Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Alpha Kinase EhAK1 Phosphorylates Actin and Regulates Phagocytosis in Entamoeba histolytica

Phagocytosis plays a key role in nutrient uptake and virulence of the protist parasite Entamoeba histolytica. Phagosomes have been characterized by proteomics, and their maturation in the cells has been studied. However, there is so far not much understanding about initiation of phagocytosis and formation of phagosomes at the molecular level. Our group has been studying initiation of phagocytosis and formation of phagosomes in E. histolytica, and have described some of the molecules that play key roles in the process. Here we show the involvement of EhAK1, an alpha kinase and a SH3 domain containing protein in the pathway that leads to formation of phagosomes using red blood cell as ligand particle. A number of approaches, such as proteomics, biochemical, confocal imaging using specific antibodies or GFP tagged molecules, expression down regulation by antisense RNA, over expression of wild type and mutant proteins, were used to understand the role of EhAK1 in phagocytosis. EhAK1 was found in the phagocytic cups during the progression of cups, until closure of phagosomes, but not in the phagosomes themselves. It is recruited to the phagosomes through interaction with the calcium binding protein EhCaBP1. A reduction in phagocytosis was observed when EhAK1 was down regulated by antisense RNA, or by over expression of the kinase dead mutant. G-actin was identified as one of the major substrates of EhAK1. Phosphorylated actin preferentially accumulated at the phagocytic cups and over expression of a phosphorylation defective actin led to defects in phagocytosis. In conclusion, we describe an important component of the pathway that is initiated on attachment of red blood cells to E. histolytica cells. The main function of EhAK1 is to couple signalling events initiated after accumulation of EhC2PK to actin dynamics.
The strength of sharply bounded induction

We prove that the sharply bounded arithmetic T02 in a language containing the function symbol ⌊x /2y ⌋ (often denoted by MSP) is equivalent to PV1. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical Investigation of Iterative Phase Retrieval Algorithm for Quasi-Optical Millimeter-Wave RF Beams

In this paper, we present a detailed analysis of the iterative phase retrieval approach (IPRA) for determining the phase profile of the output microwave beam of a gyrotron from known intensity patterns emphasizing the field propagation techniques which are used to propagate the RF field of the microwave beam between known intensity planes. The propagation method, based on first Rayleigh-Sommerfeld diffraction integral (RSDI), is solved using fast Fourier transform (FFT) technique and zero padding. It is observed that the use of FFT and, therefore, the discretization of the RSDI propagation kernel introduce aberrations in the propagated field due to the superposition of the original field with its replicated versions. This problem is solved by approximations leading to the Huygens-Fresnel propagation method which further imposes the restrictions on the distances of propagation depending on the size of the transverse plane used to discretize the intensity pattern. This constraint of the distance of propagation causes problem in the iterative phase retrieval approach (IPRA) when more than two intensity planes are used. A method based on interpolation is proposed to overcome this restriction. IPRA is then further discussed to optimize several parameters, such as plane separation, plane dimension, mesh size, and measurement accuracies, which become more of an issue during the measurements of infrared intensity thermograms of the output microwave beam.
Effects of rising temperatures and [CO2] on the physiology of tropical forest trees

Using a mixture of observations and climate model outputs and a simple parametrization of leaf-level photosynthesis incorporating known temperature sensitivities, we find no evidence for tropical forests currently existing ‘dangerously close’ to their optimum temperature range. Our model suggests that although reductions in photosynthetic rate at leaf temperatures (TL) above 30°C may occur, these are almost entirely accountable for in terms of reductions in stomatal conductance in response to higher leaf-to-air vapour pressure deficits D. This is as opposed to direct effects of TL on photosynthetic metabolism. We also find that increases in photosynthetic rates associated with increases in ambient [CO2] over forthcoming decades should more than offset any decline in photosynthetic productivity due to higher D or TL or increased autotrophic respiration rates as a consequence of higher tissue temperatures. We also find little direct evidence that tropical forests should not be able to respond to increases in [CO2] and argue that the magnitude and pattern of increases in forest dynamics across Amazonia observed over the last few decades are consistent with a [CO2]-induced stimulation of tree growth.
Lung Cancer Risk and Past Exposure to Emissions from a Large Steel Plant

