bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 infection causes depletion of monocytic cells through a non-canonical cell death pathway
Authors: Stuck Michelle , Arnow Nicolas D. , Kazmierski Julia , Walper Felix , Goffinet Christine , Bannert Norbert , Cingöz Oya 
Published: December 2022

AbstractProgrammed cell death is a regulatory mechanism to eliminate infected or damaged cells. Several programmed cell death pathways exist, including apoptosis, necroptosis and pyroptosis, which can be distinguished by the cellular molecules involved. Here we show that infection of monocytic cells with HIV-1 causes cell death, which is dose- and cell type dependent and occurs independently of nucleic acid sensing or interferon (IFN) signaling. Death is observed in the case of near full-length viruses that produce viral proteins upon infection, but not in case of a minimal lentiviral vector that does not express viral gene products, demonstrating the necessity of viral gene products or a near-full length RNA genome to trigger death. Inhibition of reverse transcription or integration rescues cells, indicating that a step after integration is responsible. Using mutant viruses, we further narrow down the step in the retroviral replication cycle that triggers death. Inhibition of diverse cell death pathways individually cannot rescue cells from death following infection, consistent with PANoptosis, a cellular death process that cannot be accounted for by any single programmed cell death pathway alone. Our results elucidate the viral and cellular determinants of cell death caused by HIV-1 infection and outline cellular responses that result in the depletion of specific cell populations.
Plant-PLMview: a database for identifyingcis-regulatory sequences with preferential positions in gene-proximal regions of plants
Authors: Rozière Julien , Samson Franck , Guichard Cécile , Correa Margot , Coursol Sylvie , Martin Marie-Laure , Brunaud Véronique 
Published: December 2022

AbstractBackgroundEstablishing relationships between transcription factors and target genes is essential for understanding the mechanisms regulating gene expression, which play a fundamental role in plant adaptation to the local environment. Despite the importance of this research area and the tremendous progress in sequencing methods such as ChIP-seq and DAP-seq, we are still far from a complete reconstruction of thecis-regulatory landscape. Only a small number of transcription factors can be assessed from experimental data to identify theircis-regulatory binding sites. This highlights the role thatin silicoapproaches can play to complement experimental data.ResultsWe have developed Plant-PLMview, a web-accessible database for detecting preferentiallycis-regulatory sequences in the gene-proximal regions of 20 plant species. Users of Plant-PLMview can (i) access the proximal regions of controlled genes from 20 plant species, (ii) query their own DNA motifs or access 840cis-regulatory sequences from various plant resources, and (iii) use a tool called PLMdetect to search for preferentially located motifs in the gene-proximal regions of a list of genes. Results are displayed via a web interface with a list of DNA motifs preferentially located in a region near the start or end of genes, the distribution of these motifs and associated annotations. In addition, a graphical map of the preferential locations of the motifs in the 5’ and 3’-proximal regions of genes provides an overview of all motifs and genes examined.ConclusionPlant-PLMview provides the opportunity to study the proximal landscape of gene regulation in 20 plant genomes. The originality of the database lies in its ease of use thanks to the curated data (cis-regulatory sequences and proximal regions of genes) and the possibility to search through PLMdetect in the 5’-gene-proximal region, but also in the 3’-gene-proximal region, which is rarely explored. The web interface provides numerous graphical views that allow the users to get an overview and interpret the results more easily.
Pro- and anti-tumour activities of CD146/MCAM in breast cancer result from its heterogeneous expression and association with epithelial to mesenchymal transition
Authors: Mannion Aarren J. , Odell Adam F. , Baker Syed Murtuza , Matthews Laura C. , Jones Pamela F. , Cook Graham P. 
Published: December 2022

