bluuebunny/crossref_metadata_2025 huggingface dataset:
David Livingstone
Authors: Simpson Kathryn
Published: July 2023

David Livingstone was a Scottish doctor, missionary and traveler. He was born in 1813 in tied accommodation at the Monteith, Bogle & Co. Cotton Mill in Blantyre Scotland. David was the second child of Neil and Agnes (née Hunter). He worked up to fourteen hours a day from the age of ten in the mill, and at age 19 he had saved enough money to attend Anderson College in Glasgow. He joined the London Missionary Society (LMS) in 1838 and gained his medical license in November 1840. Livingstone was intending to go to China but this was prevented due the Opium Wars (1839–1860). He went to South Africa in 1841, having heard the famous Scottish missionary Robert Moffat speak of the opportunities for missionaries there. His first eleven years in inland mission stations were centered around his association with Sechele, the leader of the Kwêna. In February 1844 Livingstone was bitten by a lion after an ill-judged attempt to disperse a pride who were harassing the animals of a village he was working in. While recuperating at the Moffat mission station, he fell in love with Robert’s daughter Mary. He married Mary in Kuruman, in the northern Cape province of South Africa, in 1845. They went on to have six children. In 1852, after a few years of traveling with them, Livingstone sent his family to Britain so he would be free to travel in earnest. From 1852 to 1856 Livingstone roamed the Zambezi with the support of Sekeletu, leader of the Kololo; during this trip Livingstone walked across the continent. In 1857 Livingstone resigned from the LMS and became British Consul to the African interior. The second Zambezi trip, known as the Zambezi Expedition, was primarily funded by the British government, and built on Livingstone’s understanding that if he could find a navigable route along the Zambezi this would facilitate trade, no such route is possible due to the Cabora Bassa rapids. Livingstone’s final journey was to identify the source of the Nile. He died in Chitambo, present-day Chipundu in Zambia, in April 1873. His body was taken to the coast by his associates and returned to Britain; his funeral was at Westminster Abbey in April 1874. Livingstone and his legacy were central to British ideas of imperialism, and it is from him that the concept of the three C’s of colonialism came: Christianity, commerce, and civilization, the purported answer to stopping the traffic in enslaved people.
Adventure Literature
Authors: Holterhoff Kate
Published: July 2023

Adventure factors into the plots of much 19th-century British fiction, but what sets the adventure literature genre apart is its charismatic heroes, terrible adversaries, and plotting that emphasizes action over character development. The form of Victorian adventure fiction is indebted to the exoticism, excitement, and danger central to the plots of Daniel Defoe’s Robinson Crusoe (1719) and Sir Walter Scott’s historical romances beginning with Waverley (1814). This genre came into its own during the era of New Imperialism (1875–1914), and literary critics typically credit two fictions with inspiring the popularity of adventure during this period: Robert Louis Stevenson’s Treasure Island (serialized in Young Folks 1 October 1881 to 28 January 1882) and H. Rider Haggard’s King Solomon’s Mines (1885) and She (1887). These thrilling, wild-minded fictions gained a foothold in the popular imagination which continues into the present. Literary and cultural studies scholarship concerned with adventure literature tends to focus on this genre’s contributions to the discourses of aesthetics, imperialism, children’s literature, print history, gender and sexuality, and the history of science.
Roger Williams
Authors: Glover Jeffrey
Published: July 2023

Roger Williams (b. 1603?–d. 1683) was an English colonist, religious dissenter, and the founder of Rhode Island. He was born in London, England, and embraced Puritanism as a youth, emigrating with his wife to the Massachusetts Bay Colony in 1631. Williams was an outspoken critic of the Puritan church in New England, steadfastly holding that state involvement in church affairs intruded on matters of individual religious conscience. In 1635 the Massachusetts Bay Colony banished Williams and he founded Rhode Island on land purchased from the Narragansett Indians. For the next five decades, Williams was a Protestant minister, prolific writer, political leader, trader, diplomat to the Indigenous peoples of southern New England, and fluent scholar of the Narragansett language. His views on the separation of church and state seemed to foretell later conceptions of religious liberty, and his writings about the Narragansetts influenced modern anthropology and history.
Biological Rhythms
Authors: Refinetti Roberto
Published: July 2023

Biological rhythms are oscillatory processes observed in living beings—while the beings are alive or even after their death, as is the case for populational oscillations determined by the study of geological cycles using fossilized organisms. Until life on other planets can be documented, biological rhythms are considered to be restricted to organisms on planet Earth. The most obvious separation between types of biological rhythms is the one between rhythms that are purely caused by environmental cycles on one hand and rhythms that are generated endogenously and are only modulated by environmental cycles on the other hand. Technically, the term “circa” should be used only for rhythms that have been demonstrated to be endogenously generated and to be susceptible to synchronization by environmental cycles, which as of today applies only to circatidal, circalunar, circadian, and circannual rhythms. However, there are many other oscillatory patterns that have been observed in living organisms, and they are undoubtedly biological rhythms even if many of them may not be controlled by biological clocks. Biological rhythms are usually classified into three main categories: those that oscillate about once a day (circadian), those that oscillate faster than once a day (ultradian), and those that oscillate slower than once a day (infradian). Bibliographies in these three categories will be detailed below, after a brief discussion of professional journals and considerations about the reliability of oscillations presumed to constitute biological rhythms.
Crime and Policing in Israel
Authors: Yogev Dikla , Levenkron Nomi
Published: July 2023

