Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high flexibility of the peptides. Based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique, we have developed a new computational method “Pep-GaMD”, which selectively boosts essential potential energy of the peptide in order to effectively model its high flexibility. In addition, another boost potential is applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Independent 1 μs dual-boost Pep-GaMD simulations have captured repetitive peptide dissociation and binding events, which enable us to calculate peptide binding thermodynamics and kinetics. The calculated binding free energies and kinetic rate constants agreed very well with available experimental data. Furthermore, the all-atom Pep-GaMD simulations have provided important insights into the mechanism of peptide binding to proteins that involves long-range electrostatic interactions and mainly conformational selection. In summary, Pep-GaMD provides a highly efficient, easy-to-use approach for unconstrained enhanced sampling and calculations of peptide binding free energies and kinetics. Significance Statement We have developed a new computational method “Pep-GaMD” for enhanced sampling of peptide-protein interactions based on the Gaussian accelerated molecular dynamics (GaMD) technique. Pep-GaMD works by selectively boosting the essential potential energy of the peptide to effectively model its high flexibility. In addition, another boost potential can be applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Dual-boost Pep-GaMD has captured repetitive peptide dissociation and binding events within significantly shorter simulation time (microsecond) than conventional molecular dynamics. Compared with previous enhanced sampling methods, Pep-GaMD is easier to use and more efficient for unconstrained enhanced sampling of peptide binding and unbinding, which provides a novel physics-based approach to calculating peptide binding free energies and kinetics.
Metabolic flux fingerprinting differentiates planktonic and biofilm states of Pseudomonas aeruginosa and Staphylococcus aureus

The challenges of defining the biofilm phenotype has been clear for decades. Many biomarkers for biofilm are known, but methods for identifying these are often invasive and/or complicated. These methods often rely on disrupting the biofilm matrix or examining virulence factors and compounds, which may only be expressed under certain conditions. We used microcalorimetric measurements of metabolic energy release to investigate whether unchallenged, planktonic Pseudomonas aeruginosa displayed differences in metabolism compared to surface-bound and non-attached biofilms. The pattern of energy release observed in the recorded microcalorimetric thermograms clearly depended on growth state, though the total energy expenditure was not different between growth states. To characterize these differences, we developed a classification pipeline utilizing machine learning algorithms to classify growth state, based on the observed patterns of energy release. With this approach, we could with high accuracy detect the growth form of blinded samples. To challenge the algorithm, we attempted to limit the amount of training data. By training the algorithm with only a single data point from each growth form, we obtained a mean accuracy of 90.5% using two principal components. Further validation of the classification pipeline showed that the approach was not limited to P. aeruginosa but could also be used for detection of gram-positive Staphylococcus aureus biofilm. We propose that microcalorimetric measurements, in combination with this new quantitative framework, can be used as a non-invasive biomarker to detect the presence of biofilm. These results could have a significant potential in clinical settings where the detection of biofilms in infections often means a different outcome and treatment regime for the patient.
Towards accountable decision aiding : explanations for the aggregation of preferences

We consider providing a decision aiding process with tools aiming at complying to the demands of accountability. Decision makers, seeking support, provide preference information in the form of reference cases, that illustrates their views on the way of taking into account conflicting points of view. The analyst, who provides the support, assumes a generic representation of the reasoning with preferences, and fits the aggregation procedure to the preference information. We assume a robust elicitation process, where the recommendations stemming from the fitted procedure can be deduced from dialectical elements. Therefore, we are interested in solving an inverse problem concerning the model, and in deriving explanations, if possible sound, complete, easy to compute and to understand. We address two distinct forms of reasoning: one aimed at comparing pairs of alternatives with an additive value model, the other aimed at sorting alternatives into ordered categories with a noncompensatory model.
Embryotoxicity of extracts from lake ontario rainbow trout (oncorhynchus mykiss) to japanese medaka (oryzias latipes)

