bluuebunny/crossref_metadata_2025 huggingface dataset:
The TARCiS statement: Guidance on terminology, application, and reporting of citation searching
Authors: Hirt Julian , Nordhausen Thomas , Fuerst Thomas , Ewald Hannah ,   TARCiS study group, Appenzeller-Herzog Christian
Published: October 2023

Evidence syntheses adhering to systematic literature searching techniques are a cornerstone of evidence-based health care. Beyond term-based searching in electronic databases, citation searching is a prevalent search technique to identify relevant sources of evidence. However, for decades, citation searching methodology and terminology has not been standardized. We performed an evidence-guided four-round Delphi consensus study with 27 international methodological experts in order to develop the Terminology, Application, and Reporting of Citation Searching (TARCiS) statement. TARCiS comprises ten specific recommendations on when and how to conduct and report citation searching in the context of systematic literature searches and four research priorities. We encourage systematic reviewers and information specialists to incorporate TARCiS into their standardized workflows.
Policy impact evaluation: A potential use case for longitudinal monitoring of viruses in wastewater at small geographic scales
Authors: Chan Elana M. G. , Bidwell Amanda , Li Zongxi , Tilmans Sebastien , Boehm Alexandria B.
Published: October 2023

We used wastewater monitoring data to evaluate the impact of public health policies and interventions on the spread of COVID-19 among a university population. We first evaluated the correlation between incident, reported COVID-19 cases and wastewater SARS-CoV-2 RNA concentrations and observed changes to the correlation over time. Using a difference-in-differences approach, we evaluated the association between university COVID-19 policy changes and levels of SARS-CoV-2 RNA concentrations in wastewater. Policy changes associated with a significant change in campus wastewater SARS-CoV-2 RNA concentrations included changes to face covering recommendations, indoor gathering bans, and routine surveillance testing requirements and availability. We did not observe changes in SARS-CoV-2 RNA concentrations associated with other policy changes. The work presented herein demonstrates how longitudinal wastewater monitoring of viruses may be used for causal inference such as policy impact evaluation, especially at small geographic scales.
Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer’s Disease
Authors: Lee Donghoon , Vicari James M. , Porras Christian , Spencer Collin , Pjanic Milos , Wang Xinyi , Kinrot Seon , Weiler Philipp , Kosoy Roman , Bendl Jaroslav , Prashant N M , Psychogyiou Konstantina , Malakates Periklis , Hennigan Evelyn , Monteiro Fortes Jennifer , Zheng Shiwei , Therrien Karen , Mathur Deepika , Kleopoulos Steven P. , Shao Zhiping , Argyriou Stathis , Alvia Marcela , Casey Clara , Hong Aram , Beaumont Kristin G. , Sebra Robert , Kellner Christopher P. , Bennett David A. , Yuan Guo-Cheng , Voloudakis George , Theis Fabian J. , Haroutunian Vahram , Hoffman Gabriel E. , Fullard John F. , Roussos Panos
Published: October 2023

The complex roles of myeloid cells, including microglia and perivascular macrophages, are central to the neurobiology of Alzheimer’s disease (AD), yet they remain incompletely understood. Here, we profiled 832,505 human myeloid cells from the prefrontal cortex of 1,607 unique donors covering the human lifespan and varying degrees of AD neuropathology. We delineated 13 transcriptionally distinct myeloid subtypes organized into 6 subclasses and identified AD-associated adaptive changes in myeloid cells over aging and disease progression. The GPNMB subtype, linked to phagocytosis, increased significantly with AD burden and correlated with polygenic AD risk scores. By organizing AD-risk genes into a regulatory hierarchy, we identified and validatedMITFas an upstream transcriptional activator ofGPNMB, critical for maintaining phagocytosis. Through cell-to-cell interaction networks, we prioritizedAPOE-SORL1andAPOE-TREM2ligand-receptor pairs, associated with AD progression. In both human and mouse models,TREM2deficiency disrupted GPNMB expansion and reduced phagocytic function, suggesting that GPNMB’s role in neuroprotection wasTREM2-dependent. Our findings clarify myeloid subtypes implicated in aging and AD, advancing the mechanistic understanding of their role in AD and aiding therapeutic discovery.
Rationale and protocol for a safety, tolerability and feasibility randomized, parallel group, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms
Authors: Stubbs Brianna J. , Alvarez-Azanedo Gabriela , Peralta Sawyer , Roa-Diaz Stephanie , Gray Wyatt , Alexander Laura , Silverman-Martin Wendie , Garcia Thelma , Blonquist Traci M. , Upadhyay Vaibhav , Turnbaugh Peter J. , Johnson James B. , Newman John C.
Published: October 2023

Background

Frailty is a geriatric syndrome characterized by chronic inflammation and metabolic insufficiency that creates vulnerability to poor outcomes with aging. We hypothesize that geroscience interventions, which target mechanisms of aging, could ameliorate frailty. Metabolites such as ketone bodies are candidate geroscience interventions, having pleiotropic effects on inflammo-metabolic aging mechanisms. Ketone esters (KEs) induce ketosis without dietary changes, but KEs have not been studied in an older adult population. Our long-term goal is to examine if KEs modulate geroscience mechanisms and clinical outcomes relevant to frailty in older adults.

