Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of haplotype networks: The randomized minimum spanning tree method

Haplotype network construction is a widely used approach for analysing and visualizing the relationships among DNA sequences within a population or species. This approach has some problems such as how to quantify alternative links among sequences or how to plot efficiently networks to compare them easily. In this paper, a new method is presented: the randomized minimum spanning tree method, based on randomizing the input order of the data in order to produce alternative branchings in the haplotype network. It is shown that this new method can produce, at least in some situations, networks with less alternative links than the minimum spanning network method. A new graphical display of haplotype networks is introduced here. This is based on calculating the coordinates of the haplotypes from a multidimensional scaling of the haplotype distance matrix. The display can be done in two or three dimensions. The eigenvalues extracted from the multidimensional scaling analysis give an indication of the relevant number of dimensions. These tools are illustrated with the analyses of published data on the leopard and on the jaguar. These analyses show interesting and contrasting patterns between these two species of big cats. All tools are implemented in R and available in the package pegas.
Design and verification for CDC synchronization based on TMR

Triple modular redundancy (TMR) is widely used in FPGA/ASIC circuits to protect circuits against single event upsets (SEUs). However, because of the interference of metastability on signal transmis- sion across clock domains, the TMR circuits’ capability against SEUs is reduced greatly. In order to solve this problem, a cross-clock transmission solution which could be applied in TMR circuits are presented. In ad-dition, simulation-based veriﬁcation which combined protocol assertions, metastableinjectionandforcedinversionisproposedtosucceedinverifyingtheavailabilityofthesolutionbasedonTMRcircuits.
Systematic review of the incidence and risk factors for cerebral vasculopathy and stroke after cranial proton and photon radiation for childhood brain tumors.

Background The aim of our study is to determine the incidence, timing, and risk factors for cerebral vasculopathy after cranial proton and photon radiation for pediatric brain tumors. Methods We performed a single-institution retrospective review of a cohort of children treated with proton radiation for brain tumors. MRA and/or MRI were reviewed for evidence of cerebral vascular stenosis and infarcts. Twenty-one similar studies (17 photon, 4 proton) were identified by systematic literature review. Results For 81 patients with median follow-up of 3 years, the rates of overall and severe vasculopathy were 9.9% and 6.2% respectively, occurring a median of 2 years post radiation. Dose to optic chiasm greater than 45 Gy and suprasellar location were significant risk factors. Results were consistent with 4 prior proton studies (752 patients) that reported incidence of 5% to 6.7%, 1.5 to 3 years post radiation. With significantly longer follow-up (3.7-19 years), 9 studies (1108 patients) with traditional photon radiation reported a higher rate (6.3%-20%) and longer time to vasculopathy (2-28 years). Significant risk factors were neurofibromatosis type 1 (NF-1; rate 7.6%-60%) and suprasellar tumors (9%-20%). In 10 studies with photon radiation (1708 patients), the stroke rate was 2% to 18.8% (2.3-24 years post radiation). Conclusions Childhood brain tumor survivors need screening for vasculopathy after cranial radiation, especially with higher dose to optic chiasm, NF-1, and suprasellar tumors. Prospective studies are needed to identify risk groups, and ideal modality and timing, for screening of this toxicity.
DIGITAL PAYMENT: PROBABILITY IN MILLENIAL (CASE STUDY OF UINSU FEBI STUDENTS)

The rapid technological advances with a very strong internet penetration make the Indonesian people connect to communicate instantly. This has indirectly changed the pattern of human life, especially in the activities of shopping, communicating and working and transacting money in order to spend their income. Therefore with the activities carried out the hope of access to financial services that are affordable, fast and easy to personally connect with various activities. Someone in the internet world makes demands that need to be addressed by modern financial service providers. Internet access has shown a significant increase. This is consistent with the publication of the Association of Internet Service Providers (APJII) in March 2015 stating an increase in internet users, namely from 71.9 million in 2013 to 88.1 million users at the end of 2014, or about 34.9% of the total population currently. This digital payment research shows that there is an increase in the quality of banking services in Indonesia. This is because the banking management has implemented it to reach all levels of Indonesian society, especially for millennials living in the FOR (frontier, outermost, and remote) areas.
Can climate matching predict the current and future climatic suitability of the UK for the establishment of non-native birds?

