Miracle-dz/UniFAR-FTUs huggingface dataset:
The unfolding of iRFP713 in a crowded milieu

The exploring of biological processes in vitro under conditions of macromolecular crowding is a way to achieve an understanding of how these processes occur in vivo. In this work, we study the unfolding of the fluorescent probe iRFP713 in crowded environment in vitro. Previously, we showed that the unfolding of the dimeric iRFP713 is accompanied by the formation of a compact monomer and an intermediate state of the protein. In the intermediate state, the macromolecules of iRFP713 have hydrophobic clusters exposed to the surface of the protein and are prone to aggregation. Concentrated solutions of polyethylene glycol (PEG-8000), Dextran-40 and Dextran-70 with a molecular mass of 8000, 40000 and 70000 Da, respectively, were used to model the conditions for macromolecular crowding. A limited available space provided by all the crowding agents used favors to the enhanced aggregation of iRFP713 in the intermediate state at the concentration of guanidine hydrochloride (GdnHCl), at which the charge of protein surface is neutralized by the guanidine cations. This is in line with the theory of the excluded volume. In concentrated solutions of the crowding agents (240–300 mg/ml), the stabilization of the structure of iRFP713 in the intermediate state is observed. PEG-8000 also enhances the stability of iRFP713 in the monomeric compact state, whereas in concentrated solutions of Dextran-40 and Dextran-70 the resistance of the protein in the monomeric state against GdnHCl-induced unfolding decreases. The obtained data argues for the excluded volume effect being not the only factor that contributes the behavior of biological molecules in a crowded milieu. Crowding agents do not affect the structure of the native dimer of iRFP713, which excludes the direct interactions between the target protein and the crowding agents. PEGs of different molecular mass and Dextran-40/Dextran-70 are known to influence the solvent properties of water. The solvent dipolarity/polarizability and basicity/acidity in aqueous solutions of these crowding agents vary in different ways. The change of the solvent properties in aqueous solutions of crowding agents might impact the functioning of a target protein.
ARGUING OVER [THE] REMOTE CONTROL: WHY INDIGENOUS POLICY NEEDS TO BE BASED ON EVIDENCE AND NOT HYPERBOLE

Recent public debate on Indigenous issues has been provoked, inter alia, by a 2005 Centre for Independent Studies paper by Helen Hughes and Jenness Warin, who focused on the extent to which policies have been effective in improving the living conditions of Indigenous Australians since the era of self-determination commenced. Unfortunately, the quality of historical data is questionable, and hence we need an appreciation of the reliability of estimates. The 2002 National Aboriginal and Torres Strait Islander Social Survey allows a detailed interrogation of the reliability of estimates. This paper critically analyses socioeconomic changes between 1994 and 2002 for remote and other areas by comparing the recent data with analogous data collected in 1994. Changes in health status and a range of socio-economic indicators are documented to provide a more balanced assessment of the level of economic and social development in the respective areas.
Monitoring and modeling land subsidence at the Cerro Prieto Geothermal Field, Baja California, Mexico, using SAR interferometry

Images derived from repeat‐pass spaceborne interferometric synthetic aperture radar (InSAR) systems offer the possibility of mapping surface deformation of small spatial extent and monitoring its spatio‐temporal evolution. A slow local subsidence has been detected at the Cerro Prieto geothermal field from images acquired by the European Space Agency remote sensing satellites ERS‐1/2 between 1993 and 1997. Although agricultural activity in the area limited the investigation, interferometric monitoring revealed that the ground deformation is associated with the withdrawal of geothermal fluid and agreed with the leveling data. Modeling of the subsidence was carried out assuming elastic deformation in a half‐space from simple point sources, of which five were necessary to reproduce the fringe patterns observed on the interferograms. The depths and locations of three of the sources are compatible with the location of the known reservoir. The study improves prior knowledge of the displacement field and of the mecanisms involved in the subsidence phenomenon.
Avaliação da diversidade genética entre acessos de mamoneira (Ricinus communis L.) por meio de caracteres morfoagronômicos

