bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidation of the MicroRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity
Authors: Yang Xiaozeng , Fishilevich Elane , German Marcelo A. , Gandra Premchand , McEwan Robert E. , Billion André , Knorr Eileen , Vilcinskas Andreas , Narva Kenneth E. 
Published: February 2021

Abstract
Diabrotica virgifera virgifera (western corn rootworm, WCR) is one of the most destructive agricultural insect pests in North America. It is highly adaptive to environmental stimuli and crop protection technologies. However, little is known about the underlying genetic basis of WCR behavior and adaptation. More specifically, the involvement of small RNAs (sRNAs), especially microRNAs (miRNAs), a class of endogenous small non-coding RNAs that regulate various biological processes, has not been examined, and the datasets of putative sRNA sequences have not previously been generated for WCR. To achieve a comprehensive collection of sRNA transcriptomes in WCR, we constructed, sequenced, and analyzed sRNA libraries from different life stages of WCR and northern corn rootworm (NCR), and identified 101 conserved precursor miRNAs (pre-miRNAs) in WCR and other Arthropoda. We also identified 277 corn rootworm specific pre-miRNAs. Systematic analyses of sRNA populations in WCR revealed that its sRNA transcriptome, which includes PIWI-interacting RNAs (piRNAs) and miRNAs, undergoes a dynamic change throughout insect development. Phylogenetic analysis of miRNA datasets from model species reveals that a large pool of species-specific miRNAs exists in corn rootworm; these are potentially evolutionarily transient. Comparisons of WCR miRNA clusters to other insect species highlight conserved miRNA-regulated processes that are common to insects. Parallel Analysis of RNA Ends (PARE) also uncovered potential miRNA-guided cleavage sites in WCR. Overall, this study provides a new resource for studying the sRNA transcriptome and miRNA-mediated gene regulation in WCR and other Coleopteran insects.
redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-Cell RNA-Seq Data and Applications in Cancer
Authors: Xie Kaikun , Liu Zehua , Chen Ning , Chen Ting 
Published: February 2021

Abstract
The recent advancement of single-cell RNA sequencing (scRNA-seq) technologies facilitates the study of cell lineages in developmental processes and cancer. In this study, we developed a computational method, called redPATH, to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric Hamiltonian path algorithm. Besides, we developed a novel approach to visualize the trajectory development and implemented visualization methods to provide biological insights. We validated the performance of redPATH by segmenting different stages of cell development on multiple neural stem cell and cancer datasets, as well as other single-cell transcriptome data. In particular, we identified a stem cell-like subpopulation in malignant glioma cells. These cells express known proliferative markers, such as GFAP, ATP1A2, IGFBPL1, and ALDOC, and remain silenced for quiescent markers such as ID3. Furthermore, we identified MCL1 as a significant gene that regulates cell apoptosis and CSF1R for reprogramming macrophages to control tumor growth. In conclusion, redPATH is a comprehensive tool for analyzing scRNA-seq datasets along the pseudo developmental time. redPATH is available at https://github.com/tinglabs/redPATH.
kLDM: Inferring Multiple Metagenomic Association Networks Based on the Variation of Environmental Factors
Authors: Yang Yuqing , Wang Xin , Xie Kaikun , Zhu Congmin , Chen Ning , Chen Ting 
Published: February 2021

Abstract
Identification of significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose; however, they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors (EFs), which can result in inaccurate estimations. Therefore, in this study, we propose a computational model, called the k-Lognormal-Dirichlet-Multinomial (kLDM) model, which estimates multiple association networks that correspond to specific environmental conditions, and simultaneously infers microbe–microbe and EF–microbe associations for each network. The effectiveness of the kLDM model was demonstrated on synthetic data, a colorectal cancer (CRC) dataset, the Tara Oceans dataset, and the American Gut Project dataset. The results revealed that the widely-used Spearman’s rank correlation coefficient method performed much worse than the other methods, indicating the importance of separating samples by environmental conditions. Cancer fecal samples were then compared with cancer-free samples, and the estimation achieved by kLDM exhibited fewer associations among microbes but stronger associations between specific bacteria, especially five CRC-associated operational taxonomic units, indicating gut microbe translocation in cancer patients. Some EF-dependent associations were then found within a marine eukaryotic community. Finally, the gut microbial heterogeneity of inflammatory bowel disease patients was detected. These results demonstrate that kLDM can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and Python scripts, together with all experimental datasets, are accessible at https://github.com/tinglab/kLDM.git.
The European Geopolitical Space and the Long Path to Brexit (TheGovernment and Opposition/Leonard Schapiro Lecture 2020)
Authors: Thompson Helen 
Published: February 2021

