bluuebunny/crossref_metadata_2025_split huggingface dataset:
The topoisomerase II/condensin II axis silences transcription during germline specification in Caenorhabditis elegans
Authors: Belew Mezmur D , Chien Emilie , Wong Matthew , Michael W Matthew 
Published: October 2024

Abstract
In Caenorhabditis elegans, the germline is specified via a preformation mechanism that relies on the PIE-1 protein's ability to globally silence mRNA transcription in germline precursor cells, also known as the P lineage. Recent work from our group has identified additional genome silencing events in C. elegans during oogenesis and in starved L1 larvae, and these require the condensin II complex, topoisomerase II, and components of the H3K9me/heterochromatin pathway. Interestingly, silencing in oocytes also requires PIE-1, but this is not the case in starved L1s. Here, we ask if additional genome silencing components besides PIE-1 are required to repress gene expression in the P lineage of early embryos, and we find that condensin II and topoisomerase II are required and the H3K9me/heterochromatin pathway is not. We show that depletion of topoisomerase II/condensin II activates the normally suppressed RNA polymerase II to inappropriately transcribe somatic genes in the P lineage. We also present evidence that while both PIE-1 and topoisomerase II/condensin II are required for genome silencing in the P lineage, PIE-1 can silence transcription independently of topoisomerase II/condensin II when misexpressed in somatic cells. Thus, in oocytes, all three genome silencing systems (topoisomerase II/condensin II, H3K9me, and PIE-1) are operational, while in both early embryos and starved L1s two of the three are active. Our data show that multiple, redundantly acting genome silencing mechanisms act in a mix-and-match manner to repress transcription at different developmental stages in the C. elegans germline.
Palaeognaths Reveal Evolutionary Ancestry of the Avian Major Histocompatibility Complex Class II
Authors: Minias Piotr , Babik Wiesław 
Published: October 2024

Abstract
The multigene family of the major histocompatibility complex (MHC) codes for the key antigen-presenting molecules of the vertebrate immune system. In birds, duplicated MHC class II (MHC-II) genes are highly homogenized by concerted evolution, and thus, identification of their orthologous relationships across long evolutionary timescales remains challenging. Relatively low evolutionary rate of avian MHC class IIA genes has been expected to provide a promising avenue to allow such inferences, but availability of MHC-IIA sequences in nonmodel bird species has been limited until recently. Here, taking advantage from accumulating genomic resources, we identified and analyzed MHC-IIA sequences from the most basal lineage of extant birds (Palaeognathae). Conserved region of the MHC-IIA membrane-proximal domain was used to search for orthologous relationships between palaeognath birds and nonavian reptiles. First, analyses of palaeognath sequences revealed the presence of a separate MHC-IIA gene lineage (DAA3) in kiwis, which did not cluster with previously described avian MHC-IIA lineages (DAA1 and DAA2). Next, phylogenetic reconstruction showed that kiwi DAA3 sequences form a single well-supported cluster with turtle MHC-IIA. High similarity of these sequences most likely reflects their remarkable evolutionary conservation and retention of ancient orthologous relationships, which can be traced back to basal archosauromorphs ca. 250 million years ago. Our analyses offer novel insights into macroevolutionary history of the MHC and reinforce the view that rapid accumulation of high-quality genome assemblies across divergent nonmodel species can substantially advance our understanding of gene evolution.
Stability of L2-Invariants on Stratified Spaces
Authors: Bei Francesco , Piazza Paolo , Vertman Boris 
Published: October 2024

Abstract
Let $\overline{M}$ be a compact smoothly stratified pseudo-manifold endowed with a wedge metric $g$. Let $\overline{M}_{\Gamma }$ be a Galois $\Gamma $-covering. Under additional assumptions on $\overline{M}$, satisfied for example by Witt pseudo-manifolds, we show that the $L^{2}$-Betti numbers and the Novikov–Shubin invariants are well defined. We then establish their invariance under a smoothly stratified codimension-preserving homotopy equivalence, thus extending results of Dodziuk, Gromov, and Shubin to these pseudo-manifolds.
Objects at Work: Cybersecurity Certificates Making Topological Expertise
Authors: Leander Anna 
Published: October 2024