ABSTRACT Capsule: Current UK distributions of non-native birds poorly match areas identified as being climatically suitable. Aims: Non-native species are spreading at unprecedented rates and though invasions are expected to increase under climate change, evidence for this is mixed. We assess climatic suitability throughout the UK based on the apparent match to the climate in species’ native ranges and investigate potential climatic limitation within the non-native range. Methods: Climate was characterized within polygons representing the native ranges of 167 potentially invasive species. Parts of the UK with current and future climate similar to that in the native range were deemed climatically suitable. The incidence of recent observations inside and outside suitable areas was used to test hypotheses about climatic limitation of non-native ranges. Results: Climate matching suggests that 69 of 167 non-native bird species could currently find climatically suitable areas for establishment in the UK. Future climate change would see this number increase by 14% by 2080. However, observed occurrences of non-native species in the UK were not significantly correlated to climatic suitability. Only 44 of the 69 species with suitable climate in the UK were present. Moreover, 85% of species observed in the UK had some UK occurrences in climatically unsuitable areas and for 57 species their entire UK range was in climatically unsuitable areas. Similar results were apparent for the subset of 12 species with established UK populations. Conclusions: Climate matching provides a relatively poor indication of the extent of current and future suitable areas because species can adapt to new climates or other factors constrain the native range and many climatically suitable areas are currently unoccupied. Improvements to climate matching techniques and ongoing surveillance are required to refine predictions to support effective management policies.
Feruloyl esterase from Aspergillus clavatus improves xylan hydrolysis of sugarcane bagasse

Feruloyl esterase is a subclass of carboxylic acid esterases with the capacity to release ferulic acid and other cinnamic acids from plant cell walls and synthetic substrates. Feruloyl esterases act synergistically with xylanases removing ferulic acid residues esterified to arabinoxylans. Feruloyl esterase type D from Aspergillus clavatus (AcFAE) was expressed in Escherichia coli , purified, and applied with a commercial xylanase consortium (Novozymes) for hydrolysis of sugarcane bagasse. Feruloyl esterase plus xylanase increased 5.13-fold the releasing of ferulic acid from sugarcane bagasse. Removal of only 7.7% of ferulic acid content by AcFAE increased 97.3% the sugarcane bagasse hydrolysis by xylanase. These data support the use of AcFAE as an interesting adjuvant enzyme to improve lignocellulose digestion and biotechnological tool for biorefineries.
Selection for an improved disease resistance using factorial mating designs and molecular based pedigree in fish: a simulation study

Diseases are a major threat for fish farming all over the world. Selective breeding for natural genetic resistance is considered as a promising tool to reduce the economical impact of disease outbreaks and the environmental issue associated with the use of veterinary drugs. When available, heritability estimates are usually medium to high for a wide range of diseases (Quillet et al., 2007), supporting the idea that a potential for progress through selection does exist. Yet, few commercial breeding programmes have been implemented up to now, one reason being the cost of the facilities dedicated to infectious challenges for many families. Using a posteriori marker-based parentage rebuilding now makes it possible to get the pedigree information when families are reared in a common garden environment since fertilization. The feasibility and power of such a system has been well established for growth and quality traits (Dupont-Nivet et al., 2008; Vandeputte et al., 2008). The limitation comes from the cost of genotyping, which must be designed in order to optimize the associated genetic gain. This paper aims at simulating a selection procedure for disease resistance considered as a binary trait (0 if the fish dies, 1 if it survives) in a population of mixed families where the parentage of both selection candidates and challenged animals is established a posteriori. The Bayesian methods based on the maximization of the posterior distribution of unknowns (MAP) as proposed by Gianola and Foulley (1983) and Harville and Mee (1984) are used to estimate breeding values. The expected genetic progress is simulated according to the genetic determinism of the trait, the number of genotyped individuals and their distribution among candidates and related challenged animals, considering that for sanitary reasons, challenged animals cannot be used anymore as future breeders.
Subclinical Hypothyroidism (SH) and Atherogenic Index of Plasma (AIP) in Women: A Case-Control Study From a Tertiary Care Hospital in South India

