Miracle-dz/UniFAR-FTUs huggingface dataset:
Groundwater as a source of phosphorus and silicate in an estuarine zone: results from continuous monitoring of nutrients and 222Rn

The concentrations of 222Rn and dissolved inorganic nutrients in river water at a fixed station of the Nakdong River estuary which has an artificial barrage were continuously measured from October 2014 to May 2015. Monthly benthic 222Rn flux from the river bottom was estimated using a simple mass balance model, taking into account 222Rn sources and sinks. The estimated benthic 222Rn flux shows a significant correlation with groundwater level, suggesting that groundwater level can be used as a representative of the groundwater input. Based on correlation analyses, the concentration of dissolved inorganic nitrogen (DIN) was found to be dependent primarily on river water input. In contrast, the concentrations of dissolved inorganic phosphorus (DIP) and dissolved inorganic silicate (DSi) were predominantly controlled by groundwater input. Our results suggest that groundwater input may be an important source of DIP, especially under P-limited condition, which can affect marine primary production and ecological problems such as eutrophication and algal blooms in the coastal zones.
Phylogeography of Walnut-Infesting Rhagoletis suavis (Diptera: Tephritidae) Flies

Abstract Discerning the biogeography and historical ranges of organisms is important to understanding the processes causing population divergence and speciation. Mountainous regions in North America have contributed to widespread divergence within animals and plants as species become geographically isolated and diverge. Here, we investigate patterns of divergence for six species of walnut-infesting flies in the Rhagoletis suavis species group (Diptera: Tephritidae) in the United States and Mexico based on sequence analysis of mitochondrial DNA (mtDNA) encoded Cytochrome Oxidase I and II genes (COI and COII). We resolved the relationship of the newly described species, Rhagoletis ramosae, found in the highlands of Mexico, within the R. suavis species group to test alternate hypotheses of migration and divergence. Bayesian phylogenetic analysis supported a clade in which R. ramosae was most closely related to Rhagoletis zoqui/Rhagoletis completa, found in eastern Mexico. This implies that the Sierra Madre Oriental and not the Sierra Madre Occidental have been a major conduit of migration, isolation, and speciation for walnut flies between Mexico and the United States. Comparisons of mtDNA divergence for R. suavis group flies with the Rhagoletis pomonella and Rhagoletis cingulata species groups suggested that despite current similarities in geographic distributions, these taxa do not share a common biogeographic history, diverging in different regions at different times in the past. Patterns displayed by Rhagoletis flies can be compared to patterns seen in other organisms through the Southwestern and Eastern United States, and Mexico to develop a fuller understanding of the biogeography of these regions of North America.
The complete mitochondrial genome of Sympiezomias velatus (Coleoptera: Curculionidae)

Abstract Here, we determined the complete mitogenome sequence of Sympiezomias velatus (Coleoptera: Curculionidae: Entiminae). This mitogenome was 15,592 bp long with an A + T content of 74.1% and contains 13 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), 2 ribosomal RNA unit genes and a large non-coding region (putative control region). The trnI gene was not found in the S. velatus mitogenome. The order and orientation of the mitochondrial genes were identical to the inferred ancestral arrangement of insects except for trnR which was changed to be adjacent the nad3 gene. All tRNAs had the typical cloverleaf structure, except for trnS1 which lacked the dihydrouridine arm. The Bayesian phylogenetic tree of 10 Entiminae species based on the concatenated nucleotide sequences of 13 PCGs strong supported a sister relationship of S. velatus and Barynotus obscures.
A Biologists Guide to Analysis of DNA Microarray Data

Let's read! We will often find out this sentence everywhere. When still being a kid, mom used to order us to always read, so did the teacher. Some books are fully read in a week and we need the obligation to support reading. What about now? Do you still love reading? Is reading only for you who have obligation? Absolutely not! We here offer you a new book enPDFd a biologists guide to analysis of dna microarray data to read.
Classification of vehicles’ types using histogram oriented gradients: comparative study and modification

