Miracle-dz/UniFAR-FTUs huggingface dataset:
The Nature of Automated Essay Scoring Feedback

The purpose of this study is to explore the nature of feedback that English as a Second Language (ESL) students received on their writings either from an automated essay scoring (AES) system or from the teacher. The participants were 12 adult ESL students who were attending an intensive English center at a university in Florida. The drafts of the students were analyzed in depth from a case-study perspective. While the document (essay) analysis was the main data collection method, observations and interviews provided crucial information regarding the context in which the students wrote and the nature of each type of feedback they received. The results revealed that the nature of the AES feedback and written teacher feedback (TF) feedback was different from each other. While the written TF was shorter and more focused, the AES feedback was quite long, generic, and redundant. The findings suggested that AES systems are not entirely ready to meet the needs of ESL or English as a Foreign Language (EFL) students. The developing companies need to improve the feedback capabilities of the program for nonnative English-speaking students, that is, less redundancy, shorter feedback, simpler language for feedback, and feedback for short/off topic/repetitious essays.
Wood mouse feeding effort and decision-making when encountering a restricted unknown food source

Animals making foraging decisions must balance the energy gained, the time invested, and the influence of key environmental factors. In our work, we examined the effect of predation risk cues and experience on feeding efforts when a novel food resource was made available. To achieve this, we live-trapped wood mouse Apodemus sylvaticus in Monte de Valdelatas (Madrid), where 80 Sherman traps were set in four plots. Traps were subjected to two food-access difficulties in treatments consisting of three consecutive nights: open plastic bottles (easy) and closed bottles (difficult), both using corn as bait. To simulate predation risk, we set fox faeces in half of the traps in each plot. We also considered moonlight (medium/low) as an indirect predation risk cue. We analysed whether bottles had been bitten by mice and the gnawed area of each bottle was measured. Our results indicated that food access difficulty, experience, and predation risk determined mice feeding decisions and efforts. The ability of mice to adapt feeding effort when a new food source is available was demonstrated because a higher proportion of closed bottles exhibited bite marks and the gnawed area was bigger. Moreover, mouse experience was determinant in the use of this new resource since recaptured mice gnawed broader orifices in the bottles and the gnawed area increased each time an individual was recaptured. Additionally, direct predation risk cues prompted mice to bite the bottles whereas the effect of different moon phases varied among the food access treatments. This study provides direct evidence of formidable efficacy of wild mice to exploit a new nutrient resource while considering crucial environmental factors that shape the decision-making procedure.
An $\alpha$ -Divergence-Based Approach for Robust Dictionary Learning

In this paper, a robust sequential dictionary learning (DL) algorithm is presented. The proposed algorithm is motivated from the maximum likelihood perspective on dictionary learning and its link to the minimization of the Kullback–Leibler divergence. It is obtained by using a robust loss function in the data fidelity term of the DL objective instead of the usual quadratic loss. The proposed robust loss function is derived from the <inline-formula> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula>-divergence as an alternative to the Kullback–Leibler divergence, which leads to a quadratic loss. Compared to other robust approaches, the proposed loss has the advantage of belonging to class of redescending M-estimators, guaranteeing inference stability from large deviations from the Gaussian nominal noise model. The algorithm is obtained by solving a sequence of penalized rank-1 matrix approximation problems, where the <inline-formula> <tex-math notation="LaTeX">$\ell _{1}$ </tex-math></inline-formula>-norm is introduced as a penalty promoting sparsity and then using a block coordinate descent approach to estimate the unknowns. Performance comparison with similar robust DL algorithms on digit recognition, background removal, and gray-scale image denoising is performed highlighting efficacy of the proposed algorithm.
Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling

Mast cell tumours (MCTs) are common neoplasms in dogs and are usually regarded as potentially malignant. Several studies have attempted to identify biomarkers to better predict biological behaviours for this tumour. The aim of this study was to identify pathways connected to clinical and histopathological malignancies, shorter survival times, and poor prognoses associated with MCTs. We performed genome-wide gene expression analyses on tissues obtained from 15 dogs with single MCTs, and identified two distinct tumour subtypes—high-risk and low-risk—associated with differences in histological grades, survival times, Ki67 indices, and occurrence of death due the disease. Comparative analyses of RNA sequence profiles revealed 71 genes that were differentially expressed between high- and low-risk MCTs. In addition to these analyses, we also examined gene co-expression networks to explore the biological functions of the identified genes. The network construction revealed 63 gene modules, of which 4 were significantly associated with the more aggressive tumour group. Two of the gene modules positively correlated with high-risk MCTs were also associated with cell proliferation and extracellular matrix-related terms. At the top of the extracellular matrix module category, genes with functions directly related to those of cancer-associated fibroblasts (CAFs) were identified. Immunohistochemical analyses also revealed a greater number of CAFs in high-risk MCTs. This study provides a method for the molecular characterisation of canine MCTs into two distinct subtypes. Our data indicate that proliferation pathways are significantly involved in malignant tumour behaviours, which are known to be relevant for the induction and maintenance of MCTs. Finally, animals presenting high-risk MCTs overexpress genes associated with the extracellular matrix that can be robustly linked to CAF functions. We suggest that CAFs in the MCT stroma contribute to cancer progression.
Associations between brain morphology and motor performance in chronic neck pain: A whole‐brain surface‐based morphometry approach