This article on policing and crime in Israel reflects the complex heterogeneous nature of the state of Israel as well as its police. The two largest minority communities in Israel are the Israeli Arabs (c. 21 percent) and the ultra-Orthodox Jews (c. 10 percent). Another group, although much smaller in size (c. 2 percent), is the Ethiopians. Due to Israel’s geopolitical and national history, the Arabs are perceived as a security threat by the public as well as by the police. Consequently, much of the research about minority policing focuses on policing the Arab society. Ethiopians are subject to similar discriminatory policing as the Arabs, but in their case the police are making greater efforts to rectify the situation. The ultra-Orthodox community has been responsible for most of the mass clashes with the state since its early days, despite or maybe due to the persistent ideological tension against the existence of the state that is accompanied with a growing integration into Israeli society. Israeli policing, which has received very little scholarly attention to date, has some similarities to and differences from police forces elsewhere. Similarities are seen in the steadily increasing number of women in police force (28 percent) as well as the number of women officers in senior positions. In addition, as in other police forces, there is growing success in recruitment of police officers from minority groups, especially Arabs, ultra-Orthodox, and Ethiopians. Yet, unlike other countries, the number of volunteer and military police officers in the Israeli police is alarmingly high, as such police officers tend to be older and tend to function according to military rather than civilian norms. Military service in the Israeli Defense Forces inevitably affects the way officers perceive Arab citizens, and it contributes to stress, burnout, and trauma. Moreover, the police are forbidden from striking, which affects employment conditions, the quality of the workforce, and morale.
Shakira
Authors: O’Dell Cary
Published: July 2023

Shakira (nee Shakira Isabel Mebarak Ripoll), born 2 February 1977, in Barranquilla, Columbia, is a singer, prolific songwriter, musician, record producer, actress, voice actress (Zootopia, 2016), television personality, television producer, philanthropist, and humanitarian. Known internationally as the “Queen of Latin Music,” she is a multiple Grammy Award winner, multiple Latin Grammy Award winner, multiple Billboard Music Award winner, and MTV Video Music Award winner, as well as the possessor of a star on the Hollywood Walk of Fame and several mentions in the Guinness Book of World Records, among other accolades. Having begun her professional performing career in her native Columbia, Shakira released her first album, Magia (1991) for Sony Music Columbia when she was thirteen years old. Her subsequent Latin recordings include Peligro (1993), Pies Descalzos (1995), and Donde Estan los Ladrones? (1998). Shakira entered the American marketplace in 2001 with her fifth album, the English-language Laundry Service, which would eventually sell over ten million copies. Her subsequent albums, recorded in English or Spanish and sometimes in both languages, have sold in excess of 80 million copies. In 2018, Forbes magazine designated Shakira as the best-selling Latin artist of all time. Along with Laundry Service, Shakira’s other albums include the Spanish-language Fijacion Oral, Vol. 1 (2005), Sale el Sole (2010) and El Dorado (2017). Her English-language releases include Oral Fixation, Vol. 2 (2005), She Wolf (2009) and Shakira (2014). As a collaborator, Shakira has worked with Maluma, Wyclef Jean, Rhianna, Pitbull, the Black Eyed Peas, and Beyonce, among others. Shakira is one of the world’s more recently minted global superstars, a categorization that was solidified by her co-headlining the February 2020 Super Bowl halftime show with Jennifer Lopez, her reoccurring involvement with the World Cup, and her role on two nonsequential seasons as one of the judges/coaches on the hit NBC-TV musical competition series The Voice. Subsequently, Shakira acted as both co-creator/co-producer of the 2022 reality competition show Dancing with Myself, where she also acted as a judge. In 1997, Shakira founded the Columbian-based Barefoot Foundation (Pies Fundacion Descalozos). Its mission is “to ensure that every Colombian child can exercise their right to a quality education. Our model targets displaced and vulnerable communities by addressing their unique needs.” Since its establishment, the foundation has created twenty-seven schools and educational spaces in Columbia that have provided both food and education to over 100,000 impoverished children.
Book Publishing and Printing Technologies in Premodern China (Seventh-Nineteenth Centuries)
Authors: Brokaw Cynthia
Published: July 2023

