Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure et dynamique de systèmes unidimensionnels modèles : les nano-peapods de carbone

Ce travail de these est consacre a l'etude sur une large gamme de temperatures d'un systeme unidimensionnel modele, les nano-peapods de carbone. Ces composes sont constitues de fullerenes (C60, dans notre cas) inseres dans des nanotubes de carbone monofeuillets. Les diametres des fullerenes et des tubes etant concordant, les fullerenes s'arrangent selon un reseau 1D.Dans le premier chapitre de ce manuscrit, nous decrivons la synthese des peapods de carbone. Dans les deux chapitres suivants, nous decrivons les differents modeles et methodes experimentales qui nous permettent de determiner l'evolution de la structure moyenne des chaines de fullerenes, ainsi que la dynamique de rotation et de translation des molecules.Dans les trois derniers chapitres, nous decrivons l'evolution de la structure et de la dynamique des chaines sur trois gammes de temperatures, que nous appelons hautes (500-1100 K), basses (0-200 K), et intermediaires (200-500 K). Les resultats experimentaux concernant deux types d'echantillons, les peapods monomeres et les peapods polymeres (dans lesquels les degres de liberte de rotation sont restreints) sont confrontes a des modeles analytiques. Nous mettons en evidence trois comportements differents des chaines dans ces trois gammes de temperature.
Techniques for screening Cercospora leaf spot resistant fenugreek genotypes

Abstract: Cercospora leaf spot (CLS) caused by Cercospora traversiana is an important phyto-pathological problem of fenugreek (Trigonella foenum-graecum L.), a multiuse legume crop. Field screenings for resistant plants, although accurate and effective, demand significant time and a sizable workforce to accomplish. Also, weather conditions in the field may not always be favourable for uniform disease spread, which eventually may lead to failure of the overall experiment. Whole-plant assays (WPA) and detached leaf assays (DLA) with artificial inoculation not only help in scaling up the number of plants screened but also reduce the space, time, and amount of inoculum needed for the experiment. The results from our two experiments indicate that both the WPA and DLA methods can be used reliably to differentiate resistant and susceptible genotypes of fenugreek. In addition, the correlation coefficient between WPA and DLA (r = 0.875, P < 0.01), derived from the mean disease score of each genotype, shows that they can be used interchangeably while screening fenugreek for CLS. DLA was found to be temperature-sensitive for the development of CLS symptoms and wounded leaves developed symptoms faster than non-wounded leaves. These indoor methods can be used for the development of CLS-resistant fenugreek cultivars in areas where disease development is difficult under field conditions.
Environmental and Radar Characteristics of Gargantuan Hail-Producing Storms

Storms that produce gargantuan hail (defined here as ≥ 6 inches or 15 cm in maximum dimension), although seemingly rare, can cause extensive damage to property and infrastructure, and cause injury or even death to humans and animals. Currently, we are limited in our ability to accurately predict gargantuan hail and detect gargantuan hail on radar. In this study, we analyze the environments and radar characteristics of gargantuan hail-producing storms to define the parameter space of environments in which gargantuan hail occurs, and compare environmental parameters and radar signatures in these storms to storms producing other sizes of hail. We find that traditionally used environmental parameters used for severe storms prediction, such as most unstable convective available potential energy (MUCAPE) and 0–6 km vertical wind shear, display considerable overlap between gargantuan hail-producing storm environments and those that produce smaller hail. There is a slight tendency for larger MUCAPE values for gargantuan hail cases, however. Additionally, gargantuan hail-producing storms seem to have larger low-level storm-relative winds and larger updraft widths than those storms producing smaller hail, implying updrafts less diluted by entrainment and perhaps maximizing the liquid water content available for hail growth. Moreover, radar reflectivity or products derived from it are not different from cases of smaller hail sizes. However, inferred mesocyclonic rotational velocities within the hail growth region of storms that produce gargantuan hail are significantly stronger than the rotational velocities found for smaller hail categories.
Study of Chemical Composition of Cattle Meat and Sheep Meat in Khartoum State

This study was conducted in the College of Animal Production Science and Technology, Sudan University of Science and Technology to investigate the chemical composition of beef and sheep meat (mutton) are marketed in Khartoum State, (longissimus muscle from different carcass of mature animals). The chemical composition determined according to the Association of Official Analytical Chemists methods (AOAC. 2007). The samples were analyzed in three different brands of these raw cuts in duplicate. The results showed that the chemical composition of beef and mutton was no significant difference (P> 0.05) between beef and mutton in the moisture and ash content. Also the study showed no significant difference (P <0.05) between beef and mutton in the protein and fat percentage. In this study beef had higher moisture content (74.83%) compared to mutton (73.25%). Whereas sheep meat (mutton) had higher protein content (18.61%) compared to beef (17.41%). In this study beef had the lower fat content (3.0%) compared to sheep meat (3.87%). However, the beef had the higher ash content (1.88%) compared to sheep meat (1.0%). Chemically beef had low fat concentration compared to sheep meat with favorable nutritional quality. Also in this study there was a decrease in moisture content by a significant increase in fat content.
Comparing Ecosystem Service Preferences between Urban and Rural Dwellers