Abstract
Objects do work creating expertise. This article parses how. It works with, revisits, and develops the notion of “boundary-work” located at the core of science and technology studies by Thomas Gieryn, Susan Leigh Star, and others and adds to it the notion of “orienting work” borrowing from the work of materialist feminists such as Sarah Ahmed and Maria do Mar Pereira. Working with these concepts, it shows that cybersecurity certificates make expertise topological. They demarcate, connect, create affective attachments to, and prefigure shapeshifting boundaries of cybersecurity expertise. They orient toward a maze of routes to cybersecurity expertise, a multiplicity of shifting locations in it, and toward fences that are stretched and straddled. Departing from conventional assumptions about the role of certificates in the formation of expertise, I show that rather than close off and stabilize expertise, the work of cybersecurity certificates opens and unsettles it. The cybersecurity expertise they make is preserved in continuous deformation. I also show that rather than fragment and fracture expertise, the work of certificates stretches, bends, and twists an expertise that remains connected. The work makes expertise of a distinctly topological quality. Engaging this moving, shapeshifting terrain politically is both exceptionally challenging and fundamentally important. The shifting expert terrain is generating a steadily expanding range of cybersecurity concerns that are inscribed ever more firmly in the socio-technical infrastructures of cybersecurity with ramifications for everyday life.
High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts
Authors: Voulgari-Kokota Anna , Boatta Francesco , Rijkers Ruud , Wertheim Bregje , Beukeboom Leo W , Ellers Jacintha , Salles Joana Falcao 
Published: October 2024

Abstract
The housefly (Musca domestica) is a common insect species with only a few recurrent bacterial taxa in its gut microbiota, because the numerous microbial acquisition routes in its septic habitats can favor transient microbes. Here, we investigated the role of the diet on the microbiota and the developmental success of a housefly strain reared on three substrates. We used a control wheat bran-based substrate, and added clotted cream and sucrose to make a high-fat, and a high-sugar substrate, respectively. The conducted survey revealed that, in contrast to the high-fat diet, the high-sugar diet caused lower developmental success and less diverse microbiota, in which several lactobacilli were replaced with Weissella bacterial phylotypes. Cultures with sucrose as the sole carbon source confirmed that a Weissella confusa strain, isolated from larvae, could utilize sucrose more efficiently than other tested lactic acid bacteria; a result also supported by gene function prediction analysis. Enhancing the rearing substrate with Limosilactobacillus fermentum and Lactiplantibacillus plantarum strains, which were isolated from control larvae, could not only revert the negative effect of the high-sucrose diet on development, but also increase the gut bacterial diversity. In our study, we show that the microbiota shifts in response to the high-sucrose diet did not benefit the host, that showed lower developmental success. In contrast, high-sucrose favored specific components of the microbiota, that continued to be enriched even after multiple generations, outcompeting beneficial bacteria. Also, microbiome manipulation showed the potential of probiotics to rescue host performance and restore the microbiome.
More than Foodsaving Machines: Insights from Communities Fighting Food Waste in the Digital Age
Authors: Ntouros Vasilis , Vlachokyriakos Vasilis , Engelbutzeder Philip 
Published: October 2024

