bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated pupillometry is a predictor of outcome of stroke patients: an observational, prospective, cohort study
Authors: Scala Irene , Miccoli Massimo , Di Giovanni Jacopo , Cerulli Fabiana , Rizzo Pier A , Bellavia Simone , Vitali Francesca , Colò Francesca , Abruzzese Serena , della Marca Giacomo , Guglielmi Valeria , Brunetti Valerio , Di Iorio Riccardo , Broccolini Aldobrando , Profice Paolo , Calabresi Paolo , Monforte Mauro , Frisullo Giovanni
Published: February 2025

Automated Pupillometry (AP) is a rapid, non-invasive tool to assess the pupillary light reflex, extensively used for monitoring patients with traumatic brain injury. In acute ischemic stroke, quantitative tools to monitor neurological status and predict outcome are lacking. This study aims to evaluate the ability of AP to predict stroke outcome, defined trough the modified Rankin Scale (mRS) scores. In this observational, cohort study, we enrolled adult patients with anterior circulation stroke admitted to the stroke unit of a comprehensive stroke center between 2021 and 2024 who underwent AP evaluation within 72 hours of stroke onset. Exclusion criteria were: intracranial hypertension, severe eye diseases, pathologies involving the autonomic nervous system, and lack of 3-month follow-up data. The AP evaluation was repeated three consecutive times in each patient using the NPi-200® and mean parameters of the two eyes and those of the eye homolateral and contralateral to the ischemic lesion were considered. Mann-Whitney U-test, t-test and χ2-tets were used for univariate comparisons. Binary and ordinal multivariable logistic regression were used for the adjusted analysis. The primary outcome measure was the dichotomization of the three-month mRS of 0-2 vs 3-6. Secondary outcomes were the score on the 3-month mRS, 3-month dichotomization of mRS 0-3 vs 4-6, three-month and in-hospital death. Receiver operating characteristic curves (ROC) were computed to evaluate the prognostic ability of AP. Two-hundred and nine patients (123 men, median age 75 years) were included in the study. Among included patients, 11 (5.3%) died during the hospital stay and 124 (59.33%) had a 3-month mRS<3. In multivariable logistic regression models corrected for all possible confounders, a low dilatation velocity (DV) in the eye homolateral to the stroke lesion was an independent predictor of poor prognosis, defined as both mRS>2 and mRS>3 at three months (p=0.028 and p=0.024, respectively). Furthermore, homolateral DV resulted to be a significant predictor of a shift towards a better outcome on the three-month mRS in the ordinal logistic regression (p=0.036). A DV≥0.865 mm/s was able to predict a good stroke outcome at 90 days with 60% sensitivity and specificity (area under the curve 0.651; p<0.001). No other AP parameters were independent predictors of stroke outcome. A reduction in the DV in the eye ipsilateral to the ischemic lesion is associated with poor in-hospital and 3-month stroke outcome and it could be useful for identifying patients who need a tailored monitoring and treatment path to improve their prognosis.
Comparing rates of molecular and morphological evolution identifies multiple speciation trajectories in a diverse radiation of skinks
Authors: Schembri Rhiannon , Bromham Lindell , Moritz Craig , Hua Xia
Published: February 2025

There is increasing recognition that the process of species divergence is not uniform across the tree of life, and that newly diverged taxa may differ in their levels of phenotypic and genetic divergence. We investigate the relationship between phenotypic and genetic differentiation across the speciation continuum using sister pairs from a large ecologically diverse radiation of Australian skinks, the Tribe Eugongylini, a high-quality alignment of genomic sequence data, and morphometric data for 90 lineages across the radiation. Based on the framework proposed by Struck et al. (2018) for comparative study of species divergence, we used latent class regression to test for multiple speciation “trajectories”. We found evidence for multiple relationships between genetic divergence and morphological disparity for recently diverged sister taxa, which we summarise into two broad patterns. One of these patterns is characterised by relatively rapid morphological differentiation for pairs with greater disparity in environmental variables, consistent with expectations of ecological speciation. The second pattern shows accumulation of both morphological and genetic differences in proportion to each other, consistent with gradual speciation. Our study shows how heterogeneity in speciation processes can be captured in a comparative framework.
Screening Aging And Homelessness
Authors: Capp Rose , VandenBosch Jim
Published: February 2025

This special issue on Homelessness and Older Adults offers us the opportunity to consider how both fiction and non-fiction films address this topic and what kinds of insights they offer. In exploring this significant issue, we decided to address fiction and non-fiction films separately. Rose Capp discusses a selection of feature fiction films from the United States, Australia and the United Kingdom, while Jim VandenBosch explores an expansive range of short and feature length documentaries from Portland to Finland.
Emerging mechanism and Therapeutic Potential of Neurofibromatosis Type 1-Related Nerve System Tumor: Advancing Insights into Tumor Development
Authors: Yu Xuan , Gu Yihui , Liu Jun , Huang Jingxuan , Li Qingfeng , Wang Zhichao
Published: February 2025