Introduction Subclinical hypothyroidism (SH) is defined as an increase in serum-thyroid stimulating hormone (S-TSH) above the normal level with free triiodothyronine (T4) and free thyroxine (T3) within the normal range. It is more common in females. The association between SH and dyslipidemia is unclear. There are many controversial studies regarding the same. This is the single largest study of Atherogenic index of plasma (AIP) in SH among women from our country. Our aim is to study the lipid profile and AIP in SH patients. We will also study the correlation between AIP and S-TSH levels in SH patients. Materials and methods It was a retrospective study conducted in a tertiary care center. A total of 97 females with SH were taken as cases and 86 normal females were taken as euthyroid (ET) controls. They were matched for demographic characteristics. T3, T4, S-TSH, total cholesterol, S-triglycerides (S-TG), high-density lipoprotein - cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and AIP were compared between the two groups. Spearman’s correlation between TSH and AIP was studied in the SH group. Mann-Whitney U test was performed. Results The TG, HDL, AIP levels were significantly different between both groups. TG, AIP was higher in the SH group compared to the ET group (p value of TG= 0.01, p value of AIP <0.0001). HDL was lower in the ET group compared to the SH group (p value <0.0001). AIP showed a significant positive correlation with S-TSH levels in the SH group. (r value=0.72, p value=<0.001). Conclusion It is important to regularly monitor SH patients for dyslipidemia, in order to start early therapy with levothyroxine/statins. Emphasis should be laid on lifestyle changes such as diet and exercise from the time of diagnosis. Community level education and awareness should be encouraged. Also, AIP is a better parameter to assess cardiovascular risk in SH patients than a conventional lipid profile.
Influence of fungal exudates of Alternaria dauci on carrot partial resistance

Alternaria leaf blight, caused by the necrotrophic fungus Alternaria dauci, is the most damaging foliar disease in carrot production. Fungicide use has variable efficiency, and presents economic and ecological costs. Popular partially resistant cultivars exist, but their resistance level is still unsatisfactory. A better knowledge on carrot A. dauci resistance mechanisms may help to produce more resistant cultivars faster. More generally, partial resistance mechanisms in plants are still poorly understood. In order to better understand partial resistance to leaf blight in carrot, we implemented an a priori approach, investigating the role of different resistance mechanisms in the carrot-A. dauci interaction. It has been suggested that Alternaria dauci produces toxins, such as zinniol. The work presented here is centered on the role played by these toxins in the plant-fungus interaction, and more especially plant resistance. Plant cell suspensions from several genotypes were treated with raw fungal extracts. A good correlation was found between whole plant resistance to the fungus and metabolic activity of the cell suspensions after 48 h of exposure. Similar results were obtained using different techniques and different exposure times. Additionally, it was found that the toxicity of fungal extracts was due to secreted apolar compounds, which did not include zinniol. Zinniol is only produced when the fungus is grown in anoxic conditions. Nevertheless, fungal growth condition and zinniol content do not impact extract toxicity. Moreover, zinniol was not toxic to plant cells at physiological concentration.
Crystal structure of chlorido{hydridotris[3-phenyl-5-methylpyrazol-1-yl-κN3]borato}copper(II), C30H28BClCuN6

