bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phagocytosis underpins the biotrophic lifestyle of intracellular parasites in the class Phytomyxea (Rhizaria)
Authors: Garvetto Andrea , Murúa Pedro , Kirchmair Martin , Salvenmoser Willibald , Hittorf Michaela , Ciaghi Stefan , Harikrishnan Srilakshmy L. , Gachon Claire M.M. , Burns John A. , Neuhauser Sigrid 
Published: September 2022

SummaryPhagocytosis is a complex multi-gene trait of eukaryotes and allegedly one of the very defining features of this group. Although well documented for free-living unicellular eukaryotes and in specific cellular types of animals, data on phagocytosis in intracellular biotrophic parasites are scant. Indeed, the definition of intracellular biotrophy as complete reliance of a parasite on a living host, with which it constantly negotiates for the exchange of nutrients, is at odd with the consumption of particulate matter suggested by phagocytosis. Phytomyxea are intracellular biotrophic parasites infecting a broad group of hosts, ranging from plants to stramenopiles. They belong to the clade Rhizaria, where phagotrophy (i.e., phagocytosis as main mode to acquire nutrients) is the main mode of nutrition. The exact mode of nutrition of the biotrophic phytomyxea, including the agriculturally impactful phytomyxid Plasmodiophora brassicae, is still unresolved; despite investigations and the availability of molecular data. For other Phytomyxea, observations are patchy and molecular data altogether lacking. Here, using available genomic and transcriptomic data for Phytomyxea and the de novo sequenced transcriptome of the brown algae parasite Maullinia ectocarpii, we investigate the likelihood that the genetic machinery underpinning phagotrophy is conserved within the clade. We further document intracellular phagocytosis in P. brassicae and M. ectocarpii by transmission electron microscopy and fluorescent in situ hybridization. Our investigations confirm that molecular signatures underpinning phagocytosis exist in Phytomyxea and hint at a smaller subset of genes used for intracellular phagocytosis, which is similar between the two parasites. Microscopic evidence confirms the existence of intracellular phagocytosis, which seems to coexist with the manipulation of host physiology typical of biotrophic interactions. In both phytomyxid parasites investigated intracellular phagocytosis has adapted to the intracellular environment and seemingly targets specific organelles. Our findings shed light on the feeding behaviour of Phytomyxea, providing new molecular data for the class; and suggest a paramount and previously unrecognised role for phagocytosis in biotrophic interactions between host and parasite.
Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy
Authors: Sayin Serkan , Rosener Brittany , Li Carmen G , Ho Bao , Ponomarova Olga , Ward Doyle V , Walhout Albertha JM , Mitchell Amir 
Published: September 2022

AbstractDrug metabolism by the microbiome can influence anti-cancer treatment success. We previously suggested that chemotherapies with antimicrobial activity can select for adaptations in bacterial drug metabolism that can inadvertently influence the host’s chemoresistance. We demonstrated that evolved resistance against fluoropyrimidine chemotherapy lowered its efficacy in worms feeding on drug-evolved bacteria (Rosener et al., 2020). Here we examine a model system that captures local interactions that can occur in the tumor microenvironment. Gammaproteobacteria colonizing pancreatic tumors can degrade the nucleoside-analog chemotherapy gemcitabine and, in doing so, can increase the tumor’s chemoresistance. Using a genetic screen inEscherichia coli, we mapped all loss-of-function mutations conferring gemcitabine resistance. Surprisingly, we found that one third of resistance mutations increase or decrease bacterial drug breakdown and therefore can either lower or raise the gemcitabine load in the local environment. Experiments in threeE. colistrains revealed that evolved adaptation converged to inactivation of the nucleoside permease NupC, an adaptation that increased the drug burden on co-cultured cancer cells. The two studies provide complementary insights on the potential impact of microbiome adaptation to chemotherapy by showing that bacteria-drug interactions transpire locally and systemically and can influence chemoresistance in the host.
The DEPDC1 protein LET-99 is required for cortical stability and antagonizes branched actin formation to promote robust cytokinesis
Authors: Price Kari L. , Lamb Helen , Alvarado Jocelyn V. , Rose Lesilee S. 
Published: September 2022

