Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Alterations of NTRK, POLE, ERBB2, and Microsatellite Instability Status in Chinese Patients with Colorectal Cancer

Abstract Background The increasing molecular characterization of colorectal cancers (CRCs) has spurred the need to look beyond RAS, BRAF, and microsatellite instability (MSI). Genomic alterations, including ERBB2 amplifications and mutations, POLE mutations, MSI, and NTRK1–3 fusions, have emerged as targets for matched therapies. We sought to study a clinically annotated Chinese cohort of CRC subjected to genomic profiling to explore relative target frequencies. Methods Tumor and matched whole blood were collected from 609 Chinese patients with CRC. Extracted DNA was analyzed for all classes of genomic alterations across 450 cancer‐related genes, including single‐nucleotide variations (SNVs), short and long insertions and deletions (indels), copy number variations, and gene rearrangements. Next‐generation sequencing–based computational algorithms also determined tumor mutational burden and MSI status. Results Alterations in TP53 (76%), APC (72%), and KRAS (46%) were common in Chinese patients with CRC. For the first time, the prevalence of NTRK gene fusion was observed to be around 7% in the MSI‐high CRC cohort. Across the cohort, MSI was found in 9%, ERBB2 amplification in 3%, and POLE pathogenic mutation in 1.5% of patients. Such results mostly parallel frequencies observed in Western patients. However, POLE existed at a higher frequency and was associated with large tumor T‐cell infiltration. Conclusion Comparing to the Western counterparts, POLE mutations were increased in our cohort. The prevalence of NTRK gene fusion was around 7% in the MSI‐high CRC cohort. Increased adoption of molecular profiling in Asian patients is essential for the improvement of therapeutic outcomes. Implications for Practice The increasing use of genomic profiling assays in colorectal cancer (CRC) has allowed for the identification of a higher number of patient subsets benefiting from matched therapies. With an increase in the number of therapies, assays simultaneously evaluating all candidate biomarkers are critical. The results of this study provide an early support for the feasibility and utility of genomic profiling in Chinese patients with CRC.
Evaluation of diagnostic pigments to estimate phytoplankton size classes

Phytoplankton accessory pigments are commonly used to estimate phytoplankton size classes, particularly during development and validation of biogeochemical models and satellite ocean color‐based algorithms. The diagnostic pigment analysis (DPA) is based on bulk measurements of pigment concentrations and relies on assumptions regarding the presence of specific pigments in different phytoplankton taxonomic groups. Three size classes are defined by the DPA: picoplankton, nanoplankton, and microplankton. Until now, the DPA has not been evaluated against an independent approach that provides phytoplankton size calculated on a per‐cell basis. Automated quantitative cell imagery of microplankton and some nanoplankton, used in combination with conventional flow cytometry for enumeration of picoplankton and nanoplankton, provide a novel opportunity to perform an independent evaluation of the DPA. Here, we use a data set from the North Atlantic Ocean that encompasses all seasons and a wide range of chlorophyll concentrations (0.18–5.14 mg m−3). Results show that the DPA overestimates microplankton and picoplankton when compared to cytometry data, and subsequently underestimates the contribution of nanoplankton to total biomass. In contrast to the assumption made by the DPA that the microplankton size class is largely made up of diatoms and dinoflagellates, imaging‐in‐flow cytometry shows significant presence of diatoms and dinoflagellates in the nanoplankton size class. Additionally, chlorophyll b is commonly attributed solely to picoplankton by the DPA, but Chl b‐containing phytoplankton are observed with imaging in both nanoplankton and microplankton size classes. We suggest revisions to the DPA equations and application of uncertainties when calculating size classes from diagnostic pigments.
The rolling circle amplification and next generation sequencing approaches reveal genome wide diversity of Kenyan cassava mosaic geminivirus

