bluuebunny/crossref_metadata_2025_split huggingface dataset:
A practical guide for mutational signature analysis in hematological malignancies
Authors: Maura Francesco , Degasperi Andrea , Nadeu Ferran , Leongamornlert Daniel , Davies Helen , Moore Luiza , Royo Romina , Ziccheddu Bachisio , Puente Xose S. , Avet-Loiseau Herve , Campbell Peter J. , Nik-Zainal Serena , Campo Elias , Munshi Nikhil , Bolli Niccolò 
Published: July 2019

AbstractAnalysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and result interpretation. Using whole-genome sequencing of multiple myeloma (MM), chronic lymphocytic leukemia (CLL) and acute myeloid leukemia, we compare the performance of public signature analysis tools. We describe caveats and pitfalls of de novo signature extraction and fitting approaches, reporting on common inaccuracies: erroneous signature assignment, identification of localized hyper-mutational processes, overcalling of signatures. We provide reproducible solutions to solve these issues and use orthogonal approaches to validate our results. We show how a comprehensive mutational signature analysis may provide relevant biological insights, reporting evidence of c-AID activity among unmutated CLL cases or the absence of BRCA1/BRCA2-mediated homologous recombination deficiency in a MM cohort. Finally, we propose a general analysis framework to ensure production of accurate and reproducible mutational signature data.
Comparing socioeconomic inequalities between early neonatal mortality and facility delivery: Cross-sectional data from 72 low- and middle-income countries
Authors: Lohela Terhi J. , Nesbitt Robin C. , Pekkanen Juha , Gabrysch Sabine 
Published: July 2019

AbstractFacility delivery should reduce early neonatal mortality. We used the Slope Index of Inequality and logistic regression to quantify absolute and relative socioeconomic inequalities in early neonatal mortality (0 to 6 days) and facility delivery among 679,818 live births from 72 countries with Demographic and Health Surveys. The inequalities in early neonatal mortality were compared with inequalities in postneonatal infant mortality (28 days to 1 year), which is not related to childbirth. Newborns of the richest mothers had a small survival advantage over the poorest in unadjusted analyses (−2.9 deaths/1,000; OR 0.86) and the most educated had a small survival advantage over the least educated (−3.9 deaths/1,000; OR 0.77), while inequalities in postneonatal infant mortality were more than double that in absolute terms. The proportion of births in health facilities was an absolute 43% higher among the richest and 37% higher among the most educated compared to the poorest and least educated mothers. A higher proportion of facility delivery in the sampling cluster (e.g. village) was only associated with a small decrease in early neonatal mortality. In conclusion, while socioeconomically advantaged mothers had much higher use of a health facility at birth, this did not appear to convey a comparable survival advantage.
Etv2 transcriptionally regulates Yes1 and promotes cell proliferation during embryogenesis
Authors: Singh Bhairab N. , Gong Wuming , Das Satyabrata , Theisen Joshua W. M. , Sierra-Pagan Javier E. , Yannopoulos Demetris , Skie Erik , Shah Pruthvi , Garry Mary G. , Garry Daniel J. 
Published: July 2019