AbstractAlthough Brexit had its short-term roots in economic and constitutional legitimation issues, it cannot be explained without considering the European geopolitical space, the EU's contrasting political formations in the security and economic spheres, and the fault lines these produce. Seen from a long-term geopolitical perspective, there have been recurrent problems in Britain's efforts to deal with the EU and its predecessors, and persistent patterns of crisis. The geopolitical environment, especially around NATO and energy security in the Middle East, first rendered non-membership of the EEC a problem, then made entry impossible for a decade, helped make EU membership politically very difficult for British governments to sustain, and then constrained the May governments’ Article 50 negotiations. These problems have a singularly British shape, but they cannot be separated from more general fault lines in the European geopolitical space.
Accelerating future mass loss of Svalbard glaciers from a multi-model ensemble
Authors: van Pelt Ward J. J. , Schuler Thomas V. , Pohjola Veijo A. , Pettersson Rickard 
Published: February 2021

AbstractProjected climate warming and wettening will have a major impact on the state of glaciers and seasonal snow in High Arctic regions. Following up on a historical simulation (1957–2018) for Svalbard, we make future projections of glacier climatic mass balance (CMB), snow conditions on glaciers and land, and runoff, under Representative Concentration Pathways (RCP) 4.5 and 8.5 emission scenarios for 2019–60. We find that the average CMB for Svalbard glaciers, which was weakly positive during 1957–2018, becomes negative at an accelerating rate during 2019–60 for both RCP scenarios. Modelled mass loss is most pronounced in southern Svalbard, where the equilibrium line altitude is predicted to rise well above the hypsometry peak, leading to the first occurrences of zero accumulation-area ratio already by the 2030s. In parallel with firn line retreat, the total pore volume in snow and firn drops by as much as 70–80% in 2060, compared to 2018. Total refreezing remains largely unchanged, despite a marked change in the seasonal pattern towards increased refreezing in winter. Finally, we find pronounced shortening of the snow season, while combined runoff from glaciers and land more than doubles from 1957–2018 to 2019–60, for both scenarios.
Palynological indications for Silurian – earliest Devonian age strata in the Netherlands
Authors: Houben Alexander J.P. , Vis Geert-Jan 
Published: February 2021

Abstract
Knowledge of the stratigraphic development of pre-Carboniferous strata in the subsurface of the Netherlands is very limited, leaving the lithostratigraphic nomenclature for this time interval informal. In two wells from the southwestern Netherlands, Silurian strata have repeatedly been reported, suggesting that these are the oldest ever recovered in the Netherlands. The hypothesised presence of Silurian-aged strata has not been tested by biostratigraphic analysis. A similar lack of biostratigraphic control applies to the overlying Devonian succession. We present the results of a palynological study of core material from wells KTG-01 and S05-01. Relatively low-diversity and poorly preserved miospore associations were recorded. These, nonetheless, provide new insights into the regional stratigraphic development of the pre-Carboniferous of the SW Netherlands. The lower two cores from well KTG-01 are of a late Silurian (Ludlow–Pridoli Epoch) to earliest Devonian (Lochkovian) age, confirming that these are the oldest sedimentary strata ever recovered in the Netherlands. The results from the upper cored section from the pre-Carboniferous succession in well KTG-01 and the cored sections from the pre-Carboniferous succession in well S05-01 are more ambiguous. This inferred Devonian succession is, in the current informal lithostratigraphy of the Netherlands, assigned to the Banjaard group and its subordinate Bollen Claystone formation, of presumed Frasnian (i.e. early Late Devonian) age. Age-indicative Middle to Late Devonian palynomorphs were, however, not recorded, and the overall character of the poorly preserved palynological associations in wells KTG-01 and S05-01 may also suggest an Early Devonian age. In terms of lithofacies, however, the cores in well S05-01 can be correlated to the upper Frasnian – lower Famennian Falisolle Formation in the Campine Basin in Belgium. Hence, it remains plausible that an unconformity separates Silurian to Lower Devonian strata from Upper Devonian (Frasnian–Famennian) strata in the SW Netherlands. In general, the abundance of miospore associations points to the presence of a vegetated hinterland and a relatively proximal yet relatively deep marine setting during late Silurian and Early Devonian times. This differs markedly from the open marine depositional settings reported from the Brabant Massif area to the south in present-day Belgium, suggesting a sediment source to the north. The episodic presence of reworked (marine) acritarchs of Ordovician age suggests the influx of sedimentary material from uplifted elements on the present-day Brabant Massif to the south, possibly in relation to the activation of a Brabant Arch system.
Late-Holocene sea-level reconstruction (1200 BC–AD 100) in the Westergo terp region of the northern Netherlands
Authors: Vos Peter C. , Nieuwhof Annet 
Published: February 2021