AbstractCD146, also known as melanoma cell adhesion molecule (MCAM), is expressed in numerous cancers and has been implicated in the regulation of metastasis. We show that CD146 negatively regulates transendothelial migration (TEM) in breast cancer. This tumour suppressor-like activity is supported by a reduction in MCAM gene expression and increased promoter methylation in tumour tissue compared to normal breast tissue. However, increased CD146/MCAM expression is associated with poor prognosis in breast cancer, a characteristic that is difficult to reconcile with inhibition of TEM by CD146 and its epigenetic silencing. Single cell transcriptome data revealed MCAM expression in multiple cell types, including the tumour vasculature and malignant epithelial cells. MCAM expressing tumour cells were in the minority and expression was associated with epithelial to mesenchymal transition (EMT). Furthermore, gene expression signatures defining invasiveness and a stem cell-like phenotype were most strongly associated with mesenchymal-like tumour cells with low levels of MCAM mRNA, likely to represent an intermediate or hybrid E/M state. Our results show that high levels of MCAM gene expression are associated with poor prognosis in breast cancer because they reflect tumour vascularisation and EMT. However, the inhibitory effects of CD146 on TEM are likely to be weakest in an intermediate state between the epithelial and mesenchymal phenotypes, consistent with highly tumourigenic nature of this population.
Single-cell profiling uncovers aMuc4-expressing metaplastic gastric cell type sustained byHelicobacter pylori-specific inflammation
Authors: O’Brien Valerie P. , Kang Yuqi , Shenoy Meera K. , Finak Greg , Young William C. , Dubrulle Julien , Koch Lisa , Rodriguez Martinez Armando E. , Snow Jazmine A. , Williams Jeffery , Donato Elizabeth , Batra Surinder K. , Yeung Cecilia C.S. , Bullman Susan , Koch Meghan A. , Gottardo Raphael , Salama Nina R. 
Published: December 2022

AbstractMechanisms forHelicobacter pylori(Hp)-driven stomach cancer are not fully understood. In a transgenic mouse model of gastric preneoplasia, concomitantHpinfection and induction of constitutively active KRAS (Hp+KRAS+) alters metaplasia phenotypes and elicits greater inflammation than either perturbation alone. Gastric single-cell RNA-seq showed thatHp+KRAS+ mice had a large population of metaplastic pit cells that expressed the intestinal mucinMuc4and the growth factor amphiregulin. Metaplastic pit cells were associated with macrophage and T cell inflammation and prevented by gastric immunosuppression. Lineage tracing showed thatMuc4was not dependent on cell-intrinsic KRAS activity, and lineage-derived cells had a limited propensity for growth as organoids, demonstrating that metaplastic pit cells are largely not self- renewing. Finally, MUC4 expression was significantly associated with proliferation in human gastric cancer samples. These studies identify anHp-associated metaplastic pit cell lineage, also found in human gastric cancer tissues, whose expansion is driven byHp-dependent inflammation.Statement of SignificanceUsing a mouse model, we have delineated metaplastic pit cells as a pre-cancerous cell type whose expansion requiresH. pylori-driven inflammation. In humans, metaplastic pit cells show enhanced proliferation as well as enrichment in precancer and early cancer tissues, highlighting an early step in the gastric metaplasia to cancer cascade.
Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri
Authors: Ragupathy R , Jolley K. A. , Zamuner C. , Jones J. B. , Redfern J. , Behlau F. , Ferreira H. , Enright M.C. 
Published: December 2022

