Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characterization of Rare and Threatened Local Populations of Peas (Pisum sativum L.) Cultivated in the Arid Region of Southern Tunisia

Pea (Pisum sativum L.) is an important legume for human and animal consumption, cultivated in many temperate regions of the world. In the present investigation, the seeds of twelve pea accessions collected from the arid regions of southern Tunisia, characterized by different colors of flowers and seed coats, were evaluated for their proteins, phenolic compounds and antioxidant activities. The protein content determined by the Bradford method ranged from 46.91 to 151.08 mg/g DW. The content of total phenol, total flavonoid and condensed tannin, ranging from 36.85 to 102.52 mg GAE/100 g DW, 6.95 to 48.11 mg QE/100 g DW, and 12.37 to 70.43 mg CE/100 g DW, respectively. These parameters were characterized respectively by the following three methods, the Folin‐Ciocalteu reagent, the aluminum chloride and the vanillin assay. The LC‐ESI/MS analysis identified the presence of 8 phenolic acids and 9 flavonoids which quinic acid, protocatechuic acid, hyperoside, and quercetin‐3‐O‐rhamnosidewere detected as the most abundant compounds. Moreover, the antioxidant activity of pea seeds was evaluated by the ABTS+and DPPH tests. Indeed, DPPH and ABTS anti‐free radical activity values ranged from 1.92 to 14.11 μmoL TEAC/g DW and 2.3 to 14.95 μmoL TEAC/g DW, respectively. The variability across the assessed traits revealed significant differences as computed by ANOVA tests. Else, the results showed significant correlations between seed coat color, seed shape, flower color and phenolic compounds. Therefore, genotypes characterized by a purple flower, brown seed coat, and wrinkled form had the highest levels of phenolic compounds and antioxidant activity. Correlation analysis revealed that phenolic compounds presented a strong positive correlation with antioxidant activities, while being negatively correlated with protein content. UPGMA cluster and Principal component analysis (PCA) revealed two main groups. This work highlights the nutritional value of P. sativum seeds as a good source of natural antioxidant compounds that may be useful in the food and pharmaceutical industries.
HbA1c and biomarkers of diabetes mellitus in Clinical Chemistry and Laboratory Medicine: ten years after

Abstract Since its discovery in the late 1960s, HbA1c has proven to be a major biomarker of diabetes mellitus survey and diagnosis. Other biomarkers have also been described using classical laboratory methods or more innovative, non-invasive ones. All biomarkers of diabetes, including the historical glucose assay, have well-controlled strengths and limitations, determining their indications in clinical use. They all request high quality preanalytical and analytical methodologies, necessitating a strict evaluation of their performances by external quality control assessment trials. Specific requirements are needed for point-of-care testing technologies. This general overview, which describes how old and new tools of diabetes mellitus biological survey have evolved over the last decade, has been built through the prism of papers published in Clinical Chemistry and Laboratory Medicine during this period.
Convergence of secretory, endosomal, and autophagic routes in trans-Golgi–associated lysosomes

Zhou et al. document that the vicinity of the trans-Golgi is the main location for lysosomes in Drosophila cells. They also show that the trans-Golgi–associated degradative compartment, where basal microautophagy of secretory cargos normally takes place, additionally contributes to autophagic vesicle formation under stress conditions.
Overcoming Limitations in Peer-Victimization Research That Impede Successful Intervention: Challenges and New Directions

Peer victimization at school is a worldwide problem with profound implications for victims, bullies, and whole-school communities. Yet the 50-year quest to solve the problem has produced mostly disappointing results. A critical examination of current research reveals both pivotal limitations and potential solutions. Solutions include introducing psychometrically sound measures to assess the parallel components of bullying and victimization, analyzing cross-national data sets, and embracing a social-ecological perspective emphasizing the motivation of bullies, importance of bystanders, pro-defending and antibullying attitudes, classroom climate, and a multilevel perspective. These solutions have been integrated into a series of recent interventions. Teachers can be professionally trained to create a highly supportive climate that allows student-bystanders to overcome their otherwise normative tendency to reinforce bullies. Once established, this intervention-enabled classroom climate impedes bully-victim episodes. The take-home message is to work with teachers on how to develop an interpersonally supportive classroom climate at the beginning of the school year to catalyze student-bystanders’ volitional internalization of pro-defending and antibullying attitudes and social norms. Recommendations for future research include studying bullying and victimization simultaneously, testing multilevel models, targeting classroom climate and bystander roles as critical intervention outcomes, and integrating school-wide and individual student interventions only after improving social norms and the school climate.
Changes in Chinese students' academic emotions after examinations: Pride in success, shame in failure, and self‐loathing in comparison

