bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA‐Seq data normalization and interpretation
Authors: Pirrello Julien , Deluche Cynthia , Frangne Nathalie , Gévaudant Frédéric , Maza Elie , Djari Anis , Bourge Mickaël , Renaudin Jean‐Pierre , Brown Spencer , Bowler Chris , Zouine Mohamed , Chevalier Christian , Gonzalez Nathalie 
Published: November 2017

SummaryAs part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene‐specific ploidy‐regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing (RNA‐Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry‐sorted nuclei based on their DNA content. Here we show that cell‐based approaches to the study of RNA‐Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy‐specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location.
Sequential gene activation and gene imprinting during early embryo development in maize
Authors: Meng Dexuan , Zhao Jianyu , Zhao Cheng , Luo Haishan , Xie Mujiao , Liu Renyi , Lai Jinsheng , Zhang Xiaolan , Jin Weiwei 
Published: November 2017

SummaryGene imprinting is a widely observed epigenetic phenomenon in maize endosperm; however, whether it also occurs in the maize embryo remains controversial. Here, we used high‐throughput RNA sequencing on laser capture microdissected and manually dissected maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3–13 days after pollination, DAP) to analyze allelic gene expression patterns. Co‐expression analysis revealed sequential gene activation during maize embryo development. Gene imprinting was observed in maize embryos, and a greater number of imprinted genes were identified at early embryo stages. Sixty‐four strongly imprinted genes were identified (at the threshold of 9:1) on manually dissected embryos 5–13 DAP (more imprinted genes at 5 DAP). Forty‐one strongly imprinted genes were identified from laser capture microdissected embryos at 3 and 5 DAP (more imprinted genes at 3 DAP). Furthermore, of the 56 genes that were completely imprinted (at the threshold of 99:1), 36 were not previously identified as imprinted genes in endosperm or embryos. In situ hybridization demonstrated that most of the imprinted genes were expressed abundantly in maize embryonic tissue. Our results shed lights on early maize embryo development and provide evidence to support that gene imprinting occurs in maize embryos.
High‐throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates
Authors: Gallaher Sean D. , Fitz‐Gibbon Sorel T. , Strenkert Daniela , Purvine Samuel O. , Pellegrini Matteo , Merchant Sabeeha S. 
Published: November 2017

SummaryChlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal‐based platform for producing biofuels and bio‐products. Its highly repetitive, ~205‐kbp circular chloroplast genome and ~15.8‐kbp linear mitochondrial genome were sequenced prior to the advent of high‐throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA‐Seq was used to quantify their relative abundances across 12 different growth conditions. Forty‐six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA‐Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine‐rich polynucleotide tails were observed at the 3’‐end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.
The influence of inflammation and hematocrit on clot strength in canine thromboelastographic hypercoagulability
Authors: Marschner Clara B. , Wiinberg Bo , Tarnow Inge , Markussen Bo , Kühnel Line , Bochsen Louise , Kristensen Annemarie T. 
Published: November 2017

AbstractObjectiveTo investigate parameters causing canine thromboelastographic hypercoagulability and to investigate whether thromboelastography (TEG) with Cytochalasin D (Cyt D) added is related to parameters of platelet activity.DesignProspective observational study on hemostatic and inflammatory parameters. Data were collected between November 2012 and July 2013.SettingUniversity teaching hospital.AnimalsTwenty‐eight dogs suffering from diseases predisposing to thrombosis and 19 clinically healthy dogs. Diseased dogs were enrolled if they fulfilled inclusion criteria regarding age, size, informed client consent, and obtained a diagnosis of a disease that has been associated with thrombosis or hypercoagulability.InterventionsNone.Measurements and Main ResultsParameters of coagulation and anticoagulation, fibrinolysis, and antifibrinolysis, platelet activity, inflammation, platelet count, and hematocrit were measured using CBC, TEG, platelet aggregation on multiplate, platelet activity on flow cytometry, and hemostatic and inflammatory markers on plasma and serum analyses. ANOVA and multilinear regression analyses indicated that especially hematocrit and the inflammatory parameters C‐reactive protein and interleukin‐8 showed best association with overall clot strength in diseased dogs with hypercoagulable TEG tracings. Ratios presumed to reflect platelet contribution to the TEG tracing obtained in TEG analyses with Cyt D were related especially with hematocrit and P‐selectin expression of platelets measured after γ‐Thrombin activation on flow cytometry.ConclusionOverall clot strength in TEG analyses of the hypercoagulable dogs included in the present study appears to be primarily associated with inflammation as well as hematocrit. Furthermore, the ratio between standard TEG analyses and TEG analyses with Cyt D may reflect some degree of platelet activity.
Transpalpebral ultrasonographic measurement of the optic nerve sheath diameter in healthy dogs
Authors: Smith Joshua J. , Fletcher Daniel J. , Cooley Stacy D. , Thompson Margret S. 
Published: November 2017

