Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotyping and phylogenetic construction of Hepatitis C virus from the thalassemic patients in Al-Amara city in Iraq

Hepatitis C virus (HCV)is an enveloped and positive single strand RNA virus. The length of HCV genome is up to 9.6 kb, it isheterogeneous molecule due to the high mutation rate of the genome, it has two vital regions at the flanks of the genome, named untranslated region, 3'UTR and 5'UTR, these regions regulate the replication and translation of the genome, and they could be used for detection of this virus. Investigation of the genotypes and serotypes of HCV is a crucial technique for treatment of the patients who have been infected by this virus, the treatment of these patients depends on the identification of the genotypes of HCV because the certain genotypes do not respond to the therapy as well as the time course of the therapy also depend on the genotypes and subtypes of HCV. Bioinformatics application such as the alignment and phylogenetic tree has so important approaches to know the genetic relationship evolution and the development of HCV genotypes and subtypes. Objective the current cross-sectional study conducts to identify and investigate of the genotypes and subtypes as well as the phylogenic tree of HCV. Subject and methods the current study targeted the seropositive HCV of the sixtyfive thalassemic patients who were attendinginto the Thalassemia Center in Al Amara city for getting the blood. The nested PCR was the technique that used in this study, then the phylogenetic tree and the sequence of nucleotide alignment was achieved by certain software such as MEGA 6.0 and Unweighted Pair Group method with Arithmetic Mean (UPGMA tree). Resultthe current study displayed the genotype 1a of HCV was the high prevalence rate that accounted 11 (55%), while the lowest was 2b (3, 15%), whereas the 2a was 6 (30%). The resident Hepatitis C virus isolates with the numbers 1, 2, 5, 7, 8, 9, 10, 14, 15, 18, and 20) were so show closed related to all NCBI-Blast Hepatitis C virus genoptype 1a (AF009606.1), the local Hepatitis C virus isolates numbered 3, 4, 6, 16, 17, and 19) were so show closed related to all NCBI-Blast Hepatitis C virus genoptype 2a (AF169004.1). The local Hepatitis C virus isolates numbered 11, 12, and 13) were shown closed related to all NCBI-Blast Hepatitis C virus genoptype 2b (D10988.1) at total genetic change (0.005%). Conclusion the genotypes of HCV in the current study were only 1a, 2a and 2b, with the different occurrence 11 (55%), 6 (30%) and 3 (15%) respectively.
Association Mapping and Genomic Selection for Yield and Agronomic Traits in Soft Winter Wheat

Tools such as genome-wide association study (GWAS) and genomic selection (GS) have expedited the development of crops with improved genetic potential. While GWAS aims to identify significant markers associated with a trait of interest, the goal of GS is to utilize all marker effects to predict the performance of new breeding lines prior to testing. A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft winter wheat (SWW) lines evaluated in eight site-years in Arkansas and Oklahoma. Broad sense heritability of GY (H=0.48) was moderate compared to other traits including plant height (H=0.81) and kernel weight (H=0.77). Markers associated with multiple traits on chromosomes 1A, 2D, 3B, and 4B serve as potential targets for marker assisted breeding to select for GY improvement. Validation of GY-related loci using spring wheat from the International Maize and Wheat Improvement Center (CIMMYT) in Mexico confirmed the effects of three loci in chromosomes 3A, 4B, and 6B. Lines possessing the favorable allele at all three loci (A-C-G allele combination) had the highest mean GY of possible haplotypes. The same population of 239 lines was used in a GS study as a training population (TP) to determine factors that affect the predictability of GY. The TP size had the greatest effect on predictive ability across the measured traits. Adding covariates in the GS model was more advantageous in increasing prediction accuracies under single population cross validations than in forward predictions. Forward validation of the prediction models on two new populations resulted in a maximum accuracy of 0.43 for GY. Genomic selection was “superior” to marker-assisted selection in terms of response to selection and combining phenotypic selection with GS resulted in the highest response. Results from this study can be used to accelerate the process of GY improvement and increase genetic gains in wheat breeding programs. ©2018 by Dennis Nicuh Lozada All Rights Reserved
Cellular Subscriber Lines (CSL): A Wireless-Wireline Physically Converged Architecture

Wireless-wireline convergence and cellular wireless deployment can economically accelerate through partial transmission of wireless 4G, 5G (generally 3GPP-standards-compliant), and/or Wi-Fi 6 baseband signals on the billions of copper phone, Ethernet, coaxial cable, and other wireline connections. This article poses such a Cellular Subscriber Lines (CSL) re-use architecture and investigates large bandwidth-efficiency gains, as well as the consequent cost-efficiency improvement that accrues for CSL’s deployment infrastructure. In-home wireless signals’ seamless distribution partially over copper links can achieve good data-rate-versus-distance profile. Results here also expand to Wi-Fi (possibly with MIMO use) on Ethernet multi-pair cables, finding very large gains over existing enterprise mesh (ad-hoc or otherwise) approaches.
One-Class Remote Sensing Classification From Positive and Unlabeled Background Data

