bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of the causative pathogen in the 2023 conjunctivitis outbreak of Nepal using unbiased metagenomic next generation sequencing
Authors: Shrestha Eliya , Katuwal Nishan , Kharel Sitaula Ranju , Gurung Harimaya , Shrestha Aastha , Karki Pratap , Shrestha Rajeev
Published: April 2024

In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudden-onset redness, foreign body sensation, watery discharge, and occasional lid swelling. A majority of cases exhibited acute hemorrhagic conjunctivitis, with management involving ocular lubricants, personal hygiene, and topical antibiotics. This study details the genomic epidemiology and clinical characteristics of conjunctivitis cases during the outbreak. To understand the causative agents, conjunctival swabs from patients were evaluated using unbiased metagenomic next-generation sequencing (mNGS) in Illumina iSeq100 at Dhulikhel Hospital Kathmandu University Hospital. This case series revealed the presence of Enterovirus C (coxsackievirus strain A24) as the major pathogen responsible for the outbreak. This case series contributes valuable insights into the genomic diversity of conjunctivitis-associated viruses, highlighting the potential of mNGS in enhancing diagnostic capabilities and guiding public health responses.
Aggressive responses to rivals depend on the interaction between the vocal traits of territory-holder and mimicked intruders in a miniature tropical frog
Authors: Munoz Matias I. , Camargo-Rodriguez Nicolas , Halfwerk Wouter
Published: April 2024

Territory defence is an important aspect of animal behaviour, and tightly linked to rival assessment and species recognition processes. An important component of these two processes is signalling, and animals must decide how to respond to a challenge based on the signals they perceive from their rivals. Here we manipulated the note repetition rate of rocket frog calls to simulate rivals with high and low vocal performances, and tested the aggressive responses of males in the field. We found that the probability of aggression depended on the interaction between the stimulus treatment and the peak frequency of the territorial males. Low-frequency calling males were more likely to respond aggressively to the fast call, while high-frequency calling males showed a higher probability of aggression towards the slow call. Frogs that responded aggressively approached the slow call 2.4-times faster than the fast call. Low-frequency calling males also increased their peak frequencies in response to the playbacks, while high-frequency calling males did not modify their vocalizations. Body weight was not correlated with the peak frequency or the inter-note interval of males. Peak frequency and amplitude (loudness) are positively interrelated in frogs, and are potential indicators of the motivational state of the signaller. We argue that low-frequency males were not singing at their maximum capacity, and they increased their vocal output when challenged by a rival, especially when the rival was a high-performance individual. We show that rocket frog aggression depends on the temporal parameters of the rival, but also on how territory-holders compare their own calls to those of challengers in terms of their frequency, and therefore demonstrate that frogs pay attention to different aspects of signals during aggressive decision-making.
Human iPSCs from aged donors retain their mitochondrial aging signature
Authors: Lejri Imane , Cader Zameel , Grimm Amandine , Eckert Anne
Published: April 2024

Aging represents the main risk factor for developing neurodegenerative disorders. One of the hallmarks of aging is mitochondrial dysfunction. Age-related mitochondrial alterations have been shown to affect mitochondrial energy metabolism and redox homeostasis as well as mitochondrial dynamics. In the present study, we addressed the question of whether or not, induced pluripotent stem cells (iPSCs) may be used as a model of “aging in a dish” to identify therapies at alleviating the aging of mitochondria. Notably, we could demonstrate that compared to human iPSCs from young donors, those from aged donors show impaired mitochondrial bioenergetics and exhibit a rise in reactive oxygen species generation. Furthermore, we demonstrate that iPSCs from aged donors present low mitochondrial mass and alterations of the morphology of the mitochondrial network. This study provides evidence that the aging phenotype is present at the mitochondrial level in iPSCs from aged donors, ranging from bioenergetics to dynamics. Thus, this model can be used for high through put screening to identify drugs that improve mitochondrial function.

Graphical abstract
Identification and characterization of innate immunity inActinidia melanandrain response toPseudomonas syringaepv.actinidiae
Authors: Hemara Lauren M. , Chatterjee Abhishek , Yeh Shin-Mei , Chen Ronan K.Y. , Hilario Elena , Le Lievre Liam , Crowhurst Ross N. , Bohne Deborah , Arshed Saadiah , Patterson Haileigh R. , Barrett-Manako Kelvina , Thomson Susan , Allan Andrew C. , Brendolise Cyril , Chagné David , Templeton Matthew D. , Jayaraman Jay , Tahir Jibran
Published: April 2024