AbstractXanthomonas citrisubspeciescitri(XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. OtherX. citrisubsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread ofX. citridisease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes.In this study we developed a core genome multilocus typing scheme (cgMLST) forX. citribased upon 250 genomes comprising multiple examples ofX. citrisubsp.citripathotypes A, A* and Aw,X. citrisubsp.malvacearumandX. citripathovarsaurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vignicolaand single isolates ofX. citripathovarsdieffenbachiaeandpunicae. This dataset included genomic sequencing of 100 novel XCC isolates. The cgMLST scheme, based upon 1618 core genes across 250 genomes, has been implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). Grapetree minimum-spanning, and iTOL Neighbour-joining phylogenies generated from cgMLST data resolved almost identical groupings of isolates to a core genome SNP - based neighbour joining phylogeny taking 4 min, 15 min and 36 h respectively. These resolved identical groupings of XCC pathotypes andX. citrisubsp. and pathovars.X. citricgMLST should prove to be an increasingly valuable resource for the study of this key species of plant pathogenic bacteria. Users can submit genomic and associated metadata to compare with previously characterised isolates atPubMLST.orgto allow rapid characterization of local, national and global epidemiology of these pathogens and examine evolutionary relationships.
Unpacking the value conversion in a circular business model: exploring the effect of competitive criteria
Authors: Galvão Graziela Darla Araujo , Ferrer Paulo Sergio Scoleze , Evans Steve , Carvalho Marly Monteiro de 
Published: December 2022

PurposeThis research aims to investigate the influence of the implementation of technical cycles on both captured value and shared value in the circular economy context. Moreover, it analyses the moderating effect of competitive criteria on the relationship between technical cycles and captured value. Finally, it examines the relationship between the captured value and the shared value.Design/methodology/approachThis research follows survey-based research with data gathered from 50 countries and 16 sectors, whose final sample represented 233 organisations. In order to validate the structural and measurement model, the authors applied the partial least squares structural equation modelling technique in the strict rigour of the confirmatory algorithm.FindingsThe validated research model demonstrates the value flow through technical cycles. Moreover, it shows the crucial role of the competitive criteria in the value stream through direct, moderate and indirect effects by influencing the relationship between technical cycles and captured and shared values. Finally, the study fills the gap for quantitative studies in the circular economy field.Practical implicationsFrom a practical perspective, this study contributes to structuring circular business models more robustly, by understanding the influence of competitive criteria (cost, quality, flexibility and delivery) on the conversion of operation strategy in the implementation of the technical cycles in the circular economy context. It contributes to decision-makers, in deciding on which competitive criteria to invest more, which brings more consistent results for technical cycle implementation. It also confirms the importance of partnerships, demonstrating how value cascades from the company through the value network.Originality/valueAs far as is known to date, this is the first study investigating the influence of competitive criteria in the circular economy context. Furthermore, it sheds light on the direct and indirect effects of the technical cycles on value captured by organisations and flow shared value with other players.
Ultrasonic washing as an abiotic elicitor to increase the phenolic content in fruits and vegetables: A review
Authors: Hong Chen , Zhao Yi‐Ming , Zhou Cunshan , Guo Yiting , Ma Haile 
Published: December 2022

AbstractUltrasonic washing has been widely applied to the postharvest storage of fruits and vegetables as a residue‐free physical washing technology, which plays an important role in improving shelf‐life, safety, and nutritional value. Phenolics are a large group of phytochemicals widespread in fruits and vegetables, and they have been considered potential protective factors against some diseases because of potent antioxidative properties. Previous studies have shown that ultrasonic washing can increase the phenolic content of fruits and vegetables immediately or during storage through the induction of plant stress responses, which is of great significance for improving the functional and nutritional value of fruits and vegetables. However, the mechanisms of ultrasound as an elicitor to improve the phenolic content remain controversial. Therefore, this review summarizes the applications of ultrasonic washing to increase the phenolic content in fruits and vegetables. Meanwhile, the corresponding physiological stress response mechanisms of the phenolic accumulation in terms of immediate stress responses (i.e., higher extractability of phenolics) and late stress responses (i.e., metabolism of phenolics) are expounded. Moreover, a hypothetical model is proposed to explain phenolic biosynthesis triggered by signaling molecules produced under ultrasound stress, including primary signal (i.e., extracellular adenosine triphosphate) and secondary signals (e.g., reactive oxygen species, Ca2+, NO, jasmonates, and ethylene). Additionally, the techno‐economic feasibility of ultrasonic washing technology is also discussed. Further, challenges and trends for further development of ultrasonic washing as an abiotic elicitor applied to the postharvest storage of fruits and vegetables are presented.
Worksite health promotion for employees working from home: A vignette experiment examining intentions to participate
Authors: van der Put Anne C. , Mandemakers Jornt J. , de Wit John B. F. , van der Lippe Tanja 
Published: December 2022

