Miracle-dz/UniFAR-FTUs huggingface dataset:
STABILITY ANALYSIS OF BARLEY GENOTYPES UNDER DIFFERENT WATER STRESS LEVELS

Water deficit is the main yield-limiting factor in Egypt and overall the world. Thus the main objective from this work was to evaluate eighteen barley genotypes differed in their genetic makeup under six varied environments which are the combination between, two growing seasons (2013/2014 and 2014/2015) and three water irrigation levels (800, 1100 and 1400 m/fad.) as severe stress, moderate stress and adequate, respectively in newly reclaimed sandy soil of South El-Qantara Shark, Ismailia, Egypt, for days to 50% heading, flag leaf area, plant height, 1000-grain weight, biological yield and grain yield. The combined analyses of variance and the mean square of joint regression analysis of variance revealed significant differences among genotypes (G), environments (E) and the G × E interaction for all the traits. Environment + Genotype × Environment (E + G × E), mean squares due to environment (linear) and linear interaction (G × E linear) had highly significant effects for all characters. Severe and moderate water stress levels were significantly reduced all studied traits except 1000-grain weight for all barley genotypes than adequate water supply treatment. Grain yield reduced in the 1 year by an average of 25.67% and 13.44% and in the 2 year by an average of 26.82% and 12.67% under 1 and 2 irrigation levels, respectively, compared with the 3 level. Phenotypic stability parameters showed that barely genotypes, Line 9, Rihane 3 and Line 11 were highly adapted to favorable environments for days to 50% heading; Line 6, Line 5 and Giza 2000 for plant height; Giza 126 for flag leaf area; Line 1, Line 11and Rihane 3 for 1000-grain weight; Line 9, Line 7 and Line 2 for biological yield and Line 6, Line 9 and line 10 for grain yield. Genotypic stability parameters indicated that barley genotypes Line 11 and Giza 2000 was highly adapted to favorable environments for days to 50% heading; Line 2 for plant height, 1000-grain weight and biological yield; California mariout, Giza 123, Line 4, Line 6 and Line 7 for grain yield. The additive main effects and multiplicative interaction (AMMI) analysis of variance showed highly significant difference among genotypes, environments, G × E, IPCA1 and IPCA2. AMMI stability value (ASV) and GE biplot revealed that, the most desired and stable genotypes were Line 1, Giza 123, California mariout, Line 8 and Line 6 for grain yield. According to genotype plus genotype × environment (GGE) biplots, the ideal genotype was Line 9 for days to 50% heading; Line 6 for plant height; Line 11 for flag leaf area; Line 1 for 1000-grain weight; Line 9 for biological yield and Line 6 for grain yield.
Influence of Human Activities on the Water Quality of Ogun River in Nigeria

The quality of Ogun River in south-west, Nigeria was investigated by a field survey; covering the dry season and rainy season. Water samples were collected from seven sites (including an Abattoir, a market, residential community and a brewery); analysis of the physico-chemical parameters using standard methods and their environmental effects on the river were investigated. Generally, the value/degree of dissolved oxygen, phosphate, BOD, COD, pH, temperature, hardness from the sites during the rainy and dry seasons were compared with the World Health Organization (WHO) standards for domestic and commercial water. The traces of some hazardous physical and chemical impurities in the river were above the acceptable limits; and thereby pose a health risk to several rural communities who rely heavily on the river primarily as their source of domestic water. The study revealed a need for continuous pollution monitoring and management program of surface water in Nigeria. Keywords: surface water, water quality, water pollution, field survey, physico-chemical analysis
Chromosome Evolution Based on Variation in Chromosome Number and Chiasma Frequency in the Genus Ocimum L. from Thailand