Pseudomonas syringaepv.actinidiaebiovar 3 (Psa3) has decimated kiwifruit orchards growing susceptible kiwifruitActinidia chinensisvarieties. Effector loss has occurred recently in Psa3 isolates from resistant kiwifruit germplasm, resulting in strains capable of partially overcoming resistance present in kiwiberry vines (A. arguta, A. polygama, andA. melanandra). Diploid maleA. melanandrarecognises several effectors, sharing recognition of at least one avirulence effector (HopAW1a) with previously studied tetraploid kiwiberry vines. Sequencing and assembly of theA. melanandragenome enabled the characterisation of the transcriptomic response of this non-host to wild-type and genetic mutants of Psa3.A. melanandraappears to mount a classic effector-triggered immunity (ETI) response to wildtype Psa3 V-13, as expected. Surprisingly, the type III secretion (T3S) system-lackingPsa3 V-13 ΔhrcCstrain did not appear to trigger pattern-triggered immunity (PTI) despite lacking the ability to deliver immunity-suppressing effectors. Contrasting theA. melanandraresponses to an effectorless Psa3 V-13 Δ33Estrain and to Psa3 V-13 ΔhrcCsuggested that PTI triggered by Psa3 V-13 was based on the recognition of the T3S itself. The characterisation of both ETI and PTI branches of innate immunity responses withinA. melanandrafurther enables breeding for durable resistance in future kiwifruit cultivars.
Brain and Blood Transcriptome-Wide Association Studies Identify Five Novel Genes Associated with Alzheimer’s Disease
Authors: Mews Makaela A. , Naj Adam C. , Griswold Anthony J. ,   Alzheimer’s Disease Genetics Consortium, Below Jennifer E. , Bush William S.
Published: April 2024

INTRODUCTION

Transcriptome-wide Association Studies (TWAS) extend genome-wide association studies (GWAS) by integrating genetically-regulated gene expression models. We performed the most powerful AD-TWAS to date, using summary statistics fromcis-eQTL meta-analyses and the largest clinically-adjudicated Alzheimer’s Disease (AD) GWAS.

METHODS

We implemented the OTTERS TWAS pipeline, leveragingcis-eQTL data from cortical brain tissue (MetaBrain; N=2,683) and blood (eQTLGen; N=31,684) to predict gene expression, then applied these models to AD-GWAS data (Cases=21,982; Controls=44,944).

RESULTS

We identified and validated five novel gene associations in cortical brain tissue (PRKAG1,C3orf62,LYSMD4,ZNF439,SLC11A2) and six genes proximal to known AD-related GWAS loci (Blood:MYBPC3; Brain:MTCH2,CYB561,MADD,PSMA5,ANXA11). Further, using causal eQTL fine-mapping, we generated sparse models that retained the strength of the AD-TWAS association forMTCH2,MADD,ZNF439,CYB561, andMYBPC3.

DISCUSSION

Our comprehensive AD-TWAS discovered new gene associations and provided insights into the functional relevance of previously associated variants.
Latiné immigrant heterogeneity: Striking health differences among Cuban refugee/migration waves to the United States
Authors: Hernandez M. , Perry G.H.
Published: April 2024

Latiné people differ markedly in our lived experiences in ways that are underappreciated. Meanwhile, variations in social experiences are known to be associated with differential health outcomes. We test whether immigration history is associated with health differences among U.S.-based Cuban refugees. Cubans from the circum-1980 Mariel Boatlift migration wave reported significantly higher instances of disability than Early Cuban Exiles, Freedom Flight refugees, and Special Period refugees. We also interviewed Miami-based Cubans. Participants described heightened discrimination in 1980s Cuba and U.S., which we hypothesize contributed to higher instances of disability refugees of that era. By understanding how differential social experiences shape health, we aim to provide a nuanced understanding of the social determinants of health and the ways adverse experiences can be combated.

One-Sentence Summary

Even within a Latiné community from a single country of origin, we find that differential social experiences of immigrating to the U.S. are associated with variation in health outcomes.
Increasing the resolution of malaria early warning systems for use by local health actors
Authors: Evans Michelle V , Ihantamalala Felana A , Randriamihaja Mauricianot , Herbreteau Vincent , Revillion Christophe , Catry Thibault , Delaitre Eric , Bonds Matthew H , Roche Benjamin , Mitsinjoniala Ezra , Ralaivavikoa Fianamirindra A , Razafinjato Bénédicte , Raobela Omega , Garchitorena Andres
Published: April 2024

Background: The increasing availability of electronic health system data and remotely-sensed environmental variables has led to the emergence of statistical models capable of producing malaria forecasts. Many of these models have been operationalized into malaria early warning systems (MEWSs), which provide predictions of malaria dynamics several months in advance at national and regional levels. However, MEWSs do not generally produce predictions at the village-level, the operational scale of community health systems and the first point of contact for the majority of rural populations in malaria-endemic countries. Methods: We developed a hyper-local MEWS for use within a health-system strengthening intervention in rural Madagascar. It combined bias-corrected, village-level case notification data with remotely sensed environmental variables at spatial scales as fine as a 10m resolution. A spatio-temporal hierarchical generalized linear regression model was trained on monthly malaria case data from 195 communities from 2017-2020 and evaluated via cross-validation. The model was then integrated into an automated workflow with environmental data updated monthly to create a continuously updating MEWS capable of predicting malaria cases up to three months in advance at the village-level. Predictions were transformed into indicators relevant to health system actors by estimating the quantities of medical supplies required at each health clinic and the number of cases remaining untreated at the community level. Results: The statistical model was able to accurately reproduce village-level case data, performing nearly five times as well as a null model during cross-validation. The dynamic environmental variables, particularly those associated with standing water and rice field dynamics, were strongly associated with malaria incidence, allowing the model to accurately predict future incidence rates. When compared to historical stock data, the MEWS predicted stock requirements within 50 units of reported stock requirements 68% of the time. Conclusion: We demonstrate the feasibility of developing an automatic, hyper-local MEWS leveraging remotely-sensed environmental data at fine spatial scales. As health system data become increasingly digitized, this method can be easily applied to other regions and be updated with near real-time health data to further increase performance.
Leveraging transformers and large language models with antimicrobial prescribing data to predict sources of infection for electronic health record studies
Authors: Yuan Kevin , Yoon Chang Ho , Gu Qingze , Munby Henry , Walker A Sarah , Zhu Tingting , Eyre David W
Published: April 2024

Background

Electronic health records frequently contain extensive unstructured free-text data, but extracting information accurately from these data and at scale is challenging. Using free-text from antibiotic prescribing data as an example, we investigate the performance of modern natural language processing methods (NLP) and large language models (LLMs) as tools for extracting features from medical records.