Objectives

The primary objective of this randomized, placebo-controlled, double-blinded, parallel-group, pilot trial is to determine tolerability of 12-weeks of KE ingestion in a generalizable population of older adults (≥ 65 years). Secondary outcomes include safety and acute blood ketone kinetics. Exploratory outcomes include physical function, cognitive function, quality of life, aging biomarkers and inflammatory measures.

Methods

Community-dwelling adults who are independent in activities of daily living, with no unstable acute medical conditions (n=30) will be recruited. The study intervention is a KE or a taste, appearance, and calorie matched placebo beverage. Initially, acute 4-hour ketone kinetics after 12.5g or 25g of KE consumption will be assessed. After collection of baseline safety, functional, and biological measurements, subjects will randomly be allocated to consume KE 25g or placebo once daily for 12-weeks. Questionnaires will assess tolerability daily for 2-weeks, and then via phone interview at bi-monthly intervals. Safety assessments will be repeated at week 4. All measures will be repeated at week 12.

Conclusion

This study will evaluate feasibility, tolerability, and safety of KE consumption in older adults and provide exploratory data across a range of geroscience-related endpoints. This data will inform design of larger trials to rigorously test KE effects on geroscience mechanisms and clinical outcomes relevant to frailty.
Association between combined sewer overflow events and gastrointestinal illness in Massachusetts municipalities with and without river-sourced drinking water, 2014-2019
Authors: Haley Beth M. , Sun Yuantong , Jagai Jyotsna S. , Leibler Jessica H. , Fulweiler Robinson , Ashmore Jacqueline , Wellenius Gregory A. , Heiger-Bernays Wendy
Published: October 2023

Background

Combined sewer overflow (CSO) events release untreated wastewater into surface waterbodies during heavy precipitation or snowmelt. Combined sewer systems serve approximately 40 million people in the United States, primarily in urban and suburban municipalities in the Midwest and Northeast. Predicted increases in heavy precipitation events driven by climate change underscore the importance of quantifying potential health risks associated with CSO events.

Objectives

The aims of this study were: to 1) estimate the association between CSO events (2014-2019) and emergency department (ED) visits for acute gastrointestinal illness (AGI) among Massachusetts municipalities that border a CSO-impacted river, and 2) determine if associations differ by municipal drinking water source.

Methods

A case time series design was used to estimate the association between daily cumulative upstream CSO discharge in the prior four days and ED visits for AGI, adjusting for temporal trends, temperature, and precipitation. Associations between CSO events and AGI were also compared by municipal drinking water source (CSO-impacted river vs. other sources).

Results

Extreme upstream CSO discharge events (>95th percentile by cumulative volume) were associated with a cumulative risk ratio (CRR) of AGI of 1.22 (95% CI: 1.05, 1.42) over the next four days for all municipalities, and the association was robust after adjusting for precipitation (1.17 [0.98, 1.39]). In municipalities with CSO-impacted drinking water sources, the adjusted association was somewhat less pronounced following 95th percentile CSO events (1.05 [0.82, 1.33]). The adjusted CRR of AGI was 1.62 in all municipalities following 99th percentile CSO events (95% CI: 1.04, 2.51) and not meaningfully different across strata defined by drinking water source.

Discussion

In municipalities bordering a CSO-impacted river in Massachusetts, extreme CSO events are associated with higher risk of AGI within four days. The largest CSO events are associated with increased risk of AGI regardless of drinking water source.
Navigating vaccination choices: The intersecting dynamics of institutional trust, belonging and message perception among Congolese migrants in the UK (A reflexive thematic analysis)
Authors: Crawshaw Alison F , Vandrevala Tushna , Knights Felicity , Deal Anna , Lutumba Laura Muzinga , Nkembi Sarah , Kitoko Lusau Mimi , Hickey Caroline , Forster Alice S , Hargreaves Sally
Published: October 2023

Background

The COVID-19 pandemic has disproportionately impacted intersectionally marginalised migrants, revealing systemic disparities in health outcomes and vaccine uptake. An in-depth understanding of the underlying social and structural factors influencing health behaviours is necessary to develop tailored interventions for migrants but has been seldom explored. Therefore, this qualitative study aimed to explore the contextual factors shaping COVID-19 vaccination decision-making among Congolese migrants in the UK.

Methods

A community-based participatory research study was designed and led by a community-academic partnership in London, UK (2021–2022). Peer-led, semi-structured interviews were conducted in Lingala with 32 adult Congolese migrants and explored beliefs, perceptions and lived experiences of migration, healthcare and vaccination and the pandemic. Reflexive thematic analysis generated two themes and a model conceptualising the vaccination decision-making process was developed. Participants and community partners were financially compensated, and the study received ethical approval from the University of London ethics committee (REC: 2021.0128).

