bluuebunny/crossref_metadata_2025_split huggingface dataset:
The changing mouse embryo transcriptome at whole tissue and single-cell resolution
Authors: He Peng , Williams Brian A. , Trout Diane , Marinov Georgi K. , Amrhein Henry , Berghella Libera , Goh Say-Tar , Plajzer-Frick Ingrid , Afzal Veena , Pennacchio Len A. , Dickel Diane E. , Visel Axel , Ren Bing , Hardison Ross C. , Zhang Yu , Wold Barbara J. 
Published: July 2020

AbstractDuring mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.
Using multiple short epochs optimises the stability of infant EEG connectivity parameters
Authors: Haartsen Rianne , van der Velde Bauke , Jones Emily J. H. , Johnson Mark H. , Kemner Chantal 
Published: July 2020

AbstractAtypicalities in connectivity between brain regions have been implicated in a range of neurocognitive disorders. We require metrics to assess stable individual differences in connectivity in the developing brain, while facing the challenge of limited data quality and quantity. Here, we examine how varying core processing parameters can optimise the test–retest reliability of EEG connectivity measures in infants. EEG was recorded twice with a 1-week interval between sessions in 10-month-olds. EEG alpha connectivity was measured across different epoch lengths and numbers, with the phase lag index (PLI) and debiased weighted PLI (dbWPLI), for both whole-head connectivity and graph theory metrics. We calculated intra-class correlations between sessions for infants with sufficient data for both sessions (N’s = 19–41, depending on the segmentation method). Reliability for the whole brain dbWPLI was higher across many short epochs, whereas reliability for the whole brain PLI was higher across fewer long epochs. However, the PLI is confounded by the number of available segments. Reliability was higher for whole brain connectivity than graph theory metrics. Thus, segmenting available data into a high number of short epochs and calculating the dbWPLI is most appropriate for characterising connectivity in populations with limited availability of EEG data.
Estimation of the ultimate tensile strength and yield strength for the pure metals and alloys by using the acoustic wave properties
Authors: Mohammed Arshed Abdulhamed , Haris Sallehuddin Mohamed , Al Azzawi Wessam 
Published: July 2020

AbstractIn this paper, the acoustic impedance property has been employed to predict the ultimate tensile strength (UTS) and yield strength (YS) of pure metals and alloys. Novel algorithms were developed, depending on three experimentally measured parameters, and programmed in a MATLAB code. The measured parameters are longitudinal wave velocity of the metal, density, and crystal structure. 19-samples were considered in the study and divided into 3-groups according to their crystal structure; 7-FCC, 6-BCC, and 6-HCB. X-ray diffraction was used to examine the crystal structure of each sample of each group, while longitudinal wave velocity and metals’ density were measured experimentally. A comparison between mechanical properties predicted by the model and the ASTM standards was done to investigate the validity of the model. Furthermore, predicted stress–strain curves were compared with corresponding curves in the pieces literature as an additional validation check. The results revealed the excellence of the model with 85–99% prediction accuracy. The study also proved that if metals are grouped according to their crystal structure, a relation between UTS, YS, and modulus of elasticity (E) properties and wave pressure transmission coefficient (Tr) could be formulated.
Inter- and intra-annual wind speed variabilities in wide valley regions of the middle reaches of the Yarlung Tsangpo River, China
Authors: Ben Yue , Mei Yadong , Chen Yiming , Hu Tiesong , Zhu Di 
Published: July 2020