AbstractEtv2, an Ets-transcription factor, governs the specification of the earliest hemato-endothelial progenitors during embryogenesis. While the transcriptional networks during hemato-endothelial development have been well described, the mechanistic details are incompletely defined. In the present study, we described a new role for Etv2 as a regulator of cellular proliferation via Yes1 in mesodermal lineages. Analysis of an Etv2-ChIPseq dataset revealed significant enrichment of Etv2 peaks in the upstream regions of cell cycle regulatory genes relative to non-cell cycle genes. Our bulk-RNAseq analysis using the doxycycline-inducible Etv2 ES/EB system showed increased levels of cell cycle genes including E2f4 and Ccne1 as early as 6 h following Etv2 induction. Further, EdU-incorporation studies demonstrated that the induction of Etv2 resulted in a ~2.5-fold increase in cellular proliferation, supporting a proliferative role for Etv2 during differentiation. Next, we identified Yes1 as the top-ranked candidate that was expressed in Etv2-EYFP+ cells at E7.75 and E8.25 using single cell RNA-seq analysis. Doxycycline-mediated induction of Etv2 led to an increase in Yes1 transcripts in a dose-dependent fashion. In contrast, the level of Yes1 was reduced in Etv2 null embryoid bodies. Using bioinformatics algorithms, biochemical, and molecular biology techniques, we show that Etv2 binds to the promoter region of Yes1 and functions as a direct upstream transcriptional regulator of Yes1 during embryogenesis. These studies enhance our understanding of the mechanisms whereby Etv2 governs mesodermal fate decisions early during embryogenesis.
Comparative transcriptome analysis of cultivated and wild seeds of Salvia hispanica (chia)
Authors: Peláez Pablo , Orona-Tamayo Domancar , Montes-Hernández Salvador , Valverde María Elena , Paredes-López Octavio , Cibrián-Jaramillo Angélica 
Published: July 2019

AbstractSalvia hispanica (chia) constituted an important crop for pre-Columbian civilizations and is considered a superfood for its rich content of essential fatty acids and proteins. In this study, we performed the first comprehensive comparative transcriptome analysis between seeds from cultivated varieties and from accessions collected from native wild populations in Mexico. From the 69,873 annotated transcripts assembled de novo, enriched functional categories and pathways revealed that the lipid metabolism was one of the most activated processes. Expression changes were detected among wild and cultivated groups and among growth conditions in transcripts responsible for triacylglycerol and fatty acid synthesis and degradation. We also quantified storage protein fractions that revealed variation concerning nutraceutical proteins such as albumin and glutelin. Genetic diversity estimated with 23,641 single nucleotide polymorphisms (SNPs) revealed that most of the variation remains in the wild populations, and that a wild-type cultivated variety is genetically related to wild accessions. Additionally, we reported 202 simple sequence repeat (SSRs) markers useful for population genetic studies. Overall, we provided transcript variation that can be used for breeding programs to further develop chia varieties with enhanced nutraceutical traits and tools to explore the genetic diversity and history of this rediscovered plant.
Immune heterogeneity of head and tail pancreatic lymph nodes in non-obese diabetic mice
Authors: Li Xiaofei , Bean Asher , Uehara Mayuko , Banouni Naima , Ben Nasr Moufida , Kasinath Vivek , Jiang Liwei , Fiorina Paolo , Abdi Reza 
Published: July 2019

AbstractThe pancreatic lymph node is critical to the pathogenesis of autoimmune diabetes, as it constitutes the initial site for the priming of autoreactive T cells. In this study, we compared the histopathology of the head pancreatic lymph node (HPLN) to the tail pancreatic lymph node (TPLN) in NOD mice. HPLNs and TPLNs were harvested from 4 week-, 8 week-, and 12 week-old NOD mice, and their microvasculature, extracellular matrix, and immune cell subsets were characterized. The percentages of B cells and antigen-presenting cells (APCs) were much higher in the HPLN, as compared to the TPLN. Notably, the HPLNs of 12 week-old mice were characterized by greater expansion of high endothelial venules (HEVs) and lymphatic vessels in comparison to the TPLNs. Finally, we observed a higher density of extracellular matrix (ECM) fibers surrounding the lymphatic vasculature in the HPLNs than in the TPLNs. These data for the first time demonstrate that the HPLN possesses a different immune microanatomy and organization from the TPLN. These novel observations unveil a major phenotypic difference between two types of LNs from the same organ and may highlight an independent fundamental role played by each PLN during the establishment of T1D.
Metabolic cost adaptations during training with a soft exosuit assisting the hip joint
Authors: Panizzolo Fausto A. , Freisinger Gregory M. , Karavas Nikos , Eckert-Erdheim Asa M. , Siviy Christopher , Long Andrew , Zifchock Rebecca A. , LaFiandra Michael E. , Walsh Conor J. 
Published: July 2019

