bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets
Authors: De‐Kayne Rishi , Frei David , Greenway Ryan , Mendes Sofia L. , Retel Cas , Feulner Philine G. D. 
Published: December 2020

AbstractTechnological advances in DNA sequencing over the last decade now permit the production and curation of large genomic data sets in an increasing number of nonmodel species. Additionally, these new data provide the opportunity for combining data sets, resulting in larger studies with a broader taxonomic range. Whilst the development of new sequencing platforms has been beneficial, resulting in a higher throughput of data at a lower per‐base cost, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four‐channel system to a two‐channel system. We caution that when data are combined from these two systems, erroneous guanine base calls that result from the two‐channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artefacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever‐changing sequencing platform technology.
Metalloids in plants: A systematic discussion beyond description
Authors: Parveen Nishat , Berni Roberto , Sudhakaran Sreeja , Bhat Javaid A. , Shinde Suhas , Ramawat Naleeni , Singh Vijay P. , Sahi Shivendra , Deshmukh Rupesh , Chauhan Devendra K. , Tripathi Durgesh Kumar 
Published: December 2020

AbstractMetalloids represent a wide range of elements with intermediate physiochemical properties between metals and non‐metals. Many of the metalloids, like boron, selenium, and silicon are known to be essential or quasi‐essential for plant growth. In contrast, metalloids viz. arsenic and germanium are toxic to plant growth. The toxicity of metalloids largely depends on their concentration within the living cells. Some elements, at low concentration, may be beneficial for plant growth and development; however, when present at high concentration, they often exert negative effects. In this regard, understanding the molecular mechanisms involved in the uptake of metalloids by roots, their subsequent transport to different tissues and inter/intra‐cellular redistribution has great importance. The mechanisms of metalloids' uptake have been well studied in plants. Also, various transporters, as well as membrane channels involved in these processes, have been identified. In this review, we have discussed in detail the aspects concerning the positive/negative effects of different metalloids on plants. We have also provided a thorough account of the uptake, transport, and accumulation, along with the molecular mechanisms underlying the response of plants to these metalloids. Additionally, we have brought up the previous theories and debates about the role and effects of metalloids in plants with insightful discussions based on the current knowledge.
Directly converted astrocytes retain the ageing features of the donor fibroblasts and elucidate the astrocytic contribution to human CNS health and disease
Authors: Gatto Noemi , Dos Santos Souza Cleide , Shaw Allan C. , Bell Simon M. , Myszczynska Monika A. , Powers Samantha , Meyer Kathrin , Castelli Lydia M. , Karyka Evangelia , Mortiboys Heather , Azzouz Mimoun , Hautbergue Guillaume M. , Márkus Nóra M. , Shaw Pamela J. , Ferraiuolo Laura 
Published: December 2020

AbstractAstrocytes are highly specialised cells, responsible for CNS homeostasis and neuronal activity. Lack of human in vitro systems able to recapitulate the functional changes affecting astrocytes during ageing represents a major limitation to studying mechanisms and potential therapies aiming to preserve neuronal health. Here, we show that induced astrocytes from fibroblasts donors in their childhood or adulthood display age‐related transcriptional differences and functionally diverge in a spectrum of age‐associated features, such as altered nuclear compartmentalisation, nucleocytoplasmic shuttling properties, oxidative stress response and DNA damage response. Remarkably, we also show an age‐related differential response of induced neural progenitor cells derived astrocytes (iNPC‐As) in their ability to support neurons in co‐culture upon pro‐inflammatory stimuli. These results show that iNPC‐As are a renewable, readily available resource of human glia that retain the age‐related features of the donor fibroblasts, making them a unique and valuable model to interrogate human astrocyte function over time in human CNS health and disease.
SPATA4 improves aging‐induced metabolic dysfunction through promotion of preadipocyte differentiation and adipose tissue expansion
Authors: Li Zhongchi , Xu Kang , Zhao Sen , Guo Yannan , Chen Huiling , Ni Jianquan , Liu Qingfei , Wang Zhao 
Published: December 2020

