Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiative Energy Budgets of Phototrophic Surface-Associated Microbial Communities and their Photosynthetic Efficiency Under Diffuse and Collimated Light

We investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O2, temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under light-limiting conditions and amounted to ~13% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis and light distribution. The light acclimation index, Ek was >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident 45 irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. Our results suggest that the optical properties and the structural organization of phytoelements are important traits affecting the photosynthetic efficiency of biofilms and sediments.
Unifying Population and Landscape Ecology with Spatial Capture-recapture

Spatial heterogeneity in the environment induces variation in population demographic rates and dispersal patterns, which result in spatio-temporal variation in density and gene flow. Unfortunately, applying theory to learn about the role of spatial structure on populations has been hindered by the lack of mechanistic spatial models and inability to make precise observations of population structure. Spatial capture-recapture (SCR) represents an individual-based analytic framework for overcoming this fundamental obstacle that has limited the utility of ecological theory. SCR methods make explicit use of spatial encounter information on individuals in order to model density and other spatial aspects of animal population structure, and have been widely adopted in the last decade. We review the historical context and emerging developments in SCR models that enable the integration of explicit ecological hypotheses about landscape connectivity, movement, resource selection, and spatial variation in density, directly with individual encounter history data obtained by new technologies (e.g., camera trapping, non-invasive DNA sampling). We describe ways in which SCR methods stand to revolutionize the study of animal population ecology.
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

Motivation: Genotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single lineage (auto polyploids), inbreeding can result from mixed mating and/or double reduction. For WGDs that involve hybridization (allopolyploids), alleles are typically inherited through independently segregating subgenomes. Results: We present two new models for estimating genotypes and population genetic parameters from genotype likelihoods for auto- and allopolyploids. We then use simulations to compare these models to existing approaches at varying depths of sequencing coverage and ploidy levels. These simulations show that our models typically have lower levels of estimation error for genotype and parameter estimates, especially when sequencing coverage is low. Finally, we also apply these models to two empirical data sets from the literature. Overall, we show that the use of genotype likelihoods to model non-standard inheritance patterns is a promising approach for conducting population genomic inferences in polyploids. Availability: A C++ program, EBG, is provided to perform inference using the models we describe. It is available under the GNU GPLv3 on GitHub: https://github.com/pblischak/polyploid-genotyping. Contact: blischak.4@osu.edu.
Chimeric 14-3-3 proteins for unravelling interactions with intrinsically disordered partners

In eukaryotes, several proteins act as “hubs”, integrating signals from a variety of interacting partners that bind to the hub through intrinsically disordered regions. Not surprisingly, one of the major hubs, the 14-3-3 protein, that plays wide-ranging roles in cellular processes, has been linked with a number of disorders including neurodegenerative diseases and cancer. A partner protein usually binds with its phosphopeptide accommodated in an amphipathic groove (AG) of 14-3-3, a promising platform for therapeutic intervention. Protein plasticity in the groove allows to accommodate a range of phosphopeptides with different sequences. So far, in spite of mammoth effort, accurate structural information has been derived only for few 14-3-3 complexes with phosphopeptide-containing proteins or various short synthetic peptides. The progress has been prevented by intrinsic disorder of partner proteins and, in case of transient interactions, by the low affinity of phosphopeptides. We reasoned that these problems could be resolved by using chimeric 14-3-3 proteins with incorporated peptide sequences. We tested this hypothesis and found that such chimeric proteins are easy to design, express, purify and crystallize. We show that when attached to the C terminus of 14-3-3 via an optimal linker, peptides become stoichiometrically phosphorylated by protein kinase A during bacterial co-expression. We determined crystal structures for complexes of chimeric 14-3-3 protein fused with three different peptides. In most of the cases, the phosphopeptide is bound inside the AG, providing invaluable information on its interaction with the protein. This approach can reinvigorate studies of 14-3-3 protein complexes, including those with otherwise challenging low affinity phosphopeptides. Furthermore, 14-3-3-phosphopeptide chimeras can be useful for the design of novel biosensors for in vitro and in vivo imaging experiments.
Mathematical constraints on FST: multiallelic markers in arbitrarily many populations

FST is one of the most widely used statistics in population genetics. Recent mathematical studies have identified constraints on FST that challenge interpretations of FST as a measure with potential to range from 0 for genetically similar populations to 1 for divergent populations. We generalize results obtained for population pairs to arbitrarily many populations, characterizing the mathematical relationship between FST, the frequency M of the more frequent allele at a polymorphic biallelic marker, and the number of subpopulations K. We show that for fixed K, FST has a peculiar constraint as a function of M, with a maximum of 1 only if M = i/K for integers i with ⌈K/2⌉ ≤ i ≤ K − 1. For fixed M, as K grows large, the range of FST becomes the full closed or half-open unit interval. For fixed K, however, some M < (K − 1)/K always exists at which the upper bound on FST is constrained to be below . In each of three migration models—island, rectangular stepping-stone, and linear stepping-stone—we use coalescent simulations to show that under weak migration, FST depends strongly on the allele frequency M when K is small, but not when K is large. Finally, using data on human genetic variation, we employ our results to explain the generally smaller FST values between pairs of continents relative to global FST values. We discuss implications for the interpretation and use of FST.
Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map

