ORegAnno 3.0: A community-driven resource for curated regulatory annotation

The Open Regulatory Annotation database (ORegAnno) is a resource for curated regulatory annotation. It contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. ORegAnno differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information. The current release is an update of the database previously featured in the NAR Database Issue, and now contains 1 948 307 records, across 18 species, with a combined coverage of 334 215 080 bp. Complete records, annotation, and other associated data are available for browsing and download at http://www.oreganno.org/

Design, Construction, and Validation of a Critical Pedagogy Attitude Questionnaire in Iran

The application of the principles of critical pedagogy to the field of ELT in the last few decades has contributed to the immergence of critical perspectives toward ELT industry and the role of English in the world. These views known as the critical standpoint acknowledges the existence of non-neutral hidden aspects in ELT and regards English as a tool to promote selected ideologies and to pursue hidden goals. Despite the rapid spread of English in Iran and the relevance of the issues addressed by the critical standpoint in ELT to this specific context, few studies have been conducted to survey Iranian EFL teachers' critical attitude towards ELT industry and the lack of an instrument to measure their critical attitude was highly remarkable. The present study, therefore, aimed at developing a Critical Pedagogy Attitude Questionnaire that could be used to evaluate Iranian ELT community’s critical attitude towards ELT industry. The newly developed questionnaire was validated by administering it among 100 English professors and institute teachers in 21 cities of Iran. This study investigated the internal consistency and the construct validity of the newly-developed instrument which both indicated acceptable results

Design, Construction, and Validation of a Critical Pedagogy Attitude Questionnaire in Iran

The application of the principles of critical pedagogy to the field of ELT in the last few decades has contributed to the immergence of critical perspectives toward ELT industry and the role of English in the world. These views known as the critical standpoint acknowledges the existence of non-neutral hidden aspects in ELT and regards English as a tool to promote selected ideologies and to pursue hidden goals. Despite the rapid spread of English in Iran and the relevance of the issues addressed by the critical standpoint in ELT to this specific context, few studies have been conducted to survey Iranian EFL teachers' critical attitude towards ELT industry and the lack of an instrument to measure their critical attitude was highly remarkable. The present study, therefore, aimed at developing a Critical Pedagogy Attitude Questionnaire that could be used to evaluate Iranian ELT community’s critical attitude towards ELT industry. The newly developed questionnaire was validated by administering it among 100 English professors and institute teachers in 21 cities of Iran. This study investigated the internal consistency and the construct validity of the newly-developed instrument which both indicated acceptable results

Design, Construction, and Validation of a Critical Pedagogy Attitude Questionnaire in Iran

The application of the principles of critical pedagogy to the field of ELT in the last few decades has contributed to the immergence of critical perspectives toward ELT industry and the role of English in the world. These views known as the critical standpoint acknowledges the existence of non-neutral hidden aspects in ELT and regards English as a tool to promote selected ideologies and to pursue hidden goals. Despite the rapid spread of English in Iran and the relevance of the issues addressed by the critical standpoint in ELT to this specific context, few studies have been conducted to survey Iranian EFL teachers' critical attitude towards ELT industry and the lack of an instrument to measure their critical attitude was highly remarkable. The present study, therefore, aimed at developing a Critical Pedagogy Attitude Questionnaire that could be used to evaluate Iranian ELT community’s critical attitude towards ELT industry. The newly developed questionnaire was validated by administering it among 100 English professors and institute teachers in 21 cities of Iran. This study investigated the internal consistency and the construct validity of the newly-developed instrument which both indicated acceptable results

Investigating Two Aspects of Teachers' Contribution to Classroom Discourse across Proficiency Levels: Corrective Feedback and Use of L1

In EFL contexts where the language learners' input, output, and interactions are primarily provided within the four walls of the classroom, the success of learning depends to a large extent on the righteousness and adequacy of classroom discourse to which the teachers' contribution has a decisive role. Drawing upon this assumption, the present study aimed at investigating teachers' contribution to classroom discourse at two levels of proficiency, namely low intermediate and high intermediate levels, based on two of the five categories proposed by Ellis (2008). In so doing, the discourse of eight English classes at the aforementioned levels taught by four male and female teachers (two classes per teacher, one low intermediate and one high intermediate) was audio-recorded, transcribed, and then analyzed quantitatively and qualitatively to determine whether the teachers intentionally and professionally modified their contributions to classroom discourse according to the learners' proficiency levels. The analysis of the results revealed that there was no marked and intentional adjustment on the part of participating teachers to the classroom discourse when interacting with the learners at those levels. At the end, the implications of the present study for classroom teachers, teacher trainers, supervisors, and observers were discussed

Long-range three-dimensional tracking of nanoparticles using interferometric scattering (iSCAT) microscopy

Tracking nanoparticle movement is highly desirable in many scientific areas, and various imaging methods have been employed to achieve this goal. Interferometric scattering (iSCAT) microscopy has been particularly successful in combining very high spatial and temporal resolution for tracking small nanoparticles in all three dimensions. However, previous works have been limited to an axial range of only a few hundred nanometers. Here, we present a robust and efficient strategy for localizing nanoparticles recorded in high-speed iSCAT videos in three dimensions over tens of micrometers. We showcase the performance of our algorithm by tracking gold nanoparticles as small as 10 nm diffusing in water while maintaining 5 {\mu}s temporal resolution and nanometer axial localization precision. Our results hold promise for applications in cell biology and material science, where the three-dimensional motion of nanoparticles in complex media is of interest

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN