bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preconception indicators and associations with health outcomes reported in UK routine primary care data: a systematic review
Authors: Schoenaker Danielle , Lovegrove Elizabeth M , Cassinelli Emma H , Hall Jennifer , McGranahan Majel , McGowan Laura , Carr Helen , Alwan Nisreen A , Stephenson Judith , Godfrey Keith M 
Published: February 2024

AbstractBackgroundRoutine primary care data may be a valuable resource for preconception health research and informing provision of preconception care.AimTo review how primary care data could provide information on the prevalence of preconception indicators and examine associations with maternal and offspring health outcomes.Design and SettingSystematic review of observational studies using UK routine primary care data.MethodLiterature searches were conducted in five databases (March 2023) to identify observational studies that used national primary care data from individuals aged 15-49 years. Preconception indicators were defined as medical, behavioural and social factors that may impact future pregnancies. Health outcomes included those that may occur during and after pregnancy. Screening, data extraction and quality assessment were conducted by two reviewers.ResultsFrom 5,259 records screened, 42 articles were included. The prevalence of 30 preconception indicators was described for female patients, ranging from 0.01% for sickle cell disease to >20% for each of advanced maternal age, previous caesarean section (among those with a recorded pregnancy), overweight, obesity, smoking, depression and anxiety (irrespective of pregnancy). Few studies reported indicators for male patients (n=3) or associations with outcomes (n=5). Most studies had low risk of bias, but missing data may limit generalisability.ConclusionFindings demonstrate that routinely collected UK primary care data can be used to identify patients’ preconception care needs. Linking primary care data with health outcomes collected in other datasets is underutilised but could help quantify how optimising preconception health and care can reduce adverse outcomes for mothers and children.How this fits inProvision of preconception care is not currently embedded into routine clinical practice but may be informed by routinely collected primary care data.This systematic review demonstrates that UK primary care data can provide information on the prevalence of a range of medical, behavioural and social factors among female patients of reproductive age, while limited research has examined male preconception health or associations with maternal and offspring health outcomes.Routinely recorded electronic patient record data can be used by primary healthcare professionals to search for preconception risk factors and thereby support individualised preconception care, while aggregate data can be used by public health agencies to promote population-level preconception health.Further data quality improvements and linkage of routine health datasets are needed to support the provision of preconception care and future research on its benefits for maternal and offspring health outcomes.
Acute kidney injury outcomes of COVID-19 confirmed patients in a Philippine tertiary hospital: A retrospective study
Authors: Sayson Joberly , Kalaw Reginald , Ordona Bernadette Ecunar , Lim Marissa Elizabeth 
Published: February 2024

AbstractThe novel coronavirus (COVID-19) is known to be the fifth pandemic causing massive deaths worldwide. This virus has not only been deeply associated with acute respiratory distress, but also acute kidney injury (AKI). This study describes the baseline characteristics and various outcomes of AKI based on the KDIGO 2012 Clinical Practice Guidelines in patients hospitalized with COVID-19 at a Philippine tertiary hospital. A total of 195 patient records were retrospectively reviewed for the study. Of the 195 patients, 81(42%) patients developed AKI. Significant baseline characteristics included older age (56.28 + 14.12), presence of hypertension (p=0.004), diabetes mellitus (p=0.002), and cardiovascular disease (p=0.003). Also, the use of diuretics, inotropes and antibiotics were more prevalent in patients who developed AKI. Most of the patients who had AKI were categorized as stage 1 (49.38%). Mechanical ventilation was significantly (p<0.001) more prevalent in patients with AKI (20.99%) compared to patients without AKI (5.26%). There was significantly higher rates (p<0.001) of renal replacement therapy in patients with AKI (30.86%). Lastly, higher mortality rates were observed in patients with AKI (50.62%) versus patients without AKI (12.28%). Our study demonstrated that patients with COVID-19 can develop AKI and tend to have a poorer prognosis.
[ICoN: Integration using Co-attention across Biological Networks
Authors: Tasnina Nure , Murali T. M. 
Published: February 2024

