swelling power of pre-gelatinized starch increased from 2.15 at 60 o C to 3.00 at 70 o C but the values decreased at 80 to 90 o C. Acid-treated starch exhibited higher paste clarity at refrigerated temperature than ambient temperature but at ambient temperature, oxidized starch had high paste clarity during storage. Acid and alkali-treated starches had higher water exudate at day 0 which later decreased with storage. Acetylated starch had higher peak viscosity (3833.00 cP). Acid and alkali treatment reduced the viscosities and had low freezethaw stability. Keywords : Colour, Modification, Physicochemical, Trifoliate yam starch
The First Step to Learning Place Value: A Role for Physical Models?

Very few questions have cast such an enduring effect in cognitive science as the question of “symbol-grounding”: Do human-invented symbol systems have to be grounded to physical objects to gain meanings? This question has strongly influenced research and practice in education involving the use of physical models and manipulatives. However, the evidence on the effectiveness of physical models is mixed. We suggest that rethinking physical models in terms of analogies, rather than groundings, offers useful insights. Three experiments with 4- to 6-year-old children showed that they can learn about how written multi-digit numbers are named and how they are used to represent relative magnitudes based on exposure to either a few pairs of written multi-digit numbers and their corresponding names, or exposure to multi-digit number names and their corresponding physical models made up by simple shapes (e.g., big-medium-small discs); but they failed to learn with traditional mathematical manipulatives (i.e., base-10 blocks, abacus) that provide a more complete grounding of the base-10 principles. These findings have implications for place value instruction in schools and for the determination of principles to guide the use of physical models.
Quantitative image features from radiomic biopsy differentiate oncocytoma from chromophobe renal cell carcinoma

Abstract. Purpose: To differentiate oncocytoma and chromophobe renal cell carcinoma (RCC) using radiomics features computed from spherical samples of image regions of interest, “radiomic biopsies” (RBs). Approach: In a retrospective cohort study of 102 CT cases [68 males (67%), 34 females (33%); mean age ± SD, 63 ± 12 years], we pathology-confirmed 42 oncocytomas (41%) and 60 chromophobes (59%). A board-certified radiologist performed two RB rounds. From each RB round, we computed radiomics features and compared the performance of a random forest and AdaBoost binary classifier trained from the features. To control for overfitting, we performed 10 rounds of 70% to 30% train-test splits with feature-selection, cross-validation, and hyperparameter-optimization on each split. We evaluated the performance with test ROC AUC. We tested models on data from the other RB round and compared with the same round testing with the DeLong test. We clustered important features for each round and measured a bootstrapped adjusted Rand index agreement. Results: Our best classifiers achieved an average AUC of 0.71 ± 0.024. We found no evidence of an effect for RB round (p = 1). We also found no evidence for a decrease in model performance when tested on the other RB round (p = 0.85). Feature clustering produced seven clusters in each RB round with high agreement (Rand index = 0.981 ± 0.002, p < 0.00001). Conclusions: A consistent radiomic signature can be derived from RBs and could help distinguish oncocytoma and chromophobe RCC.
Spontaneous Alpha-Band Oscillations Bias Subjective Contrast Perception

Perceptual decisions depend both on the features of the incoming stimulus and on the ongoing brain activity at the moment the stimulus is received. Specifically, trial-to-trial fluctuations in cortical excitability have been linked to fluctuations in the amplitude of prestimulus α oscillations (∼8-13 Hz), which are in turn are associated with fluctuations in subjects' tendency to report the detection of a stimulus. It is currently unknown whether α oscillations bias postperceptual decision-making, or even bias subjective perception itself. To answer this question, we used a contrast discrimination task in which both male and female human subjects reported which of two gratings (one in each hemifield) was perceived as having a stronger contrast. Our EEG analysis showed that subjective contrast was reduced for the stimulus in the hemifield represented in the hemisphere with relatively stronger prestimulus α amplitude, reflecting reduced cortical excitability. Furthermore, the strength of this spontaneous hemispheric lateralization was strongly correlated with the magnitude of individual subjects' biases, suggesting that the spontaneous patterns of α lateralization play a role in explaining the intersubject variability in contrast perception. These results indicate that spontaneous fluctuations in cortical excitability, indicated by patterns of prestimulus α amplitude, affect perceptual decisions by altering the phenomenological perception of the visual world. SIGNIFICANCE STATEMENT Our moment-to-moment perception of the world is shaped by the features of the environment surrounding us, as much as by the constantly evolving states that characterize our brain activity. Previous research showed how the ongoing electrical activity of the brain can influence whether a stimulus has accessed conscious perception. However, evidence is currently missing on whether these electrical brain states can be associated to the subjective experience of a sensory input. Here we show that local changes in patterns of electrical brain activity preceding visual stimulation can bias our phenomenological perception. Importantly, we show that the strength of these variations can help explain the great interindividual variability in how we perceive the visual environment surrounding us.
Role of AMH in Prediction of Menopause

