Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of cadmium on cellular protein and glutathione synthesis and expression of stress proteins in eastern oysters, Crassostrea virginica Gmelin

SUMMARY Cadmium (Cd) is an important toxicant in estuarine and coastal environments that can strongly affect energy balance of aquatic organisms by increasing the organism's basal energy demand and reducing its aerobic capacity. Mechanisms of cadmium-induced increase in basal metabolic costs are not well understood and may involve elevated detoxification costs due to the synthesis of cellular protective proteins and glutathione. We studied the short-term effects of cadmium exposure (4 h) on protein and glutathione (GSH) synthesis and expression of stress proteins (heat shock proteins HSP60, HSP70 and HSP90) and metallothioneins in isolated gill and hepatopancreas cells of the eastern oyster, Crassostrea virginica. Our study showed that exposure to cadmium resulted in a dose-dependent increase in the rate of protein synthesis in oyster cells, which reached 150% of the control at the highest tested Cd level (2000 μmol l–1). GSH synthesis was significantly inhibited by the highest Cd concentrations, especially in hepatopancreas, which resulted in a slight but significant decrease in the total GSH concentrations. Elevated protein synthesis was associated with the increased expression of metallothioneins and heat shock proteins. Interestingly, stress protein response differed considerably between gill and hepatopancreas cells. In hepatopancreas, expression of metallothionein mRNA (measured by real-time PCR) increased 2–8-fold in response to Cd exposure, whereas no significant increase in metallothionein expression was found in Cd-exposed gill cells. By contrast, HSP60 and HSP70 protein levels increased significantly in Cd-exposed gill cells (by 1.5–2-fold) but not in hepatopancreas. No change in HSP90 expression was detected in response to Cd exposure in oyster cells. These data indicate that metallothionein expression may provide sufficient protection against Cd-induced damage to intracellular proteins in hepatopancreas, alleviating the need for overexpression of molecular chaperones. By contrast, Cd detoxification mechanisms such as inducible metallothioneins and GSH appear to be insufficient to fully prevent protein damage in gill cells, thus necessitating induction of HSPs as a secondary line of cellular defense. Therefore, gills are likely to be among the most Cd-sensitive tissues in oysters, which may have important implications for impaired oxygen uptake contributing to energy misbalance and reduced aerobic scope in Cd-exposed oysters.
A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

Marine bivalves show among the greatest allozyme diversity ever reported in Eukaryotes, putting them historically at the heart of the neutralist−selectionist controversy on the maintenance of genetic variation. Although it is now acknowledged that this high diversity is most probably a simple consequence of a large population size, convincing support for this explanation would require a rigorous assessment of the silent nucleotide diversity in natural populations of marine bivalves, which has not yet been done. This study investigated DNA sequence polymorphism in a set of 37 nuclear loci in wild samples of the flat oyster Ostrea edulis. Silent diversity was found to be only moderate (0.7%), and there was no departure from demographic equilibrium under the Wright-Fisher model, suggesting that the effective population size might not be as large as might have been expected. In accordance with allozyme heterozygosity, nonsynonymous diversity was comparatively very high (0.3%), so that the nonsynonymous to silent diversity ratio reached a value rarely observed in any other organism. We estimated that one-quarter of amino acid-changing mutations behave as neutral in O. edulis, and as many as one-third are sufficiently weakly selected to segregate at low frequency in the polymorphism. Finally, we inferred that one oyster is expected to carry more than 4800 non-neutral alleles (or 4.2 cM−1). We conclude that a high load of segregating non-neutral amino-acid polymorphisms contributes to high protein diversity in O. edulis. The high fecundity of marine bivalves together with an unpredictable and highly variable success of reproduction and recruitment (sweepstakes reproduction) might produce a greater decoupling between Ne and N than in other organisms with lower fecundities, and we suggest this could explain why a higher segregating load could be maintained for a given silent mutation effective size.
Semantic Part Segmentation with Deep Learning