Methods

We used 938,150 hospital antibiotic prescriptions from Oxfordshire, UK. The 4000 most frequently used free-text indications justifying antibiotic use were labelled by clinical researchers into 11 categories describing the infection source/clinical syndrome being treated and used for model training. Traditional classification methods, fuzzy regex matching and n-grams with XGBoost, were compared against modern transformer models: we fine-tuned generic and domain-specific BERT models, fine-tuned GPT3.5, and investigated few-shot learning with GPT4. Models were evaluated on internal and external test datasets (2000 prescriptions each). Infection sources determined from ICD10 codes were also used for comparisons.

Results

In internal and external test datasets, the fine-tuned domain-specific Bio+Clinical BERT model averaged an F1 score of 0.97 and 0.98 respectively across the classes and outperformed the traditional regex (F1=0.71 and 0.74) and n-grams/XGBoost (F1=0.86 and 0.84). OpenAI’s GPT4 model achieved F1 scores of 0.71 and 0.86 without using labelled training data and a fine-tuned GPT3.5 model F1 scores of 0.95 and 0.97. Comparing infection sources extracted from ICD10 codes to those parsed from free-text indications, free-text indications revealed 31% more specific infection sources.

Conclusion

Modern transformer-based models can efficiently and accurately categorise semi-structured free-text in medical records, such as prescription free-text. Finetuned local transformer models outperform LLMs currently for structured tasks. Few shot LLMs match the performance of traditional NLP without the need for labelling. Transformer-based models have the potential to be used widely throughout medicine to analyse medical records more accurately, facilitating beter research and patient care.
Barriers and facilitators to physical activity among Black women: a qualitative systematic review and thematic synthesis
Authors: Howard Sherron L. , Bartholomew John B.
Published: April 2024

American Black women are less physically active than other American women. While several qualitative studies have investigated this issue, there has been no effort to synthesize this literature.

Purpose

This study aimed to utilize qualitative thematic synthesis to employ an intersectionality framework in synthesizing existing published qualitative studies on barriers to and facilitators of physical activity for Black women and reflect constructs related to (a) all American women, (b) Black Americans, and (c) Black women. This qualitative thematic synthesis included 18 studies published from 2011 to the present. Studies were coded for quality and then reviewed with their themes identified and inductively integrated across the studies. The resulting themes were then deductively placed within a broader structure of an intersectionality framework. Reflecting this framework, three categories were identified: (1) general experience of physical activity for women, regardless of race, with themes of (a) motivation, (b) structured support, (c) overall health, (d) environment; (2) general experiences of physical activity for Black Americans, with a sub-theme of (a) low access; and (3) specific, intersectional experiences of physical activity for Black women, with sub-themes of (a) black hair, and (b) body ideal. Our synthesis of the existing qualitative research revealed that Black women experience PA related to being a woman, to being Black, and to the intersectional nature of being a Black woman. Interventions might target these intersectional themes to tailor interventions to support PA in Black women.
Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML
Authors: Truong Peter , Shen Sylvie , Joshi Swapna , Islam Md Imtiazul , Zhong Ling , Raftery Mark J. , Afrasiabi Ali , Alinejad-Rokny Hamid , Nguyen Mary , Zou Xiaoheng , Bhuyan Golam Sarower , Sarowar Chowdhury H. , Ghodousi Elaheh S. , Stonehouse Olivia , Mohamed Sara , Toscan Cara E. , Connerty Patrick , Kakadia Purvi M. , Bohlander Stefan K. , Michie Katharine A. , Larsson Jonas , Lock Richard B. , Walkley Carl R. , Thoms Julie A. I. , Jolly Christopher J. , Pimanda John E.
Published: April 2024

Hypomethylating agents (HMAs) are frontline therapies effective at altering the natural course of Myelodysplastic Neoplasms (MDS) and Acute Myeloid Leukemia (AML).