AbstractSpermatogenesis‐associated protein 4 (SPATA4) is conserved across multiple species. However, the function of this gene remains largely unknown. In this study, we generated Spata4 transgenic mice to explore tissue‐specific function of SPATA4. Spata4 overexpression mice displayed increased subcutaneous fat tissue compared with wild‐type littermates at an old age, while this difference was not observed in younger mice. Aging‐induced ectopic fat distribution, inflammation, and insulin resistance were also significantly attenuated by SPATA4. In vitro, SPATA4 promoted preadipocyte differentiation through activation of the ERK1/2 and C/EBPβ pathway and increased the expression of adipokines. These data suggest SPATA4 can regulate lipid accumulation in a tissue‐specific manner and improve aging‐induced dysmetabolic syndromes. Clarifying the mechanism of SPATA4 functioning in lipid metabolism might provide novel therapeutic targets for disease interventions.
Evaluation of 3 different treatment modalities for conservative management of attrited, sensitive molar teeth – A preliminary 12‐week report
Authors: Vishanth Subashri , Sherwood I Anand , Gutmann James L , Murugadoss Vaanjay , Prince Ernest 
Published: December 2020

AbstractManagement of symptomatic attrited molar teeth presents various challenges. Aim of the study was to manage and evaluate the outcome of sensitive, attrited molar teeth using three different treatment options, including bioglass‐containing desensitising toothpaste, Gluma desensitiser and coronal a pulpotomy using a calcium silicate‐based product, Biodentine. A total of 61 attrited molar teeth, for which the patients had expressed tooth sensitivity, were included. Depending on the pulp status, treatment groups were allotted using block randomisation. Post‐treatment sensitivity was assessed at 48 h, 4 and 12 weeks using 10‐point visual analog scale (VAS) and Schiff Cold Air Sensitivity Scale (SCASS). Data were analysed using non‐parametric statistical tests. Pulpotomies achieved significantly the least post‐treatment sensitivity scores at all scheduled recalls. This interim 12‐week report on management concludes that a pulpotomy, using Biodentine, was able to achieve significantly higher number of asymptomatic teeth when compared to other treatment choices.
Effect of different irrigation protocols for applications in regenerative endodontics on mechanical properties of root dentin
Authors: Elnaggar Semha E. , El Backly Rania M. , Zaazou Ashraf Mamdouh , Morsy Elshabrawy Sonia , Abdallah Amr Ahmed 
Published: December 2020

AbstractThe objective of this study was to evaluate the effect of different concentrations of NaOCl with and without passive ultrasonic irrigation (PUI) on mechanical properties of human dentin for applications in regenerative endodontics (RE). Sixty single‐rooted teeth were sectioned into 2 halves (n = 120). Dentin bars were produced from one half for flexural strength and the other half was used for microhardness. Specimens were randomly assigned into 10 groups: G1 and G2 (control): distilled water for 30 and 60 min, respectively; G3: 1.5%NaOCl for 30 min; G4:1.5%NaOCl for 60 min; G5: 1.5%NaOCl + PUI for 30 min; G6: 1.5%NaOCl + PUI for 60 min; G7: 5.25%NaOCl for 30 min; G8: 5.25%NaOCl for 60 min; G9: 5.25%NaOCl + PUI for 30 min; G10: 5.25%NaOCl + PUI for 60 min. An increase in NaOCl concentration showed highly significant reduction in mechanical properties. There was no significant difference between 1.5% NaOCl and control group except for specimens treated with PUI for 60 min. NaOCl in concentrations recommended for RE did not have a significant effect on mechanical properties of dentin. However, PUI with increased irrigation time might have an effect even with low NaOCl concentration.
Seasonal variations in the morphology of the seminal vesicles of the African straw‐coloured fruit bat (Eidolon helvum)
Authors: Abiaezute Clifford Nwabugwu , Nwaogu Innocent Chima , Obidike Ikechukwu Reginald , Igwebuike Udensi Maduabuchi 
Published: December 2020