In this work we address the task of segmenting an object into its parts, or semantic part segmentation. We start by adapting a state-of-the-art semantic segmentation system to this task, and show that a combination of a fully-convolutional Deep CNN system coupled with Dense CRF labelling provides excellent results for a broad range of object categories. Still, this approach remains agnostic to high-level constraints between object parts. We introduce such prior information by means of the Restricted Boltzmann Machine, adapted to our task and train our model in an entirely discriminative fashion, as a hidden CRF, demonstrating that prior information can yield additional improvements. We evaluate the performance of our approach on the Penn-Fudan and LFW datasets for the tasks of pedestrian parsing and face labelling respectively. We show superior performance with respect to competitive methods that have been extensively engineered on these benchmarks, as well as realistic qualitative results on part segmentation, even in challenging cases, such as occluded or deformable objects. We also provide quantitative and extensive qualitative results on three classes from the PASCAL Parts dataset.
Journal of Economic Behavior & Organization Performance Pay and Worker Cooperation: Evidence from an Artefactual Field Experiment

We report the results of an artefactual field experiment with bicycle messengers in Switzer-land and the United States. Messenger work is individualized enough that firms can choose to condition pay on it, but significant externalities in messenger behavior nonetheless give their on-the-job interactions the character of a social dilemma. Second-mover behavior in our sequential prisoner's dilemma allows us to characterize the cooperativeness of our participants. Among messengers, we find that employees at firms that pay for performance are significantly less cooperative than those at firms that pay hourly wages or who are members of cooperatives. To examine whether the difference is the result of treatment or selection we exploit the fact that firm type is location-specific in Switzerland and that entering messengers must work in performance pay firms in the U.S.
Stochastic boosting for large-scale image classification

Boosting has been extensively used in image processing. Many work focuses on the design or the usage of boosting, but training boosting on large-scale datasets tends to be ignored. To handle the large-scale problem, we present stochastic boosting (StocBoost) that relies on stochastic gradient descent (SGD) which uses one sample at each iteration. To understand the efficacy of StocBoost, the convergence of training algorithm is theoretically analyzed. Experimental results show that StocBoost is faster than the batch ones, and is also comparable with the state-of-the-arts.
Prediction of Cement Physical Properties by Virtual Testing

Assuring the quality of the massive quantities of cement produced worldwide each year is a daunting task. Currently, the cement industry performs extensive physical testing to assess the quality of their product, resulting in large costs for both materials (and their disposal) and labor. One of the major goals of the Virtual Cement and Concrete Testing Laboratory (VCCTL) consortium is to provide the technology to reduce the number of necessary physical tests. In this paper, the ability of the VCCTL to successfully predict a wide variety of cement paste physical properties is demonstrated. Predicted physical properties are compared to experimental measurements for degree of hydration, heat of hydration, chemical shrinkage, setting times, compressive strength development, and pore solution concentrations. When the starting materials are characterized in detail, good agreement is exhibited between VCCTL model predictions and experimental measurements, highlighting the potential for this virtual technology to ultimately save the cement industry both time and money.
A Pro-Apoptotic Fragment of the p75 Neurotrophin Receptor Is Expressed in p75NTRExonIV Null Mice

The p75 neurotrophin receptor (p75NTR) regulates neuronal survival, apoptosis, and growth. Recent studies have reported that disruption of Exon IV produces a null mouse lacking all p75NTR gene products (p75NTRExonIV-/-), whereas mice lacking p75NTR Exon III (p75NTRExonIII-/-) maintain expression of an alternatively spliced form of p75NTR (s-p75NTR). Here, we report that p75NTRExonIV-/- mice express a p75NTR gene product that encodes a truncated protein containing the extracellular stalk region together with the entire transmembrane and intracellular domains. The gene product is initiated from a cryptic Kozak consensus/initiator ATG sequence within a region of Exon IV located 3′ to the pGK-Neo insertion site. Overexpression of this fragment in heterologous cells results in activation of Jun kinase and induces Pro-caspase-3 cleavage, indicating that it activates p75NTR signaling cascades. These results indicate that aspects of the p75NTRExonIV-/- phenotype may reflect a gain-of-function mutation rather than loss of p75NTR function.
Multiple parasite infections and their relationship to self-reported morbidity in a community of rural Côte d'Ivoire.

