Miracle-dz/UniFAR-FTUs huggingface dataset:
Toolkit for Weighting and Analysis of Nonequivalent Groups: A Tutorial on the TWANG Shiny App for Two Treatments

This tutorial describes how to use a menu-driven Shiny app based on the Toolkit for Weighting and Analysis of Nonequivalent Groups (TWANG) R package. It can be used to estimate propensity score weights and related treatment effects for comparing two treatment groups when using observational data. The tutorial demonstrates use of the Shiny app through an illustrative example and explains key inputs and outputs of the TWANG Shiny app.
Development of in vitro propagation system for Atriplex halimus L.

Syrian Arab Republic is located on the Eastern coast of the Mediterranean Sea with an area of 18.517. 071 ha and a population of about 20.376 million (Anon 2009). Dry land in Syria accounts for about 10 million ha, about 55% of the entire country, with annual rainfall of <200 mm per year for the last 20 years (Wardeh 2005). Desertification is threatening large areas in Syria mainly due to salinity, which has expanded to the irrigated areas in the Eastern part of the country (Harba 2006). Therefore, it is crucial to prevent salinity and desertification in any way possible. One way to rehabilitate and reclaim these soils is by planting salt-tolerant forage species. Among these species is the genus Atriplex, which has recently raised interest where some 100.000 ha have been planted in the Mediterranean basin, Species of the genus Atriplex are known for their high tolerance to aridity and salinity (Le Houerou 1992). Using halophytes to produce forage in saline lands is the best economic solution (Khan and Duke 2001). Halophytes can play a role in soil reclamation in degraded lands (Le Houerou 1992). Atriplex are the dominant plants in arid and semi-arid lands of the world, especially when soil is combined with salinity (Ortíz et al. 2005). Atriplex halimus L. is a member of the Chenopodiaceae and one of the major species used in combating desertification due to its salt tolerance, which is defined as a plant’s ability to grow under saline stress (Munns 2002). A. halimus is an important Mediterranean xerohalophyte salt bush species highly resistant to drought (Le Houerou 2000), salinity (Bajji et al. 1998) and heavy metal stress (Lutts et al. 2004). Therefore, this study was carried out to develp an efficient micropropagation system for large-scale rapid clonal multiplication and spreading its cultivation to contribute in alleviating desertification impact on the environment and Humans. Another objective was the selection of in vitro of highly salt-tolerant clones by increasing concentrations of NaCl on in vitro grown plantlets.
Eighteen years of ecological monitoring reveals multiple lines of evidence for tundra vegetation change

The Arctic tundra is warming rapidly, yet the exact mechanisms linking warming and observed ecological changes are often unclear. Understanding mechanisms of change requires long-term monitoring of multiple ecological parameters. Here, we present the findings of a collaboration between government scientists, local people, park rangers, and academic researchers that provide insights into changes in plant composition, phenology, and growth over 18 yr on Qikiqtaruk-Herschel Island, Canada. Qikiqtaruk is an important focal research site located at the latitudinal tall shrub line in the western Arctic. This unique ecological monitoring program indicates the following findings: (1) nine days per decade advance of spring phenology, (2) a doubling of average plant canopy height per decade, but no directional change in shrub radial growth, and (3) a doubling of shrub and graminoid abundance and a decrease by one-half in bare ground cover per decade. Ecological changes are concurrent with satelliteobserved greening and, when integrated, suggest that indirect warming from increased growing season length and active layer depths, rather than warming summer air temperatures alone, could be important drivers of the observed tundra vegetation change. Our results highlight the vital role that long-term and multi-parameter ecological monitoring plays in both the detection and attribution of global change.
The Notch and EGFR signaling regulate caspase inhibitor Diap1 to match supply with intestinal demand