We studied the spatial distribution of cancer incidence rates around a large steel plant and its association with historical exposure. The study population was close to 600,000. The incidence data was collected for 1995–2006. From historical emission data the air pollution concentrations for polycyclic aromatic hydrocarbons (PAH) and metals were modelled. Data were analyzed using Bayesian hierarchical Poisson regression models. The standardized incidence ratio (SIR) for lung cancer was up to 40% higher than average in postcodes located in two municipalities adjacent to the industrial area. Increased incidence rates could partly be explained by differences in socioeconomic status (SES). In the highest exposure category (approximately 45,000 inhabitants) a statistically significant increased relative risk (RR) of 1.21 (1.01–1.43) was found after adjustment for SES. The elevated RRs were similar for men and women. Additional analyses in a subsample of the population with personal smoking data from a recent survey suggested that the observed association between lung cancer and plant emission, after adjustment for SES, could still be caused by residual confounding. Therefore, we cannot indisputably conclude that past emissions from the steel plant have contributed to the increased risk of lung cancer.
Refining video annotation by exploiting pairwise concurrent relation

Video annotation is a promising and essential step for content-based video search and retrieval. Most of the state-of-the-art video annotation approaches detect multiple semantic concepts in an isolated manner, which neglect the fact that video concepts are usually correlated in semantic nature. In this paper, we propose to refine video annotation by leveraging the pairwise concurrent relation among video concepts. Such concurrent relation is explicitly modeled by a concurrent matrix and then a propagation strategy is adopted to refine the annotations. Through spreading the scores of all related concepts to each other iteratively, the detection results approach stable and optimal. In contrast with existing concept fusion methods, the proposed approach is computationally more efficient and easy to implement, not requiring to construct any contextual model. Furthermore, we show its intuitive connection with the PageRank algorithm. We conduct the experiments on TRECVID 2005 corpus and report superior performance compared to existing key approaches.
A Chandra observation of the z= 2.285 galaxy FSC 10214+4724: evidence for a Compton-thick quasar?

We present a ≈20 ks Chandra ACIS-S observation of the strongly lensed z = 2.285 ultraluminous infrared galaxy FSC 10214 + 4724. Although this observation achieves the equivalent sensitivity of an up to ≈ 4M sChandra exposure (when corrected for gravitational lensing), the rest-frame 1.6‐26.3 keV emission from FSC 10214 + 4724 is weak (L X ≈ 2 × 10 42 erg s −1 for a lensing boost of ≈100); a significant fraction of this X-ray emission appears to be due to vigorous star formation activity. If FSC 10214 + 4724 hosts a quasar, as previously suggested, then it must be obscured by Compton-thick material. We compare FSC 10214 + 4724 to high-redshift SCUBA galaxies and discuss the X-ray identification of Compton-thick AGNs at high redshift.
Coupling of Cellular Processes and Their Coordinated Oscillations under Continuous Light in Cyanothece sp. ATCC 51142, a Diazotrophic Unicellular Cyanobacterium