Neurofibromatosis Type 1 (NF1) is a genetic disorder resulting from mutations in the NF1 gene, which increases susceptibility to various nervous system tumors, including plexiform neurofibromas, malignant peripheral nerve sheath tumors, and optic pathway gliomas. Recent research has shown that these tumors are intricately connected to the complex, dynamic interactions within neurons, culminating in neuronal signaling that fosters tumor growth. These interactions offer crucial insights into the molecular mechanisms underpinning tumor development, as well as broader implications for therapeutic strategies. This review summarizes the mechanisms through which mutations in the NF1 gene within neural tissues trigger tumorigenesis, while examining the role of the neuron—via factors such as visual experience, neurotransmitter, tumor microenvironment, and psychological influences—in both promoting tumor progression and being affected by the tumors themselves. By investigating the dynamic relationship between NF1-associated nervous system tumor cells and neurons, we aim to shed light on novel biological pathways and disease processes, emphasizing the potential of interdisciplinary approaches that combine neurobiology, oncology, and pharmacology to enhance treatment strategies and even inhibit the tumorigenesis.
Substance Use Disorders
Authors: Mangum Anna , Ling Diana , Velasquez Mary
Published: February 2025

Substance use disorders (SUDs) are medical and mental health conditions that affect millions of people worldwide, of all ages, races, genders and socioeconomic levels. Men are affected at a higher rate than women, but substance misuse among women is increasing. SUDs range from mild to severe and occur when the use of alcohol and/or other legal or illicit drugs cause clinically significant impairment, including health problems, disability, and failure to meet major responsibilities at work, school, and/or home. The disorders are recurrent and often serious, but treatable, and many people do recover. The most severe SUDs are sometimes called “addictions,” though the terms “addiction” or “addicts” can be stigmatizing. This terminology often poses a barrier to seeking and receiving help. In more recent work, the term that is used in professional and clinical contexts is “substance misuse.” According to The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, Text Revision, SUDs encompass ten separate classes of legal and illicit drugs: alcohol; caffeine; cannabis (marijuana); hallucinogens; inhalants; opioids; sedatives, hypnotics or anxiolytics; stimulants (amphetamine-type substances, cocaine, etc.); and tobacco. The overall costs of SUDs to individuals, their families, and their communities are staggering. These costs include compromised physical and mental health; reduced quality of life; increased crime and violence; increased motor vehicle crashes; abuse and neglect of children; loss of productivity; and health care costs. The United States ranks twenty-seventh among developed countries in life expectancy; the rate has plateaued and is declining for certain subpopulations. This trend is due largely to substance misuse. This article outlines a comprehensive range of resources on the complex, evolving subject of SUDs, through a social work lens. It begins with a general overview of SUDs, followed by works on diagnosis, and resources regarding SUDs and certain subpopulations: people of color, people with mental illness, older adults, youth, and lesbian, gay, bisexual, transgender, questioning, intersex, asexual and other gender/sexual identity (LGBTQIA+) people. References focusing on screening, brief intervention, and referral to treatment (SBIRT); and treatment approaches are also included. Specific subsections are devoted to outlining resources on alcohol, marijuana/cannabis, opioids and tobacco use disorders as well. The article concludes with resources regarding significant policy dimensions of SUDs and the neuroscience behind these disorders.
Sultan Muhammad Shah Aga Khan III
Authors: Mukherjee Swati
Published: February 2025

Born in 1877 in Karachi into an illustrious family that left Qajar Persia and sought shelter in colonial India, Sultan Muhammad Shah became the forty-eighth Imam of the Nizari Ismaʿili branch of the Shiʿa Muslims at the tender age of eight. Succeeding his father Ali Shah Aga Khan II (b. 1830–d. 1885) as the Shiʿa Ismaʿili community’s spiritual leader in 1885, a genealogy traced back to the son-in-law of the Prophet Muhammad, that is, Imam Ali, Sultan Muhammad Shah Aga Khan III held office of the imamate until his demise in 1957. During his imamate the Nizari Ismaʿilis witnessed momentous socioreligious reforms in the face of colonial modernity, with early experiments beginning in South Asia and parts of Africa but gradually radiating outward along transregional and increasingly global pathways. Yet, there were also critiques and schisms. Striking at once a delicate balance between an Enlightenment-inspired European modernity and a reassertion of core Shiʿa Ismaʿili traditions, Aga Khan III guided and repositioned the Nizari Ismaʿili community amid the changing politico-social exigencies in colonial South Asia as well as in the larger global arena. This was made possible not only in the realm of ideas and abstract notions but effectively on the ground thanks to a robust institutional framework that forged a global community of believers subsumed within a larger pan-Islamic vision under the auspices of the imamate. Yet, distinctive denominational traits were not only retained but were recast within the mold of the burgeoning institutional enterprise. Indeed, such features were often argued to be the very fount of the community’s strength and resilience amid the vicissitudes of historical processes. Furthermore, an important feature of this venture of institutionalization was the guiding vision to both conceptualize and articulate within its institutional mechanism discourses of social service and community development, gradually also marking the early stirrings of an enduring process that went on to cater to a much larger audience beyond the Ismaʿili community. This period thus marked the emergence of a modern Ismaʿili community under the guidance of an imamate that had come to redefine its leadership in terms of a significantly expanded role. It also left behind a template for the succeeding imam of the time, Shah Karim Aga Khan IV (b. 1936–), to emulate and further build on. Much of this history, however, becomes better intelligible when read against the larger backdrop of the 19th-century developments in colonial South Asia. The present article provides a critical review of the existing corpus of English-language scholarship in this field.
Personhood and the Body
Authors: Farman Abou , Tuckett Miranda
Published: February 2025