AbstractWind speed and variability are the most critical climatic factors affecting sand/dust storms, which have not been sufficiently studied in the middle reaches of the Yarlung Tsangpo River (MYR). In this study, wind speed variability was investigated using the moving average over shifting horizon method (MASH), combined with the modified Mann–Kendall test and Sen’s slope based on data from the Tsetang, Lhasa, and Nyêmo meteorological stations during 1960–2015. The results indicated that annual wind speeds for the MYR wide valley regions declined significantly at decadal rates of − 0.216 m/s and underwent three stages from 1960 to 2015: an increasing trend from 1960 to 1975 (0.44 m/s per decade), a weakening until 2006 (− 0.46 m/s per decade), and a remarkable subsequent recovery (1.05 m/s per decade). Different variability trends were observed for the three stations: wind speed decreased significantly during all months at the Tsetang and Nyêmo stations, particularly in the spring, while for Lhasa, a non-significant wind speed increase was detected in summer, and the highest decline occurred in winter. The MASH method resulted in the effective visualization of different patterns, making seasonal process analysis and trend detection easier. In addition, the possible main causes for wind speed change were also discussed. The wind speed change in the study region was strongly associated with the large-scale atmospheric patterns, and the surface pressure gradient variability between the mid and low latitudes may have been a primary driving force. Positive/negative phases of the Pacific Decadal Oscillation (PDO) corresponded well with wind speed decreases/increases and were regarded as an indicator of wind speed variations. The effects of human activities associated with surface roughness change in the MYR were minor compared with the climatic changes.
Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1
Authors: Roszczenko-Jasińska Paula , Vu Huong N. , Subuyuj Gabriel A. , Crisostomo Ralph Valentine , Cai James , Lien Nicholas F. , Clippard Erik J. , Ayala Elena M. , Ngo Richard T. , Yarza Fauna , Wingett Justin P. , Raghuraman Charumathi , Hoeber Caitlin A. , Martinez-Gomez Norma C. , Skovran Elizabeth 
Published: July 2020

AbstractLanthanide elements have been recently recognized as “new life metals” yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.
Genetic and environmental variation in educational attainment: an individual-based analysis of 28 twin cohorts
Authors: Silventoinen Karri , Jelenkovic Aline , Sund Reijo , Latvala Antti , Honda Chika , Inui Fujio , Tomizawa Rie , Watanabe Mikio , Sakai Norio , Rebato Esther , Busjahn Andreas , Tyler Jessica , Hopper John L. , Ordoñana Juan R. , Sánchez-Romera Juan F. , Colodro-Conde Lucia , Calais-Ferreira Lucas , Oliveira Vinicius C. , Ferreira Paulo H. , Medda Emanuela , Nisticò Lorenza , Toccaceli Virgilia , Derom Catherine A. , Vlietinck Robert F. , Loos Ruth J. F. , Siribaddana Sisira H. , Hotopf Matthew , Sumathipala Athula , Rijsdijk Fruhling , Duncan Glen E. , Buchwald Dedra , Tynelius Per , Rasmussen Finn , Tan Qihua , Zhang Dongfeng , Pang Zengchang , Magnusson Patrik K. E. , Pedersen Nancy L. , Dahl Aslan Anna K. , Hwang Amie E. , Mack Thomas M. , Krueger Robert F. , McGue Matt , Pahlen Shandell , Brandt Ingunn , Nilsen Thomas S. , Harris Jennifer R. , Martin Nicholas G. , Medland Sarah E. , Montgomery Grant W. , Willemsen Gonneke , Bartels Meike , van Beijsterveldt Catharina E. M. , Franz Carol E. , Kremen William S. , Lyons Michael J. , Silberg Judy L. , Maes Hermine H. , Kandler Christian , Nelson Tracy L. , Whitfield Keith E. , Corley Robin P. , Huibregtse Brooke M. , Gatz Margaret , Butler David A. , Tarnoki Adam D. , Tarnoki David L. , Park Hang A. , Lee Jooyeon , Lee Soo Ji , Sung Joohon , Yokoyama Yoshie , Sørensen Thorkild I. A. , Boomsma Dorret I. , Kaprio Jaakko 
Published: July 2020

