Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of Genetic Background and Cell Lineage on the Level and Pattern of Position Effect Variegation

Background Chromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is juxtaposed with heterochromatin. Here we closely examine the impact of genetic background on PEV phenotypes in the fruit fly, Drosophila melanogaster. Results Using consecutive generations of selective breeding, we isolated, from a single laboratory population, two inbred lines exhibiting contrasting degrees of variegation (A1: low expression, D1: high expression). Within each inbred population, remarkable similarity is observed in both the degree and the pattern of variegation. 89.63% of the differences between the two inbred lines in the degree of silencing can be explained by genotype, while a modest but significant sex effect is also observed. Further analyses of the PEV phenotype in the progeny of crosses between A1 and D1 suggest that the genotypic effect is the result of the combined effect of multiple independent trans-acting loci. While the initial observations are based on a PEV phenotype scored in the fly eye (hsp70-white reporter), similar degrees of silencing were observed using a beta-gal reporter that can be scored across the whole fly. The pattern of variegating hsp70-white expression among individual flies becomes almost identical after five generations of inbreeding. Using a reporter inserted into the heterochromatic fourth chromosome, image analysis found significant enrichment of pigmentation in the ventral-posterior quadrant in both the A1 and D1 lines, and in the F1 and F2 progeny produced from a cross between A1 and D1, despite different degrees of expression. Conclusions Combining these results with the spreading model for local heterochromatin formation, we propose an augmented stochastic model to describe PEV. In this model, the genetic background, which determines the overall level of silencing, works with the cell lineage specific regulatory environment to determine the on/ off probability at the reporter locus in each cell. This model acknowledges cell-type specific events, as well as the general impact of heterochromatin formation.
Exploring the Relationship Between Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17

Characterizing and engineering microbial communities for lignocellulosic biofuel production has received widespread attention. Previous research has established that Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17 coculture significantly improves overall cellulosic biofuel production efficiency. Here, we investigated this interaction and revealed the mechanism underlying the improved efficiency observed. In contrast to the previously reported mutualistic relationship, a harmful effect toward C. thermocellum JN4 was observed in these microbial consortia. Although T. thermosaccharolyticum GD17 relieves the carbon catabolite repression of C. thermocellum JN4 regarding obtaining more cellobiose or glucose released from lignocellulose, T. thermosaccharolyticum GD17 significantly hampers the growth of C. thermocellum JN4 in coculture. The increased formation of end products is due to the strong competitive metabolic advantage of T. thermosaccharolyticum GD17 over C. thermocellum JN4 in the conversion of glucose or cellobiose into final products. The possibility of controlling and rebalancing these microbial consortia to modulate cellulose degradation was achieved by adding T. thermosaccharolyticum GD17 stimulants into the system. As cellulolytic bacteria are usually at a metabolic disadvantage, these discoveries may apply to a large proportion of cellulosic biofuel-producing microbial consortia. These findings provide a reference for engineering efficient and modular microbial consortia for modulating cellulosic conversion.
Influences of Habitat and Hybridization on the Genetic Structure of Redband Trout in the Upper Snake River Basin, Idaho

Abstract The genetic structure of redband trout Oncorhynchus mykiss gairdnerii in the upper Snake River basin was investigated at various scales using 13 microsatellite loci. The majority of the genetic variation was partitioned between streams, although differentiation among watersheds was significant. This diversity was probably historically partitioned at the watershed scale when steelhead O. mykiss (anadromous rainbow trout) were present, with the exception of small, isolated, headwater streams where there may have been only resident trout. Genetic structure appears to have been altered by a combination of factors, including habitat fragmentation and hybridization with hatchery trout. Redband trout populations in the desert and montane environments both experienced reduced gene flow, but the desert populations displayed higher degrees of genetic differentiation. There was also a significant inverse relationship between the degree of genetic differentiation and the level of allelic diversity. Interspec.
A nonlinear mixed‐effects modeling approach for ecological data: Using temporal dynamics of vegetation moisture as an example

