bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutrophils prime unique transcriptional responses in intestinal organoids during infection with nontyphoidalSalmonella entericaserovars
Authors: Lawrence Anna-Lisa E. , Berger Ryan P. , Hill David R. , Huang Sha , Yadagiri Veda K. , Bons Brooke , Fields Courtney , Knight Jason S. , Wobus Christiane E. , Spence Jason R. , Young Vincent B. , Abuaita Basel H. , O’Riordan Mary X. 
Published: August 2022

AbstractNontyphoidal strains ofSalmonella entericaare a major cause of foodborne illnesses and infection with these bacteria result in inflammatory gastroenteritis. Neutrophils are a dominant immune cell type found at the site of infection inSalmonella-infected individuals, but how they regulate infection outcome is not well understood. Here we used a co-culture model of primary human neutrophils and human intestinal organoids to probe the role of neutrophils during infection with two of the most prevalentSalmonellaserovars:Salmonella entericaserovar Enteritidis and Typhimurium. Using a transcriptomics approach, we identified a dominant role for neutrophils in mounting differential immune responses including production of pro-inflammatory cytokines, chemokines, and antimicrobial peptides. We also identified specific gene sets that are induced by neutrophils in response to Enteritidis or Typhimurium infection. By comparing host responses to these serovars, we uncovered differential regulation of host metabolic pathways particularly induction of cholesterol biosynthetic pathways during Typhimurium infection and suppression of RNA metabolism during Enteritidis infection. Together these findings provide insight into the role of human neutrophils in modulating different host responses to pathogens that cause similar disease in humans.ImportanceNontyphoidal serovars ofSalmonella entericaare known to induce robust neutrophil recruitment in the gut during early stages of infection, but the specific role of neutrophils in regulating infection outcome of different serovars is poorly understood. Due to differences in human infection progression compared to small animal models, characterizing the role of neutrophils during infection has been challenging. Here we used a co-culture model of human intestinal organoids with human primary neutrophils to study the role of neutrophils during infection of human intestinal epithelium. Using a transcriptomics approach, we define neutrophil-dependent reprogramming of the host response toSalmonella, establishing a clear role in amplifying pro-inflammatory gene expression. Additionally, the host response driven by neutrophils differed between two similar nontyphoidalSalmonellaserovars. These findings highlight the importance of building more physiological infection models to replicate human infection conditions to study host responses specific to individual pathogens.
Retrotransposons facilitates tissue specific horizontal transfer of circulating tumor DNA between human cells
Authors: Cinar Munevver , Martinez-Medina Lourdes , Puvvula Pavan K. , Arakelyan Arsen , Vardarajan Badri N. , Anthony Neil , Nagaraju Ganji P. , Park Dongkyoo , Feng Lei , Sheff Faith , Mosunjac Marina , Saxe Debra , Flygare Steven , Alese Olatunji B. , Kaufman Jonathan , Lonial Sagar , Sarmiento Juan , Lossos Izidore S. , Vertino Paula M. , Lopez Jose A. , El-Rayes Bassel , Bernal-Mizrachi Leon 
Published: August 2022

AbstractA variety of organisms have been shown to have altered physiology or developed pathology due to gene transfer, but mammals have never been shown to do so. Here, we show that circulating tumor DNA (ct) can promote cell-specific horizontal gene transfer (HGT) between human cancer cells and explain the mechanisms behind this phenomenon. Once ctDNA enters the host cell, it migrates to the nucleus and integrates into the cell’s genome, thereby transferring its genetic information. We determine that retrotransposons of the ERVL, SINE, and LINE families are necessary for cell targeting and the integration of ctDNA into host DNA. Using chemically synthesized retrotransposons, we found that AluSp and MER11C reproduced multiple myeloma’s (MM) ctDNA’s cell targeting and integration into MM cells. We also discovered that ctDNA might, as a result of HGT, influence the treatment response of multiple myeloma and pancreatic cancer models. Overall, this is the first study to show that retrotransposon-directed HGT can promote genetic material transfer in cancer. There is, however, a broader impact of our findings than just cancer since cell-free DNA has also been found in physiological and other pathological conditions as well. Furthermore, with the discovery of transposons-mediated tissue-specific targeting, a new avenue for the delivery of genes and therapies will emerge.
A genomic timescale for placental mammal evolution
Authors: Foley Nicole M. , Mason Victor C. , Harris Andrew J. , Bredemeyer Kevin R. , Damas Joana , Lewin Harris A. , Eizirik Eduardo , Gatesy John ,   Zoonomia Consortium, Springer Mark S. , Murphy William J. 
Published: August 2022

