Miracle-dz/UniFAR-FTUs huggingface dataset:
Ensemble of Deep Recurrent Neural Networks for Identifying Enhancers via Dinucleotide Physicochemical Properties

Enhancers are short deoxyribonucleic acid fragments that assume an important part in the genetic process of gene expression. Due to their possibly distant location relative to the gene that is acted upon, the identification of enhancers is difficult. There are many published works focused on identifying enhancers based on their sequence information, however, the resulting performance still requires improvements. Using deep learning methods, this study proposes a model ensemble of classifiers for predicting enhancers based on deep recurrent neural networks. The input features of deep ensemble networks were generated from six types of dinucleotide physicochemical properties, which had outperformed the other features. In summary, our model which used this ensemble approach could identify enhancers with achieved sensitivity of 75.5%, specificity of 76%, accuracy of 75.5%, and MCC of 0.51. For classifying enhancers into strong or weak sequences, our model reached sensitivity of 83.15%, specificity of 45.61%, accuracy of 68.49%, and MCC of 0.312. Compared to the benchmark result, our results had higher performance in term of most measurement metrics. The results showed that deep model ensembles hold the potential for improving on the best results achieved to date using shallow machine learning methods.
Dietary Intake by Food Source and Eating Location in Low- and Middle-Income Chilean Preschool Children and Adolescents from Southeast Santiago

Background: Food source and eating location are important factors associated with the quality of dietary intake. In Chile the main food sources and eating locations of preschool children and adolescents and how these relate to dietary quality are unknown. Methods: We analyzed 24 h dietary recalls collected in 2016 from low- and middle-income Chilean preschool children (3–6 years, n = 839) and adolescents (12–14 years, n = 643) from southeastern Santiago. Surveys collected the food source and eating location for each food reported during the recall. We estimated the mean intake of calories and key nutrients of concern, such as saturated fats, total sugars, and sodium, by food source and eating location. Results: Foods obtained and eaten at home contributed the greatest proportion of total calories and the key nutrients of concern. Foods obtained at home tended to have lower caloric densities but higher sugar and sodium densities than foods obtained away from home in both age groups. With regard to location, for preschool children foods consumed at home had lower caloric and sugar densities than foods eaten at school, while for adolescents foods consumed at home had lower caloric, saturated fat, and sugar densities than foods eaten at school. For both children and adolescents, home was the primary source of sugar-sweetened beverages (SSBs) calories. SSBs were important calorie contributors among foods across all settings, but the highest absolute amount of calories from these beverages was consumed at home. Conclusions: While most of Chilean youths’ calories and key nutrients of concern are obtained and consumed at home, these foods tended to have lower caloric densities than foods obtained and consumed away from home. Home was the main food source for SSBs, but the relative consumption of these beverages was high in all eating locations. More research will be needed to inform and evaluate policies and interventions to improve children’s dietary quality across settings.
Radiobiological and dosimetric impact of RayStation pencil beam and Monte Carlo algorithms on intensity‐modulated proton therapy breast cancer plans

Abstract Purpose RayStation treatment planning system employs pencil beam (PB) and Monte Carlo (MC) algorithms for proton dose calculations. The purpose of this study is to evaluate the radiobiological and dosimetric impact of RayStation PB and MC algorithms on the intensity‐modulated proton therapy (IMPT) breast plans. Methods The current study included ten breast cancer patients, and each patient was treated with 1–2 proton beams to the whole breast/chestwall (CW) and regional lymph nodes in 28 fractions for a total dose of 50.4 Gy relative biological effectiveness (RBE). A total clinical target volume (CTV_Total) was generated by combining individual CTVs: AxI, AxII, AxIII, CW, IMN, and SCVN. All beams in the study were treated with a range shifter (7.5 cm water equivalent thickness). For each patient, three sets of plans were generated: (a) PB optimization followed by PB dose calculation (PB‐PB), (b) PB optimization followed by MC dose calculation (PB‐MC), and (c) MC optimization followed by MC dose calculation (MC‐MC). For a given patient, each plan was robustly optimized on the CTVs with same parameters and objectives. Treatment plans were evaluated using dosimetric and radiobiological indices (equivalent uniform dose (EUD), tumor control probability (TCP), and normal tissue complication probability (NTCP)). Results The results are averaged over ten breast cancer patients. In comparison to PB‐PB plans, PB‐MC plans showed a reduction in CTV target dose by 5.3% for D99% and 4.1% for D95%, as well as a reduction in TCP by 1.5–2.1%. Similarly, PB overestimated the EUD of target volumes by 1.8─3.2 Gy(RBE). In contrast, MC‐MC plans achieved similar dosimetric and radiobiological (EUD and TCP) results as the ones in PB‐PB plans. A selection of one dose calculation algorithm over another did not produce any noticeable differences in the NTCP of the heart, lung, and skin. Conclusion If MC is more accurate than PB as reported in the literature, dosimetric and radiobiological results from the current study suggest that PB overestimates the target dose, EUD, and TCP for IMPT breast cancer treatment. The overestimation of dosimetric and radiobiological results of the target volume by PB needs to be further interpreted in terms of clinical outcome.
Technical and Non-Technical Skills in Surgery: A Simulated Operating Room Environment Study.

