Miracle-dz/UniFAR-FTUs huggingface dataset:
A mitochondrial genetic divergence proxy predicts the reproductive 1 compatibility of mammalian hybrids 2

Despite the significant genetic barriers that arise during the process of reproductive 35 isolation between species, numerous hybrid offspring of divergent mammalian 36 species pairs have been catalogued. In some cases, these hybrids are only able to 37 produce offspring through backcrosses with a parent species due to unisexual 38 sterility (Haldane’s Rule). In other instances, F1 hybrids are able to produce F2s 39 through matings with F1s. Here, we explicitly tested whether genetic distance can be 40 used as a proxy to predict the relative fertility of the hybrid offspring resulting from 41 numerous pairs of terrestrial mammals. We assessed the proxy’s predictive power 42 using a well characterised felid hybrid system, and applied it to modern and ancient 43 hominins. Our results revealed a small overlap in mitochondrial genetic divergence 44 values that distinguish species pairs whose divergence values fall within two 45 categories: those whose hybrid offspring follow Haldane’s Rule, and those whose 46 hybrid offspring can produce F2s. The strong correlation between genetic distance 47 and hybrid fertility demonstrated here suggests that this proxy can be employed to 48 predict whether the hybrid offspring of two mammalian species will follow Haldane’s 49 Rule. 50
Seabird ecology in relation to fisheries

Previous research has hinted at changes in the migratory patterns of seabirds nesting in Scotland, including a decreasing number of Northern Gannets Morus bassanus wintering in the North Sea, and an increase in numbers of Northern Gannets and Great Skuas Stercorarius skua spending the winter off north-western Africa (NWA). Both species show increasing numbers of colonies in northern areas, including Norway and Russia. These seabird species move through the North Sea during autumn migration, and from there search for favourable wintering grounds mainly around Iberia, including the Atlantic coast of Portugal, the Bay of Biscay and the Gulf of Cadiz. By means of historic ring recovery data, provided by the British Trust for Ornithology, it was possible to establish that the number of records of adults of both species are increasing in recent years from NWA coasts, despite having to attend their nests in the colonies and, as a result, having limited time to migrate south. Differences were observed in ring recovery locations between years and months. The number of ring recoveries by month coincides with records from observation points along the coast of Western Europe. However, ring recovery data are limited and potentially biased. Using data loggers, it was possible to establish that both species are diurnal in habits during the entire winter period, showing noticeable differences in the times spent flying during the migration months (September-October) and during the wintering and breeding months (January and March respectively), and to confirm the increasing tendency to winter off NWA in recent years. Analyses of fishing landings, discard rates, and sea surface temperature data, show that food available to Northern Gannets and Great Skuas is increasing in NWA coasts where oceanographic conditions are stable; in contrast in the North Sea fisheries are decreasing and the sea surface is warming. Both species are apparently changing their migratory behaviour in order to face the constant changes in the abundance of food. Given the long life-span of Northern Gannets and Great Skuas, genetic changes can be ruled out of an explanation for the changes in migration behaviour, and the fact that the changes in winter distribution appear to be occurring within one generation of the birds. The winter distribution of Northern Gannets and Great Skuas may be due to an ideal free distribution over a wide range, in response to changes in the distribution of fish and the availability of discards.
Title: Use of Evolved Artificial Regulatory Networks to Simulate 3d Cell Differentiation Use of Evolved Artificial Regulatory Networks to Simulate 3d Cell Differentiation

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Abstract Cell differentiation has a crucial role in both artificial and natural development. This paper presents results from simulations in which a genetic algorithm (GA) was used to evolve artificial regulatory networks (ARNs) to produce predefined 3D cellular structures through the selective activation and inhibition of genes. The ARNs used in this work are extensions of a model previously used to create 2D geometrical patterns. The GA worked by evolving the gene regulatory networks that were used to control cell reproduction, which took place in a testbed based on cellular automata (CA). After the final chromosomes were produced, a single cell in the middle of the CA lattice was allowed to replicate controlled by the ARN found by the GA, until the desired cellular structures were formed. Two simple cubic layered structures were first developed to test multiple gene synchronization. The model was then applied to the problem of generating a 3D French flag pattern using morphogenetic gradients to provide cells with positional information that constrained cellular replication.
The Australian Government's environmental impact assessment (EIA) regime: using surveys to identify proponent views on cost-effectiveness