AbstractDifferent adaptation rates have been reported in studies involving ankle exoskeletons designed to reduce the metabolic cost of their wearers. This work aimed to investigate energetic adaptations occurring over multiple training sessions, while walking with a soft exosuit assisting the hip joint. The participants attended five training sessions within 20 days. They walked carrying a load of 20.4 kg for 20 minutes with the exosuit powered and five minutes with the exosuit unpowered. Percentage change in net metabolic cost between the powered and unpowered conditions improved across sessions from −6.2 ± 3.9% (session one) to −10.3 ± 4.7% (session five), indicating a significant effect associated with training. The percentage change at session three (−10.5 ± 4.5%) was similar to the percentage change at session five, indicating that two 20-minute sessions may be sufficient for users to fully adapt and maximize the metabolic benefit provided by the exoskeleton. Retention was also tested measuring the metabolic reduction five months after the last training session. The percent change in metabolic cost during this session (−10.1 ± 3.2%) was similar to the last training session, indicating that the adaptations resulting in reduced metabolic cost are preserved. These outcomes are relevant when evaluating exoskeletons’ performance on naïve users, with a specific focus on hip extension assistance.
Absorbing phase transition in the coupled dynamics of node and link states in random networks
Authors: Saeedian Meghdad , San Miguel Maxi , Toral Raul 
Published: July 2019

AbstractWe present a stochastic dynamics model of coupled evolution for the binary states of nodes and links in a complex network. In the context of opinion formation node states represent two possible opinions and link states represent positive or negative relationships. Dynamics proceeds via node and link state update towards pairwise satisfactory relations in which nodes in the same state are connected by positive links or nodes in different states are connected by negative links. By a mean-field rate equations analysis and Monte Carlo simulations in random networks we find an absorbing phase transition from a dynamically active phase to an absorbing phase. The transition occurs for a critical value of the relative time scale for node and link state updates. In the absorbing phase the order parameter, measuring global order, approaches exponentially the final frozen configuration. Finite-size effects are such that in the absorbing phase the final configuration is reached in a characteristic time that scales logarithmically with system size, while in the active phase, finite-size fluctuations take the system to a frozen configuration in a characteristic time that grows exponentially with system size. There is also a class of finite-size topological transition associated with group splitting in the network of these final frozen configurations.
Direct and indirect effects of urban gardening on aboveground and belowground diversity influencing soil multifunctionality
Authors: Tresch Simon , Frey David , Bayon Renée-Claire Le , Mäder Paul , Stehle Bernhard , Fliessbach Andreas , Moretti Marco 
Published: July 2019

AbstractUrban gardens are popular green spaces that have the potential to provide essential ecosystem services, support human well-being, and at the same time foster biodiversity in cities. We investigated the impact of gardening activities on five soil functions and the relationship between plant (600 spp.) and soil fauna (earthworms: 18 spp., springtails: 39 spp.) in 85 urban gardens (170 sites) across the city of Zurich (Switzerland). Our results suggest that high plant diversity in gardens had a positive effect on soil fauna and soil multifunctionality, and that garden management intensity decreased plant diversity. Indices of biological activity in soil, such as organic and microbial carbon and bacterial abundance, showed a direct positive effect on soil multifunctionality. Soil moisture and disturbance, driven by watering and tilling, were the driving forces structuring plant and soil fauna communities. Plant indicator values proved useful to assess soil fauna community structure, even in anthropogenic plant assemblages. We conclude that to enhance soil functions, gardeners should increase plant diversity, and lower management intensity. Soil protective management practices, such as applying compost, mulch or avoiding soil tilling, should be included in urban green space planning to improve urban biodiversity and nature’s contribution to people.
Direct Observation of Long-Chain Branches in a Low-Density Polyethylene
Authors: Shinohara Ken-ichi , Yanagisawa Masahiro , Makida Yuu 
Published: July 2019