In the world history of printing, China is distinctive for the number and variety of different technologies employed in the premodern era—that is, between the seventh century, when xylography or woodblock (muban木版, diaoban雕版, diaoke雕刻) printing was invented, and the late nineteenth century, when mechanized movable type and other imports from the West began to supplant indigenous print technologies. The Chinese also developed several methods of movable-type printing as early as the Song dynasty (960–1279): earthenware or clay movable type (nihuozi泥活字) and wooden movable type (muhuozi木活字) printing. Metal movable type (jinshu huozi金屬活字), first invented in Korea in the thirteenth century, was also in limited use in China by the Ming dynasty (1368–1644); Chinese printers experimented with bronze or copper (tong銅), tin (xi錫), lead (qian鉛), and, eventually, porcelain (ciban磁版) types. In the Qing (1644–1911), wooden movable type or wax tablets (laban蠟板) were used for rapid reproduction of news sheets and public announcements. Each method had different practical, economic, technological, and/or aesthetic advantages. For example, xylography reproduced calligraphy more effectively and allowed publishers to reprint works easily and relatively cheaply as the market demanded, whereas movable type was the most efficient way of speedily publishing texts of immediate relevance but short shelf life, or texts in which the same characters were frequently repeated (e.g., genealogies). The variety of print technologies thus offered Chinese publishers, whether official, private, commercial, or institutional, considerable flexibility in adapting technology to content and use. But, generally speaking, throughout the long twelve-century history of premodern Chinese printing, woodblock printing remained the dominant technology, as it was most suitable for printing the Chinese language and could most effectively reproduce the aesthetic quality of Chinese calligraphy. This bibliography gathers sources, primary (where available) and secondary, to provide information about these different printing technologies, their origins, their development, and their uses—and the ways in which they shaped Chinese book culture from the late Tang dynasty (618–907) through much of the last imperial dynasty, the Qing (1644–1911). Some attention is also devoted to the techniques of Chinese color printing, the materials and tools of printing, craft labor and publishing organization, and the economics of printing. A final section treats the fate of the premodern technologies in the modern era. For works that treat the history of Chinese publishing and book culture, see the Oxford Bibliographies in Chinese Studies article “Printing and Book Culture.”
Multinational comparison study of aircraft pilot healthcare avoidance behaviour
Authors: Hoffman W R , Patel P K , Aden J , Willis A , Acker J P , Bjerke E , Miranda E , Luster J , Tvaryanas A
Published: July 2023

Background

US and Canadian pilots are required to meet medical standards to secure their active flying status, but a subgroup exhibit healthcare avoidance behaviour due to fear of loss of that status. This phenomenon has the potential to impact pilot health, aeromedical screening and aviation safety. No international comparison study of pilot healthcare avoidance currently exists between US and Canadian pilots.

Aims

To compare the rate and subtypes of healthcare avoidance behaviour secondary to fear for loss of flying status between US and Canadian pilots.

Methods

A comparison analysis of data collected during two independent, non-probabilistic, cross-sectional internet surveys including any individual certified to perform flying duties in the USA (US survey) or Canada (Canadian survey).

Results

There were 4320 US pilots and 1415 Canadian pilots who completed informed consent and 3765 US pilots and 1405 Canadian pilots were included in the results. There were 56% of US pilots who reported a history of healthcare avoidance behaviour compared to 55% of Canadian pilots (P = 0.578). A multivariable logistic regression that included age, pilot type and gender showed that US pilots were slightly more likely than Canadian pilots to report this behaviour (odds ratio 1.22, 95% confidence interval 1.06–1.4).

Conclusions

Healthcare avoidance behaviour due to fear of loss of flying status has a relatively high prevalence in both US and Canadian pilot populations.
Parliamentary Committees and Ex-post Oversight: Institutional Options and Design
Authors: West Hallbera
Published: July 2023

Parliamentary oversight of executive power is a parliamentary system concern, considering weaker ex-post institutional oversight mechanisms and actor incentive challenges. Yet, institutional options are precondition for making parliamentary ex-post oversight work and this article investigates which type of options in fact exists within the vital committee system and how they are designed. The expectation is that ex-post oversight options depend on distributional power structures, being stronger for systems with traditions for minority compared to majority governments. For the design, the expectation is an institutional ‘efficient’ outcome in terms of ex-post oversight options being placed in a controlled central oversight committee, and that this applies regardless of government traditions. Empirically, focus is on the five most similar Nordic state parliamentary cases that vary in committee settings and in government traditions. For the investigation focus is on specific ex-post oversight options, the design of these options and overall de-facto use. The findings show a clear difference between the Scandinavian minority cases and the Icelandic and Finnish majority cases. For the design, most cases have ex-post oversight options designed for specific oversight committees, but where the Danish Folketing deviates by providing several options in different committees.
The centimeter-to-submillimeter broad-band radio spectrum of the central compact component in a nearby type-II Seyfert galaxy NGC 1068
Authors: Michiyama Tomonari , Inoue Yoshiyuki , Doi Akihiro
Published: July 2023

