Immune Literacy: Reading, Writing, and Editing Adaptive Immunity.
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ABSTRACT:
SUBMITTER: Csepregi L
PROVIDER: S-EPMC7462589 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Scientific literacy, marked by the ability and willingness to engage with scientific information, is supported through a new genre of citizen science-course-based research in association with undergraduate laboratories. A three-phased progressive learning module was developed to enhance student engagement in such contexts while supporting three learning outcomes: I) present an argument based on evidence, II) analyze science and scientists within a social context, and III) experience, reflect upon, and communicate the nature of scientific discovery. Phase I entails guided reading and reflection of citizen science-themed texts. In Phase II, students write, peer-review, and edit position and counterpoint papers inspired by the following prompt, "Nonscientists should do scientific research." Phase III involves two creative assignments intended to communicate the true nature of science. Students work collaboratively to develop public service announcement-like poster campaigns to debunk a common misconception about the nature of science or scientists. Individually, they create a work of art to communicate a specific message about the raw experience of performing scientific research. Suggestions for implementation and modifications are provided. Strengths of the module include the development of transferable skills, temporal distribution of grading demands, minimal in-class time needed for implementation, and the inclusion of artistic projects to support affective learning domains. This citizen science-themed learning module is an excellent complement to laboratory coursework, as it serves to surprise, challenge, and inspire students while promoting disciplinary values.
| S-EPMC4798826 | biostudies-other
Project description:During the last years, digital writing devices are increasingly replacing handwriting with pencil and paper. As reading and writing skills are central for education, it is important to know, which writing tool is optimal for initial literacy education. The present training study was therefore set up to test the influence of the writing tool on the acquisition of literacy skills at the letter and word level with various tests in a large sample of kindergarten children (n = 147). Using closely matched letter learning games, children were trained with 16 letters by handwriting with a pencil on a sheet of paper, by writing with a stylus on a tablet computer, or by typing letters using a virtual keyboard on a tablet across 7 weeks. Training using a stylus on a touchscreen is an interesting comparison condition for traditional handwriting, because the slippery surface of a touchscreen has lower friction than paper and thus increases difficulty of motor control. Before training, immediately after training and four to five weeks after training, we assessed reading and writing performance using standardized tests. We also assessed visuo-spatial skills before and after training, in order to test, whether the different training regimens affected cognitive domains other than written language. Children of the pencil group showed superior performance in letter recognition and improved visuo-spatial skills compared with keyboard training. The performance of the stylus group did not differ significantly neither from the keyboard nor from the pencil group. Keyboard training, however, resulted in superior performance in word writing and reading compared with handwriting training with a stylus on the tablet, but not compared with the pencil group. Our results suggest that handwriting with pencil fosters acquisition of letter knowledge and improves visuo-spatial skills compared with keyboarding. At least given the current technological state, writing with a stylus on a touchscreen seems to be the least favorable writing tool, possibly because of increased demands on motor control. Future training studies covering a more extended observation period over years are needed to allow conclusions about long-term effects of writing tools on literacy acquisition as well as on general cognitive development.
| S-EPMC6987467 | biostudies-literature
Project description:Reading-to-write is an essential skill in academic writing, and reading-writing tasks have been widely adopted in standardized English tests. Much more recent literature on integrated reading-writing tasks has focused on writers' use of source texts or the validity of integrated writing assessment, while little is known about whether the nature of the types of reading texts has any bearing on integrated reading-writing tasks. This study examines whether the types of reading texts (i.e., similar views or opposing views on a debatable issue) have any influence on second language (L2) students' argumentative writing in terms of the use of argument elements and its overall quality. Fifty-four Chinese second-year university students majoring in English language teaching were asked to write an argumentative essay after reading texts with either similar views or opposing views. Results show that students reading texts with opposing viewpoints presented more data and higher overall quality of argumentative essays than students reading texts with similar viewpoints, although the latter group presented more counterargument data. Pedagogical implications on teaching argumentative writing are discussed.