Findings

Participants highlighted the incompatibility of lockdown restrictions with their communal culture, which intensified feelings of exclusion and alienation. Concerns about COVID-19 vaccination were attributed to safety and effectiveness, partly informed by experiences and legacies of discrimination and exploitation of Black Africans. Inequality in the pandemic response and COVID-19 outcomes heightened participants’ sense that their views and needs were being overlooked and government sources and information were perceived as coercive. Drawing on this data, our model depicts the interplay between institutional trust, belonging, and message perception which shaped participants’ vaccination decisions and led to (non-)engagement with COVID-19 vaccination.

Conclusion

This research enhances understanding of how social and contextual factors may influence migrants’ engagement with health interventions. It underscores the necessity of partnering with migrant communities to understand their needs in context and co-design tailored interventions and inclusive messaging strategies which foster trust and belonging. Implementing systemic changes to address structural inequalities will be crucial to create an environment that supports engagement with health-protective behaviours and enhances health outcomes among migrant communities.
Both HFrEF and HFpEF Should be Included in Calculating CHA2DS2–VASc score: a Taiwanese Longitudinal Cohort
Authors: Cheng Chien-Chien , Huang Pang-Shuo , Chen Jien-Jiun , Chiu Fu-Chun , Chang Sheng-Nan , Wang Yi-Chih , Wu Cho-Kai , Hwang Juey-Jen , Tsai Chia-Ti
Published: October 2023

Background

Congestive heart failure (CHF) in the context of AF-related stroke risk, was coined when it mainly referred to patients with left ventricular systolic dysfunction (HFrEF). However, the term now encompasses patients with preserved ejection fraction (HFpEF) as well. Given this change, it becomes essential to investigate the variation in stroke risk between atrial fibrillation (AF) patients with HFpEF and HFrEF for enhancing risk assessment and subsequent management strategies.

Methods

In a longitudinal study utilizing the National Taiwan University Hospital Integrated Medical Database (iMED), 8358 patients with AF were followed up for 10 years from January 2010 to December 2020 (mean follow-up 3.76 years). The study evaluated the risk of ischemic stroke, using Cox models adjusted for potential risk factors of AF-related stroke.

Results

Comparing AF patients of different CHF subgroups, HFpEF patients had a higher mean CHA2DS2–VASc score (4.08±1.502 vs. 3.83±1.571, p<0.001) and a higher risk of stroke during follow-up (HR 1.151 (1.013-1.308), p=0.031). In contrast, patients with HFrEF had a higher prevalence of myocardial infarction (MI) and coronary artery disease (CAD). After adjusting for other risk factors, there was no significant difference in the risk of new-onset stroke between HFpEF and HFrEF patients (HR 1.001 (0.877-1.142), p=0.994).

Conclusion

After adjusting for other risk factors of stroke, both HFpEF and HFrEF were found to have a similar risk of stroke in AF patients. Therefore, it is important to extend the criteria for “C” in the CHA2DS2–VASc score to include HFpEF patients. Prior to multivariable adjustment, HFpEF patients had a higher risk than those with HFrEF, likely due to their higher CHA2DS2–VASc score, indicating a greater prevalence of stroke-related comorbidities.
Temporally distinct roles of Aurora A in polarization of theC. eleganszygote
Authors: Manzi Nadia I. , de Jesus Bailey N. , Shi Yu , Dickinson Daniel J.
Published: October 2023

During asymmetric cell division, coordination of cell polarity and the cell cycle is critical for proper inheritance of cell fate determinants and generation of cellular diversity. InCaenorhabditis elegans(C. elegans), polarity is established in the zygote and is governed by evolutionarily conserved Partitioning defective (PAR) proteins that localize to distinct cortical domains. At the time of polarity establishment, anterior and posterior PARs segregate to opposing cortical domains that specify asymmetric cell fates. Timely establishment of these PAR domains requires a cell cycle kinase, Aurora A (AIR-1 inC.elegans). Aurora A depletion by RNAi causes a spectrum of phenotypes including no posterior domain, reversed polarity, and excess posterior domains. How depletion of a single kinase can cause seemingly opposite phenotypes remains obscure. Using an auxin-inducible degradation system, drug treatments, and high-resolution microscopy, we found that AIR-1 regulates polarity via distinct mechanisms at different times of the cell cycle. During meiosis I, AIR-1 acts to prevent the formation of bipolar domains, while in meiosis II, AIR-1 is necessary to recruit PAR-2 onto the membrane. Together these data clarify the origin of the multiple polarization phenotypes observed in RNAi experiments and reveal multiple roles of AIR-1 in coordinating PAR protein localization with the progression of the cell cycle.
Elevated epigenetic age in wild compared to lab-raised house mice
Authors: Hanski Eveliina , Joseph Susan , Raulo Aura , Wanelik Klara M , O’Toole Áine , Knowles Sarah C L , Little Tom J
Published: October 2023