Changes in brain morphology are hypothesized to be an underlying process that drive the widespread pain and motor impairment in patients with chronic neck pain. However, no earlier research assessed whole‐brain cortical morphology in these patients. This case–control study assesses group‐differences in whole‐brain morphology between female healthy controls (HC; n = 34), and female patients with chronic idiopathic neck pain (CINP; n = 37) and whiplash‐associated disorders (CWAD; n = 39). Additionally, the associations between whole‐brain morphology and motor performance including balance, strength, and neuromuscular control were assessed. Cortical volume, thickness, and surface area were derived from high resolution T1‐weighted images. T2*‐weighted images were obtained to exclude traumatic brain injury. Vertex‐wise general‐linear‐model‐analysis revealed cortical thickening in the left precuneus and increased volume in the left superior parietal gyrus of patients with CINP compared to HC, and cortical thickening of the left superior parietal gyrus compared to HC and CWAD. Patients with CWAD showed a smaller cortical volume in the right precentral and superior temporal gyrus compared to HC. ANCOVA‐analysis revealed worse neuromuscular control in CWAD compared to HC and CINP, and in CINP compared to HC. Patients with CWAD showed decreased levels of strength and sway area compared to CINP and HC. Partial correlation analysis revealed significant associations between the volume of the precentral gyrus, and neuromuscular control and strength together with an association between the volume of the superior temporal gyrus and strength. Our results emphasize the role of altered gray matter alterations in women with chronic neck pain, and its association with pain and motor impairment.
Effects of State Anxiety and Ego Depletion on Performance Change in Golf Putting: A Hierarchical Linear Model Application

This study employed a hierarchical linear model analysis to examine the effects of ego depletion and state anxiety on performance changes in golf putting. We randomly assigned 51 female college students with no previous golf putting experience to either an ego-depletion (experimental) group (n = 26) or a non-ego-depletion (control) group (n = 25). Putting performance changes over repeated trials displayed a quadratic curve, and both ego depletion and state anxiety exerted negative effects on early, but not late, putting performance. Contrary to previous findings, the interaction effect between ego depletion and state anxiety on performance was nonsignificant.
Effects of carfilzomib alone and in combination with cisplatin on the cell death in cisplatin-sensitive and cisplatin-resistant ovarian carcinoma cell lines.

BACKGROUND Previous studies on the efficacy of platinum-based drugs and selective inhibitors of proteasome have revealed promising outcomes. This study is aimed to evaluate the effects of the combination of cisplatin and carfilzomib on the cell death induction and drug efflux transporters expression in cisplatin-sensitive (A2780s) and cisplatin-resistant (A2780cp) ovarian cancer cells lines. METHODS MTT cytotoxic assay was conducted to determine the cytotoxicity. Drug interactions were analyzed based on Chou-Talalay's principles and real-time PCR analysis was performed to determine possible alterations in mRNA levels of MRP1 and BCRP. RESULTS A2780s cells were more susceptible to both cisplatin and carfilzomib while analyses of drug interactions between the two agents showed synergistic effects in all affected fractions of drug-treated A2780s and A2780cp cells (CI<0.9) with the combination indices being significantly lower in A2780cp cells (p < 0.01). We also found that although mRNA levels of BCRP and MRP1 were significantly altered in both cells exposed to each drug alone, only the combination regimen was able to significantly reduce the mRNA levels of these genes in A2780cp cells (p<0.001). CONCLUSION This combination might be a potential strategy for suppressing cell growth via downregulating the drug efflux transporters expression, especially in cisplatin-resistant ovarian cancer cells (Fig. 3, Ref. 45).
Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants

Background Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic analysis of transcriptomic data, especially in cases with cSVs, is a complex and challenging task, and the development of proper bioinformatic tools for transcriptome studies is necessary. Methods We designed a bioinformatic workflow for the analysis of total RNA-Seq data consisting of two separate parts (pipelines): The first pipeline incorporates a statistical solution for differential gene expression analysis in a biologically heterogeneous sample set. We utilized results from transcriptomic arrays which were carried out in parallel to increase the precision of the analysis. The second pipeline is used for the identification of de novo fusion genes. Special attention was given to the filtering of false positives (FPs), which was achieved through consensus fusion calling with several fusion gene callers. We applied the workflow to the data obtained from ten patients with chronic lymphocytic leukemia (CLL) to describe the consequences of their cSVs in detail. The fusion genes identified by our pipeline were correlated with genomic break-points detected by genomic arrays. Results We set up a novel solution for differential gene expression analysis of individual samples and de novo fusion gene detection from total RNA-Seq data. The results of the differential gene expression analysis were concordant with results obtained by transcriptomic arrays, which demonstrates the analytical capabilities of our method. We also showed that the consensus fusion gene detection approach was able to identify true positives (TPs) efficiently. Detected coordinates of fusion gene junctions were in concordance with genomic breakpoints assessed using genomic arrays. Discussion Byapplying our methods to real clinical samples, we proved that our approach for total RNA-Seq data analysis generates results consistent with other genomic analytical techniques. The data obtained by our analyses provided clues for the study of the biological consequences of cSVs with far-reaching implications for clinical outcome and management of cancer patients. The bioinformatic workflow is also widely applicable for addressing other research questions in different contexts, for which transcriptomic data are generated.
Treatment of Gynecomastia by Endoscopic Subcutaneous Mastectomy in Adolescents.

Background: Morbidity of traditional open surgery for the treatment of gynecomastia includes asymmetry, retraction of the nipple, and poor scarring. Other approaches were described to improve the results. Endoscopic subcutaneous mastectomy (ESCM) was reported in adult series, including a few adolescents. This technique was considered as safe with good aesthetic results. The aim of this study was to evaluate the results of ESCM in an adolescent series. Patient and Methods: We treated 19 adolescents with Simon's grade IIB and III gynecomastia between June 2014 and July 2018. They could choose open surgery through the nipple or endoscopic surgery by axillary approach. To perform ESCM, three trocars were placed on the midaxillary line to dissect the gland. The resection was performed leaving 1 cm thickness of gland behind the nipple. The gland was extracted after morcellation through the 10 mm trocar. A drainage tube was placed in the cavity. The patients wore a thoracic belt smoothly compressing the operative areas for 15 days. The result was considered as good when there was no remaining gland, good symmetry, and no nipple retraction or nipple lateral displacement. Results: During the study period, 12 adolescents were treated by ESCM and 7 preferred open surgery. Among the 12 ESCM patients, 7 had bilateral and 5 unilateral gynecomastia. A subcutaneous injection of serum was done in the last 6 patients to facilitate the creation of the work space. A 2- or 3-mm second-degree burn occurred in 4 cases, 2 on the nipple and 2 just above the nipple, with a 2 mm remaining scar above the nipple in 1 case. The postoperative course was uneventful in 11 adolescents. One subcutaneous seroma expanded at 15 days postoperative and resolved after 3 weeks of prolonged compression by thoracic belt. The adolescents had 11 good results and 1 persistent asymmetry; 2 other asymmetries had a spontaneous improvement after 1 or 2 years. Conclusion: ESCM is feasible and safe for the treatment of gynecomastia in adolescents. This technique is challenging but permits to reach good aesthetic results and avoids scars on the anterior wall of the thorax.
Compiler Optimizations for a Time-constrained Environment

Over the last several decades, two important shifts have taken place in the computing world: first, the speed of processors has vastly outstripped the speed of memory, making memory accesses by far the most expensive operations that a typical symbolic program performs. Second, dynamically compiled languages such as Java and C# have become popular, placing new pressures on compiler writers to create effective systems for run-time code generation. This paper addresses the need created by the lagging speeds of memory accesses in the context of dynamically compiled systems. In such systems memory access optimization is important for resultant program performance, but the compilation time required by most traditional memory access optimizations is prohibitively high for use in such contexts. In this paper, we present a new analysis, memory dependence analysis, which amortizes the cost of performing memory access analysis to a level that is acceptable for dynamic compilation. In addition, we present two memory access optimizations based on this new analysis, and present empirical evidence that using this approach results in significantly improved compilation times without significant loss in resultant code quality.
Graphene- and Graphene Oxide-Based Nanocomposite Platforms for Electrochemical Biosensing Applications

Graphene and its derivatives such as graphene oxide (GO) and reduced GO (rGO) offer excellent electrical, mechanical and electrochemical properties. Further, due to the presence of high surface area, and a rich oxygen and defect framework, they are able to form nanocomposites with metal/semiconductor nanoparticles, metal oxides, quantum dots and polymers. Such nanocomposites are becoming increasingly useful as electrochemical biosensing platforms. In this review, we present a brief introduction on the aforementioned graphene derivatives, and discuss their synthetic strategies and structure–property relationships important for biosensing. We then highlight different nanocomposite platforms that have been developed for electrochemical biosensing, introducing enzymatic biosensors, followed by non-enzymatic biosensors and immunosensors. Additionally, we briefly discuss their role in the emerging field of biomedical cell capture. Finally, a brief outlook on these topics is presented.
RNA-seq data in pain research-an illustrated guide.