However, acquired resistance and treatment failure are hallmarks of HMA therapy. To address this clinical need, we performed a genome-wide CRISPR-Cas9 screen in a human MDS-derived cell line, MDS-L, and identified TOPORS as a highly ranked loss-of-function target that synergizes with HMAs, reducing leukemic burden and improving survival in xenograft models. We demonstrate that the depletion of TOPORS mediates sensitivity to HMAs by predisposing leukemic blasts to an impaired DNA damage response (DDR) accompanied by an accumulation of SUMOylated DNMT1 in HMA-treated TOPORS-depleted cells. Importantly, the combination of HMAs with targeting of TOPORS did not functionally impair healthy hematopoiesis. While inhibitors of TOPORS are currently unavailable, we show that inhibition of protein SUMOylation (upstream of TOPORS functions) with TAK-981 partially phenocopies HMA-sensitivity and DDR impairment. Overall, our data suggest that the combination of HMAs with the inhibition of SUMOylation or TOPORS demonstrates a favourable therapeutic index and is a rational treatment framework for High-Risk MDS (HR-MDS) or AML.
Pangenomes of Human Gut Microbiota Uncover Links Between Genetic Diversity and Stress Response
Authors: Shoer Saar , Reicher Lee , Pilpel Yitzhak , Segal Eran
Published: April 2024

The human gut microbiota has been the subject of many studies, establishing its central role in host health and disease. Interplay between mutations, horizontal gene transfer, natural selection, and genetic drift, lead to genetic diversity within these species, resulting in different phenotypes and effects on the host. Pangenome represents the collective gene pool of different strains of the same species. Here, we created pangenomes for 728 human gut prokaryotic species, holding four times more genes than the highest quality individual genome, showcasing the genetic diversity inherent in the human gut population. We find these species have a core set of about a thousand genes that defines them, distinct even between closely related species, and an accessory set of genes that are unique to the different strains. Furthermore, we show a spectrum of microbial behavior, while some species exhibit a saturated or “closed” pangenome, suggesting a limited set of genetic capabilities, others maintain an “open” pangenome, indicating elevated adaptability through genetic diversity. We discover that high strain variability is associated with the capacity of species to undergo sporulation, whereas low strain variability is associated with carrying genes that facilitate antibiotic resistances, suggesting different evolutionary strategies for survival taken by these microbes. We further map the landscape of antibiotic resistance genes across the human gut population, and find 237 cases of extreme resistance, predominantly of Enterobacteriaceae species, even to last resort antibiotics kept for cases where traditional treatments have failed. Lastly, we associate microbial strain level differences with human age and sex, exemplifying how the presence of specific genes inAkkermansia muciniphilaandPhocaeicola vulgatusrelate to host characteristics. Overall, our research provides a comprehensive overview of the evolution, genetic complexity and functional potential of the human gut microbiota, emphasizing its significant implications for human health and disease. The pangenomes and the antibiotic resistances map constitute a valuable resource for further scientific research and therapeutic advancements.
Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites
Authors: Abaeva Irina S. , Pestova Tatyana V. , Hellen Christopher U. T.
Published: April 2024

Viral internal ribosomal entry sites (IRESs) form several classes that use distinct mechanisms to mediate end-independent initiation of translation. The origin of viral IRESs is a longstanding question. The simplest IRESs comprise tandem pseudoknots and occur in the intergenic region (IGR) ofDicistroviridaegenomes (orderPicornavirales). Larger IGR IRESs contain additional elements that determine specific properties such as binding to the head of the ribosoma l 40S subunit. Metagenomic analyses reported here identified novel groups of structurally distinct IGR-like IRESs. The smallest of these (∼120nt long) comprise three pseudoknots and bind directly to the ribosomal P site. Others are up to 260nt long: insertions occurred at specific loci, possibly reflecting non-templated nucleotide insertion during replication. Various groups can be arranged in order, differing by the cumulative addition of single structural elements, suggesting an accretion mechanism for the structural elaboration of IRESs. Identification of chimeric IRESs implicates recombinational exchange of domains as a second mechanism for the diversification of IRES structure. Recombination likely also accounts for the presence of IGR-like IRESs at the 5’-end of some dicistrovirus-like genomes (e.g. Hangzhou dicistrovirus 3) and in the RNA genomes ofTombusviridae(orderTolivirales),Marnaviridae(orderPicornavirales), and the ‘Ripiresk’ picorna-like clade (orderPicornavirales).
The variable genomic landscape during osteosarcoma progression: insights from a longitudinal WGS analysis
Authors: Meijer Debora M. , Ruano Dina , Briaire-de Bruijn Inge H. , Wijers-Koster Pauline M. , van de Sande Michiel A.J. , Gelderblom Hans , Cleton-Jansen Anne-Marie , de Miranda Noel F.C.C. , Kuijjer Marieke L. , Bovée Judith V.M.G.
Published: April 2024

Osteosarcoma is a primary bone tumor that exhibits a complex genome characterized by gross chromosomal abnormalities. Osteosarcoma patients often develop metastatic disease, resulting in limited therapeutic options and poor survival rates. To gain knowledge on the mechanisms underlying osteosarcoma heterogeneity and metastatic process, it is important to obtain a detailed profile of the genomic alterations that accompany osteosarcoma progression. We performed WGS on multiple tissue samples from six patients with osteosarcoma, including the treatment naïve biopsy of the primary tumor, resection of the primary tumor after neoadjuvant chemotherapy, local recurrence and distant metastases. SNVs and structural variants were found to accumulate over time, contributing to an increased complexity of the genome of osteosarcoma during progression. Phylogenetic trees based on SNVs and structural variants reveal distinct evolutionary patterns between patients, including linear, neutral and branched patterns. The majority of osteosarcomas showed variable copy number profiles or gained whole genome doubling in later occurrences. Additionally, chromothripsis is not confined to a single early event, as multiple other chromothripsis events may appear in later occurrences. Together, we provide a detailed analysis of the complex genome of osteosarcomas and show that five out of six osteosarcoma genomes are highly dynamic and variable during progression.
Differential risk of cardiovascular complications in patients with adult type-2 diabetes mellitus in Ghana using clustering analysis: A hospital-based cross-sectional study
Authors: Obirikorang Christian , Adu Evans Asamoah , Afum-Adjei Awuah Anthony , Darko Samuel Nkansah , Ghartey Frank Naku , Ametepe Samuel , Nyarko Eric NY , Anto Enoch Odame
Published: April 2024

Aim

To characterize clinically relevant subgroups of patients with T2DM based on adiposity, insulin secretion, and resistance indices.