Abstract Background Several attempts have been made to examine students' academic emotions (AEs) in Western contexts, but less is known about how students' self‐reported emotions vary over time. Aims The study aimed to understand Chinese students' emotional responses to academic events and the impact of high‐stakes testing on their AEs in the first year with a repeated‐measures survey after the Semester 1 and Semester 2 mid‐term examinations. Samples 351 first‐year university students completed both surveys in an elite Chinese university, where the top 10% of first‐year students were assigned to an honours programme. Methods Self‐reported AEs survey responses were evaluated with confirmatory factor analysis. Invariance testing between honours and ordinary students and between semesters was used to examine between‐group differences across time. Results A three‐factor model of AEs (i.e., admired, shame, and self‐loathing) was found in both semesters, with strong invariance between semesters. Mean scores between groups were equivalent and semester. However, self‐loathing had the lowest mean (mean = 2.50; between mostly disagree and slightly agree), admired was at moderately agree (mean = 4.00), and shame was strongest at just over moderately agree (mean = 4.20). Conclusions This study reveals a three‐factor structure of AEs and the stability of these emotions among highly successful Chinese learners. Despite being elite students, this sample of Chinese learners felt shame and pride in response to mid‐term examinations.
Evidence for high gene flow, nonrandom mating, and genetic bottlenecks of Ganoderma boninense infecting oil palm (Elaeis guineensis Jacq.) plantations in Malaysia and Indonesia

ABSTRACT Ganoderma boninense, the causal agent of basal stem rot (BSR) disease, has been recognized as a major economic threat to commercial plantings of oil palm (Elaeis guineensis Jacq.) in Southeast Asia, which supplies 86% of the world’s palm oil. High genetic diversity and gene flow among regional populations of 417 G. boninense isolates collected from Sabah, Sarawak, and Peninsular Malaysia (Malaysia) and Sumatra (Indonesia) were demonstrated using 16 microsatellite loci. Three genetic clusters and different admixed populations of G. boninense across regions were detected, and they appeared to follow the spread of the fungus from the oldest (Peninsular Malaysia and Sumatra) to younger generations of oil palm plantings (Sabah and Sarawak). Low spatial genetic differentiation of G. boninense (FST = 0.05) among the sampling regions revealed geographically nonrestricted gene dispersal, but isolation by distance was still evident. Analysis of molecular variance (AMOVA) confirmed the little to no genetic differentiation among the pathogen populations and the three genetic clusters defined by STRUCTURE and minimum spanning network. Despite G. boninense being highly outcrossing and spread by sexual spores, linkage disequilibrium was detected in 7 of the 14 populations. Linkage disequilibrium indicated that the reproduction of the fungus was not entirely by random mating and genetic drift could be an important structuring factor. Furthermore, evidence of population bottleneck was indicated in the oldest oil palm plantations as detected in genetic clusters 2 and 3, which consisted mainly of Peninsular Malaysia and Sumatra isolates. The population bottleneck or founding event could have arisen from either new planting or replanting after the removal of large number of palm hosts. The present study also demonstrated that migration and nonrandom mating of G. boninense could be important for survival and adaptation to new palm hosts.
Hypoglycemic and hypolipidemic effects of Garcinia cambogia extracts in streptozotocin-nicotinamide induced diabetic rat model.

BACKGROUND AND OBJECTIVES Diabetes mellitus, a global health problem, is associated with metabolic complications such as hyperglycemia, hyperlipidemia, hypertension, cardiovascular diseases, and loss of vision. The present study evaluated the antidiabetic and antihyperlipidemic effects of ethanol extract of Garcinia cambogia (L.) N. Robson (G. cambogia) fruit rind in a streptozotocin-nicotinamide induced diabetic Wistar Rat model. MATERIALS AND METHODS Streptozotocin-nicotinamide was injected intraperitoneally to induce diabetes in Wistar rats. Five groups of rats (n=6) - normal control, diabetic, diabetic treated with G. cambogia at 400 mg/kg and 800 mg/kg body weight, and diabetic treated with metformin at 500 mg/kg body weight, were studied. Blood samples were collected after three weeks of treatment. Random blood glucose (RBG), Serum total cholesterol levels (TCL), serum total triglyceride levels (TGL), high-density lipoprotein levels, and body weight were measured. RESULTS Although G. cambogia treatment did not have any antidiabetic activity (p>0.05) rind in the streptozotocin-nicotinamide induced diabetic Wistar Rat model, it decreased the serum TCL, and body weight significantly (P<0.05). CONCLUSIONS Ethanolic extract of G. cambogia fruit rind possesses anti-obesity activity and significantly reduces total cholesterol but does not have antidiabetic activity.
Readability, Content, and Accountability Assessment of Online Health Information for Retinitis Pigmentosa & Retinitis Pigmentosa Treatment Options