This paper proposes an efficient model for recognizing and classifying a vehicle type. The model localizes each object in the image then identifies the vehicle type. The features of an image are extracted using the histogram oriented gradients (HOG) and ant colony optimization (ACO). A vehicle type is determined using different classifiers namely: the k-nearest neighbor (KNN), support vector machine (SVM), random forest (RF), and Softmax classifiers. The model is implemented and operated on two datasets of vehicles' images as test-beds. From the comparative study, the SVM outperforms the other adopted classifiers and is also better using HOG than that using ACO. A modification is done on HOG by adding the Laplacian filter to select the most significant image features. The accuracy of the SVM classifier using modified HOG outperforms that one using the traditional HOG. The proposed model is analyzed and discussed regardless the local geometric and photometric transformations like illumination variations.
Potential Pathological Biomarkers in Multiple Sclerosis

Multiple Sclerosis (MS) is a complex disease of the central nervous system (CNS) that involves the intricate interplay of different immune cells going awry leading to inflammation, demyelination, and neurodegeneration. Its diagnosis is quite arduous because of the baffling number of symptoms it elicits and the varied clinical manifestation it presents. The simplified criteria (in form of Macdonald’s Criteria) which have got modified several times is now the single most important criteria accepted by neurology bodies for diagnosing MS. Biomarkers from time to time have been explored to simplify the diagnosis and prognosticate MS along with a necessity to monitor treatment outcome. In recent years, research on biomarkers has advanced rapidly due to their ability to be easily and rapidly measured, their specificity, safety, and their ability to yield precise results. Biomarkers are classified into various categories including predictive, diagnostic, prognostic, related to disease activity, and monitoring treatment outcome. Each representative of the disease activity category reflects a variety of pathological processes of MS such as neuroaxonal loss, gliosis, demyelination, disability progression, remyelination, etc. This review discusses several promising serum and cerebrospinal fluid biomarkers and imaging biomarkers used in clinical practice. Myelin oligodendrocyte glycoprotein antibody disease which is recently recognized as a definite disease will also be discussed. Furthermore, it sheds light on the criteria and the challenges a biomarker faces to be considered as a standard one.
Analysis of the properties of NetcodICN protocols

Information Centric Networking (ICN) is a family of recent protocols based on a paradigm different from traditional IP networks. A natural and well-adapted extension to this type of networks is the use of network coding: this has been exploited in the previously proposed family of NetcodCCN/NetcodNDN protocols, which are capable of reaching network capacity. However, this has been observed with heuristics, and on a few examples of networks. We analyze more formally the properties of several variants of the protocol.
Bioprinting and biomaterials for dental alveolar tissue regeneration

Three dimensional (3D) bioprinting is a powerful tool, that was recently applied to tissue engineering. This technique allows the precise deposition of cells encapsulated in supportive bioinks to fabricate complex scaffolds, which are used to repair targeted tissues. Here, we review the recent developments in the application of 3D bioprinting to dental tissue engineering. These tissues, including teeth, periodontal ligament, alveolar bones, and dental pulp, present cell types and mechanical properties with great heterogeneity, which is challenging to reproduce in vitro. After highlighting the different bioprinting methods used in regenerative dentistry, we reviewed the great variety of bioink formulations and their effects on cells, which have been established to support the development of these tissues. We discussed the different advances achieved in the fabrication of each dental tissue to provide an overview of the current state of the methods. We conclude with the remaining challenges and future needs.
Effect of melting modes on microstructure and tribological properties of selective laser melted AlSi10Mg alloy

ABSTRACT This paper focuses on the effect of melting modes on microstructural evolution and tribological properties of AlSi10Mg alloy fabricated by selective laser melting (SLM). The results showed that the microstructures of SLM AlSi10Mg consisted of primary α-Al surrounded by cellular Si networks (∼500 nm) when fabricated in conduction mode, but has a finer cellular-like Si phase (∼200 nm) when fabricated in keyhole mode. The strong convection caused by the melt reflow and Marangoni convection under keyhole mode also resulted in deposition of nano-scale Si particles at the bottom of the molten pool. The SLM AlSi10Mg fabricated in keyhole mode exhibited better wear resistance than that fabricated in conduction mode. Compared to traditional as-cast specimens, both SLM specimens showed better wear resistance due to the unique cellular-like networks. The SLM technique offers a new approach for material processing that can be used to refine microstructures for improved tribological properties.
The effect of environmental factors and growth hormone receptor gene polymorphism on growth curve and live weight parameters in buffalo calves.

