bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homologue Series Detection and Management in LC-MS data with homologueDiscoverer
Authors: Mildau Kevin , van der Hooft Justin J.J. , Flasch Mira , Warth Benedikt , Abiead Yasin El , Koellensperger Gunda , Zanghellini Jürgen , Büschl Christoph 
Published: July 2022

AbstractSummaryUntargeted metabolomics data analysis is highly labor intensive and can be severely frustrated by both experimental noise and redundant features. Homologous polymer series are a particular case of features that can either represent large numbers of noise features, or alternatively represent features of interest with large peak redundancy. Here we present homologueDiscoverer, an R package which allows for the targeted and untargeted detection of homologue series as well as their evaluation and management using interactive plots and simple local database functionalities.AvailabilityhomologueDiscoverer is freely available at github https://github.com/kevinmildau/homologueDiscoverer.Contactkevin.mildau@univie.ac.at, christoph.bueschl@boku.ac.at, juergen.zanghellini@univie.ac.at
CCR2 identifies tendon resident macrophage and T cell populations while CCR2 deficiency impedes late tendon healing
Authors: Muscat Samantha , Nichols Anne E.C. , Gira Emma , Loiselle Alayna E. 
Published: July 2022

ABSTRACTDuring tendon healing, macrophages are thought to be a key mediator of scar tissue formation, which prevents successful functional restoration of the tendon. However, macrophages are critical for successful tendon healing as they aid in wound debridement, extracellular matrix deposition, and promote fibroblast proliferation. Recent work has sought to better define the multi-faceted functions of macrophages using depletion studies, while other studies have identified a tendon resident macrophage population. To begin to delineate the functions of tendon-resident versus circulation-derived macrophages, we examined the tendon healing phenotype in Chemokine Receptor 2 (CCR2) reporter (CCR2GFP/+), and knockout mice. CCR2 is a chemokine receptor primarily found on the surface of circulating bone marrow derived monocytes, with CCR2 being an important mediator of macrophage recruitment to wound environments. Surprisingly, CCR2GFP/+ cells were present in the tendon during adult homeostasis, and single cell RNA sequencing identified these cells as tendon-resident macrophages and T cells. During both homeostasis and healing, CCR2 knockout resulted in a substantial decrease in CCR2GFP+ cells and pan-macrophages. Additionally, loss of CCR2 resulted in reduced numbers of myofibroblasts and impeded functional recovery during late healing. This study highlights the heterogeneity of tendon-resident and recruited immune cells and their contributions following injury, and establishes an important role for CCR2 in modulating both the adult tendon cell environment and tendon healing process.
Grape-seed proanthocyanidin extract (GSPE) modulates diurnal oscillations of key hepatic metabolic genes and metabolites alleviating hepatic lipid deposition in cafeteria-fed obese rats in a time-of-day-dependent manner
Authors: Rodríguez Romina M , de Assis Leonardo Vinícius Monteiro , Colom-Pellicer Marina , Quesada-Vázquez Sergio , Cruz-Carrión Álvaro , Escoté Xavier , Oster Henrik , Aragonès Gerard , Mulero Miquel 
Published: July 2022

