bluuebunny/crossref_metadata_2025_split huggingface dataset:
Populism and public procurement: an EU response to increased corruption and collusion risks in Hungary and Poland
Authors: Bernatt Maciej , Jones Alison 
Published: January 2023

Abstract
This article examines how illiberal changes, both in the political system and the economy, by populist governments in Hungary and Poland are increasing the risk of corruption and collusion in public procurement processes in those countries. It notes that these developments have significant consequences not only for Hungary and Poland, but also for the EU both generally, in terms of their impact on EU law and fundamental values, and specifically in relation to its finances. It thus considers what role EU law can play in reducing, mitigating, or reversing these risks. It offers several recommendations of a legal-systemic and more practical nature. The article recognises that although many steps taken by the EU to date have failed to deliver meaningful change, the EU does possess a powerful toolkit which, if fully utilised, provide the means to challenge individual cases of suspected corruption and collusion in Hungary and Poland (and other Member States), and systematic and serious violations of EU law through legal actions and financial mechanisms. It also makes proposals designed to protect EU funds better from misuse in national public procurement processes, including through closer cooperation between EU and national agencies, more proactive, real-time monitoring of processes, the use of integrity pacts, and the development of the EU’s early detection and exclusion and remedies systems.
A deep learning-based stripe self-correction method for stitched microscopic images
Authors: Wang Shu , Liu Xiaoxiang , Li Yueying , Sun Xinquan , Li Qi , She Yinhua , Xu Yixuan , Huang Xingxin , Lin Ruolan , Kang Deyong , Wang Xingfu , Tu Haohua , Liu Wenxi , Huang Feng , Chen Jianxin 
Published: January 2023

AbstractThe stitched fluorescence microscope images inevitably exist in various types of stripes or artifacts caused by uncertain factors such as optical devices or specimens, which severely affects the image quality and downstream quantitative analysis. In this paper, we present a deep learning-based Stripe Self-Correction method, so-called SSCOR. Specifically, we propose a proximity sampling scheme and adversarial reciprocal self-training paradigm that enable SSCOR to utilize stripe-free patches sampled from the stitched microscope image itself to correct their adjacent stripe patches. Comparing to off-the-shelf approaches, SSCOR can not only adaptively correct non-uniform, oblique, and grid stripes, but also remove scanning, bubble, and out-of-focus artifacts, achieving the state-of-the-art performance across different imaging conditions and modalities. Moreover, SSCOR does not require any physical parameter estimation, patch-wise manual annotation, and raw stitched information in the correction process, which provides an intelligent image quality optimization solution for microscopist or even microscope company, and facilitates more precise biomedical applications for researchers.
PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow
Authors: Fogg John , Allman Elizabeth S. , Ané Cécile 
Published: January 2023

AbstractWe consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages, or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example. We implemented the simulation of gene trees under these network coalescent models in the Julia packagePhyloCoalSimulations, which depends onPhyloNetworksand its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial athttps://github.com/cecileane/PhyloCoalSimulations.jl.
Simulated-to-real Benchmarking of Acquisition Methods in Metabolomics
Authors: Wandy Joe , McBride Ross , Rogers Simon , Terzis Nikolaos , Weidt Stefan , van der Hooft Justin J.J. , Bryson Kevin , Daly Rónán , Davies Vinny 
Published: January 2023

ABSTRACTData-Dependent and Data-Independent Acquisition modes (DDA and DIA, respectively) are both widely used to acquire MS2 spectra in untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS) metabolomics analyses. Despite their wide use, little work has been attempted to systematically compare their performance due to the difficulty and cost of performing comparisons with real experimental data due to the lack of ground truth and the costs involved in running large number of acquisitions. Here, we present a systematicin-silicocomparison of these two acquisition methods. To do so, we extended our Virtual Metabolomics Mass Spectrometer (ViMMS) framework with a DIA module. Our results show that the performance of these methods varies with the average number of co-eluting ions as the most important factor. At low numbers, DIA outperforms DDA, but at higher numbers, DDA has an advantage as DIA can no longer deal with the large amount of overlapping ion chromatograms. Results from simulation were further validated on an actual mass spectrometer, demonstrating that using ViMMS we can draw conclusions from simulation that translate well into the real world. Embedding this work within ViMMS also allows for researchers to easily simulate DDA and DIA LC-MS/MS runs, validate them on actual instrument, and potentially prototype novel methods that best combine the characteristics of both approaches. We believe that this work provides a useful guide to the choice of DIA or DDA for scientists involved in metabolomics data acquisition.
Mechanistic insights into robust cardiac IKspotassium channel activation by aromatic polyunsaturated fatty acid analogues
Authors: Bohannon Briana M. , Jowais Jessica J. , Nyberg Leif , Liin Sara I. , Larsson H. Peter 
Published: January 2023