Rolling circle amplification is a simple approach of enriching populations of single-stranded DNA plant begomovirus genomes (genus, Begomovirus; family, Geminiviridae). This is an innovative approach that utilizes the robustness of the bacteriophage phi29 DNA polymerase used in circle amplification, together with deep sequencing using Illumina Miseq and bioinformatics to assess population diversity of begomoviruses in naturally infected cassava. The approach is suitable for detecting rare members in a population in begomoviral populations in situation where mixtures of isolates, strains, and multiple species occur. The main objectives were to increase the sensitivity of detection of next generation sequencing by enriching it using rolling circle amplification then determination of the diversity of the cassava mosaic geminivirus. This was done by total nucleic acids isolated from symptomatic, field cassava infected plants, then using rolling circle amplification to multiply the less abundant viral sequences. Enriched and non-enriched virus-libraries were subjected to deep sequencing using Illumina Miseq. Using bioinformatic CLC Genomics 5.5. 1 software programs the quality assessment of reads and contig assembly of viral sequences. This was done through de novo and reference-guided assembly. The identity and diversities of the begomoviral sequences were compared with sequences in Sanger sequencing of viral components deposited in the NCBI Gene Bank. In this study we have demonstrated that RCA increases the chances of detecting the virus by approximately 10 to 1000 fold and wide genome diversity of cassava mosaic geminivirus in various cassava growing zones in Kenya were detected. In conclusion, this approach described herein is simple and will enhance the exploration of begomovirus diversities from cassava infected plants, irrespective of their viral abundance. This will make it possible for routine screening of field samples as the cost of deep sequencing NGS is decreasing and the advances of bioinformatic software development become enhanced. This is the first report of the RCA-Illumina-NGS approach to explore cassava infected with begomoviruses under field conditions and their diversities. Key words: Illumina Miseq sequencing, geminivirus, ssDNA viruses, viral sequence enrichment, de novo genome assembly, rolling cycle amplification (RCA).
Calculus for software engineering: Students’ perception towards flipped classroom

The research aimed to analyse the learning readiness and perception of informatics engineering students about calculus. More top-level students taken remedial teaching and the student stated that calculus was dominated by mathematics and lecturers did not relate to software application. The research method which was a case study analysed the learning readiness was further examined by providing an open questionnaire to new students about the calculus learning. The lecture was then carried out as many as 4 meetings. The overall research data was a description of the questionnaire and quiz results. The questionnaire stated that 82% of new students have not yet learned that calculus belongs to the field of mathematics. After lectures using flipped classroom models were implemented, the quiz results show that 38 students reached a score of more than 80. Students also respond positively to the learning using flipped classroom models increased the spirit of learning calculus because all records and exercises were well stored and can be downloaded at any time. Learning using flipped classroom models provided easy learning for new students, practicality in task collection, and effectiveness for communicating with lecturers and group members without being tied to place and time.
Flood susceptibility mapping in Erythropotamos river basin with the aid of Remote Sensing and GIS

Erythropotamos is a tributary of river Evros and during the last decade its drainage basin flooded many times, causing extensive damage on properties. In order to assess flood susceptibility in the aforementioned study area, the inundated areas of floods that occurred in 2010, 2017 and 2018 were initially delineated with the aid of SAR (Synthetic Aperture Radar) imagery by applying an established flood delineation methodology. Subsequently, flood susceptibility mapping was conducted for the study area by applying the Analytical Hierarchy Process (AHP). Topographical, hydrological and meteorological factors were used and each one of them was classified into three (3) flood susceptibility categories (low, medium and high). The determination of the importance for each factor over the others, which is the main objective of this research, was decided according to the proportion of the 2010 inundated area, captured by ENVISAT/ASAR imagery, which intersected with each factor’s high susceptibility class. Finally, the resulting flood susceptibility map was validated according with the inundated areas of the 2017 and 2018 flood events, captured by SENTINEL – 1 A/B imagery, indicating that approximately 60% of both of these areas intersected with the map’s high susceptibility zone.
Verifying the Utility of Black Locust (Robinia pseudoacacia L.) in the Reclamation of a Lignite Combustion Waste Disposal Site in Central European Conditions