ABSTRACT Purpose New therapies for retinitis pigmentosa (RP) have led to patients desiring more information about their disease. We assessed the readability, content, and accountability of online health information for RP and its treatments. Methods Two internet queries were performed: one pertaining to the condition RP, and another pertaining to treatments of RP. Three analyses were performed on the top search results that met eligibility criteria: (1) A readability analysis produced an average reading level; (2) A content analysis was conducted to score each source on the accuracy, completeness, clarity, and organization of the content; and (3) An accountability analysis was performed to evaluate adherence to accountability benchmarks, including authorship, attribution, disclosure, and currency. Results The mean reading level was 12.0 (SD = 3.2, 95% CI = 11.0–13.0) for the 8 RP webpages and 12.5 (SD = 3.1, 95% CI = 11.7–13.4) for the 10 RP treatment webpages. The mean content score for RP sites was 21.3 of 32 points (SD = 4.1, 95% CI = 19.5–23.0). The mean content score for RP treatment sites was 5.5 out of 16 points (SD = 3.7, 95% CI = 4.1–6.9). The inter-rater reliability was 0.973 (Cronbach’s alpha). For RP sites, the mean accountability score was 2.6 out of 4 points (SD = 0.9, 95% CI = 1.9–3.4). For RP treatment sites, the mean accountability score was 2 out of 4 points (SD = 0.9, 95% CI = 1.4–2.6). Conclusion Our data suggest that the online information available to patients regarding RP and RP treatment options exceeds the AMA-recommended sixth-grade reading level and contains gaps in content relevant to patients.
Multiorgan neutrophilic inflammation in a Border Collie with “trapped” neutrophil syndrome

Abstract Trapped neutrophil syndrome is a rare congenital disease recognized in Border Collies and is characterized by persistent neutropenia with myeloid hyperplasia. The mechanism of neutropenia has not been described. We document the case of a young Border Collie diagnosed with trapped neutrophil syndrome based on clinical features, blood and bone marrow evaluation, and presence of the associated homozygous mutation. Results from flow cytometric and storage studies suggested lower neutrophil survival time. The dog had substantial neutrophilic inflammation in multiple organs, indicating that neutrophils could leave the marrow and enter tissues, making the term “trapped” neutrophil syndrome a misnomer.
Application of a simple DNA damage model developed for electrons to proton irradiation

Proton beam therapy allows irradiating tumor volumes with reduced side effects on normal tissues with respect to conventional x-ray radiotherapy. Biological effects such as cell killing after proton beam irradiations depend on the proton kinetic energy, which is intrinsically related to early DNA damage induction. As such, DNA damage estimation based on Monte Carlo simulations is a research topic of worldwide interest. Such simulation is a mean of investigating the mechanisms of DNA strand break formations. However, past modellings considering chemical processes and DNA structures require long calculation times. Particle and heavy ion transport system (PHITS) is one of the general-purpose Monte Carlo codes that can simulate track structure of protons, meanwhile cannot handle radical dynamics simulation in liquid water. It also includes a simple model enabling the efficient estimation of DNA damage yields only from the spatial distribution of ionizations and excitations without DNA geometry, which was originally developed for electron track-structure simulations. In this study, we investigated the potential application of the model to protons without any modification. The yields of single-strand breaks, double-strand breaks (DSBs) and the complex DSBs were assessed as functions of the proton kinetic energy. The PHITS-based estimation showed that the DSB yields increased as the linear energy transfer (LET) increased, and reproduced the experimental and simulated yields of various DNA damage types induced by protons with LET up to about 30 keV μm−1. These results suggest that the current DNA damage model implemented in PHITS is sufficient for estimating DNA lesion yields induced after protons irradiation except at very low energies (below 1 MeV). This model contributes to evaluating early biological impacts in radiation therapy.
Global trends and regional differences in non-transport unintentional injuries mortality among children and adolescents, 1990 to 2019: results from the Global Burden of Disease 2019 study

