cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12851900.v1
title: Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

description: Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in <i>Arabidopsis thaliana</i>, which exhibited many anciently conserved similarities with humans but also positions that appear to be ‘hot spots’ for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
DOI: 10.6084/m9.figshare.12851900
title: Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

description: Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in <i>Arabidopsis thaliana</i>, which exhibited many anciently conserved similarities with humans but also positions that appear to be ‘hot spots’ for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
DOI: 10.1285/i9788883051616p67
title: Orientamento in bilico tra formazione e lavoro

description: La funzione orientativa si connota per comportamenti di aiuto e collaborazione con l'obiettivo di esplicitare l'implicito delle opinioni e dei valori che orientano la personale predisposizione verso una determinata scelta. Oltre ai compiti di natura informativa della professionalità orientativa, dunque, ad essa si richiede di saper promuovere, attraverso un atto dialogico costruttivo di razionalità emergenti, specifiche abilità di autoriflessione (esplicitazione dell'implicito) e riflessione (scelta critica) sul portato culturale delle proprie esperienze e delle credenze maturate nel corso della vita, guardando al contempo alla progettazione esistenziale che si annuncia nella stessa richiesta consulenziale. L'orientamento segue il cambio dei paradigmi tanto scientifici che sociali e, di fatto, nella tensione tra obiettivi formativi e occupazionali, esso ha attraversato diverse fasi e rappresentazioni. Si tratta di trovare il modo di gestire livelli estremamente elevati di complessità rispetto ai quali è assolutamente indispensabile lavorare con soggettività proattive che siano aiutate a conoscere le proprie capacità, interessi, valori, saper identificare i punti di forza e le aree critiche, maturare una disponibilità al cambiamento per gestire l'incertezza. L'università e le competenze in esse insegnate delineano, oggi la migliore risposta alla richiesta di saperi la cui funzione sia anche orientativa.
DOI: 10.1285/i9788883051616p79
title: La formazione del personale docente: prospettive di sviluppo

description: La Legge 107/15 stabilisce che 'la formazione in servizio dei docenti di ruolo è obbligatoria, permanente e strutturale'. Ogni scuola individua le attività di formazione per i docenti di ruolo sulla base del 'Piano nazionale di formazione', che presenta il corpo docente come la risorsa chiave per il miglioramento della qualità dei sistemi educativi in Europa. Il punto di partenza riguarda le competenze culturali, disciplinari, didattiche e metodologiche in relazione ai traguardi di competenza e agli obiettivi di apprendimento previsti dagli ordinamenti scolastici; il possesso delle competenze relazionali e organizzative; la partecipazione responsabile all'organizzazione scolastica, al lavoro collaborativo in rete; la cura della propria formazione in forma di ricerca didattica, documentazione, riflessione sulle pratiche, di diffusione di esperienze di eccellenza. La rilevazione dei bisogni formativi è stata effettuata utilizzando format condivisi a livello regionale che hanno riguardato sia i singoli docenti, che le istituzioni scolastiche e gli ambiti territoriali. Fondamentale è stato il ruolo del tutor, sia nell'affiancamento ai formatori durante le attività di formazione, sia nel sostegno ai docenti formati nelle attività di ricerca.
DOI: 10.6084/m9.figshare.12851582
title: Geneseek_GOAT53KV1_20191219_DNAReportSM0.zip

description: 52K SNP chip-seq
DOI: 10.6084/m9.figshare.12851582.v1
title: Geneseek_GOAT53KV1_20191219_DNAReportSM0.zip

description: 52K SNP chip-seq
DOI: 10.1285/i9788883051616p89
title: Il modello DidaSco per lo sviluppo professionale dell'insegnante in servizio

description: Lo sviluppo professionale continuo è la prospettiva entro cui i responsabili politici promuovono oggi la qualità dell'insegnamento. Lo sviluppo dell'identità professionale degli insegnanti richiede autoconsapevolezza, riflessione su/in azione, dispositivi per il miglioramento di diversi tipi di abilità professionali (abilità disciplinari; abilità pedagogiche e trasversali; competenze trasversali; capacità organizzative e capacità di gestione ecc.). Negli ultimi anni il Piano nazionale italiano per la formazione degli insegnanti (PNF) ha dovuto occuparsi del processo continuo di formazione professionale, fornendo un modello di governance univoco e standard di qualità. In questo contributo si descrivono il modello pedagogico, le metodologie di organizzazione e i dispositivi specifici del Progetto DidaSco, un programma di formazione per insegnanti di Sviluppo professionale continuo, sviluppato presso l'Università di Bari. Il Progetto DidaSco si basa su un approccio collaborativo che nasce dalla partnership tra ricercatori e insegnanti ed è realizzato sulla base del PNF; la struttura di ciascun corso riunisce conoscenze teoriche, documentazione e ricerca d'azione; il dispositivo 'prototipo' è testato all'interno delle pratiche di insegnamento a scuola. Come esempio di programma di formazione 'multi-livello', il modello del progetto DidaSco potrebbe essere oggetto specifico di studi per la formazione permanente.
DOI: 10.6084/m9.figshare.12851444.v1
title: Expt1116_Validation