Basil, Ocimum L. , is an economically important member of the family Lamiaceae. It has been widely used for many purposes, such as culinary herbs. The genus harbors large variation in chromosome number and size, which is believed to be a consequence of centuries of cultivation and selection for desirable traits. Meiosis was examined in five Ocimum species from Thailand, from five populations of each species. The results revealed that three of these species are cytogenetically related, forming a polyploid series with a base chromosome number of x=13: O. americanum L. (2n=2x=26, a new number for Thai plants), O. basilicum L. (2n=4x=52) and O. africanum Lour. (2n=6x=78, a new number for the genus). Two species with small chromosomes, O. tenuiflorum L. (2n=36) and O. gratissimum L. (2n=40), seem probably tetraploids with base numbers x=9 and 10, respectively. Meiotic irregularities in O. basilicum and O. africanum suggested that the species may be newly formed polyploids undergoing diploidization. Unlike recent polyploids, the meiotic chromosomes of O. tenuiflorum and O. gratissimum are entirely stable. Statistically significant intraspecific variation in chiasma frequencies was found in O. basilicum and O. africanum and the variation appeared to be geographically associated. The results presented here are useful both in the conservation of native basil species and in the breeding of elite accessions.
Prey partitioning between sympatric canid species revealed by DNA metabarcoding

The recovery of apex predators relies on restoring the full suite of trophic interactions within the ecosystem. Diet analysis with DNA metabarcoding technology can help deliver insights into these trophic interactions with fine-grained resolution. The recovery of wolves in Washington state offers an excellent case to study the trophic cascade impacts of the apex predators on the ecosystem and explore prey partitioning between sympatric canid species. We used DNA metabarcoding technology on scats to characterize the diet composition and its spatiotemporal variations of wolves and coyotes and quantified the diet niche overlap between these two canid species in northeastern Washington. In total, 19 different prey taxa were detected. Frequency of occurrence data showed that wolves primarily preyed upon deer (Odocoileus sp.) (47.47%) and moose (Alces alces) (42.42%). Coyotes also consumed moose (30.10%) and deer (21.36%), but snowshoe hares (Lepus americanus) were the most common prey (61.17%) in their diet. There were significant spatial variations in the wolf diet composition (p = 0.001) with wolves in the Dirty Shirt pack range consuming more moose (71.43%). Coyotes showed significant spatial and temporal dietary variations (season: p = 0.037; pack: p = 0.003; pack:season p = 0.043). Our data suggested that coyotes use ungulate carrion subsidies from wolves as food resources. DNA metabarcoding with fecal DNA provides an excellent noninvasive tool to characterize diet profile at the fine-grained level and can be applied to other carnivore species to help understand the impacts of recovery of apex predators on the local ecosystems.
Estimation of speed, armature temperature, and resistance in brushed DC machines using a CFNN based on BFGS BP

In this paper, a sensorless speed and armature resistance and temperature estimator for Brushed (B) DC machines is proposed, based on a Cascade-Forward Neural Network (CFNN) and Quasi-Newton BFGS backpropagation (BP). Since we wish to avoid the use of a thermal sensor, a thermal model is needed to estimate the temperature of the BDC machine. Previous studies propose either non-intelligent estimators which depend on the model, such as the Extended Kalman Filter (EKF) and Luenberger's observer, or estimators which do not estimate the speed, temperature and resistance simultaneously. The proposed method has been verified both by simulation and by comparison with the simulation results available in the literature
Modification of the structure of a metallopeptide: Synthesis and biological evaluation of 111in-labeled DOTA-conjugated rhenium-cyclized α-MSH analogues

Rhenium-cyclized CCMSH analogues are novel melanoma-targeting metallopeptides with high tumor uptake, long tumor retention, and low background in normal tissues, which make these metallopeptides an ideal structural motif for designing novel melanoma-targeting agents. ReCCMSH has been derivatized with a 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelate so that it can be labeled with a wide variety of radionuclides for imaging and therapeutic applications. This study involved optimization of the in vivo biological properties of DOTA-ReCCMSH (S), through modification of the structure of the metallopeptide. Several DOTA-ReCCMSH analogues, Ac-Lys(DOTA)-ReCCMSH (4) DOTA-ReCCMSH(Arg11) (6), DOTA-ReCCMSH-OH (8), and DOTA-ReCCMSH-Asp-OH (10), were synthesized using solid phase peptide synthesis followed by rhenium cyclization. The IC50 values of the metallopeptides were determined through competitive binding assays against 125I-(Tyr2)-NDP. Radiolabeling of the DOTA-rhenium-cyclized peptides w.
Daylight Transport Systems for Buildings at High Latitudes

