Miracle-dz/UniFAR-FTUs huggingface dataset:
Scaling effects of temperature on parasitism from individuals to host–parasite systems

Parasitism is expected to change in a warmer future, but whether warming leads to substantial increases in parasitism remains unclear. Understanding how warming effects on parasitism in individual hosts (e.g., parasite load) translate to effects on population-level parasitism (e.g., prevalence, R0) remains a major knowledge gap. We analyzed the temperature dependence of parasitism at both host and population levels in thirteen empirical vector-borne host–parasite systems and found a strong, significant positive correlation between the thermal optima of individual- and population-level parasitism. We also found a significant, positive correlation in eleven environmentally-transmitted parasite systems, though several of these systems exhibited thermal optima >5ºC apart between individual and population levels. Similarly, parasitism thermal optima were close to host performance thermal optima in vector-borne systems but not in environmentally-transmitted systems. We then adapted and simulated simple models for both transmission modes and found a similar pattern to the empirical systems: thermal optima in vector-borne systems were more strongly correlated across scales compared to environmentally-transmitted systems. Generally, our results suggest that information on the temperature-dependence, and specifically the thermal optimum, at either the individual- or population-level should provide a useful—though not quantitatively exact—baseline for predicting temperature dependence at the other level, especially in vector-borne parasite systems. Environmentally-transmitted parasitism may operate by a different set of rules, in which temperature-dependence is decoupled in some systems, requiring the need for trait-based studies of temperature-dependence at individual and population levels.
Threat induces changes in cardiac activity and metabolism negatively impacting survival in flies

Adjusting to a dynamic environment involves fast changes in the body’s internal state, characterized by coordinated alterations in brain activity, physiological and motor responses. Threat-induced defensive states are a classic example of coordinated adjustment of bodily responses, being cardiac regulation one of the best characterized in vertebrates. A great deal is known regarding the neural basis of invertebrate defensive behaviours, mainly in Drosophila melanogaster. However, whether physiological changes accompany these remains unknown. Here, we set out to describe the internal bodily state of fruit flies upon an inescapable threat and found cardiac acceleration during running and deceleration during freezing. In addition, we found that freezing leads to increased cardiac pumping from the abdomen towards the head-thorax, suggesting mobilization of energy resources. Concordantly, threat-triggered freezing reduces sugar levels in the hemolymph and renders flies less resistant to starvation. The cardiac responses observed during freezing were absent during spontaneous immobility, underscoring the active nature of freezing response. Finally, we show that baseline cardiac activity predicts the amount of freezing upon threat. This work reveals a remarkable similarity with the cardiac responses of vertebrates, suggesting an evolutionarily convergent defensive state in flies. Our findings are at odds with the widespread view that cardiac deceleration while freezing has first evolved in vertebrates and that it is energy sparing. Investigating the physiological changes coupled to defensive behaviours in the fruit fly has revealed that freezing is costly, yet accompanied by cardiac deceleration, and points to heart activity as a key modulator of defensive behaviours.
The Synthesis of High Yield PbS Nanocrystalline and its Photovoltaic Applications

High quality PbS nanorcrystallines (NCs) have been fabricated in high yield by a simple hydrothermal method using unique ligands. We find that the experiment conditions such as different ligands,the reaction temperature greatly influence the morphology and the size of PbS NCs. Specifically, the complex ligands OPA and butylamine have great effects on the final products compared with no ligand. We can obtain PbS nanocrystalline with more homogeneous size and higher optical properties. On the other hand, higher external quantum efficiency (EQE) of the solar cell will be achieved with Schottky device structure of ITO/PbS/Al.
Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens

Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics has led to the identification of mechanisms that are used by beneficial microorganisms to overcome these challenges such as the production of iron-chelating compounds, the formation of strong biofilms, or the concealment of characteristic microbial molecular patterns that trigger the host immune system. However, how such mechanisms arose from an evolutionary perspective is much less understood. To study bacterial adaptation in the rhizosphere, we employed experimental evolution to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant-one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We identified 35 mutations, including single-nucleotide polymorphisms, insertions, and deletions, distributed over 28 genes. We found that mutations in genes encoding global regulators, and in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel, underlining that bacterial adaptation to the rhizosphere follows multiple strategies. Notably, we observed that motility increased in parallel across multiple independent evolutionary lines. Altogether these results underscore the strength of experimental evolution to identify key genes, pathways, and processes for bacterial rhizosphere colonization, and a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future. Importance Beneficial root-associated microorganisms carry out many functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming many challenges. Previously, diverse mechanisms that are used by beneficial microorganisms to overcome these challenges were identified. However, how such mechanisms have developed from an evolutionary perspective is much less understood. Here, we employed experimental evolution to track the evolutionary dynamics of a root-dwelling pseudomonad on the root of Arabidopsis. We find that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility accumulate in parallel, underlining these strategies for bacterial adaptation to the rhizosphere. We identified 35 mutations distributed over 28 genes. Altogether our results demonstrate the power of experimental evolution to identify key pathways for rhizosphere colonization and a methodology for the development of elite beneficial microorganisms that can support sustainable agriculture.
A thermodynamic model of protein structure evolution explains empirical amino acid rate matrices

Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. Averaged over time and across proteins, these evolutionary pressures are sufficiently consistent to produce global substitution patterns that can be used to successfully find homologues, infer phylogenies, and reconstruct ancestral sequences. Although the factors which govern the variation of protein substitution rates has received much attention, the influence of thermodynamic stability constraints remains unresolved. Here we develop a simple model to calculate amino acid rate matrices from evolutionary dynamics controlled by a fitness function that reports on the thermodynamic effects of amino acid mutations in protein structures. This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi-nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein stability. We find that our theoretical model accurately recapitulates the complex pattern of empirical rates observed in common global amino acid substitution matrices used in phylogenetics. These results suggest that selection for thermodynamically stable proteins, coupled with nucleotide mutation bias filtered by the structure of the genetic code, is the primary global driver behind the amino acid substitution patterns observed in proteins throughout the tree of life.
IN SITU INFRARED MEASUREMENTS OF FREE-FLYING SILICATE DURING CONDENSATION IN THE LABORATORY

We developed a new experimental system for infrared (IR) measurements on free-flying nucleating nanoparticles in situ and applied it to studies on silicate particles. We monitored the condensation of magnesium-bearing silicate nanoparticles from thermally evaporated magnesium and silicon monoxide vapor under an atmosphere of oxygen and argon. The IR spectrum of newly condensed particles showed a spectral feature for non-crystalline magnesium-bearing silicate that is remarkably consistent with the IR spectrum of astronomically observed non-crystalline silicate around oxygen-rich evolved stars. The silicate crystallized at <500 K and eventually developed a high crystallinity. Because of the size effects of nanoparticles, the silicate would be expected to be like a liquid at least during the initial stages of nucleation and growth. Our experimental results therefore suggest decreasing the possible formation temperature of crystalline silicates in dust formation environments with relatively higher pressure.
Chemical kinetics and energy transfer in moderate pressure H2 plasmas used in diamond MPACVD processes

A kinetic model for moderate-pressure microwave H2 plasmas obtained in diamond deposition reactors is presented. This model involves three groups of reactions which describe the vibrational kinetics of H2, the chemistry of H2 and H electronically excited states and the groundstate species kinetics, respectively. The set of species kinetic equations resulting from this model, coupled to the electron Boltzmann equation and the total energy equation were solved under a quasi-homogenous plasma assumption. This enables the estimation of the species densities, the electron distribution function and related electron properties, as well as the gas temperature. The results show that the most important ionization channel is that due to the quenching of H (n = 2) excited states by H2. The production of the H-atom is mainly due to electron impact dissociation at low microwave power density and to thermal dissociation at high power density. A simplified physical model which may be used for describing the non-equilibrium H2 plasma flow in diamond deposition microwave plasmas reactors is also proposed.
Graphene Solution‐Gated Field‐Effect Transistor Array for Sensing Applications

Graphene, with its unique combination of physical and electronic properties, holds great promise for biosensor and bioelectronic applications. In this respect, the development of graphene solution‐gated field‐effect transistor (SGFET) arrays capable of operation in aqueous environments will establish the real potential of graphene in this rapidly emerging field. Here, we report on a facile route for the scalable fabrication of such graphene transistor arrays and provide a comprehensive characterization of their operation in aqueous electrolytes. An on‐chip structure for Hall‐effect measurements allows the direct determination of charge carrier concentrations and mobilities under electrolyte gate control. The effect of the solution‐gate potential on the electronic properties of graphene is explained using a model that considers the microscopic structure of water at the graphene/electrolyte interface. The graphene SGFETs exhibit a high transconductance and correspondingly high sensitivity, together with an effective gate noise as low as tens of μV. Our study demonstrates that graphene SGFETs, with their facile technology, high transconductance, and low noise promise to far outperform state‐of‐the‐art Si‐based devices for biosensor and bioelectronic applications.
Gene Expression in Vascular Smooth Muscle

