bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proportions of taxa belonging to the gut core microbiome change throughout the life cycle and season of the bark beetleIps typographus
Authors: Veselská Tereza , Švec Karel , Kostovčík Martin , Peral-Aranega Ezequiel , Garcia-Fraile Paula , Křížková Barbora , Havlíček Václav , Saati-Santamaría Zaki , Kolařík Miroslav 
Published: June 2023

AbstractThe European spruce bark beetle, Ips typographus, is a serious pest of spruce forests in Europe, and its invasion and development inside spruce tissues are facilitated by microorganisms. We investigated the core gut bacterial and fungal microbiomes of I. typographus throughout its life cycle in spring and summer generations. We used cultivation techniques and molecular identification in combination with DNA and RNA metabarcoding. Our results revealed that communities differ throughout their life cycle and across generations in proportion of dominantly associated microbes, rather than changes in species composition. The bacteriome consisted mostly of the phylum Gammaproteobacteria, with the most common orders and genera being Enterobacteriales (Erwinia and Serratia), Pseudomonadales (Pseudomonas), and Xanthomonadales. The fungal microbiome was dominated by yeasts (Saccharomycetes—Wickerhamomyces, Kuraishia, and Nakazawaea), followed by Sordariomycetes (Ophiostoma bicolor and Endoconidiophora polonica). We did not observe any structure ensuring long-term persistence of microbiota on any part of the gut epithelium, suggesting that microbial cells are more likely to pass through the beetle’s gut with chyme. The most abundant taxa in the beetle’s gut were also identified as dominant in intact spruce phloem. Therefore, we propose that these taxa are acquired from the environment rather than specifically vectored between generations.
Characterization of direct and/or indirect genetic associations for multiple traits in longitudinal studies of disease progression
Authors: Brossard Myriam , Paterson Andrew D , Espin-Garcia Osvaldo , Craiu Radu V , Bull Shelley B 
Published: June 2023

Abstract
When quantitative longitudinal traits are risk factors for disease progression and subject to random biological variation, joint model analysis of time-to-event and longitudinal traits can effectively identify direct and/or indirect genetic association of single nucleotide polymorphisms (SNPs) with time-to-event. We present a joint model that integrates: (1) a multivariate linear mixed model describing trajectories of multiple longitudinal traits as a function of time, SNP effects, and subject-specific random effects and (2) a frailty Cox survival model that depends on SNPs, longitudinal trajectory effects, and subject-specific frailty accounting for dependence among multiple time-to-event traits. Motivated by complex genetic architecture of type 1 diabetes complications (T1DC) observed in the Diabetes Control and Complications Trial (DCCT), we implement a 2-stage approach to inference with bootstrap joint covariance estimation and develop a hypothesis testing procedure to classify direct and/or indirect SNP association with each time-to-event trait. By realistic simulation study, we show that joint modeling of 2 time-to-T1DC (retinopathy and nephropathy) and 2 longitudinal risk factors (HbA1c and systolic blood pressure) reduces estimation bias in genetic effects and improves classification accuracy of direct and/or indirect SNP associations, compared to methods that ignore within-subject risk factor variability and dependence among longitudinal and time-to-event traits. Through DCCT data analysis, we demonstrate feasibility for candidate SNP modeling and quantify effects of sample size and Winner's curse bias on classification for 2 SNPs identified as having indirect associations with time-to-T1DC traits. Joint analysis of multiple longitudinal and multiple time-to-event traits provides insight into complex traits architecture.
Hydrodynamic Diversity of Jets Mediated by Giant and Non-Giant Axon Systems in Brief Squid
Authors: Li Diana H , Bartol Ian K , Gilly William F 
Published: June 2023