AbstractThe precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signal using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic timetrees reveal an accumulation of cladogenic events before and immediately following the KPg boundary implying important roles for Cretaceous continental vicariance and the KPg extinction in the placental radiation.One-Sentence SummaryA comprehensive whole genome phylogeny of extant placental mammals reveals timing and patterns of ordinal diversification.
Mouse SAS-6 is required for centriole formation in embryos and integrity in embryonic stem cells
Authors: Grzonka Marta , Bazzi Hisham 
Published: August 2022

AbstractCell division fidelity is crucial for stem cell propagation and the maintenance of pluripotency. Centrosomes, which organize the mitotic spindle microtubules to ensure proper bipolar cell division, have a core of a pair of centrioles that duplicate once per cell cycle. At the onset of centriole biogenesis, SAS-6 forms a cartwheel structure, which is the precursor for the forming procentrioles. SAS-6 is essential for centriole formation in human cell lines and other organisms. However, the functions of SAS-6 in mouse stem cells remain to be elucidated. Here, we report thatSas-6-null mouse embryos lack centrioles, activate the mitotic surveillance cell death pathway and arrest at mid-gestation. In contrast, SAS-6 is not strictly required for centriole formation in mouse embryonic stem cells (mESCs)in vitro, but is still important to regulate centriole length, symmetry and ability to template cilia. Remarkably, centrioles appeared after just one day of culture ofSas-6-null blastocysts, from which mESCs are normally derived. Finally, the number of cells with centrosomes is drastically decreased upon the exit from a pluripotent state. Collectively, our data suggest a differential requirement for mouse SAS-6 in centriole formation or integrity depending on the cellular context, and highlight the robustness of mESCs in using SAS-6-independent centriole-duplication pathways.
Fission yeast Dis1 is an unconventional TOG/XMAP215 that induces microtubule catastrophe to drive chromosome pulling
Authors: Murase Yuichi , Yamagishi Masahiko , Okada Naoyuki , Toya Mika , Yajima Junichiro , Hamada Takahiro , Sato Masamitsu 
Published: August 2022

AbstractThe shortening of microtubules attached to kinetochores is the driving force of chromosome movement during cell division. Specific kinesins are believed to shorten microtubules but are dispensable for viability in yeast, implying the existence of additional factors responsible for microtubule shortening. Here, we demonstrate that Dis1, a TOG/XMAP215 ortholog in fission yeast, promotes microtubule shortening to carry attached chromosomes. Although TOG/XMAP215 orthologs are generally accepted as microtubule polymerases, Dis1 promoted microtubule catastrophe in vitro and in vivo. Notably, microtubule catastrophe was promoted when the tip was attached to kinetochores, as they steadily anchored Dis1 at the kinetochore-microtubule interface. Engineered Dis1 oligomers artificially tethered at a chromosome arm region induced the shortening of microtubules in contact, frequently pulling the chromosome arm towards the vicinity of spindle poles in meiocytes. Thus, unlike Alp14 and other TOG/XMAP215 orthologs, Dis1 plays an unconventional role in promoting microtubule catastrophe, thereby driving chromosome movement.
‘Targeting’ the Search: An Upgraded Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets
Authors: Ravichandran Shashank , Avatapalli Sai Supriya , Narasimhan Yatindrapravanan , Kaushik Karishma S , Yennamalli Ragothaman M 
Published: August 2022

AbstractBacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein function, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations (∼1.18 µs). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional classification in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.
Stock liquidity and the accrual anomaly
Authors: Cheng Zhuo (June) , Fang Jing (Bob) 
Published: August 2022