Abstract
Grassroots initiatives promoting sharing-for-community are viewed as contributing to the transition towards a more socially equitable and environmentally sustainable world. However, along with other challenges, they often encounter technological barriers. In this article we report on our engagement with a number of self-organised foodsaving and sharing communities active in Europe which use the open-source platform Karrot to coordinate their activities. Our aim has been to explore the use of Karrot, across various contexts. We have also been interested in understanding Karrot’s impact on community-led foodsaving and sharing daily practices, as well as on community governance and organising; aspects which distinguish grassroots initiatives from more top-down anti-food waste models. We found that while Karrot facilitates certain processes, it does not fully meet the needs of the researched communities, which in turn have been configuring Karrot and have been developing unique digital ecologies, combining Karrot with off-the-shelf commercial tools. By recognising foodsaving and sharing communities as elements of a larger transformational ecosystem, we broaden our discussion to include the role of technology beyond just community-led foodsaving and sharing initiatives. Reflecting on the process of developing digital ecologies, we explore interoperability as a design element that can enhance sharing-for-community practices. Next, we propose strategies to strengthen community governance and organisation. Finally, we seed Community-Supported Software as an evolving framework that can facilitate the collaboration between grassroots place-based and software communities.
“Nerves Need Nourishment”: Advertising Phospho-Energon Pills in Early Twentieth-Century Sweden
Authors: O’Hagan Lauren Alex , Runefelt Leif 
Published: October 2024

Abstract
This paper offers the first case study of Phospho-Energon — an early twentieth-century Swedish patent medicine believed to cure nervousness. Using a large dataset of newspaper advertisements, it explores how the product was presented through scientific and medical language, which drew upon a range of visual and verbal rhetoric to convince consumers of its benefits. It finds that pseudoscientific discourse focusing on self-help was regularly used to sell Phospho-Energon, with consumers warned that their nerves were “not allowed to fail” and required “protection” in order to remain healthy. Furthermore, the “science” supporting this discourse gradually shifted over time as neurosis replaced neurasthenia as a diagnostic category and the concept of spring lethargy became popularised. Overall, this study argues that Phospho-Energon stands as an important example of how partial scientific/medical claims can be used as a rhetorical device to sell products to consumers looking for a quick-fix cure for their perceived mental health conditions.
Pharmaceutical industry promotional activities on social media: a scoping review
Authors: Mor Jessica , Kaur Tina , Menkes David B , Peter Elizabeth , Grundy Quinn 
Published: October 2024

Abstract

Objectives
The rise of social media has broadened the reach and impact of pharmaceutical promotion across countries. This scoping review synthesizes available literature on the nature, extent, and impacts of such promotion, with a particular focus on public health implications.

Methods
Using a systematic strategy, we searched six multidisciplinary scholarly databases for empirical studies, both peer-reviewed and grey, published since 2004, which had collected data on pharmaceutical promotion via social media. Data were synthesized qualitatively into outcome domains.

Key findings
We included 45 studies, primarily conducted in the USA (20/45, 44%) and multi-nationally (15/45, 33%), and published after 2013 (40/45, 89%). Studies used content analyses, surveys, and interviews to measure pharmaceutical industry presence or impacts on the following indicators: social media, social media strategy, consumer reach and engagement, health information quality, ethical and regulatory guideline adherence, and consumer attitudes and behaviours. Taken together, these studies indicate a gradual increase in industry use of social media, notably including the development of novel consumer engagement strategies, such as targeted promotion and influencer sponsorship. Studies also showed that, in some cases, health information provided on social media is of low quality, ethically and legally questionable, and potentially harmful to public health.

Conclusions
Appreciating the regulatory and reputational risks of consumer engagement on social media, the pharmaceutical industry has gradually increased promotional activities on social media since its inception. Evidence of harmful content and promotional activities that have become more covert and targeted suggests the need for regulatory development.
Games for hybrid logic from semantic games to analytic calculi
Authors: Freiman Robert 
Published: October 2024

Abstract
Game semantics and winning strategies offer a potential conceptual bridge between semantics and proof systems of logics. We illustrate this link for hybrid logic—an extension of modal logic that allows for explicit reference to worlds within the language. We lift a Hintikka-style semantic game to a disjunctive game. The disjunctive game adequately models entailment and validity over classes of frames characterizable in the hybrid language. The search for winning strategies in this game can be reformulated as a sequent-style proof system.
soibean: High-Resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs
Authors: Vogel Nicola Alexandra , Rubin Joshua Daniel , Pedersen Anders Gorm , Sackett Peter Wad , Pedersen Mikkel Winther , Renaud Gabriel 
Published: October 2024