AbstractIn the early 20th century, archaeological research in the terp (artificial dwelling-mound) region of the northern Netherlands focused, besides settlement history, on natural salt-marsh dynamics and sea-level rise. In particular Van Giffen used salt-marsh deposits under dated terp layers to reconstruct the rate of sedimentation of the developing salt marsh and relative sea-level rise.This line of research in archaeology was rekindled during excavations in the terp of Wijnaldum-Tjitsma between 1991 and 1993. Since then, geology has become an integral part of archaeological research in the terp region. This paper focuses on the northwestern part of the province of Friesland (Westergo), where most archaeological terp research during the past three decades has been carried out, owing to several research programmes by the Province of Friesland. The primary aim of the geoarchaeological research is to better understand the interaction between human inhabitants and the salt-marsh landscape. The sedimentary record exposed in the excavation trenches makes it possible to collect data on the development of the coastal environments of the Wadden Sea prior to habitation, including data on sea-level rise. The sea-level data collected in the geoarchaeological studies in Westergo are the topic of this paper. The measured levels of the tidal-flat/salt-marsh boundary underneath the terps make it possible to reconstruct palaeo-Mean High Water (palaeo-MHW) levels. Such sea-level index points (SLIPs), based on marine shell data points from 12 locations, now make it possible to establish a palaeo-MHW diagram for this part of the Wadden Sea, for the period between 1200 BC and AD 100. In this period the palaeo-MHW in the Westergo region rose fromc.1.8 m to 0.3 m −NAP: a mean sea-level rise ofc.0.12 m per century.We discuss the fact that elevation of the palaeo-MHW SLIP is not only determined by relative sea level (RSL), but also by the magnitude of the tidal amplitude. The tidal range, and therefore the MHW elevations in a tidal basin, can change from place to place and also in time. Also in a single tidal basin the tidal range is variable, due to the distortion of the tidal wave as a result of the morphology of the tidal system. Such local tidal range fluctuations – not related to sea-level rise – influence the palaeo-MHW curve of Westergo and other tidal basins in the Wadden Sea and need to be taken into account when interpreting the curve.In this paper, we will go into the causes of changes in palaeotidal ranges in meso- and macrotidal systems, analyse the tidal range variations in recent and subrecent basins and estuaries and discuss the implications of these changes on the sea-level curve of the Westergo region in NW Friesland.
Edge overlap in weighted and directed social networks
Authors: Mattie Heather , Onnela Jukka-Pekka 
Published: February 2021