This study was conducted to determine the effects of some environmental factors and growth hormone receptor gene polymorphisms (GHR) on Brody growth curve coefficients and different body weights parameters in buffalo calves. The records and blood samples of 27 buffalo calves, born in 2009, bred at Afyon Kocatepe University Animal Research Center were analyzed. A, B and k parameters for the Brody model were estimated as 366.589±31.698, 0.932±0.011 and 0.002±0.000 respectively. In addition, live weights at birth, 180 and 360 days were 30.696±1.043 kgs, 121.701±5.071 kgs and 188.834±8.442 kgs respectively. Three polymorphic regions were detected at G3676A, G3679A and G3680del bases in exon 10 of the GHR gene. Effects of sex on parameter A and birth weight on weight at 180 days were statistically significant (P<0.05). Findings indicated that G3676A and G3679A mutations and haplotypes consisting of mentioned SNPs may result in significant differences in growth traits, but the available data were not enough to reveal this fact.
Hybrid-Vlasov modeling of three-dimensional dayside magnetopause reconnection

Dayside magnetic reconnection at the magnetopause, which is a major driver of space weather, is studied for the first time in a three-dimensional (3D) realistic setup using a hybrid-Vlasov kinetic model. A noon–midnight meridional plane simulation is extended in the dawn–dusk direction to cover 7 Earth radii. The southward interplanetary magnetic field causes magnetic reconnection to occur at the subsolar magnetopause. Perturbations arising from kinetic instabilities in the magnetosheath appear to modulate the reconnection. Its characteristics are consistent with multiple, bursty, and patchy magnetopause reconnection. It is shown that the kinetic behavior of the plasma, as simulated by the model, has consequences on the applicability of methods such as the four-field junction to identify and analyze magnetic reconnection in 3D kinetic simulations.
In vivo assessment of bisphenol A induced histopathological alterations and inflammatory gene expression in lungs of male Wistar rats

Bisphenol A (BPA), an imperative environmental contaminant used in polycarbonate plastics. Due to limited information concerning the effect of BPA on lungs, this study design to assess whether BPA cause alterations in histopathology and trace metal content in lungs of rats. They were divided into five groups with five rats per group. Group I was named as control group. Group L6 and L12 were received BPA (10 mg/kg body weight/day) for 6 weeks and 12 weeks respectively. Group H6 and L12 were given BPA (25 mg/kg body weight/day) for 6 weeks and 12 weeks respectively. Considerable alteration in Cu, Zn and Fe was detected in experimental groups. BPA also caused significant increase in the expression of tumor necrosis factor α that mediate the pulmonary inflammatory response. Comparative study of resolved proteins i.e. 72 KDa (matrix metalloproteinase 2 fragment) and 109 KDa (nucleolin) on SDS-PAGE showed their altered expression in experimental groups. Histopathology of experimental groups revealed altered architecture of lungs. Special staining of BPA treated groups showed significant number of mast cells in alveoli and bronchioles. Prolonged administration of BPA causes deleterious aggravating lung damage even at extremely low dose, so the use of BPA should be prohibited in plastic synthesizing industries.
Segmentation Effect on the Transferability of International Safety Performance Functions for Rural Roads in Egypt