Methods

A cross-sectional study was conducted at Eastern Regional Hospital in Ghana from July to October 2021 to investigate long-term patients with T2DM. To select participants, a systematic random sampling method was employed. Demographic data was collected using a structured questionnaire and fasting blood samples were taken to measure glycemic and lipid levels. Blood pressure and adiposity indices were measured during recruitment. The risk of cardiovascular disease (CVD) was defined using Framingham scores and standard low-density lipoprotein thresholds. To analyze the data, k-means clustering algorithms and regression analysis were used.

Results

The study identified three groups in female patients according to body mass index, relative fat mass, glycated hemoglobin, and triglyceride-glucose index. These groups included the obesity-related phenotype, the severe insulin resistance phenotype, and the normal weight phenotype with improved insulin resistance. Among male patients with T2DM, two groups were identified, including the obesity-related phenotype with severe insulin resistance and the normal weight phenotype with improved insulin sensitivity. The severe insulin resistance phenotype in female patients was associated with an increased risk of high CVD (OR=5.34, 95%CI:2.11-13.55) and MetS (OR=7.07; 95%CI:3.24-15.42). Among male patients, the obesity-related phenotype with severe insulin resistance was associated with an increased intermediate (OR=21.78, 95%CI:4.17-113.78) and a high-risk CVD (OR=6.84, 95%CI:1.45-32.12).

Conclusions

The findings suggest that there are specific subgroups of patients with T2DM characterized by obesity and uncontrolled insulin resistance leading to poor glycemic control. This underscores the importance of considering differences in adiposity, insulin secretion, and sensitivity indices when making clinical decisions for patients with T2DM.
High measles and rubella vaccine coverage and seroprevalence among Zambian children participating in a measles and rubella supplementary immunization activity
Authors: Prosperi Christine , Truelove Shaun A. , Carcelen Andrea C. , Chongwe Gershom , Mwansa Francis D. , Ndubani Phillimon , Simulundu Edgar , Bwalya Innocent C. , Hamahuwa Mutinta , Kapungu Kelvin , Matakala Kalumbu H. , Musukwa Gloria , Mutale Irene , Betha Evans , Chaavwa Nchimunya , Kampamba Lombe , Matoba Japhet , Munachoonga Passwell , Mufwambi Webster , Situtu Ken , Thuma Phillip E. , Sakala Constance , Kayeye Princess , Winter Amy K. , Ferrari Matthew J , Moss William J. , Mutembo Simon
Published: April 2024

Post-campaign coverage surveys estimate the number and proportion of previously unvaccinated children vaccinated during a supplementary immunization activity (SIA) but cannot address whether susceptible children seronegative to measles and rubella viruses were vaccinated during the SIA.

We conducted a cross-sectional serosurvey nested within the November 2020 measles-rubella SIA in Zambia. Children aged 9 months to 5 years were systematically sampled at 30 SIA sites in Choma and Ndola Districts. A questionnaire was administered to the caregiver to collect the child’s demographic information and history of routine measles-rubella (MR) vaccination, and dried blood spot specimens were collected from the child. Specimens were tested for Immunoglobulin-G antibodies to measles and rubella viruses by enzyme immunoassay.

Among children enrolled with MR vaccination data (N=2,364), 2,214 (94%) reported at least one routine MR dose before the SIA. We estimate 5.0% (118/2364) of children would not have otherwise received routine MR dose 1 without the SIA and 23.4% (553/2364) would not have otherwise received routine MR dose 2. Thus, 1 in 3.5 doses were given to an MR un- or under-vaccinated child who may not have received that dose in the absence of an SIA. Eighty-six percent of children were measles seropositive and 90% were rubella seropositive before vaccination during the SIA. Thirty-six percent of children with no prior routine MR dose were measles seropositive while nine percent of children with two prior routine MR doses were measles seronegative.

Although children vaccinated during this SIA were highly likely to already have received routine vaccinations, the SIA reached a considerable number of susceptible children. Monitoring SIA effectiveness and efficiency is important to understand the benefits of vaccine delivery strategies in reaching un- and under-vaccinated children and may guide alternative strategies.
CerebellarEx VivoMagnetic Resonance Imaging at its Feasibility Limit: Up to 77-Microns Isotropic Resolution using Low-Bandwidth Balanced Steady State Free Precession (LoBa-bSSFP) Sequences and 3T Standard Equipment
Authors: Weigel Matthias , Dechent Peter , Galbusera Riccardo , Bahn Erik , Lu Po-Jui , Kappos Ludwig , Brück Wolfgang , Stadelmann Christine , Granziera Cristina
Published: April 2024

Background

Ultra-high-resolution magnetic resonance imaging of the ex vivo brain is increasingly becoming an indispensable tool for studying the morphology and potential pathology of the brain. Despite the important role of the cerebellum in nervous system functions and motor control, as well as its potential damage in neurological diseases, it remains relatively understudied compared to other brain regions. One major reason is the even finer structures.

