bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircAST: Full-Length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs
Authors: Wu Jing , Li Yan , Wang Cheng , Cui Yiqiang , Xu Tianyi , Wang Chang , Wang Xiao , Sha Jiahao , Jiang Bin , Wang Kai , Hu Zhibin , Guo Xuejiang , Song Xiaofeng 
Published: January 2020

Abstract
Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms at the same locus. However, the challenges of reconstruction and quantification of alternatively spliced full-length circRNAs remain unresolved. On the basis of the internal structural characteristics of circRNAs, we developed CircAST, a tool to assemble alternatively spliced circRNA transcripts and estimate their expression by using multiple splice graphs. Simulation studies showed that CircAST correctly assembled the full sequences of circRNAs with a sensitivity of 85.63%–94.32% and a precision of 81.96%–87.55%. By assigning reads to specific isoforms, CircAST quantified the expression of circRNA isoforms with correlation coefficients of 0.85–0.99 between theoretical and estimated values. We evaluated CircAST on an in-house mouse testis RNA-seq dataset with RNase R treatment for enriching circRNAs and identified 380 circRNAs with full-length sequences different from those of their corresponding cognate linear RNAs. RT-PCR and Sanger sequencing analyses validated 32 out of 37 randomly selected isoforms, thus further indicating the good performance of CircAST, especially for isoforms with low abundance. We also applied CircAST to published experimental data and observed substantial diversity in circular transcripts across samples, thus suggesting that circRNA expression is highly regulated. CircAST can be accessed freely at https://github.com/xiaofengsong/CircAST.
Sexual Desire Changes in Transgender Individuals Upon Initiation of Hormone Treatment: Results From the Longitudinal European Network for the Investigation of Gender Incongruence
Authors: Defreyne Justine , Elaut Els , Kreukels Baudewijntje , Fisher Alessandra Daphne , Castellini Giovanni , Staphorsius Annemieke , Den Heijer Martin , Heylens Gunter , T'Sjoen Guy 
Published: January 2020

Abstract

Introduction
Several steps in the transitioning process may affect sexual desire in transgender people. This is often underexposed by those providing gender-affirming care.

Aim
To prospectively assess sexual desire during the first 3 years of hormonal therapy (HT) in transgender people.

Methods
This prospective cohort study was part of the European Network for the Investigation of Gender Incongruence. At baseline, different psychological questionnaires were administered. Sex steroids were measured at each follow-up visit. Data were analyzed cross-sectionally and prospectively.

Main Outcome Measure
Prospective analysis of total, dyadic (with another person), and solitary (with oneself) sexual desire in 766 participants (401 transgender women [TW], 364 transgender men [TM]) was carried out using the Sexual Desire Inventory (SDI) questionnaire during a 3-year follow-up period, starting at the initiation of HT. Other factors associated with prospective changes were assessed.

Results
In TW, total, dyadic, and solitary SDI scores decreased during the first 3 months of HT. However, after 36 months, total and dyadic SDI scores were higher than baseline scores. Solitary scores after 36 months were comparable with baseline scores. In TM, total, dyadic, and solitary SDI scores increased over the first 3 months, remaining stable thereafter. However, total and dyadic SDI scores after 36 months were comparable with baseline scores, whereas solitary scores remained higher than baseline. Factors associated with a prospective increase in SDI scores included having undergone gonadectomy, no longer experiencing menstrual bleeding or higher gender dysphoria levels at baseline (in TM only).

Clinical Implications
This study offers clear data on the time course of sexual desire after starting HT and thereby helps to inform people who want to start HT. Transgender people can be informed that changes in sexual desire after initiating HT are temporary. Over a longer period of time, the current research does not suggest induction of hypoactive sexual disorder in TW or long-term increased sexual desire in TM.

Strength & Limitations
Strengths include the prospective design of this large multicentric study, the well-defined cohort, controlling for HT, sex steroids, and other factors. Limitations include performing a data lock, the absence of an objective measure of sexual desire, and the timing of laboratory measurements.

