bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of ten-year cardiovascular disease risk in Bangladesh: A comparative analysis of laboratory and non-laboratory-based WHO risk prediction models
Authors: Monower Md Mostafa , Abid Shehab Uddin Al , Bhuiyan Mahfuzur Rahman , Mamun Mohammad Abdullah Al , Choudhury Sohel Reza 
Published: July 2024

AbstractObjectivesThis study aimed to estimate the 10-year cardiovascular diseases (CVD) risk in Bangladeshi adults using updated 2019 WHO laboratory-based and non-laboratory-based models, identify key CVD risk determinants, and assess the agreement between two models.MethodsWe conducted a cross-sectional analysis of nationally representative Bangladesh STEPS 2018 survey data, involving 2767 adults aged 40-69 years without prior CVDs, using both versions of the updated 2019 WHO 10-year CVD risk prediction models. Logistic regression identified determinants and model agreement was assessed using Bland-Altman Plot, concordance, and Kappa statistics with STATA version 17.ResultsIn the laboratory-based model, 10.32% (95% CI: 8.78-12.11) of the population was at elevated risk (≥10%), while the non-laboratory-based model showed 9.25% (95% CI: 7.7-11.08). Males had significantly higher risk than females in both models (p<0.0001). Elevated 10-year CVD risk was associated with age increments of five years (OR=4.29, 95% CI: 3.48-5.30), being female (OR=0.31, 95% CI: 0.18-0.53), urban residence (OR=1.82, 95% CI: 1.20-2.74), residing in Dhaka division (OR=2.44, 95% CI: 1.26-4.73), and higher education (OR=2.42, 95% CI: 1.06-5.51). Key metabolic factors included high waist-hip ratio (OR=2.08, 95% CI: 1.22-3.52) and elevated triglycerides (OR=2.70, 95% CI: 1.65-4.41). Comparing models, Bland-Altman plots showed limit of agreement (-3.16, 3.52) with mean difference of 0.18, proportional bias (males: y=-0.43 + 1.11x; females: y=-0.43 + 1.16x), Lin’s Concordance Correlation Coefficient (LCCC) 0.90 (95% CI: 0.89-0.91), and a Kappa statistic of 0.69 (95%CI: 0.67-0.72).ConclusionA substantial portion of the adult Bangladeshi population is at elevated risk of a cardiovascular event within the next decade, with males at higher risk per both models. Sociodemographic, and metabolic factors indicating potential target groups for intervention. The non-laboratory-based model generally shows agreement with the laboratory-based model and can serve as an alternative in settings with limited laboratory resources, though caution is advised for high-risk individuals.
Tattoo ink exposure is associated with lymphoma and skin cancers – a Danish study of twins
Authors: Clemmensen Signe B. , Mengel-From Jonas , Kaprio Jaakko , Frederiksen Henrik , Hjelmborg Jacob vB. 
Published: July 2024

AbstractWe aim to study the possible association between tattoo ink exposure and development of certain cancers in the recently established Danish Twin Tattoo Cohort.Tattoo ink is known to transfer from skin to blood stream and accumulate in regional lymph nodes. We are concerned that tattoo ink induce inflammation at deposit site that may eventually become chronic and increase risk of abnormal cell proliferation, especially skin cancer and lymphoma.We conducted two designs of study in twins in order to improve confounder control: A cohort study of 2,367 randomly selected twins and a case-control study of 316 twins born in the period 1960-1996. Cancer diagnoses (ICD-10) were retrieved from the Danish Cancer Registry and tattoo ink exposure from the Danish Twin Tattoo survey from 2021. The analysis addressed effects of time-varying exposure.In the case-control study, individual level analysis resulted in a hazard of skin cancer (of any type except basal cell carcinoma) that was 1.62 times higher among tattooed (95% CI: 1.08-2.41). Twin-matched analysis of 14 twin pairs discordant for tattoo ink exposure and skin cancer show HR=1.33 (95% CI: 0.46-3.84). For skin cancer and lymphoma, increased hazards were found for tattoos larger than the palm of a hand: HR=2.37 (95% CI: 1.11-5.06) and HR=2.73 (95% CI: 1.33-5.60), respectively. In the cohort study design, individual level analysis resulted in a hazard ratio of 3.91 (95% CI: 1.42-10.8) for skin cancer and 2.83 (95% CI: 1.30-6.16) for basal cell carcinoma.In conclusion, we are very concerned that tattoo ink interacting with surrounding cells may have severe consequences. Further studies are needed beneficial to public health – the sooner the better.
Airway smooth muscle tone curbs hyperresponsiveness in experimental asthma
Authors: Gazzola Morgan , Boucher Magali , Henry Cyndi , Rojas-Ruiz Andrés , Marsolais David , Bossé Ynuk 
Published: July 2024