The regenerative activity of adult stem cells carries a high risk of cancer, particularly in highly renewable tissues. To guarantee that the correct organ size is attained and to cope with the continual risk of cancer, developing tissues often use programmed cell death (PCD) as an adaptive mechanism to cull excess and abnormal cells. Members of the family of Inhibitor of Apoptosis Proteins (IAPs) inhibit caspases and cell death and are often overexpressed in cancer. Here, we show that Diap1 is expressed in committed progenitor (enteroblast) cells in the adult Drosophila intestine. Blocking endogenous caspases uncovered that more than half of enteroblasts produced by intestinal stem cells (ISCs) are actively eliminated by apoptosis in the physiological intestine and also led to tumorigenesis. We find that antagonistic interplay between the Notch and EGFR signaling on Diap1 regulation governs the enteroblast cell death or survival decision via the conserved Klumpfuss/WT1-Lozenge/RUNX axis, which also regulates of differentiation plasticity of enteroblasts. These data provide new insights into how apoptosis drives adult tissue renewal and protection against tumors.
Analysis of the molecular diversity of R. solani isolates from five Ugandan agro-ecological zones using inter - simple sequence repeat markers

This study used seven inter-simple sequence repeat (ISSR) markers to characterize 55 R. solani isolates in order to establish their genetic diversity. The isolates were from five common bean growing agro-ecological zones of Uganda; the Southwest highlands (SW), Lake Victoria crescent and Mbale farmlands (LVC), Teso farming system (TFS), the Northern mixed farmlands (N) and the Western highlands and Semliki flats (W). DNA was extracted from 7-day old R. solani isolates growing on potato dextrose agar and amplified using PCR. Molecular analysis based on the ISSR fingerprints established moderate genetic diversity (mean = 0.389 ± 0.022). In addition, a high degree of intraspecific variation was observed by cluster analysis which generated a dendrogram with 5 highly reliable clusters (p ≥ 0.95) whose composition was independent of agro-ecological zones. Further evidence of intraspecific variation was provided by analysis of molecular variance which ascribed all the observed variation to genetic differences within the isolates. Isolates from SW, W, TFS and N had significant standardized index of association values indicative of clonal reproduction while isolates from LVC did not have significant values whence were sexual. The genetic diversity revealed by our study means that screening common bean germplasm for sources of resistance to R. solani should be done using diverse pathotypes and secondly, the breeders should pyramid many disease resistance genes in elite cultivars to provide durable resistance against R. solani.
Replacement of Yolk of the Chicken Embryo in ovo with Fresh Yolk or Yolk Varying in Granule and Cholesterol Content

A method has been devised to study the nutritional role of yolk cholesterol in the development of the chicken (Gallus gallus domesticus) embryo using egg yolk replacement. Preliminary experiments revealed that 11 mL of yolk in medium-sized eggs were adequate to support embryos from 4 to 20 days of incubation, and that low levels of β-cyclodextrin (β-CD) and amyloglucosidase (AG) in yolk were tolerated by the embryo. Fresh egg yolk was treated with β-CD at 50 °C, centrifuged to remove the insoluble β-CD-cholesterol complex, and incubated with AG to degrade residual β-CD. The cholesterol content was reduced from 13.1 mg g−1 in fresh egg yolk to 1.3 mg g−1 in cholesterol-reduced yolk supernatant (CRYS). Yolk granules co-precipitated with the β-CD-cholesterol complex. The cholesterol concentration of CRYS supplemented with granules from fresh yolk (i.e. CRYSg) was 3.2 mg g−1. When yolks of early 5-day embryos were replaced with 11 mL of CRYS, the maximum survival was 17 days of incubation. When yolks were replaced with 11 mL CRYSg, 30% of embryos survived to 20 days, a significant increase in survival compared to CRYS (P < 0.05). Sixty per cent of embryos receiving fresh yolk (yolk controls) and 83% of embryos in intact eggs (intact controls) survived to 20 days. The controls did not differ significantly (P > 0.05). Embryos in the CRYS and CRYSg groups had shorter survivals than yolk controls (P < 0.001) and intact controls (P < 0.005). These results suggest a methodological approach for investigations of egg yolk cholesterol and yolk granules in chick embryo development.
Differential dropout analysis captures biological variation in single-cell RNA sequencing data