Abstract Increasingly, often ecologist collects data with nonlinear trends, heterogeneous variances, temporal correlation, and hierarchical structure. Nonlinear mixed‐effects models offer a flexible approach to such data, but the estimation and interpretation of these models present challenges, partly associated with the lack of worked examples in the ecological literature. We illustrate the nonlinear mixed‐effects modeling approach using temporal dynamics of vegetation moisture with field data from northwestern Patagonia. This is a Mediterranean‐type climate region where modeling temporal changes in live fuel moisture content are conceptually relevant (ecological theory) and have practical implications (fire management). We used this approach to answer whether moisture dynamics varies among functional groups and aridity conditions, and compared it with other simpler statistical models. The modeling process is set out “step‐by‐step”: We start translating the ideas about the system dynamics to a statistical model, which is made increasingly complex in order to include different sources of variability and correlation structures. We provide guidelines and R scripts (including a new self‐starting function) that make data analyses reproducible. We also explain how to extract the parameter estimates from the R output. Our modeling approach suggests moisture dynamic to vary between grasses and shrubs, and between grasses facing different aridity conditions. Compared to more classical models, the nonlinear mixed‐effects model showed greater goodness of fit and met statistical assumptions. While the mixed‐effects approach accounts for spatial nesting, temporal dependence, and variance heterogeneity; the nonlinear function allowed to model the seasonal pattern. Parameters of the nonlinear mixed‐effects model reflected relevant ecological processes. From an applied perspective, the model could forecast the time when fuel moisture becomes critical to fire occurrence. Due to the lack of worked examples for nonlinear mixed‐effects models in the literature, our modeling approach could be useful to diverse ecologists dealing with complex data.
EXOTIC MARINE MACROALGAE ON THE BRAZILIAN COAST: A REVISION

The introduction of exotic marine species is a recent concern in Brazil, and seaweeds are the least studied group. The first publications deal with intentional introduction of species for aquaculture. Recent papers focus on putative accidental introductions. In this review we summarize the existing knowledge about the presence of non-indigenous seaweeds on the Brazilian coast. Nevertheless, the labeling of a species as an exotic one can be a complex issue. Kappaphycus alvarezii and K. striatum were the only authorized and well documented intentional introductions in Brazil, aiming to carrageenan production. Caulerpa scalpelliformis , known from a large stretch of the northeast and east Brazilian coast, seems to have spread to Rio de Janeiro state and can be considered as the only invasive species in Brazil so far. Available data indicate that this species is impacting benthic communities on Ilha Grande Bay. In this same region, Laurencia caduciramulosa populations appeared in 2001 and begun to spread. Other introductions are mere suspicions: Anotrichium yagii and Dasya brasiliensis are suspected to be exotic for being conspicuous species not reported previously to well studied areas. Cladophora corallicola, Laurencia venusta, Pedobesia ryukyuensis, Porphyra leucosticta, Porphyra rizzinii and Porphyra suborbiculata , all reported on recent surveys and suspected to be newcomers, should rather be considered as cryptogenic because they may have been overlooked or misidentified on previous surveys.
Market Integration and Efficiency in the Presence of Cross-border Trade Restrictions: Evidence from selected Maize Markets in Southern Africa