BACKGROUND Concomitant parasitic infections are common in the developing world, yet most studies focus on a single parasite in a narrow age group. We investigated the extent of polyparasitism and parasite associations, and related these findings to self-reported morbidity. METHODS Inhabitants of 75 randomly selected households from a single village in western Côte d'Ivoire provided multiple faecal specimens and a single finger prick blood sample. The Kato-Katz technique and a formol-ether concentration method were employed to screen faecal samples for Schistosoma mansoni, soil-transmitted helminths and intestinal protozoa. Giemsa-stained blood smears were analysed for malaria parasites. A questionnaire was administered for collection of demographic information and self-reported morbidity indicators. RESULTS Complete parasitological data were obtained for 500/561 (89.1%) participants, similarly distributed among sex, with an age range from 5 days to 91 years. The prevalences of Plasmodium falciparum, hookworms, Entamoeba histolytica/E. dispar, and S. mansoni were 76.4%, 45.0%, 42.2%, and 39.8%, respectively. Three-quarters of the population harboured three or more parasites concurrently. Multivariate analysis revealed significant associations between several pairs of parasites. Some parasitic infections and the total number of parasites were significantly associated with self-reported morbidity indicators. CONCLUSIONS Our data confirm that polyparasitism is very common in rural Côte d'Ivoire and that people have clear perceptions about the morbidity caused by some of these parasitic infections. Our findings can be used for the design and implementation of sound intervention strategies to mitigate morbidity and co-morbidity.
An Energy-Efficient High-Throughput Mesh-Based Photonic On-Chip Interconnect for Many-Core Systems

Future high-performance embedded and general purpose processors and systems-on-chip are expected to combine hundreds of cores integrated together to satisfy the power and performance requirements of large complex applications. As the number of cores continues to increase, the employment of low-power and high-throughput on-chip interconnect fabrics becomes imperative. In this work, we present a novel mesh-based photonic on-chip interconnect, named PHENIC-II, for future high-performance many-core systems. The novel architecture is based on an energy-efficient non-blocking photonic switch and a contention-aware routing algorithm. Simulation results show that the proposed system provides better bandwidth and energy efficiency when compared to conventional hybrid photonic NoC systems.
Linked Knowledge Sources for Topic Classification of Microposts: A Semantic Graph-Based Approach

Short text messages, a.k. a microposts (e.g., tweets), have proven to be an effective channel for revealing information about trends and events, ranging from those related to disaster (e.g., Hurricane Sandy) to those related to violence (e.g., Egyptian revolution). Being informed about such events as they occur could be extremely important to authorities and emergency professionals by allowing such parties to immediately respond. In this work we study the problem of topic classification (TC) of microposts, which aims to automatically classify short messages based on the subject(s) discussed in them. The accurate TC of microposts however is a challenging task since the limited number of tokens in a post often implies a lack of sufficient contextual information. In order to provide contextual information to microposts, we present and evaluate several graph structures surrounding concepts present in linked knowledge sources (KSs). Traditional TC techniques enrich the content of microposts with features extracted only from the microposts content. In contrast our approach relies on the generation of different weighted semantic meta-graphs extracted from linked KSs. We introduce a new semantic graph, called category meta-graph. This novel meta-graph provides a more fine grained categorisation of concepts providing a set of novel semantic features. Our findings show that such category meta-graph features effectively improve the performance of a topic classifier of microposts. Furthermore our goal is also to understand which semantic feature contributes to the performance of a topic classifier. For this reason we propose an approach for automatic estimation of accuracy loss of a topic classifier on new, unseen microposts. We introduce and evaluate novel topic similarity measures, which capture the similarity between the KS documents and microposts at a conceptual level, considering the enriched representation of these documents. Extensive evaluation in the context of Emergency Response (ER) and Violence Detection (VD) revealed that our approach outperforms previous approaches using single KS without linked data and Twitter data only up to 31.4% in terms of F1 measure. Our main findings indicate that the new category graph contains useful information for TC and achieves comparable results to previously used semantic graphs. Furthermore our results also indicate that the accuracy of a topic classifier can be accurately predicted using the enhanced text representation, outperforming previous approaches considering content-based similarity measures.
Magnetic braking in young late-type stars : The effect of polar spots