Conclusion
Gender-affirming HT only induces short-term changes in sexual desire in transgender people. Over a longer period of time, a net increase in dyadic sexual desire in TW receiving feminizing HT and sexual desire scores comparable with baseline in TM receiving virilizing HT, were observed.
A Review and Roadmap of Online Learning Platforms and Tutorials in Digital Archaeology
Authors: Daems Dries 
Published: January 2020

OverviewWith an ever-growing range of computational tools and applications now available for archaeological practice, the potential of digital archaeology is greater than ever before. Yet, archaeological curricula have not always followed suit, and many archaeologists are not up-to-date with the necessary digital skills. To fill this gap, online tutorials and learning platforms are being developed to familiarize archaeologists and students with the potential of digital media for archaeological research practices. Given the essential pedagogical role of these platforms, their quality is deserving of deeper interrogation. Here, I review three major platforms offering tutorials on digital archaeology: the Programming Historian, Project MERCURY-SIMREC, and the Open Digital Archaeology Textbook. These are evaluated and compared based on their goals, design (intuitiveness, ease of use), accessibility (use of jargon, required prerequisite knowledge, software requirements), scope (target audience, range of skills addressed, targeted level of improvement), and efficiency (whether or not they achieve their intended goals). The review concludes with a road map contextualizing the current state of available resources in light of the wider state of digital archaeology, and it considers pathways toward future development.
ON THE OPTIMAL COMBINATION OF ANNUITIES AND TONTINES
Authors: Chen An , Rach Manuel , Sehner Thorsten 
Published: January 2020

AbstractTontines, retirement products constructed in such a way that the longevity risk is shared in a pool of policyholders, have recently gained vast attention from researchers and practitioners. Typically, these products are cheaper than annuities, but do not provide stable payments to policyholders. This raises the question whether, from the policyholders' viewpoint, the advantages of annuities and tontines can be combined to form a retirement plan which is cheaper than an annuity, but provides a less volatile retirement income than a tontine. In this article, we analyze and compare three approaches of combining annuities and tontines in an expected utility framework: the previously introduced “tonuity”, a product very similar to the tonuity which we call “antine” and a portfolio consisting of an annuity and a tontine. We show that the payoffs of a tonuity and an antine can be replicated by a portfolio consisting of an annuity and a tontine. Consequently, policyholders achieve higher expected utility levels when choosing the portfolio over the novel retirement products tonuity and antine. Further, we derive conditions on the premium loadings of annuities and tontines indicating when the optimal portfolio is investing a positive amount in both annuity and tontine, and when the optimal portfolio turns out to be a pure annuity or a pure tontine.
Assessing Characteristics of Unplanned School Closures that Occurred in the United States in Response to Hurricane Harvey in 2017
Authors: Jackson Ashley M. , Ahmed Faruque 
Published: January 2020

ABSTRACTObjective:Hurricane Harvey, which made landfall in Texas on August 24, 2017, caused catastrophic damage that resulted in the closure of many schools and school districts across 4 states. We evaluated the underlying reasons and characteristics of the unplanned school closures to gain insight on how communities may cope with recommended preemptive closures as an intervention for pandemic influenza.Methods:Information was extracted from news articles, school websites, and Twitter and Facebook posts previously collected through daily systematic searches of Google, Google News, and Lexis-Nexis. This information was sorted into predefined categories describing the characteristics that may be associated with unplanned school closures that occur during a natural disaster.Results:Across Texas, Louisiana, Kentucky, and Tennessee, there were 3026 unplanned closures. Sixty-three percent of the closures occurred in Texas. The main reasons for the closures were flooding, power outages, and structural damage. The closed schools in Texas were sometimes used as shelters or as locations for providing food or other resources.Conclusion:School closures associated with Hurricane Harvey were attributed to both the effects of the hurricane and use for resource allocation. These findings can help inform preparedness planning and response for future hurricane seasons and other large-scale emergencies.
Comparing the measurement of different social networks: Peer nominations, online communication, and proximity data
Authors: van Woudenberg T. J. , Bevelander K. E. , Burk W. J. , Smit C. R. , Buijs L. , Buijzen M. 
Published: January 2020

AbstractBackground:Technological progress has enabled researchers to use new unobtrusive measures of relationships between actors in social network analysis. However, research on how these unobtrusive measures of peer connections relate to traditional sociometric nominations in adolescents is scarce. Therefore, the current study compared traditional peer nominated networks with more unobtrusive measures of peer connections: Communication networks that consist of instant messages in an online social platform and proximity networks based on smartphones’ Bluetooth signals that measure peer proximity. The three social network types were compared in their coverage, stability, overlap, and the extent to which the networks exhibit the often observed sex segregation in adolescent social networks.Method:Two samples were derived from theMyMovezproject: a longitudinal sample of 444 adolescents who participated in the first three waves of the first year of the project (Y1; 51% male;Mage= 11.29,SDage= 1.26) and a cross-sectional sample of 774 adolescents that participated in fifth wave in the third year (Y3; 48% male;Mage= 10.76,SDage= 1.23). In the project, all participants received a research smartphone and a wrist-worn accelerometer. On the research smartphone, participants received daily questionnaires such as peer nomination questions (i.e., nominated network). In addition, the smartphone automatically scanned for other smartphones via Bluetooth signal every 15 minutes of the day (i.e., proximity network). In the Y3 sample, the research smartphone also had a social platform in which participants could send messages to each other (i.e., communication network).Results:The results show that nominated networks provided data for the most participants compared to the other two networks, but in these networks, participants had the lowest number of connections with peers. Nominated networks showed to be more stable over time compared to proximity or communication networks. That is, more connections remained the same in nominated networks than in proximity networks over the three waves of Y1. The overlap between the three networks was rather small, indicating that the networks measured different types of connections. Nominated and communication networks were segregated by sex, whereas this was less the case in proximity networks.Conclusion:The communication and proximity networks seem to be promising unobtrusive measures of peer connections and are less of a burden to the participant compared to a nominated network. However, given the structural differences between the networks and the number of connections per wave, the communication and proximity networks should not be used as direct substitutes for sociometric nominations, and researchers should bear in mind what type of connections they wish to assess.
What do beginning teachers make of task-based language teaching? A comparative re-production of East (2014)
Authors: East Martin 
Published: January 2020