AbstractThis study explores which factors affect employees' intention to participate in worksite health promotion (WHP) when they work from home. Employees increasingly work from home, yet existing WHP is mainly tied to the workplace. We lack knowledge on what might stimulate employees to make use of WHP specifically when they work from home. Drawing on the theory of reasoned action, we studied whether type of activity, duration, if WHP takes place during work time, how often employees work from home (shaping employees' attitude) and colleague participation (social norms) explain employees' intention to participate in WHP when working from home. To do so, we employed a vignette experiment. Results show that employees' intentions are higher for walking and taking breaks than for an online sports class. Moreover, intentions are higher for shorter activities and when participating in WHP can be done during work time. The more colleagues participate, the higher intentions of employees to do so too. By offering WHP for employees at home, employers can promote employees' health even when these are not present in the workplace. Our study provides leads into how employers may create conditions under which employees use WHP when working from home.
The oncogenic driving force of CD30 signaling‐induced chromosomal instability in adult T‐cell leukemia/lymphoma
Authors: Nakashima Makoto , Utsunomiya Atae , Watanabe Toshiki , Horie Ryouichi , Uchimaru Kaoru 
Published: December 2022

AbstractAdult T‐cell leukemia/lymphoma (ATL) develops via stepwise accumulation of gene mutations and chromosome aberrations. However, the molecular mechanisms underlying this tumorigenic process are poorly understood. We previously reported the presence of a biological link between the expression of CD30, which serves as a marker for ATL progression, and the actively proliferating fraction of human T‐cell leukemia virus type 1 (HTLV‐1)‐infected cells that display polylobulation. Here, we demonstrated that CD30 signaling induced chromosomal instability with clonal expansion through DNA double‐strand breaks (DSBs) via an increase of intracellular reactive oxygen species. CD30+ATL cells were composed of subclones with additional genomic aberrations compared with CD30−ATL cells in ATL patients. Furthermore, we found an accumulation of copy number loss of DSB repair‐related genes as the disease progressed. Taken together, CD30 expression on ATL cells appears to be correlated with genomic instability, suggesting that CD30 signaling is one of the oncogenic factors of ATL progression with clonal evolution. This study provides new insight into the biological roles of CD30 signaling and could improve our understanding of tumorigenic processes of HTLV‐1‐infected cells.
Prostaglandins differentially modulate mucosal‐associated invariant T‐cell activation and function according to stimulus
Authors: Mehta Hema , Tasin Irene , Hackstein Carl Philipp , Willberg Christian , Klenerman Paul 
Published: December 2022

AbstractMucosal‐associated invariant T (MAIT) cells are an innate‐like T‐cell type conserved in many mammals and especially abundant in humans. Their semi‐invariant T‐cell receptor (TCR) recognizes the major histocompatibility complex–like molecule MR1 presenting riboflavin intermediates associated with microbial metabolism. Full MAIT cell triggering requires costimulation via cytokines, and the cells can also be effectively triggered in a TCR‐independent manner by cytokines [e.g. interleukin (IL)‐12 and IL‐18 in combination]. Thus, triggering of MAIT cells is highly sensitive to local soluble mediators. Suppression of MAIT cell activation has not been well explored and could be very relevant to their roles in infection, inflammation and cancer. Prostaglandins (PG) are major local mediators of these microenvironments which can have regulatory roles for T cells. Here, we explored whether prostaglandins suppressed MAIT cell activation in response to TCR‐dependent and TCR‐independent signals. We found that protaglandin E2 (PGE2) and to a lesser extent protaglandin D2 (PGD2), but not leukotrienes, suppressed MAIT cell responses to Escherichia coli or TCR triggers. However, there was no impact on cytokine‐induced triggering. The inhibition was blocked by targeting the signaling mediated via PG receptor 2 (PTGER2) and 4 (PTGER4) receptors in combination. These data indicate that prostaglandins can potentially modulate local MAIT cell functions in vivo and indicate distinct regulation of the TCR‐dependent and TCR‐independent pathways of MAIT cell activation.
Some Metabolic Characteristics of Dairy Cows with Different Post Partum Ovarian Function
Authors: Huszenicza G. , Haraszti J. , Molnár L. , Solti L. , Fekete S. , Ekés K. , Yaro A. C. 
Published: December 2022

