Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic biomarkers for prediction/classification of sample conditions in marine microeukaryotes (diatoms)

Marine microeukaryotes express large and complex transcriptomes that often respond dynamically to environmental and physiological conditions. In parallel to developments in human disease research, the opportunity exists to employ transcriptomic features as “biomarkers” to understand and predict cellular and environmental states. Here, the prediction and classification of basic physiological and environmental states including light, growth phase and inorganic carbon status was explored for the model diatom T. pseudonana using publicly available data including 56 microarray and 316 mRNA-seq samples. Simple “machine learning” methods combined with integrative bootstrapped clustering were able to detect, recapitulate and expand biologically and environmentally relevant signals evident across hundreds of samples collected and processed independently by multiple laboratories. Agnostic, integrative and empirical “data-driven” approaches are likely applicable to modern questions in new environmental and experimental contexts.
Remote sensing of forest health and vitality: a South African perspective

Commercial forestry plantations are an important and valuable segment of the South African economy and forest managers are required to maximise and sustain forest productivity. However, various factors such as the outbreak of damaging agents are constantly hampering forest health and thus decrease productivity. It is therefore important to detect the presence and spread of these agents within plantation forests, a task efficiently achieved using remote sensing technology. A wide assortment of sensors with varying resolutions are available and have been extensively used for this purpose. This paper reviews the current status of remote sensing of forest health in South Africa by providing insight on the latest developments on the use of the technology in forest plantations. A systematic search was executed on Google Scholar, ScienceDirect® and EBSCOhost® databases that identified 627 articles of which 29 made reference to remote sensing of forest health in South Africa. Four key results were found: (1) the latest technology is capable of detecting and monitoring forest health with great accuracy, especially with the adoption of machine learning methods; (2) studies employing remote sensing to characterise forest health have burgeoned since 2006 with even more applying hyperspectral data; (3) most studies were spatially concentrated in the KwaZulu-Natal Midlands region around Pietermaritzburg with only a few over the Western Cape; and (4) the remote detection of pest outbreaks and pathogens have received much attention followed by alien invasive plants and a few studies directed to fragmentation. Present and future partnerships may open up opportunities for exploit- ing remote sensing further; this should address growing expectations from government and industry for more detailed and accurate information concerning the health and condition of South Africa's plantation forests.
Clarification of the taxonomic confusion between Ilex formosana and I. tetramera (Aquifoliaceae), with the description of a new species I. shukunii

Ilex formosana and I. tetramera, both occurring in subtropical forests of China, are easily confused in morphology and distribution. To unravel their identities, phylogenetic analyses of multiple accessions of the two species and their possible relatives using two nuclear DNA loci (ITS and ETS) are conducted in present study. Our results show that I. formosana (sampled from type locality) is closest to I. matanoana and I. mertensii, and I. tetramera (sampled from type locality) is sister to I. nuculicava, while the remaining samples, which were originally identified as I. formosana or I. tetramera, form a strongly supported clade sister to I. cinerea, representing a cryptic new species, which is named here as I. shukunii. Despite the homogeneity in morphology, the divergence in the distribution of I. formosana, I. shukunii, and I. tetramera also supports our phylogenetic results. Insulated by the Taiwan Strait, the re-defined I. formosana is restricted to Taiwan Island. Separated by the Tanaka-Kaiyong Line, a major phytogeographic boundary of Sino-Himalayan and Sino-Japanese Floras, I. shukunii occurs from southeast Yunnan to southeast mainland of China, whereas the re-defined I. tetramera is endemic to southwest Yunnan.
Novel nematic and glassy liquid crystalline oligomers as electroluminescent organic semiconductors

ABSTRACT Several oligomers (MWs > 1000 g mol−1) with highly rigid and conjugated aromatic cores, incorporating 1,4-disubstituted phenylene, 2,7-disubstituted fluorene, 1,4-disubstituted thiophene and/or 2,7-disubstituted carbazole rings with lateral and terminal substituents were synthesised as novel organic semiconductors. These novel liquid crystalline oligomers exhibit glass transition temperatures above room temperature, high clearing points and a broad nematic temperature range as well as electroluminescent behaviour in solution-processed devices.
Moment dipolaire de CH3CN

Le moment dipolaire de l'acetonitrile (CH 3 CN) a ete determine par spectroscopie millimetrique a absorption saturee et effet Stark. La methode des moindres carres correles et la methode de la mediane ont ete utilisees pour verifier la validite du resultat de l'estimation du moment dipolaire. Sa valeur est : μ = 3,92197 (13) D.
MIDAS: Aplicación informática para la identificación de microsatélites exactos e inexactos en secuencias genómicas.