ABSTRACTBackground & ObjectivesA sustained contraction of airway smooth muscle, hereinafter called tone, increases the response to methacholine in healthy mice and humans. However, the effect of tone in the context of an active inflammation remains to be investigated. The objective of the present study was to test the effect of tone on thein vivoresponse to methacholine in mice during an active inflammatory phase of experimental asthma.MethodsMale BALB/c mice were exposed once-daily to either intranasal saline or house dust mite for 10 consecutive days to induce experimental asthma. They then underwent one of two methacholine challenges 24 h after the last exposure. While the same cumulative dose was administered in both challenges, one was preceded by a 20-min period of tone induced by nebulizing low doses of methacholine at 5-min intervals. Respiratory mechanics were monitored before and throughout the methacholine challenge by oscillometry. Bronchoalveolar lavages (BAL) and histology were also performed.ResultsBAL inflammation and histological alterations were consistent with experimental asthma. In accordance with previous studies, tone potentiated the response to methacholine in control mice, mainly by stiffening the lung periphery. The lung was even stiffer upon methacholine challenge during an active phase of inflammation in mice with experimental asthma, but this was not further potentiated by tone. In fact, in mice with experimental asthma, tone mitigated hyperresponsiveness by preventing further airway narrowing and, more importantly, small airway narrowing heterogeneity and closure.ConclusionDuring an active inflammatory phase of experimental asthma, tone protects against hyperresponsiveness.Take-home messageThe effect of airway smooth muscle tone on the methacholine response was investigated in mice with or without experimental asthma. While tone potentiated the methacholine response in control mice, it mitigated hyperresponsiveness in experimental asthma. These results unveiled a protective role of the airway smooth muscle in experimental asthma.
Optimization and model averaging of histogram-based place cell firing rate maps using the point process framework
Authors: Okatan Murat 
Published: July 2024

AbstractBackgroundThe firing rate of hippocampal place cells depends on the spatial position of the organism in an environment. This position dependence is often quantified by constructing spike-in-location and time-in-location histograms, the ratio of which yields a firing rate map.New MethodThe purpose of this study is to present a new method for optimizing the spatial resolution of histogram-based firing rate maps.ResultsIt is pointed out that histogram-based firing rate maps are conditional intensity functions of inhomogeneous Poisson process models of neural spike trains, and, as such, they can be optimized through model selection within the point process framework.ResultsThe point process framework is used here for optimizing the size and the aspect ratio of the histogram bins using the Akaike Information Criterion (AIC). It is also used for model averaging using Akaike weights, when maps of various bin sizes provide comparable fits. Application of the method is illustrated on data from real rat hippocampal place cells.Comparison with existing methodsExisting methods do not optimize the number of bins used in each dimension of the firing rate map.ConclusionThe proposed approach allows for the construction of the AIC-best histogram-based firing rate map for each individual place cell.
Chemogenetic control of GABAergic activity within the interpeduncular nucleus reveals dissociable behavioral components of the nicotine withdrawal phenotype
Authors: Miguelez Fernández Anabel M. M. , Netherton Shana , Niladhuri Seshadri B. , Rivera Patricia , Tseng Kuei Y. , Peters Christian J. 
Published: July 2024