AbstractWith the increasing availability of behavioral data from diverse digital sources, such as social media sites and cell phones, it is now possible to obtain detailed information about the structure, strength, and directionality of social interactions in varied settings. While most metrics of network structure have traditionally been defined for unweighted and undirected networks only, the richness of current network data calls for extending these metrics to weighted and directed networks. One fundamental metric in social networks is edge overlap, the proportion of friends shared by two connected individuals. Here, we extend definitions of edge overlap to weighted and directed networks and present closed-form expressions for the mean and variance of each version for the Erdős–Rényi random graph and its weighted and directed counterparts. We apply these results to social network data collected in rural villages in southern Karnataka, India. We use our analytical results to quantify the extent to which the average overlap of the empirical social network deviates from that of corresponding random graphs and compare the values of overlap across networks. Our novel definitions allow the calculation of edge overlap for more complex networks, and our derivations provide a statistically rigorous way for comparing edge overlap across networks.
Immune status, well-being and gut microbiota in military supplemented with synbiotic ice cream and submitted to field training: a randomised clinical trial
Authors: Valle Maria C. P. R. , Vieira Isabel A. , Fino Luciana C. , Gallina Darlila A. , Esteves Andrea M. , da Cunha Diogo T. , Cabral Lucélia , Benatti Fabiana B. , Marostica Junior Mario R. , Batista Ângela G. , Santos Rosangela , Pastore Glaucia M. , Sartoratto Adilson , Sivieri Katia , Tizioto Polyana C. , Coutinho Luiz L. , Antunes Adriane E. C. 
Published: February 2021

AbstractStrenuous physical activity, sleep deprivation and psychological stress are common features of military field training. The present study aimed to evaluate the effects of supplementation with a synbiotic ice cream on salivary IgA, gastrointestinal symptoms, well-being indicators and gut microbiota in young military participants undergoing field training. Sixty-five military completed the study: one group was supplemented for 30 d with synbiotic ice cream containing: 2·1 × 108CFU/g forLactobacillus acidophilusLA-5 and 2·7 × 109CFU/g forBifidobacterium animalisBB-12 and 2·3 g of inulin in the 60 g of ice cream at manufacture, and the other with a placebo ice cream. Volunteers were evaluated at pre-supplementation (baseline), post-supplementation and after a 5-d military training.BifidobacteriumandLactobacillusgenera were measured in stool samples and both showed a higher differential abundance post-supplementation and training. Salivary IgA and gastrointestinal symptoms decreased at post-training in both groups (P< 0·05; main effect of time); however, supplementation with synbiotic did not mitigate this effect. Tenseness and sleepiness were decreased in the synbiotic-treated group, but not in the placebo group at post-military training (P= 0·01 and 0·009, respectively; group × time effect). The other well-being indicators were not affected by the synbiotic supplementation. In conclusion, 30 d of synbiotic ice cream supplementation containing inulin,L. acidophilusLA-5 andB. animalisBB-12 favourably modulated gut microbiota and improved tenseness and sleepiness in healthy young military undergoing a 5-d field training. These improvements may be relevant to this population as they may influence the decision-making process in an environment of high physical and psychological stress.
Usury and Poverty: A Case Study of the Post-Rabbinic Moment in Midrash and Piyyut
Authors: Gvaryahu Amit 
Published: February 2021

AbstractThe Hebrew Bible prohibits lending at interest. This is usually linked to care for the poor. A similar connection is found in post-biblical literature as well. In Deut 23:20–21, however, usury is disconnected from the poverty laws. Classical rabbinic literature (second to sixth centuries) follows Deuteronomy in sharply de-coupling usury from poverty: the usury prohibition in that corpus regulates commerce and property, and is not intended to benefit the poor. In a sharp break with classical rabbinic tradition, the usury prohibition is reassociated with the poor in piyyut and in the Tanhuma midrashim, two late antique genres of Jewish literature associated but not entirely contiguous with classical rabbinic literature. Both genres bring this tradition to the fore through the use of earlier rabbinic materials, which do not espouse it. This combination of usury and care for the poor mirrors fourth-century Christian writings on usury.
Three Ways to Imitate Paul in Late Antiquity: Ekstasis, Ekphrasis, Epektasis
Authors: Motia Michael 
Published: February 2021