AbstractThe study investigated seasonal changes in the morphology of the seminal vesicles of Eidolon helvum in a typical African tropical environment. Seminal vesicles of forty‐eight bats were examined during the early rainy, late rainy and peak dry seasons, using gross anatomical, histological and ultrastructural techniques. The interlobular connective tissue septa from the external capsule demarcated the glandular parenchyma into numerous lobules of tubulo‐alveolar glands. A simple cuboidal epithelium of mono‐ or bi‐nucleated cuboidal cells lined the glandular mucosa during the rainy season. This was replaced by a bistratified cuboidal epithelium, whose upper layer of cells showed evidence of degeneration, during the dry season. The PAS‐positive secretory products appeared to be numerous during the rainy season, but few and clumped together during the dry season. The mean gross weight, interlobular septal thickness, acini diameter and epithelial height of the glands varied significantly with season. Ultrastructural features of the secretory cells during the rainy season showed well‐developed cytoplasmic organelles, numerous electron lucid secretory vesicles and electron‐dense granules. Secretory epithelial cells of the seminal vesicles are very active during the rainy season, while regeneration of degenerated epithelium in preparation for the next reproductive cycle occurs during the dry season.
The World We (Re)Build: An Ethnography of the Future
Authors: Willow Anna J. 
Published: December 2020

SummaryThis essay directs the theoretical energy of the emerging anthropology of the future genre toward the essential task of generating new anthropological prospects for making positive world contributions. Embracing visioning as a promising ethnographic technique, I develop an ethnography of the future drawn from central Ohio Transition participants’ prefigurative actions and descriptions of desirable futures. I suggest that temporal imaginings have very real effects on the world we ultimately (re)build and outline anthropology’s roles in the future‐making process.
Methyl‐beta cyclodextrin and creatine work synergistically under hypoxic conditions to improve the fertilization ability of boar ejaculated sperm
Authors: Umehara Takashi , Tsujita Natsumi , Goto Masaaki , Tonai Shingo , Nakanishi Tomoya , Yamashita Yasuhisa , Shimada Masayuki 
Published: December 2020

AbstractAlthough successful fertilization is completed by only 150 sperm in the pig oviduct, more than 50,000 sperms are required to achieve a fertilization rate of more than 70% by pig in vitro fertilization (IVF). In this study, to improve the efficiency of pig IVF, the effects of hypoxic conditions and treatment with creatine and methyl‐beta cyclodextrin (MβCD) on the glycolytic pathway were investigated. Under low O2 conditions, zig‐zag motility was strongly induced within 30 min; however, the induction disappeared at 60 min. Although caffeine suppressed zig–zag motility under low O2 conditions, creatine induced and sustained zig–zag motility until 120 min. Additionally, pretreatment with MβCD for 15 min greatly enhanced zig–zag motility via ATP production in sperm incubated with creatine under low O2 conditions. Sperm pretreated with MβCD were used for IVF in medium containing creatine under low O2 conditions. A fertilization rate of approximately 70% was achieved with only 1.0 x 104 sperms/mL, and there were few polyspermic embryos. Therefore, our novel method was beneficial for efficient production of pig embryos in vitro. Moreover, the zig–zag motility may be a novel movement which boar capacitated sperm exhibit in the culture medium.
Clinical and biological features of B‐cell neoplasms with CDK6 translocations: an association with a subgroup of splenic marginal zone lymphomas displaying frequent CD5 expression, prolymphocytic cells, and TP53 abnormalities
Authors: Gailllard Baptiste , Cornillet‐Lefebvre Pascale , Le Quoc‐Hung , Maloum Karim , Pannetier Mélanie , Lecoq‐Lafon Carinne , Grange Béatrice , Jondreville Ludovic , Michaux Lucienne , Nadal Nathalie , Ittel Antoine , Luquet Isabelle , Struski Stéphanie , Lefebvre Christine , Gaillard Jean‐Baptiste , Lafage‐Pochitaloff Marina , Balducci Estelle , Penther Dominique , Barin Carole , Collonge‐Rame Marie Agnès , Jimenez‐Poquet Mélanie , Richebourg Steven , Lemaire Pierre , Defasque Sabine , Radford‐Weiss Isabelle , Bidet Audrey , Susin Santos A. , Nguyen‐Khac Florence , Chapiro Elise ,   the Groupe Francophone de Cytogénétique Hématologique
Published: December 2020