Genetic divergence is one of the most important breeding parameters evaluated in the initial phase of a genetic improvement program. The objective of this work was to characterize 15 accessions of castor bean using morphoagronomic traits. The trial was carried out in Lavras, MG, Brazil, from February to August 2008. The experimental design was a randomized complete block design with three replicates and 25 plants per plot. The traits evaluated were: plant height (cm), stem height (cm), number of nodes, diameter of stem and number of clusters. Significant differences (F test: P < 0.01) were found for accession effects on all studied traits. Genetic distances among accessions were estimated using the Euclidean method. Four distinct groups were formed using the methods of Tocher and the hierarchical nearest neighbor clustering, based on the Euclidean distance. The results of this work indicate crossings between accessions from groups I and IV, II and IV and III and IV.
Working Group on Development and Environment in the Americas

The Working Group on Development and Environment in the Americas, founded in 2004 under the initiative of the Global Development and Environment Institute at Tufts University, brings together economic researchers from several countries in the Americas who have carried out empirical studies of the social and environmental impacts of economic liberalization. The Working Group's goal is to contribute empirical research and policy analysis to the ongoing policy debates on national economic development strategies and international trade. The Working Group has completed three projects, with associated policy reports and books, most in Spanish, English, and Portuguese: Executive Summary Ownership matters when it comes to Chinese overseas foreign direct investment (OFDI) in Latin America and the Caribbean (LAC) during 2000-2011. Chinese OFDI is a new global trend that will continue to increase by leaps and bounds into the future. How will economies respond to this profound and aggressive investment growth in the future? Will laissez-faire, protectionism or ignorance prevail? No country in the world neither China itself, nor the US or Mexico will be able to isolate itself from this global trend. Do we understand the source and characteristics of Chinese OFDI? Despite the burgeoning amount of new research on the China-Latin America relationship, there have been few concrete studies on China's OFDI. This paper helps to fill that gap and finds that China's OFDI is qualitatively different than the rest of foreign direct investment (FDI) in the region. In recent history, there is no single country that has undergone such a profound level of structural change as China from massive capital importer to a capital exporter. China's OFDI shows additional characteristics that are different to the rest of the world's FDI: there are a group of state-run institutions – from the central government down to local institutions-that provide catalogues and guidelines that allow or reject for products, processes and specific OFDI from the private and public sectors. Thus, OFDI in China is not permitted unless given approval by powerful public institutions such as the National Development and Reform Commission, among several others. This in part explains why China has the largest share state-owned transnational enterprises-26.7 percent of total public FDI in 2010-in contrast to most of the world's FDI. This analysis focuses on China's OFDI in Latin America during 2000-2011, and concludes that Latin America and the Caribbean (LAC) has become the second largest recipient of Chinese OFDI during this period. …
Dexterous In-hand Manipulation by Guiding Exploration with Simple Sub-skill Controllers

Recently, reinforcement learning has led to dexterous manipulation skills of increasing complexity. Nonetheless, learning these skills in simulation still exhibits poor sample-efficiency which stems from the fact these skills are learned from scratch without the benefit of any domain expertise. In this work, we aim to improve the sample efficiency of learning dexterous in-hand manipulation skills using controllers available via domain knowledge. To this end, we design simple sub-skill controllers and demonstrate improved sample efficiency using a framework that guides exploration toward relevant state space by following actions from these controllers. We are the first to demonstrate learning hard-to-explore finger-gaiting in-hand manipulation skills without the use of an exploratory reset distribution. Video results can be found at https://roamlab.github. io/vge
Variation of orbital features in adapine skulls