Age is a key parameter in population ecology, with myriad biological processes changing with age as organisms develop early in life and later senesce. As age is often hard to accurately measure with non-lethal methods, epigenetic methods of age estimation (epigenetic clocks) have become a popular tool in animal ecology, and are often developed or calibrated using captive animals of known age. However, few studies have directly compared epigenetic age estimates between wild and captive or lab-reared animals of the same species, even though age-related epigenetic changes can be influenced by environmental conditions. Here, we built an epigenetic clock from standard laboratory house mice (C57BL/6,Mus musculus)and then used it to estimate age in a population of wild mice (Mus musculus domesticus) of unknown age. We show that this clock accurately predicts adult wild mice to be older than juveniles and that wild mice typically increase in epigenetic age over time, but with wide variation in epigenetic ageing rate among wild individuals. We further show that, for a given body mass, wild mice are epigenetically older than lab mice, and that this difference is not explained by accelerated ageing post-capture but is observed even among the smallest juvenile mice. This suggests different epigenetic age profiles in mice with contrasting genetic and environmental backgrounds arise very early in life and may be driven by peri- and postnatal effects on offspring DNA methylation.
DEVELOPMENT AND EVALUATION OF COATED RICOTTA CHEESE WITH WHEY PROTEIN AND CLOVE OIL
Authors: Aamir Muhammad , Sarwar Eram , Ahmad Aftab , Saeed Farhan , Ikram Ali , Afzaal Muhammad , Kiran Faiza , Ateeq Huda , Akram Noor , Hussain Shahzad , Khan Mahbubur Rehman
Published: October 2023

Cheese, oldest dairy product which is used to preserve the nutrients of milk for long time. It is available in different shapes, sizes, flavors and textures. Ricotta is fresh soft cheese, is prepared through coagulating the whey proteins. It is a value-added product manufactured from cheese whey. Microbial spoiling occurs as a result of unmanaged conditions, resulting in the unfavorable changes in odor, flavor, and texture. That leads to food poisoning when infected food is consumed. Natural preservatives are preferred by consumers over synthetic preservatives since they are safer and extend the shelf life of food goods. Synthetic preservatives are poisonous and have negative health consequences. Edible coatings are biodegradable, natural films that can improve the product’s safety, quality, and nutritional content until it is consumed. This research was carried out to analyse the effect of whey protein and clove essential oil on the shelf life of ricotta cheese due to their excellent gas barrier properties, antioxidant and antimicrobial properties. Different concentrations of clove oil (0.1, 0.2, 0.3 %) are incorporated in whey protein coating solution (2.5,5,7.5%). The overall findings for all groups showed that there was gradual decrease in acidity and moisture content. Therefore, sample TRC3treated with 0.75 % whey protein and 0.3% clove oil showed significant results (P<0.05). They showed less microbial count, increased fat and protein value. But it also had great impact on sensory analysis such as on color, texture, aroma while it showed significant overall acceptability due to high clove oil and whey protein concentrations. Hence, this study showed significant effect on shelf life of ricotta cheese and its shelf life increased from 7 to 21 days.
Lifecycle of a predatory bacterium vampirizing its prey through the cell envelope and S-layer
Authors: Santin Yoann G. , Sogues Adrià , Bourigault Yvann , Remaut Han K. , Laloux Géraldine
Published: October 2023

Predatory bacteria feed upon and kill other bacteria in various natural environments. Obligate epibiotic predators likeBdellovibrio exovorusconsume their prey whilst remaining attached to the outside of the prey. How these predators achieve epibiotic feeding through the prey cell envelope has not been explored previously. Whereas the S-layer is the only proposed defensive structure against predatory bacteria, it remains unclear how this thin outer layer of the envelope might prevent epibiotic attacks. Similarly, the lifecycle ofB. exovorusduring the predator-prey interaction is poorly understood, with current models suggesting a binary division. Here we imaged the entire predatory lifecycle ofB. exovorusand the fate of itsCaulobacter crescentusprey by time-lapse microscopy and cryo-electron microscopy to monitor predator attack, growth and division and assess the impact of the S-layer on epibiotic predation. Our data reveal thatB. exovorususes non-binary division in a novel proliferation pattern that mainly generates three progenies. Moreover, we found thatB. exovoruspredates regardless of the presence of an S-layer, calling for revisiting its protective role against predators. Finally, our results indicate that epibiotic predation relies on the establishment of a secured junction between the prey and predator outer membranes, which must be resolved unilaterally to maintain cellular integrity of the predator departing from the prey surface.
The prevalence ofFusobacterium nucleatumsubspecies in the oral cavity stratifies by local health status
Authors: Krieger Madeline , AbdelRahman Yasser M. , Choi Dongseok , Palmer Elizabeth A. , Yoo Anna , McGuire Sean , Kreth Jens , Merritt Justin
Published: October 2023