Abstract
Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems, overcoming the limitations of conventional fossil records. However, several methodological challenges remain, particularly for classifying the DNA to species level and conducting phylogenetic analysis. Current methods, primarily tailored for modern datasets, fail to capture several idiosyncrasies of aeDNA, including species mixtures from closely related species and ancestral divergence. We introduce soibean, a novel tool that utilizes mitochondrial pangenomic graphs for identifying species from aeDNA reads. It outperforms existing methods in accurately identifying species from multiple closely related sources within a sample, enhancing phylogenetic analysis for aeDNA. soibean employs a damage-aware likelihood model for precise identification at low coverage with a high damage rate. Additionally, we reconstructed ancestral sequences for soibean’s database to handle aeDNA that is highly diverged from modern references. soibean demonstrates effectiveness through simulated data tests and empirical validation. Notably, our method uncovered new empirical results in published datasets, including using porpoise whales as food in a Mesolithic community in Sweden, demonstrating its potential to reveal previously unrecognized findings in aeDNA studies.
Isolated adrenocorticotropic hormone deficiency presenting with arthritis: A case report
Authors: Yamashita Yuya , Sato Seidai , Nii Kaori , Mori Kensuke , Haji Keiko , Naito Nobuhito , Ogino Hirokazu , Kawawno Hiroshi , Hanibuchi Masaki , Endo Itsuro , Nishioka Yasuhiko 
Published: October 2024

ABSTRACT
This case report describes a case of isolated adrenocorticotropic hormone (ACTH) deficiency that presented with arthritis. Initial investigations, including blood tests, imaging, and musculoskeletal ultrasonography, did not confirm any specific connective tissue disease, making it initially difficult to identify the cause of the arthritis. Subsequent adrenal crisis led to the diagnosis of isolated ACTH deficiency through comprehensive endocrine evaluation. The patient’s musculoskeletal symptoms, together with generalised symptoms, were resolved following corticosteroid replacement therapy. This report highlights isolated ACTH deficiency as a rare but one of the causes of polyarticular joint pain and underscores the importance of considering endocrine disorders in the differential diagnosis of unexplained arthritis, particularly when accompanied by systemic symptoms.
Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package
Authors: Pirrotta Stefania , Masatti Laura , Bortolato Anna , Corrà Anna , Pedrini Fabiola , Aere Martina , Esposito Giovanni , Martini Paolo , Risso Davide , Romualdi Chiara , Calura Enrica 
Published: October 2024

Abstract
Understanding cancer mechanisms, defining subtypes, predicting prognosis and assessing therapy efficacy are crucial aspects of cancer research. Gene-expression signatures derived from bulk gene expression data have played a significant role in these endeavors over the past decade. However, recent advancements in high-resolution transcriptomic technologies, such as single-cell RNA sequencing and spatial transcriptomics, have revealed the complex cellular heterogeneity within tumors, necessitating the development of computational tools to characterize tumor mass heterogeneity accurately. Thus we implemented signifinder, a novel R Bioconductor package designed to streamline the collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Leveraging publicly available signatures curated by signifinder, users can assess a wide range of tumor characteristics, including hallmark processes, therapy responses, and tumor microenvironment peculiarities. Through three case studies, we demonstrate the utility of transcriptional signatures in bulk, single-cell, and spatial transcriptomic data analyses, providing insights into cell-resolution transcriptional signatures in oncology. Signifinder represents a significant advancement in cancer transcriptomic data analysis, offering a comprehensive framework for interpreting high-resolution data and addressing tumor complexity.
Associations between central nervous system tumor diagnosis stage and survival and Medicaid enrollment among children, adolescents, and young adults
Authors: Johnson Kimberly J , Brown Derek S , Thompson Tess , Barnes Justin M , King Allison A 
Published: October 2024

Abstract

Background
Medicaid enrollment has been associated with disparities in younger cancer patient survival. To further understand this association for central nervous system (CNS) tumor patients, we used Surveillance, Epidemiology, and End Results (SEER)-Medicaid-linked data to examine associations between Medicaid enrollment and enrollment timing and (1) diagnosis stage, and (2) CNS tumor death.