N-fixing tree species, such as black locust, have achieved very promising results in the reclamation of technosols, especially those at combustion waste disposal sites, which have extremely poor nutrients and adverse physicochemical parameters. This paper presents an assessment of the survival rates, growth parameters, and quality and vitality of and nutrient supply (NPK) to black locust (Robinia pseudoacacia L.) specimens that were experimentally planted on a lignite combustion waste disposal site. The black locust seedlings were introduced directly into the combustion waste using two variants of NPK (7% N, 5.5% P2O5, and 9% K2O) fertilisation, at doses of 250 and 500 kg ha−1, and in control plots with no mineral fertilisation. No significant impacts of the applied mineral fertilisation were found on the soil properties, growth parameters, or nutrient supplies to the trees. Black locust introduced to the landfill after three years of revegetation was characterised by a very high survival rate of 95%–100%, as well as good growth parameters (height and diameter at the root collar). Nutrient supply was determined on the basis of the chemical composition of the leaves, which indicated an adequate supply of nitrogen, similar to levels found under natural conditions. In the case of K and P, the supply levels were lower than optimal when compared with data from the literature. However, at this initial stage of tree development on the combustion waste disposal site, nutrient supply is similar on all variants and is not a critical factor for successful black locust introduction. We suggest using growth parameters, survival, and vitality of trees as decisive factors for the reclamation of combustion waste landfill sites strategy. All these factors confirmed the usefulness of black locust to the reclamation of combustion waste disposal sites.
Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells

1 Report Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells Piyush Joshi 2, , Tatsuya Seki , Shinobu Kitamura, Andrea Bergano, Bongyong Lee 3 and Ranjan J. Perera* 2, 3,5 1 Department of Oncology, Johns Hopkins University School of Medicine, 401 N. Broadway, Baltimore, MD 21287 USA 2 Department of Cancer and Blood Disorders Institute, Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701 USA 3 Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger road, Orlando, FL 32827 USA 4 Medical and Biological Laboratories, Nagoya 460-0008, Japan 5 The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 401 N. Broadway, Baltimore, MD 21287 USA *Corresponding author email: jperera2@jhmi.edu
Managerial equity incentives and R&D investments in emerging economies: study based on threshold effects

ABSTRACT Do managerial equity incentives benefit or impede R&D investments? To address this question and the inconsistent empirical findings on the topic, this study investigates the relationship between equity incentives and R&D investments as well as the threshold effects of some contextual factors. Our study evidence a curvilinear inverted U-shaped relationship between equity incentives and R&D investments by using GMM system estimators for a sample of 158 Chinese firms for the 2006–2018 period. Our findings also indicated that the influence of equity incentives on R&D investments is constrained by contextual factors such as financial slack and equity concentration, suggesting that financial slack plays a double threshold effect on the above relationship, while equity concentration performed a significant single threshold effect.
Seed quality improvement with fruit extracts in blackgram

The present study was conducted to know the effect of extracts from parts of papaya and pomegranate fruits containing enormous amount of antioxidants on the seed quality parameters of blackgram (Vigna mungo L.). Blackgram seeds were soaked in papaya peel, pulp, seeds and pomegranate peel, seeds extracts viz., 2.5 %, 5 %, 7.5 % and 10 % concentration for 1 hour. The physiological parameters were evaluated under laboratory conditions. The results revealed that seeds treated with 2.5 % papaya seed extract recorded high physiological and biochemical changes in terms of field emergence, germination percentage, seedling length, dry matter production, vigour index and ? - amylase activity when compared to rest of treatments and control.
Molecular Anion Spectroscopy and Stability