This paper examines the transferability of the Safety Performance Function (SPF) of the Highway Safety Manual (HSM) and other 10 international SPFs for total crashes on rural multi-lane divided roads in Egypt. Four segmentation approaches are assessed in the transferability of the international SPFs, namely: (1) one-kilometer segments (S1); (2) homogenous sections (S2); (3) variable segments with respect to the presence of curvatures (S3); and (4) variable segments with respect to the presence of both curvatures and U-turns (S4). The Mean Absolute Deviation (MAD), Mean Prediction Bias (MPB), Mean Absolute Percentage Error (MAPE), Pearson χ2 statistic, and Z-score parameters are used to evaluate the performance of the transferred models. The overdispersion parameter (k) for each transferred model and each segmentation approach is recalibrated using the local data by the maximum likelihood method. Before estimating the transferability calibration factor (Cr), three methods were used to adjust the local crash prediction of the transferred models, namely: (1) the HSM default crash modification factors (CMFs); (2) local CMFs; and (3) recalibrating the constant term of the transferred model. The latter method is found to outperform the first two methods. Besides, the results show that the segmentation method would affect the performance of the transferability process. Moreover, the Italian SPFs based on the S1 segmentation method outperforms the HSM and all of the investigated international SPFs for transferring their models to the Egyptian rural roads.
Up to 40% of COVID-19 Critically Ill Patients Have Vitamin D Deficiency

Background: Coronavirus disease (COVID-19) has caused more than 745,000 deaths worldwide. Vitamin D has been identified as a potential strategy to prevent or treat this disease. The purpose of the study was to measure vitamin D at hospital admission of COVID-19; Methods: We included critically ill patients with the polymerase chain reaction positive test for COVID-19, from March to April, 2020. Statistical significance was defined as P &lt; . 05. All tests were 2-tailed; Results: A total of 35 patients (median age, 60 years; 26 [74.3%] male) were included. Vitamin D levels were categorized as deficient for 14 participants (40%). Vitamin D deficiency was associated with vitamin A (P= 0.003) and Zinc (P= 0.019) deficiency and lower levels of albumin (P= 0.026) and prealbumin (P= 0.009). Overall, none of the studied variables were associated with vitamin D status: mortality, intensive care unit (ICU) or hospital stay, necessity of vasoactive agents, intubation, prone position, C reactive protein (CRP), Dimer-D, Interleukin 6 levels (IL-6), ferritin levels, or bacterial superinfection; Conclusions: In this single-center, retrospective cohort study, deficient vitamin D status was found in 40% in COVID-19 critically ill patients. However, deficient vitamin D status was not associated with inflammation or outcome.
A low-jitter 2.4 GHz all-digital MDLL with a dithering jitter reduction scheme for 256 times frequency multiplication

A new all-digital multiplying delay-locked loop (MDLL) based frequency multiplier architecture with a high frequency multiplication factor N of 256 is presented. The proposed MDLL utilizes a dithering jitter reduction scheme based on a delta-sigma modulation to achieve a low deterministic jitter and a large N factor. Additionally, a new stochastic phase detector is proposed to reduce static phase oﬀset and improve jitter performance. Implemented in a 65-nm 1.0-V CMOS process, the proposed all-digital MDLL generates 2.4-GHz output clock and achieves a peak-to-peak jitter of 6.47 ps with N = 256 . It occupies an active area of 0.032 mm 2 and achieves a power eﬃciency of 0.875 mW/GHz.
Spatial transcriptomics reveals the heterogeneity and FGG+CRP+ inflammatory cancer-associated fibroblasts replace islets in pancreatic ductal adenocarcinoma

Background Understanding the spatial heterogeneity of the tumor microenvironment (TME) in pancreatic cancer (PC) remains challenging. Methods In this study, we performed spatial transcriptomics (ST) to investigate the gene expression features across one normal pancreatic tissue, PC tissue, adjacent tumor tissue, and tumor stroma. We divided 18,075 spatial spots into 22 clusters with t-distributed stochastic neighbor embedding based on gene expression profiles. The biological functions and signaling pathways involved in each cluster were analyzed with gene set enrichment analysis. Results The results revealed that KRT13+FABP5+ malignant cell subpopulation had keratinization characteristics in the tumor tissue. Fibroblasts from adjacent tumor tissue exhibited a tumor-inhibiting role such as “B-cell activation” and “positive regulation of leukocyte activation. ” The FGG+CRP+ inflammatory cancer-associated fibroblasts replaced the islets in tumor stroma. During PC progression, the damage to pancreatic structure and function was heavier in the pancreatic exocrine (AMYA2+PRSS1+) than in the endocrine (INS+GCG+). Conclusion Our results revealed the spatial heterogeneity of dynamic changes and highlighted the significance of impaired exocrine function in PC.
Accelerated hypometabolism with disease progression associated with faster cognitive decline among amyloid positive patients