SummaryA translocation involving the cyclin‐dependent kinase 6 (CDK6) gene [t(CDK6)] is a rare but recurrent abnormality in B‐cell neoplasms. To further characterise this aberration, we studied 57 cases; the largest series reported to date. Fluorescence in situ hybridisation analysis confirmed the involvement of CDK6 in all cases, including t(2;7)(p11;q21) immunoglobulin kappa locus (IGK)/CDK6 (n = 51), t(7;14)(q21;q32) CDK6/immunoglobulin heavy locus (IGH) (n = 2) and the previously undescribed t(7;14)(q21;q11) CDK6/T‐cell receptor alpha locus (TRA)/T‐cell receptor delta locus (TRD) (n = 4). In total, 10 patients were diagnosed with chronic lymphocytic leukaemia, monoclonal B‐cell lymphocytosis or small lymphocytic lymphoma, and 47 had small B‐cell lymphoma (SmBL) including 36 cases of marginal zone lymphoma (MZL; 34 splenic MZLs, one nodal MZL and one bronchus‐associated lymphoid tissue lymphoma). In all, 18 of the 26 cytologically reviewed cases of MZL (69%) had an atypical aspect with prolymphocytic cells. Among the 47 patients with MZL/SmBL, CD5 expression was found in 26 (55%) and the tumour protein p53 (TP53) deletion in 22 (47%). The TP53 gene was mutated in 10/30 (33%); the 7q deletion was detected in only one case, and no Notch receptor 2 (NOTCH2) mutations were found. Immunoglobulin heavy‐chain variable‐region (IGHV) locus sequencing revealed that none harboured an IGHV1‐02*04 gene. Overall survival was 82% at 10 years and not influenced by TP53 aberration. Our present findings suggest that most t(CDK6)+ neoplasms correspond to a particular subgroup of indolent marginal zone B‐cell lymphomas with distinctive features.
The effects of a ‘pretend play‐based training’ designed to promote the development of emotion comprehension, emotion regulation, and prosocial behaviour in 5‐ to 6‐year‐old Swiss children
Authors: Richard Sylvie , Baud‐Bovy Gabriel , Clerc‐Georgy Anne , Gentaz Edouard 
Published: December 2020

The objective of this study was to evaluate the effects of a pretend play‐based training designed to promote the development of socio‐emotional competences. 79 children aged 5 to 6 years were evaluated before and after a pretend play‐based training. The experimental group (39 children) received this programme on emotion comprehension, negative emotion regulation, and prosocial behaviour one hour a week for eleven weeks during class hours, while the control group (40 children) received no specific intervention. The programme was implemented by 5 teachers. The results show improvements in the ability to understand emotions in children who benefited from the training. These findings are discussed in the broader context of using this form of play as a privileged pedagogical tool to allow children to develop these competences.
A novel temporal‐predominant neuro‐astroglial tauopathy associated with TMEM106B gene polymorphism in FTLD/ALS‐TDP
Authors: Llibre‐Guerra Jorge J. , Lee Suzee E. , Suemoto Claudia K. , Ehrenberg Alexander J. , Kovacs Gabor G. , Karydas Anna , Staffaroni Adam , Franca Resende Elisa De Paula , Kim Eun‐Joo , Hwang Ji‐Hye , Ramos Eliana Marisa , Wojta Kevin J. , Pasquini Lorenzo , Pang Shirley Yin‐Yu , Spina Salvatore , Allen Isabel E. , Kramer Joel , Miller Bruce L. , Seeley William W. , Grinberg Lea T. 
Published: December 2020

AbstractPolymorphisms in TMEM106B, a gene on chromosome 7p21.3 involved in lysosomal trafficking, correlates to worse neuropathological, and clinical outcomes in frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) with TDP‐43 inclusions. In a small cohort of C9orf72 expansion carriers, we previously found an atypical, neuroglial tauopathy in cases harboring a TMEM106B rs1990622 A/A genotype. To test whether TMEM106B genotype affects the risk of developing atypical tauopathy under a recessive genotype model (presence versus absence of two major alleles: A/A vs. A/G and G/G). We characterized the atypical tauopathy neuropathologically and determined its frequency by TMEM106B rs1990622 genotypes in 90 postmortem cases with a primary diagnosis of FTLD/ALS‐TDP [mean age at death 65.5 years (±8.1), 40% female]. We investigated the effect of this new atypical tauopathy on demographics and clinical and neuropsychological metrics. We also genotyped TMEM106B in an independent series with phenotypically similar cases. Sixteen cases (16/90, 17.7 %) showed the temporal‐predominant neuro‐astroglial tauopathy, and 93.7% of them carried an A/A genotype (vs. ~35% in a population cohort). The odds ratio of FTLD/ALS‐TDP individuals with the A/A genotype showing neuro‐astroglial tauopathy was 13.9. Individuals with this tauopathy were older at onset (p = 0.01). The validation cohort had a similarly high proportion of rs1990622 A/A genotype. TDP‐43 and tau changes co‐occur in a subset of neurons. Our data add to the growing body of evidence that TMEM106B polymorphisms may modulate neurodegeneration. A distinctive medial temporal predominant, 4‐repeat, neuro‐astroglial tauopathy strongly correlates to TMEM106B A/A genotype in FTLD/ALS‐TDP cases.
Determinants of dental prosthetic treatment need: A birth cohort study
Authors: Chisini Luiz Alexandre , Sarmento Hugo Ramalho , Collares Kauê , Horta Bernardo Lessa , Demarco Flávio Fernando , Correa Marcos Britto 
Published: December 2020

AbstractObjectivesTo estimate the incidence of the need for a dental prosthesis during early adulthood and its association with socioeconomic and oral disorder trajectories.MethodsIn 1982, in the city of Pelotas, all live births (n = 5914) and their mothers were assessed. A representative sample of this cohort study was examined for oral health conditions at 15, 24 and 31 years (Oral Health Study–OHS). The need for a dental prosthesis was assessed at 24 and 31 years of age, and variables of interest (gender, skin colour, socioeconomic status (SES), use of dental services, caries and periodontal disease) were collected from different waves of this cohort. Longitudinal association between outcome and variables of interest was assessed using multilevel mixed models.ResultsA total of 539 individuals were assessed in 2013 (60.7% response rate). The need for a dental prosthesis was 28.9% at 24 years. (95% CI 24.9‐33.2) and 49.0% at 31 years (95% CI 44.7‐53.3). Risk of presenting with a need for a dental prosthesis was higher in users of public services. Downwardly mobile and lower SES trajectory groups presented a higher risk of the need for a dental prosthesis. High‐risk caries trajectory group showed a higher risk of presenting with the need for a dental prosthesis from 24 to 31 years.ConclusionsOur findings demonstrate that the need for dental prosthesis from 24 to 31 years old was determined by trajectories of exposure during the life cycle, reinforcing that tackling socioeconomic inequalities at any stage of life can have an effect on an individual's oral health.
Upregulation of spinal ASIC1 by miR‐485 mediates enterodynia in adult offspring rats with prenatal maternal stress
Authors: Xu Xue , Li Yong‐Chang , Wu Yan‐Yan , Xu Yu‐Cheng , Weng Rui‐Xia , Wang Cai‐Lin , Zhang Ping‐An , Zhang Ying , Xu Guang‐Yin 
Published: December 2020

AbstractAimsIrritable bowel syndrome (IBS) is a common functional gastrointestinal disease characterized by abdominal pain. Our recent study has shown that the acid‐sensitive ion channel 1 (ASIC1) in dorsal root ganglion (DRG) is involved in stomachache of adult offspring rats subjected with prenatal maternal stress (PMS). MiR‐485 is predicted to target the expression of ASIC1. The aim of the present study was designed to determine whether miR‐485/ASIC1 signaling participates in enterodynia in the spinal dorsal horn of adult offspring rats with PMS.MethodsEnterodynia was measured by colorectal distension (CRD). Western blotting, qPCR, and in situ hybridization were performed to detect the expression of ASICs and related miRNAs. Spinal synaptic transmission was also recorded by patch clamping.ResultsPMS offspring rats showed that spinal ASIC1 protein expression and synaptic transmission were significantly enhanced. Administration of ASICs antagonist amiloride suppressed the synaptic transmission and enterodynia. Besides, PMS induced a significant reduction in the expression of miR‐485. Upregulating the expression markedly attenuated enterodynia, reversed the increase in ASIC1 protein and synaptic transmission. Furthermore, ASIC1 and miR‐485 were co‐expressed in NeuN‐positive spinal dorsal horn neurons.ConclusionsOverall, these data suggested that miR‐485 participated in enterodynia in PMS offspring, which is likely mediated by the enhanced ASIC1 activities.