This paper is a literature study of daylight transport systems aiming at selecting the most appropriate ones for application at high latitudes. It is limited to the systems that transport light at a long distance from the façade and distribute it either in the building core or at a rear place in a room adjacent to the façade. The literature is spanning from the 80s’ to the present. It covers the theoretical background and development of the systems from their infancy, through technical development of the design elements and to the adaptation of the systems to different climatic conditions. Since the most literature comes from equatorial and tropical climate, a short contextualization with high latitudes climate is included. Findings are systematized and presented in tables for easier comparison of efficiency, visual comfort, design efficacy, maintenance need, cost and/or availability on the market, and energy-saving potential in different climates. Conclusions confirm that the daylight condition at the location is the main prerequisite when deciding on the type of collector while the building structure and room functionality are the basis for choosing the type of the transport element. Finally, the distribution element showed to be the key factor when discussing applicability in a functional space where the final success depends on human acceptance. This paper can be useful to get an overview of performance characteristics and application preferences of different daylight transport systems or just their components in daylight conditions at high latitudes. © 2019 The Author(s). Published by solarlits.com. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Estimating the Sequencing of Evacuation Destination and Accommodation Type in Hurricanes

Abstract Hurricanes are one of the most dangerous catastrophes faced by the USA. The associated life losses can be reduced by proper planning and estimation of evacuation demand by emergency planners. Traditional evacuation demand estimation involves a sequential process of estimating various decisions such as whether to evacuate or stay, evacuation destination, and accommodation type. The understanding of this sequence is not complete nor restricted to strict sequential ordering. For instance, it is not clear whether the evacuation destination decision is made before the accommodation type decision, or the accommodation type decision is made first or both are simultaneously made. In this paper, we develop a nested logit model to predict the relative ordering of evacuation destination and accommodation type that considers both sequential and simultaneous decision making. Household survey data from Hurricane Matthew is used for computing empirical results. Empirical results underscore the importance of developing a nested structure among various outcomes. In addition to variables related to risk perception and household characteristics, it is found that social networks also affect this decision-making process.
SEGMENTATION STRATEGIES FOR ROAD SAFETY ANALYSIS

OF DISSERTATION SEGMENTATION STRATEGIES FOR ROAD SAFETY ANALYSIS This dissertation addresses the relationship between roadway segment length and roadway attributes and their relationship to the efficacy of Safety Performance Function (SPF) models. This research focuses on three aspects of segmentation: segment length, roadway attributes, and combinations of the two. First, it is shown that choice of average roadway segment length can result in markedly different priority lists. This leads to an investigation of the effect of segment length on the development of SPFs and identifies average lengths that produce the best-fitting SPF. Secondly, roadway attributes are filtered to test the effect that homogeneity has on SPF development. Lastly, a combination of segment length and attributes are examined in the same context. In the process of conducting this research a tool was developed that provides objective goodness-of-fit measures as well as visual depictions of the model. This information can be used to avoid things like omitted variable bias by allowing the user to include other variables or filter the database. This dissertation also discusses and offers examples of ways to improve the models by employing alternate model forms. This research revealed that SPF development is sensitive to a variety of factors related to segment length and attributes. It is clear that strict base condition filters based on the most predominant roadway attributes provide the best models. The preferred functional form was shown to be dependent on the segmentation approach (fixed versus variable length). Overall, an important step in SPF development process is evaluation and comparison to determine the ideal length and attributes for the network being analyzed (about 2 miles or 3.2 km for Kentucky parkways). As such, a framework is provided to help safety professionals employ the findings from this research.
Genetic Evaluation for Some Productive and Reproductive Traits by Using Animal Model in A Commercial Friesian Herd in Egypt