As an analytic category in anthropology proper, personhood dates only to Marcel Mauss’s 1938 seminal essay on the topic, “A Category of the Human Mind: The Notion of Person; The Notion of Self.” But as a central concern in European and American legal and philosophical thought it dates back much further—indeed, as Mauss himself points out, its genealogy may well be traced to Roman law where it appears as a way of distinguishing aspects of a public persona (legal and political) from a private or metaphysical identity. For Mauss, coming from a Durkheimian lineage where a key distinction was between organism and social being, the category of person offered the possibility of carving out a domain of analysis for the social sciences, distinct from the ascendant biological, cognitive, psychological, and metaphysical forms which were increasingly describing the figure of the human through essentialized, universal, and materially reductive determinations. Thus, only two years after Mauss, AR Radcliffe-Brown 1940 elaborates on functionalism in the essay “On Social Structure,” by writing: “Every human being living in society is two things: he is an individual and he is also a person. As an individual he is a biological organism. . . . . The human being as a person is a complex of social relationships. . . . ” In other words, the person has had analytic and moral value for the social sciences precisely in so far as it could be separated from a materially-determined (and thereby also racialized and sexed) body. And yet, given the metaphysical ambiguities and juridicopolitical histories (including the history of slavery and modern race-making), the separation has never been clean; neither have personhood and humanity been neatly coterminous categories. Yet it is precisely this tangle that has generated the dynamic anthropological reflections on the overlaps and separations of persons, bodies, and things across cultures and histories, especially in light of the perennial anthropological problem of translation across languages and cultural forms. Today, with increasing technological intervention into bodies and minds around the globe, the distinction has become more salient if muddled and so the tangle has rather thickened. As rivers, mountains and robots gain status as persons, the criteria of personhood and the secular human behind it are expanding beyond the older metaphysical assumptions that divided the world into humans and things, thus raising new questions about what it is to have mind or to have body, and to have philosophical, legal, and political frameworks around these.
Abundance/Biomass Comparison Method
Authors: Smith Walter H.
Published: February 2025

Detecting signatures of disturbance in ecological communities has long been a challenge for ecologists, particularly for complex communities composed of many species. Individual species’ responses to disturbance are often variable, while many forms of disturbance may not be visually apparent in some ecosystems. Other disturbances may also produce ecological legacies whose signatures may persist in organismal assemblages long after a disturbance event has passed. In spite of this variability, researchers have acknowledged that many disturbed communities are dominated by small-bodied taxa that contribute disproportionately to overall community abundance. By contrast, undisturbed communities are often dominated by large-bodied species that are less abundant but contribute disproportionately to overall community biomass. The abundance/biomass comparison (ABC) method provides an analytical framework for examining species’ dominance in terms of abundance and biomass in a community, allowing researchers to use an organismal assemblage to quantify the amount of perturbation in a habitat or sample of interest. Specifically, the method provides researchers with a potential snapshot of the ecological condition of a species assemblage made without reliance on a series of control samples collected across time and space. This article will examine the historical foundations of the ABC method, detail its general theoretical principles and analytical techniques, and explore its applications and critiques across a variety of ecosystem types and taxa.
Chofetz Chaim (Rabbi Yisrael Meir Kagan) and his Mishna Berura
Authors: Broyde Michael J. , Liberman Ariel
Published: February 2025

Rabbi Yisrael Meir Kagan, known as the Chofetz Chaim, holds a paramount position among 20th-century gedolim. Beyond his image as a devout, humble, and visionary community leader, he is celebrated for his extensive writings, most notably the Mishna Berura. This six-volume opus, published intermittently from 1884 to 1907, continues to wield authority in Orthodox Jewish law, offering a comprehensive guide to daily religious life by synthesizing traditions, laws, and customs. However, despite his profound scholarly impact, Rabbi Kagan’s early life and influences remain mysterious. Few robust contemporary scholarly biographies have been written, and background literature, apart from commentaries on his works, especially the Mishna Berura, tends to be sparse and nearly exclusively written in Hebrew. This article likewise focuses on his scholarly and ethical works rather than delving into his personal life. Within his writings, particularly the Mishna Berura and its commentaries, Rabbi Kagan strikes a balance between traditionalism and iconoclasm, diverging from established halakhic norms. Throughout the Mishna Berura especially, Rabbi Kagan champions an innovatively pragmatic and ethical approach to daily life within the framework of Jewish law. His writings emphasize nuanced understanding, engagement, and flexibility, avoiding rigid adherence to a few principles. He does so with editorial precision, harmonizing multiple propositions and offering resolutions and recommendations while acknowledging diverse individual standards. Although scholars may vary in interpreting Rabbi Kagan’s decision-making methodology, there is no disputing that the Mishna Berura marked a significant halakhic innovation as a major historical transition was taking place for eastern European Jewry in the early twentieth century. Rabbi Kagan’s personal legacy, therefore, can be said to be one of resilience and innovation. And, though a veil of obscurity cloaks his personal life, Rabbi Kagan left a clear literary legacy that serves as a guiding light for many navigating faith amidst societal upheaval.
Colonialism and the Environment
Authors: Parsons Meg
Published: February 2025