Microsatellites are tandem repeat, frequent and diverse short sequences in the genomes of all species, constituting important markers in multiple areas of genomics-based research. Associations of these markers have been found in a significant number of human diseases. Vaccine development has shown how pathogens can evade the immune response by simply altering the composition of repeat sequences in their genes. There are numerous computer applications for the detection of these sequences, but they do not meet all expectations due to the divergence of criteria and approaches applied to solving the problem of their detection. MIDAS implements a non-heuristic solution based on two combinatorial algorithms in series: the first one detects exact microsatellites, and the second one, if the model parameters allow it, extends the sequences to their optimal inaccurate version. The application has as input the genomic sequence in GBFF or FASTA format and its output provides the microsatellite positions in the genomic sequence, as well as sizes, alignments, flanks and other statistics. The algorithm is highly efficient and comprehensive, detecting all possible repeat sequences regardless of their nucleotide composition. Keywords: SSR; microsatellite; molecular marker; data mining; algorithms
COMPARISON OF ANALGESIC AND ANTI-INFLAMMATORY ACTIVITIES OF PURIFIED ANTHOCYANIN FROM OSBECKIA ASPERA (L.) BLUME AND OSBECKIA RETICULATA BEDD. USING ANIMAL MODELS

Objective: The objective of the present work is to isolate, purify, and fractionate anthocyanin from selected Osbeckia species and also to compare the analgesic and anti-inflammatory potentiality using animal models.Methods: Methodologies include extraction of anthocyanin from the in vitro callus culture of Osbeckia aspera and Osbeckia reticulata, purification using amberlite column chromatography, and fractionation by liquid chromatography-tandem mass spectrometry. The analgesic activity was determined by tail immersion method, analgesy meter, hot plate, and acetic acid-induced writhing test. Anti-inflammatory activity was evaluated by carrageenan-induced paw inflammation in mice.Results: Anthocyanin-producing callus cultures were established in MS medium fortified with various combinations of phytohormones and sucrose. Optimal callus formation in O. aspera was initiated on cultures containing 0.5 mg/L of 2, 4-D, and 0.5 mg/L 6-benzylaminopurine (BA). In O. reticulata callus was initiated in the presence of 1.2 mg/L BA and 1.4 mg/L naphthalene acetic acid. The same hormonal combination on extended treatments turned the white friable callus into red compact callus. Anthocyanins obtained from Osbeckia species were purified and fractionated containing malvidin-3-diglucoside, delphinidin, cyanidin aglycone, and peonidin. Purified anthocyanin of O. aspera at the concentrations 50, 100, 150, and 200 mg/kg after 120 min exhibited significant analgesic activity by tail immersion method, in comparison to O. reticulata. However, with hot plate method, anthocyanin of O. reticulata produced a significant analgesic activity even at lower doses (50 and 100 mg/kg) after 120 min. However, in writhing test, theepurified anthocyanin of O. aspera significantly stopped the number of writhes at a dose of 200 mg/kg and also by the anthocyanin of O. reticulata. In the evaluation of anti-inflammatory effect using plethysmometer, anthocyanin at doses of 100,150 and 200 mg/kg started producing anti-inflammatory effect after 30 min, which lasted until 120 min.Conclusion: It is concluded from the present study that the purified anthocyanin of Osbeckia possesses potent analgesic and anti-inflammatory activities.
Breast cancer histopathology image classification using kernelized weighted extreme learning machine

