Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclooxygenase (COX)-2 Inhibitors Reduce Toxoplasma gondii Infection and Upregulate the Pro-inflammatory Immune Response in Calomys callosus Rodents and Human Monocyte Cell Line

Toxoplasma gondii is able to infect a wide range of vertebrates, including humans. Studies show that cyclooxygenase-2 (COX-2) is a modulator of immune response in multiple types of infection, such as Trypanosoma cruzi. However, the role of COX-2 during T. gondii infection is still unclear. The aim of this study was to investigate the role of COX-2 during infection by moderately or highly virulent strains of T. gondii in Calomys callosus rodents and human THP-1 cells. C. callosus were infected with 50 cysts of T. gondii (ME49), treated with COX-2 inhibitors (meloxicam or celecoxib) and evaluated to check body weight and morbidity. After 40 days, brain and serum were collected for detection of T. gondii by real-time PCR and immunohistochemistry or cytokines by CBA. Furthermore, peritoneal macrophages or THP-1 cells, infected with RH strain or uninfected, were treated with meloxicam or celecoxib to evaluate the parasite proliferation by colorimetric assay and cytokine production by ELISA. Finally, in order to verify the role of prostaglandin E2 in COX-2 mechanism, THP-1 cells were infected, treated with meloxicam or celecoxib plus PGE2, and analyzed to parasite proliferation and cytokine production. The data showed that body weight and morbidity of the animals changed after infection by T. gondii, under both treatments. Immunohistochemistry and real-time PCR showed a reduction of T. gondii in brains of animals treated with both COX-2 inhibitors. Additionally, it was observed that both COX-2 inhibitors controlled the T. gondii proliferation in peritoneal macrophages and THP-1 cells, and the treatment with PGE2 restored the parasite growth in THP-1 cells blocked to COX-2. In the serum of Calomys, upregulation of pro-inflammatory cytokines was detected, while the supernatants of peritoneal macrophages and THP-1 cells demonstrated significant production of TNF and nitrite, or TNF, nitrite and MIF, respectively, under both COX-2 inhibitors. Finally, PGE2 treatment in THP-1 cells triggered downmodulation of pro-inflammatory mediators and upregulation of IL-8 and IL-10. Thus, COX-2 is an immune mediator involved in the susceptibility to T. gondii regardless of strain or cell types, since inhibition of this enzyme induced control of infection by upregulating important pro-inflammatory mediators against Toxoplasma.
Functional Genes and Bacterial Communities During Organohalide Respiration of Chloroethenes in Microcosms of Multi-Contaminated Groundwater

Microcosm experiments with CE-contaminated groundwater from a former industrial site were set-up to evaluate the relationships between biological CE dissipation, dehalogenase genes abundance and bacterial genera diversity. Impact of high concentrations of PCE on organohalide respiration was also evaluated. Complete or partial dechlorination of PCE, TCE, cis-DCE and VC was observed independently of the addition of a reducing agent (Na2S) or an electron donor (acetate). The addition of either 10 or 100 μM PCE had no effect on organohalide respiration. qPCR analysis of reductive dehalogenases genes (pceA, tceA, vcrA, and bvcA) indicated that the version of pceA gene found in the genus Dehalococcoides [hereafter named pceA(Dhc)] and vcrA gene increased in abundance by one order of magnitude during the first 10 days of incubation. The version of the pceA gene found, among others, in the genus Dehalobacter, Sulfurospirillum, Desulfuromonas, and Geobacter [hereafter named pceA(Dhb)] and bvcA gene showed very low abundance. The tceA gene was not detected throughout the experiment. The proportion of pceA(Dhc) or vcrA genes relative to the universal 16S ribosomal RNA (16S rRNA) gene increased by up to 6-fold upon completion of cis-DCE dissipation. Sequencing of 16S rRNA amplicons indicated that the abundance of Operational Taxonomic Units (OTUs) affiliated to dehalogenating genera Dehalococcoides, Sulfurospirillum, and Geobacter represented more than 20% sequence abundance in the microcosms. Among organohalide respiration associated genera, only abundance of Dehalococcoides spp. increased up to fourfold upon complete dissipation of PCE and cis-DCE, suggesting a major implication of Dehalococcoides in CEs organohalide respiration. The relative abundance of pceA and vcrA genes correlated with the occurrence of Dehalococcoides and with dissipation extent of PCE, cis-DCE and CV. A new type of dehalogenating Dehalococcoides sp. phylotype affiliated to the Pinellas group, and suggested to contain both pceA(Dhc) and vcrA genes, may be involved in organohalide respiration of CEs in groundwater of the study site. Overall, the results demonstrate in situ dechlorination potential of CE in the plume, and suggest that taxonomic and functional biomarkers in laboratory microcosms of contaminated groundwater following pollutant exposure can help predict bioremediation potential at contaminated industrial sites.
Transcriptional Shifts Highlight the Role of Nutrients in Harmful Brown Tide Dynamics

Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.
The Key Factors in Physical Activity Type Detection Using Real-Life Data: A Systematic Review

Background: Physical activity (PA) is paramount for human health and well-being. However, there is a lack of information regarding the types of PA and the way they can exert an influence on functional and mental health as well as quality of life. Studies have measured and classified PA type in controlled conditions, but only provided limited insight into the validity of classifiers under real-life conditions. The advantage of utilizing the type dimension and the significance of real-life study designs for PA monitoring brought us to conduct a systematic literature review on PA type detection (PATD) under real-life conditions focused on three main criteria: methods for detecting PA types, using accelerometer data collected by portable devices, and real-life settings. Method: The search of the databases, Web of Science, Scopus, PsycINFO, and PubMed, identified 1,170 publications. After screening of titles, abstracts and full texts using the above selection criteria, 21 publications were included in this review. Results: This review is organized according to the three key elements constituting the PATD process using real-life datasets, including data collection, preprocessing, and PATD methods. Recommendations regarding these key elements are proposed, particularly regarding two important PA classes, i.e., posture and motion activities. Existing studies generally reported high to near-perfect classification accuracies. However, the data collection protocols and performance reporting schemes used varied significantly between studies, hindering a transparent performance comparison across methods. Conclusion: Generally, considerably less studies focused on PA types, compared to other measures of PA assessment, such as PA intensity, and even less focused on real-life settings. To reliably differentiate the basic postures and motion activities in real life, two 3D accelerometers (thigh and hip) sampling at 20 Hz were found to provide the minimal sensor configuration. Decision trees are the most common classifier used in practical applications with real-life data. Despite the significant progress made over the past year in assessing PA in real-life settings, it remains difficult, if not impossible, to compare the performance of the various proposed methods. Thus, there is an urgent need for labeled, fully documented, and openly available reference datasets including a common evaluation framework.
Polymer Solar Cells—Interfacial Processes Related to Performance Issues

Harnessing solar energy with solar cells based on organic materials (in particular polymeric solar cells) is an attractive alternative to silicon-based solar cells due to the advantages of lower weight, flexibility, lower manufacturing costs, easier integration with other products, low environmental impact during manufacturing and operations and short energy payback times. However, even with the latest efficiencies reported up to 17%, the reproducibility of these efficiencies is not up to par, with a significant variation in the efficiencies reported across the literature. Since these devices are based on ultrathin multilayer organic films, interfaces play a major role in their operation and performance. This review gives a concise account of the major interfacial issues that are responsible for influencing the device performance, with emphasis on their physical mechanisms. After an introduction to the basic principles of polymeric solar cells, it briefly discusses charge generation and recombination occurring at the donor-acceptor bulk heterojunction interface. It then discusses interfacial morphology for the active layer and how it affects the performance and stability of these devices. Next, the formation of injection and extraction barriers and their role in the device performance is discussed. Finally, it addresses the most common approaches to change these barriers for improving the solar cell efficiency, including the use of interface dipoles. These issues are interrelated to each other and give a clear and concise understanding of the problem of the underperformance due to interfacial phenomena occurring within the device. This review not only discusses some of the implemented approaches that have been adopted in order to address these problems, but also highlights interfacial issues that are yet to be fully understood in organic solar cells.
Feasibility of Human Neural Stem Cell Transplantation for the Treatment of Acute Subdural Hematoma in a Rat Model: A Pilot Study

Human neural stem cells (hNSCs) transplantation in several brain injury models has established their therapeutic potential. However, the feasibility of hNSCs transplantation is still not clear for acute subdural hematoma (ASDH) brain injury that needs external decompression. Thus, the aim of this pilot study was to test feasibility using a rat ASDH decompression model with two clinically relevant transplantation methods. Two different methods, in situ stereotactic injection and hNSC-embedded matrix seating on the brain surface, were attempted. Athymic rats were randomized to uninjured or ASDH groups (F344/NJcl-rnu/rnu, n = 7–10/group). Animals in injury group were subjected to ASDH, and received decompressive craniectomy and 1-week after decompression surgery were transplanted with green fluorescent protein (GFP)-transduced hNSCs using one of two approaches. Histopathological examinations at 4 and 8 weeks showed that the GFP-positive hNSCs survived in injured brain tissue, extended neurite-like projections resembling neural dendrites. The in situ transplantation group had greater engraftment of hNSCs than matrix embedding approach. Immunohistochemistry with doublecortin, NeuN, and GFAP at 8 weeks after transplantation showed that transplanted hNSCs remained as immature neurons and did not differentiate toward to glial cell lines. Motor function was assessed with rotarod, compared to control group (n = 10). The latency to fall from the rotarod in hNSC in situ transplanted rats was significantly higher than in control rats (median, 113 s in hNSC vs. 69 s in control, P = 0.02). This study first demonstrates the robust engraftment of in situ transplanted hNSCs in a clinically-relevant ASDH decompression rat model. Further preclinical studies with longer study duration are warranted to verify the effectiveness of hNSC transplantation in amelioration of TBI induced deficits.
Linking Hypothesis and Number of Response Options Modulate Inferred Scalar Implicature Rate