AbstractMetabolic syndrome (MS) and its related diseases, including obesity and non-alcoholic fatty liver disease (NAFLD), have become a public health issue due to their increasing prevalence. Polyphenols, such as grape seed proanthocyanidin extract (GSPE), are bioactive compounds present in fruits and vegetables that show promise for MS treatment. We have previously demonstrated that the efficacy of this phenolic extract in the modulation of liver circadian clocks was affected by the time of the day at which it was ingested. Thus, we wondered if the beneficial effects of GSPE consumption in NAFLD could be mediated by diurnal modulation of hepatic lipid and glucose metabolism and whether GSPE effects on liver metabolism are impacted by the timing of administration. Results from hepatic lipid profiling, expression rhythm analysis of metabolic genes together with liver metabolomics in rats revealed that the CAF diet impaired glucose homeostasis and enhanced lipogenesis in the liver, leading to the generation of hepatosteatosis. Chronic consumption of GSPE at the onset of the active phase was able to restore the daily oscillation of liver mass and of key lipogenic and glycogenic genes, along with the reestablishment of liver metabolite rhythms, demonstrating hepatoprotective properties by decreasing triglyceride accumulation and lipid droplet formation in the liver, thus mitigating the development of CAF-induced NAFLD. Furthermore, in vitro data suggest that catechin, one of the main phenolic compounds found in the GSPE extract, may be involved in the ameliorating effects of GSPE against NAFLD.
Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms
Authors: Powers Christopher , Gomaa Fatma , Billings Elizabeth B. , Utter Daniel R. , Beaudoin David J. , Edgcomb Virginia P. , Hansel Colleen M. , Wankel Scott D. , Filipsson Helena L. , Zhang Ying , Bernhard Joan M. 
Published: July 2022

AbstractCertain benthic foraminifera are known to thrive in marine sediments with low oxygen or even without detectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain somewhat elusive. To better understand the metabolic versatility of foraminifera, we studied two benthic species that thrive in oxygen-depleted marine sediments. Here we detail, via transcriptomics and metatranscriptomics, differential gene expression of Nonionella stella and Bolivina argentea, collected from Santa Barbara Basin, California, USA, in response to varied oxygenation and chemical amendments. Organelle-specific metabolic reconstructions revealed that these two species utilize adaptable mitochondrial and peroxisomal metabolism that reflect their differing lifestyles. N. stella, most abundant in anoxia and characterized by the lack of food vacuoles and the abundance of intracellular lipid droplets, was predicted to couple the putative peroxisomal beta-oxidation and glyoxylate cycle with a versatile electron transport system and a partial TCA cycle running in the reductive direction. In contrast, B. argentea, most abundant in hypoxia and contains food vacuoles, was predicted to utilize the putative peroxisomal gluconeogenesis and a full TCA cycle but lacks the expression of key beta-oxidation and glyoxylate cycle genes. These metabolic adaptations likely confer ecological success while encountering deoxygenation and illuminate the importance of metabolic modifications and interactions between mitochondria and peroxisomes in protists.ImportanceForaminiferan protists are nearly ubiquitous in today’s oceans and likely were major components of the Neoproterozoic protistan community. While largely considered aerobic, certain foraminifera demonstrate surprising adaptability to hypoxia and anoxia, contributing to biogeochemical cycling in benthic environments. The analyses of Rhizarian adaptive metabolism set the stage for studying other microeukaryotes under increasing ocean deoxygenation. Revealing the metabolic roles of foraminifera in anaerobic biogeochemical cycling should spur reassessments of existing paleoecological datasets as well as new perspectives on the metabolic evolution of eukaryotic cells.
Phenome-wide Mendelian randomization study of plasma triglycerides and 2,600 disease traits
Authors: Park Joshua K. , Bafna Shantanu , Forrest Iain S. , Duffy Áine , Marquez-Luna Carla , Petrazzini Ben O. , Vy Ha My , Jordan Daniel M. , Verbanck Marie , Narula Jagat , Rosenson Robert S. , Rocheleau Ghislain , Do Ron 
Published: July 2022