description: Dataset for Training Cohort (Experiment 1116). New Cohort was enrolled to validate machine learning regression model trained on Experiment 1068. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851444
title: Expt1116_Validation

description: Dataset for Training Cohort (Experiment 1116). New Cohort was enrolled to validate machine learning regression model trained on Experiment 1068. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851909.v1
title: Accurate characterization of <i>Escherichia coli</i> tRNA modifications with a simple method of deep-sequencing library preparation

description: In conventional RNA high-throughput sequencing, modified bases prevent a large fraction of tRNA transcripts to be converted into cDNA libraries. Recent proposals aiming at resolving this issue take advantage of the interference of base modifications with RT enzymes to detect and identify them by establishing signals from aborted cDNA transcripts. Because some modifications, such as methyl groups, do almost not allow RT bypassing, demethylation and highly processive RT enzymes have been used to overcome these obstacles. Working with <i>Escherichia coli</i> as a model system, we show that with a conventional (albeit still engineered) RT enzyme and key optimizations in library preparation, all RT-impairing modifications can be highlighted along the entire tRNA length without demethylation procedure. This is achieved by combining deep-sequencing samples, which allows to establish aborted transcription signal of higher accuracy and reproducibility, with the potential for differentiating tiny differences in the state of modification of all cellular tRNAs. In addition, our protocol provides estimates of the relative tRNA abundance.
DOI: 10.6084/m9.figshare.12851915
title: Profiling of cis- and trans-acting factors supporting noncanonical splice site activation

description: Recently, by combining transcriptomics with functional splicing reporter assays we were able to identify GT&gt;GC&gt;TT as the three highestranked dinucleotides of human 5ʹ splice sites (5’ss)(Erkelenz et al., 2018). Here, we have extended our investigations to theproteomic characterization of nuclear proteinsthat bindto canonical and noncanonical 5’ss. Surprisingly, we found that U1 snRNP binding to functional 5’ss sequences prevented components of the DNA damage response (DDR) from binding to the RNA, suggesting a close link between spliceosome arrangement and genome stability. We demonstrate that all tested noncanonical 5’ss sequences are bona-fide targets of the U2-type spliceosome and are bound by U1 snRNP, including U1-C, in the presence of splicing enhancers. The quantity of precipitated U1-C protein was similar for all noncanonical 5’ss dinucleotides, so that the highly different 5’ss usage was likely due to a later step after early U1 snRNP binding. In addition, we show that an internal GT at positions +5/+6 can be advantageous for splicing at position +1 of noncanonical splice sites. Likewise, and in agreement with previous observations, splicing inactive U1 snRNP binding sites could serve as splicing enhancers, which may also explain the higher abundance of U1 snRNPs compared to other U snRNPs.Finally, we observe thatan arginine-serine (RS)-rich domain recruitment to stem loop I of the U1 snRNA is functionally sufficient to promoteexon-definition and upstream 3’ss activation.
DOI: 10.6084/m9.figshare.12851915.v1
title: Profiling of cis- and trans-acting factors supporting noncanonical splice site activation

description: Recently, by combining transcriptomics with functional splicing reporter assays we were able to identify GT&gt;GC&gt;TT as the three highestranked dinucleotides of human 5ʹ splice sites (5’ss)(Erkelenz et al., 2018). Here, we have extended our investigations to theproteomic characterization of nuclear proteinsthat bindto canonical and noncanonical 5’ss. Surprisingly, we found that U1 snRNP binding to functional 5’ss sequences prevented components of the DNA damage response (DDR) from binding to the RNA, suggesting a close link between spliceosome arrangement and genome stability. We demonstrate that all tested noncanonical 5’ss sequences are bona-fide targets of the U2-type spliceosome and are bound by U1 snRNP, including U1-C, in the presence of splicing enhancers. The quantity of precipitated U1-C protein was similar for all noncanonical 5’ss dinucleotides, so that the highly different 5’ss usage was likely due to a later step after early U1 snRNP binding. In addition, we show that an internal GT at positions +5/+6 can be advantageous for splicing at position +1 of noncanonical splice sites. Likewise, and in agreement with previous observations, splicing inactive U1 snRNP binding sites could serve as splicing enhancers, which may also explain the higher abundance of U1 snRNPs compared to other U snRNPs.Finally, we observe thatan arginine-serine (RS)-rich domain recruitment to stem loop I of the U1 snRNA is functionally sufficient to promoteexon-definition and upstream 3’ss activation.
DOI: 10.1285/i9788883051616p99
title: Formare a scuola. Per un'educazione sociolinguistica democratica