AbstractMotivationMolecular interaction networks are powerful tools for studying cellular functions. Integrating diverse types of networks enhances performance in downstream tasks such as gene module detection and protein function prediction. The challenge lies in extracting meaningful protein feature representations due to varying levels of sparsity and noise across these heterogeneous networks.ResultsWe propose ICoN, a novel ‘co-attention’-based, denoising, unsupervised graph neural network model that takes multiple protein-protein association networks as inputs and generates an integrated single network by computing a unified feature representation for each protein. A key contribution of ICoN is a novel approach that enables cross-network communication through co-attention during training. The model also incorporates a denoising training technique, introducing perturbations to each input network and training the model to reconstruct the original network from its corrupted version, a method previously unexplored in network integration.Our experimental results demonstrate that ICoN surpasses individual networks across three downstream tasks: gene module detection, gene coannotation prediction, and protein function prediction. Compared to existing unsupervised network integration models, ICoN exhibits superior performance across the majority of downstream tasks and exhibits enhanced robustness against noise. This work introduces a promising approach for effectively integrating diverse protein-protein association networks, aiming to achieve a biologically meaningful unified representation of proteins.AvailabilityThe ICoN software is available under the GNU Public License v3 athttps://github.com/Murali-group/ICoN.
Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genusDipodiumand provides insights into plastid gene degeneration
Authors: Goedderz Stephanie , Clements Mark A. , Bent Stephen J. , Nicholls James A. , Patel Vidushi S. , Crayn Darren M. , Schlüter Philipp M. , Nargar Katharina 
Published: February 2024

AbstractThe orchid genusDipodiumR.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, the latter confined to sect.Dipodium. This study examined plastome degeneration inDipodiumin a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24Dipodiumsamples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect.Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found sect.Leopardanthusas sister lineage to sect.Dipodium. Dipodium ensifolium, the only leafy autotrophic species in sect.Dipodiumwas found sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence time estimations found thatDipodiumarose ca. 33.3 Ma near the lower boundary of the Oligocene and crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect.Dipodium. The comparative assessment of plastome structure and gene degradation inDipodiumrevealed that plastidndhgenes were pseudogenised or physically lost in allDipodiumspecies, including in leafy autotrophic species of bothDipodiumsections. Levels of plastidndhgene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus.Dipodiumexhibits an early stage of plastid genome degradation as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.
Trophic niche partitioning in symbiotic marine invertebrates
Authors: Guibert Isis , Conti-Jerpe Inga Elizabeth , Pons Leonard , Tayaban Kuselah , Sayco Sherry Lyn , Cabaitan Patrick , Conaco Cecilia , Baker David Michael 
Published: February 2024

AbstractFierce competition for food and space underpins coral reefs’ biodiversity - supported by photosymbiotic foundational species. In contrast to other ecosystems, there is scant evidence that competition is mitigated by niche partitioning. Indeed, the dynamic evolutionary lineages of symbiotic partners and their syntrophy create layers of nutritional complexity that obfuscate patterns that structurn reef communities. As conspicuous members of Indo-Pacific reefs - giant clams co-occur with reef-building corals and similarly associate with algal symbionts. Using a common garden experiment, we analyzed stable isotope values from six giant clam species in the Philippines. These data, along with published data from ten sympatric corals, were used to calculate a novel metric - the Host Evaluation: Reliance on Symbionts (HERS) index - to assess variations in relative trophic strategies. Consistent with trophic niche partitioning – all species fell along an autotrophy-heterotrophy gradient with little overlap. We found a significant phylogenetic signal in clam HERS score, highlighting the role of selection in their nutritional ecology. We conclude that niche partitioning comes with tradeoffs, where predominantly autotrophic species showed higher growth rates but higher susceptibility to stress and consequently - greater conservation concern.TeaserTrophic niche partitioning plays a role in symbiotic marine invertebrate evolution with benefits and costs.
Building Blocks of Understanding: Constructing a Reverse Genetics Platform for studying determinants of SARS-CoV-2 replication
Authors: Olguin-Nava Marco , Bohn Patrick , Hennig Thomas , Börtlein Charlene , Gribling-Burrer Anne-Sophie , Schmidt Nora , Caliskan Neva , Dölken Lars , Munschauer Mathias , Smyth Redmond P. 
Published: February 2024

