Miracle-dz/UniFAR-FTUs huggingface dataset:
Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease

The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calculated by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromolecular crowding.
Prospective evaluation of a rapid diagnostic test for Trypanosoma brucei gambiense infection developed using recombinant antigens

Background Diagnosis and treatment are central elements of strategies to control Trypanosoma brucei gambiense human African trypanosomiasis (HAT). Serological screening is a key entry point in diagnostic algorithms. The Card Agglutination Test for Trypanosomiasis (CATT) has been the most widely used screening test for decades, despite a number of practical limitations that were partially addressed by the introduction of rapid diagnostic tests (RDTs). However, current RDTs are manufactured using native antigens, which are challenging to produce. Methodology/Principal findings The objective of this study was to evaluate the accuracy of a new RDT developed using recombinant antigens (SD BIOLINE HAT 2.0), in comparison with an RDT produced using native antigens (SD BIOLINE HAT) and CATT. A total of 57,632 individuals were screened in the Democratic Republic of the Congo, either passively at 10 health centres, or actively by 5 mobile teams, and 260 HAT cases were confirmed by parasitology. The highest sensitivity was achieved with the SD BIOLINE HAT 2.0 (71.2%), followed by CATT (62.5%) and the SD BIOLINE HAT (59.0%). The most specific test was CATT (99.2%), while the specificity of the SD BIOLINE HAT and SD BIOLINE HAT 2.0 were 98.9% and 98.1%, respectively. Sensitivity of the tests was lower than previously reported, as they identified cases from partially overlapping sub-populations. All three tests were significantly more sensitive in passive than in active screening. Combining two or three tests resulted in a markedly increased sensitivity: When the SD BIOLINE HAT was combined with the SD BIOLINE HAT 2.0, sensitivity reached 98.4% in passive and 83.0% in active screening. Conclusions/Significance The recombinant antigen-based RDT was more sensitive than, and as specific as, the SD BIOLINE HAT. It was as sensitive as, but slightly less specific than CATT. While the practicality and cost-effectiveness of algorithms including several screening tests would need to be investigated, using two or more tests appears to enhance sensitivity of diagnostic algorithms, although some decrease in specificity is observed as well.
Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis

The human Y chromosome shows frequent structural variants, some of which are selectively neutral, while others cause impaired fertility due to the loss of spermatogenic genes. The large‐scale use of multiple Y‐chromosomal microsatellites in forensic and population genetic studies can reveal such variants, through the absence or duplication of specific markers in haplotypes. We describe Y chromosomes in apparently normal males carrying null and duplicated alleles at the microsatellite DYS448, which lies in the proximal part of the azoospermia factor c (AZFc) region, important in spermatogenesis, and made up of “ampliconic” repeats that act as substrates for nonallelic homologous recombination (NAHR). Physical mapping in 26 DYS448 deletion chromosomes reveals that only three cases belong to a previously described class, representing independent occurrences of an∼1.5‐Mb deletion mediated by recombination between the b1 and b3 repeat units. The remainder belong to five novel classes; none appears to be mediated through homologous recombination, and all remove some genes, but are likely to be compatible with normal fertility. A combination of deletion analysis with binary‐marker and microsatellite haplotyping shows that the 26 deletions represent nine independent events. Nine DYS448 duplication chromosomes can be explained by four independent events. Some lineages have risen to high frequency in particular populations, in particular a deletion within haplogroup (hg) C*(xC3a,C3c) found in 18 Asian males. The nonrandom phylogenetic distribution of duplication and deletion events suggests possible structural predisposition to such mutations in hgs C and G. Hum Mutat 0, 1–10, 2008. © 2008 Wiley‐Liss, Inc.
Particle trapping in three-dimensional fully developed turbulence

The statistical properties of fluid particles transported by a three-dimensional fully developed turbulent flow are investigated by means of high resolution direct numerical simulations. Single trajectory statistics are investigated in a time range spanning more than three decades, from less than a tenth of the Kolmogorov time scale, τη, up to one large-eddy turnover time. Our analysis reveals the existence of relatively rare trapping events in vortex filaments which give rise to enhanced intermittency on Lagrangian observables up to 10τη. Lagrangian velocity structure function attain scaling properties in agreement with the multifractal prediction only for time lags larger than those affected by trapping.
Relation among quality traits of chicken breast meat during cold storage: correlations between freshness traits and torrymeter values