One-class classification is a common situation in remote sensing, where researchers aim to extract a single land type from remotely sensed data. Learning a classifier from labeled positive and unlabeled background data, which is the case-control sampling scenario, is efficient for one-class remote sensing classification because labeled negative data are not necessary for model training. In this study, we propose a novel positive and background learning with constraints (PBLC) algorithm to address this one-class classification problem. With user-specified information of maximum probability as the constraint, PBLC infers the posterior probability of positive class directly in one-step model training. We test PBLC on a synthetic dataset and a real aerial photograph to perform different one-class classification tasks. Experimental results demonstrate that PBLC can successfully train linear and nonlinear classifiers including generalized linear model, artificial neural network, and convolutional neural network. Probabilistic and binary predictions by PBLC are more similar to the gold-standard positive-negative method, outperforming the two-step positive and background learning algorithm that post-calibrates a naïve classifier based on an estimated constant. Hence, the proposed PBLC algorithm has the potential to solve one-class classification problems in the case-control sampling scenario.
Performance Analysis of a Semiblind Channel Estimator in One-Bit Massive MIMO Systems

Massive multiple-input multiple-output (MIMO) suffers from RF hardware complexity, cost, and circuit power consumption. The high-resolution analog-to-digital converter (ADC) at the RF front end is one of the major contributors in power depletion. Thus, one-bit massive MIMO becomes an effective solution. However, the availability of accurate channel state information (CSI) at the base station remains a challenging task. In this article, we propose a semiblind channel estimator for one-bit massive MIMO systems and evaluate its uplink (UL) performance. The proposed algorithm consists of two stages: initialization and iteration. The initial channel estimate is obtained from a pilot-aided initialization stage, which is refined in the iteration stage with the help of both pilot and a few data symbols. The semiblind approach simultaneously improves the estimation accuracy and spectral efficiency with minimum pilot length. We also derive a theoretical lower bound on the UL achievable rate under perfect and imperfect CSI. Through simulations, we show that the semiblind scheme achieves a considerable improvement in mean square error, bit-error-rate, spectral efficiency, and bit energy against the existing one-bit pilot based estimators at the cost of a nominal increase in computational complexity.
Integrating Multiresolution and Multitemporal Sentinel-2 Imagery for Land-Cover Mapping in the Xiongan New Area, China

Accurate land use/land cover (LULC) mapping over a large area is essential to environmentally sustainable development. Recently, the Chinese government established a new national economic zone called the Xiongan New Area, and along with the upcoming large-scale urban construction, this area will inevitably experience a dramatic LULC change, which will threaten the local ecological balance. In this article, we proposed a two-stage approach for LULC mapping in the Xiongan New Area ahead of the forthcoming dense urban construction. The first stage is to obtain base-class maps through a supervised imagery classification. Specifically, we designed a new object-based framework consisting of automatic image segmentation, pixel-based probabilistic estimation, and area-weighted probability statistics for Sentinel-2 multiresolution imagery classification. The second stage is an LULC map refinement process in which the temporal features of each land use category are extracted to refine the LULC classification. Through the implementation of the proposed two-stage approach, an LULC map containing permanent water, temporal water, natural vegetation, barren land, built-up land, and cropland categories can be produced. Through an accuracy assessment, the proposed multiresolution imagery classification method achieved the highest overall accuracy of 88.58% and an average accuracy (AA) of 87.78% compared with conventional classification methods. After obtaining the refined LULC map, we find that the current Xiongan New Area is in a less developed state, that is, cropland accounts for the highest proportion of 51.59%, which is followed by natural vegetation (22.38%) and built-up land (15.69%).
Tests in a semi-natural environment suggest that bait and switch strategy could be used to control invasive Common Carp

There are four files: 1) PIT_tagged_FISH contains unique PIT tag for every fish, plus length, species, pond, date of mortality, 2) Raw_detections contains all fish detected during study, 3) Summarized_mortalities contains summaries of the fish mortalities by pond and species before and after experimental treatment, and 4) R_code contains a summary of and code for the R analysis used.
The Impact of Time Spent Student Teaching on the Decision to Enter the Field: A Longitudinal Study

Due to the lack of qualified agricultural education teachers needed to fill yearly vacancies on the secondary school level, educators at Texas Tech University conducted a longitudinal study concerning how student teachers spend their time during their student teaching experience in an attempt to identify if this time spent has an impact on the decision to enter the field. Findings showed student teachers were engaged for a total of 713.83 to 931.23 hours on average during their student teaching experience. Longitudinally, time spent in the classroom, in FFA activities, and in SAE observations varied at different points in the semester. A logistic regression revealed 18-28% of the variance in the decision to teach may be explained by the amount of time grading student work and with laboratory preparation and maintenance. Recommendations for practice include encouraging student teachers to participate in as many activities as possible. Further research should be conducted to identify more factors influencing the decision of student teachers to enter the field.
Advancing Revolving Funds for the Sustainable Development of Rural Regions