Histopathology is considered as the gold standard for diagnosing breast cancer. Traditional machine learning (ML) algorithm provides a promising performance for cancer diagnosis if the training dataset is balanced. Nevertheless, if the training dataset is imbalanced the performance of the ML model is skewed toward the majority class. It may pose a problem for the pathologist because if the benign sample is misclassified as malignant, then a pathologist could make a misjudgment about the diagnosis. A limited investigation has been done in literature for solving the class imbalance problem in computer‐aided diagnosis (CAD) of breast cancer using histopathology. This work proposes a hybrid ML model to solve the class imbalance problem. The proposed model employs pretrained ResNet50 and the kernelized weighted extreme learning machine for CAD of breast cancer using histopathology. The breast cancer histopathological images are obtained from publicly available BreakHis and BisQue datasets. The proposed method achieved a reasonable performance for the classification of the minority as well as the majority class instances. In comparison, the proposed approach outperforms the state‐of‐the‐art ML models implemented in previous studies using the same training‐testing folds of the publicly accessible BreakHis dataset.
A systematic review of factors associated with uncontrolled diabetes and meta‐analysis of its prevalence in Saudi Arabia since 2006

The study aims to systematically review the literature for risk factors associated with poor glycaemic control among type 2 diabetes mellitus (T2DM) patients in Saudi Arabia (SA) and conducts a meta‐analysis of its prevalence. Following the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) protocol, we searched the Scopus, PubMed, PsycINFO, Web of Science, and CINAHL Plus databases from May to November 2018. The search terms were T2DM, glycaemic control, and SA. The inclusion criteria include the following: observational studies which were conducted in T2DM patients in SA reporting prevalence or/and personal, psychological or behavioural predictors in papers published after 2006. Articles were assessed using a modified Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) tool. Studies included in the meta‐analysis defined uncontrolled T2DM as glycated haemoglobin ≥7% (53 mmol/mol), and reported results were based on a random‐effects model. Eighteen of the following articles (3 retrospective cohort studies, 1 case–control study, and 14 cross‐sectional studies) were included. The quality of the studies (high: 2; moderate: 7, and low: 9) varied. The pooled prevalence of uncontrolled T2DM in SA was 77.7% (95% CI, 71.2–84.2). In the included studies, the most consistent predictors of poor glycaemic control were longer diabetes duration, lack of self‐efficacy, and low knowledge of diabetes. However, significant variations in research designs were observed across the studies. A national diabetes prevention and treatment program is needed to lessen the burden of diabetes in SA. Future studies should address the personal, psychological, and behavioural factors of poor glycaemic control in SA at national level.
Caractérisation et modélisation des plasmas micro-onde multi-dipolaires : application à la pulvérisation assistée par plasma multi-dipolaire

L'extension d'echelle des procedes plasma fonctionnant a tres faibles pressions est l'une des problematiques a resoudre pour leur essor au niveau industriel. Une solution consiste a distribuer uniformement des sources de plasma elementaires dans lesquelles le plasma est produit par couplage a la resonance cyclotronique electronique (RCE). Ces sources elementaires sont constituees d'un aimant permanent cylindrique (dipole magnetique) dispose a l'extremite d'une structure coaxiale d'amenee des micro-ondes. Bien que conceptuellement simple, l'optimisation de ces sources de plasma dipolaires est complexe. Elle requiert la connaissance, d'une part, des configurations de champ magnetique statique et electrique micro-onde, et, d'autre part, des mecanismes de production du plasma, dans les zones de champ magnetique fort (condition RCE), et des mecanismes de diffusion. Ainsi, une caracterisation experimentale des domaines de fonctionnement et des parametres plasma par sonde de Langmuir et par spectroscopie d'emission optique a ete menee sur differentes configurations de sources dipolaires. Parallelement, une premiere modelisation analytique a permis de calculer des champs magnetiques de configurations simples, le mouvement et la trajectoire des electrons dans ces champs magnetiques, l'acceleration des electrons par couplage RCE. Ces resultats ont permis ensuite de valider la modelisation numerique des trajectoires electroniques par une methode hybride Particle In Cell / Monte-Carlo. L'etude experimentale a mis en evidence des domaines de fonctionnement pression/puissance tres larges, entre 15 et 200 W de puissance micro-onde et depuis 0,5 jusqu'a 15 mTorr dans l'argon. L'etude des parametres plasma a permis de localiser la zone de couplage RCE pres du plan equatorial de l'aimant et de confirmer l'influence de la geometrie de l'aimant sur cette derniere. Ces caracterisations appliquees a un reacteur cylindrique utilisant 48 sources ont montre la possibilite d'atteindre au centre de l'enceinte des densites entre 1011 et 1012 cm-3 pour des pressions d'argon de quelques mTorr. La modelisation des trajectoires electroniques au voisinage des aimants indique un meilleur confinement radial pour des aimants presentant un rapport longueur/diametre eleve. De plus, cette etude numerique confirme les resultats de l'etude experimentale, a savoir une zone de couplage RCE pres du plan equatorial et non au voisinage de l'extremite du guide coaxial micro-onde. Enfin, ces resultats ont ete appliques avec succes a la pulverisation assistee par plasma multi-dipolaire de cibles, permettant en particulier une usure uniforme de ces dernieres.
TgCentrin2 is required for invasion and replication in the human parasite Toxoplasma gondii