AbstractTo better understand viral pathogenesis, host-virus interactions, and potential therapeutic interventions, the development of robust reverse genetics systems for SARS-CoV-2 is crucial. Here, we present a reverse genetics platform that enables the efficient manipulation, assembly, and rescue of recombinant SARS-CoV-2. The versatility of our reverse genetics system was demonstrated by generating recombinant SARS-CoV-2 viruses. We used this system to generate N501Y and Y453F spike protein mutants. Characterization studies revealed distinct phenotypic effects, impact on viral fitness, cell binding, and replication kinetics. We also investigated a recently discovered priming site for NSP9, which is postulated to produce a short RNA antisense leader sequence. By introducing the U76G mutation into the 5’UTR, we show that this priming site is necessary for the correct production of genomic and subgenomic RNAs, and also for efficient viral replication. In conclusion, our developed reverse genetics system provides a robust and adaptable platform for the efficient generation of recombinant SARS-CoV-2 viruses for their comprehensive characterization.Significance statementIn this study, we present a versatile reverse genetics platform facilitating the efficient manipulation, assembly, and rescue of recombinant SARS-CoV-2. Demonstrating its adaptability, we successfully engineered N501Y and Y453F spike protein mutants, each exhibiting distinct phenotypic effects on viral fitness, cell binding, and replication kinetics. We also investigated a novel negative sense priming site for NSP9, demonstrating a role in RNA production and viral replication. This straightforward reverse genetic system is therefore a powerful tool to generate recombinant viruses for advancing our understanding of SARS-CoV-2 biology.
Genome-wide CRISPR screen identifies AC9 as a key regulator of ER Ca2+homeostasis involved in neuronal differentiation
Authors: Wang Liuqing , Li Jia , Wang Yiping , Zhong Ziyi , Wang Yuqing , Huang Rui , Zhang Bingwei , Liu Panpan , Ye Erkejiang , Cao Ruotong , Ali Sher , Ke Yuepeng , Yang Junjie , Yokoyama Tatsushi , Liu Jin , Zhang Xiaoyan , Sakamoto Masayuki , Sun Lin , Zhou Yubin , Wang Youjun 
Published: February 2024

AbstractEndoplasmic reticulum (ER) calcium (Ca2+) homeostasis is essential for maintaining normal cellular physiological functions. Its disturbance is strongly linked to the onset and progression of human diseases, including cancer, developmental defects, and neurodegenerative disorders. The lack of sensitive ratiometric ER Ca2+indicators, nevertheless, hinders systematic investigation of ER Ca2+modulators and the underlying mechanisms. Capitalizing on two ultra-sensitive ER Ca2+indicators and CRISPR-based genome-wide screening, we identified a set of proteins capable of reducing the ER Ca2+content. Further comparative analysis and qPCR validation pinpointed adenylate cyclase 9 (AC9), which is upregulated during neuronal differentiation, as a key ER-Ca2+-reducing regulator. Mechanistically, AC9-mediated production of cAMP is not essential for its ability to reduce ER Ca2+content. Instead, AC9 inhibits store operated calcium entry (SOCE) by acting on Orai1, ultimately causing attenuation of ER Ca2+level. More physiologically relevant, upregulation of AC9 in neurons is essential for reducing ER Ca2+levels duringDrosophilabrain development. Collectively, this study lays a solid groundwork for further in-depth exploration of the regulatory mechanisms dictating ER Ca2+homeostasis during neuronal differentiation and brain development.
Neural signatures of opioid-induced risk-taking behavior in the prelimbic prefrontal cortex
Authors: Quave Cana B. , Vasquez Andres M. , Aquino-Miranda Guillermo , Marín Milagros , Bora Esha P. , Chidomere Chinenye L. , Zhang Xu O. , Engelke Douglas S. , Do-Monte Fabricio H. 
Published: February 2024