Methods
Individuals diagnosed with a first malignant primary CNS tumor between 0 and 39 years from 2006 to 2013 were included. Medicaid enrollment was first classified as enrolled versus not enrolled with those enrolled further classified as having continuous, discontinuous (at diagnosis or other discontinuous), or other enrollment. We used logistic and Cox Proportional Hazards regression stratified by age to calculate adjusted odds ratios (ORs) and hazard ratios (HRs) for those 0–14 and 15–39 years.

Results
Among 10 107 CNS tumor patients, we found significantly higher odds of regional/distant versus in situ/localized stage diagnoses for those with other discontinuous (OR0–14 = 1.50, 95% CI: 1.15–1.95) and at diagnosis (OR15–39 = 1.41, 95% CI: 1.11–1.78) Medicaid enrollment versus those not enrolled. Those enrolled versus not enrolled in Medicaid had a higher hazard of CNS tumor death for both age groups (HR0–14 = 1.60 95% CI: 1.37–1.86; HR15–39 = 1.50, 95% CI: 1.39–1.62) with the highest hazards for those enrolled at diagnosis (HR0–14 = 1.83, 95% CI: 1.51–2.22; HR15–39 = 1.93, 95% CI: 1.77–2.10).

Conclusions
Medicaid enrollment is associated with a higher risk of CNS tumor death with an almost 2-fold higher risk for young CNS tumor patients enrolled at diagnosis. These results support the critical need for consistent health insurance coverage for young CNS tumor patients.
Ancestral origins and post-admixture adaptive evolution of highland Tajiks
Authors: Wen Jia , Liu Jiaojiao , Feng Qidi , Lu Yan , Yuan Kai , Zhang Xiaoxi , Zhang Chao , Gao Yang , Wang Xiaoji , Mamatyusupu Dolikun , Xu Shuhua 
Published: October 2024

ABSTRACT
It remains debatable how many genes and how various the mechanisms are behind human adaptation to extreme environments, such as high altitudes. Despite extensive studies on Tibetans, Andeans and Ethiopians, new insights are expected to be provided with careful analysis of underrepresented highlanders living in a different geographical region, such as the Tajiks, who reside on the Pamir Plateau at an average altitude exceeding 4000 meters. Moreover, genetic admixture, as we observed in the current whole-genome deep-sequencing study of Xinjiang Tajiks (XJT), offers a unique opportunity to explore how admixture may facilitate adaptation to high-altitude environments. Compared with other extensively studied highlanders, XJT showed pronounced admixture patterns: most of their ancestry are derived from West Eurasians (34.5%–48.3%) and South Asians (21.4%–40.0%), and some minor ancestry from East Asians and Siberians (3.62%–17.5%). The greater genetic diversity in XJT than in their ancestral source populations provides a genetic basis for their adaptation to high-altitude environments. The admixture gain of functional adaptive components from ancestral populations could facilitate adaptation to high-altitude environments. Specifically, admixture-facilitated adaptation was strongly associated with skin-related candidate genes that respond to UV radiation (e.g. HERC2 and BNC2) and cardiovascular-system-related genes (e.g. MPI and BEST1). Notably, no adaptive variants of genes showing outstanding natural selection signatures in the Tibetan or Andean highlanders were identified in XJT, including EPAS1 and EGLN1, indicating that a different set of genes contributed to XJT's survival on the Pamir Plateau, although some genes underlying natural selection in XJT have been previously reported in other highlanders. Our results highlight the unique genetic adaptations in XJT and propose that admixture may play a vital role in facilitating high-altitude adaptation. By introducing and elevating diversity, admixture likely induces novel genetic factors that contribute to the survival of populations in extreme environments like the highlands.