We analyze all the available Atacama Large Millimeter/submillimeter Array archival data for the nearby type-II Seyfert galaxy NGC 1068, including new 100 GHz data with an angular resolution of 005, which was not included in previous continuum spectral analyses. By combining with the literature data based on the Very Large Array, we investigate the broad-band radio continuum spectrum of the central ≲7 pc region of NGC 1068. We find that the flux density is between ≈10 and 20 mJy at 5–700 GHz. Due to the inability of the model in previous studies to account for the newly added 100 GHz data point, we proceeded to update the models and make the necessary adjustments to the parameters. One possible interpretation of this broad-band radio spectrum is a combination of emission from the jet base, the dusty torus, and the compact X-raying corona with a magnetic field strength of ≈20 G on scales of ≈30 Schwarzschild radii from the central black hole. In order to firmly identify the compact corona by omitting any other possible extended components (e.g., free–free emission from ionized gas in the vicinity), high-resolution/sensitivity observations achieved by next-generation interferometers will be necessary.
Management of febrile neutropenia in immunocompetent children and youth
Authors: Lirette Marie-Pier , Wright Nicola , Trottier Evelyne D , Beck Carolyn E
Published: July 2023

Febrile neutropenia is a common clinical presentation in children that can be associated with invasive bacterial infection (IBI). However, in otherwise healthy children and youth with fever and neutropenia, the risk for IBI is low, with most cases being caused by viral infections. Well-appearing, non-oncologic, and presumed immunocompetent children aged 6 months to 18 years experiencing a first episode of neutropenia, with no additional risk factors, typically do not require empiric antibiotics. However, a thorough assessment, including complete history and physical exam, is indicated, and a blood culture should be performed when the absolute neutrophil count is <0.5 × 109/L. Close follow-up, a repeat complete blood count, and strong anticipatory guidance are recommended.
Crustal Growth Identified by High-δ18O Zircon and Olivine: A Perspective from Ultramafic Arc Cumulates in Southern Tibet
Authors: Wang Jun , Wang Qiang , Sun Peng , Dan Wei , Kerr Andrew C , Zhang Zhi-Ping , Zhang Le , Wei Gangjian , Dong Han , Hu Wan-Long , Yang Zong-Yong , Zhang Xiu-Zheng , Qi Yue
Published: July 2023

In recent studies of crustal growth using global zircon Hf–O isotopic datasets, high-δ18O zircons are typically attributed to intra-crustal reworking during which very little juvenile mantle-derived magmas were added to the crust. Although arc magmas may originate from a high-δ18O mantle wedge, it has been difficult to decipher the contribution of high-δ18O mantle to zircon-saturated felsic magma due to superimposed intra-crustal processes. We address this issue by combining the data from high-δ18O zircon-bearing ultramafic cumulates and coeval lavas from a Cretaceous magmatic arc in southern Tibet. The cumulates mainly consist of different proportions of cumulus olivine and intercumulus amphibole. Amphibole analyses show a transition from increasing to decreasing Zr with increasing SiO2 (50–74 wt.%) contents in the intercumulus melts, indicating zircon saturation in late-stage interstitial melts. The εNd(t) values (2.4 ± 1.4) of the apatite grains crystallized before and after zircon remain almost constant. Interstitial zircons have δ18O (6.1–7.2‰) values similar to the earliest crystallized olivine (δ18O = 6.3–7.1‰) in the cumulates. The coeval lavas may represent the intercumulus melts extracted from amphibole-rich cumulates at different depths. Both the lavas and cumulates were ultimately derived from high-δ18O arc mantle modified by small amounts (<12%) of subducted sediments, and crystallized zircon during intra-crustal magma evolution without involving crustal contamination or melting. These high-δ18O zircons therefore are not products of crustal reworking, but record crustal growth during their crystallization (110 ± 2 Ma). Our study shows that the combination of zircon and olivine oxygen isotopes for ultramafic to felsic rocks is more effective than zircon data alone in evaluating the role of crustal growth vs. reworking in an arc system. The implication is that global zircon-based crustal evolution models that attribute all high-δ18O zircons to crustal reworking may conceal recent crustal growth.
Examining what factors affect inter-agency working in missing children investigations
Authors: Waring Sara , Monaghan Paige , Yates Amy , Girgiel Nikola , Giles Susan , O’Brien Freya
Published: July 2023

Despite responsibility for missing children belonging to multiple agencies, police perceive this to be falling heavily on their shoulders, placing substantial demand on finite resources. Drawing on thematic analysis of 24 interviews conducted with police, local authority, social service, and care home staff from across three UK boroughs, the following study seeks to identify what factors facilitate and hinder inter-agency working in the prevention and response to missing children and why. Findings highlight that inter-agency working is facilitated by having ‘direct points of contact’ across agencies to facilitate information sharing. Inter-agency working is hindered by ‘inconsistent definitions of missing’, limited ‘understanding of roles and responsibilities’, ‘service demand’, ‘technological issues’, ‘fear’, and ‘discrepancies in responses to missing’. Evidence suggests that partnership working would be facilitated by improving shared understanding of missing, roles and responsibilities, and having direct points of contact across agencies.
Digital disruption diversified—FinTechs and the emergence of a coopetitive market ecosystem
Authors: Larsson Bengt , Rolandsson Bertil , Ilsøe Anna , Larsen Trine Pernille , Lehr Alex , Masso Jaan
Published: July 2023