The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or “anchors” are associated with CTCF protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of Polycomb Repressive Complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer-promoter communication, our results indicate that loops are also associated with gene repression.
How to identify low-abundance modified peptides with proteomics mass spectrometry

Traditional analytics rely largely on search engine “similarity” scores (e.g. XCorr, ion-score, hyperscore) that quantify the degree of similarity between the measured spectrum and a predicted spectrum, the latter derived from a candidate peptide sequence using a sequence-to-spectrum ionization model. They evolved mainly for abundant peptides with robust spectral signals. Efforts to improve the search engine score, for example by incorporating accurate fragment data, have had limited success or worse. Some ad hoc efforts identify unexpectedly numerous peptides having near-identical mass, charge, and chromatographic retention time i.e. same isotopic envelopes at the same split-second in a multihour experiment better explained by faulty analytics.
Social caching and vehicular social networks: two contributions to the theory and practice of online social networks

OF THE DISSERTATION Social Caching and Vehicular Social Networks: Two Contributions to The Theory and Practice of Online Social Networks by Lu Han Dissertation Director: Liviu Iftode Recent years have witnessed an explosive growth of the Online Social Networks (OSNs), which serve as a fertile ground for research such as, examining individual and group behaviors, identifying information dissemination patterns, and building unconventional OSNs. This dissertation explores the design and implementation of two emerging OSNs, a distributed social network (DOSN) and a vehicular social network (VSN), both from theoretical and practical perspectives, with the goal of improving the performance and functionality of the systems. Distributed OSNs have been proposed as an alternative to centralized OSNs. DOSNs neither have central repository of all user data, nor they impose control regarding how the data will be accessed, hence, enable users to keep control of their private data. One of the critical challenges in building DOSNs is the performance of the distributed social update dissemination. To address this, we propose Social Caches, nodes that cache updates of their friends in order to reduce the number of peer-to-peer network connections. We formulate social cache selection as an instance of the Neighbor-Dominating Set Problem, and propose a set of approximation, regression and heuristic social cache selection algorithms to solve it. Performance evaluation based on real social traffic data and five well-known social graphs shows that the proposed social caching mechanism can reduce P2P network connections by an order of magnitude. In the second part of the dissertation, we introduce a new class of online social networks
Prevalência de anticorpos para alphavirus em equinos do estado do Pará, Brasil

The State of Para comprises 26% of Brazilian Amazon region, where a large diversity of arboviruses has been described. This study sought to assess the prevalence and distribution of hemagglutination inhibition (HI) antibodies against antigens of four alphaviruses (Togaviridae: Alphavirus ) from the species: Eastern equine encephalitis (EEEV), Western equine encephalitis (WEEV), Mayaro virus (MAYV), and Mucambo virus (MUCV) in 753 serum samples of horses in Para State, Brazil. All investigated arboviruses were detected and indicate that horses are susceptible to these alphaviruses, and show evidences of their active circulation in farm animals in the Brazilian Amazon.
Faster and better training of multi-layer perceptron for forecasting problems

New methods for training multi-layer perceptron network for forecasting problems are presented. The first method exploits spectral characteristics of time series to get faster learning and improved prediction accuracy. A neural network scheme for real time implementation of this method is also presented. The second method suggests the use of two new weight initialization schemes which give very fast convergence besides giving better prediction. The foreign exchange time series is used to illustrate the efficacy of the proposed methods. <<ETX>>
Continuous and interval training exercise programme: its relationship with biochemical parameters among some Nigerian undergraduates

The importance of exercise and fitness in the management of diabetes has dominated the scientific research space in recent years. This present study therefore emphasizes the advances and facts relating metabolic stress hormones, diabetes and exercise. Twenty apparently healthy Nigerian students whose mean age was 23.67±2.78 years, mean heights 1.77±0.84m and average body weight 66.26±7.53kg participated in the study with internal training exercise programme for six weeks and continuous for the last two weeks. The testosterone, cortisol and Gamma Glutamyltransferase (GGT) levels were increased while the insulin level decreased although only cortisol and testosterone mean differences were significant after the exercise. From the result, it can be concluded that continuous and internal training exercise programmes are effective in managing stress-induced pathological (degenerative) diseases. Exercise is therefore recommended as a non-pharmacological adjunct in managing some metabolic syndrome such as non-insulin dependent diabetes and obesity among Nigerian students who are to an extent prone to stress.
Three-dimensional object recognition using cross-sections

Describes a method for recognizing 3D objects from their serial cross-sections. Object regions of interest in cross-sectional binary images of successive slices are aligned with those of the models. Cross-sectional differences between the object and the models are measured in the direction of the gradient of the cross-section boundary. This is repeated in all the cross-sectional images. The model with minimum average cross-sectional difference is selected as the best match to the given object. The method is tested using computer-generated surfaces, and results are presented. <<ETX>>
Les nanoparticules polymères pour la délivrance de principes actifs anticancéreux