Colonialism has far-reaching environmental effects. Colonial enterprises allowed people to accidentally and knowingly introduce exotic plants, animals, and diseases to colonies and bring biota back to Europe and other colonial settings. Colonial actors transformed the landscapes and waterscapes, introducing new land use systems, but many were (and still are) unsustainable and unsuited to local climates and environments. Monoculture agriculture, for instance, depletes soil nutrients, reduces biodiversity, and makes ecosystems more vulnerable to global climate change. Colonial authorities frequently prioritized export crops over local food security, increasing food insecurity and heightening the risk of famine. In the name of colonial progress, civilization, and productivity, vast swaths of endemic forests were cut down, wetlands were drained, and land reclaimed to create farms, plantations, towns, and cities. Natural resources, including timber, spices, and minerals, were extracted from colonies and exported to fuel colonial powers’ lifestyles and economic development, with colonialism and capitalism interwoven with environmental changes. Even the creation of biodiversity conservation measures followed colonial actors’ desires to secure their continuous access to natural resources and protect their commercial interests. Studies show that pre-colonial societies were complex and dynamic, with long-standing and effective environmental governance and management arrangements that sustainably used resources. However, global colonialism severely disrupted local environmental governance and management regimes. Colonized peoples lost vital resources and were excluded from decision making, resulting in countless environmental injustices. Historically marginalized social groups, including but not limited to Indigenous peoples living in colonial territories, settler colonial societies, and postcolonial nations continue to experience various environmental injustices traced back to colonial and neocolonial policies, economic practices, and racial ideologies. Climate change is also reinforcing existing old environmental injustices and creates new ones for people living in colonial situations. Industrialized Global North nations (current or former colonial powers) are primarily responsible for causing climate change due to their high greenhouse gas emissions. At the same time, Global South countries (mostly former colonies) and Indigenous peoples in settler colonial societies contribute little to emissions but suffer the worst climate impacts. Moreover, climate colonialism is happening around the globe. Those in the Global North are buying land and establishing carbon offset projects in the Global South, undermining local peoples’ ways of life. Colonial mindsets still hinder decision makers from recognizing the value of Indigenous and postcolonial solutions to environmental issues, despite promising examples of enhanced resilience, social and environmental justice, and environmental guardianship practices tied to the resurgence of Indigenous knowledge.
Artists in Seventeenth-Century Dutch Brazil
Authors: Brienen Rebecca
Published: February 2025

The drawings and paintings created in the colony of Dutch Brazil (1630–1654) represent the global reach of Dutch-sponsored artistic production in the seventeenth century. Johan Maurits van Nassau-Siegen (b. 1604–d. 1679) was a German count, a cousin of Dutch Stadholder Frederick Hendrick, and Dutch Brazil’s only colonial governor. He arrived in northeastern Brazil (present-day Recife) in 1637; by 1640 his retinue likely included up to three professional painters from the Netherlands: Frans Post (b. 1612–d. 1680) of Haarlem, Albert Eckhout (b. c. 1607–d. c. 1666) of Groningen, and the little-known Utrecht artist Abraham Willaerts (b. c. 1613–d. 1669). They were joined in Brazil by Dutch physician Willem Piso (b. 1611–d. 1678) and German natural historian Georg Marggrafe (b. 1610–d. 1644). During their time in Brazil, these men studied the human population, the plants and animals, the topography, and even the constellations of the South American colony. Together, they created the first written and visual record by Europeans of their interaction with Brazil. Post is known for his landscapes of Brazil, some produced in situ, and others that became the staple of his post-Brazilian career. Topographical drawings and a series of natural history studies may also be attributed to the artist. Engravings after his designs also appeared in Dutch humanist Caspar Barlaeus’s 1647 history of Dutch Brazil, Rerum per octennium in Brasilia. Eckhout’s Brazilian oeuvre includes life-sized images, often called ethnographic portraits, of the men and women of the colony (excluding Europeans); paintings of fruits and vegetables grown in Brazil; and a large corpus of drawings and oil studies on paper. Many of the latter were used for woodcuts in Marggrafe and Piso’s 1648 Historia Naturalis Brasiliae. Later European work by Eckhout included tapestry cartoons and Brazilian-inspired ceiling paintings. Willaerts was a marine specialist whose oeuvre includes a recently identified View of Recife from 1640. While Piso was not artistically inclined, Marggrave created maps, and multiple watercolors of Brazilian flora and fauna have also been attributed to him. The German quartermaster Zacharias Wagener was not part of the governor’s official retinue, nor was he a trained artist. Nonetheless, his Thierbuch copied and interpreted works by the colony’s official artists. Piso, Marggrafe, Eckhout, Post, and possibly Willaerts were not leading artists or scientists in the Dutch Republic when they were chosen for this remarkable experience. They had training, but more importantly, they were young, unwed, and likely interested in traveling to the New World as a means of making a name for themselves.
Transforming Understanding of Congenital Heart Disease Through a Virtual Reality Innovation
Authors: da Silva Maria Jocelane Nascimento , de Souza Soares Antônio Marcos , Braga Hévila Ferreira Gomes Medeiros , Rosa Benedita Shirley Carlos , Filho Pedro Pedrosa Rebouças , Guedes Nirla Gomes , Felipe Gilvan Ferreira , Monteiro Flávia Paula Magalhães , Oliveira John Anderson Muniz , da Silva Barros Antônio Carlos , Melo Emanuella Silva Joventino
Published: February 2025