Methods

A balanced steady state free precession approach with receiver bandwidths as low as 50Hz/pixel and long repetition times of 36ms is suggested and optimized, called “LoBa-bSSFP”, which enhances the signal-to-noise ratio and alleviates strain on the gradient system for the ultra-high spatial resolutions. A radiofrequency phase cycle scheme is used to reduce potential artifacts. Only 3T MRI standard equipment is utilized for acquisition and basic image reconstruction of the ex vivo brain immersed in perfluoropolyether.

Results

The presented LoBa-bSSFP approach provides images with very good soft tissue contrast and a detailed visualization of cerebellar morphology. It enables isotropic resolutions of 98-microns for the entire cerebellum, a further refinement allows even up to 77-microns isotropic on a purely clinical MR system. The acquisitions preserved the integrity of the ex vivo cerebellum, so maintaining its connection to the cerebrum and brainstem.

Conclusions

Our findings demonstrate the feasibility of employing 3T based LoBa-bSSFP for true ultra-high-resolution ex vivo imaging of the cerebellum, reaching resolutions up to 77-microns isotropic and the potential to reveal subtle microscopic abnormalities of the cerebellar cortex. LoBa-bSSFP may be superior to conventional FLASH sequences in terms of acquisition efficiency and - in some cases - even contrast.
Arabidopsis produces distinct subpopulations of extracellular vesicles that respond differentially to biotic stress
Authors: Koch Benjamin L. , Rutter Brian D. , Innes Roger W.
Published: April 2024

Extracellular vesicles (EVs) secreted by mammalian cells are highly heterogenous in contents and function. Whether this is also true for EVs secreted by plant cells is not yet known. To address this knowledge gap, we used high-resolution density gradient ultracentrifugation to separate distinct subpopulations of Arabidopsis EVs. We analyzed the protein content, morphology, and purity of these subpopulations, confirming the presence of three distinct EV subpopulations. The EV marker protein TETRASPANIN 8 (TET8) was detected only in medium-density EVs and was not associated with cell wall nanofilaments, which was unique among EV proteins. TET8 and PENETRATION 1 (PEN1) were confirmed to be secreted on mostly separate EV populations using total internal fluorescence microscopy. We found that EV marker proteins are differentially secreted in response to phytohormones, changes in growth temperature, and infection with fungal pathogensColletotrichumandGolovinomyces cichoracearum. EV subpopulations marked by TET8, PEN1, and RPM1-INTERACTING PROTEIN 4 (RIN4) were highly increased as soon as one day after fungal infection, while other EV populations remained unaffected. Together these data indicate that Arabidopsis EVs are highly heterogenous and suggest that specific EV subpopulations may contribute to plant immunity.
SLC17 transporters mediate renal excretion of Lac-Phe in mice and humans
Authors: Li Veronica L. , Xiao Shuke , Schlosser Pascal , Scherer Nora , Wiggenhorn Amanda L. , Spaas Jan , Tung Alan Sheng-Hwa , Karoly Edward D. , Köttgen Anna , Long Jonathan Z.
Published: April 2024

N-lactoyl-phenylalanine (Lac-Phe) is a lactate-derived metabolite that suppresses food intake and body weight. Little is known about the mechanisms that mediate Lac-Phe transport across cell membranes. Here we identify SLC17A1 and SLC17A3, two kidney-restricted plasma membrane-localized solute carriers, as physiologic urine Lac-Phe transporters. In cell culture, SLC17A1/3 exhibit high Lac-Phe efflux activity. In humans, levels of Lac-Phe in urine exhibit a strong genetic association with theSLC17A1-4locus. Urine Lac-Phe levels are also increased following a Wingate sprint test. In mice, genetic ablation of either SLC17A1 or SLC17A3 reduces urine Lac-Phe levels. Despite these differences, both knockout strains have normal blood Lac-Phe and body weights, demonstrating that urine and plasma Lac-Phe pools are functionally and biochemically de-coupled. Together, these data establish SLC17 family members as the physiologic urine transporters for Lac-Phe and uncover a biochemical pathway for the renal excretion of this signaling metabolite.
Evolution engineering of methylotrophic E. coli enables faster growth than native methylotrophs
Authors: Nieh Liang-Yu , Chen Frederic Y.-H. , Jung Hsin-Wei , Su Kuan-Yu , Tsuei Chao-Yin , Lin Chun-Ting , Lee Yue-Qi , Liao James C.
Published: April 2024