STUDY DESIGN Observational simulation study OBJECTIVE. : The goal of this study was to investigate the relationship between technical and non-technical skills in a simulated surgical procedure. SUMMARY OF BACKGROUND DATA Although surgeons' technical and non-technical skills during surgery are crucial determinants for clinical outcomes, little literature is available in spine surgery. Moreover, evidence regarding how surgeons' technical and non-technical skills are related is limited. METHODS A mixed-reality and full-scale simulated operating room environment was employed for the surgical team. Eleven surgeons performed the vertebroplasty procedure (VP). Technical skills were assessed using Objective Structured Assessment of Technical Skill (OSATS) scores and senior expert-evaluated VP outcome assessment. Non-technical skills were assessed with the Observational Teamwork Assessment for Surgery (OTAS). Kendall-Tau-b tests were performed for correlations. We further controlled the influence of surgeons' experience (based on professional tenure and number of prior VPs performed). RESULTS Surgeons' non-technical skills correlated significantly with their technical performance (τ=0.63; p = 0.006) and surgical outcome scores (τ=0.60; p = 0.007). This association was attenuated when controlling for surgeons' experience. CONCLUSION Our results suggest that spine surgeons with higher levels of technical skill levels also apply better communication, leadership and coordination behaviors during the procedure. Yet, the role of surgeons' experience needs further investigation for improving surgeons' intraoperative performance during spine surgery. LEVEL OF EVIDENCE 3.
Ant Lion Optimizer based Approach for Optimal Scheduling of Thermal Units for Small Scale Electrical Economic Power Dispatch Problem

A novel nature inspired algorithm ant lion optimizer (ALO) is recently developed which is motivated from the hunting mechanism of ant lions . Inherit steps of hunting prey such as the random walk of ants, building traps, entrapment of ants in traps, catching preys, and re-building are simulated to find the optimal solution of real life problems . Intelligent and Optimization techniques based on evolutionary computing, metaheuristic,biological base,nature inspired, search method establish their applications in the area of electrical economic power dispatch planning(EEPDP) to reach global optimal solution for this multi scale, multi-decision, multi-objective combinatorial problem subjected to different constraints.An application of ALO to solve non linear electric economic power dispatch problem(EEPDP) is proposed in this paper. Efficient and optimal planning of economic electrical power dispatch problem is an integral part of economic electrical energy generation planning and it is the need of time for the electrical engineers to browse this area in multi-scale planning scenarios. The performance of s ant lion optimizer (ALO) to solve electrical economic power dispatch problem is tested on three and six unit system.Test results are compared with other techniques grey wolf optimization(GWO),cuckoo search(CS),artificial bee colony(ABC),firefly algorithm(FA),particle swarm optimization(PSO),shuffled frog leap (SFL) ,bacteria foraging algorithm(BFO),harmony search(HS) applied in literature. Simulation results proved that the ALO technique is better as compared to other nature inspired,heuristic,metaheuristic techniques to find global minima and maintain the solution quality in terms of low fuel cost.
PENERAPAN METODE RESITASI DAN DISKUSI UNTUK MENINGKATKAN PRESTASI BELAJAR MAHASISWA PROGRAM STUDI ILMU KEPERAWATAN UNIVERSITAS GALUH THE APPLICATION OF RECITATION AND DISCUSSION METHOD TO IMPROVE SOPHOMORE STUDENTS ACHIEVEMENT IN NURSING PROGRAM AT GALUH UNIVERSITY