This article analyses the development of FinTech companies in relation to traditional banks in four countries: Denmark, Estonia, the Netherlands and Sweden. Based on approaches drawn from the sociology of markets and field theory, we analyse and theorize about empirical data from secondary sources, official documents and 38 interviews with key actors. Whereas digital technologies have been commonly depicted as a source of disruption for established business models, suggesting that the rise of FinTech leads to competitive upheaval in the financial sector, more recent studies argue that such interpretations are exaggerated. Here, we propose the emergence of a ‘coopetitive’ market ecosystem that combines co-operative and competitive connections between incumbents and challengers who often share the same infrastructure. FinTech firms are shown to function as catalysts in the transformation towards this ecosystem shaped by coopetitive interdependence between the actors.
Effect of Fluopyram on Pratylenchus penetrans on Corn in the Field and In Vitro
Authors: Han Jaeyeong , Ficca Alyson , Kleczewski Nathan , Schroeder Nathan
Published: July 2023

The effects of a fluopyram seed treatment on lesion nematodes (Pratylenchus spp.) and other plant-parasitic nematodes (PPNs) were evaluated on corn in multiple field locations in 2020 and 2021. The highest rate of fluopyram seed treatment (0.15 mg seed−1) reduced early season population density of lesion nematodes compared with the base treatment control in 2020 only. However, fluopyram did not affect late season lesion nematode population density and corn yields. Fluopyram seed treatment also had minimal or nonsignificant effects on other PPN species. Based on these results, the effects of fluopyram were tested in vitro on Pratylenchus penetrans. Results demonstrated that fluopyram severely affected motility in P. penetrans. The sensitivity of P. penetrans second-stage juveniles (J2s) to fluopyram was significantly higher than at J4 and adult, suggesting that sensitivity to fluopyram is dependent on developmental stage. In addition, the effects of fluopyram were reversible at an EC50 but were irreversible at the maximum concentration (25 μg/ml). Overall, our results indicate that fluopyram has potential for controlling P. penetrans, but its efficacy is variable depending on nematode developmental stage and chemical concentration. Further research is needed to determine if these impacts can translate to field scenarios.
Commentary on Pang et al. (2023)Nature
Authors: Faskowitz Joshua , Moyer Daniel , Handwerker Daniel A. , Gonzalez-Castillo Javier , Bandettini Peter A. , Jbabdi Saad , Betzel Richard
Published: July 2023

Pang et al. (2023) present novel analyses demonstrating that brain dynamics can be understood as resulting from the excitation of geometric modes, derived from the shape of the brain. Notably, they demonstrate that linear combinations of geometric modes can reconstruct patterns of fMRI data more accurately, and with fewer dimensions, than comparable connectivity-derived modes. Equipped with these results, and underpinned by neural field theory, the authors contend that the geometry of the cortical surface provides a more parsimonious explanation of brain activity than structural brain connectivity. This claim runs counter to prevailing theories of information flow in the brain, which emphasize the role of long-distance axonal projections and fasciculated white matter in relaying signals between cortical regions (Honey et al. 2009; Deco et al. 2011; Seguin et al., 2023). While we acknowledge that cortical geometry plays an important role in shaping human brain function, we feel that the presented work falls short of establishing that the brain’s geometry is “a more fundamental constraint on dynamics than complex interregional connectivity” (Pang et al. 2023). Here, we provide 1) a brief critique of the paper’s framing and 2) evidence showing that their methodology lacks specificity to the brain’s orientation and shape. Ultimately, we recognize that the geometric mode approach is a powerful representational framework for brain dynamics analysis, but we also believe that there are key caveats to consider alongside the claims made in the manuscript.
Unraveling membrane protein localization and stabilization in nanodiscs
Authors: Kim So-Jung , Koh Young Hoon , Roh Soung-Hun
Published: July 2023

Nanodiscs are nanoscale structures consisting of a lipid bilayer surrounded by membrane scaffold proteins (MSPs). They are widely used in the study of membrane proteins (MPs) because they provide a stable lipid environment. However, the precise mechanism governing MP behavior within the nanodisc remains elusive. Here, we examined the cryo-EM structures of various MPs reconstituted in nanodiscs from an electron microscopy database (EMPIAR). By analyzing the heterogeneity and interactions in the nanodiscs, we found that MPs within nanodiscs display a distinct spatial preference toward the edges of the nanodisc shells. Furthermore, we observed that MPs can establish direct, amphipathic interactions with the MSPs, promoting protein stability. These interactions may induce a rearrangement of the MSP-MSP interactions, leading to the formation of MP-MSP interactions Collectively, our study provides structural and biophysical insights into how nanodiscs contribute to MP structural behavior and stability.