Centrins are EF-hand containing proteins ubiquitously found in eukaryotes and are key components of centrioles/basal bodies as well as certain contractile fibers. We previously identified three centrins in the human parasite Toxoplasma gondii, all of which localized to the centrioles. However, one of them, TgCentrin2 (CEN2), is also targeted to ring-shaped structures at the apical and basal ends of the parasite, as well as to multiple annuli at the junction between the apical cap and the rest of the membrane cortex. The role(s) that TgCentrin2 plays in these locations was unknown. Here we report the functional characterization of TgCentrin2 in the parasite lytic cycle. After multiple unsuccessful attempts to knock out or knock down the TgCentrin2 gene with existing tools, we designed a new conditional knockdown method that combines transcriptional and protein stability control to achieve tight regulation of TgCentrin2 levels in the parasite. We discovered that under knockdown conditions, there was an ordered loss of TgCentrin2 from its four compartments, due to differences in incorporation kinetics and structural inheritance over successive generations. This was correlated with the development of major invasion deficiency at early stages of CEN2 knockdown, and replication defects at later stages. These results indicate that TgCentrin2 is incorporated into multiple cytoskeletal structures to serve distinct functions in T. gondii that are required for parasite survival.
A multistage optimisation algorithm for the large vehicle routing problem with time windows and synchronised visits

Abstract We propose a multistage algorithm for the vehicle routing problem with time windows and synchronised visits, which is capable of solving large problem instances arising in home health care applications. The algorithm is based on a constraint programming formulation of the daily home care scheduling and routing problem. It contains visits with hard time windows and pairwise synchronisation to be staffed by carers who have different skills and work custom shift patterns with contractual breaks. In a computational study, we first experiment with a benchmark set from the literature for the vehicle routing problem with time windows and synchronised visits. Our algorithm reproduced the majority of the best-known solutions, and strictly improved results for several other instances. Most importantly, we demonstrate that the algorithm can effectively solve real scheduling instances obtained from a UK home care provider. Their size significantly surpass similar scheduling problems considered in the literature. The multistage algorithm solved each of these instances in a matter of minutes, and outperformed human planners, scheduling more visits and significantly reducing total travel time.
Binding energy and photostability of the β-cyclodextrin encapsulates of lornoxicam and tenoxicam drugs: A combined experimental and theoretical study