Synopsis
Neural input is critical for establishing behavioral output, but understanding how neuromuscular signals give rise to behaviors remains a challenge. In squid, locomotion through jet propulsion underlies many key behaviors, and the jet is mediated by two parallel neural pathways, the giant and non-giant axon systems. Much work has been done on the impact of these two systems on jet kinematics, such as mantle muscle contraction and pressure-derived jet speed at the funnel aperture. However, little is known about any influence these neural pathways may have on the hydrodynamics of the jet after it leaves the squid and transfers momentum to the surrounding fluid for the animal to swim. To gain a more comprehensive view of squid jet propulsion, we made simultaneous measurements of neural activity, pressure inside the mantle cavity, and wake structure. By computing impulse and time-averaged forces from the wake structures of jets associated with giant or non-giant axon activity, we show that the influence of neural pathways on jet kinematics could extend to hydrodynamic impulse and force production. Specifically, the giant axon system produced jets with, on average, greater impulse magnitude than those of the non-giant system. However, non-giant impulse could exceed that of the giant system, evident by the graded range of its output in contrast to the stereotyped nature of the giant system. Our results suggest that the non-giant system offers flexibility in hydrodynamic output, while recruitment of giant axon activity can provide a reliable boost when necessary.
Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology
Authors: Baden Tom , Briseño John , Coffing Gabrielle , Cohen-Bodénès Sophie , Courtney Amy , Dickerson Dominick , Dölen Gül , Fiorito Graziano , Gestal Camino , Gustafson Taryn , Heath-Heckman Elizabeth , Hua Qiaz , Imperadore Pamela , Kimbara Ryosuke , Król Mirela , Lajbner Zdeněk , Lichilín Nicolás , Macchi Filippo , McCoy Matthew J , Nishiguchi Michele K , Nyholm Spencer V , Otjacques Eve , Pérez-Ferrer Pedro Antonio , Ponte Giovanna , Pungor Judit R , Rogers Thea F , Rosenthal Joshua J C , Rouressol Lisa , Rubas Noelle , Sanchez Gustavo , Santos Catarina Pereira , Schultz Darrin T , Seuntjens Eve , Songco-Casey Jeremea O , Stewart Ian Erik , Styfhals Ruth , Tuanapaya Surangkana , Vijayan Nidhi , Weissenbacher Anton , Zifcakova Lucia , Schulz Grace , Weertman Willem , Simakov Oleg , Albertin Caroline B 
Published: June 2023

Synopsis
Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.
Military spending and innovation: learning from 19th-century world fair exhibition data
Authors: Danzer Alexander M , Danzer Natalia , Feuerbaum Carsten 
Published: June 2023

Abstract
We provide quantitative evidence on the relationship between military spending and innovation in the 19th century. Combining innovation data from world fairs and historical military data across Europe, we show that national military spending is associated with national innovation toward war logistics such as food processing, but less toward war technology such as guns. This innovation pattern reflects differences in the historical markets for war supplies: while the armed forces sourced weapons globally, the food market remained local.
Grooming and agonistic behaviors in the semi-terrestrial crabsOcypode quadrata(Fabricius, 1787) andMinuca(Uca) burgersi(Holthuis, 1967) (Decapoda: Brachyura: Ocypodidae)
Authors: Dakin Maggie , Wortham Jen L 
Published: June 2023

AbstractGrooming behaviors reduce body fouling and are well documented in crustaceans. There are more detailed laboratory-based grooming studies on fully aquatic crabs compared to semi-terrestrial crabs. By contrast, semi-terrestrial crabs are predicted to have different grooming time budgets than fully aquatic crabs because semi-terrestrial crabs are not constantly submerged in water that can mechanically remove sedimentary fouling, whereas fully aquatic crustaceans have increased fouling from algae and epibionts. We studied the grooming behaviors of two semi-terrestrial crab species. Crabs (N = 50 ghost crabs, Ocypode quadrata (Fabricius, 1787); N = 50 fiddler crabs, Minuca (Uca) burgersi (Holthuis, 1967)) were observed in isolation for 45-min trials. We recorded grooming frequency, location, appendage, and time. Ghost crabs were also observed in agonistic encounters to determine how grooming varied in the presence of a conspecific individual. Ghost crabs and fiddler crabs have different grooming time budgets, (0.526 and 0.895%, respectively) with both species having lower grooming time budgets than fully aquatic crustaceans. Some similarities and differences in grooming between the two semi-terrestrial crabs exist, with both species frequently grooming their eyes and maxillipeds using a brush or scrape mechanism, but with fiddler crabs using their eyes as a grooming appendage more frequently than ghost crabs. Ghost crab males groom less than females, whereas fiddler crab males and females groom equally. In agonistic interactions in ghost crabs, the grooming time budget decreased compared with isolated observations and individuals engaged in a “playing dead” behavior (thanatosis) after engaging in a fight. Semi-terrestrial crabs were found to groom significantly less than fully aquatic crustaceans.
Protection of Biocultural Heritage in the Anthropocene: Towards Reconciling Natural, Cultural, Tangible and Intangible Heritage
Authors: Bhati Harsh Vardhan , Epstein Yaffa 
Published: June 2023