SIGNIFICANCE

By thoroughly examining multiple deposited datasets of membrane proteins (MPs) reconstituted in nanodiscs, we have gathered compelling evidence that MPs exhibit a clear spatial inclination toward the periphery of the nanodisc shells. Moreover, we have observed that MPs establish direct and amphipathic interactions with membrane scaffold proteins (MSPs). These interactions have the potential to induce a rearrangement of the MSP-MSP interactions, consequently forming MP-MSP interactions. Through quantitative analysis, we have successfully characterized the significant role played by these interactions in ensuring the overall stability of the proteins.
In-silicoidentification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA binding proteins inAedes aegypti
Authors: Sumitha Melveettil Kishor , Kalimuthu Mariapillai , Aarthy Murali , Paramasivan Rajaiah , Kumar Ashwani , Gupta Bhavna
Published: July 2023

Background

RNA binding proteins (RBPs) are the proteins that bind RNAs and regulate their functioning. RBPs in mosquitoes are gaining attention due to their ability to bind flaviviruses and regulate their replication and transmission. Despite their relevance, RBPs in mosquitoes have not been explored much. In this study, we screened the whole genome ofAedes aegypti,the primary vector of several pathogenic viruses, and identified the proteins containing RNA recognition motif (RRM), the most abundant protein domain in eukaryotes.

Results

Using severalin-silicostrategies, a total of 135 RRM containing RBPs were identified inAe. aegypti. The proteins were characterized based on their available annotations and the sequence similarity with theDrosophila melanogaster.Ae. aegyptiRRM containing RBPs included serine/arginine-rich (SR) proteins, polyadenylate binding proteins (PABP), heteronuclear ribonucleoproteins (hnRNP), small nuclear ribonucleoproteins (snRNP), splicing factors, eukaryotic initiation factors, transformers, nucleolysins,etc. Phylogenetic analysis revealed that the proteins and the domain organisation is conserved amongAe. aegypti,Bombyx moriandDrosophila melanogaster. However, the gene length and the intron-exon organisation varied across the insect species. Expression analysis of the genes encoding RBPs using publicly available RNA sequencing data for different developmental time points of the mosquito life cycle starting from the ovary and eggs up to the adults revealed stage-specific expression with several genes preferentially expressed in early embryonic stages and blood-fed female ovary.

Conclusions

This is the first database for theAe. aegyptiRBPs that can serve as the reference base for future investigations. The stage-specific genes can be further explored to determine their role in mosquito growth and development with a focus to develop novel mosquito control strategies.
Taxor: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
Authors: Ulrich Jens-Uwe , Renard Bernhard Y.
Published: July 2023

Metagenomic long-read sequencing is gaining popularity for various applications, including pathogen detection and microbiome studies. To analyze the large data created in those studies, software tools need to taxonomically classify the sequenced molecules and estimate the relative abundances of organisms in the sequenced sample. Due to the exponential growth of reference genome databases, the current taxonomic classification methods have large computational requirements. This issue motivated us to develop a new data structure for fast and memoryefficient querying of long reads. Here we present Taxor as a new tool for long-read metagenomic classification using a hierarchical interleaved XOR filter data structure for indexing and querying large reference genome sets. Taxor implements several k-mer-based approaches such as syncmers for pseudoalignment to classify reads and an Expectation-Maximization algorithm for metagenomic profiling. Our results show that Taxor outperforms competing shortand long-read tools regarding precision, while having a similar recall. Most notably, Taxor reduces the memory requirements and index size by more than 50% and is among the fastest tools regarding query times. This enables real-time metagenomics analysis with large reference databases on a small laptop in the field. Taxor is available athttps://gitlab.com/dacs-hpi/taxor.
Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain
Authors: Hegarty Brianna E. , Gruenhagen George W. , Johnson Zachary V. , Baker Cristina M. , Streelman Jeffrey T.
Published: July 2023

The telencephalon has undergone remarkable diversification and expansion throughout vertebrate evolution, exhibiting striking differences in structural and functional complexity. Nevertheless, fundamental features are shared across vertebrate taxa, such as the presence of distinct regions including the pallium, subpallium, and olfactory structures. Teleost fishes have a uniquely ‘everted’ telencephalon, which has made it challenging to compare brain regions in fish to those in other vertebrates. Here we combine spatial transcriptomics and single-nucleus RNA-sequencing to generate a spatially-resolved transcriptional atlas of the cichlid fish telencephalon. We then compare cell-types and anatomical regions in the cichlid telencephalon with those in amphibians, reptiles, birds, and mammals. We uncover striking transcriptional similarities between cell populations in the fish telencephalon and subpallial, hippocampal, and cortical cell populations in tetrapods. Ultimately, our work lends new insights into the organization and evolution of conserved cell-types and regions in the vertebrate forebrain.
Mutational profile of the regenerative process andde novogenome assembly of the planarianSchmidtea polychroa
Authors: Póti Ádám , Szüts Dávid , Vermezovic Jelena
Published: July 2023

