bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial-transcriptomics reveals unique defining molecular features of fluorescence-sorted 5-aminolevulinic acid+ infiltrative tumor cells associated with glioblastoma recurrence and poor survival
Authors: Andrieux Geoffroy , Das Tonmoy , Griffin Michaela , Smith Stuart J. , Rahman Ruman , Chakraborty Sajib 
Published: May 2021

AbstractSpatiotemporal-heterogeneity of glioblastoma (GBM) originating from the genomic and transcriptional variation in spatially distinct intra-tumor sites, may contribute to subtype switching in GBM prior to and upon recurrence. Fluorescence-guided neurosurgical resection utilizing 5-aminolevulinic acid (5ALA) has enabled the isolation of infiltrative margin tumor cells (5ALA+ cells) from a background of non-neoplastic cells. We have explored the spatial-transcriptomic (ST) landscape to interrogate molecular signatures unique to infiltrating 5ALA+ cells in comparison to GBM core, rim, and invasive margin non-neoplastic cells. ST analysis reveals that GBM molecular subtype plasticity is not restricted to recurrence, but manifests regionally in a cell-type-specific manner. Whilst GBM core and rim are highly enriched with Classical and Proneural subtypes, the unique enrichment of the Mesenchymal subtype (MES) in 5ALA+ cells supports the hypothesis that MES 5ALA+ cells may drive GBM recurrence. Upregulation of the wound response pathway in 5ALA+ cells signifies the possibility of hijacking the wound healing pathway of neural cells to promote tumor growth. Exon-intron split analysis revealed an upregulation of exonic counts for MES and wound-response genes in 5ALA+ cells, implying that these genes are under active post-transcriptional control. Network analysis suggests that wound response genes, including chemokineCCL2that recruits regulatory T-cells and monocytic myeloid-derived suppressor cells, are controlled by anIRF8-mediated transcriptional program in 5ALA+ cells. A higher stemness signature both in 5ALA+ cells and non-neoplastic cells of the invasive margin emphasizes the role of this microenvironment in stemness acquisition and defines 5ALA+ cells as a rare sub-population of GBM stem cells. Finally, we establish a link between the unique molecular signatures of 5ALA+ cells and poor survival and GBM recurrence. Characterization of the 5ALA+ infiltrative sub-population offers an opportunity to develop more effective GBM treatments and urges focus away from the GBM proliferative core, upon which failed targeted therapies have been predicated.
A comprehensive mass spectral library for human thyroid tissues
Authors: Sun Yaoting , Li Lu , Ge Weigang , Dong Zhen , Liu Wei , Chen Hao , Xiao Qi , Cai Xue , Zhang Fangfei , Xiao Junhong , Wang Guangzhi , He Yi , Kon Oi Lian , Iyer N. Gopalakrishna , Zhao Yongfu , Guo Tiannan 
Published: May 2021

AbstractThyroid nodules occur in about 60% of the population. Current diagnostic strategies, however, often fail at distinguishing malignant nodules before surgery, thus leading to unnecessary, invasive treatments. As proteins are involved in all physio/pathological processes, a proteome investigation of biopsied nodules may help correctly classify and identify malignant nodules and discover therapeutic targets. Quantitative mass spectrometry data-independent acquisition (DIA) enables highly reproducible and rapid throughput investigation of proteomes. An exhaustive spectral library of thyroid nodules is essential for DIA yet still unavailable. This study presents a comprehensive thyroid spectral library covering five types of thyroid tissue: multinodular goiter, follicular adenoma, follicular and papillary thyroid carcinoma, and normal thyroid tissue. Our library includes 925,330 transition groups, 157,548 peptide precursors, 121,960 peptides, 9941 protein groups, and 9826 proteins from proteotypic peptides. This library resource was evaluated using three papillary thyroid carcinoma samples and their corresponding adjacent normal thyroid tissue, leading to effective quantification of up to 7863 proteins from biopsy-level thyroid tissues.
Parasite-driven cascades or hydra effects: susceptibility and foraging depression shape parasite-host-resource interactions
Authors: Walsman Jason C. , Strauss Alexander T. , Hall Spencer R. 
Published: May 2021

