bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benthic diversity along an Arctic fjord: which are the key factors?
Authors: Lebrun Anaïs , Comeau Steeve , Gazeau Frédéric , Gattuso Jean-Pierre 
Published: August 2023

AbstractArctic coastal ecosystems include benthic communities that hold an important role within the marine food chain. Kelps, fucoid species, and coralline algae dominate rocky habitats, offering food and shelter for various species. Kelps and fucoid species also aid in carbon sequestration, sediment stabilization, and erosion mitigation. In summer, the influx of freshwater from glacier and permafrost melt alters coastal waters conditions. The input of turbid freshwater influences underwater light, salinity, and substrate, impacting benthic organism distribution. This study investigates possible link between environmental conditions and benthic diversity through environmental DNA (eDNA). Six sites were monitored along Kongsfjorden (Svalbard,Norway) during the summer of 2021. Contrary to expectations, macroalgal distribution didn’t correlate with light, and suspension feeders showed no clear links with chlorophyll a or nutrient concentrations. Glacial influence may have contributed to higher benthic diversity. Predators’ presence, tied to glacier proximity, possibly explained this trend. However, further studies are needed to validate these observations and assumptions.
Averaging a local PLSR pipeline to predict chemical compositions and nutritive values of forages and feed from spectral near infrared data
Authors: Lesnoff Matthieu 
Published: August 2023

AbstractPartial least squares regression (PLSR) is a reference method in chemometrics. In agronomy, it is used for instance to predict components of chemical composition (response variablesy) of vegetal materials from spectral near infrared (NIR) dataXcollected from spectrometers. The principle of PLSR is to reduce the dimension of the spectral dataXby computing vectors that are then used as latent variables (LVs) in a multiple linear model. A difficulty is to determine the relevant dimensionality (number of LVs) of the model for the given available data. This step can also become time consuming when many different datasets have to be processed and/or the datasets are frequently updated. An alternative to determinate the relevant PLSR dimensionality is the ensemble learning method “PLSR averaging”. In the past, this method has been demonstrated to be efficient for complex biological materials such as mixed forages, and facilitates to automatize predictions (e.g. in user-friendly web interface platforms). This article presents the extension of the PLSR averaging to ak-nearest neighbors locally weighted PLSR pipeline (kNN-LWPLSR). The kNN-LWPLSR pipeline has the advantage to account for non-linearity betweenXandyexisting for instance in heterogeneous data (e.g. mixing of vegetal species, collection from different geographical areas, etc.). In the article, kNN-LWPLSR averaging is applied to an extensive NIR database built to predict the chemical composition of European and tropical forages and feed. The main finding of the study was the overall superiority of the averaging compared to the usual kNN-LWPLSR. Averaging may therefore be recommended in local PLSR pipelines to predict NIR forage and feed data.
Colibactin-induced genotoxicity and colorectal cancer exacerbation critically depends on adhesin-mediated epithelial binding
Authors: Jans Maude , Kolata Magdalena , Blancke Gillian , Ciers Maarten , Dohlman Anders B. , Kusakabe Takato , Sze Mozes , Thiran Alexandra , Berx Geert , Tejpar Sabine , van Loo Geert , Iliev Iliyan D. , Remaut Han , Vereecke Lars 
Published: August 2023

AbstractVarious bacteria are suggested to contribute to colorectal cancer (CRC) development, includingpks+ E. coliwhich produce the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. It remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells and its DNA to cause harm. Using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we found thatpks+ E. colidrives CRC exacerbation and tissue invasion in a colibactin-dependent manner. Using isogenic mutant strains, we further demonstrate that CRC exacerbation critically depends on expression of theE. colitype-1 pilus adhesin FimH and the F9-pilus adhesin FmlH. Blocking bacterial adhesion using a pharmacological FimH inhibitor attenuates colibactin-mediated genotoxicity and CRC exacerbation. Together, we show that the oncogenic potential ofpks+ E. colicritically depends on bacterial adhesion to host epithelial cells and is critically mediated by specific bacterial adhesins. Adhesin-mediated epithelial binding subsequently allows production of the genotoxin colibactin in close proximity to host epithelial cells, which promotes DNA damage and drives CRC development. These findings present promising therapeutic avenues for the development of anti-adhesive therapies aiming at mitigating colibactin-induced DNA damage and inhibiting the initiation and progression of CRC, particularly in individuals at risk for developing CRC.
CASi: A multi-timepoint scRNAseq data analysis framework
Authors: Wang Yizhuo , Flowers Christopher R , Wang Michael , Huang Xuelin , Li Ziyi 
Published: August 2023