AbstractChronic exposure to nicotine results in the development of a dependent state such that a withdrawal syndrome is elicited upon cessation of nicotine. The habenulo-interpeduncular (Hb-IPN) circuit contains a high concentration of nAChRs and has been identified as a main circuit involved in nicotine withdrawal. Here we investigated the contribution of two distinct subpopulations of IPN GABAergic neurons to nicotine withdrawal behaviors. Using a chemogenetic approach to specifically target Amigo1-expressing or Epyc-expressing neurons within the IPN, we found that activity of the Amigo1 and not the Epyc subpopulation of GABAergic neurons is critical for anxiety-like behaviors both in naïve mice and in those undergoing nicotine withdrawal. Moreover, data revealed that stimulation of Amigo1 neurons in nicotine-naïve mice elicits opposite effects on affective and somatic signs of withdrawal. Taken together, these results suggest that somatic and affective behaviors constitute dissociable components of the nicotine withdrawal phenotype and are likely supported by distinct subpopulations of neurons within the IPN.
Origin of division of labor is decoupled from polymorphism in colonial animals
Authors: Leventhal Sarah , Edie Stewart M. , Morrison Rebecca , Simpson Carl 
Published: July 2024

AbstractDivision of labor, the specialization of sometimes phenotypically divergent cell types or group members, is often associated with ecological success in eukaryotic colonial organisms. Despite its many independent evolutionary origins, how division of labor originates remains unclear. Conventional hypotheses tend towards an “economic” model, so that biological division of labor may reflect a partitioning of pre-existing tasks and morphologies into specialized colony members. Here, we present an alternative model of the origin of division of labor, which can explain the evolution of new functions within a colony. We show that in colonies of the Cretaceous aged (103-96 Ma) fossil bryozoan of the genusWilbertopora, the first cheilostome bryozoan to evolve polymorphism, new member morphologies were not a simple partitioning of pre-existing morphologies, but instead expanded into novel morphospace as they lost functions, specifically feeding. This expansion into new morphologies occurred primarily during two pulses of heightened morphological disparity, suggesting that the evolution of polymorphism corresponded to relaxed constraints on morphology and perhaps to the exploration of novel functions. Using a simple model of physiological connections, we show that regardless of the functionality of these new colony members, all non-feeding members could have been supported by neighboring feeding members. This suggests that the geometric constraints and physiological connectedness could be prerequisites for evolving both polymorphism and division of labor in modular organisms, and that a classic partitioning model of specialization cannot be broadly applied to biological systems.One Sentence summaryIn cheilostome bryozoans, polymorphism evolved through the loss of preexisting functions, rather than the gain of new functions, suggesting that polymorphism can evolve through drift rather than division of labor.
A NovelEx VivoApproach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices
Authors: Vierhout Megan , Ayoub Anmar , Ali Pareesa , Kumaran Vaishnavi , Naiel Safaa , Isshiki Takuma , Koenig Joshua F. , Kolb Martin R.J. , Ask Kjetil 
Published: July 2024

ABSTRACTIdiopathic pulmonary fibrosis (IPF) is fatal interstitial lung disease characterized by excessive scarring of the lung tissue and declining respiratory function. Given its short prognosis and limited treatment options, novel strategies to investigate emerging experimental treatments are urgently needed. Macrophages, as the most abundant immune cell in the lung, have key implications in wound healing and lung fibrosis. However, they are highly plastic and adaptive to their surrounding microenvironment, and thus to maximize translation of research to lung disease, there is a need to study macrophages in multifaceted, complex systems that are representative of the lung. Precision-cut lung slices (PCLS) are living tissue preparations derived from the lung that are culturedex vivo,which bypass the need for artificial recapitulation of the lung milieu and architecture. Our objective was to establish and validate a moderate-throughput, biologically- translational, viable model to study profibrotic polarization of macrophages in the lung using murine PCLS. To achieve this, we used a polarization cocktail (PC), consisting of IL-4, IL-13, and IL-6, over a 72-hour time course. We first demonstrated no adverse effects of the PC on PCLS viability and architecture. Next, we showed that multiple markers of macrophage profibrotic polarization, including Arginase-1, CD206, YM1, and CCL17 were induced in PCLS following PC treatment. Through tissue microarray-based histological assessments, we directly visualized and quantified Arginase-1 and CD206 staining in PCLS in a moderate-throughput manner. We further delineated phenotype of polarized macrophages, and using high-plex immunolabelling with the Iterative Bleaching Extends Multiplexity (IBEX) method, showed that the PC effects both interstitial and alveolar macrophages. Substantiating the profibrotic properties of the system, we also showed expression of extracellular matrix components and fibrotic markers in stimulated PCLS. Finally, we demonstrated that clodronate treatment diminishes the PC effects on profibrotic macrophage readouts. Overall, our findings support a suitable complex model for studying ex vivo profibrotic macrophage programming in the lung, with future capacity for investigating experimental therapeutic candidates and disease mechanisms in pulmonary fibrosis.
Metagenome-assembled genomes of Estonian Microbiome cohort reveal novel species and their links with prevalent diseases
Authors: Pantiukh Kateryna , Aasmets Oliver , Krigul Kertu Liis , Org Elin 
Published: July 2024