As methanol can be derived from either CO2or methane, methanol economy may play a role in combating climate change. In this scenario, rapid utilization of methanol by an industrial microorganism is the first and crucial step for efficient utilization of the C1 feedstock chemical. Here, we report the development of a methylotrophic E. coli strain (SM6) with a doubling time of 3.5 hours, outpacing that of common native methylotrophs. We accomplish this using evolution engineering with dynamic copy number variation (CNV). We developed a bacterial artificial chromosome (BAC) with dynamic CNV to facilitate overcoming the formaldehyde-induced DNA-protein cross-linking (DPC) problem in the evolution process. The growth rate of the organism in methanol minimal medium improved significantly after it acquired a loss-of-function mutation inmutS. We tracked the genome variations of 72 cultures along the evolution process by next-generation sequencing, and identified the metabolic features of the fast-growing strain. This study illustrates the potential of dynamic CNV as an evolution tool and synthetic methylotrophs as a platform for sustainable biotechnological applications.
Delineation of the Complete Reaction Cycle of a Natural Diels-Alderase
Authors: Maschio Laurence , Back Catherine R , Alnawah Jawaher , Bowen James I , Johns Samuel T , Mbatha Sbusisiwe Z , Han Li-Chen , Lees Nicholas R , Zorn Katja , Stach James E M , Hayes Martin A , van der Kamp Marc W , Pudney Christopher R , Burston Steven G , Willis Christine L , Race Paul R
Published: April 2024

The Diels-Alder reaction is one of the most effective methods for the synthesis of substituted cyclohexenes. The development of protein catalysts for this reaction remains a major priority, affording new sustainable routes to high value target molecules. Whilst a small number of natural enzymes have been shown capable of catalysing [4+2] cycloadditions, there is a need for significant mechanistic understanding of how these prospective Diels-Alderases promote catalysis to underpin their development as biocatalysts for use in synthesis. Here we present a molecular description of the complete reaction cycle of the bona fide natural Diels-Alderase AbyU, which catalyses formation of the spirotetronate skeleton of the antibiotic abyssomicin C. This description is derived from X-ray crystallographic studies of AbyU in complex with a non-transformable synthetic substrate analogue, together with transient kinetic analyses of the AbyU catalysed reaction and computational reaction simulations. These studies reveal the mechanistic intricacies of this enzyme system and establish a foundation for the informed reengineering of AbyU and related biocatalysts.
nP-collabs: Investigating counterion mediated bridges in the multiply phosphorylated tau-R2 repeat
Authors: Marien Jules , Prévost Chantal , Sacquin-Mora Sophie
Published: April 2024

Tau is an instrinsically disordered (IDP), microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated via multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer’s disease. Using all-atom molecular dynamics (MD) simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289 and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs, and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termednP-collab(for nPhosphate collaboration, withnbeing an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations, and is likely to impact the peptide overall dynamics, and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidues spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one to six residues apart. Three new metrics specifically tailored for IDPs (Proteic Menger Curvature, Local Curvature and Local Flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.

Abstract Figure
ACE2-independent sarbecovirus cell entry is supported by TMPRSS2-related enzymes and reduces sensitivity to antibody-mediated neutralization
Authors: Zhang Lu , Cheng Hsiu-Hsin , Krüger Nadine , Hörnich Bojan , Graichen Luise , Hahn Alexander S. , Schulz Sebastian R. , Jäck Hans-Martin , Stankov Metodi V. , Behrens Georg M.N. , Müller Marcel A. , Drosten Christian , Mörer Onnen , Winkler Martin Sebastian , Qian ZhaoHui , Pöhlmann Stefan , Hoffmann Markus
Published: April 2024

The COVID-19 pandemic, caused by SARS-CoV-2, demonstrated that zoonotic transmission of animal sarbecoviruses threatens human health but the determinants of transmission are incompletely understood. Here, we show that most spike (S) proteins of horseshoe bat and Malayan pangolin sarbecoviruses employ ACE2 for entry, with human and raccoon dog ACE2 exhibiting broad receptor activity. The insertion of a multibasic cleavage site into the S proteins increased entry into human lung cells driven by most S proteins tested, suggesting that acquisition of a multibasic cleavage site might increase infectivity of diverse animal sarbecoviruses for the human respiratory tract. In contrast, two bat sarbecovirus S proteins drove cell entry in an ACE2-independent, trypsin-dependent fashion and several ACE2-dependent S proteins could switch to the ACE2-independent entry pathway when exposed to trypsin. Several TMPRSS2-related cellular proteases but not the insertion of a multibasic cleavage site into the S protein allowed for ACE2-independent entry in the absence of trypsin and may support viral spread in the respiratory tract. Finally, the pan-sarbecovirus antibody S2H97 enhanced cell entry driven by two S proteins and this effect was reversed by trypsin. Similarly, plasma from quadruple vaccinated individuals neutralized entry driven by all S proteins studied, and use of the ACE2-independent, trypsin-dependent pathway reduced neutralization sensitivity. In sum, our study reports a pathway for entry into human cells that is ACE2-independent, supported by TMPRSS2-related proteases and associated with antibody evasion.
Proteomic Insights into Circadian Transcription Regulation: Novel E-box Interactors Revealed by Proximity Labeling
Authors: Torres Manon , Kramer Achim
Published: April 2024