Abstract
This article examines the effectiveness, legitimacy, and fairness of heritage conservation outcomes under the 1972 World Heritage Convention (1972 WHC), with a focus on recognising and respecting the rights of Indigenous Peoples in heritage nomination, protection, and management. Examining conflicts surrounding World Heritage sites in Kenya and Sweden, this article argues that recognition of biocultural heritage and biocultural rights can promote environmental justice and help meet global environmental challenges. To promote the conservation of both built and natural landscapes, the article recommends expanding protection for the relationship between humans and their environment. Recognising biocultural heritage under UNESCO conventions could promote Indigenous sovereignty, protect cultural and natural heritage, and contribute to global efforts to address climate change. The article calls for further research mapping biocultural heritage in natural and mixed heritage sites and advocates for fuller engagement with Indigenous Peoples to increase the ability of the 1972 WHC to promote sustainability as it enters its second half-century.
Symptomatic acinar cell cystadenoma of the pancreas
Authors: Sergi William , D’Ugo Stefano , Libia Annarita , Depalma Norma , Marchese Tiziana , Garritano Stefano , Vadrucci Stefania , Stasi Elisa , Botrugno Ivan , Manoochehri Farshad , Spampinato Marcello , Sergi William 
Published: June 2023

Abstract
Acinar cystic transformation (ACT), also known as ‘acinar cell cystadenoma’, is an uncommon cystic neoplasm of pancreas with unknown malignant potential. This case regards a woman with symptomatic pancreatic head ACT, revealed with pathological exam of specimen after pancreaticoduodenectomy. A 57-years-old patient presented mild hyperbilirubinemia and recurrent cholangitis; she underwent to ERCP, EUS and MRI, and these exams revealed a large cyst of the pancreatic head that caused biliary compression. The discussion of the case by the multidisciplinary group indicated surgical resection. Pancreatic ACT is so rare, and its preoperative diagnosis is difficult. The symptoms of the patients and the features of the cyst are the criteria to choose a surgical resection.
First case of primary appendiceal tuberculosis presented as stump appendicitis
Authors: Mathew Midhun , Mathew Tony , Joseph Elizabeth 
Published: June 2023

Abstract
Tuberculosis (TB) remains as a significant global public health issue, especially in developing and underdeveloped nations. Extrapulmonary TB comprises 20% of the TB cases; of which 34.4% were in the lymphatics, 25.2% pleural, followed by 12.8% gastrointestinal and 9.4% in the central nervous system. Ileocecal involvement is the most common among gastrointestinal TB. Although it can cause secondary damage to the appendix, primary type of appendicular TB is rare and can occur with no other signs of the disease. A high index of suspicion is necessary for early diagnosis and treatment of TB. Similarly, stump appendicitis (SA) is a rare and delayed complication of appendectomy. Here we report a case of primary appendicular TB in a patient presented to a multi-specialty hospital in Kerala, India, with SA.
Wooded streets, but not streetlight dimming, favour bat activity in a temperate urban setting
Authors: Stanley Christopher , Bagniewska Joanna Maria , Grabowska-Zhang Ada , Hesselberg Thomas 
Published: June 2023

Abstract
Urbanization damages biodiversity, reducing people’s connection to nature and negatively impacting the survivability of local species. However, with small adjustments, the damage could be mitigated. In temperate regions, several bat species inhabit urban areas, and with urbanization set to increase, adapting urban areas to improve their suitability for bats is imperative. Therefore, we investigated if wooded streets and streetlight dimming in an urban setting influenced bat activity. Static bat detectors were used to compare wooded versus non-wooded, and bright versus dim streets in Leicester, UK, on predominantly residential streets. The collected calls were quantified into bat activity (passes per night). Six species were identified, but the common pipistrelle (Pipistrellus pipistrellus) was dominant, making up 94.1% of all calls, so it was the sole species included in the statistical model. Wooded streets had significantly higher bat activity than non-wooded streets, but bright and dim streets were not significantly different. The results suggest that wooded streets were being used as green corridors, with common pipistrelles possibly following them to conceal themselves from predators, such as the tawny owl, and the proliferation of wooded streets in urban areas could allow the formation of better-connected populations. Streetlight dimming did not affect bat activity, but no light-averse bats were detected, likely because even the most dimmed streets deterred them despite street lighting increasing food availability by attracting insects. Therefore, an alternate solution, such as part-night lighting, may be required to increase the suitability of urban areas to light-averse species.
Synchrotron science for sustainability: life cycle of metals in the environment
Authors: Smieska Louisa , Guerinot Mary Lou , Olson Hoal Karin , Reid Matthew , Vatamaniuk Olena 
Published: June 2023

