Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Temporal Distribution of Lantana Mites Phoretic on Butterflies

A flower-dwelling mite, Proctolaelaps lobata, is specific to Lantana florets and phoretic on a variety of Lepidoptera. A study of the spatial and temporal distribution of the mite shows significant differences between sites in Costa Rica and Texas in numbers of mites/floret and mites/butterfly such that the site with more mites/floret has fewer mites/butterfly. In both sites, first-day florets contain more mites than older florets. The number of mites/floret is significantly affected by the number of neighboring flowerheads, although the effect varies with the site. There is no distinctive change in number of mites/floret or mites/butterfly with time of day. The Texas site is recolonized annually, perhaps by mites carried by Lepidoptera from the south. ANIMALS LIVING IN HABITATS that are temporally brief compared with their generation time must possess effective dispersal mechanisms. Phoresy, or travel on another animal, is a potentially efficient dispersal mechanism, particularly if the host animal routinely visits a number of similar habitat patches in rapid succession. Flower dwelling mites that are phoretic on nectar foragers are striking examples of such behavior. Proctolaelaps vandenbergi (Ryke) rides among Protea flowers on the heads of honeybirds (Ryke 1954), and numerous Rhinoseius and Proctolaelaps species ride in the nasal cavities of hummingbirds (Baker & Yunker 1964; Colwell 1979, 1985). Here we show that another mite, P. lobata DeLeon (Mesostigmata: Ascidae) (A. Treat, pers. comm.), is phoretic on Lepidoptera and specific to flowers of Lantana spp. We examine the spatial and temporal variation in the mites' occurrence on butterflies and on flowers at the level of florets, bushes and regions. These data increase the available information on the relationship between phoretic habits and distribution of individuals in ephem-
Robustness of individualized inferences from longitudinal resting state dynamics

Individual human brains plastically reorganize over extended timescales ranging from days to years, which makes these changes difficult to track. One promising tracking indicator is the neural activity at rest. However, the rest state (RS) is vulnerable to incidental inter-day cognitive variability that can confound the detection of changes to underlying neurophysiology. Here we show that this confounding is minimized by tracking changes to the distinctiveness of an individual’s RS activity, which is shaped by individual neurophysiology. Using longitudinal (5-day) RS acquired with EEG, we devised empirical simulations of distinctiveness changes confounded by cognitive variation. These inter-day changes were correctly classified with over 96% accuracy from 2-second snapshots of instantaneous oscillatory power from RS and confounded-RS. Surprisingly, the individual indicators of distinctiveness were concentrated at characteristic fronto-central and occipital zones. These findings support the suitability of longitudinal RS for individualized inferences about neurophysiological change in health and disease.
Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut

Archaea of the order Methanomassiliicoccales use methylated-amines such as trimethylamine as a substrate for methane production. They form two large phylogenetic clades and reside in diverse environments, from soil to the human gut. Two genera, one from each clade, inhabit the human gut: Methanomassiliicoccus, which has one cultured representative, and “candidatus Methanomethylophilus”, which has none. Questions remain regarding their distribution across different biomes and human populations, their association with other taxa in the human gut, and whether host genetics correlate with their abundance. To gain insight into the Methanomassiliicoccales, and the human-associated members in particular, we performed a genomic comparison of 72 Methanomassiliicoccales genomes and assessed their presence in metagenomes derived from the human gut (n=4472 representing 25 populations), nonhuman animal gut (n=145) and nonhost environments (n=160). Our analyses showed that all taxa are generalists: they were detected in animal gut and environmental samples. We confirmed two large clades, one enriched in the gut, the other enriched in the environment, with notable exceptions. Genomic adaptations to the gut include genome reduction, a set of adhesion factors distinct from that of environmental taxa, and genes involved in the shikimate pathway and bile resistance. Genomic adaptations differed by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, the relative abundance of Methanomassiliicoccales correlated with trimethylamine-producing bacteria and was unrelated to host genotype. Our results shed light on the microbial ecology of this group may help guide Methanomassiliicoccales-based strategies for trimethylamine mitigation in cardiovascular disease. Importance Methanomassiliicoccales are a lesser known component of the human gut microbiota. This archaeal order is composed of methane producers that use methylated amines, such as trimethylamine, in methane production. This group has only one cultured representative; how they adapted to inhabit the mammalian gut and how they interact with other microbes is largely unknown. Using bioinformatics methods applied to DNA from a wide range of samples, we profiled the relative abundances of these archaea in environmental and host-associated microbial communities. We observed two groups of Methanomassiliicoccales, one largely host-associated and one largely found in environmental samples, with some exceptions. When host-associated, these archaea have a distinct set of genes related to adhesion and possess genes related to bile resistance. We did not detect Methanomassiliicoccales in all human populations tested but when present, they are correlated with Bacteria known to produce trimethylamine. Since trimethylamine is linked to cardiovascular disease risk, these intriguing Archaea may also be involved.
Pushing Out the Classroom Walls: A Scalability Benchmark for a Virtual Audience Behaviour Model in Virtual Reality