The past 15 years have seen increasing experimental investigations of core pragmatic questions in the ever more active and lively field of experimental pragmatics. Within experimental pragmatics, many of the core questions have relied on the operationalization of the theoretical notion of “implicature rate. ” Implicature rate based results have informed the work on acquisition, online processing, and scalar diversity, inter alia. Implicature rate has typically been quantified as the proportion of “pragmatic” judgments in two-alternative forced choice truth value judgment tasks. Despite its theoretical importance, this linking hypothesis from implicature rate to behavioral responses has never been extensively tested. Here we show that two factors dramatically affect the “implicature rate” inferred from truth value judgment tasks: (a) the number of responses provided to participants; and (b) the linking hypothesis about what constitutes a “pragmatic” judgment. We argue that it is time for the field of experimental pragmatics to engage more seriously with its foundational assumptions about how theoretical notions map onto behaviorally measurable quantities, and present a sketch of an alternative linking hypothesis that derives behavior in truth value judgment tasks from probabilistic utterance expectations.
Follicle Stimulating Hormone Receptor (FSHR) Polymorphisms and Polycystic Ovary Syndrome (PCOS)

Polycystic ovary syndrome (PCOS) is the commonest endocrine abnormality in women of reproductive age typically presenting with chronic oligo- or anovulation, clinical, or biochemical hyperandrogenism and polycystic ovarian morphology (PCOM). Restoring mono-ovulation is the ultimate goal of ovulation induction and most women do respond to ovulation inducing agents causing their Follicle-stimulating hormone (FSH) levels to rise. Familial clustering and the results from twin studies strongly support an underlying genetic basis for PCOS. Recent Genome wide association studies (GWAS) have identified several genetic variants being genome wide significantly associated with PCOS. Amongst those are variants in or near the Luteinizing hormone (LH) and FSH receptor genes as well as a variant in the FSH-β gene. The aim of this review is to summarize the available evidence as to whether single nucleotide polymorphisms are able to modify the PCOS phenotype or whether they constitute a risk factor for the syndrome. Data on the role of FSHR polymorphisms in PCOS are conflicting. It seems that in large Chinese studies FSHR polymorphisms are not associated with either PCOS risk or with PCOS treatment outcome. However, in large scale studies in Caucasians these polymorphisms seem to influence the risk of having PCOS. Moreover, these studies also showed that some polymorphisms might affect some clinical features of PCOS as well as treatment outcome. Although most research has focussed on the role of FSHR polymorphisms there seems to be also some evidence showing that single nucleotide polymorphisms (SNPs) in the LHCG-Receptor as well as those in FSH-β gene might also alter the phenotype of PCOS. In conclusion most studies confirm that FSHR polymorphisms do alter the phenotype of PCOS in that they either alter the response to exogenous FSH or hat they increase the risk of having PCOS.
HUSH, a Link Between Intrinsic Immunity and HIV Latency

A prominent obstacle to HIV eradication in seropositive individuals is the viral persistence in latent reservoir cells, which constitute an HIV sanctuary out of reach of highly active antiretroviral therapies. Thus, the study of molecular mechanisms governing latency is a very active field that aims at providing solutions to face the reservoirs issue. Since the past 15 years, another major field in HIV biology focused on the discovery and study of restriction factors that shape intrinsic immunity, while engaging in a molecular battle against HIV. Some of these restrictions factors act at early stages of the virus life cycle, alike SAMHD1 antagonized by the viral protein Vpx, while others are late actors. Until recently, no such factor was identified in the nucleus and found active at the level of provirus expression, a crucial step where latency may take place. Today, two studies highlight Human Silencing Hub (HUSH) as a potential restriction factor that controls viral expression and is antagonized by Vpx. This Review discusses HUSH restriction in the light of the actual knowledge of intrinsic immunity and HIV latency.
Localization and dynamics of Wolbachia infection in Asian citrus psyllid Diaphorina citri, the insect vector of the causal pathogens of Huanglongbing