A detailed and thorough computational investigation of the SF – 6 anion is undertaken, with additional calculations of other stable SF−n anions. The calculations are used to interpret recent infrared multi-photon dissociation (IRMPD) experiments of SF6 and SF − 5 anions done with the FELIX free electron tunable infrared laser in the spectral range of 450-850 cm−1. The vibrational spectroscopy of negative molecular ions is crucial towards understanding the dynamics of electron transfer processes, as well as providing experimental validation for computational models of molecular bonding in anions. Many molecular negative ions have been shown to exhibit long (i.e. > 1μs) lifetimes with respect to electron autodetachment, and a recent reformulation of QET, or quasiequilibrium theory, has shown success in reproducing these experimental lifetimes for a variety of molecules. In particular, the SF6 anion has an interesting history of disparate results for autodetachment lifetime measurements, largely dependent upon the type of experimental method employed. Analysis of the experimental data in reference to the theoretical predictions of QET suggests this disparity may be related to the degree of IVR, or inter-vibrational coupling occurring in the anion. Calculation of the electron autodetachment lifetime according to QET requires accurate values for the electron affinity as well as the vibrational frequencies for both the neutral and the anion. Ab-initio and DFT computations are extremely useful for providing reasonable estimates of the anion vibrational frequencies, however, experimental constraints upon these values are essential. An additional benefit of anion vibrational spectroscopy is the elucidation of molecular structure and symmetry. This is particularly relevant for the case of SF 6 , as certain computational methods show interesting results in regard to the distortion to lowered C4v symmetry. This is in contradiction to the expected Oh symmetry of the SF6 anion, and the potential energy surface along this multi-dimensional vector of S-F bond dissociation is further computationally explored, as are the theoretical implications of a multiple-well potential surface.
The challenge-based learning to students’ spatial mathematical ability

The low ability of students thinking in geometry requires a new perspective in creating a more challenging and better mathematics learning process. This study aims to improve mathematical spatial ability through challenge-based learning using the Quasi-Experiment Method and Non-equivalent Pretest-Posttest Control Group Design. The instruments used PAM test and spatial thinking ability test. Analysis of quantitative data used t-test, Mann–Whitney U test, and Adjusted Rank Transform, two-way ANOVA. The study conducted at a university in Bandung, Indonesia. It involved 62 prospective Madrasah Ibtidaiyah teacher candidates as samples, which categorized into two classes, 32 class B as an experimental class and 30 class A as a control class. The findings show: There is a higher increase in mathematical spatial abilities of students who obtain challenge-based learning than students who obtain expository learning based on the overall student sample and students’ initial mathematical knowledge. There was an interaction effect between type aspects (challenge-based learning and expository learning) and initial mathematical knowledge on students’ mathematical spatial abilities. Challenge-based learning can facilitate the process of conflict, discovery, social interaction, and the reflective process of students. The material is easy to understand and exciting to learn. Thus, spatial ability is better than expository learning.
Structured event memory: a neuro-symbolic model of event cognition

Humans spontaneously organize a continuous experience into discrete events and use the learned structure of these events to generalize and organize memory. We introduce the Structured Event Memory (SEM) model of event cognition, which accounts for human abilities in event segmentation, memory, and generalization. SEM is derived from a probabilistic generative model of event dynamics defined over structured symbolic scenes. By embedding symbolic scene representations in a vector space and parametrizing the scene dynamics in this continuous space, SEM combines the advantages of structured and neural network approaches to high-level cognition. Using probabilistic reasoning over this generative model, SEM can infer event boundaries, learn event schemata, and use event knowledge to reconstruct past experience. We show that SEM can scale up to high-dimensional input spaces, producing human-like event segmentation for naturalistic video data, and accounts for a wide array of memory phenomena.
Factors Predicting Low-Intermediate French Learners’ Vocabulary Use in Speaking Tasks