| S-EPMC8017206 | biostudies-literature
Project description:The chromatin-binding E3 ubiquitin ligase Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) maintains DNA methylation patterning in cancer cells through multivalent histone and DNA recognition. The tandem Tudor domain (TTD) of UHRF1 is well-characterized as a reader of lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and, more recently, lysine 126 di- and tri- methylation on DNA ligase 1 (LIG1K126me2/me3). However, the functional significance and selectivity of these interactions remains unclear. In this study, we used protein domain microarrays to search for additional readers of LIG1K126me2, the preferred methyl state bound by the UHRF1 TTD. We show that the UHRF1 TTD binds LIG1K126me2 with high affinity and selectivity compared to other known methyllysine readers. Notably, and unlike H3K9me2/me3, the UHRF1 plant homeodomain (PHD) and its N-terminal linker (L2) do not contribute to multivalent LIG1K126me2 recognition along with the TTD. To test the functional significance of this interaction, we designed a LIG1K126me2 cell-penetrating peptide (CPP). Consistent with LIG1 knockdown in somatic cells, uptake of the CPP had no effect on the DNA methylation maintenance function of UHRF1. Further, we did not detect changes in bulk DNA methylation after chemical or genetic disruption of lysine methyltransferase activity. Collectively, these studies identify UHRF1 as a selective reader of LIG1K126me2 in vitro, implicate the UHRF1 TTD as a dispensable domain for DNA methylation maintenance, and call into question existing models of methyllysine-dependent DNA methylation maintenance in somatic cancer cells.
2020-04-05 | GSE148086 | GEO
Project description:Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands the thermodynamic analysis of stochastic chains made up of material subunits to abstract strings of symbols. We introduce a non-Markovian treatment of operational rules over the symbols of the chain that parallels the physical interactions responsible for memory effects in material chains. Our theory underlies any communication system, ranging from human languages and computer science to gene evolution.
| S-EPMC7512888 | biostudies-literature
Project description:PurposeTo investigate the effect of reading or writing on a smartphone in terms of intraocular pressure (IOP) changes.DesignProspective, comparative case series.ParticipantsThirty-nine (39) healthy young (age < 40) volunteers.MethodsThe participants were requested to conduct standardized work (i.e., read a sample text on single mobile device and subsequently type it on the same device) under daylight [300 lux] and low-light [100 lux] conditions independently on consecutive days. On each day, three sets of IOP measurements (total: 7) using a rebound tonometer (iCare PRO; Tiolat, Helsinki, Finland) were performed: (1) pre-work (baseline) [2 measurements], (2) during smartphone work [5, 15, and 25 minutes], and (3) post-work [5 and 15 minutes].Main outcome measuresChanges in IOP at different check-out points.ResultsUnder the daylight condition, the mean baseline IOP was 13.7 ± 1.8 mmHg, and the mean IOP increased after 5 minutes of work (14.1 ± 1.8 mmHg; +2.0 ± 1.9%; P < 0.001). When the smartphone work lasted for 15 minutes, the IOP showed a further significant increase (15.5 ± 1.7 mmHg; +12.9 ± 4.4%; P < 0.001), which persisted over the course of the 25 minutes of smartphone work (15.3 ± 1.8 mmHg; +11.1 ± 3.9%; P < 0.001); then, after stopping work for 5 minutes, the IOP was restored (13.9 ± 1.7 mmHg; +0.9 ± 2.1%; P = 0.220). Under the low-light condition, the mean IOP was significantly increased immediately after 5 minutes of smartphone work (from 13.9 ± 1.9 to 15.6 ± 1.8 mmHg; +12.1 ± 4.8%; P < 0.001); this IOP increase continued: 17.3 ± 1.9 [+24.7 ± 10.3%] at 15 minutes' work, and 17.0 ± 1.7 mmHg [+23.1 ± 9.5%] at 25 minutes' work (P < 0.001 at both check-out points). Five minutes after stopping the smartphone work, interestingly, the IOP significantly dropped, to a level even lower than that of the pre-work (12.8 ± 1.9 mmHg; -8.1 ± 3.0%; P < 0.001), and at post-work 15 minutes, the IOP returned to the baseline (13.9 ± 1.8 mmHg; -0.3 ± 2.6%; P = 0.360).ConclusionsIn healthy young subjects, reading or writing on smartphone significantly increased IOP, and the changes of IOP were faster and greater under the low-light condition. Smartphone users who are concerned about IOP fluctuation are advised to (1) take a break if they read or write on smartphone for more than 5 minutes, and (2) avoid using smartphones wherever possible in dark places.