Urbanization can profoundly alter socioecological relationships, but its influence on how people perceive and value ecosystem services (ES) is poorly understood. We reviewed an emerging literature in which sociocultural valuation of ES is compared among urban and rural dwellers. This research suggests that, although regulating and cultural ES were highly valued by both rural and urban dwellers, urban dwellers tended to value provisioning ES less than rural dwellers did. Differences in ES valuation could result from different experiences, uses, and needs for ES of urban and rural dwellers. We also identified two key gaps in the literature that relate to understanding how diverse ES contribute differently to the well-being of rural and urban populations (and the relevance of these differences for environmental education and policy) and the changing roles of ES in developing countries and vulnerable ecosystems, such as small islands, that face pressing environmental, social, and economic challenges.
Combining multiple data sets to unravel the spatiotemporal dynamics of a data-limited fish stock

The biological status of many commercially exploited fishes remains unknown, mostly due to a lack of data necessary for their assessment. Investigating the spatiotemporal dynamics of such species can lead to new insights into population processes and foster a path towards improved spatial management decisions. Here, we focused on striped red mullet (Mullus surmuletus), a widespread yet data-limited species of high commercial importance. Aiming to quantify range dynamics in this data-poor scenario, we combined fishery-dependent and -independent data sets through a series of Bayesian mixed-effects models designed to capture monthly and seasonal occurrence patterns near the species’ northern range limit across 20 years. Combining multiple data sets allowed us to cover the entire distribution of the northern population of M. surmuletus, exploring dynamics at different spatiotemporal scales and identifying key environmental drivers (i.e., sea surface temperature, salinity) that shape occurrence patterns. Our results demonstrate that even when process and (or) observation uncertainty is high, or when data are sparse, if we combine multiple data sets within a hierarchical modelling framework, accurate and useful spatial predictions can still be made.
Fiscal policy and expectations in Brazil

Este artigo estuda os efeitos de notícias fiscais sobre a economia brasileira, baseando-se na nova literatura que procura identificar choques na política fiscal por meio de informações de previsões profissionais. É construída uma estrutura a termo de expectativas de superávit primário para o Brasil, e estimadas funções de reação para diferentes maturidades. As notícias fiscais são decompostas em um componente esperado e outro não esperado, baseados nos valores previstos e nos resíduos das funções de reação. Notícias fiscais esperadas e não esperadas são identificadas respectivamente como o primeiro fator das séries de valores previstos e dos resíduos das funções de reação, procurando capturar as notícias que tendem a persistir no horizonte de previsão. Embora com substancial incerteza, notícias sobre um aperto fiscal provocam um aumento de curto prazo no produto, uma queda da inflação, um declínio do salário real e uma depreciação da taxa de câmbio real.
IMPACT OF PRIVI-SILIXOL FOLIAR FERTILIZER IN COMBINATION WITH DI-AMMONIUM PHOSPHATE AND MYCORRHIZA ON PERFORMANCE, NPK UPTAKE, DISEASE AND PEST RESISTANCE ON SELECTED CROPS IN A GREENHOUSE EXPERIMENT

Despite silicon not considered an essential nutrient, it is typically abundant in soils and is known to have beneficial effects when added to rice crops and several other plants. These beneficial effects include disease and pest resistance, structural fortification, and regulation of the uptake of other ions. In this study, the effect of silicic acid fertilization (Privi-Silixol) on the increased biomass, economic yields, pest and disease tolerance or resistance, NPK uptake and chlorophyll content for five crop plants (Cowpea, common beans, cabbage, maize, and rice) was evaluated. The approach was executed through a controlled greenhouse experiment using Acid Washed Sand as a neutral medium. Crops planted with Privi-Silixol alone or in combination with full or half rates of recommended inorganic fertilizer performed significantly (P≤0.05) better compared to all other treatments. Plants treated with Privi-Silixol had higher dry matter yield (DMY), chlorophyll content and NPK uptake. Maize, common bean, cowpea, cabbage and rice had better disease and pest resistance compared to the control plants. Collectively, these results indicate beneficial effects of silicon in DMY, chlorophyll content, pest and disease resistance, but additional studies are needed under farmers’ conditions to conclusively understand the interactions of silicon with other interacting factors in the field.
Productivity and diversity of annually harvested reconstructed prairie communities