Abstract
The movement of metals through the environment links together a wide range of scientific fields: from earth sciences and geology as weathering releases minerals; to environmental sciences as metals are mobilized and transformed, cycling through soil and water; to biology as living things take up metals from their surroundings. Studies of these fundamental processes all require quantitative analysis of metal concentrations, locations, and chemical states. Synchrotron X-ray tools can address these requirements with high sensitivity, high spatial resolution, and minimal sample preparation. This perspective describes the state of fundamental scientific questions in the lifecycle of metals, from rocks to ecosystems, from soils to plants, and from environment to animals. Key X-ray capabilities and facility infrastructure for future synchrotron-based analytical resources serving these areas are summarized, and potential opportunities for future experiments are explored.
ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors
Authors: Jeusset Lucile , Abdollahi Nika , Verny Thibaud , Armand Marine , De Septenville Anne Langlois , Davi Frédéric , Bernardes Juliana Silva 
Published: June 2023

Abstract
High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, it performs clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.
Clinical outcome of pediatric medulloblastoma patients with Li–Fraumeni syndrome
Authors: Kolodziejczak Anna S , Guerrini-Rousseau Lea , Planchon Julien Masliah , Ecker Jonas , Selt Florian , Mynarek Martin , Obrecht Denise , Sill Martin , Autry Robert J , Stutheit-Zhao Eric , Hirsch Steffen , Amouyal Elsa , Dufour Christelle , Ayrault Olivier , Torrejon Jacob , Waszak Sebastian M , Ramaswamy Vijay , Pentikainen Virve , Demir Haci Ahmet , Clifford Steven C , Schwalbe Ed C , Massimi Luca , Snuderl Matija , Galbraith Kristyn , Karajannis Matthias A , Hill Katherine , Li Bryan K , Walsh Mike , White Christine L , Redmond Shelagh , Loizos Loizou , Jakob Marcus , Kordes Uwe R , Schmid Irene , Hauer Julia , Blattmann Claudia , Filippidou Maria , Piccolo Gianluca , Scheurlen Wolfram , Farrag Ahmed , Grund Kerstin , Sutter Christian , Pietsch Torsten , Frank Stephan , Schewe Denis M , Malkin David , Ben-Arush Myriam , Sehested Astrid , Wong Tai-Tong , Wu Kuo-Sheng , Liu Yen-Lin , Carceller Fernando , Mueller Sabine , Stoller Schuyler , Taylor Michael D , Tabori Uri , Bouffet Eric , Kool Marcel , Sahm Felix , von Deimling Andreas , Korshunov Andrey , von Hoff Katja , Kratz Christian P , Sturm Dominik , Jones David T W , Rutkowski Stefan , van Tilburg Cornelis M , Witt Olaf , Bougeard Gaëlle , Pajtler Kristian W , Pfister Stefan M , Bourdeaut Franck , Milde Till 
Published: June 2023

Abstract

Background
The prognosis for Li–Fraumeni syndrome (LFS) patients with medulloblastoma (MB) is poor. Comprehensive clinical data for this patient group is lacking, challenging the development of novel therapeutic strategies. Here, we present clinical and molecular data on a retrospective cohort of pediatric LFS MB patients.

Methods
In this multinational, multicenter retrospective cohort study, LFS patients under 21 years with MB and class 5 or class 4 constitutional TP53 variants were included. TP53 mutation status, methylation subgroup, treatment, progression free- (PFS) and overall survival (OS), recurrence patterns, and incidence of subsequent neoplasms were evaluated.

Results
The study evaluated 47 LFS individuals diagnosed with MB, mainly classified as DNA methylation subgroup “SHH_3” (86%). The majority (74%) of constitutional TP53 variants represented missense variants. The 2- and 5-year (y-) PFS were 36% and 20%, and 2- and 5y-OS were 53% and 23%, respectively. Patients who received postoperative radiotherapy (RT) (2y-PFS: 44%, 2y-OS: 60%) or chemotherapy before RT (2y-PFS: 32%, 2y-OS: 48%) had significantly better clinical outcome then patients who were not treated with RT (2y-PFS: 0%, 2y-OS: 25%). Patients treated according to protocols including high-intensity chemotherapy and patients who received only maintenance-type chemotherapy showed similar outcomes (2y-PFS: 42% and 35%, 2y-OS: 68% and 53%, respectively).

Conclusions
LFS MB patients have a dismal prognosis. In the presented cohort use of RT significantly increased survival rates, whereas chemotherapy intensity did not influence their clinical outcome. Prospective collection of clinical data and development of novel treatments are required to improve the outcome of LFS MB patients.