AbstractEast (2014) presented a largely qualitative study that uncovered how beginning teachers of languages other than English developed their understandings about task-based language teaching (TBLT) as they took part in a year-long initial teacher education programme in New Zealand. This paper reports a comparative re-production. It complements a recent New Zealand based study, experimental in nature, and its approximate replication (Erlam & Ellis, 2018a, b). The present paper argues that TBLT remains in practice a contested endeavour. Positive experimental research findings are not necessarily finding their way into classrooms, and practitioner-focused studies play a crucial role in adding to our knowledge of what works and what does not work in authentic contexts. The original study and the comparative re-production addressed the same research questions and drew on parallel data sources. The findings of the comparative study, which supported those of the original study, helped in identifying more clearly the issues at stake for the profession and the variables that require attention. It is apparent that the challenges reside in upskilling and supporting practising teachers, who need to become a stronger focus of dedicated and long-term professional development opportunities that will introduce them to the innovation, and sustain them in its implementation.
Disability, Options and Well-Being
Authors: Crawley Thomas 
Published: January 2020

AbstractMany endorse the Bad-Difference View (BDV) of disability which says that disability makes one likely to be worse off even in the absence of discrimination against the disabled. Others defend the Mere-Difference View (MDV) of disability which says that, discounting discrimination, disability does not make one likely to be worse (or better) off. A common motivation for the BDV is theOptions Argumentwhich identifies reduction in valuable options as a harm of disability. Some reject this argument, arguing that disabled people's prospects aren't hindered by having fewer options. In this article, I defend the Options Argument by arguing that, in disability cases, possessing a greater number of valuable options seems to overall improve well-being prospects. As such, the Options Argument appears to be sound and – although it doesn't establish the BDV – it lends plausibility to the BDV by identifying a potentially significant cost of disability.
An “Ingenious Moralist”: Bernard Mandeville as a Precursor of Bentham
Authors: Susato Ryu 
Published: January 2020

AbstractThis article argues that Bernard Mandeville's ideas were more likely to have influenced Jeremy Bentham's writings than previously believed. The conventional interpretation of Mandeville as a forerunner of the Hayekian “theory of spontaneous order” has obscured Mandeville and Bentham's shared emphasis on legal and interventionist solutions for the issues of prostitution and prisoners. This influence is evinced by focusing on some of Mandeville's minor works, which anticipated some of Bentham's arguments. It is unlikely that Bentham directly knew of Mandeville's minor works, but his reformist and interventionist bent was consistent and discernible in the Fable, which Jeremy Bentham read in his youth.
How Close Are Things To Us? On the Relation Between the Incidental and the Valuable
Authors: Hahn Hans Peter 
Published: January 2020

Je mehr man außer sich ist, desto besser beschaut man das ObjektKant ([1772] 1923, 664)
As pointed out in the introduction, incidentalness is a challenge for the study of culture. This applies not only to anthropological and archaeological approaches, but to any discipline that produces descriptions of cultures. As I will explain in more detail, in the framework of more detailed empirical studies dealing with things, the challenge is not only one of ‘method’, but also in terms of ‘research artefacts’, such as the tendency to overestimate meaning. Basically, this is about the question of how cultures should be described and what role everyday things play in cultural change. In this comment, I shall develop the hypothesis that the place of the individual in a society and in his or her material environment as part of everyday culture is adequately described only when incidentalness has a prominent role. Furthermore, I argue that incidentalness is a condition that is unstable, if not transient and ephemeral in terms of temporality. Innovation and cultural change are often related to this specific form of instability in time. Things are eclipsed from incidentalness and, at a certain historical moment, may become central vehicles of meaning in a society, or vice versa: things are shifted to the status of casualness, and the collective awareness shifts to other fields.
Depth Profile Analysis of Thin Oxide Layers on Polycrystalline Fe–Cr
Authors: Zijlstra Gerrit , Šamořil Tomáš , Tesařová Hana , Ocelík Václav , De Hosson Jeff Th. M. 
Published: January 2020