AbstractLow-density polyethylene (LDPE) has short-chain branch (SCB) and long-chain branch (LCB). In particular, the influence of the structure of LCBs on polymer properties is remarkable; however, it has been difficult to precisely analyze LCB structures. In this study, we measured the chain length of LCBs and the distance between branch points of LDPE by atomic force microscopy. Consequently, three LCBs were confirmed in a main chain of 162 nm, and their length were measured as 10, 31, and 18 nm. The positions of the LCBs were 33, 70, and 78 nm from the main-chain end.
Sensitivity of planktic foraminiferal test bulk density to ocean acidification
Authors: Iwasaki S. , Kimoto K. , Sasaki O. , Kano H. , Uchida H. 
Published: July 2019

AbstractThe anthropogenic CO2accumulating in the ocean is lowering seawater carbonate ion concentration and may reduce calcification rates of marine calcareous organisms. Several proxies based on test weights of planktic foraminifera have been used to evaluate the impact of ocean acidification on these organisms. Unfortunately, because of the absence of a method to evaluate the bulk density of a test, the impact of seawater carbonate chemistry on test calcification is still not fully understood. In this study, we measured bulk densities of livingGlobigerina bulloides(planktic foraminifera) tests with an X-ray micro-computed tomography (XMCT) scanner and compared them with ambient seawater characteristics. Results demonstrated that test bulk densities were controlled by ambient seawater carbonate ion concentrations and that changes of test bulk densities were accompanied by changes in micron to submicron scale porosity of internal ultrastructure. These results suggest that alteration of the bulk density of foraminiferal tests due to acidification of ambient seawater can be directly observed by XMCT scanning. A useful metric of calcification intensity would therefore be physical measurements of test densities with XMCT.
Ollivier-Ricci Curvature-Based Method to Community Detection in Complex Networks
Authors: Sia Jayson , Jonckheere Edmond , Bogdan Paul 
Published: July 2019

AbstractIdentification of community structures in complex network is of crucial importance for understanding the system’s function, organization, robustness and security. Here, we present a novel Ollivier-Ricci curvature (ORC) inspired approach to community identification in complex networks. We demonstrate that the intrinsic geometric underpinning of the ORC offers a natural approach to discover inherent community structures within a network based on interaction among entities. We develop an ORC-based community identification algorithm based on the idea of sequential removal of negatively curved edges symptomatic of high interactions (e.g., traffic, attraction). To illustrate and compare the performance with other community identification methods, we examine the ORC-based algorithm with stochastic block model artificial networks and real-world examples ranging from social to drug-drug interaction networks. The ORC-based algorithm is able to identify communities with either better or comparable performance accuracy and to discover finer hierarchical structures of the network. This opens new geometric avenues for analysis of complex networks dynamics.
No Effect of Ego Depletion on Risk Taking
Authors: Koppel Lina , Andersson David , Västfjäll Daniel , Tinghög Gustav 
Published: July 2019

AbstractWe investigated the effect of ego depletion on risk taking. Specifically, we conducted three studies (total n = 1,716) to test the prediction that ego depletion results in decisions that are more strongly in line with prospect theory, i.e., that ego depletion reduces risk taking for gains, increases risk taking for losses, and increases loss aversion. Ego depletion was induced using two of the most common manipulations from previous literature: the letter ‘e’ task (Studies 1 and 3) and the Stroop task (Study 2). Risk taking was measured using a series of standard, incentivized economic decision-making tasks assessing risk preferences in the gain domain, risk preferences in the loss domain, and loss aversion. None of the studies revealed a significant effect of ego depletion on risk taking. Our findings cast further doubts about the ability of ego-depletion manipulations to affect actual behavior in experimental settings.
Harnessing Synthetic Ecology for commercial algae production
Authors: Reynolds Sam A. , Davey Matthew P. , Aldridge David C. 
Published: July 2019