PurposeThis study examines the effect of stock liquidity on the magnitude of the accrual anomaly.Design/methodology/approachThis paper examines the relation—both time-series and cross-sectional—between stock liquidity and the magnitude of the accrual anomaly and use the 2001 minimum tick size decimalization as a quasi-experiment to establish causality.FindingsThere is both cross-sectional and time-series evidence that stock liquidity is negatively related to the magnitude of the accrual anomaly. Moreover, the extent to which investors overestimate the persistence of accruals decreases with stock liquidity. Results from a difference-in-differences analysis conducted using the 2001 minimum tick size decimalization as a quasi-experiment suggest that the effect of stock liquidity on the accrual anomaly is causal. The findings of this study are consistent with the enhancing effect of stock liquidity on pricing efficiency.Originality/valueThe study's findings are well aligned with the mispricing-based explanation for the accrual anomaly, suggesting that the improvement in market-wide stock liquidity drives the contemporaneous decline in the magnitude of the accrual anomaly, at least to a great extent.
Are individual risky behaviours relevant to healthcare allocation decisions? An exploratory study
Authors: Pinho Micaela , Durão Natércia , Zahariev Boyan 
Published: August 2022

PurposeThe problematic surrounding patients' prioritization decisions are currently at the centre of political leaders' concerns. How to define whom to treat when there are not enough resources to treat everybody is the key question. This exploratory study aims to investigate the views of Bulgarian citizens regarding the relevance of the information concerning eight individual health-related behaviours in priority setting decisions: smoking, excess of alcohol, illegal drug use, overweight/obesity, speed driving, extreme sports practice, unsafe sex and overuse of internet and/or mobile devices.Design/methodology/approachData were collected through a questionnaire where 322 respondents faced hypothetical rationing dilemmas comprising option pairs of the eight risky behaviours. Descriptive statistics and non-parametric tests were performed to define the penalization of each of the risky behaviours and to test for the association between this penalization and the respondent's health habits and sociodemographic characteristics.FindingsMost respondents would refuse to grant access to healthcare based on patients' personal responsibility for the disease. Nevertheless, respondents were more willing to consider illegal drug use, excessive alcohol consumption, engagement in unsafe sex behaviours and smoking. Respondent's own interest or advantage seems to be somehow relevant in explaining the penalization of risk behaviours in priority setting.Practical implicationsThis study shows that most respondents support the lottery criterion and thus do not want to see lifestyle prioritization in action.Originality/valueThis study is the first attempt to awaken attention to the impact that personal responsibility for health may have on intergenerational access to healthcare in Bulgaria.
Drivers of behavioral intention among non-Muslims toward halal cosmetics: evidence from Indonesia, Malaysia, and Singapore
Authors: Septiarini Dina Fitrisia , Ratnasari Ririn Tri , Salleh Marhanum Che Mohd , Herianingrum Sri , Sedianingsih Sedianingsih 
Published: August 2022

Purpose
This study aims to examine the halal brand image, halal logo and halal awareness of non-Muslim customers on attitude and behavioral intention.

Design/methodology/approach
This study uses a quantitative survey approach to 400 respondents consisting of 400 non-Muslim millennials in Indonesia, Malaysia and Singapore who have to buy halal cosmetics two years later. The sampling technique is purposive sampling. The analysis technique used in this study is structural equation modeling.

Findings
This study showed that halal logo, halal awareness and halal brand image have an effect on customer attitude. Then, the halal logo, halal awareness and halal brand image have an influence on behavioral intention. The existence of this positive signal has provided a great opportunity for businesses to make profits by meeting the demand for the halal market. Consumption of halal cosmetics produced by manufacturers attracts many non-Muslim consumers because of the safety, comfort and cleanliness of product ingredients, which of them must be given by the halal product, especially for cosmetics.

Research limitations/implications
This study broadens the understanding of the attitudes and behavioral intentions of non-Muslim consumers toward halal cosmetic products. Furthermore, this research has provided a deeper interpretation of non-Muslim understanding of halal logos, halal brand images and halal awareness which have been minimal in research studies.