Abstract Background: Non-transport unintentional injuries (NTUIs) are major public concerns, especially among children and adolescents in low- and middle-income countries. With environmental and cognitive changes, a recent systematic description of global trends and regional differences concerning NTUIs is urgently needed for the global agenda of relevant policy-making and intervention target findings. Methods: We used mortality, population, and socio-demographic-index (SDI) data from Global Burden of Disease 2019 to analyze the trends of NTUIs mortality. We applied the slope index of inequality (SII) and relative index of inequality (RII) to measure the absolute and relative inequality between countries and territories. The concentration curve and concentration index (CI) were also used to measure the inequality. We conducted a sensitivity analysis to make our findings credible. Results: In 2019, there were 205,000 deaths due to NTUIs among children and adolescents aged 5 to 24 years, which decreased from 375,000 in 1990. In 2019, the age-standardized mortality rate (ASMR) was 8.13 per 100,000, ranging from the lowest in the Netherlands (0.90 per 100,000) to the highest in the Solomon Islands (29.34 per 100,000). The low-middle SDI group had the highest ASMR of NTUIs, while the low SDI group had the slowest decrease. After excluding the death caused by “exposure to forces of nature” and “other unintentional injuries”, drowning accounted for the most deaths in almost every SDI group, gender, and age group, but the major causes of death varied in different subgroups. For example, animal contact was a major cause in low and low-middle SDI groups but less in high SDI groups, while high and high-middle SDI groups had a higher proportion of deaths for foreign body and poisonings. The SII showed a declining trend, but the RII and CI did not, which might indicate that inequality was persistent. Similar results were found in the sensitivity analysis. Conclusions: Despite the declining trend of the mortality rate and the narrowing gap between countries, there were still a large number of children and adolescents dying from NTUIs, and those experiencing social-economic disadvantages remained at high mortality. Embedding the prevention of NTUIs into sustainable development goals might contribute to the progress of reducing death and inequalities, which ensures that no one is left behind.
A Global Bias-Correction DC Method for Biased Estimation under Memory Constraint

This paper establishes a global bias-correction divide-and-conquer (GBC-DC) rule for biased estimation under the case of memory constraint. In order to introduce the new estimation, a closed representation of the local estimators obtained by the data in each batch is adopted, aiming to formulate a pro forma linear regression between the local estimators and the true parameter of interest. Least square method is then used within this framework to composite a global estimator of the parameter. Thus, the main advantage over the classical DC method is that the new GBC-DC method can absorb the information hidden in the statistical structure and the variables in each batch of data. Consequently, the resulting global estimator is strictly unbiased even if the local estimator has a non-negligible bias. Moreover, the global estimator is consistent, and even can achieve root-$n$ consistency, without the constraint on the number of batches. Another attractive feature of the new method is computationally simple and efficient, without use of any iterative algorithm and local bias-correction. Specifically, the proposed GBC-DC method applies to various biased estimations such as shrinkage-type estimation and nonparametric regression estimation. Detailed simulation studies demonstrate that the proposed GBC-DC approach is significantly bias-corrected, and the behavior is comparable with the full data estimation and is much better than the competitors.
Coherent quantum ratchets driven by tunnel oscillations

We demonstrate that the tunnel oscillations of a biased double quantum dot can be employed as driving source for a quantum ratchet. As a model, we use two capacitively coupled double quantum dots. One double dot is voltage biased and provides the ac force, while the other experiences the ac force and acts as coherent quantum ratchet. The current is obtained from a Bloch-Redfield master equation which ensures a proper equilibrium limit. We find that the two-electron states of the coupled ratchet-drive Hamiltonian lead to unexpected steps in the ratchet current.
Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user‐friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi‐automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.
Draft genome of the bluefin tuna blood fluke, Cardicola forsteri

The blood fluke Cardicola forsteri (Trematoda: Aporocotylidae) is a pathogen of ranched bluefin tuna in Japan and Australia. Genomics of Cardicola spp. have thus far been limited to molecular phylogenetics of select gene sequences. In this study, sequencing of the C. forsteri genome was performed using Illumina short-read and Oxford Nanopore long-read technologies. The sequences were assembled de novo using a hybrid of short and long reads, which produced a high-quality contig-level assembly (N50 > 430 kb and L50 = 138). The assembly was also relatively complete and unfragmented, comprising 66% and 7.2% complete and fragmented metazoan Benchmarking Universal Single-Copy Orthologs (BUSCOs), respectively. A large portion (> 55%) of the genome was made up of intergenic repetitive elements, primarily long interspersed nuclear elements (LINEs), while protein-coding regions cover > 6%. Gene prediction identified 8,564 hypothetical polypeptides, > 77% of which are homologous to published sequences of other species. The identification of select putative proteins, including cathepsins, calpains, tetraspanins, and glycosyltransferases is discussed. This is the first genome assembly of any aporocotylid, a major step toward understanding of the biology of this family of fish blood flukes and their interactions within hosts.
Assessing minimum contrast parameter estimation for spatial and spatiotemporal log‐Gaussian Cox processes

The univariate log‐Gaussian Cox process (LGCP) has shown considerable potential for the flexible modelling of the spatial, and more recently, spatiotemporal, intensity functions of planar point patterns within a restricted region in space. Its flexibility and mathematical tractability are partly offset by the need to acquire sensible estimates of the parameters controlling the dependence structure of the Gaussian field given the observed data. The method of minimum contrast, which compares theoretical descriptors of the process with their non‐parametric counterparts in order to obtain the required estimates, is arguably the most popular in practice to date. This article provides a comprehensive set of simulation studies focused on gauging the performance and impact of minimum contrast methods for parameter estimation of these processes. Results indicate that concerns over arbitrariness of implementation of minimum contrast give way to satisfactory practical performance.