Financing measures and incentive schemes for (existing and new) building owners can promote the sustainable settlement development of rural regions or municipalities and, in a wider sense, entire countries or cross-border regions. In order to be used on a broad scale, the concept of revolving funds must continue to be further developed. In this research, the concept of an advanced revolving housing fund (ARF) for building owners to support the sustainable development of rural regions and potential mechanisms are introduced. The ARF is designed to reflect impacts and challenges with regard to rural regions in Germany, Europe and beyond. Based on New Institutional Economics, the Theory of Spatial Organisms, an expert workshop, interviews and discussions and further literature research, the fundamentals for incentive schemes and the essential mechanisms and design aspects of the ARF are derived. This includes the principal structure and governance of a holding fund and several regional funds. Based on this, input parameters for the financial modelling of an ARF are presented as well as guiding elements for empirical testing to promote more research in this area. It is found that the ARF should have a regional focus and must be a comprehensive instrument of settlement development with additional informal and formal measures. The developed concept promises new impulses, in particular, for rural regions. It is proposed to test the concept by means of case studies in pioneer regions of different countries.
Exploring the Locker

This article is an effort to foster grace and to create genuine, humble community. A new sense of community, that is not conditional on our abilities to censor ourselves to be more palatable to those around us. Instead, the birth of a new way of relating that considers our deep inner selves that feel shame, remember traumas, and cower in fear of these experiences. Perhaps most of all, this article is an invitation to explore our deepest inner selves, and the cost of censoring this self. This exploration is not a leisurely dive into the corners of ourselves that lie in the shallows. It is an adventure that will require a full set of SCUBA gear, and a courageous spirit. A courageous spirit that is not only willing to dig through the shame, fear, and anger that covers our raw selves, but a spirit that will then sit with these wounded and forgotten parts, and begin to build a new sense of balance.
Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy

Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene and network dosage, and changes in gene expression. In this review, we discuss the prevalence of polyploidy across the tree of life, followed by an overview of studies investigating genome evolution and gene expression. We then provide an overview of methods in network biology, phylogenomics, and population genomics that are critical for advancing our understanding of evolution post-WGD, highlighting the need for models that can accommodate polyploids. Finally, we close with a brief note on the importance of random processes in the evolution of polyploids with respect to neutral versus selective forces, ancestral polymorphisms, and the formation of autopolyploids versus allopolyploids.
Harnessing marine microclimates for climate change adaptation and marine conservation

‐Responses to climate change and large‐scale forcing can vary widely at local scales creating marine microclimates. ‐Microclimates are robust even under extreme large‐scale forcing events (ENSO, climate change) potentially creating spatial refuges or ‘safe spaces’ for important species. ‐Small/medium no‐take zones, artificial reefs, and other possible spatial management can be placed to harness local variability as an adaptation or conservation measure in the face of climate change.
Influence of particle aspect ratio and ability to aggregate on electrical conductivity of fiber-forming polymer composites

Fiber-forming polymer composites filled with carbon nanoparticles of three types (carbon black is a spherical filler; carbon nanofibers and carbon nanotubes are anisotropic nanoparticles) were produced by melt technology. Electrical conductivity of the fiber-forming polymer composites was measured; a function of the filler concentration and the percolation thresholds were determined. It was found that an increase in the aspect ratio of carbon nanoparticles leads to a decrease in the percolation threshold. The correlation between the axial ratio, stiffness, filler concentration and electrical conductivity of the percolation cluster in fiber-forming polymer composites was analysed.
ACUTE TOXICITY TEST AND HISTOLOGICAL DESCRIPTION OF ORGANS AFTER GIVING NANO HERBAL ANDALIMAN (Zanthoxylum acanthopodium)

Andaliman is a typical plant (Northen Sumatera, Indonesia) contains antioxidants and as herbal medicine in the future. This aimed in this research to determine the toxic value of nano herbal and aliman and analyze histology of the liver, lungs, heart and brain after given of this herb. Nano herbal andaliman were made using High Energy Milling (HEM). LC50 was used Brine Shrimp Lethality Test with concentrations of 10, 100, 1000, 10000 ppm while LD50 consists of 3 stages: dose orientation test (12 mice), preliminary test (20 mice) and LD50 determination (30 mice) for 14 today by the Thomson Weil formula, then the organ was investigated for histology. The results of this research: LC50 value=1737.80 ppm, LD50 =9.807g/KgBW ± 0.075 and a significant difference was noticed (p <0.05) in liver weight but no significant difference (p> 0.05) on the weight of lungs, heart and brain. A significant difference also in organ histology on the administration nano herbal andaliman in each dose level. Nano herbal andaliman belongs to the category of mild toxic so that it could be processed as a herbal medicine of the future.
Research Progress and Prospect of Liquid Metals Used as Lubricants