AbstractRobert Orsi’s argument that religion, more than a system of “meaning making,” is a “network of relationships between heaven and earth” helps us understand what is at stake in imitation for early Christians. The question for Orsi is not, “What does it mean to imitate Paul?” as much as it is, “In what kind of relationship is one engaged when one imitates Paul?” Christians argue over both what to imitate (Who is Paul?) and how to imitate (How should Christians relate to Paul in order to be like him or to render him present?). The what has received lots of scholarly attention; this paper focuses on the how. I compare the range of possibilities of how to imitate Paul by focusing on three influential accounts of mimesis: Pseudo-Dionysius the Areopagite (ekstasis), John Chrysostom (ekphrasis), and Gregory of Nyssa (epektasis).
The Market as a Means of Post-Violence Recovery: Armenians and Oriental Carpets in the Late Ottoman Empire (c.1890s–1910s)
Authors: Tolga Cora Yaşar 
Published: February 2021

AbstractCarpet production in the late Ottoman Empire developed during the second half of the nineteenth century in a context of growing trade with Western markets, until, by the turn of the century, carpets had become the empire's leading manufacturing export. This article examines the expansion of oriental carpet production in Armenian communities affected by violence in the mid-1890s and in 1909, and its role in their recovery. It shows that output of oriental carpets rose and production was moved into regions with limited or no “pre-violence” experience of carpet production. We shall see that the increases in production were firmly linked to market-based efforts to reconstruct those communities. Different actors, including local and regional merchant-entrepreneurs and multinational companies as well as individual transnational actors such as missionaries, all began to involve themselves in Armenian communities, both to promote trade in carpets and to offer the production of them as a solution to the post-violence ills. As a result, Armenian women and children in post-violence communities became an integral part of the global market in oriental carpets as a vulnerable, organizationally weak but cost-efficient workforce. The whole process was justified in the name of assistance to the needy and was closely associated with changing definitions of the work ethic and morality in the late Ottoman Empire.
Probiotic Greek yogurt: effect of the addition of prebiotic fat substitutes on the physicochemical characteristics, probiotic survival, and sensory acceptance
Authors: Dias Sofia Sestito , de Souza Vergílio Damarys , Pereira Arthur Marroni , Klososki Suellen Jensen , Marcolino Vanessa Aparecida , da Cruz Rayane Monique Sete , Costa Giselle Nobre , Barão Carlos Eduardo , Pimentel Tatiana Colombo 
Published: February 2021

AbstractIn this research communication we evaluate the impact of the addition of prebiotic components (inulin, polydextrose, and modified starch, 40 g/l) as fat substitutes on the physicochemical characteristics, probiotic survival, and sensory acceptance of probiotic (Lacticaseibacillus casei 01, 108 CFU/ml) Greek yogurts during storage (7 °C, 28 d). All formulations had probiotic counts higher than 107 CFU/ml during storage and simulated gastrointestinal conditions (SGIC). The prebiotic components increased the probiotic survival to the enteric phase of the SGIC, with inulin producing the most pronounced effect. Inulin addition resulted in products with lower pH values and consistency and higher titratable acidity during storage, with negative impact on the sensory acceptance (flavor, texture, and overall impression) at the end of the storage period. Modified starch addition impacted negatively on the acceptance of the products (appearance, flavor, texture, and overall impression). Polydextrose addition resulted in products with lower consistency, but similar sensory acceptance to the full-fat yogurt. It can be concluded that it is possible to prepare potentially synbiotic Greek yogurts by desorption technique using L. casei as probiotic culture and inulin, polydextrose or modified starch as prebiotic components, with the utilization of polydextrose being advisable.
Unusual complications of bone wax at the skull base
Authors: Panicker R , Moorthy R K , Rupa V 
Published: February 2021

AbstractObjectiveThis study aimed to describe the clinical presentation, microbiological profile and management of complications of bone wax usage for surgical procedures at the skull base.MethodThe case records of a series of five patients who developed post-operative surgical site complications because of bone wax usage during skull base surgery were reviewed.ResultsIn all five patients, persistent site-specific clinical features were noted along with intra-operative presence of excessive bone wax. Three unique cases of presentation, one with a fungal brain abscess because of Aspergillus flavus infection, another with fungal osteomyelitis because of Trichosporon beigelii infection and a third with intradural migration of bone wax into the cerebellopontine angle cistern are highlighted.ConclusionThe presentation of surgical site infection at the skull base because of excessive use of bone wax can be manifold. The need for testing appropriate cultures including fungal culture is highlighted.