Nanocarriers based on polymers are currently attracting much attention to perform efficient drug delivery, especially in cancer therapy. Over the last decades, different kinds of polymer nanoparticulate systems have been developed (e.g., simple, stealth, targeted, stimuli-responsive and prodrug) to propose novel, better and safer cancer therapies. This article will give a brief overview of the different classes of polymer nanoparticles that have been reported and discuss some key achievements deriving from their use in the field of cancer therapy.
Explicit and tacit

The aim of the present chapter is to evaluate the extent to which quantitative and qualitative methodologies used in translation studies interplay and what new insights are obtained as a consequence of investigating explicit corpus-based data with a more tacit semantic enquiry. The approach used is Cognitive Corpus-based Linguistic methodology as applied to contrastive and to corpus-based translation studies. What is presented and interpreted is a comparison between the frequency of use of lexical units, phrases (collocations) and sentence segments in the English-to-Polish or Polish-to-English original and translated texts, juxtaposed to those identified in respective mono-lingual corpora. The paper provides evidence that, combined with a comparison of keyness and collocation patterns as well as lexical equivalence patterns and metaphor inquiry (exemplified with a number of emotion words in translation), all these parameters give us a clue to language-specific imagery construal and reconceptualization processes in translation.
Outlier Detection Based OnProjection-based Ordering

Simple one-dimensional order statistics have played an important role in one-dimensional data analysis. However, extensions of these methods to high dimensional data have not been properly addressed. Even though ordering is of natural interest in many problems, the lack of natural and unambiguous methods to order or rank multi-dimensional data has hindered the adoption of these methods for more complex applications. Projection-based depth functions are mainly based on the idea of finding a “centre-outward” ordering from the “deepest” point of data. These functions are providing promising tools for ordering multi-dimensional data and may also be used for outlier detection and cluster analysis. This paper develops an outlier-detection algorithm based on a new method for projection-based ordering of multi-dimensional data.
Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation

Differentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to multiple levels of heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell RNA transcriptomics and computational modelling of temporal mixtures, we reconstructed the developmental trajectories of Th1 and Tfh cell populations during Plasmodium infection in mice at single-cell resolution. These cell fates emerged from a common, highly proliferative and metabolically active precursor. Moreover, by tracking clonality from T cell receptor sequences, we infer that ancestors derived from the same naïve CD4+ T cell can concurrently populate both Th1 and Tfh subsets. We further found that precursor T cells were coached towards a Th1 but not a Tfh fate by monocytes/macrophages. The integrated genomic and computational approach we describe is applicable for analysis of any cellular system characterized by differentiation towards multiple fates. One Sentence Summary Using single-cell RNA sequencing and a novel unsupervised computational approach, we resolve the developmental trajectories of two CD4+ T cell fates in vivo, and show that uncommitted T cells are externally influenced towards one fate by inflammatory monocytes.
tRNA-derived small RNAs target transposable element transcripts

tRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are cleaved by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that where the tRF-AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.
Theoretical Energy Release of Thermites, Intermetallics, and Combustible Metals

Thermite mixtures, intermetallic reactants, and metal fuels have long been used in pyrotechnic applications. Advantages of these systems typically include high energy density, high combustion temperature, and a wide range of gas production. They generally exhibit high temperature stability and possess insensitive ignition properties. For the specific applications of humanitarian demining and disposal of unexploded ordnance, these pyrotechnic formulations offer additional benefits. The combination of high thermal input with low brisance can be used to neutralize the energetic materials in mines and other ordnance without the "explosive" high-blast-pressure events that can cause extensive collateral damage to personnel, facilities, and the environment. In this paper, we review the applications, benefits, and characteristics of thermite mixtures, intermetallic reactants, and metal fuels. Calculated values for reactant density, heat of reaction (per unit mass and per unit volume), and reaction temperature (without and with consideration of phase changes and the variation of specific heat values) are tabulated. These data are ranked in several ways, according to density, heat of reaction, reaction temperature, and gas production.
A cell based, high throughput assay for quantitative analysis of Hedgehog pathway activation using a Smoothened phosphorylation sensor

The Hedgehog (Hh) signalling cascade is conserved across evolution and plays an important role in development and disease. In the absence of Hh, activity of the key signal transducer Smoothened (Smo) is downregulated by the Hh receptor Patched (Ptc). However, the mechanisms underlying this inhibition, and especially its release upon ligand stimulation, are still poorly understood, in part because tools for directly following Smo activation at the subcellular level were long lacking. Here we present a high throughput, cell culture assay based on a fluorescent sensor for Drosophila Smo phosphorlyation. Using this approach we could first demonstrate that the graded response to increasing Hh levels observed at the population level can be traced back to threshold responses of individual cells exhibiting differential Hh sensitivity. Second, we screened a small molecule inhibitor library for regulators of Smo phosphorylation. We observed increased Smo sensor fluorescence with compounds aimed at two major target groups, the MAPK signalling cascade and polo and aurora kinases. Biochemical validation confirmed the screen results for selected inhibitors (dobrafenib, tak-733, volasertib) and revealed differences in the mode of Smo activation, demonstrating that the assay is in principle suitable for dissecting the cell biological basis of Hh pathway activation.