SummaryThe metabolic characteristics of cows with different post partum ovarian functions were investigated in 66 third‐fifth calving animals. For monitoring the metabolic status blood samples were taken in 1st, 3rd, 5th and 8 —10th post partum week. The glutamatc‐oxalacetate transaminase (GOT) activity, blood glucose level as well as the albumin, acetoacetic acid + acetone (ketone), non‐esterified fatty acid (NEFA), total cholesterol (TCH) and total carotene values in serum/plasma were determined. Milk samples were collected twice a week for 80—90 days after calving for progesterone analysis. In the same period rectal palpation was carried out every 7—14 days.The cows with delayed onset of cyclicity, secondary acyclicity or irregular cyclicity showed considerably higher ketone and NEFA and obviously lower TCH and carotene levels than their mates with normal ovarian functions. The duration rather than the momentary degree of energy imbalance could influence the occurrence of these ovarian disorders. In case of cystic ovaries only slight metabolic differences were observed.
Local and General Effects of Salmonella typhimuHum Endotoxin in Calves
Authors: Luthman J. , Kindahl H. , Jacobsson S. O. , Thunberg L. 
Published: December 2022

SummaryEndotoxin from Salmonella typhimurium was injected intravenously and into subcutaneously implanted tissue cages in calves. Intravenous injection of the doses 2μg/kg and 0.25μg/kg was followed by severe clinical signs, but the pyrogenic response was irregular. There was a dose‐related increase in the plasma level of IS‐ketodihydro‐PGF2α the main metabolite of PGF2α. The number of blood leukocytes decreased significantly immediately after the injection, but after 24 hours there was an increase far above the preinjection number. The serum levels of iron, zinc and calcium decreased significantly after the injection. The responses were similar to both doses of endotoxin.The clinical counterparts to tissue cages are abscesses. It was concluded that endotoxin was released very slowly after injection into the cage as there were no changes in the serum concentrations of trace elements or in 15‐ketodihydro‐PGF2α Injection into the cage was followed by a dose‐ dependent increased of PGE2 in tissue cage fluid, while there were no changes in the concentration of trace elements. The leukocyte response was variable and it is therefore probable that PGE2 was produced entirely by the tissue within the cage. The results show that tissue cages may be a suitable model for the study of local inflammatory reactions.
Long‐term determinants of valuation effects
Authors: Kim Soyoung , Min Kyunghee 
Published: December 2022

AbstractThe progression of financial globalization increases the importance of valuation changes of foreign assets and liabilities, similar to that of current account in explaining the recent net foreign asset position of countries around the world. This study analyzes the long‐term determinants of valuation effects by using panel regression with 10‐year data span of 188 countries. The main findings are as follows. First, the size of foreign assets and relative portion of risky assets are positively associated with valuation effects, which suggests that general principles for long‐term individual investors also hold for an entire country. Second, current account is negatively associated with valuation effects, which suggests that these two mechanisms stabilize each other in overall international adjustment process. Third, exchange rate changes are often positively associated with valuation effects, which at times depend on foreign asset and liability positions. Fourth, per capita GDP are negatively associated with valuation effects. Fifth, current account is mainly associated with valuation effects due to asset price changes, but exchange rate changes and foreign asset and liability positions are mainly associated with valuation effects due to exchange rate changes. The relative proportion of risky assets is associated with both types of valuation effects.