This paper investigates pair wise spatial integration and efficiency for central maize markets in three southern African countries: Malawi, Mozambique, and South Africa. The goal is to evaluate the extent to which cross border trade restrictions on maize trade affect market integration and efficiency, vis-a-vis related costs of transfer. We also attempt to establish the most dominant form of efficiency barrier in those markets. The analysis employs the extended parity bounds model (Barrett and Li 2002), supported by non-parametric assessments; and uses monthly wholesale on prices, trade flow, and estimated transfer costs for the period 1996 to 2004. Results reveal significant frequency of market integration between markets in close proximity, regardless of country location, indicating tradability of commodities and contestability of markets across borders. For those markets, however, efficiency appears weak, as trade often fails to exhaust arbitrage profits. We observe inefficiency driven by insufficient arbitrage at least 60% of the time. Occasionally, trade is observed in the presence of negative returns, though at a lower frequency of about 10%. Markets not linked through trade tend to have a higher frequency of efficiency (up to 52%), so that the lack of trade often is justified by the lack of positive arbitrage returns. In those cases, market segmentation appears driven more by restrictive transport costs than cross-border trade barriers. Our results suggest that the dominant forms of inefficiency in the southern African maize markets considered in this study are (1) insufficient arbitrage resulting from supply side constraints and other non-cost barriers to trade, and (2) restrictive transport costs. Border administered tariffs and other forms of taxes on imports seem to account for a relatively low proportion of transfer costs, and generally reduce arbitrage returns marginally.
Fundamentals of Micro‐Manufacturing

During the last decade, there has been a continuing trend of compact, integrated and smaller products such as (i) consumer electronics—cell phones, PDAs (personal digital assistant), etc.; (ii) microand distributed power generators, turbines, fuel cells, heat exchangers [1–4]; (iii) micro-components/features for medical screening and diagnostic chips, controlled drug delivery and cell therapy devices, biochemical sensors, Lab-on-chip systems, stents, etc. [5–8]; (iv) micro-aerial vehicles (MAV) and micro-robots [9–12]; and (v) sensor and actuators [13,14] (Fig. 1.1). This trend requires miniaturization of components from mesoto micro-levels. Currently, micro-electromechanical systems (MEMS), mostly limited to silicon, are widely researched and used for miniaturized systems and components using layered manufacturing techniques such as etching, photolithography, and electrochemical deposition [15,16]. Such techniques are heavily dependent on technologies and processes originally developed for micro-electronics manufacturing. However, MEMS have some limitations and drawbacks in terms of (i) material types (limited to silicon in combination with sputtered and etched thin metallic coatings), (ii) component geometries (limited to 2D and 2.5D), (iii) performance requirements (i.e., types of mechanical motions that can be realized, durability, and strength), and
Predicted gamma-ray line emission from the Cygnus complex

Context. The Cygnus region harbours a huge complex of massive stars at a distance of 1.0–2.0 kpc from us. About 170 O stars are distributed over several OB associations, among which the Cyg OB2 cluster is by far the most important with about 100–120 O stars. These massive stars inject large quantities of radioactive nuclei into the interstellar medium, such as 26 Al and 60 Fe, and their gammaray line decay signals can provide insight into the physics of massive stars and core-collapse supernovae. Aims. Past studies of the nucleosynthesis activity of Cygnus have concluded that the level of 26 Al decay emission as deduced from CGRO/COMPTEL observations was a factor 2–3 above the predictions based on the theoretical yields available at that time and on the observed stellar content of the Cygnus region. We reevaluate the situation from new measurements of the gamma-ray decay fluxes with INTEGRAL/SPI (presented in a previous paper) and new predictions based on recently improved stellar models. Methods. We built a grid of nucleosynthesis yields from recent models of massive stars. Compared to previous works, our data include some of the effects of stellar rotation for the higher mass stars and a coherent estimate of the contribution from SNIb/c. We then developed a population synthesis code to predict the nucleosynthesis activity and corresponding decay fluxes of a given stellar population of massive stars. Results. The observed decay fluxes from the Cygnus complex are found to be consistent with the values predicted by population synthesis at solar metallicity; and yet, when extrapolated to the possible subsolar metallicity of the Cygnus complex, our predictions fail to account for the INTEGRAL/SPI measurements. The observed extent of the 1809 keV emission from Cygnus is found to be consistent with the result of a numerical simulation of the diffusion of 26 Al inside the superbubble blown by Cyg OB2. Conclusions. Our work indicates that the past dilemma regarding the gamma-ray line emission from Cygnus resulted from an overestimate of the 1809 keV flux of the Cygnus complex, combined with an underestimate of the nucleosynthesis yields. Our results illustrate the importance of stellar rotation and SNIb/c in the nucleosynthesis of 26 Al and 60 Fe. The effects of binarity and metallicity
Adolescents’ Computer Mediated Learning and Influences on Interpersonal Relationships