AbstractDuring cytokinesis, signals from the central spindle stimulate the accumulation of active RhoA-GTPase and thus contractile ring components at the equator, while the astral microtubules inhibit such components at the polar cortex. The DEPDC1 family protein LET-99 is required for furrow ingression in the absence of the central spindle signal, and for timely onset of furrowing even in the presence of the central spindle signal. Here we show that LET-99 works downstream or independently of RhoA-GTP and antagonizes branched F-actin and the Rac protein CED-10 to promote furrow initiation. This interaction with CED-10 is separable from LET-99’s function in spindle positioning. We also characterize a new role for LET-99 in regulating cortical stability, where LET-99 acts in parallel with the actomyosin scaffolding protein anillin, but LET-99 does not antagonize CED-10 in this case. We propose that LET-99 acts in a pathway that inhibits the Rac CED-10 to promote the proper balance of branched versus linear F-actin for cytokinesis, and that LET-99 also regulates another factor that contributes to cortical stability.
Rapid Evolution of Glycan Recognition Receptors Reveals an Axis of Host-Microbe Conflicts at Carbohydrate-Protein Interfaces
Authors: Hilbert Zoë A. , Young Hannah J. , Schwiesow Mara , Elde Nels C. 
Published: September 2022

AbstractDetection of microbial pathogens is a primary function of many mammalian immune proteins. This can be accomplished through the recognition of diverse microbial-produced macromolecules including proteins, nucleic acids and carbohydrates. Many pathogens subvert host defenses by rapidly changing these structures to avoid detection, placing strong selective pressures on host immune proteins that repeatedly adapt to remain effective. Signatures of rapid evolution have been identified in numerous host immunity proteins involved in the detection of pathogenic protein substrates, but whether the same signals can be observed in host proteins engaged in interactions with other pathogen-derived molecules has received much less attention. This focus on protein-protein interfaces has largely obscured the study of fungi as contributors to host-pathogen evolutionary conflicts, despite their importance as a formidable class of vertebrate pathogens. Here, we provide evidence that many mammalian immune receptors involved in the detection of microbial glycans have been subject to recurrent positive selection. Notably, we find that rapidly evolving sites in these genes primarily cluster in key functional domains involved in carbohydrate recognition. Further, we identified convergent patterns of substitution in distinct primate populations at a site in the Melanin Lectin gene that has been associated with increased risk of invasive fungal disease. Our results also highlight the power of evolutionary analyses to reveal uncharacterized interfaces of host-pathogen conflict by identifying genes, such as CLEC12A, with strong signals of positive selection across multiple mammalian lineages. These results suggest that the realm of interfaces shaped by host-microbe conflicts extends beyond the world of host-viral protein-protein interactions and into the world of microbial glycans and fungi.
Peptide-PAINT using a transfected-docker enables live- and fixed-cell super-resolution imaging
Authors: Maity Barun Kumar , Nall Duncan , Lee Yongjae , Selvin Paul R 
Published: September 2022

ABSTRACTPoint accumulation for imaging in nanoscale topography (PAINT) is a single-molecule technique for super-resolution microscopy, achieving ∼5-25 nanometer resolution. Here we show that by transfecting the protein-of-interest with a docker-coil, rather than by adding the docker externally—as is the norm when using DNA tethers or antibodies as dockers—we can achieve similar localization, ∼10 nm. However, using a transfected docker has several experimental advances and simplifications. Most importantly, it allows Peptide-PAINT to be applied to transfected live cells, including surface proteins in mammalian cells and neurons under physiological conditions. The enhance resolution of Peptide-PAINT is also shown for organelles in fixed cells to unravel structural details including ≈40-nm and ≈60-nm axial repeats in vimentin filaments in the cytoplasm, and fiber shapes of sub-100-nm histone-rich regions in the nucleus.
Atg1 modulates mitochondrial dynamics to promote germline stem cell maintenance inDrosophila
Authors: Ayachit Minal S. , Shravage Bhupendra V. 
Published: September 2022

AbstractMitochondrial dynamics (fusion and fission) are necessary for stem cell maintenance and differentiation. However, the relationship between mitophagy, mitochondrial dynamics and stem cell exhaustion is not clearly understood. Here we report the multifaceted role of Atg1 in mitophagy, mitochondrial dynamics and stem cell maintenance in female germline stem cells (GSCs) inDrosophila. We found that depletion ofAtg1in GSCs leads to impaired autophagy (mitophagy) as measured by reduced formation of autophagosomes, increased accumulation of p62/Ref (2)P and accumulation of damaged mitochondria. Disrupting Atg1 function led to mitochondrial fusion in developing cysts. The fusion was a result of an increase in Marf levels in both GSCs and cysts, and the fusion phenotype could be rescued by overexpression ofDrp1or by depletingMarfvia RNAi in Atg1-depleted cyst cells. Interestingly, double knockdown of bothAtg1:Marfaffected ovariole size and the number of vitellogenic oocytes. WhileAtg1:Marfknockdown led to decrease in germ cell number. Strikingly,Atg1:Marfdouble knockdown leads to a dramatic loss of GSCs, GCs and a total loss of vitellogenic stages, suggesting a block in oogenesis. Overall, our results demonstrate that Drp1, Marf and Atg1 function together to influence female GSC maintenance and their differentiation into cysts.Research HighlightsAtg1, in addition to its role in mitophagy, influences mitochondrial dynamics during oogenesis through modulation of Marf.Atg1 and Marf promote Germline stem cell maintenance in Drosophila.
Comparison of machine learning predictions of subjective poverty in rural China
Authors: Maruejols Lucie , Wang Hanjie , Zhao Qiran , Bai Yunli , Zhang Linxiu 
Published: September 2022