AbstractSurfaces of polycrystalline ferritic Fe–Cr steel with grain sizes of about 13 µm in diameter were investigated with surface sensitive techniques. Thin oxide layers, with a maximum thickness of about 100 nm, were grown by oxidation in air at temperatures up to 450°C and were subsequently characterized using time-of-flight secondary ion mass spectrometry (TOF-SIMS) and atomic force microscopy. Correlative microscopy was applied, which allows for element-specific depth profiles on selected grains with a particular crystal orientation. A strong correlation between the grain orientation and the thickness of the oxide layer was found. The sequence in the oxidation growth rate of ferritic Fe–Cr steel crystal planes is found to be {011} > {111} > {001}, which is unexpectedly opposed to known Fe-based systems. Moreover, for the first time, the Cr/Fe ratio throughout the oxide layer has been determined per grain orientation. A clear order from high to low of {001} > {111} > {011} was detected.
Development and characterization of tetraploid castor plants
Authors: Baghyalakshmi K. , Shaik Mobeen , Mohanrao Manmode Darpan , Shaw Ranjan Kumar , Lavanya C. , Manjunatha T. , Senthilvel S. 
Published: January 2020

AbstractCastor is a prime industrial crop belonging to a monotypic genus and its genetic improvement depends on creating desired variability in the primary gene pool. This study reports the development of tetraploid castor plants through colchicine treatment. Seeds of three castor genotypes were soaked in aqueous solutions of colchicine with variable concentrations, and the LD50value was determined. Of 1010 treated field-raised plants, three were identified as potential polyploids based on increases in a guard cell size and reductions in the number of stomata. The putative polyploid plants were selfed and the progeny were subjected to meiotic analysis. All the progeny were found to be tetraploid. The pairing of chromosomes was abnormal with univalent to octavalent configurations during meiosis-I, but the later parts of meiosis were normal. Seasonal variations in pollen fertility indicated the possible role of temperature-sensitive male sterility in causing the sterility in tetraploid plants. The tetraploid plants were phenotypically comparable with their diploid counterparts, but produced substantially bigger seeds. Thus, these tetraploid plants are valuable resources for basic and applied research in castor.
Drill and broadcast establishment methods influence interseeded cover crop performance in organic corn
Authors: Wallace John M. , Isbell Sarah , Hoover Ron , Barbercheck Mary , Kaye Jason , Curran William S. 
Published: January 2020

AbstractOrganic grain producers are interested in interseeding cover crops into corn (Zea mays L.) in regions that have a narrow growing season window for post-harvest establishment of cover crops. A field experiment was replicated across 2 years on three commercial organic farms in Pennsylvania to compare the effects of drill- and broadcast-interseeding to standard grower practices, which included post-harvest seeding cereal rye (Secale cereale L.) at the more southern location and winter fallow at the more northern locations. Drill- and broadcast-interseeding treatments occurred just after last cultivation and used a cover crop mixture of annual ryegrass [Lolium perenne L. ssp. multiflorum (Lam.) Husnot] + orchardgrass (Dactylis glomerata L.) + forage radish (Raphanus sativus L. ssp. longipinnatus). Higher mean fall cover crop biomass and forage radish abundance (% of total) was observed in drill-interseeding treatments compared with broadcast-interseeding. However, corn grain yield and weed suppression and N retention in late-fall and spring were similar among interseeding treatments, which suggests that broadcast-interseeding at last cultivation has the potential to produce similar production and conservation benefits at lower labor and equipment costs in organic systems. Post-harvest seeding cereal rye resulted in greater spring biomass production and N retention compared with interseeded cover crops at the southern location, whereas variable interseeding establishment success and dominance of winter-killed forage radish produced conditions that increased the likelihood of N loss at more northern locations. Additional research is needed to contrast conservation benefits and management tradeoffs between interseeding and post-harvest establishment methods.
Multiple uses of app instead of using multiple apps – a case for rethinking the digital health technology toolbox
Authors: Torous John , Vaidyam Aditya 
Published: January 2020

Abstract
There are tens of thousands of mental health-related apps available today – representing extreme duplication in this digital age. Instead of a plethora of apps, there is a need for a few that meet the needs of many. Focusing on transparency and free sharing of software, we argue that a collaborative approach towards apps can advance care through creating customisable and future proofed digital tools that allow all stakeholders to engage in their design and use.