Wolbachia is a group of intracellular bacteria that infect a wide range of arthropods including the Asian citrus psyllid (ACP), Diaphorina citri Kuwayama. This insect is the vector of Candidatus Liberibacter asiaticus (CLas), the causal pathogen of Huanglongbing or citrus greening disease. Here, we investigated the localization pattern and infection dynamics of Wolbachia in different developmental stages of ACP. Results revealed that all developmental stages of ACP including egg, 1st–5th instar nymphs, and adults of both gender were infected with Wolbachia. FISH visualization of an ACP egg showed that Wolbachia moved from the egg stalk of newly laid eggs to a randomly distributed pattern throughout the egg prior to hatching. The infection rate varied between nymphal instars. The titers of Wolbachia in fourth and fifth instar nymphs were significantly higher than those in the first and second instar nymphs. Wolbachia were scattered in all nymphal stages, but with highest intensity in the U‐shaped bacteriome located in the abdomen of the nymph. Wolbachia was confined to two symmetrical organizations in the abdomen of newly emerged female and male adults. The potential mechanisms of Wolbachia infection dynamics are discussed.
What's eating us about what we're eating.

In order to assess the time at which the distant metastases were initiated, a model has been developed to simulate the natural history of human breast cancer. The metastasis appearance curves were fitted to those observed for tumours of various sizes among the 2648 patients treated at the Institut Gustave Roussy from 1954 to 1972. The model assumes that metastases are initiated when the tumour reaches a threshold volume (distribution of this volume was estimated in a previous article). Two patterns of growth were considered: exponential and Gompertzian. Distributions of tumour and metastases doubling times are fixed according to the literature. A relationship between tumour and metastasis doubling time is estimated. Simulations were used to optimize metastases growth duration as a function of the metastasis doubling time. The ages of the metastases at tumour diagnosis are calculated. With exponential growth, it was necessary to introduce correlations to obtain a satisfactory fit of the metastases appearance curves: between the tumour volume at diagnosis and the doubling time (RI = -0.3), and between the tumour volume at metastasis initiation and the doubling time (R2=0.3). The growth duration of the metastases before their detection was found to equal about 18 metastases doubling times at detection and the mean ratio between the doubling time of a tumour and its metastases equal to 2.2. With Gompertzian growth, it was impossible to adjust satisfactorily the proportions of metastases at diagnosis as a function of the primary tumour volume. However, when we ignore this, the best fit was obtained when the duration of metastases growth before detection was about the same as for exponential growth. With either growth pattern, the model predicts that the proportion of patients with metastases would be reduced by -30% if the primary tumours were treated 12 months earlier. This prediction is consistent with the results of the screening programs for breast cancer.
Vision-Based Hierarchical Fuzzy Controller and Real Time Results for a Wheeled Autonomous Robot

One of the most important problems in robotics is motion planning problem, which its basic controversy is to plan a collision-free path between initial and target configurations for a robot. In the framework of motion planning for nonholonomic systems, the wheeled robots have attracted a significant amount of interest. The path planner of a wheeled autonomous robot has to meet nonholonomic constraints and then the movement direction must always be tangent to its trajectory (Paromtichk et. al., 1998; Latombe, 1991, Murray & Sastry, 1993; Lamiraux & Laumond, 2001; Scheuer & Fraichard, 1996). If no obstacles exist on path of the robot, then the robot task is finding the shortest path connecting two given initial and final configurations. The shortest paths for a car like vehicle consist of a finite sequence of two elementary components: arcs of circle (with minimum turning radii) and straight line segments. In any case, the problem is that the curvature is discontinuous between two elementary components, so that these shortest paths cannot be followed precisely without stopping at each discontinuity point to reorient the front wheels. To avoid these stops, several authors have proposed continuous-curvature path planners using differential geometric methods. These planners generate clothoids, cubic spirals, ┚-splines, quintic polynomials, etc., which are then followed by using a path-tracking technique based on, for example, pure-pursuit or predictive control methods (Lamiraux & Laumond, 2001; Scheuer & Fraichard, 1996). Stabilization issues of path-tracking methods for car-like vehicles using the Lyapunov method have been reported in (Walsh et. al., 1994; Tayebi & Rachid, 1996). One of the key technologies of future automobiles is the parking assist or automatic parking control. Control problems of a car-like vehicle are not easy because of the nonholonomic velocity constraints. The truck backer-upper control is a typical nonlinear control problem that cannot be solved by the conventional control techniques. The goal of controller is to back up a truck to a loading dock from any initial position as quickly and precisely as possible. Backing a truck to the loading dock or parking spot is a difficult task even for a skilled truck driver. The research in parking problem is derived from the study of general motion planning for autonomous robots. In the past few decades, many algorithms have been developed for robot parking planning (Jiang & Seneviratne, 1999; Gomez-Bravo et. al., 2001; Cuesta et. al., 2004; Reeds & Shepp, 1990). The attempts to