AbstractWe investigated the heritability of educational attainment and how it differed between birth cohorts and cultural–geographic regions. A classical twin design was applied to pooled data from 28 cohorts representing 16 countries and including 193,518 twins with information on educational attainment at 25 years of age or older. Genetic factors explained the major part of individual differences in educational attainment (heritability: a2 = 0.43; 0.41–0.44), but also environmental variation shared by co-twins was substantial (c2 = 0.31; 0.30–0.33). The proportions of educational variation explained by genetic and shared environmental factors did not differ between Europe, North America and Australia, and East Asia. When restricted to twins 30 years or older to confirm finalized education, the heritability was higher in the older cohorts born in 1900–1949 (a2 = 0.44; 0.41–0.46) than in the later cohorts born in 1950–1989 (a2 = 0.38; 0.36–0.40), with a corresponding lower influence of common environmental factors (c2 = 0.31; 0.29–0.33 and c2 = 0.34; 0.32–0.36, respectively). In conclusion, both genetic and environmental factors shared by co-twins have an important influence on individual differences in educational attainment. The effect of genetic factors on educational attainment has decreased from the cohorts born before to those born after the 1950s.
Investigating effect of climate warming on the population declines of Sympetrum frequens during the 1990s in three regions in Japan
Authors: Nakanishi Kosuke , Koide Dai , Yokomizo Hiroyuki , Kadoya Taku , Hayashi Takehiko I. 
Published: July 2020

AbstractClimate warming is of concern as a key factor in the worldwide decline in insect populations. In Japan, numbers of a common dragonfly in rice paddy fields, Sympetrum frequens, decreased sharply in the 1990s. Because S. frequens migrates to cooler mountains in summer, climate warming has been suggested as one of the main causes of the population decline in addition to agronomic factors. Here, we analysed the relation between summer temperatures and population densities of S. frequens and the related S. infuscatum, which does not migrate to mountains in summer, using published population monitoring data and temperature data from three regions (Toyama, Ishikawa, and Shizuoka) in Japan. Decadal differences in summer temperatures lay within the range of fluctuations among years, suggesting that an increase in summer temperatures cannot explain the past sharp population declines. However, regression analyses using monitoring data from Toyama showed that the population dynamics of both species in autumn are negatively correlated with summer temperatures in the same year. These results suggest that high temperatures in summer directly affect adult mortality to an extent that results in a decrease in population growth.
Assessing the current and potential future distribution of four invasive forest plants in Minnesota, U.S.A., using mixed sources of data
Authors: Reinhardt Jason R. , Russell Matthew B. , Senay Senait , Lazarus William 
Published: July 2020

AbstractInvasive plants are an ongoing subject of interest in North American forests, owing to their impacts on forest structure and regeneration, biodiversity, and ecosystem services. An important component of studying and managing forest invaders involves knowing where the species are, or could be, geographically located. Temporal and environmental context, in conjunction with spatially-explicit species occurrence information, can be used to address this need. Here, we predict the potential current and future distributions of four forest plant invaders in Minnesota: common buckthorn (Rhamnus cathartica), glossy buckthorn (Frangula alnus), garlic mustard (Alliaria petiolata), and multiflora rose (Rosa multiflora). We assessed the impact of two different climate change scenarios (IPCC RCP 6.0 and 8.5) at two future timepoints (2050s and 2070s) as well as the importance of occurrence data sources on the potential distribution of each species. Our results suggest that climate change scenarios considered here could result in a potential loss of suitable habitat in Minnesota for both buckthorn species and a potential gain for R. multiflora and A. petiolata. Differences in predictions as a result of input occurrence data source were most pronounced in future climate projections.
Importance of a vertically tilting structure for energizing the North Atlantic Oscillation
Authors: Martineau Patrick , Nakamura Hisashi , Kosaka Yu , Yamamoto Ayako 
Published: July 2020