Various preparative techniques were used to extract nonpolar organic compounds from the muscle tissue of Lake Ontario rainbow trout (Oncorhynchus mykiss). In this extract, PCBs and organochlorine compounds were detected in nanogram-per-milliliter quantities, and polychlorinated dibenzo-p-dioxins and dibenzofurans were detected in picogram-per-milliliter quantities. The extract and various subfractions of the extract were tested for embryotoxicity in a bioassay with embryos of Japanese medaka (Oryzias latipes). The whole extract was embryotoxic to medaka, as were an extract fraction containing PCBs (fraction A) and extract fractions containing nonpolar organochlorine compounds (fractions B and C). When subfractions prepared from fraction A were tested for embryotoxicity, a subfraction containing non-ortho-substituted PCB congeners was embryo-toxic, whereas subfractions containing mono-ortho- and di-ortho-substituted PCB congeners were relatively nontoxic. Pathological lesions characteristic of exposure to planar halogenated aromatic hydrocarbons were observed only in embryos exposed to the non-ortho-PCB subfraction. The non-ortho-PCB subfraction of fraction A was more toxic than the original fraction A, which indicates that nontoxic PCBs reduce the toxicity of the non-ortho-PCBs through some unknown mechanism. This study indicates that organochlorine compounds and non-ortho-substituted PCBs have the potential to be embryotoxic to early life stages of Great lakes fish, but nontoxic contaminants can modify this toxicmore » response. These data are relevant to the interpretation of correlations between embryo mortalities and concentrations of persistent organic contaminants in Great Lakes salmonids. « less
Impact of selenium spray on monocarpic senescence of soybean (Glycine Max L.)

An experiment was conducted to study the effect of selenium on senescence phenomenon in soybean. Selenium was applied both as seed treatment at 5 ppm and as foliar spray at 50 and 100 ppm on 45, 60 and 75 DAS. The impact of selenium on delaying senescence was well established by increased activity of antioxidant enzymes such as, catalase and peroxidase and more numbers of leaves. Improved source strength by retaining more leaf number and area with better partitioning efficiency was considered as the contributing factor for significant yield improvement in selenium-treated plants.
Riverina high school students views of biotechnology

Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.8 No.2, Issue of August 15, 2005 © 2005 by Pontificia Universidad Catolica de Valparaiso -- Chile Received June 29, 2004 / Accepted March 15, 2005
Intraneuronal chloride accumulation via NKCC1 is not essential for hippocampal network development in vivo

NKCC1 is the primary transporter mediating chloride uptake in immature principal neurons, but its role in the development of in vivo network dynamics and cognitive abilities remains unknown. Here, we address the function of NKCC1 in developing mice using electrophysiological, optical and behavioral approaches. We report that NKCC1 deletion from telencephalic glutamatergic neurons decreases in-vitro excitatory GABA actions and impairs neuronal synchrony in neonatal hippocampal brain slices. In vivo, it has a minor impact on correlated spontaneous activity in the hippocampus and does not affect network activity in the intact visual cortex. Moreover, long-term effects of the developmental NKCC1 deletion on synaptic maturation, network dynamics and behavioral performance are subtle. Our data reveal a neural network function of depolarizing GABA in the hippocampus in vivo, but challenge the hypothesis that NKCC1 is essential for major aspects of hippocampal development.
SEMANTIC PHOTOGRAMMETRY: BOOSTING IMAGE-BASED 3D RECONSTRUCTION WITH SEMANTIC LABELING

: Automatic semantic segmentation of images is a prominent research field with promising and reliable solutions already available, based on recent advances in machine learning. At the same time, using image labels as input to image-based 3D reconstruction is believed to have an enormous potential to improve the quality of its results. In this work we discuss this argument, exploring the contribution of semantic labelling towards 3D reconstruction in photogrammetry. We experiment with semantic information in various steps of the pipeline starting from feature matching to dense 3D reconstruction. Labelling in 2D instead of 3D is considered as an easier task in terms of data availability and algorithm maturity. However, since semantic labelling of all the images involved in the reconstruction may be a costly, laborious and time consuming task, we propose to use a deep learning architecture to automatically generate semantically segmented images. To this end, we have trained a Convolutional Neural Network (CNN) on historic building façade images that will be further enriched in the future. The first results of this study are promising, with an improved performance on the quality of the 3D reconstruction and the potentiality to transfer the labelling results and get, thus, a labelled 3D model.
In vitro antimicrobial activity of crude leaf and stem bark extracts of Gmelina arborea (Roxb) against some pathogenic species of Enterobacteriaceae.

Phytochemical screening of the Gmelina arborea reveals the presence of carbohydrates, alkaloids, saponins, tannins, anthraquinones and cardiac glycosides. The presence of these bioactive compounds in plants is linked to biological activity. Determination of antimicrobial activity using the agar diffusion method showed that the crude extracts of the leave and stembark of the plant inhibited the growth of such recalcitrant pathogenic Escherichia coli, Klebsiella pneumonieae, Proteus mirabilis, Shigella dysenteriea and Salmonella typhi that frequently show above average resistance, the extent of which depended on the solvent and organism. Activity of the extracts was consistently less than the conventional antibiotic, tetracycline. The effectiveness of the extracts was more in the acidic than in alkaline conditions and also increased with increase in temperature. Results provided the scientific bases for the folkloric application of G. arborea as a medicinal plant and ways the plant can be used as source for newer antibiotic substances for the possible control of dysentery, diarrhea, typhoid fever and wound infections associated with these bacteria.
Interactions between plant growth and soil nutrient cycling under elevated CO2: a meta‐analysis