Les auteurs explorent la production orale en français d’apprenants natifs et non natifs dans deux dialogues. L’étude vise plus précisément trois objectifs. Premièrement, celui d’étudier la relation entre la taille du vocabulaire réceptif et productif d’apprenants de français d’une part et le vocabulaire utilisé dans deux dialogues d’autre part. Deuxièmement, les auteurs veulent comparer le vocabulaire produit (c’est-à-dire le nombre de mots utilisés, le profil lexical de fréquence et la diversité lexicale mesurée à l’aide de D et HD-D) par des locuteurs non natifs avec celui des locuteurs natifs. Troisièmement, les auteurs veulent déterminer lesquelles des mesures mentionnées ci-dessus permettent de prédire l’évaluation holistique des connaissances lexicales d’apprenants de français par des experts. Cinquante apprenants de français de 17 ans ont rempli un test de vocabulaire réceptif et productif et ont participé à deux dialogues. Vingt-sept francophones du même âge ont produit les mêmes dialogues. Les résultats indiquent qu’il existe une corrélation positive et modérée entre le vocabulaire réceptif et les scores holistiques, mais pas entre le vocabulaire productif et les scores holistiques. Qui plus est, lorsqu’ils s’expriment, les locuteurs natifs produisent plus de mots et moins de mots à usage fréquent. La diversité lexicale de leur production est également plus élevée que celle des apprenants de français. Enfin, il semble qu’une combinaison de la diversité lexicale (HD-D) et du nombre de types utilisés par les locuteurs ainsi que la fréquence de ces mots expliquent une grande partie de la variance dans les scores holistiques. Les résultats de la présente étude jettent un nouvel éclairage sur le rôle de l’emploi du vocabulaire dans la production orale de locuteurs natifs et non natifs dans une langue autre que l’anglais, à savoir le français, et pour une population autre que des étudiants universitaires, c’est-à-dire des apprenants pré-intermédiaires.
Modeling and Operation of Single and Multiple Tube Membrane Bioreactors

Abstract : A mathematical model was developed and experimental work completed to examine the removal of volatile organic compounds from air using single and multiple tube membrane bioreactors. Both bench-sale and a small pilot-scale reactor's performance were reasonably predicted by the mathematical model. Both model predictions and experimental work indicated the liquid suspension does not significantly contribute to the removal of contaminants from air. Experimental results indicate that membrane bioreactor performance is not detrimentally affected by phosphorous or nitrogen limitation after an initial period with adequate nutrient supply. Stopping the liquid flow in the reactor module also did not lead to a declination in performance. VOC removal in a polyporous membrane reactor remained constant under diurnal loading conditions when compared with continuously operated bioreactors. A heated bioreactor also was found to remove contaminant at the same rate as a reactor operated at ambient temperature while measured heat transfer coefficients for several module configurations ranged from 2.9-17.4 W/sq m/K. Bioreactors operated in series provided additional removal of contaminant from the air.
THE SCIENTIFIC CREATIVITY OF FIFTH GRADERS IN A STEM PROJECT-BASED COOPERATIVE LEARNING APPROACH

This research aimed to examine the effects of an integrated STEM project-based with cooperative learning (STEM-PjBCL) approach on fifth graders’ five sub-scales of trait dimension in scientific creativity. A quasi-experimental pre-test and post-test non-equivalent control group design was employed. A total of 360 fifth graders from four randomly selected primary schools were chosen as sample and assigned to STEM-PjBCL (n=120), PjBL (n=120), and Conventional (CV) (n=120) instructional methods. The Figural Scientific Creativity Test was used as the pre-test and post-test. Multivariate Analysis of Covariance (MANCOVA) was performed on the post-test scores with pre-test scores as the covariates to examine whether a significant difference existed across the three methods. The results showed that fifth graders taught with the STEM-PjBCL method significantly outperformed their counterparts in the PjBL and CV method in Fluency, Originality, Elaboration, Abstractness of title, and Resistance to premature closure. However, fifth graders taught in the PjBL method did not significantly outperform their counterparts in the CV method in the five sub-scales of scientific creativity. Large effect sizes were obtained for comparing STEM-PjBCL with the PjBL and CV method. The results suggest that the STEM-PjBCL method produces a significant beneficial effect on promoting the five sub-scales of trait dimension of scientific creativity among fifth graders. Keywords: cooperative learning, project-based learning, scientific creativity, STEM, trait dimension.