Single-cell RNA sequencing data is characterized by a large number of zero counts, yet there is growing evidence that these zeros reflect biological variation rather than technical artifacts. We propose differential dropout analysis (DDA) to identify the effects of biological variation in single-cell RNA sequencing data. Using 16 publicly available and simulated datasets, we show that DDA accurately detects biological variation and can assess the relative abundance of transcripts more robustly than methods relying on counts. DDA is available at https://github.com/gbouland/DDA.
Biosurvey of Mercury (Hg), Cadmium (Cd), and Lead (Pb) Contamination in Reclamation Island-Jakarta Bay

: Man-made islands allegedly alter the coastline that slowing pollutants retention time. Green mussels ( Perna viridis ) are one of the organisms known to accumulate heavy metals. Biosurvey needs to be conducted to acquire information on heavy metal content in man-made habitat and biota. The aims of this research are to identify the water quality related to heavy metal presence; to measure heavy metal content in green mussels ( Perna viridis ) around the reclaimed island to determine heavy metal level pollution on reclamation island. Sampling was conducted in August 2017 in reclamation islands C and D. Heavy metal measurement values refer to the SNI method 3554-2015. Data of heavy metal content in water, sediment, and green mussels were analyzed with quantitative descriptive method. The results show biological oxygen demands (BOD), and chemical oxygen demands (COD) has exceeded the water quality standard which indicates a high level of pollution. The results of the examination of the heavy metal in seawater show that mercury (Hg), cadmium (Cd), and lead (Pb) are below the tools detection limit ( < 0.0002; < 0.00011; < 0.00086 mg/L) and below seawater pollution standard for biota. Concentrations of heavy metals mercury, cadmium, and lead in sediments around the reclaimed islands and Teluk Naga area are below heavy metal pollution standards for sediments. Mercury (Hg) levels below the tools detection limit ( < 0.0004 mg/L); cadmium (Cd) ranges from 0.02-0.20 mg/L; lead (Pb) ranges from 0.50 to 5.46 mg/L. Heavy metals examination in green mussels indicate that mercury (Hg), cadmium (Cd), and lead (Pb) are below the tools detection limit ( < 0.001; < 0.00011; < 0.00086 mg/L) and below the heavy metal pollution standard on bivalves. Generally, water and sediment around the reclaimed islands and natural habitat in August 2017 are not polluted by heavy metals so there is no harm to biota. Heavy metals quality in water, sediment and mussels are below the pollution standard and based on the USEPA system belong to grade A. The heavy metal index on Reclaimed Island is 18 and considered good. Based on the results obtained, it can be concluded that the reclaimed islands C and D in August 2017 were safe from heavy metal mercury, cadmium, and lead pollutions.
HIV reservoir size is determined prior to ART initiation and linked to CD8 T cell activation and memory expansion

Initiation of antiretroviral therapy (ART) in early compared with chronic HIV infection is associated with a smaller HIV reservoir. This longitudinal analysis of 63 individuals who commenced ART during primary HIV infection (PHI) investigates which pre-and post-therapy factors associate most closely with reservoir size (HIV DNA) following treatment initiation during PHI. The best predictor of reservoir size at one-year was pre-ART HIV DNA which was in turn significantly associated with CD8 memory differentiation (effector memory, naïve and T-betnegEomesneg subsets), CD8 T cell activation (CD38 expression) and PD-1 and Tim-3 expression on memory CD4 T cells. No associations were found for any immunological variables following one-year of ART. HIV reservoir size is determined around the time of ART initiation in individuals treated during PHI. CD8 T cell activation and memory expansion are linked to HIV reservoir size, suggesting the importance of the initial host-viral interplay in eventual reservoir size.
Single-copy Knock-In Loci for Defined Gene Expression in C. elegans