Data used in this investigation were collected from 4370 records for 874 purebred Friesian cows' daughters of 44 sires from 1985 to 2003, which belong to Shobratana Animal Production Society, located in the north part of Delta region near Tanta city in Egypt. Variance and covariance components for 305 day milk yield (305dMY, kg), lactation length (LL, day), dry period (DP, day), days open (DO, day) and calving interval, (CI, day) were estimated with REML using an animal model (Boldman, 1955), that included the fixed effects of month and year of calving and parity of cow. Random effects were animal, direct and maternal genetic effects, maternal permanent environmental effect and random effect.Overall means of (305-dMY), LL, DP, DO and CI were 4897 kg, 327 day, 120 day, 66.3 day and 401.16 day. Month and year of calving were highly significant effect (P<0.01) for all studied traits. Direct heritability (ha) of the mentioned traits was 0.38, 0.13, 0.14, 0.11 and 0.16, respectively. Heritabilities of maternal effects (hm) of (305-dMY) (0.13), LL (0.18), DP (0.23), DO (0.14) and CI (0.21), respectively. Estimates of direct-maternal genetic correlations in all traits studied ranging from -0.60 to 0.74. Genetic correlations among different studied traits ranged from -0.80 to 1.00 while the phenotypic correlations among investigated traits were positive, ranging from 0.07 to 0.99. Range of predicted breeding value (PBV's) of sires were 462 kg, 1.05 d, 0.24 d, 5.93 d and 2.26 d, for 305dMY, LL, DP, DO and CI, respectively. PBV's of cows of the mentioned traits was 1123 kg, 2.92 d, 1.64 d, 5.93 d and 2.92 d respectively. Corresponding PBV's of dams for the above same traits were 510 kg, 1.42 d, 0.80 d, 7.20 d and 3.00 d, respectively. Accuracy of (PBV's) ranged from 38 to 88, 73 to 88 and 39 to 89% for sires, cows and dams, respectively; indicating the genetic improvement could be attained through any bath of them. Estimates of temporary environmental variance as a proportion of phenotypic variance for LL, DP, DO and CI ranged from 35 to 71% indicating the improvement in these traits could be achieved by improving for these temporary factors.
Phylogenetic analysis of Black Bengal and Jamunapari goats in Bangladesh based on partial sequence of cytochrome b gene

Goats, among the livestock species, are considered the most prolific ruminant especially under callous climatic conditions. The aim of the present study was to depict the current phylogenetic status and genetic diversities of Black Bengal (BBG) and Jamunapari goat of Bangladesh and the world. Cytochrome b (cytb) gene (1140 bp) of mitochondrial DNA of Black Bengal goats (Capra hircus) was amplified by Polymerase Chain Reaction (PCR) for the first time in Bangladesh. The sequence from BBG had no nucleotide (nt) difference and 100% homology with the BBG (C. hircus) of India and also the goats (C. hircus) from China (Yangtze River Delta White Goat), Thailand (Wild Cervidae), Japan (Bezoar goat) and South Africa (Domestic goat). The sequence had 1-5 nt differences and 99% homology with the goats (C. hircus) from China, Thailand and Japan (other goats), and also with the goats (C. hircus) from Malaysia, South Korea, France, Italy, Pakistan, Slovenia, Switzerland and USA. Phylogenetic tree constructed with Black Bengal Goat (BBG-K-2) and Jamunapari goats (SG-1) of Bangladesh with cytochrome b nucleotide sequences were closely related to China-HM7. China-YP xj46, Pakistan-Lineage C1, Pakistan-Lineage C2, Slovenia- ChSo1, Switzerland-ChTo2992 and shared 98.8% to 99% and 98.3% to 98.6% similarity, respectively and 1-1.2% and 1.4 to 1.7% genetic distance, respectively. Based on Ctb gene Sequence collected from Bangladeshi Black Bengal Goats (BBG-K-2) and Jamunapari goats (SG- 1) that were closely related and shared with the same genetic lineage of China HM18 and India-BBG-DQ073048, respectively, suggesting a common origin. SAARC J. Agri. , 17(1): 23-35 (2019)
Single-cell RNA profiling of glomerular cells in diabetic kidney: a step forward for understanding diabetic nephropathy.

Transcriptomic profiling of kidney tissues or isolated glomeruli has been used to examine changes in the expression of multiple genes in diabetic kidney disease (1,2). Bulk tissue RNA-sequencing can quantitate the average expression of genes in a given tissue but the amount of cell type specific gene expression can only be roughly inferred by the different cell type proportions in each tissue.
Retinal horizontal cells use different synaptic sites for global feedforward and local feedback signaling