This study reports the findings of the several projects initiated at the Faculty of Education , “Goce Delcev “University , Stip, to investigate the motivation skills, but is uniquely specific to as interpersonal relationships and resources that influence the learner’s participation in the teaching/learning process in the context of online-learning and face to face learning (FtF). Uniquely it also explores e-mail romantic relationships with regard to the levels of relationship satisfaction, intimacy, "inclusion" and interpersonal attraction. Empirical research of this kind is arguably rare and will lead to a better understanding of the possibilities and limitations of a medium that could have large effects on the relationships we have in the lives of participants of computer mediated learning.
Chapter 19 Epiphytes of Seagrasses

In all aquatic environments, available surfaces are rapidly colonized by a variety of organisms. If these organisms grow on plants they are called epiphytes. Seagrasses provide an excellent substratum for epiphytic organisms and these organisms are an integral component of seagrass ecosystems. The ecology and physiology of seagrass epiphytes have been reviewed previously (Harlin, 1980; Borowitzka and Lethbridge, 1989) and this chapter focuses primarily on new developments in our understanding of seagrass epiphyte1 biology and ecology that have occurred since then. Seagrasses grow in a wide range of habitats ranging from the intertidal to depths of over 50 m (Long et al., 1996), from estuarine to marine environments, and from temperate regions to the tropics. The different seagrass genera also show a diversity of morphologies ranging from the simple subulate leaves of Syringodium and the strap-shaped leaves of Cymodocea, Posidonia, Thalassia, and Zostera,
Anatomical Development of the Cerebellothalamic Tract in Embryonic Mice

Cerebellar projections to the thalamus are a pivotal connection in cerebello-cerebral interactions. Apart from its role in coordinating sensorimotor integration in the adult brain, the cerebello-thalamic projection has also been implemented in developmental disorders, such as autism spectrum disorders. Although the development of the cerebellum, thalamus and cerebral cortex have been studied in many species, a detailed description of the ontogeny of the mammalian cerebello-thalamic tract (CbT) is currently missing. Here we investigated the development of the CbT at embryonic stages using transgenic Ntsr1-Cre/Ai14 mice and in utero electroporation (IUE) of wild type mice. Wide-field, confocal and 3D light-sheet imaging of immunohistochemical stainings showed that CbT fibers arrive in the prethalamus between E14.5 and E15.5, but only invade the thalamus after E16.5. We quantified the spread of CbT fibers throughout the various thalamic nuclei and found that at E17.5 and E18.5 the ventrolateral, ventromedial and parafascicular nuclei, but also the mediodorsal and posterior complex become increasingly innervated. Several CbT fiber varicosities colocalize with vGluT2, indicating that already from E18.5 the CbT synapse in various thalamic nuclei. Our results contribute to the construction of a frame of reference on the anatomical development of the CbT, which will help to guide future experiments investigating neurodevelopmental disorders. Significance statement Using various microscopic approaches, we investigated the anatomical development of the fiber tract between the cerebellum and thalamus, one of the major mammalian brain connections. Our results show that in mice cerebellar axons wait outside of the thalamus from embryonic day (E)15.5 until E17.5 before invading the thalamic complex. Cerebellar axons establish vGluT2-positive synapses at E18.5 throughout various thalamic nuclei, each of which subsequently develops its connections with dedicated cerebral cortical regions. Our data thereby advocate the cerebellar influence on the maturation of the thalamus and connected cerebral cortex. This knowledge can help to guide future experiments into neurodevelopmental disorders affecting cerebello-thalamo-cortical networks.
Demographic Expansion and Contraction in a Neotropical Fish during the Late Pleistocene-Holocene