AbstractThe North Atlantic Oscillation (NAO) is a prominent mode of atmospheric variability that influences weather and climate, including the occurrence of extreme events, over a large part of Europe and Northeastern America. The NAO has been considered to be maintained primarily by migratory weather disturbances and to have a deep structure with no vertical tilt. A careful inspection nonetheless reveals that the associated anomalies do exhibit a subtle vertical tilt, but its dynamical implications are still unknown. Here we show that this vertical tilt is of vital dynamical significance for the wintertime NAO. We find, using atmospheric reanalysis data, that the tilted anomalies transport heat across the pronounced thermal gradient associated with a background westerly jetstream, advecting air from the cooler North America and Greenland to the warmer Atlantic, thereby acting to reinforce NAO’s thermal anomalies. The resultant conversion of potential energy from the background state is a larger energy source for maintaining the NAO than the feedback from migratory disturbances. Our findings thus uncover a fundamental mechanism of the NAO dynamics, with implications for the improvement of seasonal predictions for the Euro-Atlantic climate and the representation of the NAO variability in climate models.
Plasma sphingosine 1-phosphate concentrations and cardiovascular autonomic neuropathy in individuals with type 2 diabetes
Authors: Chung Min Young , Park Seon-Young , Chung Jin Ook , Cho Dong Hyeok , Chung Dong Jin 
Published: July 2020

AbstractThe aim of this study was to test the hypothesis that plasma sphingosine 1-phosphate (S1P) levels are associated with the risk of cardiovascular autonomic neuropathy (CAN) in type 2 diabetes patients. This cross-sectional study included 287 individuals with type 2 diabetes. CAN was evaluated using cardiovascular reflex tests. Logistic regression analyses were conducted to assess the relationship between plasma S1P levels and CAN. Plasma S1P concentrations were significantly lower in individuals with CAN than in those without CAN. There was a significant interaction between plasma S1P levels and sex with respect to CAN (p for interaction = 0.003). When stratified by sex, the association between plasma S1P levels and CAN exhibited a sex difference; in multivariable analysis, plasma S1P levels were significantly associated with CAN in women (odds ratio per standard deviation increase in the log-transformed value, 0.40; 95% confidence interval, 0.23–0.70, p = 0.001). However, there was no significant association between plasma S1P and CAN in men. Plasma S1P concentrations were inversely associated with CAN only in women with type 2 diabetes.
LncRNA MALAT1 facilitates lung metastasis of osteosarcomas through miR-202 sponging
Authors: Zhang Jun , Piao Cheng-Dong , Ding Jie , Li Zheng-Wei 
Published: July 2020

AbstractLungs are the primary metastatic sites for osteosarcomas responsible for associated mortality. Recent data has documented role of long non-coding RNAs (lncRNAs) in proliferation and growth of osteosarcoma cells. We evaluated a role of lncRNAs in the lung metastasis of osteosarcoma with the goal of identifying a unique signature. Comparison of different lncRNAs in tumor samples from osteosarcoma with and without lung metastasis led to identification of MALAT1 as the most differentially upregulated lncRNA in the osteosarcoma patients with lung metastasis. MALAT1 was also high in osteosarcoma cells KRIB and MALAT1’s targeted downregulation in these cells led to decreased invasive potential and identification of miR-202 as the miRNA that is sponged by MALAT1. In the lung metastasis in vivo model, parental KRIB cells metastasized to lungs and such metastasis was significantly inhibited in KRIB cells with downregulated MALAT1. Ectopic miR-202 expression attenuated KRIB downregulation-mediated effects on lung metastasis. In yet another in vivo model involving parental SAOS-2 and lung-metastatic derivatives SAOS-2-LM, MALAT1 expression was found to be elevated in lung metastatic cells, which also correlated with reduced miR-202. In conclusion, MALAT1-miR-202 represents a potential lncRNA-miRNA signature that affects lung metastasis of osteosarcomas and could potentially be targeted for therapy.
Nonthermal phase transitions in metals
Authors: Medvedev Nikita , Milov Igor 
Published: July 2020