The purpose of this study was to examine: 1) the implementation of recitation and discussion to improve student's achievements; and 2) whether the presence of implementation recitation and discussion methods can improve student's achievements. This study used a class action research design with data collection using observations and field notes and analysis techniques to perform data reduction, inference, the follow-up stage and making conclusions. The results showed the recitation and discussion methods is one of methods that can be used to improve student understanding of a subject. Liveliness of students in the process of discussion can be stimulated through several awards as well as provide additional value for students who are active in the discussion process. This evidence showed by the smoothness in learning, writing, memorizing, and so on. As a result, the students learning process is more efficient. The conclusion of this study is that recitation and discussion methods can improve sophomore students achievement in nursing program at Galuh University.
Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and Omocestus navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean‐montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome‐wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent‐based phylogenetic reconstructions, integrative Bayesian model‐based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.
Dendrite‐Free Zinc Deposition Induced by Multifunctional CNT Frameworks for Stable Flexible Zn‐Ion Batteries

The current boom of safe and renewable energy storage systems is driving the recent renaissance of Zn‐ion batteries. However, the notorious tip‐induced dendrite growth on the Zn anode restricts their further application. Herein, the first demonstration of constructing a flexible 3D carbon nanotube (CNT) framework as a Zn plating/stripping scaffold is constituted to achieve a dendrite‐free robust Zn anode. Compared with the pristine deposited Zn electrode, the as‐fabricated Zn/CNT anode affords lower Zn nucleation overpotential and more homogeneously distributed electric field, thus being more favorable for highly reversible Zn plating/stripping with satisfactory Coulombic efficiency rather than the formation of Zn dendrites or other byproducts. As a consequence, a highly flexible symmetric cell based on the Zn/CNT anode presents appreciably low voltage hysteresis (27 mV) and superior cycling stability (200 h) with dendrite‐free morphology at 2 mA cm−2, accompanied by a high depth of discharge (DOD) of 28%. Such distinct performance overmatches most of recently reported Zn‐based anodes. Additionally, this efficient rechargeability of the Zn/CNT anode also enables a substantially stable Zn//MnO2 battery with 88.7% capacity retention after 1000 cycles and remarkable mechanical flexibility.
Melatonin prevents cadmium‐induced bone damage: First evidence on an improved osteogenic/adipogenic differentiation balance of mesenchymal stem cells as underlying mechanism

Melatonin (MLT) plays a role in preserving bone health, a function that may depend on homeostatic effects on both mature osteoblasts and mesenchymal stem cells (MSCs) of the bone tissue. In this study, these functions of MLT have been investigated in rat bone (femur) and in human adipose MSC (hMSC) during chronic exposure to low‐grade cadmium (Cd) toxicity, a serious public health concern. The in vivo findings demonstrate that MLT protects against Cd‐induced bone metabolism disruption and accumulation of bone marrow adipocytes, a cue of impaired osteogenic potential of skeletal MSC niches. This latter symptom was recapitulated in hMSCs in which Cd toxicity stimulated adipogenic differentiation. MLT was found to rescue, at least in part, the osteogenic differentiation properties of these cells. This study reports on a new bone cytoprotection function of MLT pertinent to Cd toxicity and its interfering effect on skeletal MSC differentiation properties that is worth investigating for its possible impact on human bone pathophysiology.
Using a Two-Stage System Evaluation Approach to Explore the New Adoption of an Information System in the Mobile Era

Currently, e-learning systems are being widely used in all stages of education. However, it is difficult for school administrators to accurately assess the actual usage performance of a new system, especially when an organization wishes to update the system for users from different backgrounds using new devices such as smartphones. To allow school administrators to conduct upgrades of e-learning systems that take into consideration students' current usage conditions, this study proposed a two-stage system evaluation approach to explore the adoption of new systems. We collected 352 samples in Stage I. The goal of this Stage I was to propose a research model to understand the usage intentions of college students toward campus e-learning systems and also the factors which showed significant differences between PC and smartphone usage. A total of 30 trained students participated in Stage II. The goal of Stage II was to propose a system performance evaluation method to evaluate the performance of the new and existing systems according to the concerned factors of smartphone users after actual system use. Finally, based on our research model and system performance evaluation method, we put forward conclusions and suggestions that schools could use as references for future system procurements and updates.
Polymorphism in the Promoter Region of NFE2L2 Gene Is a Genetic Marker of Susceptibility to Cirrhosis Associated with Alcohol Abuse