Cell type–specific RNA-seq studies have become increasingly common, whether they examine an entire population in bulk, or study its heterogeneity using single-cell analysis. Fortunately, bioinformaticians have worked to provide easy access to these data as well as developing re-analysis and meta-analysis tools for nonexpert users. Today, therefore, everyone can benefit from a wealth of independently replicated transcriptional information to enrich existing literature and quickly generate new hypotheses. Using some of these new resources, it takes just a fewminutes to see that, in contrast to previous suggestions, the angiotensin type II receptor (AGTR2) is absent from human dorsal root ganglia samples (https://www.utdallas.edu/bbs/painneurosciencelab/); another few minutes to find evidence that advillin (Avil), a gene which was believed tobe sensory neuron-specific, is also transcribed inmouse sympathetic neurons (mousebrain.org); and an hour of browsing various data sets, to discover that RNA-seq results currently do not support the hypothesis that Bdnf is expressed in microglia. Of course, RNA-seq data need to be considered in the context of their technical shortcomings. They are influenced by sequencing depth in a nonlinear way: typical guidelines for obtaining replicable results suggest removing the bottom third of all transcripts by expression level. Biaseswill be introduced by sortingmethods (eg, cellular stress as a result of dissociation) and choices in library preparation (eg, poly-A amplification misses many noncoding RNAs). Single-cell sequencing data suffer from a reverse transcription bottleneck where only a small fraction of all transcripts in a particular cell tend to be amplified. For instance, in a given cell, only 20 of 100 actin molecules might seem to be expressed, while lowly expressed genes may appear completely absent; however, all genes are usually visible when single-cell data are summed up to simulate a bulk profile. Unless cells are molecularly targeted, single-cell analysis also requires an additional cell type inference step, usually through clustering, that may be inaccurate. Finally, both bulk and single-cell RNA-seq experiments are very susceptible to batch effects and need to be carefully designed to avoid them. Beyond technical issues, it is best practice to validate RNA-seq with other methodologies, such as in situ hybridization and protein analyses. A good example of the latter are recent data on Agtr2 using a reporter mouse and Avil using a knockout validated antibody. Bearing this information in mind, the accompanying picture is designed as a cheat sheet–helping you understand the basics of RNA-seq and how to access and interpret the data. Navigating these resources will take some practice, but once you have mastered the art of browsing, RNA-seq data can be a great source of information and even joy–like sudden access to a secret library full of riveting books.
ASTROS Enhancements. Volume 2. ASTRO Programmer's Manual

Abstract : ASTROS (Automated STRuctural Optimization System) is a computer program for the multidisciplinary design and analysis of aerospace structures. ASTROS combines mathematical optimization algorithms with traditional structural analysis disciplines such as static forces, normal modes, static aeroelasticity, and dynamic aeroelasticity (flutter), all in a finite element context, to perform automated preliminary design of an aircraft structure. This report is a complete user's manual that documents the many features of ASTROS through version 10 of the software package. It also provides information on system architecture and other topics of interest. This report is Volume 2 of a set; Volume 1 (WL-TR-93-3025) is the user's manual.
RiboTag: Ribosomal Tagging Strategy to Analyze Cell‐Type‐Specific mRNA Expression In Vivo

Ribosome tagging has become a very useful in vivo approach for analyzing gene expression and mRNA translation in specific cell types that are difficult and time consuming to isolate by conventional methods. The approach is based on selectively expressing a hemagglutinin A (HA)–tagged ribosomal protein in a target cell type and then using antibodies against HA to purify the polysomes and associated mRNAs from the target cell. The original approach makes use of a mouse line (RiboTag) harboring a modified allele of Rpl22 (Rpl22‐HA) that is induced by the action of Cre recombinase. The Rpl22‐HA gene can also be introduced into the animal by stereotaxic injection of an AAV‐DIO‐Rpl22‐HA that is then activated in Cre‐expressing cells. Both methods for tagging ribosomes facilitate the immunoprecipitation of ribosome‐bound mRNAs and their analysis by qRT‐PCR or RNA‐Seq. This protocol will discuss the technical procedures and describe important considerations relevant to the analysis of the data. © 2019 by John Wiley & Sons, Inc.