Circadian clocks (∼24h) are responsible for daily physiological, metabolic and behavioral changes. Central to these oscillations is the regulation of gene transcription. Previous research has identified clock protein complexes that interact with the transcriptional machinery to orchestrate circadian transcription, but technological constraints have limited the identification of de novo proteins. Here we use a novel genomic locus-specific quantitative proteomics approach to provide a new perspective on time-of-day-dependent protein binding at a critical chromatin locus involved in circadian transcription - the E-box. Using proximity labeling proteomics at the E-box of the clock-controlledDbpgene in mouse fibroblasts, we identified 69 proteins at this locus at the time of BMAL1 binding. This method successfully enriched BMAL1 as well as HDAC3 and HISTONE H2A.V/Z, known circadian regulators. New E-box proteins include the MINK1 kinase and the XPO7 transporter, whose depletion in human U-2 OS cells results in disrupted circadian rhythms suggesting a role in the circadian transcriptional machinery. Overall, our approach uncovers novel circadian modulators and provides a new strategy to obtain a complete temporal picture of circadian transcriptional regulation.
Anchoring functional connectivity to individual sulcal morphology yields insights in a pediatric study of reasoning
Authors: Häkkinen Suvi , Voorhies Willa I. , Willbrand Ethan H. , Tsai Yi-Heng , Gagnant Thomas , Yao Jewelia K. , Weiner Kevin S. , Bunge Silvia A.
Published: April 2024

A salient neuroanatomical feature of the human brain is its pronounced cortical folding, and there is mounting evidence that sulcal morphology is relevant to functional brain architecture and cognition. However, our understanding of the relationships between sulcal anatomy, brain activity, and behavior is still in its infancy. We previously found the depth of three small, shallow sulci in lateral prefrontal cortex (LPFC) was linked to reasoning performance in childhood and adolescence (Voorhies et al., 2021). These findings beg the question: what is the linking mechanism between sulcal morphology and cognition? To shed light on this question, we investigated functional connectivity among sulci in LPFC and lateral parietal cortex (LPC). We leveraged manual parcellations (21 sulci/hemisphere, total of 1806) and functional magnetic resonance (fMRI) data from a reasoning task from 43 participants aged 7–18 years (20 female). We conducted clustering and classification analyses of individual- level functional connectivity among sulci. Broadly, we found that 1) the connectivity patterns of individual sulci could be differentiated – and more accurately than rotated sulcal labels equated for size and shape; 2) sulcal connectivity did not consistently correspond with that of probabilistic labels or large-scale networks; 3) sulci clustered together into groups with similar patterns, not dictated by spatial proximity; and 4) across individuals, greater depth was associated with higher network centrality for several sulci under investigation. These results highlight that functional connectivity can be meaningfully anchored to individual sulcal anatomy, and demonstrate that functional network centrality can vary as a function of sulcal depth.

Significance Statement

A salient, and behaviorally relevant, feature of the human brain is its pronounced cortical folding. However, the links between sulcal anatomy and brain function are still poorly understood – particularly for small, shallow, individually variable sulci in association cortices. Here, focusing on individually defined sulci in lateral prefrontal and parietal regions, we offer a novel, anatomically informed approach to defining functional connectomes. Further, we demonstrate, for the first time, a link between functional network centrality and sulcal morphology.
Origin of the intermediate-temperature magnetic specific heat capacity in the spin-liquid candidate
Ca10Cr7O28
Authors: Crossley Joe , Hooley Chris
Published: April 2024

We present several approximate calculations of the specific heat capacity of the model for Ca10Cr7O28 proposed by Balz [], using methods including exact diagonalization, thermal pure quantum states, and high-temperature expansions. In none of these cases are we able to reproduce the magnitude of the zero-field specific heat capacity shown in the intermediate-temperature (∼5–15K) experimental data. We discuss possible reasons for the discrepancy, and what it might tell us about the magnetic Hamiltonian for Ca10Cr7O28.

Published by the American Physical Society
2024
Muon
g−2
and proton lifetime in SUSY SU(5) GUTs with split superpartners
Authors: Kim Seong-Sik , Lee Hyun Min , Sim Sung-Bo
Published: April 2024

We consider the interplay of the muon g−2 anomaly and the proton decay in the supersymmetry (SUSY) SU(5) grand unified theories (GUTs) with generation-independent scalar soft masses. In these scenarios, we introduce a number of 5+5¯ messenger fields with doublet-triplet splitting in general gauge mediation to transmit SUSY breaking to the visible sector by gauge loops. As a result, squarks and sleptons receive generation-independent soft SUSY breaking masses, which are split already at the messenger scale. Taking into account the perturbative unification of gauge couplings as well as the bounds from electroweak precision and vacuum stability bounds, we showed the parameter space in general gauge mediation to explain the muon g−2 anomaly with smuon and sneutrino loops while evading the strong bounds on squarks and gluinos from the Large Hadron Collider. We also obtained the dominant Higgsino contributions to the proton decay mode, p→K+ν¯, with general generation-independent sparticle masses for squarks and sleptons. Even for split scalar soft masses in our model, however, we found that the bounds from the proton decay are satisfied only if the effective Yukawa couplings of the colored Higgsinos are suppressed further by a factor of order

10

−

4

–

10

−

3

. We illustrated how such a suppression factor is realized in orbifold GUTs in the extra dimension where the colored Higgsinos in the bulk are not coupled to the matter fields localized at the orbifold fixed points at the leading order.

Published by the American Physical Society
2024