AbstractWhen epidemics kill hosts and increase their resources, should the density of hosts decrease (with a resource increase, this constitutes a trophic cascade) or increase (a hydra effect)? Seeking answers, we integrate trait measurements, a resource-host-parasite model, and experimental epidemics with plankton. This combination reveals how a spectrum from cascades to hydra effects can arise. It reflects tension between parasite-driven mortality (a density-mediated effect) and foraging depression upon contact with parasite propagules (a trait-mediated one).In the model, mortality rises when higher susceptibility to infection increases infection prevalence. Epidemics release resources while suppressing hosts (creating a cascade). In contrast, when hosts are less susceptible and parasites depress their foraging, a resource feedback can elevate host density during epidemics (creating a hydra effect), particularly at higher carrying capacity of resources. This combination elevates primary production relative to per-host consumption of resources (two key determinants of host density).We test these predictions of the qualitative effects of host traits and resource carrying capacity with trait measurements and a mesocosm experiment. Trait measurements show clonal lines of zooplankton hosts differ in their foraging depression and susceptibility. We seeded resource-host-parasite mesocosms with different host genotypes and provided different nutrient supplies to test model predictions. Hydra effects and trophic cascades arose under different conditions, as predicted by the model.Hence, tension between trait-mediated and density-mediated effects of parasites governs the fate of host density during epidemics – from cascades to hydra effects - via feedbacks with resources.
Protein corona modulates interaction of spiky nanoparticles with lipid bilayers
Authors: Fleury Jean-Baptiste , Werner Marco , Guével Xavier Le , Baulin Vladimir A. 
Published: May 2021

AbstractThe impact of protein corona on the interactions of nanoparticles (NPs) with cells remains an open question. This question is particularly relevant to NPs which sizes, ranging from tens to hundreds nanometers, are comparable to the sizes of most abundant proteins in plasma. Protein sizes match with typical thickness of various coatings and ligands layers, usually present at the surfaces of larger NPs. Such size match may affect the properties and the designed function of NPs. We offer a direct demonstration of how protein corona can dramatically change the interaction mode between NPs and lipid bilayers. To this end, we choose the most extreme case of NP surface modification: nanostructures in the form of rigid spikes of 10-20 nm length at the surface of gold nanoparticles. In the absence of proteins we observe the formation of reversible pores when spiky NPs absorb on lipid bilayers. In contrast, the presence of bovine serum albumin (BSA) proteins adsorbed at the surface of spiked NPs, effectively reduce the length of spikes exposed to the interaction with lipid bilayers. Thus, protein corona changes qualitatively the dynamics of pore formation, which is completely suppressed at high protein concentrations. These results suggest that protein corona can not only be critical for interaction of NPs with membranes, it may change their mode of interaction, thus offsetting the role of surface chemistry and ligands.
Noise Reconstruction & Removal Network: A New Architecture to Denoise FIB-SEM Images
Authors: Giannios Katya , Chaurasia Abhishek , Thibault Guillaume , Riesterer Jessica L. , Stempinski Erin S. , Lo Terence P. , DeLaRosa Bambi , Gray Joe W. 
Published: May 2021

SummaryRecent advances in Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) allows the imaging and analysis of cellular ultrastructure at nanoscale resolution, but the collection of labels and/or noise-free data sets has several challenges, often immutable. Reasons range from time consuming manual annotations, requiring highly trained specialists, to introducing imaging artifacts from the prolonged scanning during acquisition. We propose a fully unsupervised Noise Reconstruction and Removal Network for denoising scanning electron microscopy images.The architecture, inspired by gated recurrent units, reconstructs and removes the noise by synthesizing the sequential data. At the same time the fully unsupervised training guides the network in distinguishing true signal from noise and gives comparable results to supervised architectures. We demonstrate that this new network specialized on 3D electron microscopy data sets, achieves comparable and even better results than supervised networks.
Modulation of the host cell transcriptome and epigenome by Fusobacterium nucleatum
Authors: Despins Cody A. , Brown Scott D. , Robinson Avery V. , Mungall Andrew J. , Allen-Vercoe Emma , Holt Robert A. 
Published: May 2021

AbstractFusobacterium nucleatum (Fn) is a ubiquitous opportunistic pathogen with an emerging role as an oncomicrobe in colorectal and other cancer types. Fn can adhere to and invade host cells in a manner that varies across Fn strains and host cell phenotypes. Here we performed pairwise co-cultures between three Fn strains and two immortalized primary host cell types (colonic epithelial cells and vascular endothelial cells) followed by RNA-seq and ChIP-seq to investigate transcriptional and epigenetic host cell responses. We observed that Fn-induced host cell transcriptional modulation involves strong upregulation of genes related to immune migration and inflammatory processes, such as TNF, CXCL8, CXCL1, and CCL20. Further, we identified genes strongly upregulated specifically in conditions of host cell invasion, including overexpression of both EFNA1 and LIF, two genes commonly upregulated in colorectal cancer and associated with poor patient outcomes, and PTGS2 (COX2), a gene associated with the protective effect of aspirin in the colorectal cancer setting. Interestingly, we also observed downregulation of numerous histone modification genes upon Fn exposure. To further explore this relationship, we used the ChIP-seq data to annotate chromatin states genome-wide. We found significant chromatin remodeling following Fn exposure in conditions of host cell invasion, with substantial increases in the frequency of states corresponding to active enhancers as well as low signal or quiescent states. Thus, our results highlight increased inflammation and chemokine gene expression as conserved host cell responses to Fn exposure, and extensive host cell epigenomic changes associated with Fn host cell invasion. These results extend our understanding of Fn as an emerging pathogen and highlight the importance of considering strain heterogeneity and host cell phenotypic variation when exploring pathogenic mechanisms of Fn.
Novel Generic Models for Differentiating Stem Cells Reveal Oscillatory Mechanisms
Authors: Farjami Saeed , Sosa Karen Camargo , Dawes Jonathan H.P. , Kelsh Robert N. , Rocco Andrea 
Published: May 2021

AbstractUnderstanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence suggest alternatives to the standard framework based on Waddington’s epigenetic landscape. The models allow us to suggest two generic dynamical scenarios that describe the differentiation process. In the first scenario gradual variation of a single control parameter is responsible for both entering and exiting the oscillatory regime. In the second scenario two control parameters vary: one responsible for entering, and the other for exiting the oscillatory regime. We analyse the standard repressilator and four variants of it and show the dynamical behaviours associated with each scenario. We present a thorough analysis of the associated bifurcations and argue that gene regulatory networks with these repressilator-like characteristics are promising candidates to describe cell fate selection through an oscillatory process.
Larger is not better: No mate preference by European Common Frog (Rana temporaria) males
Authors: Dittrich Carolin , Rödel Mark-Oliver 
Published: May 2021

AbstractAccording to classical sexual selection theory, females are the choosy sex in most species. Choosiness is defined as the individual effort to invest energy and time to assess potential mates. In explosive breeding anurans, high intrasexual competition between males leads to a sexual coercion ruled mating system, where males could have evolved preferences for specific female traits. In the current study, we tested male mating preference in the explosive breeding European Common Frog without intrasexual competition. We hypothesized that males show preferences towards larger female body size in the absence of male competition. We conducted mate choice experiments, placing a male and two differently sized females in a box and recorded their mating behavior. Males did not show any preference considering female body size, neither in the attempt to grab a female nor during the formation of pairs. We witnessed a high failure rate of male mating attempts, which might make the evolution of mate choice too costly. However, small males are faster in attempting females, which could be an alternative strategy to get access to females, because their larger competitors have an advantage during scramble competition. Nonetheless, in successfully formed pairs, the females were on average larger than the males, an observation which deviated from our null-model where pairs should be of similar size if mating would be random. This indicates that selection takes place, independent from male mating preference or scramble competition.
Individual growth models support the quantification of isotope incorporation rate, trophic discrimination and their interactions
Authors: Lefebvre Sébastien , Ballutaud Marine , Nuche-Pascual M. Teresa , Nahon Sarah , Liu Rongsong , Del Rio Carlos Martinez 
Published: May 2021

AbstractTwo large but independent bodies of literature exist on two essential components of the dynamics of isotopic incorporation: the isotopic incorporation rate (λ) and the trophic discrimination factor (Δ). Understanding the magnitude of these two parameters and the factors that shape them is fundamental to interpret the results of ecological studies that rely on stable isotopes. λ scales allometrically with body mass among species and depends on growth within species. Both are often assumed to be constant and independent of each other but evidence accumulates that might be linked and to vary with growth. We built and analyzed a model (IsoDyn) that connects individual growth and isotopic incorporation of nitrogen into whole body and muscle tissues. The model can assume a variety of individual growth patterns including exponential or asymptotic growths. λ depends on the rate of body mass gains which scales allometrically with body mass. Δ is a dynamic response variable that depends partly on the ratio between fluxes of gains and losses and covaries negatively with λ. The model can be parameterized either from existing large databases of animal growth models or directly from experimental results. The model was applied to experimental results on three ectotherms and one endotherm and compared to the results of the simpler and widely used time model. IsoDyn model gave a better fit with relatively little calibration. IsoDyn clarifies and expands the interpretation of isotopic incorporation data.
Dysgu: efficient structural variant calling using short or long reads
Authors: Cleal Kez , Baird Duncan M. 
Published: May 2021

AbstractStructural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), although paired-end sequencing offers better scalability. Here, we present dysgu, which calls SVs or indels using paired-end or long reads. Dysgu detects signals from alignment gaps, discordant and supplementary mappings, and generates consensus contigs, before classifying events using machine learning. Additional SVs are identified by remapping of anomalous sequences. Dysgu outperforms existing state-of-the-art tools using paired-end or long-reads, offering high sensitivity and precision whilst being among the fastest tools to run. We find that combining low coverage paired-end and long-reads is competitive in terms of performance with long-reads at higher coverage values.
Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers
Authors: Fatima Tanzeem , Srivastava Ashutosh , Hanur Vageeshbabu S. , Srinivasa Rao M. 
Published: May 2021

AbstractSandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study, 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127, expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannon’s information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result, individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.
Producing gender-blind drug knowledge and representations in prison spaces
Authors: White Niki Jana 
Published: May 2021

PurposeThis paper aims to examine knowledge production and problem representation with regard to new psychoactive substances (NPS) in Her Majesty’s Chief Inspector of Prisons (HMCIP) annual reports.Design/methodology/approachSeven annual reports published by HMCIP for England and Wales between 2014 and 2020 have been systematically reviewed drawing on thematic analysis.FindingsThis paper demonstrates how framing in HMCIP annual reports produced a characterisation of NPS in prisons that inadvertently obstructed gender-sensitive knowledge production and problem representation. The framing formalised knowledge silences about spice in women’s prisons.Originality/valueHMCIP annual reports monitor drugs in prisons and this affects how these spaces are represented to government and other stakeholders. This paper provides theoretical and practical insights into how gender-blind knowledge is produced by discussing examples of gender-blind drug representations in a specific policy context.
(Dis)satisfied with your choices? How to align online consumer’s self-awareness, time pressure and self-consciousness
Authors: Yin Chin-Ching , Hsieh Yi-Ching , Chiu Hung-Chang , Yu Jhih-Ling 
Published: May 2021

Purpose
The purpose of this paper is twofold. First, this study applies social presence theory to explore the influences of public self-awareness on consumers’ choice inconsistency and post-choice satisfaction. Second, the authors investigate how time pressure moderates the effects of self-awareness on choice inconsistency and post-choice satisfaction so that online sellers can better align their marketing strategies.

Design/methodology/approach
This research consists of two studies. Study 1 conducted a 3 (self-awareness: public/private/control) × 2 (time pressure: high/none) experiment, and 311 online participants were recruited to explore the influence of public self-awareness and time pressure. Study 2 used a 3 (self-awareness: public/private/control) × 2 (time pressure: high/no) × 2 (self-consciousness: high/low) quasi-experiments, and the authors used 652 online participants to examine the effect of self-awareness, time pressure and public self-consciousness on choice inconsistency and post-choice satisfaction.

Findings
The results indicate that publicly self-aware consumers under high time pressure show greater inconsistency than those under no time pressure. Also, people with higher public self-consciousness exhibited higher choice inconsistency and post-choice satisfaction in public self-awareness situations than those in private self-awareness and control conditions.

Research limitations/implications
To generalize the results, this study should be replicated using more heterogeneous populations in diverse regions and cultures, as well as other product categories.

Practical implications
This study explores the implications of evoking self-awareness during online consumption and the online purchase process by observing the moderating effect of self-consciousness and time pressure. The findings provide insights to marketing practitioners who seek to increase their companies’ competitive advantage and profits through effective online manipulations of consumers’ self-awareness.

Originality/value
Extant research does not address how time pressure affects the relationships among public self-awareness, choice inconsistency and post-choice satisfaction. In addition, prior research only focused on public self-awareness in customer consumption. This study bridges these gaps and has implications for e-commerce, consumer behavior and relationship marketing research fields.
The use of signage as a tool for social integration in tourist cities: examples of relevant cases in Catalonia
Authors: Imbert-Bouchard Ribera Daniel 
Published: May 2021

Purpose
This paper aims to expose the evolution in the use of the so-called reception tools and tourist information that are present at the time of consumption of a trip towards an interest in and a willingness to link local residents and tourists in a friendly, inclusive and conciliatory way. This is the case of territorial signage designed for pedestrians, a growing protagonist of the urban landscape of many cities, which has found in its formulation the appropriate response to unify the messages and criteria that are addressed to all audiences and people with all types of sensitivities.

Design/methodology/approach
Based on an extensive fieldwork study conducted in 2013 and 2017 in the 62 most populated cities of Catalonia, different variables related to the shape of the signage and the content presented in them were analysed. To this end, a specific pattern of ad-hoc observation and structured interviews were applied to determine the social transition of the content and approaches used in the signage.

Findings
While signage is initially considered to be a basic solution with purely informative content, poor in qualitative aspects and often neglected by those responsible for its management, over time it has emerged as a tool that serves to unify the interests of the citizens who share the same space for mutual interaction. It is characterised by providing open and transversal information for all citizens without focussing on or thematising tourism in an exclusive and segregated way, separating it from the rest of the aspects that make up the nature of the urban landscape.

Originality/value
This paper confirms that these tangible instruments of support for tourists, beyond seeking a harmonic fit in the urban planning of today's cities, are also complicit in seeking social cohesion in the present-day paradigm of the conflicts created by urban tourism.