Unicellular diazotrophic cyanobacteria such as Cyanothece sp. ATCC 51142 (henceforth Cyanothece), temporally separate the oxygen sensitive nitrogen fixation from oxygen evolving photosynthesis not only under diurnal cycles (LD) but also in continuous light (LL). However, recent reports demonstrate that the oscillations in LL occur with a shorter cycle time of ~11 h. We find that indeed, majority of the genes oscillate in LL with this cycle time. Genes that are upregulated at a particular time of day under diurnal cycle also get upregulated at an equivalent metabolic phase under LL suggesting tight coupling of various cellular events with each other and with the cell’s metabolic status. A number of metabolic processes get upregulated in a coordinated fashion during the respiratory phase under LL including glycogen degradation, glycolysis, oxidative pentose phosphate pathway, and tricarboxylic acid cycle. These precede nitrogen fixation apparently to ensure sufficient energy and anoxic environment needed for the nitrogenase enzyme. Photosynthetic phase sees upregulation of photosystem II, carbonate transport, carbon concentrating mechanism, RuBisCO, glycogen synthesis and light harvesting antenna pigment biosynthesis. In Synechococcus elongates PCC 7942, a non-nitrogen fixing cyanobacteria, expression of a relatively smaller fraction of genes oscillates under LL condition with the major periodicity being 24 h. In contrast, the entire cellular machinery of Cyanothece orchestrates coordinated oscillation in anticipation of the ensuing metabolic phase in both LD and LL. These results may have important implications in understanding the timing of various cellular events and in engineering cyanobacteria for biofuel production.
Size of the Whole versus Number of Parts in Genomes

It is known that chromosome number tends to decrease as genome size increases in angiosperm plants. Here the relationship between number of parts (the chromosomes) and size of the whole (the genome) is studied for other groups of organisms from different kingdoms. Two major results are obtained. First, the finding of relationships of the kind “the more parts the smaller the whole” as in angiosperms, but also relationships of the kind “the more parts the larger the whole”. Second, these dependencies are not linear in general. The implications of the dependencies between genome size and chromosome number are two-fold. First, they indicate that arguments against the relevance of the finding of negative correlations consistent with Menzerath-Altmann law (a linguistic law that relates the size of the parts with the size of the whole) in genomes are seriously flawed. Second, they unravel the weakness of a recent model of chromosome lengths based upon random breakage that assumes that chromosome number and genome size are independent.
Computational Analysis of Functional Single Nucleotide Polymorphisms Associated with the CYP11B2 Gene

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variations in humans and play a major role in the genetics of human phenotype variation and the genetic basis of human complex diseases. Recently, there is considerable interest in understanding the possible role of the CYP11B2 gene with corticosterone methyl oxidase deficiency, primary aldosteronism, and cardio-cerebro-vascular diseases. Hence, the elucidation of the function and molecular dynamic behavior of CYP11B2 mutations is crucial in current genomics. In this study, we investigated the pathogenic effect of 51 nsSNPs and 26 UTR SNPs in the CYP11B2 gene through computational platforms. Using a combination of SIFT, PolyPhen, I-Mutant Suite, and ConSurf server, four nsSNPs (F487V, V129M, T498A, and V403E) were identified to potentially affect the structure, function, and activity of the CYP11B2 protein. Furthermore, molecular dynamics simulation and structure analyses also confirmed the impact of these nsSNPs on the stability and secondary properties of the CYP11B2 protein. Additionally, utilizing the UTRscan, MirSNP, PolymiRTS and miRNASNP, three SNPs in the 3′UTR region were predicted to exhibit a pattern change in the upstream open reading frames (uORF), and eight microRNA binding sites were found to be highly affected due to 3′UTR SNPs. This cataloguing of deleterious SNPs is essential for narrowing down the number of CYP11B2 mutations to be screened in genetic association studies and for a better understanding of the functional and structural aspects of the CYP11B2 protein.
Analysis of solid and aqueous phase products from hydrothermal carbonization of whole and lipid-extracted algae.

Microalgae have tremendous potential as a feedstock for production of liquid biofuels, particularly biodiesel fuel via transesterification of algal lipids. However, biodiesel production results in significant amounts of algal residues, or “lipid extracted algae” (LEA). Suitable utilization of the LEA residue will improve the economics of algal biodiesel. In the present study, we evaluate the hydrothermal carbonization (HTC) of whole and lipid extracted algal ( Spirulina maxima ) feedstocks in order to produce a solid biofuel (hydrochar) and value-added co-products in the aqueous phase. HTC experiments were performed using a 2-L Parr reactor (batch type) at 175–215 °C with a 30-min holding time. Solid, aqueous and gaseous products were analyzed using various laboratory methods to evaluate the mass and carbon balances, and investigate the existence of high value chemicals in the aqueous phase. The HTC method is effective in creating an energy dense, solid hydrochar from both whole algae and LEA at lower temperatures as compared to lignocellulosic feedstocks, and is effective at reducing the ash content in the resulting hydrochar. However, under the treatment temperatures investigated, less than 1% of the starting dry algae mass was recovered as an identified high-value chemical in the aqueous phase.
Our Responsibility to The Seventh Generation Indigenous Peoples and Sustainable Development

