bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance
Authors: Connor Ryan , Yarmosh David A. , Maier Wolfgang , Shakya Migun , Martin Ross , Bradford Rebecca , Brister J. Rodney , Chain Patrick SG , Copeland Courtney A. , di Iulio Julia , Hu Bin , Ebert Philip , Gunti Jonathan , Jin Yumi , Katz Kenneth S. , Kochergin Andrey , LaRosa Tré , Li Jiani , Li Po-E , Lo Chien-Chi , Rashid Sujatha , Maiorova Evguenia S. , Xiao Chunlin , Zalunin Vadim , Pruitt Kim D. 
Published: November 2022

AbstractDuring the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.
Environmental micro‐niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield
Authors: Rolli Eleonora , Marasco Ramona , Fusi Marco , Scaglia Barbara , Schubotz Florence , Mapelli Francesca , Ciccazzo Sonia , Brusetti Lorenzo , Trombino Luca , Tambone Fulvia , Adani Fabrizio , Borin Sara , Daffonchio Daniele 
Published: November 2022

AbstractThe pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m2 area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co‐occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high‐throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche‐specific role of the micro‐environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico‐chemical and micro‐climatic variations at the site‐spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.
Primary teachers' knowledge and attitudes about autism, and experience of good practice approaches: implications for policy and practice in Croatia
Authors: Stošić Jasmina , Lisak Šegota Natalija , Preece David 
Published: November 2022

Education in Croatia is based upon principles of inclusion and individualisation. However, the effective inclusion of learners with special educational needs, including those with autism, has been identified as limited. To better understand the situation within primary education in the country, a survey of specialist teachers from mainstream and special primary schools was undertaken (n = 99), to investigate such teachers' knowledge and attitudes regarding autism, and their experience of ‘good autism practice’ methods and approaches. Knowledge was inconsistent, and inaccurate understandings were common. Attitudes regarding the inclusion of learners with autism were ambivalent. Training in ‘good practice’ approaches was extremely limited; however, despite low confidence, the use of these approaches was common. Teachers' education needs in autism were identified, and implications for future teacher education in autism, practice and policy initiatives are discussed.
Teaching, learning and philosophising as metaphysical animals: Introduction
Authors: Jamieson Lesley 
Published: November 2022

Abstract
In recent years, a new scholarly gaze has been cast on four women-Elizabeth Anscombe, Philippa Foot, Mary Midgley, and Iris Murdoch-who have come to be known as the ‘Wartime Quartet’. During the postwar period, when women were still scarce in the discipline, these four flourished as philosophers. New details about their wartime education give us materials to reflect on what enabled them to develop their unique philosophical voices. Their work dispels widespread philosophical dogmas, especially scientistic interpretations of naturalism that exclude value from the fabric of reality. Through their attention to the details of ordinary life, they avoid flattening the complexities of moral learning, especially where this involves navigating intergenerational differences. The articles in this Suite look to the Wartime Quartet's writings and learning conditions to show that, far from being of purely historical interest, they shed fresh light on the aims and challenges of moral education and offer a critical perspective on current pedagogical practices-particularly in the teaching of philosophy.
Patients with low body mass index are more likely to develop shoulder pain after laparoscopy
Authors: Jiang Yuxia , Wu Yijun , Lu Shentao , Que Yuni , Chi Yugang , Liu Qianfen 
Published: November 2022

AbstractIntroductionShoulder pain is one of the most common complications after laparoscopy. Previous studies have found a number of methods to reduce shoulder pain after laparoscopic surgery, but these methods have not been targeted to specific populations. The purpose of this study was to identify people who are more likely to develop shoulder pain.Material and methodsA total of 203 patients underwent laparoscopy for benign gynecological diseases between July 2020 and February 2021. Patients were divided into two groups according to the Chinese overweight standard, body mass index less than 24 kg/m2 group and 24 kg/m2 or more group. The baseline characteristics and intraoperative data between the two groups were compared. The intensity of the shoulder pain was quantified using a visual analog scale (VAS).ResultsThe incidence and the VAS scores of shoulder pain were significantly higher in the less than 24 kg/m2 group (63.64% vs 38.03%, p < 0.001 in incidence; median 5 (interquartile range [IQR] 3–7) vs 3 (IQR 2–5), p < 0.001 in VAS scores), and the chance of shoulder pain within 24 hours after laparoscopy was higher in the less than 24 kg/m2 group (89.29% vs 66.67%, p = 0.013). In univariate and multivariate logistic regression analysis, BMI less than 24 kg/m2 was an independent risk factor of shoulder pain after laparoscopic surgery (p = 0.001, p = 0.031, respectively). Shoulder pain scores were inversely correlated with BMI (r = −0.300, p = 0.001).ConclusionsPatients with low body mass index are more likely to develop shoulder pain after laparoscopy, with earlier onset and higher pain scores.
Adaptability and emotional, behavioural and cognitive aspects of self‐regulated learning: Direct and indirect relations with academic achievement and life satisfaction
Authors: Feraco Tommaso , Casali Nicole , Ganzit Elena , Meneghetti Chiara 
Published: November 2022