Abstract C30H28BClCuN6, triclinic, P1‾$P‾{1}$ (no. 2), a = 11.549(3) Å, b = 12.321(3) Å, c = 12.348(4) Å, α = 111.785(1)°, β = 116.664(3)°, γ = 97.513(1)°, V = 1361.3(7) Å3, Z = 2, Rgt(F) = 0.0440, wRref(F2) = 0.1063, T = 197 K.
Anger contributes to the spread of COVID-19 misinformation

A survey conducted over South Korean adults (N=513) reveals that emotions, specifically anger, contribute to the broader spread of misinformation on COVID-19 by leading angry individuals to consider false claims to be “scientifically credible. ” This pattern is more evident among conservatives than liberals. Our finding sheds light on new measures and journalistic interventions that could alleviate the public’s anger and foster science-based conversations during a public health crisis.
Reproductive success of least terns and black skimmers in southeastern North Carolina

One mixed colony of Least Terns and Black Skimmers at Wrightsville Beach, N.C. , was monitored to determine the reproductive success of these birds from 2003- 2005. Nests were visited, on average, every 3 days from April through July of each year. Mean clutch size differed significantly for both Least Terns and Black Skimmers among years. In 2005, there were significantly more 1-egg clutches for both species. Nest success differed significantly by clutch size for both species in 2005, and total nest success (2003-2005) also differed significantly for both species, with 1-egg clutches having much lower nest success. Hatching success differed significantly by clutch size in Least Terns in 2003 and 2005 and in Black Skimmers in 2005, and total hatching success (2003-2005) also differed significantly for both species among years. In Least Terns, 2-egg clutches had significantly greater hatching success in 2003 and 1-egg clutches had significantly lower hatching success in 2005. Overall (2003-2005), 2-egg clutches had the greatest hatching success and 1-egg clutches had the least. In Black Skimmers, hatching success increased as clutch size increased in 2005 and overall. There was a negative correlation between number of nests and nest success for both Least Terns and Black Skimmers, and number of eggs and hatching success for both Least Terns and Black Skimmers. This research provides important baseline data that may be used for conservation efforts for Least Terns and Black Skimmers in managed coastal habitats.
Polymorphisms of BoLA-DRB3 gene and its association with resistance / susceptibility to Leucosis in Holstein cattle from La Pampa

EBL is a disease of adult cattle caused by the retrovirus, bovine leukemia. It can manifest: aleukemic an asymptomatic form, with a normal number of B lymphocytes in the blood; a form of permanent lymphocytosis, with an increase in the number of B lymphocytes and finally a lymphoproliferative tumor presentation in the form of lymphosarcoma. The alleles of the genes of the Bovine Major Histocompatibility Complex (BoLA) have been associated with resistance and susceptibility to infectious diseases. The overall objective of this study was to associate polymorphisms of the BoLA-DRB3.2 gene, defined by the technique of polymerase chain reaction technique and polymorphisms length of the restriction fragment (PCR-RFLP), with resistance / susceptibility to leucosis in Holstein cows of La Pampa. It relied on a case/control design, for which blood samples were taken to 150 animals in 3 opportunities with intervals of three months each. The case group comprised animals that were positive in the immunodiffusion agar animals test (DIDA) and whose blood lymphocyte count was ≥ 10.000 linf/μl and the control group included cows that ware negative for DIDA and present < 10.000 linf/μl of blood. Fisher’s Exact test and Odds Ratio (OR) of Woolf-Haldane were used to study the association between lymphocyte count and DIDA results with allelic variants. In 82 animals genotyped by PCR-RFLP, the DRB3.2*22 allele showed an
High Temperature Stress Effected the Biochemical Parameters of Rice (Oryza sativa L.) Varieties and Hybrids