In the outer plexiform layer (OPL) of the mouse retina, two types of cone photoreceptors (cones) provide input to more than a dozen types of cone bipolar cells (CBCs). This transmission is modulated by a single horizontal cell (HC) type, the only interneuron in the outer retina. Horizontal cells form feedback synapses with cones and feedforward synapses with CBCs. However, the exact computational role of HCs is still debated. Along with performing global signaling within their laterally coupled network, HCs also provide local, cone-specific feedback. Specifically, it has not been clear which synaptic structures HCs use to provide local feedback to cones and global forward signaling to CBCs. Here, we reconstructed in a serial block-face electron microscopy volume the dendritic trees of five HCs as well as cone axon terminals and CBC dendrites to quantitatively analyze their connectivity. In addition to the fine HC dendritic tips invaginating cone axon terminals, we also identified “bulbs”, short segments of increased dendritic diameter on the primary dendrites of HCs. These bulbs are located well below the cone axon terminal base and make contact to other cells mostly identified as other HCs or CBCs. Using immunolabeling we show that HC bulbs express vesicular gamma-aminobutyric acid transporters and co-localize with GABA receptor γ2 subunits. Together, this suggests the existence of two synaptic strata in the mouse OPL, spatially separating cone-specific feedback and feedforward signaling to CBCs. A biophysics-based computational model of a HC dendritic branch supports the hypothesis that the spatial arrangement of synaptic contacts allows simultaneous local feedback and global feedforward signaling.
Utilizing directional information in Evolved Bat Algorithm for guiding artificial agents

In this paper, an idea of utilizing the directional information to guide the artiﬁcial agents in the searching process is led in to the Evolved Bat Algorithm (EBA). By properly using the directional information, the guided artiﬁcial agents can present higher searching accuracy than the agents in the conventional EBA. The advantage of our proposed method guides the artiﬁcial agent to cruise along the gradient information from the known near best solutions. It results in that the searching accuracy is increased with only a slight addition to the calculation. To test the accuracy on ﬁnding the near best solutions, 2 benchmark functions, whose global optimum are known, with diﬀerent dimensional criteria are used in the experiments. The experimental results are compared with the conventional EBA under the same experimental conditions. The experimental results indicate that our proposed method improves the accuracy on ﬁnding the near best solution. According to the experimental results, our proposed Directional guided Evolved Bat Algorithm (DgEBA) is signiﬁcantly improved compared with the conventional
The circadian clock protein REVERBα inhibits pulmonary fibrosis development

Significance The circadian clock plays an essential role in energy metabolism and inflammation. In contrast, the importance of the clock in the pathogenesis of fibrosis remains poorly explored. This study describes a striking alteration in circadian biology during pulmonary fibrosis where the relatively arrhythmic alveolar structures gain circadian but asynchronous rhythmicity due to infiltration by fibroblasts. Disruption of the clock in these cells, which are not widely implicated in circadian pathophysiology, results in a profibrotic phenotype. Translation of these findings in humans revealed previously unrecognized important circadian risk factors for pulmonary fibrosis (sleep length, chronotype, and shift work). In addition, targeting REVERBα repressed collagen secretion from human fibrotic lung tissue, making this protein a promising therapeutic target. Pulmonary inflammatory responses lie under circadian control; however, the importance of circadian mechanisms in the underlying fibrotic phenotype is not understood. Here, we identify a striking change to these mechanisms resulting in a gain of amplitude and lack of synchrony within pulmonary fibrotic tissue. These changes result from an infiltration of mesenchymal cells, an important cell type in the pathogenesis of pulmonary fibrosis. Mutation of the core clock protein REVERBα in these cells exacerbated the development of bleomycin-induced fibrosis, whereas mutation of REVERBα in club or myeloid cells had no effect on the bleomycin phenotype. Knockdown of REVERBα revealed regulation of the little-understood transcription factor TBPL1. Both REVERBα and TBPL1 altered integrinβ1 focal-adhesion formation, resulting in increased myofibroblast activation. The translational importance of our findings was established through analysis of 2 human cohorts. In the UK Biobank, circadian strain markers (sleep length, chronotype, and shift work) are associated with pulmonary fibrosis, making them risk factors. In a separate cohort, REVERBα expression was increased in human idiopathic pulmonary fibrosis (IPF) lung tissue. Pharmacological targeting of REVERBα inhibited myofibroblast activation in IPF fibroblasts and collagen secretion in organotypic cultures from IPF patients, thus suggesting that targeting of REVERBα could be a viable therapeutic approach.