AbstractObjectiveTo develop a reference range for ultrasonographically measured optic nerve sheath diameter (ONSD‐US) in dogs. We hypothesized that ONSD‐US can be measured reliably and is associated with weight but not age, sex, or body condition score (BCS), and that the relationship between weight and ONSD‐US in dogs is allometric due to canine size variations.DesignProspective, observational study.SettingUniversity teaching hospital.AnimalsSeventy‐eight healthy adult dogs.InterventionsThe ONSD was measured by a standardized transpalpebral approach.Measurements and Main ResultsRegression analysis showed the relationship between weight and ONSD was better fit with a linear model (R2 = 0.8510) than an allometric model (R2 = 0.7917). Multiple regression analysis showed ONSD is associated with weight (P < 0.0001), age (P = 0.0021), and BCS (P = 0.0007), but not with sex. Dominance analysis showed 94.6% of the variance explained by the model was due to weight. Intraclass correlation coefficient (ICC) analysis showed excellent interobserver (ICC = 0.9338–0.9608) and intraobserver (ICC = 0.9893) reliability.ConclusionsThese results suggest that ONSD‐US may be reliably measured in dogs using our described transpalpebral approach, and we have calculated prediction intervals based on body weight. Future studies are needed to determine if ONSD‐US measurements are associated with intracranial hypertension as shown in human medicine.
Two patients with MIRAGE syndrome lacking haematological features: role of somatic second-site reversion SAMD9 mutations
Authors: Shima Hirohito , Koehler Katrin , Nomura Yumiko , Sugimoto Kazuhiko , Satoh Akira , Ogata Tsutomu , Fukami Maki , Jühlen Ramona , Schuelke Markus , Mohnike Klaus , Huebner Angela , Narumi Satoshi 
Published: November 2017

BackgroundMyelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes and enteropathy (MIRAGE) syndrome is a recently described congenital disorder caused by heterozygous SAMD9 mutations. The phenotypic spectrum of the syndrome remains to be elucidated.Methods and resultsWe describe two unrelated patients who showed manifestations compatible with MIRAGE syndrome, with the exception of haematological features. Leucocyte genomic DNA samples were analysed with next-generation sequencing and Sanger sequencing, revealing the patients to have two de novoSAMD9 mutations on the same allele (patient 1 p.[Gln695*; Ala722Glu] and patient 2 p.[Gln39*; Asp769Gly]). In patient 1, p.Gln695* was absent in genomic DNA extracted from hair follicles, implying that the non-sense mutation was acquired somatically. In patient 2, with the 46,XX karyotype, skewed X chromosome inactivation pattern was found in leucocyte DNA, suggesting monoclonality of cells in the haematopoietic system. In vitro expression experiments confirmed the growth-restricting capacity of the two missense mutant SAMD9 proteins that is a characteristic of MIRAGE-associated SAMD9 mutations.ConclusionsAcquisition of a somatic nonsense SAMD9 mutation in the cells of the haematopoietic system might revert the cellular growth repression caused by the germline SAMD9 mutations (ie, second-site reversion mutations). Unexpected lack of haematological features in the two patients would be explained by the reversion mutations.
Oral corticosteroid dosing regimen and long-term prognosis in generalised myasthenia gravis: a multicentre cross-sectional study in Japan
Authors: Imai Tomihiro , Utsugisawa Kimiaki , Murai Hiroyuki , Tsuda Emiko , Nagane Yuriko , Suzuki Yasushi , Minami Naoya , Uzawa Akiyuki , Kawaguchi Naoki , Masuda Masayuki , Konno Shingo , Suzuki Hidekazu , Akaishi Tetsuya , Aoki Masashi 
Published: November 2017