1. Biofuel production from cellulosic feedstocks may increase during the next century. To be sustainable, this production should protect environmental quality and biodi versity. Fertilized mixed- species prairie can deliver substantial quantities of cellu losic ethanol per unit land area with minimal losses of NO 3 - N in drainage water, but the long- term maintenance of biodiversity in such systems has been uncertain. 2. We report how nitrogen, phosphorus, and potassium fertilizer application, pre cipitation, and time affected the species composition and productivity of recon structed prairie communities harvested annually as biofuel feedstocks over a 9- year period. 3. Results indicated that both precipitation and fertilizer application drove above-ground biomass production, with the greatest response to fertilizer occurring in wet ter than average years. Fertilization reduced species richness, but increased species evenness. Consequently, Simpson’s diversity index did not differ between the ferti lized and unfertilized communities, though it declined in both communities over time. 4. A total of 59 plant species was recorded, with eight of them explaining most of the differences in vegetation cover between the fertilized
Phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa

Bacterial viruses, or phage, play a key role in shaping natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Critically, phage often have a very narrow host range meaning they can only ever target a subset of strains in a community. Here we explore how strain diversity affects the success of lytic phage in structured communities. In particular, we infect a susceptible Pseudomonas aeruginosa strain PAO1 with lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies growing on agar. We find that competition between the two bacterial strains reduces the likelihood of the susceptible strain evolving resistance to the phage. This result holds in liquid culture and in colonies. However, while in liquid the phage eliminate the whole sensitive population, colonies contain refuges wherein bacteria can remain sensitive yet escape phage infection. These refuges form mainly due to reduced growth in colony centers. We find little evidence that the presence of the insensitive strain provides any additional protection against phage. Our study reveals that living in a spatially structured population can protect bacteria against phage infection, while the presence of competing strains may instead reduce the likelihood of evolving resistance to phage, if encountered.
Hepatitis C: Host and Viral Factors Associated with Response to Therapy and Progression of Liver Fibrosis

The goal of this study was to identify the baseline host and viral factors of response to antiviral therapy in patients with chronic hepatitis C. Compared with interferon/ribavirin therapy, new current direct-acting antiviral (DAA) combination regimens significantly increased rate of sustained virologic response (SVR) and shorter treatment durations, but is still limited by viral resistance, adverse effects, and high cost especially in developing countries. Human genetic factors and heterogeneity within the HCV genome may be associated with virologic treatment failure before and after antiviral therapy. Further, HCV infection may contribute to the development of HCV-related liver disease and hepatocarcinogenesis, through modulating genetic and epigenetic state of certain genes implicated in control of critical cellular pathways. Previous results confirm the impor tance of host and viral factors and virus-induced genetic and epigenetic changes in pre- dicting outcome and treatment response.
Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets*

We demonstrate the use of orthogonal methyl peptide enrichment techniques to enhance coverage of the protein “methylome” by LC-MS. Label free quantitation and unambiguous assignment of asymmetric and symmetric dimethylarginine modifications enabled the characterization of changes in protein arginine methylation following PRMT1 knockdown. We identified both PRMT1 substrates and scavenging by other PRMTs in the absence of PRMT1 activity to highlight the role of PRMT1 in regulating RNA-binding proteins. Graphical Abstract Highlights Enrichment of methyl peptides using two orthogonal techniques. Knockdown of PRMT1 leads to substantial changes in protein arginine “methylome”. Discrimination of ADMA and SDMA using characteristic neutral losses. Identification of PRMT1 targets and substrate scavenged by other PRMTs in the absence of PRMT1 activity. Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post-translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied because of the lack of robust, well-characterized techniques for methyl peptide enrichment. Here, to better investigate protein methylation, we compared two methods for methyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Using both methods, we identified 1720 methylation sites on 778 proteins. Comparison of these methods revealed that they are largely orthogonal, suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we then investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1). PRMT1 knockdown resulted in significant changes to 127 arginine methylation sites on 78 proteins. In contrast, only a single lysine methylation site was significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, we found 114 MMA sites that were either significantly downregulated or upregulated on proteins enriched for mRNA metabolic processes. PRMT1 knockdown also induced significant changes in both asymmetric dimethyl arginine (ADMA) and symmetric dimethyl arginine (SDMA). Using characteristic neutral loss fragmentation ions, we annotated dimethylarginines as either ADMA or SDMA. Through integrative analysis of methyl forms, we identified 18 high confidence PRMT1 substrates and 12 methylation sites that are scavenged by other non-PRMT1 arginine methyltransferases in the absence of PRMT1 activity. We also identified one methylation site, HNRNPA1 R206, which switched from ADMA to SDMA upon PRMT1 knockdown. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques to identify novel PRMT1 methylation targets and highlight the dynamic interplay between methyltransferases in mammalian cells.
Characterization and Antimicrobial Resistance Profile of Pseudomonas Aeruginosa Isolated from Clinical and Environmental Samples