Climate change associated phenomenon especially high temperature has become an important constraint for rice production. To develop high temperature tolerant rice genotypes, thorough understanding of genetics, biochemical and physiological processeshas become essential for identification and selection of traits and to enhance tolerance mechanism. In this connection, an experiment was formulated to study the effect of high temperature stress onbiochemical parameters of rice (Oryza sativa L.) varieties and hybrids. This was conducted for two consecutive kharif seasons 2012 and 2013 at Indian Institute of Rice Research, Rajendranagar, Hyderabad. The biochemical parameters like Enzyme activityPeroxidase(POD),Superoxide dismutase (SOD), and Catalase (CAT) activity was estimated in control as well as stressed condition at vegetative stage and reproductive stages. The results revealed that the temperature acclimated plantscompared to non-induced (control) showed higher peroxidase, super oxide dismutase and catalase activityat both vegetative and reproductive stages compared to check variety N-22. From this study, it can be inferred that high temperature stress is associated with increased activity of antioxidant enzymes in leaves may lead to withstand of heat tolerant rice genotypesfor stressthat in turn results in relative high yield.
Pathogens Contamination Level Reduction on Beef Using Organic Acids Decontamination Methods

In this study we aimed to assess the efficiency of organic acids in different concentrations regarding pathogens as Salmonella, Listeria and Escherichia on beef, which can cause food borne illness in humans. The samples were sterilized using UV radiation for 30 minutes, afterwards being contaminated with 1 ml of microbial suspension (0.5 MacFarland). We used reference bacterial strains for Salmonella Enteritidis, Escherichia coli and Listeria monocytogenes. The samples were subjected to decontamination procedure by introducing 25mL of solution of lactic, acetic or citric acid in concentration of 1%, 2% and 3%. The results showed a reduction of initial pathogen load, ranging from 0.32 to 7.78 log CFU/g, depending on the type of acid, concentration and pathogen sensitivity. After decontamination, standardized methods have been used for the isolation of pathogenic germs. Based on statistical analysis we conclude that pathogens have a different sensitivity to the action of acid solutions, their sensitivity in ascending order being: Listeria monocytogenes, Salmonella Enteritidis and Escherichia coli. Among the organic acids, the most efficient was lactic acid, followed by acetic acid and less efficient citric acid. The greatest reduction of germs was determined by the concentration of 3%.
Resilience in Socioeconomically Disadvantaged Turkish Adolescents: An Ecological Perspective

The purpose of this study was to examine the role of self-esteem as mediator in the relationships between perceived parental acceptance/involvement, perceived peer social support, sense of school belonging and resilience in adolescents attending schools located in low socioeconomic districts. The sample of the study consisted of 1312 high school students (673 female, 639 male) between the ages of 13 to 19 (M = 15.67, SD = 1.18). Structural equation modeling was conducted to test the hypothesized model. Results showed that perceived parental acceptance/involvement, perceived peer social support, sense of school belonging and self-esteem were positive and significant predictors of resilience. Furthermore, self-esteem partially mediated the association between perceived parental acceptance/involvement, perceived peer social support, sense of school belonging and resilience. The proposed model explained 33% of the variance in resilience. Overall, findings contributed to the understanding of the simultaneous influence of multilevel resources in adolescent resilience.
Risk‐based approach for power transformer replacement considering temperature, apparent age, and expected capacity

Due to the limited availability of end-of-life failure data of power transformers by electric utilities, planning the replacement of power transformers is a challenging task for utility engineers. Transformers can be replaced based on their health indices, but they do not allow utility engineers to quantify risks posed by transformer failures. In that context, the study proposes a novel risk-based approach to plan the replacement of aged power transformers considering their temperature, apparent age, and expected capacity. The approach comprises a methodology that incorporates power transformers' winding hottest-spot temperature and apparent age into the conventional end-of-life failure model, a methodology that calculates the expected capacity of power transformers, a novel transformer ranking index, and a methodology that calculates the optimum year of replacement. Subtransmission and distribution substations were included in the IEEE Reliability Test System to evaluate the performance of the approach. The results show that incorporating the winding hottest-spot temperature and the apparent age into the end-of-life failure model can make a significant improvement on transformer replacement decisions in the event of limited availability of failure data. Results further suggest that end-of-life failures of fans and oil pumps can have an impact on the prioritisation of transformer replacement.