ObjectiveWe examined the correlation between the dosing regimen of oral prednisolone (PSL) and the achievement of minimal manifestation status or better on PSL ≤5 mg/day lasting >6 months (the treatment target) in patients with generalised myasthenia gravis (MG).MethodsWe classified 590 patients with generalised MG into high-dose (n=237), intermediate-dose (n=187) and low-dose (n=166) groups based on the oral PSL dosing regimen, and compared the clinical characteristics, previous treatments other than PSL and prognosis between three groups. The effect of oral PSL dosing regimen on the achievement of the treatment target was followed for 3 years of treatment.ResultsTo achieve the treatment target, ORs for low-dose versus high-dose regimen were 10.4 (P<0.0001) after 1 year of treatment, 2.75 (P=0.007) after 2 years and 1.86 (P=0.15) after 3 years; and those for low-dose versus intermediate-dose regimen were 13.4 (P<0.0001) after 1 year, 3.99 (P=0.0003) after 2 years and 4.92 (P=0.0004) after 3 years. Early combined use of fast-acting treatment (OR: 2.19 after 2 years, P=0.02; OR: 2.11 after 3 years, P=0.04) or calcineurin inhibitors (OR: 2.09 after 2 years, P=0.03; OR: 2.36 after 3 years, P=0.02) was associated positively with achievement of treatment target.ConclusionA low-dose PSL regimen with early combination of other treatment options may ensure earlier achievement of the treatment target in generalised MG.
Prevalence of occupational exposure to asthmagens derived from animals, fish and/or shellfish among Australian workers
Authors: El-Zaemey Sonia , Carey Renee N , Darcey Ellie , Reid Alison , Glass Deborah Catherine , Benke Geza P , Driscoll Tim R , Peters Susan , Si Si , Abramson Michael J , Fritschi Lin 
Published: November 2017

ObjectiveSeveral animal, fish and/or shellfish derived substances encountered in the workplace can initiate or exacerbate asthma. The aims of this study were: to produce a population-based estimate of the current prevalence of occupational exposure to animal, fish and/or shellfish derived asthmagens, to identify the main circumstances of exposures and to identify occupations with the highest proportions of exposed respondents.MethodsWe used data from the Australian Work Exposure Study-Asthma, a national telephone survey that investigated the current prevalence of occupational exposure to asthmagens among Australian workers. A web-based tool was used to collect job task information and assign exposure to asthmagens, including animal, fish and/or shellfish derived asthmagens. Prevalence ratios to determine risk factors for exposure were estimated using modified Poisson regression.ResultsOf the 4878 respondents, 12.4% were exposed to asthmagens derived from animals, fish and/or shellfish. Exposure to these asthmagens was significantly higher in workers residing in regional and remote areas, compared with major cities. The main circumstance of exposure to animal derived asthmagens was through cleaning up rat/mice infestations, while the main circumstance of exposure to fish and/or shellfish derived asthmagens was through preparing and cooking salmon. Occupational groups with the highest proportion of exposure to animal or fish and/or shellfish derived asthmagens were farmers/animal workers and food workers, respectively.ConclusionsThis is the first study investigating occupational exposure to animal, fish and/or shellfish derived asthmagens in a nationwide working population. The results of this study can be used to inform the direction of occupational interventions and policies to reduce work-related asthma.
3-(Bromomethyl)-2-chloro-4-(methylsulfonyl)- benzoic acid: a new cause of sensitiser induced occupational asthma, rhinitis and urticaria
Authors: Suojalehto Hille , Karvala Kirsi , Ahonen Saana , Ylinen Katriina , Airaksinen Liisa , Suuronen Katri , Suomela Sari , Lindström Irmeli 
Published: November 2017