AbstractSingle-cell RNA sequencing (scRNA-seq) technology has been widely used to study the differences in gene expression at the single cell level, providing insights into the research of cell development, differentiation, and functional heterogeneity. Various pipelines and workflows of scRNA-seq analysis have been developed but few considered multi-timepoint data specifically. In this study, we develop CASi, a comprehensive framework for analyzing multiple timepoints’ scRNA-seq data, which provides users with: (1) cross-timepoint cell annotation, (2) detection of potentially novel cell types emerged over time, (3) visualization of cell population evolution, and (4) identification of temporal differentially expressed genes (tDEGs). Through comprehensive simulation studies and applications to a real multi-timepoint single cell dataset, we demonstrate the robust and favorable performance of the proposal versus existing methods serving similar purposes.
Inferring the Hoxa1 Gene Regulatory Network in Mouse Embryonic Stem Cells: Time-Series RNA-seq Data and Computational Modeling Approach
Authors: Emelogu Ugochi , Rogers Bryan , Banad Yaser , Cavalier Candice , Wilson Anna , Yi Xiaoping , D’Auverne Oswald , Almeida de Oliveira Samire , Akwaboa Nana , Martinez-Ceballos Eduardo 
Published: August 2023

AbstractThe homeotic geneHoxa1plays a pivotal role in regulating embryonic pattern formation and morphogenesis during mouse embryogenesis. However, despite the identification of a number of putative Hoxa1 target genes, the intricate regulatory relationships between these targets remain largely elusive. Leveraging the advancements in high-throughput technologies and sophisticated computational methods, we aimed to infer the Gene Regulatory Networks (GRNs) governed by Hoxa1 that direct cellular function, morphology, and/or differentiation. To achieve this, we generated time-series RNA-seq data from Retinoic Acid (RA)-treated Wild Type versusHoxa1-null mouse ES cells, enabling the construction of the Hoxa1 GRN. To create this GRN, we employed NARROMI, a published technique known for its noise reduction capabilities and improved accuracy in gene-regulation inference. Using this technique, we identified putative direct and indirect connections between Hoxa1 and a set of genes with known relevance in embryonic development. Validation through qPCR confirmed the Hoxa1-dependence on mRNA expression for selected genes, both within the immediate vicinity (direct) and in secondary interactions (indirect). Furthermore, by mapping the candidate genes to relevant Gene Ontology (GO) networks, we verified their involvement in processes likely regulated by Hoxa1. Our findings provide compelling evidence supporting the accuracy of the NARROMI analysis in generating a hierarchical network of genes under the transcriptional control of Hoxa1 Transcription Factor (TF), specifically in mouse ES cells. This network reveals a pool of promising candidate genes that may function as direct targets of Hoxa1. However, further investigations, including the characterization of Hoxa1 protein interactions with target loci DNA, are necessary to confirm their direct regulatory relationship with this TF. Moreover, the time-series RNA-seq data from Wild Type ES cells, coupled with the methodology employed in this study, hold the potential for constructing GRNs for additional TFs activated by RA. This comprehensive approach can shed further light on the intricate regulatory networks governing cellular function, morphology, and differentiation, advancing our understanding of embryonic development and gene regulation processes.
Simple synaptic modulations implement diverse novelty computations
Authors: Aitken Kyle , Campagnola Luke , Garrett Marina , Olsen Shawn , Mihalas Stefan 
Published: August 2023

AbstractSince environments are constantly in flux, the brain’s ability to identify novel stimuli that fall outside its own internal representation of the world is crucial for an organism’s survival. Within the mammalian neocortex, inhibitory microcircuits are proposed to regulate activity in an experience-dependent manner and different inhibitory neuron subtypes exhibit distinct novelty responses. Discerning the function of diverse neural circuits and their modulation by experience can be daunting unless one has a biologically plausible mechanism to detect and learn from novel experiences that is both understandable and flexible. Here we introduce a learning mechanism,familiarity modulated synapses(FMSs), through which a network response that encodes novelty emerges from unsupervised multiplicative synaptic modifications depending only on the presynaptic or both the pre- and postsynaptic activity. FMSs stand apart from other familiarity mechanisms in their simplicity: they operate under continual learning, do not require specialized architecture, and can distinguish novelty rapidly without requiring feedback. Implementing FMSs within an experimentally-constrained model of a visual cortical circuit, we demonstrate the generalizability of FMSs by reproducing three distinct novelty effects recently observed in experiments: absolute, contextual (or oddball), and omission novelty. Additionally, our model reproduces functional diversity within cell subpopulations, leading to experimentally testable predictions about connectivity and synaptic dynamics that can produce both population-level novelty responses and heterogeneous individual neuron signals. Altogether, our findings demonstrate how simple plasticity mechanisms within the cortical circuit structure can give rise to qualitatively distinct novelty responses. The flexibility of FMSs opens the door to computationally and theoretically investigating how distinct synapse modulations can lead to a variety of experience-dependent responses in a simple, understandable, and biologically plausible setup.
Granulomatous inflammatory responses are elicited in the liver of PD-1 knockout mice byde novogenome mutagenesis
Authors: Nagaretnam Ilamangai , Yoneshige Azusa , Takeuchi Fuka , Ozaki Ai , Tamura Masaru , Suzuki Shiori , Shigeoka Toshiaki , Ito Akihiko , Ishida Yasumasa 
Published: August 2023