AbstractSynthetic Ecology is a novel concept describing the design of de novo ecological communities for a designated purpose. This study is a proof of concept for harnessing Synthetic Ecology in expanding the scale of commercially relevant micro algae (Chlorella vulgaris) cultivation using stable Synthetic Ecologies in open environments as opposed to vulnerable monocultures. We focused on whether the grazing activity of zebra mussels (Dreissena polymorpha) would result in a consistent, and commercially favourable, dominance of Chlorella in cultures that were also inoculated with a competing and potentially invasive cyanobacteria (Synechocystis sp. PCC6803). The key result of this study was that in axenic mixed species co-cultures, zebra mussels had a significantly greater negative effect on Synechocystis cell numbers than Chlorella (P < 0.0001). The zebra mussels’ putative preference for Synechocystis over Chlorella suggests they could be used to maintain the dominance of Chlorella in outdoor cultivation systems prone to contamination by invasive cyanobacteria.
Neural crest stem cells from human epidermis of aged donors maintain their multipotency in vitro and in vivo
Authors: Moghadasi Boroujeni Samaneh , Koontz Alison , Tseropoulos Georgios , Kerosuo Laura , Mehrotra Pihu , Bajpai Vivek K. , Selvam Surya Rajan , Lei Pedro , Bronner Marianne E. , Andreadis Stelios T. 
Published: July 2019

AbstractNeural crest (NC) cells are multipotent stem cells that arise from the embryonic ectoderm, delaminate from the neural tube in early vertebrate development and migrate throughout the developing embryo, where they differentiate into various cell lineages. Here we show that multipotent and functional NC cells can be derived by induction with a growth factor cocktail containing FGF2 and IGF1 from cultures of human inter-follicular keratinocytes (KC) isolated from elderly donors. Adult NC cells exhibited longer doubling times as compared to neonatal NC cells, but showed limited signs of cellular senescence despite the advanced age of the donors and exhibited significantly younger epigenetic age as compared to KC. They also maintained their multipotency, as evidenced by their ability to differentiate into all NC-specific lineages including neurons, Schwann cells, melanocytes, and smooth muscle cells (SMC). Notably, upon implantation into chick embryos, adult NC cells behaved similar to their embryonic counterparts, migrated along stereotypical pathways and contributed to multiple NC derivatives in ovo. These results suggest that KC-derived NC cells may provide an easily accessible, autologous source of stem cells that can be used for treatment of neurodegenerative diseases or as a model system for studying disease pathophysiology and drug development.
Physical activity participation and the risk of chronic diseases among South Asian adults: a systematic review and meta-analysis
Authors: Paudel Susan , Owen Alice J. , Owusu-Addo Ebenezer , Smith Ben J. 
Published: July 2019

AbstractSouth Asia specific reviews on the role of physical activity (PA) domains on chronic disease prevention are lacking. This study aimed to systematically review published literature to identify the association between PA domains and chronic diseases and to provide summary estimates of the strength of association. Nine electronic databases were searched using the predefined inclusion criteria which included population (South Asian adults 40 years or older), exposure (PA or sedentary behaviour) and outcome (type 2 diabetes mellitus, breast cancer, colorectal cancer, coronary heart disease, stroke, vascular disease and musculoskeletal diseases and their markers). A random-effects meta-analysis was carried out for cardiometabolic outcomes whereas narrative synthesis was completed for other outcome variables. Inactive or less active South Asian adults were at 31% higher risk of being hypertensive. Likewise, the risk of cardiometabolic outcomes was 1.34 times higher among inactive adults. Household PA was found to have a protective effect on breast cancer risk. Total and leisure time PA had a protective effect on osteoporosis among males and females respectively. Contemporary studies with a longitudinal design, representative samples, valid and reliable assessment of different domains are needed to establish the role of PA in chronic disease prevention in the region.