Objectives3-(Bromomethyl)−2-chloro-4-(methylsulfonyl)-benzoic acid (BCMBA) has not previously been identified as a respiratory sensitiser. We detected two cases who presented respiratory and urticaria symptoms related to BCMBA and had positive skin prick tests to the agent. Subsequently, we conducted outbreak investigations at the BCMBA-producing factory and performed clinical examinations to confirm occupational diseases.MethodsThe outbreak investigations included observations of work processes, assessment of exposure, a medical survey with a questionnaire and skin prick tests with 0.5% BCMBA water solution on 85 exposed workers and 9 unexposed workers. We used specific inhalation or nasal challenge and open skin application test to investigate BCMBA-related occupational asthma, rhinitis and contact urticaria.ResultsWe identified nine workers with respiratory and/or skin symptoms and positive skin prick tests to BCMBA in a chemical factory. A survey among chemical factory workers indicated a BCMBA-related sensitisation rate of 8% among all exposed workers; the rate was highest (25%) among production workers in the production hall. Sensitisation was detected only in workers with the estimated highest exposure levels. Six cases of occupational asthma, rhinitis and/or contact urticaria caused by BCMBA were confirmed with challenge tests. Asthma-provoking doses in specific inhalation challenges were very low (0.03% or 0.3% BCMBA in lactose).ConclusionsWe identified a new low molecular weight agent causing occupational asthma, rhinitis and contact urticaria. A typical clinical picture of allergic diseases and positive skin prick tests suggest underlying IgE-mediated disease mechanisms. Stringent exposure control measures are needed in order to prevent BCMBA-related diseases.
Carotid Artery Stenosis Contralateral to Acute Tandem Occlusion: An Independent Predictor of Poor Clinical Outcome after Mechanical Thrombectomy with Concomitant Carotid Artery Stenting
Authors: Maus Volker , Behme Daniel , Borggrefe Jan , Kabbasch Christoph , Seker Fatih , Hüseyin Cicek , Barnikol Utako Birgit , Yeo Leonard Leong Litt , Brouwer Patrick , Söderman Michael , Möhlenbruch Markus  , Psychogios Marios Nikos , Liebig Thomas , Dohmen Christian , Fink Gereon Rudolf , Mpotsaris Anastasios 
Published: November 2017

<b><i>Background and Purpose:</i></b> Cerebral ischemic strokes due to extra-/intracranial tandem occlusions (TO) of the anterior circulation are responsible for causing mechanical thrombectomy (MT). The impact of concomitant contralateral carotid stenosis (CCS) upon outcome remains unclear in this stroke subtype. <b><i>Methods:</i></b> Retrospective analysis of prospectively collected data of 4 international stroke centers between 2011 and 2017. One hundred ninety-seven consecutive patients with anterior TO were treated with MT and acute carotid artery stenting (CAS). Clinical (including demographics and National Institutes of Health Stroke Scale [NIHSS]), imaging (including angiographic evaluation of CCS) and procedural data were evaluated. Favorable clinical outcome was defined as modified Rankin Scale (mRS) ≤2 at 90 days. <b><i>Results:</i></b> In 186 out of 197 TO patients preinterventional CT angiography was available for analysis, thereof 49 patients (26%) presented with CCS. Median admission NIHSS and procedural timings did not differ between groups. Reperfusion was successful in 38 out of 49 patients (78%) vs. 113 out of 148 patients (76%) without CCS. In stark contrast, rate of favorable outcome at 90 days differed significantly between groups (22 vs. 44%; <i>p</i> &#x3c; 0.05). The presence of CCS in TO was associated with an unfavorable clinical outcome independent of age and NIHSS in multivariate logistic regression (<i>p</i> &#x3c; 0.05). Final infarct volume was significantly larger in CCS patients (100 ± 127 vs. 63 ± 77 cm<sup>3</sup>; <i>p</i> &#x3c; 0.05). Neither all-cause mortality rates (25 vs. 17%) nor frequency of peri-interventional symptomatic intracranial hemorrhage differed between groups (7 vs. 6%). <b><i>Conclusion:</i></b> For patients with anterior TO undergoing MT with concomitant CAS the presence of CCS &#x3e;50% is an independent predictor of poor clinical outcome. This most likely cause is due to poorer collateral flow to the affected tissue.
Assessment of different in vitro sperm challenges and in vivo fertility of bovine semen batches
Authors: Oliveira Letícia Zoccolaro , Ribeiro Lucas Bernardes , Silva Luiz Gustavo Teodoro da , Oliveira Clara Slade , Dias Erika Aline Ribeiro , Campanholi Suzane Peres , Campos Carla Cristian , Oliveira Maiana Visoná de , Monteiro Fabio Morato 
Published: November 2017