Preface We cannot simply think of our survival; each new generation is responsible to ensure the survival of the seventh generation…Indigenous people are the poorest of the poor and the holders of the key to the future survival of humanity. The sidebar [comment above], drawn from the text of this report, captures the paradoxical situation of Indigenous people around the earth: on the one hand, policies and institutions have pushed them to the fringe of society and economy: on the other hand, the world is coming to understand their feeling that the current development path is not sound and that the survival of humanity is at stake. The voices of Indigenous people strike a resounding note, since their appeal is rooted in a deep and long time relationship to the earth. IISD believes that their message reinforces a fundamental value of sustainable development. Their call for ensuring responsibility to the seventh generation and for restoring the balance between the different elements of life on earth relates directly to the principles of fairness and equity. It emphasizes the need for environmental stewardship and the requirement of linking the economy, the environment and the well being of people within decision-making. The Institute tries to be a catalyst, incorporating views of stakeholders from many different backgrounds into decision-making about sustainable development. To do so requires a dedicated effort to listen and learn from communities and people who are shaping their own philosophies and initiatives for sustainable development. In particular we wish to highlight initiatives which otherwise might not be captured adequately or disseminated widely. Our role is to facilitate and to report as directly as possible their message, not to filter it through mainstream perspectives. This report, therefore contains the viewpoint of the authors. This report presents the vision of sustainable development through the eyes and experience of Indigenous people. It displays the suffering and pain caused by the cumulative effect of colonial policies, shortsighted development patterns and denial of Indigenous value and lifestyles; the lessons of such traumatic experience should lead decision-makers to rethink their approaches toward a sustainable society. Indigenous people invite us all to understand the root causes of past and present problems and to take an active role in the healing process. They also define what should be a caring social organization based on the principles of collective ownership and sharing, mutual respect and helping within the extended family …
Elimination of hydrophobic volatile organic compounds in fungal biofilters: Reducing start‐up time using different carbon sources

Fungal biofilters have been recently studied as an alternative to the bacterial systems for the elimination of hydrophobic volatile organic compounds (VOC). Fungi foster reduced transport limitation of hydrophobic VOCs due to their hydrophobic surface and extended gas exchange area associated to the hyphal growth. Nevertheless, one of their principal drawbacks is their slow growth, which is critical in the start‐up of fungal biofilters. This work compares the use of different carbon sources (glycerol, 1‐hexanol, wheat bran, and n‐hexane) to reduce the start‐up period and sustain high n‐hexane elimination capacities (EC) in biofilters inoculated with Fusarium solani. Four parallel experiments were performed with the different media and the EC, the n‐hexane partition coefficient, the biomass production and the specific consumption rate were evaluated. Biofilters were operated with a residence time of 1.3 min and an inlet n‐hexane load of 325 g m−3reactor h−1. The time to attain maximum EC once gaseous n‐hexane was fed was reduced in the three experiments with alternate substrates, as compared to the 36 days needed with the control where only n‐hexane was added. The shortest adaptation period was 7 days when wheat bran was initially used obtaining a maximum EC of 160 g m−3reactor h−1 and a critical load of 55 g m−3reactor h−1. The results were also consistent with the pressure drop, the amount of biomass produced and its affinity for the gaseous n‐hexane, as represented by its partition coefficient. Biotechnol. Bioeng. 2011; 108:758–765. © 2010 Wiley Periodicals, Inc.
An investigation on Foreign Language Form 3 students’ perceptions on the factors that affect their motivation to learn French at Saint Thomas High School in Trinidad and Tobago