AbstractBackgroundAdaptability regulates individuals' cognitive, behavioural and emotional responses to new, unexpected and uncertain situations, but to date no study has analysed whether adaptability contemporarily favours cognitive, behavioural and emotional aspects of learning.AimsThis study aims to address this gap by examining (i) the direct relations between adaptability and achievement emotions, self‐regulated learning strategies and academic self‐efficacy and (ii) the direct and indirect relations between adaptability and academic achievement and life satisfaction through and over the other study‐related factors.SampleA total of 1083 students (415 males, Mage = 13.37, SDage = 1.97, age range = 10–18) in grades 6–12 participated to the study.MethodQuestionnaires were used to measure students' adaptability, positive and negative achievement emotions, self‐regulated learning strategies, academic self‐efficacy and life satisfaction. Schools provided grades obtained by each student at the end of the academic year.ResultsA path analysis based on 1083 students (10–18 years old) confirmed that adaptability directly relates to the three study‐related factors considered and to life satisfaction and indirectly relates to academic achievement and life satisfaction—through the mediation of the other variables.ConclusionsThe results, discussed in accordance with the self‐regulated learning theory, enlarge the nomological framework of adaptability and highlight its importance for emotional, behavioural and cognitive aspects of self‐regulated learning.
Phase II trial of a novel chemotherapy regimen CVEP (cyclophosphamide, vinblastine, etoposide and prednisolone) for acquired immunodeficiency syndrome (AIDS)‐associated lymphomas
Authors: Sengar Manju , Jain Hasmukh , Shet Tanuja , Sridhar Epari , Gota Vikram , Rangarajan Venkatesh , Laskar Siddhartha S. , Alahari Aruna , Thorat Jayashree , Agarwal Archi , Sharma Neha , Gupta Himanshi , Kannan Sadhana , Kumar Shikhar , Nayak Lingaraj , Menon Hari , Gujral Sumeet , Bagal Bhausaheb 
Published: November 2022

SummaryManagement of acquired immunodeficiency syndrome (AIDS)‐related diffuse large B‐cell (DLBCL) and plasmablastic lymphomas (PBL) poses significant challenges. The evidence supports use of dose‐adjusted EPOCH (etoposide, prednisone, vincristine, cyclophosphamide and doxorubicin) with or without rituximab as first‐line therapy. The need for central venous access, growth factors and significant toxicities limits its use in resource‐constrained settings. To address these challenges, we have developed a novel regimen, CVEP (cyclophosphamide, vinblastine, etoposide, and prednisolone) based on the pharmacodynamic principles of dose‐adjusted EPOCH. This single‐centre phase II study evaluated the efficacy and safety of CVEP regimen in patients with de novo systemic AIDS‐related DLBCL and PBL. The primary objective was complete response (CR) rates as assessed by positron emission tomography‐computed tomography. The secondary objectives were incidence of Grade 3/4 toxicities, toxicities requiring hospitalisation, and disease‐free survival. From May 2011 to February 2017, 42 patients were enrolled. At the end of therapy the CR rates were 69% (29/42) in the intention‐to‐treat population and 80.5% (29/36) in evaluable patients. At a median follow‐up of 69 months, the 5‐year disease‐free survival was 65.3%. Out of 217 cycles administered, febrile neutropenia occurred in 19.3% and hospitalisation was required in 18.3% of cycles. There were two treatment‐related deaths. The CVEP regimen is an active and safe regimen for AIDS‐related DLBCL and PBL.
The perceived helpfulness of structural family therapy in caring for Hong Kong Chinese families of an adolescent with intellectual disabilities: A qualitative inquiry
Authors: Lo Julia W. K. , Ma Joyce L. C. 
Published: November 2022