Vascular diseases such as hypertension are marked by changes in calcium (Ca) and extracellular signal regulated kinase (ERK) signaling in the arterial wall. The overall goal of this project was to better understand pathways leading to altered gene regulation in cerebral arteries. Two models were tested to determine if, 1) Ca/cAMP response element binding protein (CREB) is regulated in intact cerebral arteries by multiple sources of Ca, and 2) hypertensive disease causes changes in genes regulated by ERK and CREB. Ca-mediated phosphorylation of CREB (P-CREB) was measured by immunofluorescence in both cultured vascular smooth muscle cells (VSMCs) and in intact cerebral arteries. The level of P-CREB was increased by both Ca influx through voltage-dependent calcium channels (VDCCs) and store-operated Ca entry (SOCE) in VSMCs. A similar increase in P-CREB was observed following stimulation of VDCCs and SOCE in intact cerebral arteries. However, unlike the results obtained from VSMCs phosphorylation of CREB following Ca store depletion using thapsigargin, was partially dependent on Ca entry through VDCCs, suggesting that communication between Ca entry pathways in intact arteries may be lost during cell culture. The second model was tested using immunocytochemistry and RNA analysis to measure differences in cerebral artery signal transduction and gene expression caused by chronic hypertension in the Dahl salt sensitive genetic hypertensive rat model. Arteries from hypertensive animals exhibited increased phosphorylation of ERK and expression of Ki-67, a marker of proliferation, when compared to controls. In addition, microarray analysis of arterial RNA revealed overexpression of the matricellular ERK-regulated genes osteopontin (OPN), and plasminogen activator inhibitor 1 (PAI-1), and the activator protein transcription factor (AP-1) member junB in cerebral arteries, with validation using RT qPCR. To elucidate a role for CREB, ERK and JunB in the transcriptional regulation of OPN and PAI-1, VSMCs were treated with angiotensin II (Ang II), a vasoconstrictor linked to hypertension, and confirmed activator of OPN and PAI-1 transcription. Ang II induced an ERK-dependent transient increase in junB mRNA and protein prior to OPN, and PAI-1 induction. Gene silencing experiments indicated that OPN and PAI-1 are reciprocally regulated by junB and CREB, respectively, and that CREB is a negative regulator of OPN. Data from cell culture confirms that the Ang II response in VSMCs is transient, in contrast to the hypertensive in vivo model, suggesting that the CREB and ERK response induces long term changes. Together, these data have revealed mechanisms for regulation of gene expression that are linked to proliferation and remodeling in the arterial wall. Future experiments will explore an in vivo role for Ang II and SOCE in the mediation of ERKand CREBregulated gene expression. This research has the potential to help in defining therapeutic strategies to prevent arterial remodeling caused by arterial pathologies such as hypertension.
The impact of source restriction on yield formation of corn (Zea mays L.) due to water deficiency.

To understand the mechanisms causing yield limitations in defoliated plants subjected to water deficiency, the ex periments were laid out as a randomized complete block design with split-plot arrangement. Soil-water regimes consisted of moderate irrigation until physiological maturity (W 1 ) or short severe water stress periods (W 2 ) at V 8 stage of ontogenesis, and tasseling which allotted to the main plots. Defoliation times (V 8 and tasseling) and intensities (cutting of one or two thirds of leaf blade) combinations and one control level (five Source restriction treatments) were allotted to subplots. Early defoliation caused reduction in grain yield at W 1 and W 2 by 19.2 and 14.8%, respectively. On the other hand, water deficiency reduced grain per ear by 23.9% and increased individual grain weight by 37.0% (plasticity of sink capacity). These results show that under water deficiency, grain yield limitation was mostly due to a reduction in dry matter allocation to grains (sink capacity) than a result of lower dry matter production (source strength). Findings suggest that in non-irrigated corn, breeders must direct their selection program to increase grain set and decrease surplus leaves.
A Perspective on the Toxicity of Petrogenic PAHs to Developing Fish Embryos Related to Environmental Chemistry

ABSTRACT Numerous studies demonstrate polynuclear aromatic hydrocarbons (PAHs) dissolved from weathered crude oil adversely affect fish embryos at 0.5 to 23 μg/l. This conclusion has been challenged by studies that claim (1) much lower toxicity of weathered aqueous PAHs; (2) direct contact with dispersed oil droplets plays a significant role or is required for toxicity; (3) that uncontrolled factors (oxygen, ammonia, and sulfides) contribute substantively to toxicity; (4) polar compounds produced by microbial metabolism are the major cause of observed toxicity; and (5) that based on equilibrium models and toxic potential, water contaminated with weathered oil cannot be more toxic per unit mass than effluent contaminated with fresh oil. In contrast, several studies demonstrate high toxicity of weathered oil; shifts in PAH composition were consistent with dissolution (not particle ablation), embryos accumulated dissolved PAHs at low concentrations and were damaged, and assumed confounding factors were inconsequential. Consistent with previous empirical observations of mortality and weathering, temporal shifts in PAH composition (oil weathering) indicate that PAHs dissolved in water should (and do) become more toxic per unit mass with weathering because high molecular weight PAHs are more persistent and toxic than the more abundant low molecular weight PAHs in whole oil.
Spatial distribution of local patch extinctions drives recovery dynamics in metacommunities