The lornoxicam (LRX) and tenoxicam (TNX) drugs form a stable 1:1 inclusion complex with b-cyclodextrin (β-CD) in aqueous solution. The experimentally determined association constants (K) of LRX- β-CD and TNX- β-CD are 13.4 and 10.3 M-1, respectively. Quantum chemical computations simulated the preferred orientation of guest molecules in the host. Geometry optimized results using the ONIOM technique provided more in-depth insights and identified the structure and showed that both drugs were partially encapsulated within the β-CD cavity. The calculated inclusion binding energy (BE, kcal mol-1) reveals the noticeable thermal stability of LRX-β-CD (-24.19 kcal/mol) over the TNX-β-CD (-13.45 kcal/mol) capsulate. Furthermore, the photostabilities of the encapsulated drugs were tested. Drug encapsulation did not result in any additional photostability. Moreover, encapsulation of the drugs in the β-CD resulted in noticeable changes in the electronic characteristics of the drugs, as reflected in their reactivity indices. The fact that the water-soluble β-CD formed inclusion complexes with water-insoluble LRX and TNX enables the drug delivery vehicle for oral administration.
The Characteristics of Crackers Made from Formulation of Wheat and Modified Water Yam Flour

The previous study showed that combination of wheat flour (70%) and modified water yam flour (30%) produced crackers which had the best characteristics. In this research, the effect of formulation of wheat and three kind of modified water yam flour on Resistant Starch (RS) content and Glycaemic index of the crackers were studied. Modified water yam flour was made from purple, white, and yellow ones which had been treated by three cycles autoclaving-cooling process. The native water yam flour, without treatment with autoclaving, were used as comparison. The result showed that sample crackers had higher resistant starch (1 . 67 -3 . 65%) and dietary fiber (16 . 65 -18 . 41%) content, compared to standard crackers from wheat flour. Furthermore , the crackers from modified yam flour with white water had the lowest GI ( 34 . 13 ) comparing with other crackers. So it could be developed as functional food for preventing diabetes mellitus or other digestive tract disrupter.
Design and Implementation of Asymmetric Extrusion Die Using Bezier Technique

Extrusion is a process that used to create objects of a fixed cross-sectional profile. A material is pushed through a die of the desired cross-section. The main advantage of this process with respect to other manufacturing processes is its ability to create very complex cross-sections, while the limitation of extrusion process is used to produced just a symmetric profile so this paper proposed an adopted algorithm that used to design and implementation the Asymmetric extrusion die that used to prevent the twisting that caused in metal when used to produce the Asymmetric product, and in other wise reduce the total extrusion power and die pressure distribution on metal during extrusion process. This adopted design was implemented in this work using Teflon material in both symmetric and asymmetric profile using CNC milling machine to demonstration the success of this algorithm.
Analysis of Surface Water Quality in Tehran

Box-Jenkins and exponential smoothing time series analysis of the monthly water quality in surface water in Tehran was conducted as a case study. Various univariate models were developed for each determinand. Most of the models were seasonal, indicating that the water quality determinands vary throughout the year. The models follow the same pattern of variations present in the data. This study shows the credibility of the models, therefore the models may be used for future design purposes.
Physical activity of children and adolescents from the Czech Republic, Hungary, Poland, and Slovakia: A systematic review.

INTRODUCTION AND OBJECTIVE Systematic monitoring of physical activity of young populations from different regions may be useful for making international comparisons, better understanding trends in physical activity and designing public health interventions to increase physical activity. Thus, the aim of the study was to comprehensively review studies examining the level of physical activity of children and adolescents from the Visegrád countries, and indicate the percentage of children and adolescents meeting the recommended level of physical activity. MATERIAL AND METHODS A systematic search of the published literature was conducted. Included were reports with original research that consisted of the proportion of children and adolescents who met physical activity recommendations or guidelines. To provide a current picture of physical activity of children and adolescents, the review was restricted to studies published between January 2015 - November 2018. RESULTS Moderate-to-vigorous physical activity recommendations were met by between 7.5% - 69.4% of children and adolescents. Vigorous physical activity recommendations were met by between 33.6% - 64.5% of children and adolescents. Daily recommendations for the number of steps taken were fulfilled by between 11.6% - 69.0% of children and adolescents. Differences between age categories, genders and countries were observed. CONCLUSIONS Public health interventions to increase physical activity are required to decrease insufficient levels of physical activity in children and adolescents, especially in girls. The review also highlights the need for studies with representative random samples that use validated measurement methods.