description: La formazione alla didattica nella preparazione del docente passa, in primo luogo, attraverso la conoscenza degli assunti di un'educazione linguistica democratica, attraverso la capacità di utilizzare, in modo adeguato, i mezzi e le modalità che favoriscono e garantiscono l'efficacia dell'insegnamento per tutti. La costruzione di una cittadinanza attiva può avvenire solo in una scuola che offra e garantisca a tutti il diritto allo studio. La storia linguistica e scolastica italiana ha portato ad un accumulo di stereotipi e di svantaggi verso una popolazione di bambini, di adolescenti, di giovani che hanno continuato a vivere nelle periferie, spesso isolate, della cultura, dell'economia, dello sviluppo e, soprattutto, fuori dalla scuola e fuori dalla democrazia della conoscenza e degli usi della lingua italiana.
DOI: 10.1285/i9788883051616p105
title: Gli Autori
DOI: 10.1285/i9788883051616p109
title: Colophon
DOI: 10.23708/s0q2qx
title: Food and beverage consumption and routines of adolescents and adults in Ghana and Kenya

description: Food intake was assessed using qualitative 24hr recall (food type information only, not quantity consumed). In 2017, interviewers noted all food and drink consumed by participants inside/outside the home in the previous 24hr period, also recording how long a food event lasts (time categories), time of day of the food event (exact time in minutes), who participants eat with and where. The 24hr dietary recall was structured around a pre-populated 24hr recall tool that we developed on a pre-programmed tablet including &gt;200 foods. Quota sampling was used to recruit participants taking the following into account: age, sex, socio-economic status, employment/education status and Body Mass Index. Sample here is for n=259 adolescents and adult (male/female) participants aged &gt;=13 years in Accra, Ghana (n=101) and Nairobi, Kenya (n=158). Data were anonymized and can be transmitted upon a data sharing agreement and regulatory compliance: refer to "Terms of Use" statement.
DOI: 10.6084/m9.figshare.12851948
title: Expt1375_Traing_Validation_NewArrayPlatform

description: Dataset for Training and Validation Cohorts (same as in Experiments 1068 and 1116) using newly designed peptide microarray format. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851948.v1
title: Expt1375_Traing_Validation_NewArrayPlatform

description: Dataset for Training and Validation Cohorts (same as in Experiments 1068 and 1116) using newly designed peptide microarray format. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851369
title: Untitled ItemExpt1102_Technical_Confirmation

description: Dataset for Technical Confirmation Cohort (Experiment 1102). A subset of samples were re-assayed from Experiment 1068. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851369.v2
title: Untitled ItemExpt1102_Technical_Confirmation

description: Dataset for Technical Confirmation Cohort (Experiment 1102). A subset of samples were re-assayed from Experiment 1068. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.6084/m9.figshare.12851369.v1
title: Untitled Item

description: Dataset for Technical Confirmation Cohort (Experiment 1102). A subset of samples were re-assayed from Experiment 1068. Dataset consists of meta data and raw foreground intensity data. Meta data uses row name ‘scan id’ as unique identifier that can be matched with other data files. The foreground intensity values are formatted with rows as peptide probes and columns as donors. Each value is in range of [0,65535]. The first column has row names, which is probe name, underscore, peptide sequence, where probe name is created based on the “X” and “Y” physical locations of where the probe is found on the array. The first row has column name ‘scan id’, which can be matched to the META rownames.
DOI: 10.15161/oar.it/30641
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.6084/m9.figshare.12852735
title: Using Multisensory Haptic Integration to Improve Monitoring in the Intensive Care Unit

description: Alarm fatigue and medical alarm mismanagement reduces the quality of patient care and creates stressful work environments for clinicians. Here, the feasibility of a novel “pre-alarm” system that utilizes multisensory integration of auditory and haptic stimuli is examined as a possible solution. Three vital signs (heart rate, blood pressure, and blood oxygenation) were represented by three musically distinct sounds that were combined into soundscapes and progressed through five pre-alarm zones (very low to very high). Three haptic conditions were tested with the auditory stimulus to determine the best combination of auditory and haptic stimulation. Qualitative data was collected through surveys and the NASA TLX index. Alterations in frequency and timbre were most effective at transmitting information regarding changing vital sign zones with comparatively higher accuracy and quicker reaction time (RT), <i>p</i> p p The current study demonstrates that multisensory signals do not diminish the perception of transmitted information and suggest efficient training benefits over unimodal signals. Multisensory training may be beneficial over time compared to unisensory training due to a stronger consolidation effect. The potential integration of haptic input with existing auditory alarm systems and training is supported.