O objetivo deste estudo foi estressar células espermáticas em diferentes desafios laboratoriais e comparar os resultados in vitro com a fertilidade in vivo do sêmen. Quatro partidas de um mesmo touro Brangus foram utilizadas em um programa de IATF de 332 vacas Brangus. Cada partida foi submetida ao seguinte procedimento: a amostra de sêmen foi descongelada a 36°C por 30 segundos (grupo controle). Foram avaliados parâmetros de motilidade espermática (CASA), integridade da membrana plasmática (PMI), morfologia e concentração espermática. Em seguida, uma alíquota da amostra descongelada foi incubada em banho-maria a 45°C durante 40 minutos (grupo de desafio térmico, TCG) e outra alíquota foi centrifugada a 500 xg (gradiente de Percoll 45%/90%) durante 15 min (grupo desafio de centrifugação, CCG). Uma aliquota do sêmen centrifugado foi ainda submetida ao desafio térmico, sendo incubado a 45°C durante 40 min (grupo de desafio térmico + centrifugação, CTCG). No final de cada desafio (CCG, TCG e CTCG), os mesmos testes laboratoriais utilizados para o grupo de controle foram realizados. A seguinte taxa de concepção (CR) foi observada para cada partida (B): B1 = 48,9% (44/90), B2 = 44,2% (23/52), B3 = 55,5% (40/72) e B4 = 43,2% (51/118); (P < 0,10). No laboratório, B3 apresentou maior (P ≤ 0,05) motilidade progressiva (PM) do que B4 logo após o descongelamento (grupo controle) e após todos os desafios laboratoriais (TCG, CCG e CTCG). Porém, apesar de B3 e B4 demonstrarem similar porcentagem de PMI no grupo controle (B3 = 66,7 ± 1,3 e B4 = 65,2 ± 3,3), B3 apresentou maior (P ≤ 0,05) PMI (37,2 ± 2,5%) do que B4 (26,7 ± 3,3%) após passar pelo maior desafio laboratorial (CTCG). A partida seminal que in vitro apresentou maior resistência aos desafios laboratoriais foi a mesma que apresentou tendência para maior fertilidade in vivo. Assim, sugere-se que submeter amostras seminais a desafios laboratoriais pode ser uma alternativa interessante para selecionar partidas com maior fertilidade a campo.
Jan Dullaert of Ghent on the Foundations of Propositional Logic
Authors: Hanke Miroslav 
Published: November 2017

Abstract
Jan Dullaert (1480-1513) was a direct student of John Mair and a teacher of Gaspar Lax, Juan de Celaya, and Juan Luis Vives. His commentary on Aristotle’s Peri Hermeneias addresses the foundations of propositional logic, including a detailed analysis of conditionals (following Paul of Venice’s Logica magna) and the semantics of logical connectives (conjunction, disjunction, and implication). Dullaert’s propositional logic is limited to the immediate implications of the semantics of these connectives, i.e., their introduction and elimination rules. In the same context, he discusses several alternative treatments of semantic paradoxes, paying most attention to the approaches derived from Martin Le Maistre (based on the idea that sentential meaning is closed under entailment) and John Mair (based on the idea that self-falsifying sentences are false).