Abstract The aim of this study was to evaluate the relation among the quality and freshness traits of chicken breast meat during storage for 12 d at 4°C. In addition, correlations between freshness traits and torrymeter values were examined. The L* and a* value of the color was constant; however, the b* value increased on day 5 of storage (P < 0.05). The shear force value significantly decreased, whereas the 2‐thiobarbituric acid reactive substances value significantly increased during storage. Regarding the sensory properties, the off‐odor and the drip loss increased along with the decrease in color and overall acceptability evaluated by the panelist. The pH, total microorganism counts, and volatile basic nitrogen (VBN) value of chicken breast significantly increased following storage, whereas the torrymeter value and overall acceptability of chicken breast meat significantly decreased from 12.80 to 4.53 and from 6.14 to 1.86, respectively. The VBN value was positively correlated with the pH and total microorganism counts, and the pH value was positively correlated with the total microorganism counts. The torrymeter value was associated with the VBN (−0.918, P < 0.01), pH (−0.973, P < 0.001), total microorganism counts (−0.975, P < 0.001), and overall acceptability (0.884, P < 0.01). These results suggest that the tested traits highly correlate with torrymeter value and it can be used as an indicator of freshness of chicken meat.
The paleopathology of pellagra: investigating the impact of prehistoric and historical dietary transitions to maize

Summary – This article outlines interdisciplinary research avenues that can aid in reinterpreting and expanding our understanding of the skeletal biology of maize intensive diets. We suggest that new and innovative perspectives can emerge from hypotheses concerning the impact of diet and health on skeletal manifestations of pellagra. Pellagra, a niacin/tryptophan deficiency disease, is prevalent in populations that have high maize/low protein diets. Historically it has been essentially a disease of undernutrition and social inequality. We offer a unique analysis of both macro- and microstructural skeletal indicators from 31 individuals known to have died from pellagra (n=14) and non-specific general malnutrition (n= 17). These cases are part of the Raymond Dart Skeletal Collection, housed at the University of Witwatersrand Medical School, Johannesburg, South Africa. This sample was drawn from a mid-to-late 20 th Century Black South African population. In earlier reports we demonstrated that these individuals were found to exhibit a high incidence of alveolar bone loss, dental caries, enamel hypoplasias, periostitic lesions, osteomyelitis, cribra orbitalia, and cranial pitting. The frequency of specific pathological indicators separated the pellagrins from those with non-specific general malnutrition; however the indicators were not pellagra specific. We strongly argue that pellagra does affect bone in a noticeable way at both the macro- and micro-level, and therefore as a dietrelated disease can not be excluded as a possible cause for lesions seen in maize dependent populations. We have also reported on the histological findings for rib samples taken from a subset of pellagra (n=10) and general malnutrition (n=14) cases. The critical difference between pellagrins and non-specific malnutrition cases was a decreased cortical area for pellagrins. Given its implications for interpreting the paleopathology of prehistoric and historical transitions to maize intensive diets we present a checklist of macro- and micro-level indicators for investigating a signature pattern for the skeletal biology of pellagra. The overall synthesis of our findings provides new interdisciplinary insights into skeletal-based interpretations of nutrition and micronutrient-related health problems for populations undergoing dietary transitions.
Spatio-temporal point processes, partial likelihood, foot and mouth disease

Spatio-temporal point process data arise in many fields of application. An intuitively natural way to specify a model for a spatio-temporal point process is through its conditional intensity at location x and time t, given the history of the process up to time t. Often, this results in an analytically intractable likelihood. Likelihood-based inference then relies on Monte Carlo methods which are computationally intensive and require careful tuning to each application. A partial likelihood alternative is proposed, which is computationally straightforward and can be applied routinely. The method is applied to data from the 2001 foot and mouth epidemic in the UK, using a previously published model for the spatio-temporal spread of the disease.
Regulation of tillering in sorghum: genotypic effects.

BACKGROUND AND AIMS Genotypic variation in tillering can be caused by differences in the carbon supply-demand balance within a plant. The aim of this study was to understand and quantify the effects of genotype on tillering as a consequence of the underlying internal competition for carbohydrates. METHODS Five sorghum hybrids, derived from inbred lines with a common genetic background and with similar phenology and plant height but contrasting tillering, were grown in five experiments. The experiments covered a wide range in radiation and temperature conditions, so that number of tillers produced varied significantly. Data on leaf area, tiller number, and biomass accumulation and partitioning were collected at regular intervals. To quantify internal plant competition for carbohydrates, a carbohydrate supply-demand index (S/D(index)) was developed and related to variation in tillering. KEY RESULTS The appearance of main shoot leaves and tillers was highly co-ordinated across genotypes. High-tillering hybrids had a greater appearance frequency of early tiller ranks than low-tillering hybrids, and this was associated with narrower and hence smaller main shoot leaves. A generalized S/D(index) of internal plant competition accounted for most of the observed variation in maximum tiller number (N(tiller,max)) across genotypes. However, genotypic differences in the relationship between the S/D(index) and N(tiller,max) suggested that high-tillering hybrids also had a lower S/D threshold at which tillers appeared, possibly associated with hormonal effects. CONCLUSIONS The results support the hypothesis that genotypic differences in tillering were associated with differences in plant carbon S/D balance, associated with differences in leaf size and in the threshold at which tillers grow out. The results provide avenues for phenotyping of mapping populations to identify genomic regions regulating tillering. Incorporating the results in crop growth simulation models could provide insight into the complex genotype-by-management-by-environment interactions associated with drought adaptation.
Effect of ADP on PGE1 Formation in Blood Platelets from Patients with Depression, Mania and Schizophrenia