Planarians are organisms with a unique capacity to regenerate any part of their body. New tissues are generated in a process that requires many swift cell divisions. How costly is this process to an animal in terms of mutational load remains unknown. Using whole genome sequencing, we defined the mutational profile of the process of regeneration in the planarian speciesSchmidtea polychroa. We assembledde novothe genome ofS. polychroaand analyzed mutations in animals that have undergone regeneration. We observed a threefold increase in the number of mutations and an altered mutational spectrum. High allele frequencies of subclonal mutations in regenerated animals suggested that relatively few stem cells with high expansion potential regenerated the animal. We provide, for the first time, the draft genome assembly ofS. polychroa, an estimation of the germline mutation rate for a planarian species and the mutational spectrum of the regeneration process of a living organism.
A natural bacterial pathogen ofC. elegansuses a small RNA to induce transgenerational inheritance of learned avoidance
Authors: Sengupta Titas , Ange Jonathan St. , Moore Rebecca , Kaletsky Rachel , Marogi Jacob , Myhrvold Cameron , Gitai Zemer , Murphy Coleen T.
Published: July 2023

Previously, we discovered that a small RNA from a clinical isolate ofPseudomonas aeruginosa, PA14, induces learned avoidance and its transgenerational inheritance inC. elegans. Pseudomonas aeruginosais an important human pathogen, and there are otherPseudomonadsinC. elegans’natural habitat, but it is unclear whetherC. elegansever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found inC. elegans’natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we found that a pathogenicPseudomonas vranovensisstrain isolated from theC. elegansmicrobiota, GRb0427, like PA14, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure to GRb0427, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. Using bacterial small RNA sequencing, we identified Pv1, a small RNA from GRb0427, that matches the sequence ofC. elegans maco-1. We find that Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain,P. mendocina; this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance are functional inC. elegans’natural environment, and that different bacterial small RNA-mediated regulation systems evolved independently but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
High performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks
Authors: Zufan Sara E. , Mercoulia Karolina , Kwong Jason , Judd Louise M. , Howden Benjamin P. , Seemann Torsten , Stinear Timothy P.
Published: July 2023

Hepatitis A virus (HAV) infections are an increasing public health concern in low-endemicity regions due to outbreaks from foodborne infections and sustained transmission among vulnerable groups, including persons experiencing homelessness, those who inject drugs, and men who have sex with men (MSM), which is further compounded by aging, unvaccinated populations. DNA sequence characterisation of HAV for source tracking is performed by comparing small subgenomic regions of the virus. While this approach has been successful when robust epidemiological data are available, poor genetic resolution can lead to conflation of outbreaks with sporadic cases. HAV outbreak investigations would greatly benefit from the additional phylogenetic resolution obtained by whole virus genome sequence comparisons. However, HAV genomic approaches can be difficult because of challenges in isolating the virus, low sensitivity of direct metagenomic sequencing in complex sample matrices like various foods such as fruits, vegetables and molluscs, and difficulty designing highly multiplexed PCR primers across diverse HAV genotypes. Here, we introduce a proof-of-concept pan-HAV oligonucleotide hybrid capture enrichment assay from serum and frozen berry specimens that yields complete and near-complete HAV genomes from as few as four input HAV genome copies. We used this method to recover HAV genomes from human serum specimens with high Cτ values (34·7—42·7), with high assay performance for all six human HAV sub-genotypes, both contemporary and historical. Our approach provides a highly sensitive and streamlined workflow for HAV WGS from diverse sample types, that can be the basis for harmonised and high-resolution molecular epidemiology during HAV outbreak surveillance.

Importance

This proof-of-concept study introduces a hybrid capture oligo panel for whole genome sequencing (WGS) of all six human pathogenic hepatitis A virus (HAV) subgenotypes, exhibiting a higher sensitivity than some conventional genotyping assays. The ability of hybrid capture to enrich multiple targets allows for a single, streamlined workflow, thus facilitating the potential harmonization of molecular surveillance of HAV with other enteric viruses. Even challenging sample matrices can be accommodated, making it suitable for broad implementation in clinical and public health laboratories. The ability to capture small amounts of virus from complex samples is promising for passive surveillance application to environmental substrates, such as wastewater. This innovative approach has significant implications for enhancing multijurisdictional outbreak investigations, as well as our understanding of the global diversity and transmission dynamics of HAV.
Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy
Authors: Xiao Sheng , Cunningham William J. , Kondabolu Krishnakanth , Lowet Eric , Moya Maria V. , Mount Rebecca , Ravasio Cara , Economo Michael N. , Han Xue , Mertz Jerome
Published: July 2023

Voltage imaging with cellular specificity has been made possible by the tremendous advances in genetically encoded voltage indicators (GEVIs). However, the kilohertz rates required for voltage imaging lead to weak signals. Moreover, out-of-focus fluorescence and tissue scattering produce background that both undermines signal-to-noise ratio (SNR) and induces crosstalk between cells, making reliablein vivoimaging in densely labeled tissue highly challenging. We describe a microscope that combines the distinct advantages of targeted illumination and confocal gating, while also maximizing signal detection efficiency. The resulting benefits in SNR and crosstalk reduction are quantified experimentally and theoretically. Our microscope provides a versatile solution for enabling high-fidelityin vivovoltage imaging at large scales and penetration depths, which we demonstrate across a wide range of imaging conditions and different GEVI classes.
Visible light-induced specific protein reaction delineates early stages of cell adhesion
Authors: Rahikainen Rolle , Vester Susan K. , Turkki Paula , Janosko Chasity P. , Deiters Alexander , Hytönen Vesa P. , Howarth Mark
Published: July 2023