free air carbon dioxide enrichment (FACE) and open top chamber (OTC) studies are valuable tools for evaluating the impact of elevated atmospheric CO2 on nutrient cycling in terrestrial ecosystems. Using meta‐analytic techniques, we summarized the results of 117 studies on plant biomass production, soil organic matter dynamics and biological N2 fixation in FACE and OTC experiments. The objective of the analysis was to determine whether elevated CO2 alters nutrient cycling between plants and soil and if so, what the implications are for soil carbon (C) sequestration. Elevated CO2 stimulated gross N immobilization by 22%, whereas gross and net N mineralization rates remained unaffected. In addition, the soil C : N ratio and microbial N contents increased under elevated CO2 by 3.8% and 5.8%, respectively. Microbial C contents and soil respiration increased by 7.1% and 17.7%, respectively. Despite the stimulation of microbial activity, soil C input still caused soil C contents to increase by 1.2% yr−1. Namely, elevated CO2 stimulated overall above‐ and belowground plant biomass by 21.5% and 28.3%, respectively, thereby outweighing the increase in CO2 respiration. In addition, when comparing experiments under both low and high N availability, soil C contents (+2.2% yr−1) and above‐ and belowground plant growth (+20.1% and+33.7%) only increased under elevated CO2 in experiments receiving the high N treatments. Under low N availability, above‐ and belowground plant growth increased by only 8.8% and 14.6%, and soil C contents did not increase. Nitrogen fixation was stimulated by elevated CO2 only when additional nutrients were supplied. These results suggest that the main driver of soil C sequestration is soil C input through plant growth, which is strongly controlled by nutrient availability. In unfertilized ecosystems, microbial N immobilization enhances acclimation of plant growth to elevated CO2 in the long‐term. Therefore, increased soil C input and soil C sequestration under elevated CO2 can only be sustained in the long‐term when additional nutrients are supplied.
Comparison of HLA ligand elution data and binding predictions reveals varying prediction performance for the multiple motifs recognized by HLA-DQ2.5

Binding prediction tools are commonly used to identify peptides presented on MHC class II molecules. Recently, a wealth of data in the form of naturally eluted ligands has become available and discrepancies between ligand elution data and binding predictions have been reported. Quantitative metrics for such comparisons are currently lacking. In this study, we assessed how efficiently MHC class II binding predictions can identify naturally eluted peptides, and investigated instances with discrepancies between the two methods in detail. We found that, in general, MHC class II eluted ligands are predicted to bind to their reported restriction element with high affinity. But, for several studies reporting an increased number of ligands that were not predicted to bind, we found that the reported MHC restriction was ambiguous. Additional analyses determined that most of the ligands predicted to not bind are either weak binders or predicted to bind other co-expressed MHC class II molecules. For selected alleles, we addressed discrepancies between elution data and binding predictions by experimental measurements, and found that predicted and measured affinities correlate well. For DQA1*05:01/DQB1*02:01 (DQ2.5) however, binding predictions did miss several peptides that were determined experimentally to be binders. For these peptides and several known DQ2.5 binders we determined key residues for conferring DQ2.5 binding capacity, which revealed that DQ2.5 utilizes two different binding motifs, of which only one is predicted effectively. These findings have important implications for the interpretation of ligand elution data and for the improvement of MHC class II binding predictions.
Task dynamics of body category and emotion representation in high-level visual, prefrontal and parietal cortex

Recent studies provided an increasingly detailed understanding of how visual objects categories like faces or bodies are represented in the brain. What is less clear is how a given task impacts the representation of the object category and of its attributes. Using (fMRI) we measured BOLD responses while participants viewed whole body expressions and alternatively performed an explicit (emotion) or an implicit (shape) recognition task. Our results based on multivariate methods, show that the type of task can be decoded in EBA, VLPFC and IPL with higher activity for the explicit task condition in the first two areas and no evidence of emotion specificity processes in any of them. This pattern indicates that during explicit recognition of the body expression, category representation would be strengthened while emotion and action related information would be suppressed. These results provide evidence that body representations in high level visual cortex and frontoparietal cortex are clearly task sensitive and that their contribution to emotional expression representation is based on task sensitive functional connectivity.
A reaction diffusion model of C-N-S-O species in a stratified sediment