We have generated a single-copy knock-in loci for defined gene expression (SKI LODGE) system to insert any cDNA by CRISPR/Cas9 at defined safe harbors in the Caenorhabditis elegans genome. Utilizing a single crRNA guide, which also acts as a Co-CRISPR enrichment marker, any cDNA sequence can be introduced as a single integrated copy, regulated by different tissue-specific promoters. The SKI LODGE system provides a fast, economical and effective approach for generating single-copy non-silenced transgenes in C. elegans.
Ultrafast Infrared And Raman Spectroscopy

Ultrafast coherent raman and infrared spectroscopy of liquid systems probing bond activation reactions with femtosecond infrared applications of broadband transient infrared spectroscopy the molecular mechanisms behind the vibrational population relaxation of small molecules in liquids time-resolved IR studies of ligand dynamics in heme proteins infrared vibrational echo experiments structure and dynamics of proteins and peptides - femtosecond two-dimensional infrared spectroscopy two-dimensional coherent infrared spectroscopy of vibrational excitons in peptides vibrational dephasing in liquids - raman echo and raman free-induction decay studies fifth order two-dimensional raman spectroscopy of the intermolecular and vibrational dynamics in liquids nonresonant intermolecular spectroscopy of liquids lattice vibrations that move at the speed of light - how to excite them, how to monitor them and how to image them before they get away vibrational energy redistribution in polyatomic liquids - ultrafast IR-raman spectroscopy Coulomb force and intramolecular energy flow effects for vibrational energy transfer for small molecules in polar solvents vibrational relaxation of polyatomic molecules in supercritical fluids and the gas phase vibrational energy relaxation in liquids and supercritical fluids.
Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects

Background: There is a dearth of information on the core oral bacteriome compositions of healthy Africans especially Nigerians, mostly due to the non-existence of apt molecular techniques. Objectives: In this study, we sought to determine the core oral bacteriome compositions of ‘healthy’ Nigerian males and females. Methods: Oral samples were collected from nineteen adult subjects comprising 11 females and 8 males. DNA was extracted and 16S rRNA V4 region amplified using pattern barcoded primers prior to sequencing with the Illumina MiSeq program. Quantitative Insights into Microbial Ecology (QIIME) pipeline was used for 16S rRNA identification. The core genera were defined as taxa Original Research Article Anukam et al.; IJRRD, 1(1): 1-11, 2018; Article no.IJRRD. 44125 2 present in all subjects and over 2.0% in abundance, while core species defined as taxa found in at least 17/19 samples and over 0.1% in abundance. Results: Overall, 111 genera and 151 species representing 14 phyla were identified from the 19 subjects. Firmicutes (43.6%) were the most abundant phyla followed by Proteobacteria (33.62%), Bacteroidetes (9.67%), Actinobacteria (8.48%), Fusobacteria (4.31%) and others. The most abundant genera were Streptococcus (27.28%) followed by Haemophilus (14.95%), Neisseria (9.67%), Veillonella (7.22%), Gemella (5.77%), Rothia (3.11%), Prevotella (3.03%), Porphyromonas (2.94%), Lautropia (2.86%), Corynebacterium (2.74%), and Leptotrichia (2.61%). The most abundant core species identified were Haemophilus parainfluenzae (29.31%), followed by Haemophilus influenzae (6.91%), Lautropia sp TeTO (6.82%), Porphyromonas catoniae (6.0%), Streptococcus thermophilus (5.23%), Actinobacillus porcinus (4.80%), Rothia dentocariosa (3.32%), Rothia mucilaginosa (2.95%), Neisseria elongata (2.66%), and Streptococcus gordonii (2.55%). Conclusions: The genera and species-level core oral bacteriome identified could be used as a reference for comparison with larger population studies.
Density-dependent growth of bivalves dominating the intertidal zone of Banc d’Arguin, Mauritania: importance of feeding mode, habitat and season

