bluuebunny/crossref_metadata_2025 huggingface dataset:
Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov., isolated from desert soil, and reclassification of Pedobacter xinjiangensis as Desertivirga xinjiangensis comb. nov. and Pedobacter mongoliensis as Paradesertivirga mongoliensis gen.nov., comb. nov.
Authors: Li Shuai , Liu Jun , Huang Jie , Mo Yi-Jun , Lian Wen-Hui , Yue Ling-Xiang , Zhao Guo-Zhen , Dong Lei , Li Wen-Jun
Published: May 2024

Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0 % 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1 % and 96.0 % similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA–DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0 % and <24.0 %, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4 % and 40.5 % DNA G+C contents, respectively. The predominant fatty acids (>10 %) of SYSU D00823T and SYSU D00873T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.
Pharmacological Ascorbate Induces Transient Hypoxia Sensitizing Pancreatic Ductal Adenocarcinoma to a Hypoxia Activated Prodrug
Authors: Kishimoto Shun , Crooks Daniel R. , Yasunori Otowa , Kota Yamashita , Yamamoto Kazutoshi , Linehan W. Marston , Levine Mark , Krishna Murali C , Brender Jeffrey R
Published: May 2024

Hypoxic tumor microenvironments pose a significant challenge in cancer treatment. Hypoxia-activated prodrugs like evofosfamide aim to specifically target and eliminate these resistant cells. However, their effectiveness is often limited by reoxygenation after cell death. We hypothesized that ascorbate’s pro-oxidant properties could be harnessed to induce transient hypoxia, enhancing the efficacy of evofosfamide by overcoming reoxygenation.

To test this hypothesis, we investigated the sensitivity of MIA Paca-2 and A549 cancer cells to ascorbate in vitro and in vivo. Ascorbate induced a cytotoxic effect at 5 mM that could be alleviated by endogenous administration of catalase, suggesting a role for hydrogen peroxide in its cytotoxic mechanism. In vitro, Seahorse experiments indicated generation of hydrogen peroxide consumes oxygen, which is offset at later time points by a reduction in oxygen consumption due to hydrogen peroxide’s cytotoxic effect.

In vivo, photoacoustic imaging showed ascorbate treatment at sublethal levels triggered a complex, multi-phasic response in tumor oxygenation across both cell lines. Initially, ascorbate generated transient hypoxia within minutes through hydrogen peroxide production, via reactions that consume oxygen. This initial hypoxic phase peaked at around 150 seconds and then gradually subsided. However, at longer time scales (approximately 300 seconds) a vasodilation effect triggered by ascorbate resulted in increased blood flow and subsequent reoxygenation. Combining sublethal levels of ascorbate with evofosfamide significantly prolonged tumor doubling time in MIA Paca-2 and A549b xenografts compared to either treatment alone. This improvement, however, was only observed in a subpopulation of tumors, highlighting the complexity of the oxygenation response.
Genetic and environmental contributions to eigengene expression
Authors: Gillespie Nathan A , Bell Tyler R. , Hearn Gentry C , Hess Jonathan L. , Tsuang Ming T. , Lyons Michael J. , Franz Carol E. , Kremen William S. , Glatt Stephen J.
Published: May 2024

Multivariate network-based analytic methods such as weighted gene co-expression network analysis are being increasingly applied to human and animal gene-expression data to estimate module eigengenes (MEs). MEs represent multivariate summaries of correlated gene-expression patterns and network connectivity across genes within a module. Although this approach has the potential to elucidate the mechanisms by which molecular genomic variations contribute to individual differences in complex traits, the genetic etiology of MEs has never been empirically established. It is unclear if and to what degree individual differences in blood derived MEs reflect random variation versus familial aggregation arising from heritable or shared environmental influences. We used biometrical genetic analyses to estimate the contribution of genetic and environmental influences on MEs derived from blood lymphocytes collected on a sample of N=661 older male twins from the Vietnam Era Twin Study of Aging (VETSA) whose mean age at assessment was 67.7 years (SD=2.6 years, range=62-74 years). Of the 26 detected MEs, 14 (56%) had statistically significant additive genetic variation with an average heritability of 44% (SD=0.08, range=35-64%). Despite the relatively small sample size, this demonstration of significant family aggregation including estimates of heritability in 14 of the 26 MEs suggests that blood-based MEs are reliable and merit further exploration in terms of their associations with complex traits and diseases.
Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility
Authors: VanderWaal Kimberly , Pamornchainvakul Nakarin , Kikuti Mariana , Linhares Daniel , Trevisan Giovani , Zhang Jianqiang , Anderson Tavis K. , Zeller Michael , Rossow Stephanie , Holtkamp Derald J. , Makau Dennis N. , Corzo Cesar A. , Paploski Igor A.D.
Published: May 2024