The ubiquitous inflammophilic pathobiontFusobacterium nucleatumis widely recognized for its strong association with a variety of human dysbiotic diseases such as periodontitis and oral/extraoral abscesses, as well as multiple types of cancer. F. nucleatumis currently subdivided into four subspecies:F. nucleatumsubspeciesnucleatum(Fn. nucleatum), animalis(Fn. animalis), polymorphum(Fn. polymorphum), andvincentii/fusiforme(Fn. vincentii). Although these subspecies have been historically considered as functionally interchangeable in the oral cavity, direct clinical evidence is largely lacking for this assertion. Consequently, we assembled a collection of oral clinical specimens to determine whetherF. nucleatumsubspecies prevalence in the oral cavity stratifies by local oral health status. Patient-matched clinical specimens of both disease-free dental plaque and odontogenic abscess were analyzed with newly developed culture-dependent and culture-independent approaches using 44 and 60 oral biofilm/tooth abscess paired specimens, respectively. Most oral cavities were found to simultaneously harbor multipleF. nucleatumsubspecies, with a greater diversity present within dental plaque compared to abscesses. In dental plaque,Fn. polymorphumis clearly the dominant organism, but this changes dramatically within odontogenic abscesses whereFn. animalisis heavily favored over all other fusobacteria. Surprisingly, the most commonly studiedF. nucleatumsubspecies,Fn. nucleatum,is only a minor constituent in the oral cavity. To gain further insights into the genetic basis for these phenotypes, we subsequently performed pangenome, phylogenetic, and functional enrichment analyses of oral fusobacterial genomes using the Anvi’o platform, which revealed significant genotypic distinctions amongF. nucleatumsubspecies. Accordingly, our results strongly support a taxonomic reassignment of eachF. nucleatumsubspecies into distinctFusobacteriumspecies. Of these,Fn. animalisshould be considered as the most clinically relevant at sites of active inflammation, despite being among the least characterized oral fusobacteria.
Role of Dopamine Neurons in Familiarity
Authors: Fleury Sixtine , Kolaric Rhonda , Espera Justin , Ha Quan , Tomaio Jacquelyn , Gether Ulrik , Sørensen Andreas Toft , Mingote Susana
Published: October 2023

Dopamine neurons signal the salience of environmental stimuli, influencing learning and motivation. However, research has not yet identified whether dopamine neurons also modulate the salience of memory content. Dopamine neuron activity in the ventral tegmental area (VTA) increases in response to novel objects and diminishes as objects become familiar through repeated presentations. We proposed that the declined rate of dopamine neuron activity during familiarization affects the salience of a familiar object’s memory. This, in turn, influences the degree to which an animal distinguishes between familiar and novel objects in a subsequent novel object recognition (NOR) test. As such, a single familiarization session may not sufficiently reduce dopamine activity, allowing the memory of a familiar object to maintain its salience and potentially attenuating NOR. In contrast, multiple familiarization sessions could lead to more pronounced dopamine activity suppression, strengthening NOR. Our data in mice reveals that, compared to a single session, multiple sessions result in decreased VTA dopamine neuron activation, as indicated by c-Fos measurements, and enhanced novelty discrimination. Critically, when VTA dopamine neurons are chemogenetically inhibited during a single familiarization session, NOR improves, mirroring the effects of multiple familiarization sessions. In summary, our findings highlight the pivotal function of dopamine neurons in familiarity and suggest a role in modulating the salience of memory content.
Highly-parallel production of designer organoids by mosaic patterning of progenitors
Authors: Porter Catherine M. , Qian Grace C. , Grindel Samuel H. , Hughes Alex J.
Published: October 2023

Human organoids are a promising approach for disease modeling and regenerative medicine. However, organoid variability and limited control over morphological outcomes remain significant challenges. Here we extend a DNA ‘velcro’ cell patterning approach, precisely controlling the number and ratio of human stem cell-derived progenitors contributing to nephron and mosaic nephron/ureteric bud organoids within arrays of microwells. We demonstrate long-term control over organoid size and morphology, decoupled from geometric constraints.
Structure-preserving fixation allows Scanning Electron Microscopy to reveal biofilm microstructure and interactions with immune cells
Authors: Wells Marilyn , Mikesh Michelle , Gordon Vernita
Published: October 2023

Pseudomonas aeruginosais a pathogen that forms robust biofilms which are commonly associated with chronic infections and cannot be successfully cleared by the immune system. Neutrophils, the most common white blood cells, target infections with pathogen-killing mechanisms that are rendered largely ineffective by the protective physicochemical structure of a biofilm. Visualization of the complex interactions between immune cells and biofilms will advance understanding of how biofilms evade the immune system and could aid in developing treatment methods that promote immune clearance with minimal harm to the host. Scanning electron microscopy (SEM) distinguishes itself as a powerful, high-resolution tool for obtaining strikingly clear and detailed topographical images. However, taking full advantage of SEM’s potential for high-resolution imaging requires that the fixation process simultaneously preserve both intricate biofilm architecture and the morphologies and structural signatures characterizing neutrophils responses at an infection site. Standard aldehyde-based fixation techniques result in significant loss of biofilm matrix material and morphologies of responding immune cells, thereby obscuring the details of immune interactions with the biofilm matrix. Here we show an improved fixation technique using the cationic dye alcian blue to preserve and visualize neutrophil interactions with the three-dimensional architecture ofP. aeruginosabiofilms.
Recombinant chimeric Horsepox Virus (TNX-801) is attenuated relative to Vaccinia Virus Strains in Human Primary Cell Lines and in Immunocompromised Mice
Authors: Trefry Stephanie V , Raney Christy N , Cregger Amy L , Gonzales Chase A , Layton Brittney L , Enamorado Robert N , Martinez Nelson A , Gohegan Deborah S , Moulaei Tinoush , Ziółkowska Natasza E , Goebel Scott J , Lederman Seth , Bavari Sina , Nasar Farooq
Published: October 2023