AbstractBackgroundCausality between plasma triglyceride (TG) levels and atherosclerotic cardiovascular disease (ASCVD) risk remains controversial despite more than four decades of study and two recent landmark trials, STRENGTH and REDUCE-IT. Further unclear is the association between TG levels and non-atherosclerotic diseases across organ systems.MethodsHere, we conducted a phenome-wide, two-sample Mendelian randomization (MR) analysis using inverse-variance weighted (IVW) regression to systematically infer the causal effects of plasma TG levels on 2,600 disease traits in the European ancestry population of UK Biobank. For replication, we externally tested 221 nominally significant associations (p < 0.05) in an independent cohort from FinnGen. To account for potential horizontal pleiotropy and the influence of invalid instrumental variables, we performed sensitivity analyses using MR-Egger regression, weighted median estimator, and MR-PRESSO. Finally, we used multivariable MR controlling for correlated lipid fractions to distinguish the independent effect of plasma TG levels.ResultsOur results identified 7 disease traits reaching Bonferroni-corrected significance in both the discovery (p < 1.92 × 10-5) and replication analyses (p < 2.26 × 10-4), supporting a causal relationship between plasma TG levels and ASCVDs, including coronary artery disease (OR 1.33, 95% CI 1.24-1.43, p = 2.47 × 10-13). We also identified 12 disease traits that were Bonferroni-significant in the discovery or replication analysis and at least nominally significant in the other analysis (p < 0.05), identifying plasma TG levels as a novel risk factor for 9 non-ASCVD diseases, including uterine leiomyoma (OR 1.19, 95% CI 1.10-1.29, p = 1.17 × 10-5).ConclusionsTaking a phenome-wide, two-sample MR approach, we identified causal associations between plasma TG levels and 19 disease traits across organ systems. Our findings suggest unrealized drug repurposing opportunities or adverse effects related to approved and emerging TG-lowering agents as well as mechanistic insights for future study.
Data collection from crystals grown in microfluidic droplets
Authors: Babnigg Gyorgy , Sherrell Darren , Kim Youngchang , Johnson Jessica L. , Nocek Boguslaw , Tan Kemin , Axford Danny , Li Hui , Bigelow Lance , Welk Lukas , Endres Michael , Owen Robin L. , Joachimiak Andrzej 
Published: July 2022

Protein crystals grown in microfluidic droplets have been shown to be an effective and robust platform for storage, transport and serial crystallography data collection with a minimal impact on diffraction quality. Single macromolecular microcrystals grown in nanolitre-sized droplets allow the very efficient use of protein samples and can produce large quantities of high-quality samples for data collection. However, there are challenges not only in growing crystals in microfluidic droplets, but also in delivering the droplets into X-ray beams, including the physical arrangement, beamline and timing constraints and ease of use. Here, the crystallization of two human gut microbial hydrolases in microfluidic droplets is described: a sample-transport and data-collection approach that is inexpensive, is convenient, requires small amounts of protein and is forgiving. It is shown that crystals can be grown in 50–500 pl droplets when the crystallization conditions are compatible with the droplet environment. Local and remote data-collection methods are described and it is shown that crystals grown in microfluidics droplets and housed as an emulsion in an Eppendorf tube can be shipped from the US to the UK using a FedEx envelope, and data can be collected successfully. Details of how crystals were delivered to the X-ray beam by depositing an emulsion of droplets onto a silicon fixed-target serial device are provided. After three months of storage at 4°C, the crystals endured and diffracted well, showing only a slight decrease in diffracting power, demonstrating a suitable way to grow crystals, and to store and collect the droplets with crystals for data collection. This sample-delivery and data-collection strategy allows crystal droplets to be shipped and set aside until beamtime is available.
Consumer responses toward LGBTQ+ diversity CSR: what differences do CSR levels and CSR fit make?
Authors: Kim Yeonsoo 
Published: July 2022

PurposeThis study investigated consumer responses to LGBTQ+ specific diversity CSR, taking into account different levels of CSR engagement and perceived CSR fit. Perceived motives were considered as a mediator in the process.Design/methodology/approachAn online experiment was conducted using real consumer samples (n = 376).FindingsAs companies actively demonstrate corporate values to promote LGBTQ+ human rights, consumers recognized that LGBTQ+ diversity CSR was being pursued out of altruistic motives for social good stemming from business ethics and morals. In addition, it was found that the more active the LGBTQ+ diversity CSR practice, the higher the evaluation of the company among consumers. Regarding CSR fit, perceived fit in LGBTQ+ diversity had a significant effect on both the consumer perception of CSR motive and the company evaluation. In addition to these direct impacts of CSR level and CSR fit, these two factors indirectly influenced corporate evaluation through perceived motivation and consequently affected purchase intention.Originality/valueDespite drastic changes in the legal and social environment related to LGBTQ+ diversity, there are few studies on how consumers will react when companies actively or passively participate in or hesitate and oppose CSR on LGBTQ+ diversity. By presenting empirical evidence of consumer response to LGBTQ+ CSR, this study provided business managers and public relations professionals with the insights they need to make informed decisions about the extent to which they engage in LGBTQ+ diversity CSR.
Premature deindustrialization risk in Vietnam
Authors: Tsukada Yuta 
Published: July 2022