AbstractAimsprogrammed death-1 (PD-1) is a negative regulator of immune responses. Upon deletion of PD-1 in mice, symptoms of autoimmunity developed only after they got old. In a model experiment in cancer immunotherapy, PD-1 was shown to prevent cytotoxic T lymphocytes from attacking cancer cells that expressed neoantigens derived from genome mutations. Furthermore, the larger number of genome mutations in cancer cells led to the more robust anti-tumor immune responses after the PD-1 blockade. In order to understand the common molecular mechanisms underlying these findings, we hypothesize that we might have acquired PD-1 during evolution in order to avoid/suppress autoimmune reactions against neoantigens derived from mutations in the genome of aged individuals. Main methods: to test the hypothesis, we introduced random mutations into the genome of young PD-1-/-and PD-1+/+mice. We employed two different procedures of random mutagenesis: administration of a potent chemical mutagen N-ethyl-N-nitrosourea (ENU) into the peritoneal cavity of mice and deletion ofMSH2, which is essential for the mismatch-repair activity in the nucleus and, therefore, for the suppression of accumulation of random mutations in the genome.Key findingswe observed granulomatous inflammatory changes in the liver of the ENU-treated PD-1 knockout (KO) mice, but not in the wild-type (WT) counterparts. Such lesions also developed in the PD-1/MSH2 double KO mice, but not in the MSH2 single KO mice. Significance: the results we obtained support our hypothesis: PD-1 probably functions to avoid/suppress inflammatory responses against neoantigens derived from genome mutations in aged individuals.
Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1with large variations in white spruce but not Norway spruce
Authors: Hung Tin Hang , Wu Ernest T. Y. , Zeltiņš Pauls , Jansons Āris , Ullah Aziz , Erbilgin Nadir , Bohlmann Joerg , Bousquet Jean , Birol Inanc , Clegg Sonya M. , MacKay John J. 
Published: August 2023

AbstractConifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genesUgt5/Ugt5band βglu-1may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of βglu-1-like,Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40P. glaucaindividuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of βglu-1andUgt5genes. We observed very large copy numbers of βglu-1, with up to 381 copies in a singleP. glaucaindividual. We observed among-provenance CNV of βglu-1inP. glaucabut notP. abies.Ugt5bwas predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.
Left behind in Covid times: the impact of the pandemic on job loss and job finding rates of vulnerable groups in Serbia
Authors: Vladisavljevic Marko , Lebedinski Lara 
Published: August 2023

Purpose
This paper aims to analyse COVID-19’s effects on job loss and job finding rate in Serbia, focusing on groups with already low employment before the pandemic, such as youth, women, low-educated and rural areas.

Design/methodology/approach
The authors exploit the panel structure of the Labour Force Survey (LFS) data for Serbia to analyse if the impact of the pandemic on transition probabilities was different for vulnerable groups and their counterparts during the first year of the pandemic.

Findings
The results indicate that stagnation in overall employment growth in Serbia during the first year of the COVID-19 crisis resulted from decreases in new hiring rather than increases in job losses. However, trends differed for vulnerable groups. Young workers faced the highest increase in job losses, partly due to their higher shares in informal wage employment. In contrast, decreases in job finding rates were particularly high among low-educated and in rural areas.

Practical implications
After the first year of the COVID-19 pandemic, employment opportunities of vulnerable groups further deteriorated, and already existing labour market inequalities were exacerbated. These effects are partially due to policies implemented to mitigate the crisis, which focused on preserving permanent employment while leaving vulnerable workers and groups unprotected.

Originality/value
The authors investigate the annual effects of the first year of the pandemic in a country with a large informal sector and explore the role of vulnerable groups’ job characteristics in transition changes.
Exploring luxury hospitality customer experience of Maldives tourists amidst COVID-19 pandemic
Authors: Kaushal Vaishali , Yadav Rajan 
Published: August 2023

Purpose
Despite the severe impact of the COVID-19, Maldives was one of the top destinations which witnessed decent tourist arrival amid the pandemic. This study aims to analyze luxury hospitality experiences of guests amid COVID-19 pandemic.