Accurate predictions of population dynamics require an understanding of the ways by which environmental conditions and species-specific traits affect the magnitude of density dependence. Here, we evaluated the potential impact of season and habitat (characterized by sediment grain size and seagrass biomass) on the magnitude of density dependence in shell growth of 3 infaunal bivalve species dominating the tropical intertidal benthic communities of Banc d’Arguin, Mauritania. Two of our focal species were filter feeders (Senilia senilis and Pelecyora isocardia) and one was a facultative mixotroph (Loripes orbiculatus), mainly relying on organic carbon provided by sulphide-oxidizing endosymbiotic gill-bacteria (i.e. chemosymbiotic). Distinguishing 2 seasons, winter and summer, we manipulated local bivalve densities across habitats (from bare sandy sediments to seagrass-covered mud). In situ growth of individually tagged and relocated clams was measured and compared with those of tagged clams that were allocated to adjacent sites where local bivalve densities were doubled. Growth was negatively density-dependent in both winter and summer in P. isocardia and L. orbiculatus, the 2 species that mainly inhabit seagrass sediments, but not in S. senilis, usually found in bare sediments. As reproduction and survival rates are generally size-dependent in bivalves, our results suggest that in our tropical study system, the bivalve community of seagrass-covered sediments is more strongly regulated than that of adjacent bare sediments, regardless of species-specific feeding mode or season. We suggest that ecosystem engineering by seagrasses enhances environmental stability, which allows bivalve populations within tropical seagrass beds to stay close to carrying capacity.
Emission dipolaire et absorption en champ proche de nanostructures

Le present document constitue le memoire redige durant ma these de doctorat, qui s'est deroulee de novembre 2008 a novembre 2011 a l'Institut Langevin (ESPCI ParisTech). Une partie de ce travail de these a consiste en l'etude experimentale des fluctuations spatiales de la densite de modes optiques (LDOS) a la surface de films d'or semi-continus, connus pour presenter des modes de surface localises au voisinage du seuil de percolation. Pour cela, nous avons disperse des nanosources fluorescentes a la surface de films de fraction surfacique d'or croissante et mesure la statistique du taux d'amortissement des emetteurs. Nous avons montre que les fluctuations spatiales de LDOS sont maximales lorsque les modes localises apparaissent. Nous avons ensuite developpe un instrument permettant de realiser l'imagerie de LDOS en accrochant une nanosource fluorescente a l'apex d'une pointe d'AFM, et realise une preuve de principe sur des echantillons de test. Une autre partie a concerne l'etude theorique de la reponse optique d'une nanoparticule metallique. Nous avons montre comment le taux d'amortissement d'un dipole en champ proche d'une nanosphere metallique est modifie lorsque les interactions microscopiques sont prises en compte. Nous avons egalement etudie l'influence de l'environnement sur la section efficace d'absorption d'une nanoparticule, et montre que cette grandeur n'est pas intrinseque, mais depend de l'environnement. Nous avons confirme ce resultat sur un exemple simple permettant de donner des ordres de grandeur.
Experimental and theoretical study of the capillary effect on the mechanical behaviour of granular media

[ANGLES] Effective stress in unsaturated soils has never been physically or mathematically defined. It is still the topic in large discussions and debates in the soil mechanics community. We therefore tried to obtain a more realistic effective stress distribution within partially saturated conditions deduced from the measurement of capillary forces between spherical particles. We investigated a monodisperse granular material in which the particle interactions are governed by a capillary force law. The cohesion force for a grain-pair with equal diameters is expressed as an explicit function of the liquid bridge (both its volume and its shape). This analytical relation is validated by experiments consisting of measuring the capillary force between two particles joined by a meniscus. A numerical simulation was created by a routine Matlab, to determine the capillary force and the water pressure between two balls in contact with different saturation parameters (given the contact angle), produced by traction micromechanical experiments. Finally, in order to evaluate the influence of capillary force on the macroscopic behaviour, shear strength tests have been carried out using different water contents.