The model represents a System Dynamics approach to the solution of a reaction-diffusion problem involving biogeochemical processes in a stratified marine sediment. The major reactants and products are represented, their interactions described by Michelis Menton-like equations and their movements controlled by diffusion equations. The model is truly dynamic: all reaction-and diffusion rates of all specified species are predicted by the model in space and time. In order to simplify the output, a steady-state situation is examined where the variation in oxygen, nitrate and ammonium concentrations, and the rates of nitrification and denitrification are seen in relation to different levels of organic matter mineralization. Nitrogen and carbon budgets are also presented. The modelling environment, Cellmatic, was designed to run models with high spatial and temporal structure. Cellmatic is easy to use for simulating any model with these characteristics.
Fire-scar formation and compartmentalization in oak

Fire scars result from the death of the vascular cambium resulting from excessive heating, which exposes sapwood to infection and initiates the wood decay process. In southeastern Ohio, prescribed fires in April 1995 and 1997 scarred Quercus prinus L. and Q. velutina Lam. Low-intensity fires scorched bark and produced scars, primarily on the downslope side of the stem. Eighteen scorched trees (4-23 cm at DBH) were dissected in November 1997, 14 of which had fire scars. The vascular cambium beneath natural bark fissures was most vulnerable to injury. No charred or scorched wood was associated with scars of trees exposed to single fires; wood exposed by scars from the 1995 fire was charred by the 1997 fire. Consistent with the compartmentalization process, discoloration and whiterot occurred within compartment boundaries of wood present at the time of wounding. Scars from the prescribed fires were consistent in size and shape with scars in nearby oak trees previously hypothesized to have been burned prior t.
Genetic variance in fitness and its cross-sex covariance predict adaptation during experimental evolution

In presence of rapid environmental changes, it is of particular importance to assess the adaptive potential of populations, which is mostly determined by the additive genetic variation (VA) in fitness. In this study we used Tribolium castaneum (red flour beetles) to investigate its adaptive potential in three new environmental conditions (Dry, Hot, Hot-Dry). We tested for potential constraints that might limit adaptation, including negative genetic covariance between female and male fitness. Based on VA estimates for fitness, we expected the highest relative fitness increase in the most stressful condition Hot-Dry and similar increases in single stress conditions Dry and Hot. High adaptive potential in females in Hot was reduced by a negative covariance with male fitness. We tested adaptation to the three conditions after 20 generations of experimental evolution and found that observed adaptation mainly matched our predictions. Given that body size is commonly used as a proxy for fitness, we also tested how this trait and its genetic variance (including non-additive genetic variance) were impacted by environmental stress. In both traits, variances were sex and condition dependent, but they differed in their variance composition, cross-sex and cross-environment genetic covariances, as well as in the environmental impact on VA.
Biological lability of dissolved organic carbon in stream water and contributing terrestrial sources

Abstract. Terrestrial sources of dissolved organic C (DOC) provide energy for stream microbial heterotrophs. Hydrologic conditions alter flow paths to the stream and influence terrestrial source quantity and quality. We used bioreactors to measure biodegradable DOC (BDOC) in water from soils, shallow wells, and spring seeps under baseflow conditions, overland flow during storms, and a stream during base flow and storm flow. Stream DOC concentrations ranged from 0.7 to 15.5 mg C/L and total BDOC ranged from 0.1 to 8.7 mg C/L. Under baseflow conditions, DOC was generally <2 mg C/L and BDOC was <0.7 mg C/L. BDOC made up 37.8% of DOC (8.2% labile and 29.6% semilabile constituents) and most DOC (62.2%) was recalcitrant. Storms increased DOC concentrations 6- to 12-fold and selectively mobilized BDOC increasing concentrations 8- to 27-fold. Labile and semilabile constituents increased 2-fold to 17.3% and 55.4%, respectively, so that storm flow DOC was largely biodegradable (73%). Terrestrial DOC concentrations declined from 2.15 mg C/L in soil water to 1.78 mg C/L in shallow wells to 1.26 mg C/L in spring seeps, and labile BDOC concentrations declined from 0.1 mg C/L in soil water to 0.04 mg C/L in shallow wells but increased to 0.13 mg C/L in spring seeps. Overland flow waters had elevated DOC (11.0 mg C/L) and labile BDOC (1.7 mg C/L) concentrations. Peak storm concentrations for 2 biological reactivity classes were coincident during 2 storms but divergent during another storm, suggesting temporal variation in hydrologic pathways. Our results demonstrate that storms deliver increased BDOC loads to a headwater stream and reveal the temporal variability of labile and semilabile BDOC constituents. Storms increase stream depth and velocity, resulting in increased uptake lengths for BDOC constituents, exporting them from the basin and probably providing a downstream subsidy.