Given the significant global burden of congenital heart disease, there is an urgent need for innovative solutions to support and educate parents facing this challenge. This study aimed to construct and validate a virtual reality software, called CardioVR, to support congenital heart disease counseling. The process involved collaboration with 18 experts and 30 parents in three carefully managed stages, closely following the rigorous criteria outlined in the International Organization for Standardization/International Electrotechnical Commission 25010 standards. Remarkably, CardioVR achieved a remarkable content validity coefficient of 0.91 and exceeded the International Organization for Standardization/International Electrotechnical Commission criteria with more than 70% consensus. It excelled in key areas such as organization, clarity, visual appeal, self-efficacy enhancement, cultural appropriateness, and effectiveness. In addition, the System Usability Scale evaluation yielded a commendable score of 73.3%, confirming its ease of use and comprehension. The CardioVR software was considered valid and appropriate by experts and the target audience and can be used in the future as a support instrument for healthcare professionals assisting parents and caregivers of children with congenital heart diseases.
Liver transplantation for cholestatic liver diseases: Timing & disease recurrence
Authors: Cançado Guilherme Grossi Lopes , Deeb Maya , Gulamhusein Aliya Fatemah
Published: February 2025

Though rare, primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) account for 8-14% of liver transplants (LT) in North America and Europe and the journey of these patients across the peri-transplant period is unique. Equitable access to LT is an important challenge, as the MELD score and its derivatives inadequately reflect the morbidity and mortality related to these diseases failing to capture disease-specific complications, such as recurrent cholangitis, malignancy risk, severe portal hypertension, and sarcopenia. The waitlist experience is high-risk, prolonged and a distinct form of “MELD purgatory”. Once barriers to access are overcome, post-transplant outcomes are generally excellent, however disease recurrence affects 15-35% at 5 to 10 years post-LT with increasing rates over time. Diagnosing recurrence is challenged by a broad differential for post-transplant biliary injury, and the risk factors for its development remain controversial. While post-LT use of ursodeoxycholic acid in PBC is clearly beneficial, no effective medical therapy currently exists for recurrent PSC. A heightened focus on control of inflammatory bowel disease activity is critical as a potentially important modifiable risk factor for rPSC, including with escalation of medical therapy as needed and timely colectomy when indicated. This review outlines the journey for patients with PBC and PSC, from transplant listing to post-transplant management, emphasizing the need for unique and tailored approaches to optimize outcomes and long-term survival.
Engineering a microfluidic-assisted 3D bioprinting approach for the hierarchical control deposition and compartmentalisation of graded bioinks
Authors: Serpe Federico , Iafrate Lucia , Bastioli Marco , Marcotulli Martina , Sanchini Caterina , De Turris Valeria , D’Orazio Michele , Palmisano Biagio , Mencattini Arianna , Martinelli Eugenio , Riminucci Mara , Casciola Carlo Massimo , Ruocco Giancarlo , Scognamiglio Chiara , Cidonio Gianluca
Published: February 2025

The advent of 3D bioprinting has revolutionised tissue engineering and regenerative medicine (TERM). Today, tissues of single cell type can be printed with extreme resolution and printing fidelity. However, the ultimate functionality of the desired tissue is limited, due to the absence of a multicellular population and diversity in micro-environment distribution. Currently, 3D bioprinting technologies are facing challenges in delivering multiple cells and biomaterials in a controlled fashion. The use of interchangeable syringe-based systems has often favoured the delamination between interfaces, greatly limiting the fabrication of interconnected tissue constructs. Microfluidic-assisted 3D bioprinting platforms have been found capable of rescuing the fabrication of tissue interfaces, but often fails to guarantee printing fidelity, cell density control and compatimentalisation. Herein, we present the convergence of microfluidic and 3D bioprinting platforms into a new deposition system capable of harnessing a microfluidic printhead for the continuous rapid fabrication of interconnected functional tissues. The use of flow-focusing and passive mixer printhead modules allowed for the rapid and dynamic modulation of fibre diameter and material composition, respectively. Cells were compartmentalised into discrete three-dimensional layers with defined density patterns, confirming the punctual control of the presented microfluidic platform in arranging cells and materials in 3D.In ovoandin vivostudies demonstrated the functionality of 3D bioprinted constructs with patterned vascular endothelial growth factor (VEGF) and transforming growth factor-β1 (TGF-β1), respectively. This, in turn, facilitated the simulation of diverse cellular environments and proliferation pathways within a single construct, which is currently unachievable with conventional 3D bioprinting techniques, offering new opportunities for the fabrication of functionally graded materials and physiologically-relevant skeletal tissue substitutes.
Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade
Authors: Raposo Colin J. , Yan Patrick K. , Chen Andy Y. , Majidi Saba , Hiam-Galvez Kamir J. , Satpathy Ansuman T.
Published: February 2025