Summary Adenosine diphosphate (ADP) stimulates the synthesis of prostaglandin E1 (PGE1) in lysed platelets from normal subjects, patients with affective illness but not in platelets from cases of schizophrenia. The stimulation is concentration-dependent and follows a curve which is mildly sigmoid in the normal, markedly sigmoid in depression and hyperbolic in mania.
A space-time rainfall generator for highly convective Mediterranean rainstorms

Abstract. Distributed hydrological models require fine resolution rainfall inputs, enhancing the practical interest of space-time rainfall models, capable of generating through numerical simulation realistic space-time rainfall intensity fields. Among different mathematical approaches, those based on point processes and built upon a convenient analytical description of the raincell as the fundamental unit, have shown to be particularly suitable and well adapted when extreme rainfall events of convective nature are considered. Starting from previous formulations, some analytical refinements have been considered, allowing practical generation of space-time rainfall intensity fields for that type of rainstorm events. Special attention is placed on the analytical description of the spatial and temporal evolution of the rainfall intensities produced by the raincells. After deriving the necessary analytical results, the seven parameters of the model have been estimated by the method of moments, for each of the 30 selected rainfall events in the Jucar River Basin (ValenciaSpain) – period 1991 to 2000, using 5-min aggregated rainfall data series from an automatic raingauge network.
On the pro-trade effects of immigrants

This paper investigates the causal effect of immigration on trade flows using Italian panel data at the province level. We exploit the exceptional characteristics of the Italian data (the fine geographical disaggregation, the very high number of countries of origin of immigrants, the high heterogeneity of social and economic characteristics of Italian provinces, and the absence of cultural or historical ties with the countries where immigrants come from) coupled with the use of a wide set of fixed effects and an ‘instrument’ based on immigrants’ enclaves. We find that immigrants have a significant positive effect on both exports and imports, but much larger for the latter. The pro-trade effects of immigrants tend to decline in space, and even turn negative when large ethnic communities are located too far away from a specific province (via a trade-diversion effect). Moreover, while our data show inter-ethnic spillovers for exports, we find no evidence that networks between different ethnicities affect provinces’ imports. Finally, we provide evidence of a substantial heterogeneity in the effects of immigrants: the impact on trade tends to be larger for immigrants coming from low-income countries, for earlier waves of immigrants, and for least advanced provinces (Southern Italy).
Secondary organic aerosol formation from idling gasoline passenger vehicle emissions investigated in a smog chamber

Gasoline vehicles have recently been pointed out as potentially the main source of anthropogenic secondary organic aerosol (SOA) in megacities. However, there is a lack of laboratory studies to systematically investigate SOA for- mation in real-world exhaust. In this study, SOA formation from pure aromatic precursors, idling and cold start gasoline exhaust from three passenger vehicles (EURO2-EURO4) were investigated with photo-oxidation experiments in a 6 m 3 smog chamber. The experiments were carried out down to at- mospherically relevant organic aerosol mass concentrations. The characterization instruments included a high-resolution aerosol mass spectrometer and a proton transfer mass spec- trometer. It was found that gasoline exhaust readily forms SOA with a signature aerosol mass spectrum similar to the oxidized organic aerosol that commonly dominates the or- ganic aerosol mass spectra downwind of urban areas. After a cumulative OH exposure of 5◊ 10 6 cm 3 h, the formed SOA was 1-2 orders of magnitude higher than the primary OA emissions. The SOA mass spectrum from a relevant mix- ture of traditional light aromatic precursors gave f43 (mass fraction at m/z = 43), approximately two times higher than to the gasoline SOA. However O : C and H : C ratios were similar for the two cases. Classical C6-C9 light aromatic precursors were responsible for up to 60 % of the formed SOA, which is significantly higher than for diesel exhaust. Important candidates for additional precursors are higher- order aromatic compounds such as C10 and C11 light aro- matics, naphthalene and methyl-naphthalenes. We conclude that approaches using only light aromatic precursors give an incomplete picture of the magnitude of SOA formation and the SOA composition from gasoline exhaust.
Distributed compression for MIMO coordinated networks with a backhaul constraint