PurposeDespite rising incomes and reduction of extreme poverty, the feeling of being poor remains widespread. Support programs can improve well-being, but they first require identifying who are the households that judge their income is insufficient to meet their basic needs, and what factors are associated with subjective poverty.Design/methodology/approachHouseholds report the income level they judge is sufficient to make ends meet. Then, they are classified as being subjectively poor if their own monetary income is inferior to the level they indicated. Second, the study compares the performance of three machine learning algorithms, the random forest, support vector machines and least absolute shrinkage and selection operator (LASSO) regression, applied to a set of socioeconomic variables to predict subjective poverty status.FindingsThe random forest generates 85.29% of correct predictions using a range of income and non-income predictors, closely followed by the other two techniques. For the middle-income group, the LASSO regression outperforms random forest. Subjective poverty is mostly associated with monetary income for low-income households. However, a combination of low income, low endowment (land, consumption assets) and unusual large expenditure (medical, gifts) constitutes the key predictors of feeling poor for the middle-income households.Practical implicationsTo reduce the feeling of poverty, policy intervention should continue to focus on increasing incomes. However, improvements in nonincome domains such as health expenditure, education and family demographics can also relieve the feeling of income inadequacy. Methodologically, better performance of either algorithm depends on the data at hand.Originality/valueFor the first time, the authors show that prediction techniques are reliable to identify subjective poverty prevalence, with example from rural China. The analysis offers specific attention to the modest-income households, who may feel poor but not be identified as such by objective poverty lines, and is relevant when policy-makers seek to address the “next step” after ending extreme poverty. Prediction performance and mechanisms for three machine learning algorithms are compared.
Corruption in NREGA: a theoretical analysis
Authors: Sanyal Tilak 
Published: September 2022

Purpose
Niehaus and Sukhtankar (2013a, 2013b) find that in response to an increase in the public wage rate in National Rural Employment Guarantee Act (NREGA), underpayment of wage and embezzlement rates increase monotonically. This paper aims to investigate theoretically whether the empirical finding of Niehaus and Sukhtankar (2013b) is valid in the long run. The author also verify whether their observation extends to the situation where multiple types of corruption coexist.

Design/methodology/approach
The author builds a theoretical model comprising of three individuals – a government official, a landlord and a representative worker. First, the author defines a no-corruption equilibrium where the official honestly reports the employment period to the government. In a two-stage game, the landlord announces the private wage rate in stage one, followed by the worker deciding on the allocation of time between private and public works and leisure. Then the author considers a single type of corruption where the official embezzles a part of public money by over-reporting the employment period. The landlord-worker game remains the same as before. Finally, the author considers multiple types of corruption where alongside embezzlement, the official takes a bribe from the worker for employing her. Here also, the author considers a two-stage game where in stage one, the official and landlord simultaneously determine embezzlement and bribe rates and the private wage rate, respectively. In stage two, the worker decides on the allocation of time. In both types of corruption, the probability of detection increases with the corruption rate.

Findings
In the case of a single type of corruption, the embezzlement rate behaves nonmonotonically in response to an increase in the public wage rate. A similar kind of result is obtained with multiple types of corruption as well.

Originality/value
First, to the best of the author’s knowledge, no paper prior to this has theoretically modeled corruption in NREGA. Also, the observations of Niehaus and Sukhtankar (2013a, 2013b) is neither valid in the long run nor extend to multiple corruptions.
Development of the cybercrime awareness scale (CAS): a validity and reliability study in a Turkish sample
Authors: Arpaci Ibrahim , Ateş Ersin 
Published: September 2022

PurposeCybercrimes increase day by day in parallel to cyber-attacks and cyber-threats. Due to such an increase, required cybersecurity precautions against all kinds of cyber-attacks and cyber-threats should be taken by both organizations and individuals. This study aims to develop a reliable and valid measurement tool to measure cybercrime awareness levels of individuals.Design/methodology/approachIn this study, a scale named as Cybercrime Awareness Scale (CAS) has been developed and psychometric properties of the scale have been tested by two separate studies.FindingsThe first study included a total of 500 respondents (294 female and 206 male). In the first study, factor structure of the proposed scale has been determined through an exploratory factor analysis. The results revealed a three-factor structure (i.e. information systems crimes, personal data crimes, and privacy and security). Cronbach's alpha reliability coefficients for the subdimensions were 0.95, 0.92, and 0.90, respectively. The sample of the second study consisted of 494 respondents (281 female and 213 male). The confirmatory-factor-analysis results revealed that three-factor structure is valid and optimal model. Further, the proposed scale demonstrated moderate concurrent validity results in relation to the Digital Data Security Awareness Scale.Originality/valueFindings indicated that the CAS is a valid and reliable measurement tool to measure individuals' cybercrime awareness level. This study makes a novel contribution to the existing cybersecurity literature by providing the CAS, which is developed by following rigorous methodological standards.Peer reviewThe peer review history for this article is available at:https://publons.com/publon/10.1108/OIR-01-2022-0023/
Empirical evidence of attribute framing: the case of unsophisticated IPO investors
Authors: Rapp Albert 
Published: September 2022