PurposeThis study aims to examine the premature deindustrialization risk in Vietnam.Design/methodology/approachThis study uses a manufacturing–income relationship to conduct an empirical estimation. The latecomer index is adopted in the regression model to identify a downward shift of latecomer's relationship.FindingsThe empirical analysis indicates that there is a risk of premature deindustrialization in the Northern Midlands and Mountain Areas. The provinces with low trade openness or foreign direct investment may experience risk of premature deindustrialization.Practical implicationsThis study proposes technology diffusion as a policy direction to prevent premature deindustrialization. Furthermore, the Vietnamese government should improve the business environment in the Northern Midlands and Mountain Areas by promoting and attracting export-oriented foreign direct investment.Originality/valueThis study is the first to examine premature deindustrialization in Vietnam based on provincial-level data.
Can Arab-origin brands go global? An exploratory study
Authors: Farrag Dalia Abdel Rahman , Abu Gharara Sahar Raafat 
Published: July 2022

Purpose
The purpose of this exploratory paper is to investigate and understand the most important factors that influence Arab-origin brands to go global and to appear in brand valuation studies.

Design/methodology/approach
Initially, content analysis on current literature has been conducted followed by qualitative research in the form of in-depth interviews with marketing experts that own or work for successful Arab-origin brands in Muslim countries. Data has been collected related to brands from Qatar, United Arab Emirates, Egypt, Kuwait and Saudi Arabia. A total of 20 in-depth interviews have been conducted by using face-to-face/online voice recorded method. Interviews have been transcribed, coded and analyzed.

Findings
Findings revealed that the main factors affecting the global branding process for Arab-origin brands are internal as compared to external factors. Some of the factors are common with factors in current literature such as dealing with local competition, however, many new factors as well have been identified like brand essence/meaning, internal marketing, top management support and entering mature markets. Cultural heritage plays a significant role in the strategy, creativity and leadership related to building global brands in Arab/Islamic countries. A preliminary model has been proposed based on the findings.

Research limitations/implications
This study is just a starting point for further research. The interaction and relationship between internal and external factors could be further investigated. For example, top management support can moderate the influence of local competition in global markets (Carpenter and Fredrickson, 2001). The proposed framework should be quantitatively measured across different brands for further analyzing the main factors that influence Arab/Islamic-origin brands to go global and generalizing findings. Furthermore, the role of each factor may differ from one industry to another. For example in service organizations, frontline employees are crucial to the success of the organization and challenging to standardize across global markets. Investigating the different combinations of strategy, creativity and leadership from one global market to another opens doors for further scholarly work in this area.

Originality/value
This is a pioneer study in attempting to understand the most relevant factors influencing Arab-origin brands to go global as compared to Western brands that are commonly researched in the literature. This study opens doors to further research related to Arab-origin brands globalization process as well as provides interesting insights to marketers and brand owners about the real reasons that may hinder and genuinely influence Arab-origin brands from taking their locally successful brands fully global.
The influence of humble leadership on employees’ work engagement: the mediating role of leader knowledge-sharing behaviour
Authors: Al Hawamdeh Nayel 
Published: July 2022

Purpose
This paper empirically aims to investigate the mediating role of leader knowledge-sharing behaviour (LKSB) in the relationship between humble leadership (HL) and work engagement (WE).

Design/methodology/approach
The responses of 321 employees in hospitality organisations in Jordan were collected via an online survey. The study data was then analysed using structural equation modelling.