We consider the uplink of a backhaul-constrained, MIMO coordinated network. That is, a single-frequency network with N + 1 multi-antenna base stations (BSs) that cooperate in order to decode the users' data, and that are linked by means of a common lossless backhaul, of limited capacity R. To implement the receive cooperation, we propose distributed compression: N BSs, upon receiving their signals, compress them using a multi-source lossy compression code. Then, they send the compressed vectors to a central BS, which performs users' decoding. Distributed Wyner-Ziv coding is proposed to be used, and is designed in this work. The first part of the paper is devoted to a network with a unique multi-antenna user, that transmits a predefined Gaussian space-time codeword. For such a scenario, the "compression noise" covariance at the BSs is optimized, considering the user's achievable rate as the performance metric. In particular, for N = 1 the optimum covariance is derived in closed form, while for N > 1 an iterative algorithm is devised. The second part of the contribution focusses on the multi-user scenario. For it, the achievable rate region is obtained by means of the optimum "compression noise" covariances for sum-rate and weighted sum-rate, respectively.
Antibody-based immunotherapeutic attempts in experimental animal models of prion diseases

Background: There has been a dramatic decrease in the risk of transmission of bovine spongiform encephalopathy to humans. In contrast, the risk of human-to-human transmission of variant Creutzfeldt-Jakob disease (vCJD) via medical treatments became potentially high since 4 vCJD cases were reported to be possibly transmitted through blood transfusion in the UK. However, no treatments are yet available for curing prion diseases. Objective: Conversion of the normal prion protein, PrPC, to the amyloidogenic PrP, PrPSc, plays a pivotal role in the pathogenesis. Recently, certain anti-PrP or anti-37/67-kDa laminin receptor (LRP/LR) antibodies were shown to have the potential to cure chronically infected cells, clearing PrPSc from the cells. This has raised the possibility of antibody based-immunotherapy for prion diseases. This article aims to introduce and discuss the recently published attempts of immunotherapy in prion diseases. Methods: Bibliographic research was carried out using the PubMed database. Patent literature was searched using the UK Intellectual Property Office website. Results/conclusion: No satisfying consequences in animals could be detected with anti-PrP antibodies directly infused into the brains of animals by the intraventricular route or by anti-PrP or anti-LRP/LR single chain fragment antibodies directly delivered into the brain by virus vector-mediated gene transfer. This is probably because such delivery systems failed to deliver the antibodies to the neurons relevant for the treatments.
Further Comparison of Traffic Noise Predictions Using the CadnaA and SoundPLAN Noise Prediction Models

This paper provides an update of information presented in a paper written for the AAS Acoustics 2008 conference in Geelong, Victoria. In particular this paper presents results of traffic noise modeling using CadnaA and SoundPLAN and compares both to noise measurements for three large recent road projects in NSW. CadnaA is a well known and internationally accepted noise modelling package, and its acceptance and use in Australia amongst acoustic professionals is growing fast. To assist the Australian acoustical profession, the appropriateness and accuracy of CadnaA under Australian conditions is currently being verified, and this paper presents actual project results for this purpose. Unlike CadnaA, the SoundPLAN noise prediction model is extensively used in Australia, particularly for road traffic noise predictions, and has been recognised and accepted nationally by various regulatory authorities including the major road authorities and environmental agencies. The aim of this paper is to provide additional comparative data for predicted traffic noise levels using the Calculation of Road Traffic Noise (CoRTN) algorithms as implemented by SoundPLAN and the CadnaA noise models for three large recent road projects in NSW. These three projects offer features and characteristics that differ significantly from the projects reported in the 2008 paper. Results from this study re-confirm that the CadnaA noise modeling package is accurate and effective for modelling road traffic noise in Australia.
Electron backscattered diffraction analysis of friction stir processed nanocomposites produced via spark plasma sintering

In the present study, Spark Plasma Sintered (SPSed) aluminium matrix composites were severely deformed through Friction stir processing (FSP). Pure aluminium powders and bimodal sized Al2O3 particles (80 nm and 25 μ m) were firstly mixed by ball milling and then consolidated by spark plasma sintering. The effect of the heat input as well the bimodal particle size of the alumina on the materials’ microstructure and texture development was evaluated by electron back scattered diffraction (EBSD) analysis. The EBSD analysis clearly showed that the SPSed nanocomposites possessed bimodal aluminium matrix grain structure as well as a crystallography characterised by random texture. In addition, microstructural examination revealed that the partial recrystallisation occurred during SPS for all the nanocomposites. Also, it is revealed that the Zener pinning effect of Al2O3 nanoparticles retarded recrystallised grain growth following recrystallisation during FSP and then leading to grain refinement of the aluminium. The results revealed that the heat generated during FSP has a remarkable effect on the grain distribution as well as on the crystallographic orientation. Also, a mixture of {112} <110> shear elements and an ideal strong B/ B¯ component were observed. The microstructural changes, occurred during FSP in the stir zone region for Al‐Al2O3 nanocomposites, were attributed to both the discontinuous along with the continuous recrystallisation (DDRX/CDRX). It should be pointed out that with increasing the heat input, recrystallised grains portion increased.