The study sought to investigate six students' perceptions of the factors affecting their motivation to learn French at the form three level at Saint Thomas High in Trinidad and Tobago. During French class children displayed behaviours that suggested a lack of motivation such as sleeping, not paying attention and lack of participation. Therefore, interviews were conducted with six students at the form three level to ascertain according to them, the factors that affected their motivation to learn French. The findings revealed that students' attitude, perceived competence, difficulty of French and activities affected their intrinsic motivation. Additionally, students' grades, the teacher, relevance of French, society and family members affected their extrinsic motivation to learn French.
Plant biology and pathology / Biologie et pathologie végétales Genetic and molecular basis of grass cell-wall degradability. I. Lignin-cell wall matrix interactions ✩

Lignification limits grass cell-wall digestion by herbivores. Lignification is spatially and temporally regulated, and lignin characteristics differ between cell walls, plant tissues, and plant parts. Grass lignins are anchored within walls by ferulate and diferulate cross-links, p-coumarate cyclodimers, and possibly benzyl ester and ether cross-links. Cell-wall degradability is regulated by lignin concentration, cross-linking, and hydrophobicity but not directly by most variations in lignin composition or structure. Genetic manipulation of lignification can improve gr ass cell-wall degradability, but the degree of success will depend on genetic background, plant modification techniques employed, and analytical methods used to characterize cell walls. To cite
The Effects of Virgin Coconut Oil on Bone Oxidative Status in Ovariectomised Rat

Virgin coconut oil (VCO) was found to have antioxidant property due to its high polyphenol content. The aim of this study was to investigate the effect of the virgin coconut oil on lipid peroxidation in the bone of an osteoporotic rat model. Normal female Sprague-Dawley rats aged 3 months old were randomly divided into 4 groups, with 8 rats in each group: baseline, sham, ovariectomised (OVX) control group, and OVX given 8% VCO in the diet for six weeks. The oxidative status of the bone was assessed by measuring the index of lipid peroxidation, which is malondialdehyde (MDA) concentration, as well as the endogenous antioxidant enzymes glutathione peroxidase (GPX) and superoxide dismutase (SOD) in the tibia at the end of the study. The results showed that there was a significant decrease in MDA levels in the OVX-VCO group compared to control group. Ovariectomised rats treated with VCO also had significantly higher GPX concentration. The SOD level seemed to be increased in the OVX-VCO group compared to OVX-control group. In conclusion, VCO prevented lipid peroxidation and increased the antioxidant enzymes in the osteoporotic rat model.
Understanding Information Systems Usage Behavior in E-Government: The Role of Context and Perceived Value

This work provides an alternative conceptualization of the information systems (IS) success model for further understanding of user behavior in government. A context-value-behavior framework is proposed. This study investigates the relationships among perceived quality, normative pressure, perceived values, satisfaction and intention to use IS in government. Analytical results indicate that user intention to use IS in government is markedly influenced by social value and functional value and not by conditional value and satisfaction. The contextual factors, i.e. normative pressure, information quality of IS, and service quality from support of IS department, are crucial for enhancing users’ intention to use IS in government.
Pyramidal multi-band antennas for GPS/Galileo/MicroSat application

There is a constant increase of interest for multi-band antennas, mainly driven by the objective to reduce the number of onboard and ground antennas by integrating several applications on a single radiating element. In the framework of the Galileo satellite navigation system, the French Space Agency (CNES) proposed to study the possibility of combining GPS, Galileo and MicroSat telemetry (TM) applications on the same multi-band antenna. The GPS / Galileo bands used here include for example ARNS as well as high precision applications. This communication introduces a novel topology of trap-loaded multi-band antenna based on pyramidal structures. The experimental results confirm the good performances observed during the electromagnetic simulations. The multi-band behavior and the required circular polarization characteristic of the proposed pyramidal antenna are validated experimentally.