Recombinant chimeric Horsepox virus (TNX-801) is a preclinical vaccine in development against Monkeypox and smallpox. In this brief report, we investigated the potential phenotypic differences inin vitroandin vivomodels between TNX-801 and older VACV-based vaccine strains (VACV-IHD, VACV-Lis, VACV-NYC) used in the eradication of smallpox virus. TNX-801 displayed a small plaque phenotype (∼1-2 mm) in both BSC-40 and Vero-E6 cells and yielded >10- to 100-fold lower infectious titers than the VACV strains in multiple-step replication kinetics. Growth kinetics in primary human cell lines from two main routes of poxvirus transmission, respiratory and dermal tracts, yielded ∼10- to 119-fold lower infectious titers of TNX-801. Intranasal infection of immunocompromised mice (C56BL/6Ifnar−/−/Ifngr−/−) with VACV strains at 6.0 and 5.0 log10PFU produced uniform lethal disease. In contrast, TNX-801 at 8.0 log10PFU was unable to produce any clinical disease in mice. These data demonstrate that TNX-801 is >10- to 1,000-fold more attenuated than older VACV-based smallpox vaccines in human primary cell lines and immunocompromised mice.
Interactions between pili affect the outcome of bacterial competition driven by the type VI secretion system
Authors: Otto Simon B. , Servajean Richard , Lemopoulos Alexandre , Bitbol Anne-Florence , Blokesch Melanie
Published: October 2023

The bacterial type VI secretion system (T6SS) is a widespread, kin-discriminatory weapon capable of shaping microbial communities. Due to the system’s dependency on contact, cellular interactions can lead to either competition or kin protection. Cell-to-cell contact is often accomplished via surface-exposed type IV pili (T4P). InVibrio cholerae,these T4P facilitate specific interactions when the bacteria colonize natural chitinous surfaces. However, it has remained unclear whether and, if so, how these interactions affect the bacterium’s T6SS-mediated killing. In this study, we demonstrate that pilus-mediated interactions can be harnessed to reduce the population ofV. choleraeunder liquid growth conditions in a T6SS-dependent manner. We also show that the naturally occurring diversity of pili determines the likelihood of cell-to-cell contact and, consequently, the extent of T6SS-mediated competition. To determine the factors that enable or hinder the T6SS’s targeted reduction of competitors carrying pili, we developed a physics-grounded computational model for autoaggregation. Collectively, our research demonstrates that T4P involved in cell-to-cell contact can impose a selective burden whenV. choleraeencounters non-kin cells that possess an active T6SS. Additionally, our study underscores the significance of T4P diversity in protecting closely related individuals from T6SS attacks through autoaggregation and spatial segregation.
Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection
Authors: Navaratnam Annalan M D , Beale Sarah , Boukari Yamina , Nguyen Vincent , Fong Wing Lam Erica , Braithwaite Isobel , Byrne Thomas E , Fragaszy Ellen , Geismar Cyril , Kovar Jana , Patel Parth , Shrotri Madhumita , Yavlinsky Alexei , Hayward Andrew C , Khreis Haneen , Aldridge Robert W
Published: October 2023

Introduction

Emerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations.

Methods

Concentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects.

Results

Single pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1µg/m3increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data.

Conclusion

Long term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.
Clinical performance of automated machine learning: a systematic review
Authors: Thirunavukarasu Arun James , Elangovan Kabilan , Gutierrez Laura , Hassan Refaat , Li Yong , Tan Ting Fang , Cheng Haoran , Teo Zhen Ling , Lim Gilbert , Ting Daniel Shu Wei
Published: October 2023

Introduction

Automated machine learning (autoML) removes technical and technological barriers to building artificial intelligence models. We aimed to summarise the clinical applications of autoML, assess the capabilities of utilised platforms, evaluate the quality of the evidence trialling autoML, and gauge the performance of autoML platforms relative to conventionally developed models, as well as each other.

Methods

This review adhered to a PROSPERO-registered protocol (CRD42022344427). The Cochrane Library, Embase, MEDLINE, and Scopus were searched from inception to 11 July 2022. Two researchers screened abstracts and full texts, extracted data and conducted quality assessment. Disagreement was resolved through discussion and as-required arbitration by a third researcher.