Pseudomonas aeruginosa has emerged as a potential problematic Gram negative pathogen. The present study investigated the distribution of P. aeruginosa from the various clinical (wound and post-surgical wound) and environmental (water, industrial effluents and air) samples. The antibiotic resistance test was performed using the disc diffusion method according to NCCLS guidelines. Multidrug resistant genes among the isolates were characterized using PCR. 18 of the isolates with multidrug resistance showed least resistance to ceftazidime (23 %), gentamicin (20 %) and ciprofloxacin (31 %) from clinical isolates and 60, 38.5 and 60 % respectively from environmental isolates. Over 78 % of the isolates were polyvalent 1 strains, 17 % were polyvalent 2 and 5 % were polyvalent 3 strains. Polyvalent 1 were mostly strains from clinical samples while polyvalent 2 and 3 were strains from both (clinical and environmental) samples investigated. PCR analysis of multidrug resistant P. aeruginosa indicates that, PA-SS species specific signature sequences were present in all (100%) the isolates investigated. There was high emergence of antibiotic resistance in the environment and hospital investigated. Proper monitoring, regulating indiscriminate use of chemicals in the environment and restricting the use of antibiotics without susceptibility tests or prescription by a qualified physician should be adopted.
Homeostatic controllers compensating for growth and perturbations

Cells and organisms have developed homeostatic mechanisms to maintain internal stabilities which protect them against a changing environment. How cellular growth and homeostasis interact is still not well understood, but of increasing interest to the synthetic and molecular biology community where molecular control circuits are sought and tried to maintain homeostasis that opposes the diluting effects of cell growth. In this paper we describe the performance of four negative feedback (inflow) controllers, which, for different observed growth laws (time-dependent increase in the cellular volume V) are able to compensate for various time-dependent removals of the controlled variable A. The four implementations of integral control are based on zero-order, first-order autocatalytic, second-order (antithetic), and derepressing inhibition kinetics. All controllers behave ideal in the sense that they for step-wise perturbations in V and A are able to drive the controlled variable precisely back to the controller’s theoretical set-point The applied increase in cellular volume includes linear, exponential and saturating growth and reflect experimentally observed growth laws of single cell organisms and other cell types. During the increase in V, additional linear or exponential time-dependent perturbations which remove A are applied, and controllers are tested with respect to their ability to compensate for both the increase in volume V and the applied perturbations removing A. Our results show that the way how integral control is kinetically implemented and the structure of the negative feedback loop are essential determinants of a controller’s performance. The results provide a ranking between the four tested controller types. Considering exponential volume increases together with an exponentially increasing removal rate of A controllers based on derepression kinetics perform best, but break down when the control-inhibitor’s concentration gets too low. The first-order autocatalytic controller is able to defend time-dependent exponential growth and removals in A, but generally with a certain offset below its theoretical set-point The controllers based on zero-order and second-order (antithetic) integral feedback can only manage linear increases in V and removals in A, in dependence of the controllers’ aggressiveness. Our results provide a theoretical basis what controller kinetics are needed in order to compensate for different growth laws.
CHARACTERIZATION AND SOLUBILIZATION OF CHITOSAN FROM THE ORIENTAL HORNET (VESPA ORIENTALIS)

Chitosan was extracted from the oriental hornet, Vespa orientalis (L.), Vespinae, Order; Hymenoptera, as a new source of insect chitosan, using chemical methods. We assessed the physical properties of the wasp’s chitosan using different approaches including: preliminary color-change identification, Fourier Transform Infrared spectroscopy (FTIR), X-ray diffraction and Nuclear Magnetic Resonance spectroscopy (1H-NMR). The results showed that it gave a higher purity, solubility and Degree of Deacetylation (DD) compared to crustacean chitosan. Also, it is soluble in a very low concentration of acetic acid from 0.25% to 0.5% while that of Crustacea was soluble in more than 1% acetic acid, so the oriental hornet could be a novel alternative source of higher pure and more soluble chitosan.
Assessing Practitioner Beliefs

Just because software developers say they believe in "X" that does not necessarily mean that "X" is true. As shown here, there exist numerous beliefs listed in the recent Software Engineering literature which are only supported by small portions of the available data. Hence we ask what is the source of this disconnect between beliefs and evidence? To answer this question we look for evidence for ten beliefs within 300,000+ changes seen in dozens of open-source projects. Some of those beliefs had strong support across all the projects; specifically, "A commit that involves more added and removed lines is more bug-prone" and "Files with fewer lines contributed by their owners (who contribute most changes) are bug-prone". Most of the widely-held beliefs studied are only sporadically supported in the data; i.e. large effects can appear in project data and then disappear in subsequent releases. Such sporadic support explains why developers believe things that were relevant to their prior work, but not necessarily their current work. Our conclusion will be that we need to change the nature of the debate with SE. Specifically, while it is important to report the effects that hold right now, it is also important to report on what effects change over time.