Findings
The study found that leaders showing humble behaviour were able to share knowledge that ultimately improved employees’ work engagement; thus, confirming that leaders sharing knowledge behaviour mediates the relationship between HL and all three dimensions of work engagement.

Originality/value
This study delves into and sheds further light on HL theory by proposing that LKSB serves as a motivational basis for the relationship between HL and employees’ work engagement. By bolstering the mediating mechanism of LKSB, the findings provide new, deeper insights into the influence of HL on all three dimensions of work engagement.
Species richness, functional traits and climate interactively affect tree survival in a large forest biodiversity experiment
Authors: Liu Xiaojuan , Huang Yuanyuan , Chen Lei , Li Shan , Bongers Franca J. , Castro‐Izaguirre Nadia , Liang Yu , Yang Bo , Chen Yuxin , Schnabel Florian , Tang Ting , Xue Yujie , Trogisch Stefan , Staab Michael , Bruelheide Helge , Schmid Bernhard , Ma Keping 
Published: July 2022

Abstract

Tree survival affects forest biodiversity, structure and functioning. However, little is known about feedback effects of biodiversity on survival and its dependence on functional traits and interannual climatic variability.

With an individual‐based dataset from a large subtropical forest biodiversity experiment, we evaluated how species richness, functional traits and time‐dependent covariates affected annual tree survival rates from age 3–12 (years) after planting 39 species across a diversity gradient from 1 to 2, 4, 8 and 16 tree species.

We found that overall survival rates marginally increased with diversity at the plot level, with large variation among plots within diversity levels. Significant variation among species in survival responses to diversity and changes in these responses with age were related to species functional traits and climatic conditions. Generally, survival rates of conservative species (evergreen, late‐successional species with thick leaves and high carbon to nitrogen ratio but low specific leaf area, leaf phosphorus and hydraulic conductivity) increased with diversity, age and yearly precipitation, whereas acquisitive species showed opposite responses.

Synthesis. Our results indicate that interactions between diversity, species functional traits and yearly climatic conditions can balance survival among species in diverse forests. Planting mixtures of species that differ in functional traits in afforestation projects may lead to a positive feedback loop where biodiversity maintains biodiversity, together with its previously reported beneficial effects on ecosystem functioning.
Pathological tumor long‐to‐short axis ratio as a prognostic factor in patients with thymic epithelial tumors
Authors: Tian Dong , Shiiya Haruhiko , Sato Masaaki , Shinozaki‐Ushiku Aya , Yan Hao‐Ji , Nakajima Jun 
Published: July 2022

AbstractBackgroundThymic epithelial tumors (TETs) exhibit irregular shapes reflective of the heterogeneity in tumor growth and invasive properties. We aimed to identify the prognostic value of the pathological tumor long‐to‐short axis (L/S) ratio in TETs.MethodsA retrospective study was performed on patients with TETs who underwent extended thymectomy between January 1999 and December 2019 in our institute. Patients were divided into two groups according to the threshold of the L/S ratio. Overall survival (OS) and progression‐free survival (PFS) were evaluated by Kaplan‐Meier analysis. The independent prognostic factors of TETs were identified by multivariate analysis. The performance of prediction models for the above survival outcomes with and without the L/S ratio was evaluated using an integrated time‐dependent area under the curve (iAUC).ResultsEligible patients were divided into two groups based on higher (n = 42) and lower (n = 94) L/S ratios according to a threshold value of 1.39. A significant difference was found between the two groups only in disease progression (p = 0.001). Poorer survival outcomes were found from Kaplan‐Meier curves in the higher L/S ratio group (p < 0.05). In the multivariable analysis, the L/S ratio showed significant effects on OS and PFS (p < 0.05). The performance of models with the L/S ratio was better than that without the L/S ratio in predicting survival outcomes.ConclusionsThe pathological tumor L/S ratio is an independent prognostic factor for OS and PFS in patients with TETs, and an L/S ratio >1.39 is associated with worse survival outcomes.