Abstract Variations of orbital features (orbital diameter, frontation, convergence, and interorbital breadth) in Adapis and Leptadapis are compared to those of living primate species. Adapis shows more variation in orbital diameter and orbital frontation than do living primate species, whereas Leptadapis shows greater variation in convergence, and particularly much greater variation in interorbital breadth than do living primates. Variation in orbital features does prove that the samples are heterogeneous, but does not allow separation into specific groups. However, interorbital breadth is the only feature which allows the Leptadapis sample to be separated into two groups which probably represent two distinct Leptadapis lineages. When allometric effects are taken into account, Leptadapis has relatively larger orbits, weaker frontation and weaker orbital convergence than Adapis . Since these features distinguish different genera, and even different families in living species, these marked differences support the retention of two separate genera for Adapis and Leptadapis. Adapis has an unusually small orbit size for a primate. Since all living primate species have relatively much larger orbits, Adapis is likely to have reduced its orbits from an adapine ancestor. Adapines have less frontation than living lemuriform species (their eyes were oriented more upwardly), but have greater convergence than living lemuroids (lemurids and indriids). This high convergence, an advanced feature, shows that they were very visually oriented animals. Skulls of Adapis (and some Leptadapis) also have smaller interorbital breadths than living lemuroid species.
The plasma sheet boundary layer

The plasma sheet boundary layer is a temporally variable transition region located between the magnetotail lobes and the central plasma sheet. We have made a survey of these regions by using particle spectra and three-dimensional velocity-space distributions sampled by the ISEE 1 LEPEDEA. Ion composition measurements obtained by the Lockheed ion mass spectrometers indicate that ionospheric ions play a crucial role in magnetotail dynamics. Eleven crossings from the lobes to the central plasma sheet taken at various local times and levels of geomagnetic activity are analyzed in detail. The average ratios of He+/H+, He++/H+, and O+/H+ are not significantly different between the plasma sheet boundary layer and central plasma sheet. Densities and temperatures intermediate between the central plasma sheet and lobes are observed in the plasma sheet boundary layer although bulk flow speeds there are typically enhanced. Counter-streaming ion beams are often observed in the plasma sheet boundary layer at energies of ∼1 keV/q to >45 keV/q. Intense antisunward-flowing beams of ionospheric origin at E/q of <1 kV are often seen in the tail lobes, the plasma sheet boundary layer, and, infrequently, in the central plasma sheet. Such beams are not commonly observed in the central plasma sheet, which is characterized by hotter and more isotropic ion and electron distributions. Our samples of ion distributions in the plasma sheet boundary layer frequently show an evolution of distribution functions from highly anisotropic single beams or counter-streaming beams toward the more isotropic distributions typical of the hot component of the central plasma sheet. Provided that the acceleration process for these beams can be identified, we can then account for the transport and injection of hot plasma into the central plasma sheet. We conclude that the plasma sheet boundary layer is a primary transport region of the magnetotail.
Pyrenophora tritici-repentis: A Worldwide Threat to Wheat

The necrotrophic fungus Pyrenophora tritici-repentis is the causal agent of tan spot of wheat, also known as yellow spot. Tan spot is one of the main foliar diseases of wheat, responsible for significant yield loss worldwide. To improve tan spot management, genetic control has been investigated and resistance in some cultivars improved; however, the complexity of the pathosystem wheat P. tritici-repentis makes integrated disease management strategies very important. In this chapter, we provide an overview of the current state of knowledge of tan spot, including a basic understanding of characterization, pathogenicity, population biology, the global distribution of races, and the genetics of the wheat P. tritici-repentis interaction. Furthermore, we describe several strategies that can be employed to control tan spot including, seed sanitation, cultural practices, fungicide and biological controls, as well as complementary alternative measures such as fertilization for efficient disease management in wheat production systems.
THREE-DIMENSIONAL COMPUTATION OF FLOW AROUND GROYNE

The three-dimensional (3D) numerical simulation of a steady, shallow turbulent flow around a groyne in a rectangular channel is presented. A method used to track a moving surface boundary and to follow its evolution, using a one-phase 3D Reynolds solver with rigid grids, by means of a transient fraction of fluid or “porosity” field is applied. Some results are compared with experimental data, such as the isolines of water depths and the mean velocity field. A comparison of the reattachment length prediction using the free-surface model and the rigid-lid assumption is given. Other results concerning the pressure field, turbulence, or shear stress distribution are presented and analyzed.
A vision based people tracking and following for mobile robots using CAMSHIFT and KLT feature tracker