： As a new material, liquid metal usually refers to a low melting point alloy with a melting point below 200 ℃ . It is an amorphous, flowable metal. The liquid metal at room temperature has a lower melting point and is liquid at room temperature. Because of this amorphous liquid form, it has good fluidity, thermal conductivity, thermal stability and other properties. It has been used in many fields. It has been studied on the lubrication properties of liquid metal in foreign countries since the 20th century, but the research on the use of liquid metals as a lubricant in China is still in its infancy. The preparation process of liquid metals is introduced. From the three aspects of lubrication performances of liquid metals, lubrication mechanisms of liquid metals and working performances of liquid metals bearings, the research status of liquid metal used as lubricant is summarized, and the direction of the research and the problems and technologies to be solved in the future using liquid metal as a lubricant in China is proposed.
Early Detection of Renal Dysfunction in Adolescents Aged 10-13 Years Born with very Low Birth Weight

Objective: Very low birth weight (VLBW), defined as less than 1500 gr, is an established risk factor for kidney disease in adulthood. To assess that, we examined whether VLBW manifests signs of renal dysfunction at as early as age 10 years, as reflected by elevated blood pressure, proteinuria and reduced glomerular filtration rate (GFR). Methods: 103 children aged 10-13 years and born with VLBW underwent consecutive blood pressure measurements, spot urine analysis, and weight and height measurements. Prevalence rates of hypertension, pre-hypertension and proteinuria were calculated. Characteristics were compared between children with normal and abnormal renal function, to identify risk factors for renal dysfunction. Results: The prevalence of systolic hypertension was 15.8% (95% CI 8.69% - 22.91%) of systolic pre-hypertension 6.9% (95% CI1.96% - 11.84%), and of proteinuria 15.7% (95% CI 8.64% - 22.76%) of the study population. Hypertension was associated with a significantly diminished mean birth weight compared to the remainder of the cohort (939.3gr vs 1111gr, P=0.024). Proteinuria and microalbuminuria were associated with lower mean current body weights: 27.2kg vs 36.7kg P=0.015 and 31.3 kg vs 36.8kg; P=0.023; and with increased mean estimated GFR (126.1 vs 108.3 mL/min per 1.73 m2; P = 0.0059). Conclusions: In a cohort of children aged 10-13 years, who were born preterm with VLBW, disturbed kidney function presented in considerably higher proportions than in general populations of this age. The findings merit considering initiation of routine screening during early adolescence, for hypertension, proteinuria and GFR in this risk group.
Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation

Horizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillus spp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment. These zones encompass and connect classically defined genomic islands. Analyzing topological and strand biases of recent and older transfer events, we show that restrictions on entry are rapidly enforced by selection and that restrictive and permissive zones have existed in their current locations for long periods of evolution. The largest zone, characterized by a high influx of metabolic genes, is centred on the terminus. The other two zones flank a narrow non-permissive zone around the origin of replication and extend to delimit the first third of the chromosome – the part of the chromosome that is confined to the forespore during early spore formation. Horizontal transfers into this area are biased towards functions classically controlled by the forespore-specific sigma factor σF: signal transduction, transcription, and particularly membrane biogenesis. Similar enrichment patterns are present in spore-forming but absent in non-spore-forming Bacilli. Our results suggest that the topology of HGT in Geobacillus, and Bacilli more generally, reflects constraints imposed by chromosomal organization for fast and sporulation, as asymmetric chromosomal entrapment in the forespore during early spore formation restricts where HGT-driven innovation in sporulation can occur.
Nutritional Relevance of Flavonoids in Disease Prevention

Flavonoids are not essential nutrients in that their absence from the diet does not produce deficiency conditions in animals and man. However, many have important similarities to pharmacological agents used in the treatment of disease. Their role as dietary components in disease prevention is less clear. Many potentially anti-carcinogenic and anti-atherogenic effects observed in cell cultures will not be of nutritional relevance unless flavonoids gain access to appropriate cellular sites. The bioavailability of flavonoids will depend on numerous factors including molecular structure, the amount consumed, the food matrix, degree of bioconversion in the gut and tissues, the nutrient status of the host and genetic factors. Moreover, extensive and rapid intestinal and hepatic metabolism of flavonoids suggests that the body may treat them as xenobiotic and potentially toxic compounds requiring rapid elimination. Consequently, in addition to potential health benefits, possible adverse effects of flavonoids in the diet also need to be considered when assessing their roles in the prevention of degenerative diseases.