AbstractIt is well known that sufficiently thick metals irradiated with ultrafast laser pulses exhibit phonon hardening, in contrast to ultrafast nonthermal melting in covalently bonded materials. It is still an open question how finite size metals react to irradiation. We show theoretically that generally metals, under high electronic excitation, undergo nonthermal phase transitions if material expansion is allowed (e.g. in finite samples). The nonthermal phase transitions are induced via an increase of the electronic pressure which leads to metal expansion. This, in turn, destabilizes the lattice triggering a phase transition without a thermal electron-ion coupling mechanism involved. We find that hexagonal close-packed metals exhibit a diffusionless transition into a cubic phase, whereas metals with a cubic lattice melt. In contrast to covalent solids, nonthermal phase transitions in metals are not ultrafast, predicative on the lattice expansion.
Anti-nucleosome antibodies increase the risk of renal relapse in a prospective cohort of patients with clinically inactive systemic lupus erythematosus
Authors: Rodriguez-Jimenez Norma Alejandra , Perez-Guerrero Edsaul Emilio , Gamez-Nava Jorge Ivan , Sanchez-Mosco Dalia Isabel , Saldaña-Cruz Ana Miriam , Alcaraz-Lopez Miriam Fabiola , Fajardo-Robledo Nicte Selene , Muñoz-Valle Jose Francisco , Bonilla-Lara David , Diaz-Rizo Valeria , Gonzalez-Lopez Laura 
Published: July 2020

AbstractAn important goal in the management of systemic lupus erythematosus (SLE) is the prediction of relapses. This study assesses whether anti-nucleosome antibodies (anti-NCS) increase the risk of renal relapse in inactive SLE. A prospective cohort of 115 patients with inactive SLE (M-SLEDAI ≤ 2) were followed for 12 months to assess the development of relapse (increase of M-SLEDAI ≥ 4) and specific renal flare (renal SLEDAI ≥ 4). At baseline, we identified potential risk factors for relapse, including anti-NCS. At baseline, 18 (16%) of the 115 patients with inactive SLE were anti-NCS positive. At the 12-month follow-up, anti-NCS-positive patients had a higher incidence of renal relapse compared to anti-NCS-negative patients (38.9% vs 13.4%, respectively). In Cox regression analysis, after adjusting for age, disease duration, anti-dsDNA, and immunosuppressive drugs, the presence of anti-NCS positivity at baseline increased the risk of renal relapse (HR: 5.31, 95% CI 2.03–13.92). Nevertheless, there were no differences in the incidence of other relapses in anti-NCS-positive versus anti-NCS-negative. Our results indicate that in inactive SLE, anti-NCS determination can be useful for identifying patients with a higher risk of developing renal relapse. Interestingly, this study identified that continued use of oral immunosuppressive therapy in patients with inactive SLE can reduce the risk of renal relapse.
Circulating miR-92b and miR-375 for monitoring the chemoresistance and prognosis of small cell lung cancer
Authors: Li Ming , Shan Wulin , Hong Bo , Zou Jinglu , Li Hong , Han Dandan , Zhang Yang , Li Lailing , Li Dan , Lin Wenchu 
Published: July 2020

AbstractmiRNAs have been reported to be stably detectable in plasma and to function as potent biomarkers in multiple cancers. The study aimed to evaluate the expression of candidate circulating miRNAs in patients with small cell lung cancer (SCLC) to identify potential noninvasive biomarkers. The expression of five miRNAs (miR-92b, miR-146a, miR-375, miR-1224, and miR-1246) was significantly upregulated in plasma after chemoresistance induction. Receiver operating characteristic curve (ROC) analysis showed that the area under the curve (AUC) values of miR-92b and miR-375 were 0.766 and 0.791, respectively. The data demonstrated that among the five miRNAs assessed, these two miRNAs had better diagnostic accuracy for monitoring drug resistance. In addition, miR-92b and miR-375 levels were decreased after effective chemotherapy. Furthermore, Kaplan–Meier survival analysis confirmed that high expression of miR-92b and miR-375 was closely related to shorter progression-free survival (PFS) in SCLC patients. In conclusion, these findings indicate that circulating miR-92b and miR-375 might be ideal noninvasive biomarkers for monitoring drug resistance during chemotherapy and evaluating the prognosis of patients with SCLC.