AbstractVoltage-gated potassium (KV) channels are important regulators of cellular excitability and control action potential repolarization in the heart and brain. KVchannel mutations lead to disordered cellular excitability. Loss-of-function mutations, for example, result in membrane hyperexcitability, a characteristic of epilepsy and cardiac arrhythmias. Interventions intended to restore KVchannel function have strong therapeutic potential in such disorders. Polyunsaturated fatty acids (PUFAs) and PUFA analogues comprise a class of KVchannel activators with potential applications in the treatment of arrhythmogenic disorders such as Long QT Syndrome (LQTS). LQTS is caused by a loss-of-function of the cardiac IKschannel - a tetrameric potassium channel complex formed by KV7.1 and associated KCNE1 protein subunits. We have discovered a set of aromatic PUFA analogues that produce robust activation of the cardiac IKschannel and a unique feature of these PUFA analogues is an aromatic, tyrosine head group. We determine the mechanisms through which tyrosine PUFA analogues exert strong activating effects on the IKschannel by generating modified aromatic head groups designed to probe cation-pi interactions, hydrogen bonding, and ionic interactions. We found that tyrosine PUFA analogues do not activate the IKschannel through cation-pi interactions, but instead do so through a combination of hydrogen bonding and ionic interactions.
Low concentrations of selenium nanoparticles enhance the performance of a generalist parasitoid and its host, with no net effect on host suppression
Authors: Miksanek James Rudolph , Adarkwah Charles , Tuda Midori 
Published: January 2023

ABSTRACTBACKGROUNDThe environmental and economic costs of conventional insecticides have stirred an interest in alternative management tactics, including the use of nanotechnologies. Selenium nanoparticles (SeNPs) have many applications in agriculture but may not be compatible with biological control; however, low concentrations of SeNPs may benefit natural enemies via hormesis. This study investigates the concentration-dependent effects of SeNPs (0–1000 mg L−1) onAnisopteromalus calandrae(Howard) (Hymenoptera: Pteromalidae), a generalist parasitoid of stored product pests.RESULTSThe LC50of SeNPs was 1540 mg L−1for female parasitoids and 1164 mg L−1for males. SeNPs had a significant hormetic effect; average lifespan increased by 10% at a concentration of 4.03 mg L−1for females and by 35% at 13.83 mg L−1for males. In a bioassay including hosts (the azuki bean beetle,Callosobruchus chinensis(L.) (Coleoptera: Chrysomelidae: Bruchinae)), a low concentration of SeNPs (25 mg L−1) enhanced the performance of female parasitoids; lifespan increased by 23% and the number of offspring increased by 88%. However, the number of emerging hosts did not significantly decrease; in the absence of parasitism, SeNPs actually improved host emergence by 17%.CONCLUSIONBecause higher concentrations of SeNPs reduced parasitoid lifespan, whereas low concentrations enhanced not only parasitoid performance but also host emergence, practitioners should exercise caution when considering SeNPs for use in integrated pest management.
Learning functional conservation between pig and human to decipher evolutionary mechanisms underlying gene expression and complex trait
Authors: Li Jinghui , Zhao Tianjing , Guan Dailu , Pan Zhangyuan , Bai Zhonghao , Teng Jinyan , Zhang Zhe , Zheng Zhili , Zeng Jian , Zhou Huaijun , Fang Lingzhao , Cheng Hao 
Published: January 2023

AbstractThe assessment of genomic conservation between human and pig at the functional level can help understand and improve the potential of pig as a human biomedical model. To address this, we developed aDeeplearning-based approach to learn theGenomicConservation at theFunctional level (DeepGCF) between species by integrating 386 and 374 epigenome and transcriptome profiles from human and pig, respectively. DeepGCF demonstrated a better prediction performance compared to the previous functional conservation prediction method. In addition, we showed that the resulting DeepGCF score captures the functional conservation by examining DeepGCF on chromatin states, sequence ontologies, and regulatory variants. Regions with higher DeepGCF score play a more important role in regulatory activities and show heritability enrichment in human complex traits and diseases. Our DeepGCF approach shows a promising application on the comparison of cross-species functional conservation, and the model framework can be easily adapted to other species. By expanding the model to integrate the functional profiles of multiple species, including human, mouse, pig, cattle, and other livestock animals in the future, the functional conservation information will provide additional insight into the genetic and evolutionary mechanisms behind complex traits and diseases.
Keratinocyte-derived paracrine factors regulate stress response of melanocytes to UVB
Authors: Jeayeng Saowanee , Saelim Malinee , Muanjumpon Phetthinee , Buraphat Pongsakorn , Kanchanapiboon Potjanee , Sampattavanich Somponnat , Panich Uraiwan 
Published: January 2023