In this paper, we describe the implementation and performance of a Virtual Audience behaviour model for Virtual Reality (VR). The model is a VR adaptation of an existing desktop model based on crowd-sourced data. The system allows a user in VR to easily build and experience a wide variety of atmospheres with small or large groups of virtual agents. The paper describes the model’s implementation and possible benefits for different applications, e.g. training, therapeutic or culture. Our first scalability benchmark results demonstrated the ability to simultaneously handle one hundred virtual agents without significantly affecting the recommended frame rate for VR applications. Lastly, we propose a set of improvements our training system can benefit from. This research is conducted in the context of a classroom simulation software for teachers’ training.
The influence of gene Rv3671c in Mycobacterium bovis to its replication and acid resistance

To study the effect of Marp protein in Mycobacterium bovis to the acid resistance and growth performance, this research constructed a knockout mutant (ΔMarp) with mycobacteriophage, complemented strain (ΔMarpComp), and overexpressing strain (PmvRv3671) of the gene Rv3671c with pmv261 plasmid. Culturing them in standard 7H9 medium to the early logarithmic phase and transferring them into 7H9 medium at pH 6.6 and pH 5.0 and maintenance solution at pH 6.6 and pH 4.5. Likewise, macrophages Raw264.7 were infected with multiple infections at 10. The results showed that while they grew in 7H9 medium at pH 5.0 or pH 6.6 and maintenance buffer at pH 4.5, the lived number of over-expressing strain PmvRv3671 is more than wild-type strain M.bovis, ΔMarpComp and ΔMarp on the 14th day. After removing the effects of citrate solution, it can be found that the acid resistance abilities of them all are significantly lower on the 14th day than that on the 5th day. Using them infected Raw264.7 macrophages with IFNγ stimulation, the growth rate of the PmvRv3671 is better than An5, ΔMarp and ΔMarpComp. In conclusion, Rv3671c over-expressing strain had shown a better growth ability than wild-type An5, ΔMarp and ΔMarpComp under acidic environment. When exposed to pH 4.5 citrate maintenance solution for a long time, acid resistance abilities of them all have become weaker.
The Wnt Effector TCF7l2 Promotes Oligodendroglial Differentiation by Repressing Autocrine BMP4-Mediated Signaling

Promoting oligodendrocyte (OL) differentiation represents a promising option for remyelination therapy for treating the demyelinating disease multiple sclerosis (MS). The Wnt effector transcription factor 7-like 2 (TCF7l2) was upregulated in MS lesions and had been proposed to inhibit OL differentiation. Recent data suggest the opposite yet underlying mechanisms remain elusive. Here, we unravel a previously unappreciated function of TCF7l2 in controlling autocrine bone morphogenetic protein (BMP)4-mediated signaling. Disrupting TCF7l2 in mice of both sexes results in oligodendroglial-specific BMP4 upregulation and canonical BMP4 signaling activation in vivo. Mechanistically, TCF7l2 binds to Bmp4 gene regulatory element and directly represses its transcriptional activity. Functionally, enforced TCF7l2 expression promotes OL differentiation by reducing autocrine BMP4 secretion and dampening BMP4 signaling. Importantly, compound genetic disruption demonstrates that oligodendroglial-specific BMP4 deletion rescues arrested OL differentiation elicited by TCF7l2 disruption in vivo. Collectively, our study reveals a novel connection between TCF7l2 and BMP4 in oligodendroglial lineage and provides new insights into augmenting TCF7l2 for promoting remyelination in demyelinating disorders such as MS. SIGNIFICANCE STATEMENT Incomplete or failed myelin repairs, primarily resulting from the arrested differentiation of myelin-forming oligodendrocytes (OLs) from oligodendroglial progenitor cells, is one of the major reasons for neurologic progression in people affected by multiple sclerosis (MS). Using in vitro culture systems and in vivo animal models, this study unraveled a previously unrecognized autocrine regulation of bone morphogenetic protein (BMP)4-mediated signaling by the Wnt effector transcription factor 7-like 2 (TCF7l2). We showed for the first time that TCF7l2 promotes oligodendroglial differentiation by repressing BMP4-mediated activity, which is dysregulated in MS lesions. Our study suggests that elevating TCF7l2 expression may be possible in overcoming arrested oligodendroglial differentiation as observed in MS patients.
A prediction tool for plaque progression based on patient-specific multi-physical modeling