Context. The existence of rapidly rotating cool stars in young clusters implies a reduction of angular momentum loss rate for a certain period of the star’s early life. Recently, the concentration of magnetic flux near the poles of these stars has been proposed as an alternative mechanism to dynamo saturation in order to explain the saturation of angular momentum loss. Aims. In this work we study the effect of magnetic surface flux distribution on the coronal field topology and angular momentum loss rate. We investigate if magnetic flux concentration towards the pole is a reasonable alternative to dynamo saturation. Methods. We construct a 1D wind model and also apply a 2-D self-similar analytical model, to evaluate how the surface field distribution affects the angular momentum loss of the rotating star. Results. From the 1D model we find that, in a magnetically dominated low corona, the concentrated polar surface field rapidly expands to regions of low magnetic pressure resulting in a coronal field with small latitudinal variation. We also find that the angular momentum loss rate due to a uniform field or a concentrated field with equal total magnetic flux is very similar. From the 2D wind model we show that there are several relevant factors to take into account when studying the angular momentum loss from a star. In particular, we show that the inclusion of force balance across the field in a wind model is fundamental if realistic conclusions are to be drawn from the effect of non-uniform surface field distribution on magnetic braking. This model predicts that a magnetic field concentrated at high latitudes leads to larger Alfven radii and larger braking rates than a smoother field distribution. Conclusions. From the results obtained, we argue that the magnetic surface field distribution towards the pole does not directly limit the braking efficiency of the wind.
The Role of CTLA-4 Exon-1 49 A/G Polymorphism and Soluble CTLA-4 Protein Level in Egyptian Patients with Behçet's Disease

This study analyzed the association of the A/G SNP at position +49 of exon-1 in the CTLA-4 gene to the susceptibility and clinical manifestations of Behcet's disease (BD). It was performed on 60 Egyptian BD patients and 95 age- and sex-matched healthy controls. The genotypes for the +49 A/G polymorphism of the CTLA-4 gene were determined by PCR-RFLP, while the serum level of CTLA-4 protein was measured by ELISA. CTLA-4 +49 A allele (P < 0.001, OR = 3.084, and CI (95%) = 1.90–4.99) and A/A genotype (P < 0.001, OR = 6.643, and CI (95%) = 2.58–17.10) frequency distribution was significantly more increased in patients than in the controls, with no significant differences between males and females with regard to the genotype or allele frequency distribution. A/A genotype was associated with a more reduced expression of sCTLA-4 protein in patients than in the controls (1.76 ± 0.19 versus 1.91 ± 0.30, resp; P < 0.0007). In addition, it is associated with the occurrence of ocular and vasculitic manifestations of BD in the patient group. The CTLA-4 gene could be considered as a susceptibility and a disease-modifying gene to BD in Egyptian population that needs further confirmatory studies on larger cohorts.
Cognitive Reserve in Granulin-Related Frontotemporal Dementia: from Preclinical to Clinical Stages

Objective Consistent with the cognitive reserve hypothesis, higher education and occupation attainments may help persons with neurodegenerative dementias to better withstand neuropathology before developing cognitive impairment. We tested here the cognitive reserve hypothesis in patients with frontotemporal dementia (FTD), with or without pathogenetic granulin mutations (GRN+ and GRN-), and in presymptomatic GRN mutation carriers (aGRN+). Methods Education and occupation attainments were assessed and combined to define Reserve Index (RI) in 32 FTD patients, i.e. 12 GRN+ and 20 GRN-, and in 17 aGRN+. Changes in functional connectivity were estimated by resting state fMRI, focusing on the salience network (SN), executive network (EN) and bilateral frontoparietal networks (FPNs). Cognitive status was measured by FTD-modified Clinical Dementia Rating Scale. Results In FTD patients higher level of premorbid cognitive reserve was associated with reduced connectivity within the SN and the EN. EN was more involved in FTD patients without GRN mutations, while SN was more affected in GRN pathology. In aGRN+, cognitive reserve was associated with reduced SN. Conclusions This study suggests that cognitive reserve modulates functional connectivity in patients with FTD, even in monogenic disease. In GRN inherited FTD, cognitive reserve mechanisms operate even in presymptomatic to clinical stages.
Sliding mode control for uncertain discrete-time system using robust model predictive control in reaching mode