Results

In 82 studies, 26 distinct autoML platforms featured. Brain and lung disease were the most common fields of study of 22 specialties. AutoML exhibited variable performance: AUCROC 0.35-1.00, F1-score 0.16-0.99, AUCPR 0.51-1.00. AutoML exhibited the highest AUCROC in 75.6% trials; the highest F1-score in 42.3% trials; and the highest AUCPRC in 83.3% trials. In autoML platform comparisons, AutoPrognosis and Amazon Rekognition performed strongest with unstructured and structured data respectively. Quality of reporting was poor, with a median DECIDE-AI score of 14 of 27.

Conclusions

A myriad of autoML platforms have been applied in a variety of clinical contexts. The performance of autoML compares well to bespoke computational and clinical benchmarks. Further work is required to improve the quality of validation studies. AutoML may facilitate a transition to data-centric development, and integration with large language models may enable AI to build itself to fulfil user-defined goals.
Mendelian randomization study of birth weight and risk of psychiatric disorders later in life
Authors: Wu Xiaoping , Geller Frank , Helenius Dorte , Grove Jakob , Albiñana Clara , Petersen Liselotte Vogdrup , Bulik Cynthia M. , Børglum Anders D. , Werge Thomas , Vilhjálmsson Bjarni J. , Feenstra Bjarke
Published: October 2023

Low birth weight has been associated with a higher risk of psychiatric disorders later in life. The underlying causal mechanisms of this relationship are however not clear. In this study, we investigate whether variation in fetal growth has a direct causal effect on mental health. Using birth weight as a proxy measure for fetal growth, we first assessed associations between observed birth weight and later diagnosis of psychiatric disorders in the Danish iPSYCH and ANGI-DK cohorts. Next, we constructed a polygenic score for birth weight based on >1 million variants and tested for association with psychiatric disorders. Finally, using 86 single-nucleotide polymorphisms with robust fetal-only genetic associations with birth weight, we assessed the causal relationship of genetically mediated fetal growth and psychiatric disorders using Mendelian randomization analyses. We found that higher observed birth weight was associated with lower risk of several psychiatric disorders. Polygenic score analyses supported this pattern for attention deficit/hyperactivity disorder, where an increase of one standard deviation in the score for birth weight corresponded to an odds ratio of 0.85 (95% confidence interval 0.79-0.92, P=6.27×10-5). However, one- and two-sample Mendelian randomization analyses did not indicate a direct causal relationship between the birth weight of children and their risk of psychiatric disorders. In conclusion, our study does not support a direct causal effect of fetal growth (as proxied by birth weight) on the risk of psychiatric disorders later in life, suggesting that the observed association between birth weight and mental health is likely to be caused by other factors.
Interactions of netrin-1 through its glycosylation sites immobilize Deleted in Colorectal Cancer (DCC) by favoring its constitutive clustering
Authors: Uriot Karen , Blanc Olivier , Audugé Nicolas , Faklaris Orestis , Blanc Olivier , Chaverot Nathalie , Bloch-Gallego Evelyne , Borghi Nicolas , Coppey-Moisan Maïté , Girard Philippe P.
Published: October 2023

Netrin-1 is a protein that attracts neurons expressing the membrane receptor Deleted in Colorectal Cancer DCC. In colon carcinoma, the interaction between netrin-1 and DCC prevents apoptosis. Crystallographic data suggest that these processes involve the clustering of DCC, the observation of which in cells remains elusive, as do the molecular determinants of DCC-netrin-1 interactions and their impact on DCC organization and mobility. To address these questions, we used fluorescence photobleaching, single-particle tracking and super-resolution techniques to characterize DCC organization and mobility on the cell surface. Our results show that netrin-1 impedes DCC mobility in the plasma membrane by promoting the growth of constitutive DCC nanoclusters at the expense of free DCC. Furthermore, we show that these effects are mediated primarily by the three glycosylation sites in the LamVI domain of netrin-1 and, to a lesser extent, by the C-terminal domain and its RGD binding site.
Rationale design of unrestricted pRN1 derivatives and their application in construction of a dual plasmid vector system forSaccharolobus islandicus
Authors: Zhao Pengpeng , Bi Xiaonan , Wang Xiaoning , Feng Xu , Shen Yulong , Yuan Guanhua , She Qunxin
Published: October 2023

Saccharolobus islandicusREY15A represents one of the very few archaeal models with versatile genetic tools, including efficient genome editing, gene silencing and robust protein expression systems. However, plasmid vectors constructed for this crenarchaeon thus far are solely based on the pRN2 cryptic plasmid. Although this plasmid co-exists with pRN1 in their original host, early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system forSa. islandicus. Herein we identified a putative target sequence inorf904encoding a putative replicase on pRN1 (TargetN1). Mutated targets were then designed (N1a, N1b, N1c) and tested for their capability of escaping from the host CRISPR immunity by using plasmid interference assay. This revealed that the original target triggers the CRISPR immunity in this archaeon whereas all three mutated targets do not, indicating that all designed target mutations evade the host immunity. These mutated targets were then incorporated intoorf904individually, yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed (pN1aSD, pN1bSD and pN1cSD).Sa. islandicustransformation revealed that pN1aSD and pN1bSD were functional shuttle vectors, but pN1cSD lost the capability of replication. In addition, pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination, and this yielded a dual plasmid system for genetic study with this important archaeal model.