| S-EPMC6201904 | biostudies-literature
Project description:Background: Maternal and zygotic mRNAs play critical roles in maternal-to-zygotic transition (MZT) stage and N6-methyladenosine (m6A) has been proven as an important RNA metabolism regulation system. However, the dynamic profiles of m6A modification during mammalian MZT and its potential functions remain largely unknown. Results: Here we utilized m6A-seq, low-input RNA-seq, LiRibo-seq and low-input proteomic analysis to examine the mRNA regulation dynamics during mouse MZT. We found that m6A could be inherited from maternal origin or de novo added after fertilization. Interestingly, we observed the de novo m6A modification on mRNA during zygotic genome activation (ZGA), especially at major ZGA. Further analysis showed that m6A modification on maternal mRNAs not only correlates with mRNA degradation after fertilization, but also maintains the stability of a small group of mRNAs thereby promoting their translation after fertilization. Using CRISPR-Cas13d mediated RNA editing, we systemically evaluated the functions of ten m6A regulators and identified Ythdc1 and Ythdf2 as key m6A readers for mouse preimplantation development. By combining low-input RNA-seq, RNA immunoprecipitation (RIP) and qRT-PCR, we uncovered and verified that Ythdc1 can associate with a small group of m6A-tagged mRNAs and participate in their mRNA stability regulation. Conclusions: Our integrated multi-omic analysis links m6A modification to the diverse fates of maternal and zygotic mRNAs and establishes a key role of m6A mediated RNA metabolism in mammalian MZT.
2023-03-28 | GSE228201 | GEO
Project description:According to the Home Literacy Model (Sénéchal and LeFevre, 2002, 2014), young children can be exposed to two distinct types of literacy activities at home. First, meaning-related literacy activities are those where print is present but is not the focus of the parent-child interaction, for example, when parents read storybooks to their children. In contrast, code-related literacy activities focus on the print, for example, activities such as when parents teach their children the names and sounds of letters or to read words. The present study was conducted to expand the Home Literacy Model by examining its relation with children's engagement in literacy activities at home and at school as Finnish children transitioned from kindergarten to Grades 1 and 2. Two facets of children's engagement were examined, namely, children's independent reading at home and their interest in literacy activities. Children (N = 378) were tested and interviewed at the ends of kindergarten, Grade 1, and Grade 2. Mothers completed questionnaires on their home literacy activities at each test time, and they reported the frequency with which their children read independently twice when children were in grade school. Tested was a longitudinal model of the hypothesized relations among maternal home literacy activities (shared reading and teaching of reading), children's reading skills, independent reading, and their interest in literacy activities/tasks as children progressed from kindergarten to Grade 2. Stringent path analyses that included all auto-regressors were conducted. Findings extended previous research in four ways. First, the frequency of shared reading and teaching of reading at home predicted the frequency of children's independent reading 1 year later. Second, children with stronger early literacy skills in kindergarten read independently more frequently once they were in Grade 1. Third, parents adapted, from kindergarten to Grade 1, their teaching behaviors to their children's progress in reading, whereas shared reading decreased over time. Fourth, children's own reports of interest in literacy activities were mostly not linked to other variables. Taken together, these results add another layer to the Home Literacy Model.
| S-EPMC7362993 | biostudies-literature
Project description:It has been well documented that morphemic structure (roots and affixes) have an impact in reading, but effects seem to depend on the reading experience of readers and lexical characteristics of the stimuli. Specifically, it has been reported that morphemes constitute reading units for developing readers and children with dyslexia when they encounter a new word. In addition, recent studies have stated that the effect of morphology is also present in spelling, as morphological information facilitates spelling accuracy and influences handwriting times. The goal of this study was to investigate the role of morphology in reading and spelling fluency in Spanish children with dyslexia. For that purpose, a group of 24 children with dyslexia was compared with an age-matched group of 24 children without reading disabilities in performing a word naming task and a spelling-to-dictation task of isolated words. Morphological condition (high frequency base, low frequency base, simple) and lexicality (words vs. pseudowords) were manipulated. We considered, for the naming task, reading latencies, reading durations, reading critical segment (three first phonemes) durations and naming accuracy; and, for the spelling task, written latencies, writing durations for the whole word, writing critical segment (three first letters) durations and spelling accuracy. Results showed that Spanish children (with and without dyslexia) benefit from a high frequency base to initiate reading and writing responses, showing that they are familiar with the letter chunks that constitute a morpheme. In addition, base frequency impacts reading critical segment duration only for children with dyslexia, but for both groups in writing. In summary, children with dyslexia benefit from a high frequency base to read and spell unfamiliar stimuli.
| S-EPMC5682102 | biostudies-literature
Project description:BackgroundSince the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.FindingsWe present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.ConclusionSince the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded >1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.
| S-EPMC7931820 | biostudies-literature