ABSTRACTOpioid use disorder occurs alongside impaired risk-related decision-making, but the underlying neural correlates are unclear. We developed an approach-avoidance conflict task using a modified conditioned place preference procedure to study neural signals of risky opioid seeking in the prefrontal cortex, a region implicated in executive decision-making. Following morphine conditioned place preference, rats underwent a conflict test in which fear-inducing cat odor was introduced in the previously drug-paired side of the apparatus. While the saline-exposed control group avoided cat odor, the morphine group included two subsets of rats that either maintained a preference for the paired side despite the presence of cat odor (Risk-Takers) or exhibited increased avoidance (Risk-Avoiders), as revealed by K-means clustering. Single-unit recordings from the prelimbic cortex (PL) demonstrated decreased neuronal activity upon acute morphine exposure in both Risk-Takers and Risk-Avoiders, but this firing rate suppression was absent after repeated morphine administration. Risk-Avoiders also displayed distinct post-morphine excitation in PL which persisted across conditioning. During the preference test, subpopulations of PL neurons in all groups were either excited or inhibited when rats entered the paired side. Interestingly, the inhibition in PL activity was lost during the subsequent conflict test in both saline and Risk-Avoider groups, but persisted in Risk-Takers. Additionally, Risk-Takers showed an increase in the proportion of PL neurons displaying location-specific firing in the drug-paired side from the preference to the conflict test. Together, our results suggest that persistent PL inhibitory signaling in the drug-associated context during motivational conflict may underlie increased risk-taking behavior following opioid exposure.SIGNIFICANCE STATEMENTRisky opioid use is well established in opioid use disorder, but the underlying neural correlates are poorly understood. In this study, we present findings from a novel behavioral task in which rats face a motivational conflict between contextual opioid reward memory and a naturalistic predator threat. Performing neuronal recordings in the prelimbic prefrontal cortex (PL), a brain region critical for executive decision-making, we demonstrate enhanced representation of drug-associated context and persistent inhibitory signaling by PL neurons that occur alongside opioid-induced risk-taking behavior. Our findings refine a preclinical model for studying addiction, establish PL as a prime region for investigating drug-environment interactions, and positions the prefrontal cortex as a candidate region for translational studies targeting risky opioid use.
The Optimization of High-Protein Duckweed Cultivation in Eutrophicated Water with Mutualistic Bacteria
Authors: Akkarajeerawat Sunyapat , Chauvanasmith Thanatkorn , Keatsirisart Chanan 
Published: February 2024

SUMMARYThe exponential increase in the human population is the leading cause of a global food crisis and the rise of humanity’s carbon footprint level. One such approach to resolve these issues is the cultivation of duckweed (Wolffia globosa) for consumption in the Northern and Northeastern provinces of Thailand. In particular, duckweed has drawn increasing attention due to its rapid growth rate, adaptability to extreme conditions, and potential as a protein alternative; however, their properties can be greatly enhanced. Our research investigates two optimizations for the cultivation of duckweeds: in the medium’s nitrogen-phosphorus concentration and the use of plant growth-promoting bacteria (PGPB). We hypothesized that using phosphorus-rich water and PGPB would significantly increase duckweed biomass production, while nitrogen-rich water would increase protein content. This was based on evidence from past research showing that aquatic plants have high nitrogen and phosphorus uptake and that PGPB can support the growth of plants by nitrogen fixation. We found that the phosphorus-rich group boosted biomass greatly, while the nitrogen-rich group significantly enhanced their protein value. Furthermore, PGPB yielded the highest increase in biomass, but had an insignificant impact on protein. Based on our results, we recommend the use of nitrogen and phosphorus-rich water and PGPB to optimize duckweed cultivation, addressing the global food crisis and environmental impact.
Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria
Authors: David Shannon C. , Schaub Aline , Terrettaz Céline , Motos Ghislain , Costa Laura J. , Nolan Daniel S. , Augugliaro Marta , Glas Irina , Pohl Marie O. , Klein Liviana K. , Luo Beiping , Bluvshtein Nir , Violaki Kalliopi , Hugentobler Walter , Krieger Ulrich K. , Peter Thomas , Stertz Silke , Nenes Athanasios , Kohn Tamar 
Published: February 2024