Atherosclerotic plaque rupture is responsible for a majority of acute vascular syndromes and this study aims to develop a prediction tool for plaque progression and rupture. Based on the follow-up coronary intravascular ultrasound imaging data, we performed patient-specific multi-physical modeling study on four patients to obtain the evolutional processes of the microenvironment during plaque progression. Four main pathophysiological processes, i.e., lipid deposition, inflammatory response, migration and proliferation of smooth muscle cells (SMCs), and neovascularization were coupled based on the interactions demonstrated by experimental and clinical observations. A scoring table integrating the dynamic microenvironmental indicators with the classical risk index was proposed to differentiate their progression to stable and unstable plaques. The heterogeneity of plaque microenvironment for each patient was demonstrated by the growth curves of the main microenvironmental factors. The possible plaque developments were predicted by incorporating the systematic index with microenvironmental indicators. Five microenvironmental factors (LDL, ox-LDL, MCP-1, SMC, and foam cell) showed significant differences between stable and unstable group (p < 0.01). The inflammatory microenvironments (monocyte and macrophage) had negative correlations with the necrotic core (NC) expansion in the stable group, while very strong positive correlations in unstable group. The inflammatory microenvironment is strongly correlated to the NC expansion in unstable plaques, suggesting that the inflammatory factors may play an important role in the formation of a vulnerable plaque. This prediction tool will improve our understanding of the mechanism of plaque progression and provide a new strategy for early detection and prediction of high-risk plaques. Author summary Besides the traditional systematic factors, the influences of the local microenvironmental factors on atherosclerotic plaque progression have been demonstrated. Mathematical and computational modeling is an important tool to investigate the complex interplay between plaque progression and the microenvironment, and provides a potential way toward the prediction of plaque vulnerability according to the comprehensive evaluation of both morphological and/or biochemical factors in tissue level with microenvironmental factors in cellular level. We performed patient-specific multi-physical modeling study on four patients to obtain the evolutional processes of the microenvironment during plaque progression and predicted the possible plaque developments. A scoring table integrating the dynamic microenvironmental indicators with the classical risk index was proposed to differentiate their progression to stable and unstable plaques. Based on patient-specific imaging data, the mathematical model will provide a novel method to predict the changes of plaque microenvironment and improve ability to access the personal therapeutic strategy for atherosclerotic plaque.
Detection of oncometabolites 1-methylnicotinamide, nicotine imine and N-Methylnicotinium in nails of oral cancer patients and prediction of them as modulators of DNMT1

Background The prominent among various existing views on the role of nicotine and nicotine-metabolized products in Oral squamous cell carcinoma (OSSC) is metabolic adaptation that allows the use of methyl-donor S-adenosylmethionine (SAM) for non-epigenetic purpose including the methylation of nicotinamide and nicotine. In fact, channeling of SAM for generation of 1-methylnicotinamide (1-MNA) and methylated nicotine products is seen as a key event in cancer cells that allows favorable epigenetic states by forcing DNA hypomethylation. A better perception of such events can be appreciated by analyzing samples like nail, which represents a perfect biological material for studying long-term metabolic reflections of the body. Methods Potential nicotine-metabolized products and 1-MNA in nails of OSCC patients were analyzed by using a novel approach of Vertical tube gel electrophoresis (VTGE)- assisted purification followed by their identification by LC-HRMS. Further, these identified nicotine metabolized products and 1-MNA were evaluated for their molecular interactions with known methyltransferases including cytosolic nicotinamide methyltransferase (NNMT), DNA methyltransferase (DNMT)1 and histone methyltransferases by molecular docking and molecular dynamics simulation (MDS) analyses. Results Our data suggests the presence of N-methylnicotinium ion and nicotine imine in the nail samples of OSCC patients. Further, 1-MNA is also detected in the nails as a major enzymatic product of a known detoxifying enzyme NNMT. Molecular docking of all nicotine and nicotine metabolized products with DNMT1revealed a specific binding affinity of nicotine imine only with a -6.2 Kcal/Mol docking energy. Importantly, binding of nicotine imine is within the CXCC regulatory domain of DNMT1 and it displays molecular interactions with the key amino acid residues, namely ARG690, PRO574, VAL658, PRO692 and ALA695. Furthermore, MDS data corroborated well with the specific binding affinity of nicotine imine to DNMT1 obtained by docking analysis. Conclusion Identification of N-methylnicotinium ion, nicotine imine and 1-MNA in nail samples indicates their potential as predictive and detectable biomarkers for OSCC. Molecular docking and MDS data lead us to propose a role of nicotine imine in modulating the activity of DNMT1. These data further suggest a novel understanding on the role of nicotine metabolized products in modulating DNA methylation that may contribute to tumorigenicity in oral cancer patients.
Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase

The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of the facility with which it can be cultured in the laboratory. Genomic and systems biology approaches have previously been used to describe how the transcriptome responds to environmental changes, but this analysis has been limited to bulk data, representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing in the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample algae communities in the wild. Second, scRNA-seq successfully separated single cells into non-overlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest cell division to economize resources. Notably, these groups of cells recapitulated known patterns observed with bulk RNA-seq, but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We propose that bulk RNA-seq data represent an average of varied cell states that hides underappreciated heterogeneity. One-sentence summary We show that single-cell RNA-seq (scRNA-seq) can be applied to Chlamydomonas cultures to reveal the that heterogenity in bulk cultures is largely driven by diurnal cycle phases The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Matteo Pellegrini (matteop@mcdb.ucla.edu)
USPTO Patents Application 09884455

(74) Agents: GOLDSTEIN, Jorge, A. et aL; Obion, Fisher, Spivak, McClelland & Maier, Crystal Square Five, Suite 400, 1755 South Jefferson Davis Highway, Arlington, VA 22202 (US). (81) Designated States: AT (European patent), BE (European patent), CH (European patent), DE (European patent), FR (European patent), GB (European patent), JP, LU (European patent), NL (European patent), SE (European patent).
Efeito da inoculação com FMA no crescimento inicial em mudas de pinhão manso de três procedências

P hysic nut is a plant widely cultivated in various regions of tropical America, Asia and Africa that adapts well to arid and degraded soils . T his essay aimed to evaluate the effect of arbuscular mycorrhizal fungi (AMF) on solarized substrate for production of seedlings with seeds from states of Pernambuco, Minas Gerais and Mato Grosso do Sul, Brazil . AMF used included a mixture of Clarum glomus , Gigaspora margarita , Scutellospora hterogama and Gigaspora calospora . Treatments consisted of inoculation in that mixture with solarized substrate, non-solarized and control (without inoculation) . T he results showed that seedlings produced with seeds from Pernambuco had the lowest values for leaf number and the ratio between height and diameter, while those formed with seeds from Mato Grosso do Sul revealed the largest height and diameter . I noculation with AMF in solarized oxisol red (LV) substrate did not alter morphology of physic nut seedlings produced from seeds of the three provenances tested .
Analyzing the polymorphisms of Takifugu rubripes with microsatellite

Two populations of Takifugu rubripes domesticated in different places were analyzed with the Takifugu frbripes microsatellite marker and the pattern of each sample was obtained.Altogether 20 primers were used in this experiment,of which 16 primers were assessed for genetic diversity for 10 individuals.The PCR products were electrophoresed by 2% agarose gel,and the data like allelic frequencies and analyzed by statistic method.The results indicated:mean number of alleles were 1.875 0 and 2.437 5,PIC value(polymorphism information content)were 0.275 1 and 0.379 4 and the observed heterozygosity values over all loci were 0.025 and 0.200. All of these indices indicated that genetic diversity of Takifugu rubripes was not inspiring.
Avifaunal diversity and endemism on tropical Indian Ocean islands

Species diversity and endemism of resident breed- ing birds (excluding pelagic and introduced species) on four- teen tropical Indian Ocean archipelagos were related to seven geographic variables using stepwise linear regression analysis. The total number of species within an archipelago and the numbers of continental species (species found in source areas) and Indian Ocean endemics (species restricted to the study area but found within more than one archipelago) were related positively to the number of large islands and total land area. The number and proportion of continental species were pre- dicted also by proximity to source areas and decreasing elevation. The number and proportion of endemic species (those found only within a single archipelago) were related positively to elevation. Relationships of species numbers and proportions in each species category to geographic variables were generally similar to those found in the known avifauna of the tropical Pacific region, but three differences between the two regions were evident. The avifauna of the Indian Ocean region (1) was much less diverse overall, (2) had proportionately more continental and fewer endemic species, and (3) had several families that were much more poorly represented despite their diversity in source areas. These differences may be interpreted by recognizing the importance of island isolation and area in contributing to both speciation and diversity. Increasing isolation decreases local (within- archipelago) diversity through lower colonization rates, but may at least partially compensate for this decrease on a regional (among-archipelago) scale through increased rates of speciation. Increasing area increases both local and regional diversity by providing space for more populations and by decreasing extinction rates.