Impact statement

When pRN1 was employed for vector construction inSaccharolobus islandicusREY15A, pRN1-derived vectors are not stable in this archaeon. Here we show that pRN1 orf904 encoding a putative replicase on pRN1 carries a DNA segment to be targeted by the host I-A CRISPR system. By designing mutated target sequences that evade the CRISPR immunity, efficient plasmid vectors were obtained with mutated pRN1 backbones. This strategy could be applied in developing host-vector systems for other microorganisms with plasmids or viruses carrying CRISPR target sequences. Moreover, the resulting dual vector system would facilitate genetic studies with this crenarchaeal model.
Transdifferentiation of fibroblasts into muscle cells to constitute cultured meat with tunable intramuscular fat deposition
Authors: Ma Tongtong , Ren Ruimin , Lv Jianqi , Yang Ruipeng , Xinyi Zheng , Hu Yang , Zhu Guiyu , Wang Heng
Published: October 2023

Current studies on cultured meat mainly focused on the muscle tissue reconstruction in vitro, but lack the formation of intramuscular fat which is a crucial factor in determining taste, texture and nutritional contents. Therefore, incorporating fat into cultured meat is of superior value. In this study, we employed the myogenic/lipogenic transdifferentiation of chicken fibroblasts in 3D to produce muscle mass and deposit fat into the same cells without the co-culture or mixture of different cells or fat substances. The immortalized chicken embryonic fibroblasts were implanted into the hydrogel scaffold and the cell proliferation and myogenic transdifferentiation were conducted in 3D to produce the whole-cut meat mimics. Compare to 2D, cells grown in 3D matrix showed elevated myogenesis and collagen production. We further induced fat deposition in the transdifferentiated muscle cells and the triglyceride content could be manipulated to match and exceed the levels of chicken meat. The gene expression analysis indicated that both lineage-specific and multi-functional signalings could contribute to the generation of muscle/fat matrix. Overall, we were able to precisely modulate muscle, fat, and extracellular matrix contents according to balanced or specialized meat preferences. These findings provide new avenues for customized cultured meat production with desired intramuscular fat contents that can be tailored to meet the diverse demands of consumers.

Graphical Abstract
GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
Authors: Liu Anguo , Wang Nini , Xie Guoxiang , Li Yang , Yan Xixi , Li Xinmei , Zhu Zhenliang , Li Zhuohui , Yang Jing , Meng Fanxin , Dou Mingle , Chen Weihuang , Ma Nange , Jiang Yu , Gao Yuanpeng , Wang Yu
Published: October 2023

Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression ofNova1and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
Authors: Zhu Iris , Landsman David
Published: October 2023

Housekeeping genes are considered to be regulated by common enhancers across different tissues. Here we report that most of the commonly expressed mouse or human genes across different cell types, including more than half of the previously identified housekeeping genes, are associated with cell type–specific enhancers. Furthermore, the binding of most transcription factors (TFs) is cell type–specific. We reason that these cell type specificities are causally related to the collective TF recruitment at regulatory sites, as TFs tend to bind to regions associated with many other TFs and each cell type has a unique repertoire of expressed TFs. Based on binding profiles of hundreds of TFs from HepG2, K562, and GM12878 cells, we show that 80% of all TF peaks overlapping H3K27ac signals are in the top 20,000–23,000 most TF-enriched H3K27ac peak regions, and approximately 12,000–15,000 of these peaks are enhancers (nonpromoters). Those enhancers are mainly cell type–specific and include those linked to the majority of commonly expressed genes. Moreover, we show that the top 15,000 most TF-enriched regulatory sites in HepG2 cells, associated with about 200 TFs, can be predicted largely from the binding profile of as few as 30 TFs. Through motif analysis, we show that major enhancers harbor diverse and clustered motifs from a combination of available TFs uniquely present in each cell type. We propose a mechanism that explains how the highly focused TF binding at regulatory sites results in cell type specificity of enhancers for housekeeping and commonly expressed genes.
Isogonal embeddings of interwoven and self-entangled honeycomb (hcb) nets and related interpenetrating primitive cubic (pcu) nets
Authors: O'Keeffe Michael , Treacy Michael M. J.
Published: October 2023

Two- and three-periodic vertex-transitive (isogonal) piecewise-linear embeddings of self-entangled and interwoven honeycomb nets are described. The infinite families with trigonal symmetry and edge transitivity (isotoxal) are particularly interesting as they have the Borromean property that no two nets are directly linked. These also lead directly to infinite families of interpenetrating primitive cubic nets (pcu) that are also vertex- and edge-transitive and have embeddings with 90° angles between edges.