Anti-Müllerian Hormone (AMH) is produced by small antral follicles and has evolved over the past three decades as an assumed potential marker of the number of follicles in the human ovaries, also known as ovarian reserve. This quantitative measure, given the gradual decline over time and its non-replenishable feature, could be the dreamed marker for predicting the final exhaustion of ovarian storage: the post-menopause. This introductory chapter summarizes current knowledge with regard to the contribution of serum AMH measurements to predict age of normal menopause and critically discuss its potential in this regard. Furthermore, its predictive role in the context of menopause in association with several frequently occurring fertility disorders such as premature menopause, polycystic ovarian syndrome and endometriosis are discussed. Overall, while ovarian reserve markers including AMH are unmistakably related to age at menopause, they are insufficiently precise to inform on an individual’s journey of ovarian aging.
Flexible Path Planning through Vicarious Trial and Error

Flexible planning is necessary for reaching goals and adapting when conditions change. We introduce a biologically plausible path planning model that learns its environment, rapidly adapts to change, and plans efficient routes to goals. Unlike prior models of hippocamapl replay, our model addresses the decision-making process when faced with uncertainty. We tested the model in simulations of human and rodent navigation in mazes. Like the human and rat, the model was able to generate novel shortcuts, and take detours when familiar routes were blocked. Similar to rodent hippocampus recordings, the neural activity of the model resembles neural correlates of Vicarious Trial and Error (VTE) during early learning or during uncertain conditions. Similar to rodent studies, after learning, the neural activity resembles forward replay or preplay predicting a future route, and VTE activity decreases. We suggest that VTE, in addition to weighing possible outcomes, is a way in which an organism may gather information for future use.
Remotely detected plant function in two midwestern prairie grassland experiments reveals belowground processes

Imaging spectroscopy provides the opportunity to incorporate leaf and canopy optical data into ecological studies, but the extent to which remote sensing of vegetation can enhance the study of belowground processes is not well understood. In grassland systems, aboveground and belowground vegetation quantity and quality are coupled, and both influence belowground microbial processes and nutrient cycling, providing a potential link between remote sensing and belowground processes. We hypothesized that ecosystem productivity, and the chemical, structural and phylogenetic-functional composition of plant communities would be detectable with remote sensing and could be used to characterize belowground plant and soil processes in two grassland biodiversity experiments—the BioDIV experiment at Cedar Creek Ecosystem Science Reserve in Minnesota and the Wood River Nature Conservancy experiment in Nebraska. Specifically, we tested whether aboveground vegetation chemistry and productivity, as detected from airborne sensors, predict soil properties microbial processes and community composition. Imaging spectroscopy data were used to map aboveground biomass and green vegetation cover, functional traits and phylogenetic-functional community composition of vegetation. We examined the relationships between the image-derived variables and soil carbon and nitrogen concentration, microbial community composition, biomass and extracellular enzyme activity, and soil processes, including net nitrogen mineralization. In the BioDIV experiment—which has low overall diversity and productivity despite high variation in each—belowground processes were driven mainly by variation in the amount of organic matter inputs to soils. As a consequence, soil respiration, microbial biomass and enzyme activity, and fungal and bacterial composition and diversity were significantly predicted by remotely sensed vegetation cover. In contrast, at Wood River, where plant diversity and productivity were consistently higher, remotely sensed functional, chemical and phylogenetic composition of vegetation predicted belowground extracellular enzyme activity, microbial biomass, and net nitrogen mineralization rates, while aboveground biomass did not. The strong, contrasting associations between the quantity and chemistry of aboveground inputs with belowground soil processes and properties provide a basis for using imaging spectroscopy to understand belowground processes across productivity gradients in grassland systems. However, a mechanistic understanding of how above and belowground components interact among different ecosystems remains critical to extending these results broadly.
Associations of Family Functioning and Social Support With Psychopathology in Children of Mentally Ill Parents: Multilevel Analyses From Different Rating Perspectives

Offspring of mentally ill parents is at heightened risk for psychological symptoms. The identification of environmental factors that predict their mental health is crucial for the development of preventive and therapeutic measures. In the current study, we addressed the combined role of family functioning and social support by taking mentally ill patients’, their partners’, and children’s perspectives into account. The cross-sectional sample included n=195 families (195 patients, 127 partners, and 295 children). Family members completed questionnaires related to family functioning, social support as well as parental and child psychopathology. We conducted multilevel analyses to investigate the associations with internalizing and externalizing problems in children. Family functioning and social support were significantly associated with child internalizing and externalizing problems. However, results varied depending on the rating perspective. We found significant interaction effects of family functioning and social support on child psychopathology. The findings point to the importance of family functioning and social support as potential targets for interventions. Findings should be replicated in future longitudinal studies.