Immune checkpoint blockade can facilitate tumor clearance by T cells, resulting in long term patient survival. However, the capacity of exhausted CD8+T cells (Tex), present during chronic antigen exposure, to form memory after antigen clearance remains unclear. Here, we performed longitudinal single cell RNA/T cell receptor sequencing and ATAC-sequencing on antigen-specific T cells after the clearance of chronic lymphocytic choriomeningitis virus (LCMV) infection. These data revealed the formation of a robust population of memory CD8+T cells that transcriptionally, epigenetically, and functionally resemble central memory T cells (Tcm) that form after clearance of acute infection. To lineage trace the origin and memory recall response of Tex-derived memory clones, we utilized T cell receptor sequencing over the course of primary infection and rechallenge. We show that chronic Tcm are a clonally distinct lineage of Tex derived from progenitor exhausted cells, persist long-term in the absence of antigen, and undergo rapid clonal expansion during rechallenge. Finally, we demonstrate that αPD-L1 immune checkpoint blockade after chronic LCMV infection preferentially expands clones which form Tcm after clearance. Together, these data support the concept that chronically stimulated T cells formbona fidefunctional memory T cells through an analogous differentiation pathway to acutely stimulated T cells, which may have significant implications for enhancing immune memory to cancer through checkpoint blockade and vaccination.
gcSV: a unified framework for comprehensive structural variant detection
Authors: Li Gaoyang , Liu Yadong , Liu Bo , Qian Long , Wang Yadong
Published: February 2025

The characterization of structural variants (SVs) is fundamental to genomic studies and advanced computational approaches are on demand to exert the ability of the ubiquitous high-throughput sequencing data. Herein, we propose gcSV, a read-length agnostic alignment-based approach to well-handle the issues of genome repeats, SV breakpoints and read alignments/assemblies for comprehensive, cost-effective and versatile SV calling. For long reads, its yield is 20-38% higher than state-of-the-art tools in HG002 benchmark. For hybrid sequencing, it provides a cost-effective solution (2-4x long plus 30-60x short reads) to achieve even higher yield than that of state-of-the-art tools using 30x long reads. For short reads, gcSV also achieves over 8% higher precision without any loss of sensitivity. Furthermore, gcSV confidently brings over 93,000 novel SVs comparing to the official callset of 1000 Genomes Project Phase4. The results suggest that gcSV is promising to make valuable SV discoveries in many cutting-edge studies.
A single-cell transcriptomic comparison between small intestinal neuroendocrine tumors and their progenitor
Authors: Axling Fredrik , Barazeghi Elham , Hellman Per , Norlen Olov , Backman Samuel , Stalberg Peter
Published: February 2025

Several studies have attempted to find the initiating drivers of small intestinal neuroendocrine tumors (SI-NET) development and the molecular mechanisms driving progression and metastatic spread. For gene expression studies using bulk microarrays and RNA sequencing, researchers commonly use normal intestinal mucosa as a control. The intestine is made up of several different cell types, and using bulk RNA-seq may generate findings that reflect factors other than the tumor transformation. This could potentially contribute to the lack of discoverable treatments and prevention strategies for SI-NETs. We performed scRNA-seq on tissue from two patients that had tumor resection surgery and separated the EC cells from the normal intestinal mucosa and used specific markers to compare them against SI-NET tumors cells. We pinpointed new genes associated with chr18 haploinsufficiency but also others with loss or gain of expression that have not previously been associated with SI-NETs, and which could be potential targets for further functional genomic studies.
Neighbor density-dependent facilitation promotes coexistence and internal oscillation
Authors: Buche Lisa , Shoemaker Lauren G. , Hallett Lauren M. , Vesk Peter , Godoy Oscar , Mayfield Margaret
Published: February 2025

The ability of species to form diverse communities is not fully understood. Species are known to interact in various ways with their neighborhood. Despite this, common models of species coexistence assume that per capita interactions are constant and competitive, even as the environment changes. In this study, we investigate how neighbor density-dependent variation in the strength and sign of species interactions changes species and community dynamics. We show that by including these sources of variation, predictions of ecological dynamics are significantly improved compared to outcomes of typical models that hold interaction strengths constant. We compared how well models based on different functions of neighbor density and identity did in describing population trajectories (i.e., persistence over time) and community dynamics (i.e., temporal stability, synchrony and degree of oscillation) in simulated two-species communities and a real diverse annual plant system. In our simulated communities, we found the highest level of coexistence between species pairs when species interactions varied from competitive to facilitative according to neighbor density (i.e., following a sigmoid function). Introducing within-guild facilitation through a nonlinear bounded function allowed populations, both simulated and empirical, to avoid extinction or runaway growth. In fact, nonlinear bounded functions (i.e., exponential and sigmoid functions) predicted population trends over time within the range of abundances observed over the last 10 years. With the sigmoid function, the simulated communities of two species displayed a higher probability of synchrony and oscillation than other functional forms. These simulated communities did not always show temporal stability but were predicted to coexist. Overall, varying species interactions lead to realistic ecological trajectories and community dynamics when bounded by asymptotes based on neighbor density. These findings are important for advancing our understanding of how diverse communities are sustained and for operationalizing ecological theory in the study of the real world.
Pneumolysin-dependent and independent non-canonical autophagy processes mediate host defense against pneumococcal infection
Authors: Michno Bartosz J , Pooranachandran Niedharsan , Smith Tonisha C , Faught Erin , Lipowska Sandra , Fenton Andrew K , Meijer Annemarie H. , Prajsnar Tomasz K.
Published: February 2025