PurposeThe purpose of this paper is to investigate the empirical relevance of attribute framing in the financial marketplace.Design/methodology/approachIncorporating a sample of German initial public offerings (IPOs) from 2010 to 2019, the author uses quantitative methods, including regression models and tests for the equality of means, to analyze whether unsophisticated investors are susceptible to attribute framing and whether this susceptibility reflects irrational behavior.FindingsUnsophisticated investors, who are typically retail investors, are susceptible to attribute framing. They are likely to subscribe to IPOs whose attribute “market valuation” is framed in a positive way, that is, IPOs with low offer prices. As low-priced IPOs are overvalued and underperform in the secondary market relative to high-priced IPOs, the susceptibility to attribute framing reflects irrational behavior. The findings are robust to controlling for sentiment.Research limitations/implicationsSince this paper includes a relatively small sample from a single stock market, future research might employ alternative approaches.Social implicationsWhen issuers and underwriters are able to exploit retail investors through attribute framing, the participation of these investors in the financial marketplace may finally decrease. Therefore, the financial literacy of retail investors needs to be improved.Originality/valueThis paper is the first to provide empirical evidence of attribute framing in a financial markets context. While most previous research on IPO offer prices focuses on US stocks, this paper is the first to incorporate German stocks.
Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds
Authors: Zhang Menghao , Zhang Chen , Hu Panyang , Shi Lidan , Ju Mingming , Zhang Ben , Li Xinjian , Han Xuelei , Wang Kejun , Li Xiuling , Qiao Ruimin 
Published: September 2022

AbstractMitochondria follow non‐Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.
Alcohol exposure prior to pregnancy—does hazardous consumption affect placenta‐ and inflammatory‐mediated pregnancy outcomes? A Swedish population‐based cohort study
Authors: Asp Joline , Bergman Lina , Lager Susanne , Axelsson Ove , Wikström Anna‐Karin , Hesselman Susanne 
Published: September 2022

AbstractIntroductionAlcohol consumption during pregnancy is related to severe birth complications such as low birthweight, preterm birth and birth defects. During the last decade, the Alcohol Use Disorders Identification Test (AUDIT) has been used as a screening tool in Swedish maternal healthcare units to identify hazardous, pre‐pregnancy alcohol use. However, evaluation of the screening with AUDIT, as well as adverse maternal or neonatal outcomes, has not been assessed at a national level.Material and methodsThis was a population‐based cohort study of 530 458 births from 2013 to 2018 using demographic, reproductive and maternal health data from the Swedish Pregnancy Register. Self‐reported alcohol consumption in the year before pregnancy, measured as AUDIT scores, was categorized into moderate (6–13 points) and high‐risk (14–40 points) consumption, with low‐risk (0–5 points) consumption as the reference group. Associations with pregnancy‐ and birth outcomes were explored with logistic regressions using generalized estimating equation models, adjusting for maternal and socioeconomic characteristics. Estimates are presented as adjusted odds ratios (aORs) with 95% confidence intervals (CIs).ResultsHigh‐risk and moderate pre‐pregnancy alcohol consumption was associated with preeclampsia, preterm birth and birth of an infant small for gestational age (SGA), but these associations were nonsignificant after adjustments. Prior moderate‐risk (aOR 1.29, 95% CI 1.17–1.42) and high‐risk consumption (aOR 1.62, 95% CI 1.17–2.25) increased the likelihood of intrapartum and neonatal infections.ConclusionsApart from identifying hazardous alcohol consumption prior to pregnancy and the offer of counseling, screening with the AUDIT in early pregnancy indicates a high risk of inflammatory‐/placenta‐mediated pregnancy and birth outcomes. For most outcomes, AUDIT was not an independent contributor when adjusting for confounding factors. Hazardous alcohol use prior to pregnancy was independently linked to intrapartum and neonatal infections; conditions associated with morbidity and long‐term sequalae. These associations may be explained by alcohol‐induced changes in the maternal or fetal immune system in early pregnancy or persistent alcohol intake during pregnancy, or may depend on unidentified confounding factors.