The Australian Government introduced a new project-based EIA regime in July 2000. Since its introduction, there has been a robust debate about its environmental effectiveness. To add to this debate, a survey was conducted of proponents of projects that were regulated under the regime between 16 July 2000 and 10 June 2009. The survey sought proponents' views on whether the regime improved the environmental outcomes of regulated actions and the costs they incurred in relation to the process. This article outlines the method applied in conducting the survey and presents key results. It also discusses the methodological issues associated with EIA cost-effectiveness studies. The results suggest that proponents believe the federal EIA regime is environmentally ineffective, producing significant improvements in environmental outcomes in only 11% of cases. The information supplied by respondents also suggests that average proponent costs were high, ranging between AU$130,000 and AU$2,230,000 per regulated action.
Preparation and characterization of konjac glucomannan (KGM) and deacetylated KGM (Da-KGM) obtained by sonication.

BACKGROUND Konjac glucomannan (KGM) has been widely applied in food industry as thickening and gelation agent due to its unique colloidal properties of viscosity enhancement and gelling ability. The current study was aimed to prepare and characterize KGM and deacetylated KGM (Da-KGM) samples obtained by sonication in neutral and alkali ethanol-water solutions. RESULTS The results showed that the deacetylation degree (DD) of Da-KGM increased exponentially with alkali concentration. Fourier transform infrared spectra (FTIR) spectra further confirmed deacetylation reaction through the dramatic decrease in the acetyl group band at 1740 cm-1 . Besides, the high similarity among the tested groups in terms of X-ray diffraction (XRD) spectra implied a similar crystalline structure, while differential scanning calorimetry (DSC) curves revealed that the water binding capacity and decomposition temperature of KGM changed slightly with alkali and sonication treatment. The rheological profiles indicated that apparent viscosity (η0 ) of sonicated KGM samples was unchanged except for the T60 group (60 min sonication treatment). Particularly, ultrasonic treatment at high alkaline conditions (0.10 mol/L NaOH) was noted to promote deacetylation reaction, and the obtained samples showed decreased apparent viscosity and weakened the gelation process in aqueous solution. Partial correction analysis indicated that alkali rather than ultrasonic treatment resulted in the change of DD and η0 in Da-KGM. Moreover, sonication contributed to off-white color by reducing the browning caused by alkali in Da-KGM products. CONCLUSION Ultrasound-mediated heterogeneous deacetylation reaction is a feasible way to prepare Da-KGM samples with lightened browning and controllable DD. This article is protected by copyright. All rights reserved.
Multitemporal spectral analysis for cheatgrass (Bromus tectorum) classification

Operational satellite remote sensing data can provide the temporal repeatability necessary to capture phenological differences among species. This study develops a multitemporal stacking method coupled with spectral analysis for extracting information from Landsat imagery to provide species‐level information. Temporal stacking can, in an approximate mathematical sense, effectively increase the ‘spectral’ resolution of the system by adding spectral bands of several multitemporal images. As a demonstration, multitemporal linear spectral unmixing is used to successfully delineate cheatgrass (Bromus tectorum) from soil and surrounding vegetation (77% overall accuracy). This invasive plant is an ideal target for exploring multitemporal methods because of its phenological differences with other vegetation in early spring and, to a lesser degree, in late summer. The techniques developed in this work are directly applicable for other targets with temporally unique spectral differences.
Sandstone porosity related to vitrinite reflectance