Streptococcus pneumoniae is an opportunistic pathogen responsible for life-threatening diseases including pneumonia and meningitis. The host defense against pneumococci relies heavily on macrophages, which can effectively internalize and degrade bacteria. Recent studies have implicated both canonical and non-canonical autophagy-related processes in bacterial clearance, but the precise pathways mediating defense against S. pneumoniae remain unknown. Here, we utilize a well-established zebrafish larval infection model to investigate the role of autophagy in host defense against pneumococci in vivo. Using a transgenic autophagy reporter line, we found the autophagy marker Lc3 being recruited to pneumococci-containing vesicles upon bacterial internalization by zebrafish macrophages. The genetic inhibition of core autophagy genes (atg5 and atg16l1) led to loss of the Lc3 associations and their impaired acidification, significantly delaying bacterial clearance. This Lc3 recruitment is partially mediated by LC3-associated phagocytosis (LAP), as knockdown of cyba and rubcn moderately reduced Lc3 association with phagosomes and diminished pneumococcal degradation. Interestingly, we observed no involvement of xenophagy components in S. pneumoniae-infected macrophages, suggesting the activation of another non-canonical autophagy pathway, distinct from LAP, targeting pneumococci-containing phagosomes. Instead, we found that production of pneumococcal pore-forming toxin - pneumolysin induces LAP-independent Lc3 lipidation, which could be abolished by knockdown of tecpr1a indicating the involvement of the sphingomyelin-TECPR1-induced LC3 lipidation (STIL) pathway. Collectively, our observations shed new light on the host immune response against S. pneumoniae, demonstrating that two distinct non-canonical autophagy pathways mediate bacterial degradation by macrophages and providing potential targets for the development of novel therapies to combat pneumococcal infections.
A phototaxis assay to measure sublethal effects of pesticides on bees
Authors: Sancho Gonzalo , Albacete Sergio , Azpiazu Celeste , Sgolastra Fabio , Rodrigo Anselm , Bosch Jordi
Published: February 2025

Pesticides are considered a main driver of world-wide bee declines. In agricultural areas, bees are exposed to combinations of pesticides at low concentrations. The extent to which these low levels may cause sublethal effects remains unknown. Laboratory methods to detect sublethal effects are needed as a first step in assessing the potential hazards of pesticides at low concentrations. Current bee risk assessment schemes rely on a single species, the highly socialApis mellifera, and provide insufficient coverage of sublethal effects. Due to fundamental life history differences, available tests cannot be applied to solitary bees. We provide a simple phototaxis assay to detect sublethal pesticide effects on bees. The assay is highly effective (only 6.63% of the bees failed to respond) and provides an unambiguous binary response (bees either walk straight to the light source or walk erratically across the arena). We validate the assay by conducting two experiments. In the first one, we estimate dose-response curves and calculate ED50 and benchmark dose (BMD) values of an insecticide onOsmia bicornisandO. tricornis. In the second one, we assess the effects of three insecticide doses, alone and in combination with a fungicide, inO. cornutaandA. mellifera. These experiments show that our assay can detect effects of field-realistic levels of acetamiprid exposure as low as 1-30 ng/bee. The phototaxis assay can be used to obtain relevant ecotoxicological endpoints at low sublethal concentrations in both solitary and honey bees, thus contributing to fill an important gap in bee risk assessment.
Quantitative Evaluation of Normal Cerebrospinal fluid flow in Sylvian aqueduct and perivascular spaces of middle cerebral artery and circle of Willis using 2D phase -contrast MRI imaging
Authors: D. Le Rosemarie Faustina , Karmonik Christof , Regnier-Golanov Angelique S. , Golanov Eugene V. , Britz Gavin W.
Published: February 2025

Recently, it was proposed that CSF flow constitutes a critical part of the glymphatic system, playing a critical role in various brain abnormalities from Alzheimer’s disease to hydrocephalus. Thus, measurement of CSF flow has been increasingly used for diagnostic and clinical monitoring purposes. Phase-contrast MRI has been used to determine CSF flow. However, CSF flow in the periarterial spaces of the circle of Willis and the middle cerebral artery which are important conduits remain unexplored. We employed phase-contrast MRI to explore CSF flow along the perivascular spaces of the circle of Willis and the middle cerebral artery to establish baseline parameters of CSF and compare them with the Sylvian aqueduct. To analyze CSF flow in the perivascular space, we developed a new, semi-automated method for outlining the perivascular space and extracting CSF flow parameters. The twenty-four healthy participants were recruited to achieve an even distribution by age (mean: 40 ± 11) and gender (13 males). We validated our routine for CSF flow measurements by comparing CSF flow in the Sylvian aqueduct (0.00700 mL/s) with the range of literature values, 0.0049-0.0432 mL/s. For all CSF parameters, the circle of Willis and middle cerebral artery were differed from the Sylvian aqueduct. For most CSF flow parameters, the 95% confidence intervals of the circle of Willis and middle cerebral artery overlap. The linear mixed models and general linear mixed models for flow indicate strong effects of the conduits. CSF velocity in these conduits were lower 0.159 cm/s and 0.198 cm/s respectively than in the Sylvian aqueduct. Overall, differences in CSF flow parameters between sex and age groups were negligible. In this study, we have validated our routine and established baseline values of CSF flow along the circle of Willis and the middle cerebral artery as well as highlighted the limited influence of sex and/or age.
The membrane skeleton density of red blood cells inMYH9-related disease patients is decreased
Authors: Sun Shaopeng , Pan Jiabin , Zhang Ning , Jin Xianghong , Zhu Tie-nan , Kang Zhijie , Hao Jihong , Li Xiang-dong
Published: February 2025