AbstractAerosol transmission remains a major challenge for the control of respiratory viruses, particularly for those that cause recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorganisms that populate the respiratory tract. The impact of microbial communities and inter-pathogen interactions upon the stability of transmitted viruses is well-characterised for pathogens of the gut, but is particularly under-studied in the respiratory niche. Here, we assessed whether the presence of 5 different species of common commensal respiratory bacteria could influence the stability of IAV within droplets deposited on surfaces and within airborne aerosol particles at typical indoor air humidity. It was found that bacterial presence within stationary droplets, either a mixed community or individual strains, resulted in 10- to 100-fold more infectious IAV remaining after 1 hour. Bacterial viability was not required for this viral stabilisation, though maintained bacterial morphology seemed to be essential. Additionally, non-respiratory bacteria tested here had little stabilising effect, indicating this phenomenon was respiratory-specific. The protective bacteria stabilised IAV in droplets via induction of early efflorescence due to flattened droplet morphology during drying. Even when no efflorescence occurred at high humidity or the bacteria-induced changes in droplet morphology were abolished by aerosolization instead of deposition on a well-plate, the bacteria remained protective. This indicates an additional stabilisation mechanism that is currently unknown. Notably, respiratory bacteria at equivalent density offered varying degrees of protection in droplets, with the Gram-positive speciesStaphylococcus aureusandStreptococcus pneumoniaebeing the most robustly stabilising. This suggests that the composition of an individual’s respiratory microbiota could be a previously un-considered host-specific factor influencing the efficacy of expelled viral spread. Identifying novel host-specific factors such as the commensal microbiota that can influence viral stability in the environment will further increase our understanding of individual transmission risks, and will provide novel opportunities to limit the spread of respiratory infections within our populations.SynopsisOur findings have significant environmental and health relevance, as they identify the host respiratory microbiota as a novel factor potentially contributing to environmental viral stability within indoor environments.
Nuclear pores safeguard the integrity of the nuclear envelope
Authors: Taniguchi Reiya , Orniacki Clarisse , Kreysing Jan Philipp , Zila Vojtech , Zimmerli Christian E. , Böhm Stefanie , Turoňová Beata , Kräusslich Hans-Georg , Doye Valérie , Beck Martin 
Published: February 2024

AbstractNuclear pore complexes (NPCs) constitute giant channels within the nuclear envelope that mediate nucleocytoplasmic exchange. NPC diameter is thought to be regulated by nuclear envelope tension, but how such diameter changes are physiologically linked to cell differentiation, where mechanical properties of nuclei are remodeled and nuclear mechanosensing occurs, remains unstudied. Here we used cryo-electron tomography to show that NPCs dilate during differentiation of mouse embryonic stem cells into neural progenitors. In Nup133-deficient cells, which are known to display impaired neural differentiation, NPCs however fail to dilate. By analyzing the architectures of individual NPCs with template matching, we revealed that the Nup133-deficient NPCs are structurally heterogeneous and frequently disintegrate, resulting in the formation of large nuclear envelope openings. We propose that the elasticity of the NPC scaffold mechanically safeguards the nuclear envelope. Our studies provide a molecular explanation for how genetic perturbation of scaffolding components of macromolecular complexes causes tissue-specific phenotypes.