Design/methodology/approach
This study is exploratory in nature. This study analyses 4,302 real-time customer reviews using sentiment and thematic analysis with the help of NVIVO 12 plus and Leximancer.

Findings
The findings suggest travel products as well as services associated with luxury resorts needs to be revisited. Staff needs to be more professional and must be proactive while redesigning services specially in situations like pandemic. While redesigning services in situations like pandemic, staff needs to be proactive, professional and must follow all protocols. Major negative experiences included long waiting time to avail frill services, privacy intrusion by bloggers and influencers, service quality issues. We recommend enhancing service quality followed by investing more in training and development, increasing the number of foreign languages spoken by staff and disseminating localized culinary experiences will enhance the experience quality with guests.

Research limitations/implications
This study has several limitations: first, this study limited itself to 15 luxury resorts of Maldives, which may not serve as a true representation of all luxury resorts of Maldives. The next limitation of this study is that the authors have collected customer reviews from TripAdvisor only, and the reviews were only in English language.

Practical implications
The findings of the research can be beneficial for the policymakers, hospitality practitioners and academicians who study luxury tourism industry to carve appropriate strategies for enhancing the customers’ luxury experience like leveraging customization in all areas and enhancing service quality, food quality, training and development of employees.

Originality/value
Maldives has become one of the most expensive traveler destinations and is home to world’s most expensive resorts. This study is original in nature and has a forward-looking approach which studies the disruptive effect of pandemic, intangible nature of luxury as a concept can be used by hospitality industry to redesign the luxury customer experience which can improve marketing strategies aiming to potentiate this niche. In addition, to the best of the authors’ knowledge, this study will be the first one to capture the real customer experiences of luxury resorts of Maldives.
The antecedents of career decision self-efficacy: a meta-analysis on 20 years of research
Authors: Wang Nan , Luan Yuxiang , Zhao Guolong , Ma Rui 
Published: August 2023

PurposeThis study aims to examine the antecedents of career decision self-efficacy (CDSE) and provide a comprehensive understanding of the factors that influence this critical construct in career development and decision-making.Design/methodology/approachThis study employed a meta-analysis of 43 independent studies, comprising 90 correlations and 17,143 participants. The Hunter-Schmidt method meta-analysis was used to analyze the data and identify the factors associated with CDSE. Random-effect meta-regression analysis was applied to detect the potential moderators.FindingsThe study found that CDSE is positively associated with social support (ρ = 0.41), age (ρ = 0.05), agreeableness (ρ = 0.23), conscientiousness (ρ = 0.48), emotional intelligence (ρ = 0.48), extraversion (ρ = 0.41), openness (ρ = 0.35) and proactive personality (ρ = 0.68), while negatively related to neuroticism (ρ = −0.33). Furthermore, the results indicate that sample gender (%female) and mean age partially moderate the relationship between CDSE and age, core-self evaluations and neuroticism.Originality/valueIn this study, the authors have contributed significantly to the existing research on CDSE antecedents by conducting a thorough analysis of the various factors associated with this critical construct. The findings offer an accurate understanding of the factors that influence CDSE, and this paper's moderation analysis sheds light on the boundary conditions in the CDSE literature. Moreover, this research has practical implications for practitioners such as teachers, parents and career counselors. By leveraging the insights gained from this study, practitioners can provide more effective career support and intervention to young people, which can help increase their CDSE and improve their overall career development and well-being.
Financial misconduct and corporate innovation: evidence from China
Authors: Mbanyele William , Wang Fengrong 
Published: August 2023

Purpose
This study aims to examine the real effects of financial misconduct on corporate innovation.

Design/methodology/approach
The authors use a sample of Chinese A-share listed firms from 2006 to 2017. This study uses several empirical strategies to deal with endogeneity concerns, including Heckman’s two-stage correction approach, propensity score matching and instrumental variables.

Findings
The authors’ findings consistently show that financial misconduct impedes corporate innovation. Furthermore, the authors’ analysis demonstrates that the negative impact of financial misconduct is more pronounced in nonstate enterprises. The authors also show that financial misconduct discourages innovation through information, short-termism and financing channels.

Practical implications
This paper is of particular interest to policymakers, as firm behavior is heavily regulated and altered by securities laws and regulations over time. The authors recommend firms to observe financial regulatory laws to promote capital market integrity and enhance shareholder value through innovation projects. The authors also recommend that regulators provide incentives that encourage corporate transparency and use new technologies to detect financial misconduct quickly.

Originality/value
Few studies in literature investigate the real consequences of financial misconduct on firm investments. Hence, this paper fills this gap by analyzing the implications of financial misconduct on corporate innovation. This study is one of the first to provide new insights into the adverse effects of financial misconduct on firm-level innovation, supported by empirical evidence.