Objective To evaluate the progression of brain glucose metabolism among participants with biological signature of Alzheimer’s disease (AD) and its relevance to cognitive decline. Method We studied 602 amyloid positive individuals who underwent 18F-fluorodeoxyglucose PET (FDG-PET) scan, 18F-AV-45 amyloid PET (AV45-PET) scan, structural MRI scan and neuropsychological examination, including 116 cognitively normal (CN) participants, 314 participants diagnosed as mild cognitive impairment (MCI), and 172 participants diagnosed as AD dementia. The first FDG-PET scan satisfying the inclusion criteria was considered as the baseline scan. Cross-sectional analysis were conducted with the baseline FDG-PET data to compare the regional differences between diagnostic groups after adjusting confounding factors. Among these participants, 229 participants (55 CN, 139 MCI, and 35 AD dementia) had two-year follow-up FDG-PET data available. Regional glucose metabolism was computed and the progression rates of regional glucose metabolism were derived from longitudinal FDG-PET scans. Then the group differences of regional progression rates were examined to assess whether glucose metabolism deficit accelerates or becomes stable with disease progression. The association of cognitive decline rate with baseline regional glucose metabolism, and progression rate in longitudinal data, were evaluated. Results Participants with AD dementia showed substantial glucose metabolism deficit than CN and MCI at left hippocampus, in addition to the traditionally reported frontal and parietal–temporal lobe. More substantial metabolic change was observed with the contrast AD – MCI than the contrast MCI – CN, even after adjusting time duration since cognitive symptom onset. With the longitudinal data, glucose metabolism was observed to decline the most rapidly in the AD dementia group and at a slower rate in MCI. Lower regional glucose metabolism was correlated to faster cognitive decline rate with mild–moderate correlations, and the progression rate was correlated to cognitive decline rate with moderate-large correlations. Discussion and conclusion Hippocampus was identified to experience hypometabolism in AD pathology. Hypometabolism accelerates with disease progression toward AD dementia. FDG-PET, particularly longitudinal scans, could potentially help predict how fast cognition declines and assess the impact of treatment in interventional trials.
Genotypic and Phenotypic Correlation Regarding Expression Level of Myosin Heavy Chain (Myh7) Gene Polymorphisms in Hypertrophic Cardiomyopathy

Hypertrophic cardiomyopathy (HCM), where it can be seen as unexplained left ventricular hypertrophy, is the most common inherited cardiac disorder. This condition is a major cause of sudden death. The clinical phenotype is heterogeneous, and mutations in a number of sarcomeric contractile protein genes are responsible for causing HCM, which is usually inherited as an autosomal dominant trait. The mode of inheritance can differ from those of HCM caused by mutations in sarcomere genes. Detailed clinical evaluation and mutation analysis are, therefore, important in providing an accurate diagnosis in order to enable genetic counseling, prognostic evaluation and appropriate clinical management. This Review summarizes current knowledge on the genetics regarding beta myosin heavy chain gene (MYH7), disease mechanisms, and correlations between phenotype and genotype in patients with HCM.
Environmentally Compatible Access to α‐Trifluoromethylseleno‐Enones

α‐Trifluoromethylselenolated enones constitute valuable building‐blocks for further synthesis of innovative fluorinated compounds. Herein, we described an easy access to such compounds in green conditions through a Morita‐Baylis‐Hillman like reaction. These conditions have also been extended to higher fluorinated homologs.