Human activities lead more and more to the disturbance of plant and animal communities with local extinctions as a consequence. While these negative effects are clearly visible at a local scale, it is less clear how such local patch extinctions affect regional processes, such as metacommunity dynamics and the distribution of diversity in space. Since local extinctions may not be isolated events in space but rather cluster together, it is crucial to investigate their effects in a spatially explicit framework. Here, we use experimental microcosms and numerical simulations to understand the relationship between local patch extinctions and metacommunity dynamics. More specifically, we investigate the effects of the amount and spatial autocorrelation of extinctions in a full factorial design. Experimentally, we found that local patch extinctions increased inter-patch (β-) diversity by creating differences between perturbed and unperturbed patches and at the same time increased local (α-) diversity by delaying the competitive exclusion of inferior competitors. Most importantly, recolonization dynamics depended more strongly on the spatial distribution of patch extinctions than on the amount of extinctions per se. Clustered local patch extinctions reduced mixing between perturbed and unperturbed patches which led to slower recovery, lower α-diversity in unperturbed patches and higher β-diversity. Results from a metacommunity model matched the experimental observations qualitatively when the model included ranked competitive interactions, giving a hint at the underlying mechanisms. Our results highlight that local patch extinctions can increase the diversity within and between communities, that the strength of these effects depends on the spatial distribution of extinctions and that the effects of local patch extinctions can spread regionally, throughout a landscape. These findings are highly relevant for conservation and management of spatially structured communities under global change.
Electronic transport through carbon nanotubes with ferromagnetic electrodes or in magnetic fields

Spin-dependent electronic transport through carbon nanotubes (CNTs) was studied, either sandwiched between ferromagnetic contacts or in external magnetic fields. Attention was paid to the conductance dependence on geometrical size (the length and diameter) of the CNTs, chirality, and conditions at CNT/contact interface. The CNTs are end-contacted to fcc (111) metallic leads, and the relative atomic positions at the interfaces are determined by the relaxation procedure. Additionally, a charge neutrality condition is imposed on the extended molecule (i.e., CNT with a few atomic layers of the leads) in order to fix the band line-up of the whole system. Using a single-band tight-binding model and a Green’s function technique, it is shown that if the electrodes are ferromagnetic, quite a considerable giant magnetoresistance effect can occur. For paramagnetic electrodes in a parallel magnetic field, clear Aharonov–Bohm oscillations are observed, with distinct minima in the conductance. The depth of the dips depends on the diameters of the CNTs, most likely due to some unintentional doping from the contacts. In the case of perpendicular geometry, pronounced conductance oscillations appear whenever the magnetic length becomes smaller than the perimeter of a CNT.
Initial MCNP6 Release Overview

MCNP6 is simply and accurately described as the merger of MCNP5 and MCNPX capabilities, but it is much more than the sum of those two computer codes. MCNP6 is the result of five years of effort by the MCNP5 and MCNPX code development teams. These groups of people, residing in Los Alamos National Laboratory’s (LANL) X Computational Physics Division, Monte Carlo Codes Group (XCP-3), and Decision Applications Division, Radiation Transport and Applications Team (D-5), respectively, have combined their code development efforts to produce the next evolution of MCNP. While maintenance and bug fixes will continue for MCNP5 1.60 and MCNPX 2.7. 0 for upcoming years, new code development capabilities only will be developed and released in MCNP6. In fact, the initial release of MCNP6 contains 16 new features not previously found in either code. These new features include the abilities to import unstructured mesh geometries from the finite element code Abaqus, to transport photons down to 1.0 eV, to transport electrons down to 10.0 eV, to model complete atomic relaxation emissions, and to generate or read mesh geometries for use with the LANL discrete ordinates code Partisn. The first release of MCNP6, MCNP6 Beta 2, is now available through the Radiation Safety Information Computational Center, and the first production release is expected in calendar year 2012. High confidence in the MCNP6 code is based on its performance with the verification and validation test suites, comparisons to its predecessor codes, the regression test suite, its code development process, and the underlying high-quality nuclear and atomic databases.