Originality/value
This study contributes to the literature related to the behavioral intentions of millennial non-Muslim consumers for halal cosmetics. Therefore, respondents in the study were specific, that is, non-Muslims who are millennial generation in the Indonesia, Malaysia and Singapore context.
Coordinating a reverse supply chain under stochastic demand and uncertain quality of returned products
Authors: Giri Bibhas Chandra , Dey Sushil Kumar 
Published: August 2022

PurposeThe purpose of this study is to investigate the impact of greening and promotional effort dependent stochastic market demand on the remanufacturer's and the collector's profits when the quality of used products for remanufacturing is uncertain in a reverse supply chain.Design/methodology/approachThe proposed model is developed to obtain optimal profits for the remanufacturer, the collector and the whole supply chain. Both the centralized and decentralized scenarios are considered. To motivate the collector through profit enhancement, the remanufacturer designs a cost-sharing contract. Through numerical examples and sensitivity analysis, the consequences of greenness and promotional effort on optimal profits are investigated.FindingsThe results show that the remanufacturer gets benefited from greening and promotional effort enhancement. However, a higher value of minimum acceptable quality level decreases the profits of the manufacturer and the collector. A cost-sharing contract coordinates the supply chain and improves the remanufacturer's and the collector's profits. Besides green innovation, remanufacturing mitigates the harmful effects of waste in the environment.Originality/valueTwo different viewpoints of remanufacturing are considered here – environmental sustainability and economic sustainability. This paper considers a reverse supply chain with a remanufacturer who remanufactures the used products collected by the collector. The quality of used products is uncertain, and customer demand is stochastic, green and promotional effort sensitive. These two types of uncertainty with green and promotional effort sensitive customer demand differs the current paper from the existing literature.
A research framework to analyse visual persuasion of photographs in sustainability reports
Authors: Chong Sabrina , Momin Mahmood , Narayan Anil 
Published: August 2022

Purpose
This paper aims to propose a theoretically informed and analytically rigorous research framework that sustainability researchers could use or further develop to examine visually persuasive messages in photographs.

Design/methodology/approach
Drawing on the theoretical constructs of Peirce’s (1991) visual semiotic system of icon, index and symbol and Aristotle’s (1984) persuasive appeals of ethos, pathos and logos, the authors propose a research methodology that provides an explicit step-by-step guidance to examine visually persuasive messages in sustainability-related photographs. The sustainability-related photographs in The Coca-Cola Company’s 2018 Business and Sustainability Report are examined to illustrate the application of the framework.

Findings
This paper develops a research framework and provides empirical evidence of the use of the framework to enhance the understanding of visually persuasive messages depicted in photographs.

Practical implications
The proposed framework serves as a springboard for further research into visually persuasive messages.

Originality/value
The research framework of visual persuasion is novel and can be used by sustainability researchers to analyse photographs in corporate reports. It can be extended/modified to capture visual representations in different contexts and other disciplines as well.
Effect of local‐ and landscape‐scale factors on the distribution of the spring‐dependent species Geothelphusa dehaani and larval Anotogaster sieboldii
Authors: Hirano Yuna , Kobayashi Miho , Hashimoto Yuka , Kato Hiroki , Nishihiro Jun 
Published: August 2022

AbstractKnowledge of the effects of local‐ and landscape‐scale environmental factors is indispensable for the conservation of wetland biodiversity. We surveyed the distribution and abundance of two spring‐dependent invertebrates, the Japanese freshwater crab Geothelphusa dehaani and larvae of dragonfly Anotogaster sieboldii, at 37 spring‐fed wetlands in the Lake Inba watershed, Japan. The relationships among local factors (water temperature, channel‐water velocity, substrate type, and abundance of the red swamp crayfish Procambarus clarkii), a landscape‐scale factor (the percentage of permeable surface in catchment; PPSC), and catch per unit effort (CPUE) of each species were analyzed using path analyses. PPSC indirectly affected the CPUE of both G. dehaani and A. sieboldii via different processes. For G. dehaani, PPSC affected the CPUE via a positive effect on channel‐water velocity and substrate composition in the wetland. On the other hand, PPSC positively affected the CPUE of A. sieboldii by decreasing the summer water temperature. Red swamp crayfish had no significant direct effects on either species, although we found a significant negative effect of channel‐water velocity on the distribution of red swamp crayfish. For conservation of these spring‐dependent species, we suggest preserving the area of permeable surface in the watershed in order to maintain flow velocity and low water temperature in wetlands.