AbstractThe skin microenvironment created by keratinocytes (KC) influences stress responses of melanocytes (MC) to UVB insult. Here, we investigated paracrine factors involved in the regulatory role of microenvironment created by KC in UVB-mediated MC responses using RNA sequencing analysis as well asin vitroandin vivomodels. RNA-Seq showed that G-CSF and CCL20 genes were highly upregulated in UVB-irradiated KC and their levels best correlated with paracrine protective effects of KC on stress responses of MC to UVB. Recombinant G-CSF and CCL20 treatment revealed the strongest modulatory effects on UVB-induced MC responses by mitigating apoptosis and ROS formation and upregulating tyrosinase and tyrosinase-related protein-1 (TRP-1) involved in the melanogenic pathway. A similar correlation between G-CSF and CCL20 expression in KC and the tyrosinase level in MC was also observed in the UVB-irradiated mouse skin. Our study reports for the first time that G-CSF and CCL20 might play a regulatory role in the KC’s paracrine effects on UVB-mediated MC damage and also provides translational insights for the development of biomarkers for predicting susceptibility to photodamage.Graphical abstract
Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping
Authors: Fossati Andrea , Mozumdar Deepto , Kokontis Claire , Mèndez-Moran Melissa , Nieweglowska Eliza , Pelin Adrian , Li Yuping , Guo Baron , Krogan Nevan J. , Agard David A. , Bondy-Denomy Joseph , Swaney Danielle L. 
Published: January 2023

AbstractHost-pathogen interactions (HPIs) are pivotal in regulating establishment, progression, and outcome of an infection. Affinity-purification mass spectrometry has become instrumental for the characterization of HPIs, however the targeted nature of exogenously expressing individual viral proteins has limited its utility to the analysis of relatively small pathogens. Here we present the use of co-fractionation mass spectrometry (SEC-MS) for the high-throughput analysis of HPIs from native viral infections of two jumbophages (ϕKZ andϕPA3) inPseudomonas aeruginosa. This enabled the detection>6000 unique host-pathogen and>200 pathogen-pathogen interactions for each phage, encompassing>50% of the phage proteome. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. Prediction of novel ORFs revealed aϕPA3 complex showing strong structural and sequence similarity toϕKZ nvRNAp, suggestingϕPA3 also possesses two RNA polymerases acting at different stages of the infection cycle. We further expanded our understanding on the molecular organization of the virion packaged and injected proteome by identifying 23 novel virion components and 5 novel injected proteins, as well as providing the first evidence for interactions between KZ-like phage proteins and the host ribosome. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction (https://phagemap.ucsf.edu/). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of hostpathogen interactomes and protein complex dynamics upon infection.
Rescue of neurogenesis and age-associated cognitive decline in SAMP8 mouse: role of transforming growth factor alpha
Authors: Gómez-Oliva Ricardo , Martínez-Ortega Sergio , Atienza-Navarro Isabel , Domínguez-García Samuel , Bernal Carlos , Geribaldi-Doldán Noelia , Verástegui Cristina , Ezzanad Abdellah , Hernández-Galán Rosario , Núnez-Abades Pedro , Garcia-Alloza Monica , Castro Carmen 
Published: January 2023

ABSTRACTNeuropathological aging is associated with memory impairment and cognitive decline, and affects several brain areas including the neurogenic niche of the dentate gyrus of the hippocampus (DG). In the healthy brain homeostatic mechanisms regulate neurogenesis in the DG to facilitate the continuous generation of neurons from neural stem cells (NSC). Nevertheless, aging reduces the number of activated neural stem cells, and diminishes the number of newly generated neurons. Strategies that promote neurogenesis in the DG may improve cognitive performance in the elderly resulting in the development of treatments to prevent the progression of neurological disorders in the aged population.Our work is aimed to discover targeting molecules to be used in the design of pharmacological agents to prevent the neurological effects of pathological aging. We study the effect of age on hippocampal neurogenesis using the SAMP8 mouse as a model of pathological aging. Thus, we show that in six-month-old SAMP8 mice, episodic and spatial memory are impaired, concomitantly the generation of neuroblasts and neurons is reduced and the generation of astrocytes is increased in this model. The novelty of our work resides in the fact that treatment of SAMP8 mice with a TGF-alpha targeting molecule, prevents the observed defects, positively regulating neurogenesis and improving cognitive performance. This compound facilitates the release of TGF-alpha in vitro and in vivo and activates signaling pathways initiated by this growth factor. We conclude that targeting the release of TGF-alpha may be the basis of pharmacological drugs to counteract the neurological effects of pathological aging.
Corporate communication on social media: a case study before and during pandemic COVID-19
Authors: Mušanović Jelena , Dorčić Jelena , Gregorić Maja 
Published: January 2023