Light is well established for control of bond breakage, but not for control of specific bond formation in complex environments. We previously engineered diffusion-limited reactivity of SpyTag003 peptide with its protein partner SpyCatcher003 through spontaneous transamidation. This system enables precise and irreversible assembly of biological building blocks, with applications from biomaterials to vaccines. Here, we establish a system for rapid control of this amide bond formation with visible light. We have generated a caged SpyCatcher003, which allows light triggering of covalent bond formation to SpyTag003 in mammalian cells. Photocaging is achieved through site-specific incorporation of an unnatural coumarin-lysine at the reactive site of SpyCatcher003. We showed uniform specific reaction in cell lysate upon light activation. We then used the spatiotemporal precision of a 405 nm confocal laser for uncaging in seconds, probing the earliest events in mechanotransduction by talin, the key force sensor between the cytoskeleton and extracellular matrix. Reconstituting talin induced rapid biphasic extension of lamellipodia, revealing the kinetics of talin-regulated cell spreading and polarization. Thereafter we determined the hierarchy of recruitment of key components for cell adhesion. Precise control over site-specific protein reaction with visible light creates diverse opportunities for cell biology and nanoassembly.
An oxadiazole-based compound potentiates anti-tuberculosis treatment by increasing host resistance via zinc poisoning
Authors: Maure Alexandra , Lawarée Emeline , Fiorentino Francesco , Pawlik Alexandre , Gona Saideep , Giraud-Gatineau Alexandre , Eldridge Matthew J.G. , Danckaert Anne , Hardy David , Frigui Wafa , Keck Camille , Aulner Nathalie , Mai Antonello , Hamon Mélanie , Barreiro Luis , Brodin Priscille , Brosch Roland , Rotili Dante , Tailleux Ludovic
Published: July 2023

Anti-tuberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains ofMycobacterium tuberculosisare constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high content imaging, we identified novel 1,2,4-oxadiazole-based compounds, that allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds,M. tuberculosisbecame even more sensitive to anti-tuberculosis drugs,in vitroandin vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.
Enucleation of theC. elegansembryo revealed the mechanism of dynein-dependent spacing between microtubule asters
Authors: Fujii Ken , Kondo Tomo , Kimura Akatsuki
Published: July 2023

The centrosome is a major microtubule-organizing center in animal cells. The intracellular positioning of the centrosomes is important for proper cellular function. One of the features of centrosome positioning is the spacing between centrosomes. The spacing activity is mediated by microtubules extending from the centrosomes; however, the underlying mechanisms are not fully understood. To characterize the spacing activity in theCaenorhabditis elegansembryo, a genetic setup was developed to produce enucleated embryos. The centrosome duplicated multiple times in the enucleated embryo, which enabled us to characterize the chromosome-independent spacing activity between sister and non-sister centrosome pairs. We knocked down genes in the enucleated embryo and found that the timely spacing was dependent on cytoplasmic dynein. Based on these results, we propose a stoichiometric model of cortical and cytoplasmic pulling forces for the spacing between centrosomes. We also found a dynein-independent but non-muscle myosin II-dependent movement of the centrosomes in a later cell cycle phase. The dynein-dependent spacing mechanisms for positioning the centrosomes revealed in this study is likely functioning in the cell with nucleus and chromosomes, including the processes of centrosome separation and spindle elongation.
Integrative determination of the atomic structure of mutant huntingtin exon 1 fibrils implicated in Huntington’s disease
Authors: Bagherpoor Helabad Mahdi , Matlahov Irina , Kumar Raj , Daldrop Jan O. , Jain Greeshma , Weingarth Markus , van der Wel Patrick C.A. , Miettinen Markus S.
Published: July 2023

Neurodegeneration in Huntington’s disease (HD) is accompanied by the aggregation of fragments of the mutant huntingtin protein, a biomarker of disease progression. A particular pathogenic role has been attributed to the aggregation-prone huntingtin exon 1 (HTTex1), generated by aberrant splicing or proteolysis, and containing the expanded polyglutamine (polyQ) segment. Unlike amyloid fibrils from Parkinson’s and Alzheimer’s diseases, the atomic-level structure of HTTex1 fibrils has remained unknown, limiting diagnostic and treatment efforts. We present and analyze the structure of fibrils formed by polyQ peptides and polyQ-expanded HTTex1 in vitro. Atomic-resolution perspectives are enabled by an integrative analysis and unrestrained all-atom molecular dynamics (MD) simulations incorporating experimental data from electron microscopy (EM), solid-state NMR, and other techniques. Alongside the use of prior data, we report new magic angle spinning NMR studies of glutamine residues of the polyQ fibril core and surface, distinguished via hydrogen-deuterium exchange (HDX). Our study provides a new understanding of the structure of the core as well as surface of aggregated HTTex1, including the fuzzy coat and polyQ–water interface. The obtained data are discussed in context of their implications for understanding the detection of such aggregates (diagnostics) as well as known biological properties of the fibrils.