SummaryDeep metagenomic data from population studies enables genome recovery and construction of population-specific references, including new species and uncovering microbial diversity that global references might miss. We constructed an Estonian population-specific reference of metagenome-assembled genomes (MAGs) from 1,878 stool samples of the EstMB-deep cohort. We assembled 84,762 MAGs, representing 2,257 species, including 353 potentially novel species (15.6%). Additionally, 607 species (26.9%) were not present in the global Unified Human Gastrointestinal Genome (UHGG) reference database and may therefore be population-specific. We further demonstrated the value ofde novoassembly of bacterial genomes by analysing associations with 33 prevalent diseases and detected 44 significant associations for 15 diseases, including with 10 potentially new species and 5 species absent from UHGG. The correlations, especially with new species, demonstrate thatde novobacterial genome assembly from population cohorts can provide significant novel insights linking the microbiome with prevalent diseases and uncovering population-specific differences.
Nemacounter: A user-friendly software to accurately phenotype SCN cysts
Authors: Mejias Joffrey , Kozlowski Djampa K. L. , Goshon Jackson , Maier Thomas R. , Baum Thomas J. 
Published: July 2024

AbstractThe soybean-cyst nematode (SCN;Heterodera glycines) is one of the most destructive pests affecting soybean crops. Effective management of SCN is imperative for the sustainability of soybean agriculture. A promising approach to achieving this goal is the development and breeding of new resistant soybean varieties. Researchers and breeders typically employ exploratory methods such as Genome-Wide Association Studies or Quantitative Trait Loci mapping to identify genes linked to resistance. These methods depend on extensive phenotypic screening. The primary phenotypic measure for assessing SCN resistance is often the number of cysts that form on a plant’s root system. Manual counting hundreds of cysts on a given root system is not only laborious but also subject to variability due to individual assessor differences. Additionally, while measuring cyst size could provide valuable insights due to its correlation with cyst development, this aspect is frequently overlooked because it demands even more hands-on work. To address these challenges, we have created Nemacounter, an intuitive software designed to detect, count, and measure the size of cysts autonomously. Nemacounter boasts a user-friendly graphical interface, simplifying the process for users to obtain reliable results. It enhances productivity by delivering annotated images and compiling data into csv files for easy analysis and reporting.
A negative correlation between the rate coefficient of repair after photoinhibition of cold acclimated plants and the mean annual temperature of the habitats ofArabidopsis thalianaecotypes
Authors: Oguchi Riichi , Nagano Soichiro , Pfleger Ana , Ozaki Hiroshi , Hikosaka Kouki , Osmond Barry , Chow Wah Soon 
Published: July 2024

SummaryBoth the activity of photosynthesis and the repair of damaged photosystems decline in cold environments, which may increase the extent of the damage of photosynthetic machinery by light, namely photoinhibition. We hypothesized that plants in colder habitats may possess greater tolerance to photoinhibition, especially in low temperature conditions.We measured the rate of photoinhibition, rate of photoinhibition repair and other thylakoid activities in cold environments using 298Arabidopsis thalianaecotypes and studied the relationships among the indicators of photoinhibition tolerance and climatic data of the habitat of each ecotype. The plants acclimated to cold conditions (12°C) for three days showed a negative correlation between the rate of photoinhibition repair at 5°C and the mean annual temperature of habitats, although we could not see this correlation with the control plants grown in 22°C. This result would indicate that the acclimation capacity of photoinhibition tolerance in cold conditions can affect the distribution of plants especially in colder regions.
Detecting somatic variants in purified brain DNA obtained from surgically implanted depth electrodes in epilepsy
Authors: Mascarenhas Rumika , Merrikh Daria , Khanbabaei Maryam , Kaur Navprabhjot , Ghaderi Navid , Maroilley Tatiana , Liu Yiping , Soule Tyler , Appendino Juan Pablo , Jacobs Julia , Wiebe Samuel ,   The Calgary Comprehensive Epilepsy Program Collaborators, Hader Walter , Pfeffer Gerald , Tarailo-Graovac Maja , Klein Karl Martin 
Published: July 2024