Many mobile robot navigation methods utilize laser scanners, ultrasonic sensors, vision camera, and so on for detecting obstacles and path following. However, human utilizes only vision(e.g. eye) information for navigation. In this paper, we study a mobile robot control method based on only the camera vision. The Gaussian Mixture Model and a shadow removal technology are used to divide the foreground and the background from the camera image. The mobile robot uses a combined CAMSHIFT and KLT feature tracker algorithms based on the information of the foreground to follow a person. The algorithm is verified by experiments where a person is tracked and followed by a robot in a hallway.
Controls on magmatism in the Munster Basin, SW Ireland

Abstract The following paper is intended as a review of the magmatism in the Munster Basin and an initial attempt to link it with the basin’s history. During the initiation, evolution and inversion of the Devono-Carboniferous Munster Basin magmatic activity was widespread, although small in volume. The episodic occurrence and diversity of the magmatism gives insights into the basement involvement and structural controls relating to the basin’s history. The differences in composition, location and structural relationship of the magmatic bodies are used as indicators for the timing of their emplacement and their relationship to the basin’s evolution. On the western Beara Peninsula in SW Ireland alone, more than 160 sheet-like intrusions, a wide variety of tuff bands and a deep-seated pipe-like structure of lamprophyric affinity occur. Other centres of magmatism in the basin are the Lough Guitane area, where rhyolitic lava flows and acidic pyroclastic rocks are associated with contemporaneous basin faults, and the Valentia Harbour area, where doleritic sills are associated with a volcanic breccia. A rhyodacitic tuff can be traced as far as St Finan’s Bay on the western shore of the Iveragh Peninsula. The chemical composition of the extrusive and intrusive magmatic bodies ranges from tholeiitic dolerites (Valentia Harbour) and subalkaline rhyolites (Lough Guitane) in Mid-Devonian time to subalkaline basalts and tuffs (e.g. Beara Peninsula) in Late Devonian time. In Late Carboniferous and possibly Permian time alkali basalts, trachytes and phonolites (e.g. Beara Peninsula) occur. The igneous activity in the Munster Basin is linked to the basin’s history by the interaction between active faults and fractures opening up during various stages of stress imposed on the basin and exploitation of these faults and fractures by rising magma.
Application of nonequilibrium fracture matrix model in simulating reactive contaminant transport through fractured porous media

Nonequilibrium and nonlinear sorption of the contaminants in the fractured porous media could significantly influence the shape of the breakthrough curve (BTC). For the fracture‐matrix system, there are very few studies which consider these processes. In this study, the nonequilibrium fracture‐matrix model with two different nonlinear sorption isotherms, namely nonlinear Freundlich and Langmuir sorption isotherms were developed. The effect of sorption nonlinearity and nonequilibrium conditions on the shape of the BTC was studied using the temporal moments. The developed models along with the linear equilibrium, linear nonequilibrium fracture matrix models, and the multirate mass transfer model were used to simulate the BTC, which were compared with the experimental data available in the literature. Both sorption nonequilibrium and nonlinearity were found to significantly influence the shape of the BTC. Presence of sorption nonlinearity reduces the solute spreading, whereas presence of nonequilibrium conditions increases the solute spreading. Considering the sorption nonequilibrium along with the sorption nonlinearity leads to an improved simulation of the BTC. The nonequilibrium nonlinear sorption models could simulate the extended BTC tailing resulting from sorption nonlinearity and rate‐limited interaction in the fracture‐matrix system.
Improved Water Use Estimates for Drilling and Hydrualic Fracturing in Northeastern Colorado

The development of unconventional resources in tight shales has stimulated considerable growth of oil and gas production in Northeastern Colorado, but has led to concerns about added demands on the region’s strained water resources. Northeastern Colorado’s semi-arid environment, population growth, competing water demands and uncertainty about drilling and hydraulic fracturing water requirements have resulted in scrutiny and conflict surrounding water use for tight shales. This study collects water use data from wells in Northeastern Colorado to improve water estimates and to better understand important contributing factors. Most water resource studies use estimates for the number of future wells to predict water demands. This study shows that the number of hydraulic fracturing stages is a better measure of the future water demands for horizontal wells. Vertical wells use significantly less water than horizontal wells and will be less prevalent in the future.
Eﬀects of heart rate variability biofeedback training on anxiety reduction and brain activity: A randomized active control study using EEG