AbstractBackgroundPrevious literature pinpointed the limitations of behavioural treatment in helping families of people with intellectual disabilities to transit lifecycle adjustment and suggested the contributions of systemic intervention made to this population.MethodsThis study aimed to explore the applicability of structural family therapy to helping Hong Kong Chinese families of adolescents with intellectual disabilities from the perspective of family members. Nine members from four families of adolescents with intellectual disabilities were recruited. Family or individual interviews were conducted. A thematic analysis was adopted for data analysis.FindingsThe families experienced two major changes after the therapy, that is, sharing the care responsibilities among family members and using more open communication styles in the family. Structural family therapy was found to be helpful in mediating family problems and promoting the active involvement of adolescents with intellectual disabilities in family interactions. However, the family participants expected clear guidance for the future development of adolescents with intellectual disabilities in a family treatment process.ConclusionsStructural family therapy can be a promising approach to working with Chinese families of adolescents with intellectual disabilities.
Does a tax deduction scheme matter for jobs and investment by multinational and domestic enterprises?
Authors: Konings Jozef , Lecocq Catherine , Merlevede Bruno 
Published: November 2022

AbstractMany countries have reduced corporate income tax rates or introduced tax deductions, exclusions and credits to attract foreign direct investment. This paper analyzes the introduction of the notional interest deduction (NID) in Belgium, which allows companies to deduct from their taxable income an interest that is calculated based on the company's equity. We use an event type study approach to analyze the evolution of employment and investment of foreign affiliates in Belgium. We find that the tax deduction has increased employment and investment in the Belgian affiliates on average by 7.4 and 6.1%, respectively, in the period after the introduction of the NID. The NID, however, also provides a higher after‐tax return on investment to domestic Belgian firms. Using a matching analysis, we find that domestic Belgian firms with low external financial dependence also respond to the NID but somewhat less strongly, domestic firms with high external financial dependence do not show NID‐driven investment nor employment creation.
Mechanism and application of ozone fading: Oxidative decolorisation of disperse dyes and waste‐dyed polyester fabrics
Authors: Lou Jiangfei , Ren Lamei , Yuan Jiugang , Xu Jin , Gu Zhengbiao , Fan Xuerong 
Published: November 2022

AbstractAs the most common synthetic fibre, polyester has consistently been in high demand and usage, but its recycling has always been a problem for the textile industry. The decolorisation of dyed polyester is the key to expanding its recycling use, and there is no rapid, effective and simple decolorisation method. In this study, ozone was used to decolorise dispersed dyes developed for polyester. Ozone was effective in decolorising CI Disperse Orange 30 and CI Disperse Blue 60, and the process was extended to the decolorisation of dyed polyester fabric. Based on single factor analysis, the optimum decolorisation technological conditions were: an ozone feed rate of 130 mg L−1 min−1, treatment time of 2 hours, wet pick‐up of 100% and pH value of 3, with which the decolorisation rate and colour difference values could exceed 45% and 6%, respectively. The changes in dye structure during the process of ozone decolorisation were analysed using scanning electron microscopy, X‐ray diffraction and Fourier Transform–infrared spectroscopy, and the mechanism of ozone decolorisation was also investigated. The results showed that the crystallinity decreased from 41.18% to 36.30% with a strength retention rate of above 80%, and demonstrated that ozone can be used on polyester fabric and dye simultaneously. The aim of entering the fibre was achieved by etching the polyester and decolorisation was achieved by oxidising the chromaticity groups.
Trapped K‐feldspar phenocrysts as a signature of melt migration pathways within active high‐strain zones
Authors: Silva David , Piazolo Sandra , Daczko Nathan R. 
Published: November 2022