Demographic changes during the late Pleistocene-Holocene left signatures in the DNA of contemporary populations. These signatures reveal demographic phenomena like the increase or decrease in effective population size. In this paper we searched for signatures of demographic change in the DNA of the Neotropical freshwater fish Poecilia vivipara. Also, we investigated whether demographic changes are correlated with palaeoclimatic events of the late Pleistocene-Holocene, in particular, if changes in effective population size are correlated with expansion and contraction of available habitats, induced by global ice-volume changes and sea-level fluctuations. We used Bayesian Skyline Plot (BSP) analysis with sequences from the mitochondrial gene cytochrome b to estimate the ancestral demography of the Neotropical freshwater fish P. vivipara. To test the assumptions of neutrality and absence of population structure we used Tajima’s D and Spatial Analysis of Molecular Variance (SAMOVA), respectively. Effective population size of P. vivipara remained stable until 75,000 years ago, increased by 10-fold reaching a maximum at approximately 25,000 years ago, then suddenly declined at the Pleistocene-Holocene boundary. Variation in effective population size in P. vivipara correlates with expansion and contraction of habitats induced by sea-level fluctuations, caused by the advance and retreat of ice sheets during the Last Glacial Maximum (LGM).
Determinants of capital structure: Evidence from the listed firms in the Netherlands

The paper contributes to the capital structure by investigating the determinants of companies from static trade-off theory and pecking order theory through providing the empirical evidence from listed firms in the Netherlands. The study use OLS regression in analysing the factors that influence capital structure decisions. The results suggest that liquidity served as a negative factor in capital structure decisions and pecking order theory prevails in explanation of capital structure determinants in Dutch firms.
Simple Additive Weighting Method in the Development of a System Assessing the Feasibility of Job Training Industry.

: The activities of the job training is an activity that must be implemented at Vocational Secondary School. To increase competence skills learners in the workforce, then the school must choose many places of the job training industry by the respective expertise of program participants. Therefore it is necessary that information systems can assist the school in selecting the job training industry by producing the decision support to determine the feasibility of the job training industry for use in the following period. The feasibility of job training industry that is purposed in this research is determined by the alignment of competency expertise on the job training industry with the program expertise of participants and other supporting criteria. That system is called “Sistem Pendukung Keputusan Kelayakan Tempat Praktik Kerja Industri (SPK-KTP)” or System Assessing The Feasibility of Job Training Industry. In decision-making, this system used the method of Simple Additive Weighting (SAW). In addition, the system is also equipped with features to manage the administrative activities of the job training industry, to recap the daily journal, and to recap the supervising report. SPK-KTP is the web-based information system which it is developed using the programming language PHP (Hypertext Preprocessor). System development method that used in the information system is Waterfall Model. The steps of Waterfall Model consist of analysis, design, code, and test. SPK-KTP has done testing to an expert of the information system with value 90,7%, an expert of the job training substance with value 91,6%, supervising teachers with value 83,3%, and learners with value 90,6%. Based on the result, so SPK-KTP is very feasible to use.
Population genetics of Bull Trout (Salvelinus confluentus) in the upper Athabasca River basin

Across its native range, Bull Trout (Salvelinus confluentus) extent and abundance are in decline due to historic overharvest and habitat degradation. Because Bull Trout are dependent on extensively connected, cold, clean headwater habitats, fragmentation from land use changes causes difficulty when determining the true extent and health of their populations, with Bull Trout of Alberta’s Eastern Slope region being no exception. Across this region, 431 Bull Trout from 20 sites were sampled from the Athabasca and Saskatchewan River basins and compared using 10 microsatellite loci to characterize within- and among-population genetic variation. The Saskatchewan and Athabasca River basins contained similar levels of heterozygosity but were differentiated from one another. Within the Athabasca River basin, five genetically differentiated clusters were found. Additionally, no isolation-by-distance pattern was observed between these sites. These results suggest these populations have ample genetic diversity, but genetic differentiation should be considered when deciding whether and how to alter connectivity between populations.