Alcoholic liver disease (ALD) is a highly prevalent spectrum of pathologies caused by alcohol overconsumption. Morbidity and mortality related to ALD are increasing worldwide, thereby demanding strategies for early diagnosis and detection of ALD predisposition. A potential candidate as a marker for ALD susceptibility is the transcription factor nuclear factor erythroid-related factor 2 (Nrf2), codified by the nuclear factor erythroid 2-related factor 2 gene (NFE2L2). Nrf2 regulates expression of proteins that protect against oxidative stress and inflammation caused by alcohol overconsumption. Here, we assessed genetic variants of NFE2L2 for association with ALD. Specimens from patients diagnosed with cirrhosis caused by ALD were genotyped for three NFE2L2 single nucleotide polymorphisms (SNP) (SNPs: rs35652124, rs4893819, and rs6721961). Hematoxylin & eosin and immunohistochemistry were performed to determine the inflammatory score and Nrf2 expression, respectively. SNPs rs4893819 and rs6721961 were not specifically associated with ALD, but analysis of SNP rs35652124 suggested that this polymorphism predisposes to ALD. Furthermore, SNP rs35652124 was associated with a lower level of Nrf2 expression. Moreover, liver samples from ALD patients with this polymorphism displayed more severe inflammatory activity. Together, these findings provide evidence that the SNP rs35652124 variation in the Nrf2-encoding gene NFE2L2 is a potential genetic marker for susceptibility to ALD.
The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows

Milk fat depression (MFD) syndrome represents a significant drawback to the dairy industry. The aim of this study was to unravel the ruminal metabolome-microbiome interaction in response to diet-induced MFD in dairy cows. Twelve healthy second parity Holstein dairy cows (days in milk (DIM) = 119 ± 14) were randomly assigned into control (CON, n = 6) group and treatment (TR, n = 6) group. Cows in TR group received a high-starch total mixed ration (TMR) designed to induce an MFD syndrome. Decreased milk fat yield and concentration in TR cows displayed the successful development of MFD syndrome. TR diet increased the relative abundance of Prevotella and decreased the relative abundance of unclassified Lachnospiraceae, Oribacterium, unclassified Veillonellaceae and Pseudobutyrivibrio in ruminal fluid. Metabolomics analysis revealed that the ruminal fluid content of glucose, amino acids and amines were significantly increased in TR cows compared with CON cows. Correlation analysis revealed that the concentration of amines and amino acids were highly correlated with the abundance of Oribacterium, Pseudobutyrivibrio, RC9_gut_group, unclassified BS11_gut_group and Selenomonas. In general, these findings revealed that TR diet reduced the rumination time and altered rumen fermentation type, which led to changes in the composition of ruminal microbiota and metabolites, and caused MFD.
Prevalence and correlates of PTSD in first episode psychosis: Findings from the RAISE-ETP study.

Posttraumatic stress disorder (PTSD) in young individuals is associated with an increased risk to develop psychosis or mania, and both trauma and PTSD rates are elevated in people with schizophrenia and other severe mental illnesses. However, less research has examined PTSD in people who have recently developed a first episode of psychosis (FEP). The present study is a secondary analysis of the baseline data collected for the National Institute of Mental Health Recovery After an Initial Schizophrenia Episode-Early Treatment Program (RAISE-ETP) study to examine the rates of trauma and PTSD, and to explore the demographic and clinical correlates of PTSD in a representative sample of 404 persons with an FEP. Approximately 80% of the study sample reported experiencing at least one traumatic event during their lives, with females more likely to report childhood sexual abuse and spousal abuse than males. A total of 20 participants (5.0%) met criteria for a lifetime diagnosis of PTSD, while another 15 participants (3.7%) met subthreshold diagnostic criteria for PTSD. Significant correlations were found between lifetime PTSD and the Calgary Depression Scale, the Mental Health Recovery Measure, the Stigma Scale, and duration of untreated psychosis, with higher scores on each variable associated with a diagnosis of PTSD. The association between PTSD and more severe depression, as well as lower perceptions of personal recovery, suggest that PTSD may be an important target for treatment programs for persons recovering from an FEP. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Viscous Droplet Impact on Non-wettable Textured Surfaces.

Viscous droplet impact on non-wettable surfaces with complex geometry is of technological importance, but the fundamental understanding of the dynamics is not entirely understood yet. In this work, liquid drops with various viscosities and impact velocities were investigated and their behavior was correlated with contact time upon impinging non-wettable flat and textured surfaces. It was shown that in the inertial-capillary regime, the contact time between the droplet and a flat surface is independent of impact velocity while for the viscous-capillary regime, it increases with impact velocity. Drops impacting on non-wettable surfaces with single and multiple macroscopic ridges generally leave the surface at a reduced contact time, compared to flat surfaces. The incorporation of a single macrotexture results in a step-like reduction in the contact time because the impacting drop reaches the maximum spreading diameter, a condition that must happen when the Capillary number is below unity.