AbstractSomatic variants causing epilepsy are challenging to detect as they are only present in a subset of brain cells (e.g., mosaic) resulting in low variant allele frequencies. Traditional methods that rely on surgically resected brain tissue are limited to patients undergoing brain surgery. We developed an improved protocol to detect somatic variants using DNA from stereo- electroencephalography (SEEG) depth electrodes, enabling access to a larger patient cohort and diverse brain regions. This protocol mitigates issues of cell contamination and low yields by purifying neuronal nuclei using fluorescence-activated nuclei sorting. Furthermore, we employed advanced amplification techniques, stringent quality control and an optimized bioinformatic workflow to decrease false positives. Using digital droplet polymerase chain reaction, we confirmed all four selected candidate somatic variants. Our approach enhances the reliability and applicability of SEEG-derived DNA for epilepsy, offering insights into its molecular basis, facilitating identification of the epileptogenic zone and other advancements in precision medicine.
From forests to farming: identification of photosynthetic limitations in breadfruit across diverse environments
Authors: Dow Graham J. , Lincoln Noa Kekuewa , Autufuga Dolly , Paull Robert 
Published: July 2024

AbstractBreadfruit (Artocarpus altilis) is a prolific tropical tree producing highly nutritious and voluminous carbohydrate-rich fruits. Already recognized as an underutilized crop, breadfruit could ameliorate food insecurity and protect against climate-related productivity shocks in undernourished equatorial regions. However, a lack of fundamental knowledge impedes widespread agricultural adoption, from modern agroforestry to plantation schemes. Here, we used a multi-environment breadfruit variety trial across the Hawaiian Islands to determine photosynthetic limitations, understand the role of site conditions or varietal features, and define their contributions to agronomic efficiency. Photosynthetic rates were dependent on location and variety, and strongly correlated with fruit yield (r2=0.80, p<0.001). Photochemistry was suitable to full-sunlight conditions, with a saturation point of 1545 PAR,Vcmaxof 151 μmol m-2s-1, andJmaxof 128 μmol m-2s-1, which are high-end compared to other tropical and temperate tree crops. However, limitations on CO2assimilation were imposed by stomatal characteristics, including stomatal density (p<0.05) and diurnal oscillations of stomatal conductance (>50% reductions from daily maxima). These constraints on CO2diffusion are likely to limit maximum productivity more than photochemistry. Our results comprise the first comprehensive analysis of breadfruit photosynthesis, successfully links ecophysiology with fruit yield, and identifies vital traits for future research and management optimization.
Early Embryonic Development of the German CockroachBlattella germanica
Authors: Bar-Lev Viterbo Ariel , Wexler Judith R. , Mayost Lev-Ari Orel , Chipman Ariel D. 
Published: July 2024

AbstractBackgroundEarly embryogenesis is characterized by dramatic cell proliferation and movement. In most insects, early embryogenesis includes a phase called the uniform blastoderm, during which cells evenly cover the entirety of the egg. However, the embryo of the German cockroach,Blattella germanica, like those of many insects within the super order Polyneoptera, does not have a uniform blastoderm; instead, its first cells condense rapidly at the site of a future germband. We investigated early development in this species in order to understand how early gene expression is or is not conserved in these insect embryos with distinct early cell behaviors.ResultsWe present a detailed time series of nuclear division and distribution from fertilization through germband formation and report patterns of expression for the early patterning geneshunchback,caudal, and twist in order to understand early polarization and mesoderm formation. We show a detailed time course of the spatial expression of two genes involved in the segmentation cascade,hedgehogandeven-skipped,and demonstrate two distinct dynamics of the segmentation process.ConclusionsDespite dramatic differences in cell distribution between the blastoderms of many Polyneopteran insects and those of more well-studied developmental models, expression patterns of early patterning genes are mostly similar. Genes associated with axis determination in other insects are activated relatively late and are probably not maternally deposited. The two phases of segmentation – simultaneous and sequential – might indicate a broadly conserved mode of morphological differentiation. The developmental time course we present here should be of value for further investigation into the causes of this distinct blastoderm type.