Heart rate variability biofeedback (HRVBF) is a promising anxiety-reducing intervention that activates the autonomic nervous system through paced breathing, using feedback from heart rate variability (HRV). Many studies have reported the anxiety-reducing eﬀects of HRVBF; however, reports on the eﬀectiveness of training have been negative. Furthermore, the eﬀects of training and the underlying brain activity changes remain unclear. This study aimed to examine the anxiety-reducing eﬀects of HRVBF training and related brain activity changes, by randomly assigning participants, employing an active control group, and measuring anxiety-related attentional bias using the emotional Stroop task and EEG. Fifty-ﬁve right-handed healthy young students with anxiety were randomly assigned: ﬁnally, 21 to the HRVBF group and 19 to the control group. Both groups performed 10 training sessions of 20 minutes per day within three weeks and were assessed using HRV, EEG, attentional bias, and the State-Trait Anxiety Inventory-JYZ (STAI-JYZ), before and after training. Results showed increased HRV in the HRVBF group compared with the control group, but no diﬀerences in EEG, attentional bias, and STAI-JYZ. Further analyses revealed that participants with higher pre-training HRV achieved higher heart rhythm coherence in HRVBF training and had reduced attentional bias. This study suggests that individuals with higher HRV are more likely to be proﬁcient in HRVBF training and beneﬁt from its anxiety-reducing eﬀects. The ﬁndings contribute to an understanding of participant selection and modiﬁcation of HRVBF training protocols for non-responders.
Marine Ecosystem Dynamics and Biogeochemical Cycling in the Community Earth System Model [CESM1(BGC)]: Comparison of the 1990s with the 2090s under the RCP4.5 and RCP8.5 Scenarios

AbstractThe authors compare Community Earth System Model results to marine observations for the 1990s and examine climate change impacts on biogeochemistry at the end of the twenty-first century under two future scenarios (Representative Concentration Pathways RCP4.5 and RCP8.5). Late-twentieth-century seasonally varying mixed layer depths are generally within 10 m of observations, with a Southern Ocean shallow bias. Surface nutrient and chlorophyll concentrations exhibit positive biases at low latitudes and negative biases at high latitudes. The volume of the oxygen minimum zones is overestimated.The impacts of climate change on biogeochemistry have similar spatial patterns under RCP4.5 and RCP8.5, but perturbation magnitudes are larger under RCP8.5. Increasing stratification leads to weaker nutrient entrainment and decreased primary and export production (>30% over large areas). The global-scale decreases in primary and export production scale linearly with the increases in mean sea surface temperature.
NON-BOLTZMANN STATIONARY DISTRIBUTIONS AND NON-EQUILIBRIUM RELATIONS IN ACTIVE BATHS

NON-BOLTZMANN STATIONARY DISTRIBUTIONS AND NON-EQUILIBRIUM RELATIONS IN ACTIVE BATHS Aykut Argun M.S. in Physics Advisor: Giovanni Volpe September 2016 Most natural and engineered processes, such as biomolecular reactions, protein folding, and population dynamics, occur far from equilibrium and, therefore, cannot be treated within the framework of classical equilibrium thermodynamics. Here, we experimentally study how some fundamental thermodynamic quantities and relations are affected by the presence of the non-equilibrium fluctuations associated with an active bath. We show, in particular, that, as the confinement of the particle increases, the stationary probability distribution of a Brownian particle confined within a harmonic potential becomes non-Boltzmann, featuring a transition from a Gaussian distribution to a heavy-tailed distribution. Because of this, non-equilibrium relations (e.g. Jarzynski equality, Crooks fluctuation theorem) cannot be applied. We show that these relations can be restored by using the effective potential associated with the stationary probability distribution. We corroborate our experimental findings with theoretical arguments.