PurposeThe purpose of this study is to examine how hotel brands communicate on social media before and during the pandemic coronavirus disease 2019 (COVID-19) in relation to the tourism season.Design/methodology/approachTo gain insights into the communication of Italian hotel brands on social media, this study applies a qualitative methodology. Using the text mining technique, topic modelling was conducted on a sample of 5,032 posts from Italian 5-star hotel brands shared on the hotels' official Facebook pages.FindingsThe results show that hotel brands used essentially the same communication strategy in the tourism seasons before and after the pandemic outbreak, but with a particular focus on trust, safety and cordiality during the pandemic. Hotel brands focussed intensively on brand awareness, customer engagement and special activities that promote memorable and authentic experiences as well as luxury service quality.Originality/valueThis study contributes to the theoretical and empirical sense by bridging the concepts of tourism and hospitality, social media and corporate communication.
Field experiments in marketing research: a systematic methodological review
Authors: Malodia Suresh , Dhir Amandeep , Hasni Muhammad Junaid Shahid , Srivastava Shalini 
Published: January 2023

Purpose
The purpose of this study is to present a systematic methodological review of the application of field experiments in the domain of marketing research. By performing this study, the authors seek to offer necessary advice and suggestions to marketing scholars interested in the application of field experiments and to promote the adoption of field experiments as a preferred methodological choice among scholars in this domain.

Design/methodology/approach
A total of 315 field experiments published in the ten leading marketing journals in the past five decades were analyzed in this systematic methodological review. This study examines various aspects of field experiments, including the research profile of existing research, different trends and topics related to field experiments, choice of research questions, methods of observations, unobtrusive data collection, types of interventions and outcome variables.

Findings
This study identified various trends and topics, categories of manipulations, types of limitations and important considerations in designing field experiments and offered necessary advice on the future of field experiments in marketing research.

Research limitations/implications
This study provides a complete roadmap for future marketing scholars to adopt field studies in their research plans. The systematic summary of limitations and the checklist will be helpful for the researchers to design and execute field studies more effectively and efficiently.

Practical implications
This review study offers a complete roadmap for marketing scholars who are interested in adopting field experiments in their research projects. The discussion of trends and topics, manipulations, limitations, design considerations and checklist items for field experiments offers relevant insights to marketing scholars and may help them design and execute field experiments more effectively and efficiently.

Originality/value
To the best of the authors’ knowledge, this study is the first of its kind to provide a comprehensive methodological review of field experiments published in leading marketing journals throughout the past five decades. This study makes novel and unique contributions to both theory and literature on field experiments in the marketing discipline.
Changes in sick leave utilization at an academic medical center during the COVID-19 pandemic
Authors: Lancaster Kelly , Tumin Dmitry , Campbell Kendall M. 
Published: January 2023

PurposeThe coronavirus disease 2019 (COVID-19) pandemic drastically changed work arrangements, but COVID-19's impact on employee leave utilization is unclear. The authors sought to understand how sick leave and vacation leave utilization changed during the pandemic among clinical and non-clinical departments at an academic medical center (AMC).Design/methodology/approachClinical departments were defined as work units with a primary mission of providing direct patient care. Per-person, per-month leave utilization data were obtained from the AMC's time-keeping system for 3 clinical departments and 4 non-clinical departments in the first 12 months of the pandemic and the preceding 12 months. Monthly data for each department were analyzed with mixed-effects regression.FindingsAvailable data represented 402 employees from 3 clinical departments and 73 employees from 4 non-clinical departments. The authors found no statistically significant change in sick leave utilization among either clinical or non-clinical departments. Vacation leave utilization decreased during the pandemic by 5.9 h per person per month in non-clinical departments (95% confidence interval [CI]: −8.1, −3.8;p < 0.001) and by 3.0 h per person per month in clinical departments (95% CI: −4.3, −1.7;p < 0.001).Originality/valueAmong employees in clinical departments, the authors found no increase in sick leave utilization and a decrease in vacation utilization. These findings are concerning for presenteeism, risk of burnout or understaffing resulting in workers' inability to take time away from work in clinical departments.