Vitrinite reflectance (VR) and the volume fraction of quartz cement in sandstones are both measures of thermal exposure. This paper shows how porosity reduction by quartz cementation can be related to VR for heating at a constant rate, using simple models for quartz cementation and VR. This relationship reveals that the heating rate is an explicit parameter, which means that there is no pure relationship between porosity (volume fraction quartz cement) and VR. However, the rate of quartz cementation and the rate of change of TTI (time–temperature integral) have a close exponential dependence on temperature. Porosity reduction by quartz cementation as a function of VR therefore nearly follows the same curve for very different temperature histories. This property of porosity reduction by quartz cementation is used to calibrate average specific surface parameters as a function of porosity. The calibration procedure is demonstrated on two datasets, where the average specific surface depends on porosity to the power of an exponent that is somewhat greater than 3.
The contact between the Higher Himalaya Crystallines and the Tibetan Sedimentary Series: Miocene large‐scale dextral shearing

Space and time evolution of the synmetamorphic structures across the metamorphic pile have been studied in several areas along the Himalayan belt (east and central Nepal, Garhwal, Zanskar). From one area to the other the evolution is very similar: (1) At the base of the pile, in the Main Central Thrust (MCT) shear zone, the stretching lineation, penetrative and regularly oriented N0°E to N30°E, indicates the MCT transport direction, very constant all along the belt, from the Eohimalayan main metamorphic development up to the late-metamorphic movements. (2) At the top of the pile, at the contact between the crystalline unit and its sedimentary cover, gravity-driven structures are confirmed (north-vergent folds, ductile normal faulting). However, there are numerous local indications of late Miocene (syn- to late emplacement of the leucogranitic plutons) dextral shearing. (3) In between, across the medium part of the pile, the stretching lineation shows a conspicuous progressive regional clockwise rotation, clearly indicated by the strain trajectories mapped in Nepal and Garhwal. Points 1 and 2 show that the crystalline-sedimentary boundary, despite its apparent structural and metamorphic continuity, is not only a normal fault but also an important dextral shear zone, which has acted since the upper Miocene as the main southern limit of the eastward extruding Tibetan block.
The utility of De Ritis Ratio in predicting prognosis in testicular cancer

Abstract Objective We aimed to investigate the possible association between testicular cancer prognosis and De Ritis ratio (AST/ALT). Methods The medical records of all patients who underwent radical inguinal orchiectomy at a single tertiary in Istanbul, Turkey between 2006 and 2017 were retrospectively analyzed. Investigated parameters included patients’ demographics, complete blood count and blood biochemistry results, pathology results, treatment schemes, imaging results, and survival. De Ritis ratio was calculated as follows: AST/ALT. Results A total of 171 patients with a mean age of 32.6 ± 10.1 years were included in the study. 73 patients had T1, 83 had T2, 13 had T3 and 2 had T4 disease. Rete testis invasion was detected in 74 patients (43.3 %) as well as lymphovascular invasion in 93 (54.4 %) and tunica albuginea invasion in 80 (46.8 %) patients. The cut-off value for AST/ALT was set at 1.35 [Area Under Curve (AUC): 0.791 with a sensitivity of 80 % and specificity of 73 %]. No statistically significance was observed between patients with and without elevated AST/ALT according to rete testis invasion, lymphovascular invasion, tunica albuginea invasion, and tunica vaginalis invasion (p = .25, p = .63, p = 1.0 and p = 1.0, respectively). 28.2 % of patients with seminoma had AST/ALT > 1.35 however 41.9 % of patients with non-seminoma pathology had AST/ALT > 1.35 (p = .078). Mean estimated survival time of patients with AST/ALT > 1.35 was higher than those with AST/ALT < 1.35, 91.8 versus 70.4 months, p < . 001). As seen in Kaplan-Meier analysis elevated AST/ALT is associated with early-term mortality. Conclusion De Ritis ratio was shown to be significantly associated with unfavorable prognosis. De Ritis ratio might serve as a prognostic biomarker in testicular tumor besides well-known tumor markers such as beta-human chorionic gonadotropin (hCG), alpha-fetoprotein (AFP) and lactate dehydrogenase (LDH).
How sea lice from salmon farms may cause wild salmonid declines in Europe and North America and be a threat to fishes elsewhere