Disease management and epidemiological investigations of porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2) often rely on grouping together highly related sequences. In the USA, the last five years have seen a major paradigm shift within the swine industry when classifying PRRSV-2, beginning to move away from RFLP (restriction fragment length polymorphisms)-typing and adopting the use of phylogenetic lineage-based classification. However, lineages and sub-lineages are large and genetically diverse, and the rapid mutation rate of PRRSV coupled with the global prevalence of the disease has made it challenging to identify new and emerging variants. Thus, within the lineage system, a dynamic fine-scale classification scheme is needed to provide better resolution on the relatedness of PRRSV-2 viruses to inform disease management and monitoring efforts and facilitate research and communication surrounding circulating PRRSV viruses. Here, we compare potential fine-scale systems for classifying PRRSV-2 variants (i.e., genetic clusters of closely related ORF5 sequences at finer scales than sub-lineage) using a database of 28,730 sequences from 2010 to 2021, representing >55% of the U.S. pig population. In total, we compared 140 approaches that differed in their tree-building method, criteria, and thresholds for defining variants within phylogenetic trees usingTreeCluster.

Three approaches produced epidemiologically meaningful variants (i.e., ≥5 sequences per cluster), and resulted in reproducible and robust outputs even when the input data or input phylogenies were changed. In the three best performing approaches, the average genetic distance amongst sequences belonging to the same variant was 2.1 – 2.5%, and the genetic divergence between variants was 2.5-2.7%. Machine learning classification algorithms were also trained to assign new sequences to an existing variant with >95% accuracy, which shows that newly generated sequences could be assigned without repeating the phylogenetic and clustering analyses. Finally, we identified 73 sequence-clusters (dated <1 year apart with close phylogenetic relatedness) associated with circulation events on single farms. The percent of farm sequence-clusters with an ID change was 6.5-8.7% for our best approaches. In contrast, ∼43% of farm sequence-clusters had variation in their RFLP-type, further demonstrating how our proposed fine-scale classification system addresses shortcomings of RFLP-typing. Through identifying robust and reproducible classification approaches for PRRSV-2, this work lays the foundation for a fine-scale system that would more reliably group related field viruses and provide better improved clarity for decision-making surrounding disease management.
Inference of continuous gene flow between species under misspecified models
Authors: Thawornwattana Yuttapong , Flouri Tomáš , Mallet James , Yang Ziheng
Published: May 2024

Gene flow between species is increasingly recognized as an important evolutionary process with potential adaptive consequences. Recent methodological advances make it possible to infer different modes of gene flow from genome-scale data, including pulse introgression at a specific time and continuous gene flow over an extended time period. However, it remains challenging to infer the history of species divergence and between-species gene flow from genomic sequence data. As a result, models used in real data analysis may often be misspecified, potentially leading to incorrect biological interpretations. Here, we characterize biases in parameter estimation under continuous migration models using a combination of asymptotic analysis and posterior inference from simulated datasets. When sequence data are generated under a pulse introgression model, isolation-with-initial-migration models assuming no recent gene flow are able to better recover gene flow with less bias than models that assume recent gene flow. When gene flow is assigned to an incorrect branch in the phylogeny, there may be large biases associated with the migration rate and species divergence times. When the direction of gene flow is incorrectly assumed, we may still detect gene flow if it is recent and between non-sister species but not when it is ancestral and between sister species. Overall, the impact of model misspecification is local in the species phylogeny. The pulse introgression model appears to be more robust to model misspecification and is preferable in real data analysis over the continuous migration model unless there is substantive evidence for continuous gene flow.
A selective GSK3β inhibitor, tideglusib, decreases intermittent access and binge ethanol self-administration in C57BL/6J mice
Authors: Gottlieb Sam , van der Vaart Andrew , Hassan Annalise , Bledsoe Douglas , Morgan Alanna , O’Rourke Brennen , Rogers Walker D. , Wolstenholme Jennifer T. , Miles Michael F.
Published: May 2024