AbstractMelt migration through high‐strain zones in the crust fundamentally influences their rheological behaviour and is important for the transfer of fluids to upper crustal regions. The inference of former melt‐present deformation, based on field observations, may be hampered if the high‐strain zone experience a low time‐integrated melt flux or high melt volume expulsion during deformation. In these cases, typical macro‐scale field evidence of former melt presence limits interpretations. In this contribution, we investigate igneous field evidence ranging from obvious to cryptic in the Gough Dam shear zone (central Australia), a 2‐ to 4‐km‐wide high‐strain zone shown to have acted as a significant melt pathway during the Alice Springs Orogeny. Within bands of the high‐strain zone, granitic lenses are easily discernible in the field and are inferred to have formed during melt present deformation. Related coarse K‐feldspar is observed in biotite‐rich (>75 vol%) schist (glimmerite) as either isolated grains, forming trails (sub)parallel to the main foliation, or in aggregates with subordinate quartz. Detailed characterization of the granitic lenses shows that pockets of phenocrysts may be entrained in the shear zone. If melt expulsion and melt‐rock interaction is severe, isolated K‐feldspar grains in glimmerite may form. These grains exhibit (i) partially preserved crystal faces; (ii) a lack of internal grain deformation; (iii) reaction textures preferentially formed along the main crystallographic axes showing dissolution of K‐feldspar and precipitation of dominantly biotite; (iv) low‐strain domains between multiple K‐feldspar grains being inferred to enclose crystallized melt pockets, with some apparently isolated grains showing connectivity in three dimensions; and (v) a weak quartz and K‐feldspar crystallographic preferred orientation. These observations suggest an igneous phenocrystic origin for the isolated K‐feldspar grains hosted in glimmerite, which is consistent with the observed REE concentration patterns with positive Eu anomaly. We propose that the K‐feldspar phenocrysts are early‐formed crystals that were entrained into the glimmerite rocks as reactive melt migrated through the actively deformatting high‐strain zone. Previously entrained K‐feldspar phenocrysts were trapped during the collapse of the melt pathway when melt flux‐related fluid pressure waned while confining pressure and tectonic stress were still significant. The active deformation facilitated expulsion or loss of the melt phase but retainment and trapping of phenocrysts. Hence, the presence of isolated or ‘trains’ of K‐feldspar phenocrysts is a cryptic signature of syndeformational melt transfer. If melt transfer occurs in an open chemical system, phenocrysts will be entrained within the reaction product of melt‐rock interaction. We suggest that these so‐called trapped phenocrysts are a viable indicator of former syntectonic melt passage through rocks.
The molecular diversity of plasticity mechanisms underlying memory: An evolutionary perspective
Authors: Zha Congyao , Sossin Wayne S. 
Published: November 2022

AbstractExperience triggers molecular cascades in organisms (learning) that lead to alterations (memory) to allow the organism to change its behavior based on experience. Understanding the molecular mechanisms underlying memory, particularly in the nervous system of animals, has been an exciting scientific challenge for neuroscience. We review what is known about forms of neuronal plasticity that underlie memory highlighting important issues in the field: (1) the importance of being able to measure how neurons are activated during learning to identify the form of plasticity that underlies memory, (2) the many distinct forms of plasticity important for memories that naturally decay both within and between organisms, and (3) unifying principles underlying the formation and maintenance of long‐term memories. Overall, the diversity of molecular mechanisms underlying memories that naturally decay contrasts with more unified molecular mechanisms implicated in long‐lasting changes. Despite many advances, important questions remain as to which mechanisms of neuronal plasticity underlie memory.image
The associated evolution among the extensive RNA editing, GC‐biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae
Authors: Kang Jong‐Soo , Yu Jigao , Zhang Xian‐Chun , Xiang Qiao‐Ping 
Published: November 2022

AbstractExtensive C‐to‐U editing has been reported from plastid genomes (plastomes) and mitochondrial genomes (mitogenomes) of spikemoss. While “reverse” U‐to‐C editing was recorded in other seed‐free plants such as hornworts, quillworts, and ferns, it was not observed in spikemosses. However, no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses. Here, we report thousands of C‐to‐U editing sites from plastomes and mitogenomes of two species: 1767 and 2394 edits in Selaginella remotifolia, and 4091 and 2786 edits in Selaginella nipponica, respectively. Comparative analyses revealed two different editing frequencies among plastomes, but one similar frequency in mitogenomes. The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity. The high guanine and cytosine (GC) content caused by GC‐biased mutations in organelle genomes might be related to the absence of U‐to‐C editing in Selaginellaceae. Using RNA‐seq and whole‐genome data, we screened the pentatricopeptide repeat (PPR) family and discovered that the number of aspartic acid–tyrosine–tryptophan (DYW) domain‐containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes. Consequently, we hypothesize that associated evolution among RNA editing, GC‐biased mutation in organelle genomes, and the PPR protein family encoded in the nuclear genome, is probably triggered by the aberrant DNA repair system in Selaginellaceae. Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae, which would contribute to understanding the evolution of post‐transcriptional modifications of organelle genomes in land plants.