MYH9-related disease (MYH9-RD) is a rare autosomal dominant disorder caused by mutations inMYH9gene, which encodes the heavy chain of nonmuscle myosin IIA. Nearly allMYH9-RD patients present with macrothrombocytopenia, characterized by decreased platelet count and increased platelet size. In this study, we collected blood samples from threeMYH9-RD patients (R702S, D1424N, and R1464C) and unexpectedly found that the actin levels in the red blood cells (RBCs) from all threeMYH9-RD patients are substantially lower than the healthy controls. We further revealed that the levels of two RBC membrane skeleton proteins, α-spectrin and tropomodulin, are also reduced inMYH9-RD RBCs. We showed that the membrane skeleton ofMYH9-RD RBCs was more porous and thatMYH9-RD RBCs produced more severe deformation under hyperosmotic pressure compared to healthy controls. We conclude thatMYH9-RD mutations reduce the RBC membrane skeleton density and impair its mechanical properties, and propose that defects in the membrane skeleton network in RBCs may be a common symptom inMYH9-RD.

Key points

The levels of membrane skeleton proteins and the density of membrane skeleton network in RBCs ofMYH9-RD patients are reduced.

MYH9-RD RBCs produce greater deformation under hypertonic conditions compared to healthy controls.
Competence of DNA Tetrahedron and Exosomes as Nanocarriers for Epirubicin drug delivery in Breast Cancer Cells
Authors: Saleem Afnan , Bhat Sahar Saleem , Gani Ubaid , Shafi Nausheen , Vaswani Payal , Dar Lateef A , Nazir Junaid , Ahmad Sheikh F , Bhatia Dhiraj , Ahmad Syed Mudasir
Published: February 2025

Epirubicin, a chemotherapeutic agent, is used in treatment of metastatic breast cancer treatment. However, poor intracellular delivery and systemic toxicity are its major limitations. Our study evaluates the use of DNA tetrahedron (TD) structures and exosomes for targeted delivery of epirubicin to enhance its therapeutic efficacy. Increased intracellular concentration of epirubicin was observed in Flow cytometer when delivered via the TD: Epi system compared to free epirubicin. Cell viability assays using Annexin V-FITC and propidium iodide staining revealed higher apoptosis rates in the TD: Epi system. Exosomes, primarily 100 ± 20 nm in size (99% of particles), exhibit a - 28.5 mV zeta potential, ensuring colloidal stability. SEM and TEM confirm their spherical shape, uniform size, and double membrane structure. The TD: Epi system showed the highest efficacy in RT-qPCR analysis, followed by Epirubicin + Exosomes systems and epirubicin alone, further corroborated with western blot results. While exosomes also provided improved delivery and therapeutic outcomes compared to free epirubicin, they were less effective than the TD: Epi system. These results suggest that the TD carrier significantly enhances the delivery and apoptotic efficacy of epirubicin when compared to exosome-based delivery or epirubicin alone offering a promising strategy for improving treatment outcomes.

Graphical Abstract
ImmunoMatch learns and predicts cognate pairing of heavy and light immunoglobulin chains
Authors: Guo Dongjun , Dunn-Walters Deborah K. , Fraternali Franca , Ng Joseph C. F.
Published: February 2025

The development of stable antibodies formed by compatible heavy (H) and light (L) chain pairs is crucial in both thein vivomaturation of antibody-producing cells and theex vivodesigns of therapeutic antibodies. We present here a novel machine learning framework, ImmunoMatch, for deciphering the molecular rules governing the pairing of antibody chains. Fine-tuned on an antibody-specific language model, ImmunoMatch learns from paired H and L sequences from single human B cells to distinguish cognate H-L pairs and randomly paired sequences. We find that the predictive performance of ImmunoMatch can be augmented by training separate models on the two types of antibody L chains in humans,κandλ, in line with thein vivomechanism of B cell development in the bone marrow. Using ImmunoMatch, we illustrate that refinement of H-L chain pairing is a hallmark of B cell maturation in both healthy and disease conditions. We find further that ImmunoMatch is sensitive to sequence differences at the H-L interface. ImmunoMatch focusses on H-L chain pairing as a specific, under-explored problem in antibody developability, and facilitates the computational assessment and modelling of stably assembled immunoglobulins towards large-scale optimisation of efficacious antibody therapeutics.