Fishes farmed in sea pens may become infested by parasites from wild fishes and in turn become point sources for parasites. Sea lice, copepods of the family Caligidae, are the best-studied example of this risk. Sea lice are the most significant parasitic pathogen in salmon farming in Europe and the Americas, are estimated to cost the world industry €300 million a year and may also be pathogenic to wild fishes under natural conditions. Epizootics, characteristically dominated by juvenile (copepodite and chalimus) stages, have repeatedly occurred on juvenile wild salmonids in areas where farms have sea lice infestations, but have not been recorded elsewhere. This paper synthesizes the literature, including modelling studies, to provide an understanding of how one species, the salmon louse, Lepeophtheirus salmonis, can infest wild salmonids from farm sources. Three-dimensional hydrographic models predicted the distribution of the planktonic salmon lice larvae best when they accounted for wind-driven surface currents and larval behaviour. Caligus species can also cause problems on farms and transfer from farms to wild fishes, and this genus is cosmopolitan. Sea lice thus threaten finfish farming worldwide, but with the possible exception of L. salmonis, their host relationships and transmission adaptations are unknown. The increasing evidence that lice from farms can be a significant cause of mortality on nearby wild fish populations provides an additional challenge to controlling lice on the farms and also raises conservation, economic and political issues about how to balance aquaculture and fisheries resource management.
Empresas de Base Cultural y Creativa: Identificación y Clasificación de sus Factores Críticos de Desempeño (Culture and creative based companies: identifying and classifying their critical performance factors)

El sector de las industrias culturales y creativas ha venido generando un interes creciente en la economia productiva; es por esto que la relacion entre economia y cultura ocupa hoy un lugar predominante, especialmente por las altas inversiones que esta industria requiere, aunadas a las significativas ganancias que reporta. Este articulo es el resultado de un estudio realizado por la Universidad EAFIT sobre el mencionado sector, y responde a la necesidad de conocer mejor el emprendimiento en industrias que se caracterizan por conjugar la creatividad y la cultura. El estudio permitio identificar los factores criticos de desempeno que hacen que estas industrias sean viables y cumplan sus objetivos. Los resultados sirven como referente para desarrollar un marco conceptual y pedagogico dirigido, en principio, a la formacion de profesionales en el campo de las empresas culturales y creativas, y se suma a los estudios que se han conducido y continuan haciendose alrededor de este particular sector del emprendimiento empresarial. ABSTRACTThe culture and creative industry sector has generated a growing interest into productive economies; thus the relationship between economy and culture is highly regarded today due to the high investment required and the high yields resulting from this sector. This paper resulted from a research by the EAFIT university about this sector and answers the need to better known entrepreneurship in industries based in both creativity and culture. We were able to identify critical performance factors that made these industries viable and reach their goals. Results can be used to develop a conceptual and pedagogical frame to form professionals able to work in them, and also adds to previous and ongoing knowledge developed for this particular entrepreneurial sector.
Developing a computationally efficient dynamic multilevel hybrid optimization scheme using multifidelity model interactions.

Many engineering application problems use optimization algorithms in conjunction with numerical simulators to search for solutions. The formulation of relevant objective functions and constraints dictate possible optimization algorithms. Often, a gradient based approach is not possible since objective functions and constraints can be nonlinear, nonconvex, non-differentiable, or even discontinuous and the simulations involved can be computationally expensive. Moreover, computational efficiency and accuracy are desirable and also influence the choice of solution method. With the advent and increasing availability of massively parallel computers, computational speed has increased tremendously. Unfortunately, the numerical and model complexities of many problems still demand significant computational resources. Moreover, in optimization, these expenses can be a limiting factor since obtaining solutions often requires the completion of numerous computationally intensive simulations. Therefore, we propose a multifidelity optimization algorithm (MFO) designed to improve the computational efficiency of an optimization method for a wide range of applications. In developing the MFO algorithm, we take advantage of the interactions between multi fidelity models to develop a dynamic and computational time saving optimization algorithm. First, a direct search method is applied to the high fidelity model over a reduced design space. In conjunction with this search, a specialized oracle is employed to more » map the design space of this high fidelity model to that of a computationally cheaper low fidelity model using space mapping techniques. Then, in the low fidelity space, an optimum is obtained using gradient or non-gradient based optimization, and it is mapped back to the high fidelity space. In this paper, we describe the theory and implementation details of our MFO algorithm. We also demonstrate our MFO method on some example problems and on two applications: earth penetrators and groundwater remediation. « less
Uniform processes of melt differentiation in the central Izu Bonin volcanic arc (NW Pacific)