In sliding mode control, state trajectory is divided to reaching mode and sliding mode. A method of robust model predictive control is employed to improve performance in reaching mode. Uncertain discrete time systems can be transformed to polytopic uncertain system. Then, the employed robust model predictive control can handle the robustness in uncertain polytopic system. The strong point of the proposed method is optimization of the cost function. As a result, the convergence rate to sliding surface is improved in reaching mode. Moreover, input constraint can be considered. A numerical example illustrates the effectiveness of the proposed method by comparison with existing methods.
Yeast G1 DNA damage checkpoint regulation by H2A phosphorylation is independent of chromatin remodeling

Recent studies of yeast G1 DNA damage response have identified characteristic changes in chromatin adjacent to double-strand breaks (DSBs). Histone H2A (yeast H2AX) is rapidly phosphorylated on S129 by the kinase Tel1 (ATM) over a domain extending kilobases from the DSB. The adaptor protein Rad9 (53BP1) is recruited to this chromatin domain through binding of its tudor domains to histone H3 diMe-K79. Multisite phosphorylation of Rad9 by Mec1 (ATR) then activates the signaling kinase Rad53 (CHK2) to induce a delay in G1. Here, we report a previously undescribed role for Tel1 in G1 checkpoint response and show that H2A is the likely phosphorylation target, in a much as S129 mutation to Ala confers defects in G1 checkpoint arrest, Rad9 phosphorylation, and Rad53 activation. Importantly, Rad9 fails to bind chromatin adjacent to DSBs in H2A-S129A mutants. Previous work showed that H2A phosphorylation allows binding of NuA4, SWR, and INO80 chromatin remodeling complexes, perhaps exposing H3 diMe-K79. Yet, mutants lacking SWR or INO80 remain checkpoint competent, whereas loss of NuA4-dependent histone acetylation leads to G1 checkpoint persistence, suggesting that H2A phosphorylation promotes two independent events, rapid Rad9 recruitment to DSBs and subsequent remodeling by NuA4, SWR, and INO80.
Key players of singlet oxygen-induced cell death in plants

The production of reactive oxygen species (ROS) is an unavoidable consequence of oxygenic photosynthesis. Singlet oxygen (1O2) is a highly reactive species to which has been attributed a major destructive role during the execution of ROS-induced cell death in photosynthetic tissues exposed to excess light. The study of the specific biological activity of 1O2 in plants has been hindered by its high reactivity and short lifetime, the concurrent production of other ROS under photooxidative stress, and limited in vivo detection methods. However, during the last 15 years, the isolation and characterization of two 1O2-overproducing mutants in Arabidopsis thaliana, flu and ch1, has allowed the identification of genetically controlled 1O2 cell death pathways and a 1O2 acclimation pathway that are triggered at sub-cytotoxic concentrations of 1O2. The study of flu has revealed the control of cell death by the plastid proteins EXECUTER (EX)1 and EX2. In ch1, oxidized derivatives of β-carotene, such as β-cyclocitral and dihydroactinidiolide, have been identified as important upstream messengers in the 1O2 signaling pathway that leads to stress acclimation. In both the flu and ch1 mutants, phytohormones act as important promoters or inhibitors of cell death. In particular, jasmonate has emerged as a key player in the decision between acclimation and cell death in response to 1O2. Although the flu and ch1 mutants show many similarities, especially regarding their gene expression profiles, key differences, such as EXECUTER-independent cell death in ch1, have also been observed and will need further investigation to be fully understood.