Abstract The intra-oceanic Izu Bonin arc (NW Pacific) has produced a bimodal spectrum of melts with maxima in the basaltic andesitic (c. 53–54 wt% SiO2) and rhyolitic range (c. 70–72 wt% SiO2) since arc inception c. 48–49 million years ago. Composition of phenocrysts and accessory minerals from 21 contemporaneous fallout tephras from ODP Site 782A confirm the bimodality and uniformity of the erupted melts. The basaltic andesite melts equilibrated with calcic plagioclase (c. An70–95), high-Mg# clino- and orthopyroxene and low-Ti titanomagnetite. Dacitic and rhyolitic melts crystallized sodic plagioclase (c. An40–60), low-Mg# clino- and orthopyroxene, apatite, Ti-rich titanomagnetite in addition to occasional ilmenite and amphibole. The Izu melts are inferred to crystallize at oxygen fugacities between c. 0 to +2.5 log10 units relative to FMQ, at temperatures between c. 775° and 1100 °C and at pressures between c. 300 and c. 1100 MPa, corresponding to c. 5–35 km lithospheric depth. The compositional uniformity of the tephra layers, which are spaced on average 230 ± 380 ka apart, suggest uniform processes of differentiation since at least c. 42 Ma ago. The tephra record shows no indication of periodic or progressive crustal growth that might correlate with the alternate periods of arc formation, arc rifting or backarc spreading, or would suggest an increasingly efficient ‘crustal filter’ with time. The tephra data tentatively conform to a model where crust grows steadily through intrusions of mafic and evolved melt body batches whereby buoyancy controls the level of solidification. While the tephra compositions demonstrate the uniformity of the processes of melt formation and differentiation through time, the data do not permit the differentiation processes themselves to be constrained. These may comprise fractional crystallization, crustal fusion, fusion of non-peridotitic sub-crustal lithologies, or any combination of these processes.
Reprogramming of human fibroblasts toward a cardiac fate

Reprogramming of mouse fibroblasts toward a myocardial cell fate by forced expression of cardiac transcription factors or microRNAs has recently been demonstrated. The potential clinical applicability of these findings is based on the minimal regenerative potential of the adult human heart and the limited availability of human heart tissue. An initial but mandatory step toward clinical application of this approach is to establish conditions for conversion of adult human fibroblasts to a cardiac phenotype. Toward this goal, we sought to determine the optimal combination of factors necessary and sufficient for direct myocardial reprogramming of human fibroblasts. Here we show that four human cardiac transcription factors, including GATA binding protein 4, Hand2, T-box5, and myocardin, and two microRNAs, miR-1 and miR-133, activated cardiac marker expression in neonatal and adult human fibroblasts. After maintenance in culture for 4–11 wk, human fibroblasts reprogrammed with these proteins and microRNAs displayed sarcomere-like structures and calcium transients, and a small subset of such cells exhibited spontaneous contractility. These phenotypic changes were accompanied by expression of a broad range of cardiac genes and suppression of nonmyocyte genes. These findings indicate that human fibroblasts can be reprogrammed to cardiac-like myocytes by forced expression of cardiac transcription factors with muscle-specific microRNAs and represent a step toward possible therapeutic application of this reprogramming approach.