Over 10% of the US population over 12 years old meets criteria for Alcohol Use Disorder (AUD), yet few effective, long-term treatments are currently available. Glycogen synthase kinase 3 beta (GSK3β) has been implicated in ethanol behaviors and poses as a potential therapeutic target in the treatment of AUD. Here we investigate the role of tideglusib, a selective GSK3β inhibitor, in ethanol consumption and other behaviors. We have shown tideglusib decreases ethanol consumption in both a model of daily, progressive ethanol intake (two-bottle choice, intermittent ethanol access) and binge-like drinking behavior (drinking-in-the-dark) without effecting water intake. Further, we have shown tideglusib to have no effect on ethanol pharmacokinetics, taste preference, or anxiety-like behavior, though there was a transient increase in total locomotion following treatment. Additionally, we assessed liver health following treatment via serum levels of alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase and showed no effect on aminotransferase levels though there was a decrease in alkaline phosphatase. RNA sequencing studies revealed a role of GSK3β inhibition via tideglusib on the canonical Wnt signaling pathway, suggesting tideglusib may carry out its effects on ethanol consumption through effects on β-catenin binding to the transcription factors TCF3 and LEF1. The data presented here further implicate GSK3β in alcohol consumption and support the use of tideglusib as a potential therapeutic in the treatment of AUD.
IL-4 Licenses B Cell Activation Through Cholesterol Synthesis
Authors: Steach Holly R. , York Autumn G. , Skadow Mathias H. , Chen Shuting , Zhao Jun , Williams Kevin J. , Zhou Quan , Hsieh Weu-Yuan , Brewer J. Richard , Qu Rihao , Shyer Justin A. , Harman Christian , Sefik Esen , Mowell Walter K. , Bailis Will , Cui Can , Kluger Yuval , Bensinger Steven J. , Craft Joe , Flavell Richard A.
Published: May 2024

Lymphocyte activation involves a transition from quiescence and associated catabolic metabolism to a metabolic state with noted similarities to cancer cells such as heavy reliance on aerobic glycolysis for energy demands and increased nutrient requirements for biomass accumulation and cell division1–3. Following antigen receptor ligation, lymphocytes require spatiotemporally distinct “second signals”. These include costimulatory receptor or cytokine signaling, which engage discrete programs that often involve remodeling of organelles and increased nutrient uptake or synthesis to meet changing biochemical demands4–6. One such signaling molecule, IL-4, is a highly pleiotropic cytokine that was first identified as a B cell co-mitogen over 30 years ago7. However, how IL-4 signaling mechanistically supports B cell proliferation is incompletely understood. Here, using single cell RNA sequencing we find that the cholesterol biosynthetic program is transcriptionally upregulated following IL-4 signaling during the early B cell response to influenza virus infection, and is required for B cell activationin vivo. By limiting lipid availabilityin vitro, we determine cholesterol to be essential for B cells to expand their endoplasmic reticulum, progress through cell cycle, and proliferate. In sum, we demonstrate that the well-known ability of IL-4 to act as a B cell growth factor is through a previously unknown rewiring of specific lipid anabolic programs, relieving sensitivity of cells to environmental nutrient availability.
ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes
Authors: Dong Jinhong , Scott Thomas G. , Mukherjee Rudradeep , Guertin Michael J.
Published: May 2024

Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. ZNF143 binds the promoter of nearly all its activated target genes. ZNF143 also binds near the site of genic transcription initiation to directly repress a subset of genes. Although ZNF143 stimulates initiation at ZNF143-repressed genes (i.e. those that increase expression upon ZNF143 depletion), the molecular context of binding leads tocisrepression. ZNF143 competes with other more efficient activators for promoter access, physically occludes transcription initiation sites and promoter-proximal sequence elements, and acts as a molecular roadblock to RNA Polymerases during early elongation. The termcontext specificis often invoked to describe transcription factors that have both activation and repression functions. We define the context and molecular mechanisms of ZNF143-mediatedcisactivation and repression.
Intensifying marine heatwaves and limited protection threaten global kelp forests
Authors: Arafeh-Dalmau Nur , Villaseñor-Derbez Juan Carlos , Schoeman David S. , Mora-Soto Alejandra , Bell Tom W. , Butler Claire L. , Costa Maycira , Dunga Loyiso V. , Houskeeper Henry F. , Lagger Cristian , Pantano Carolina , Laínez del Pozo Daniela , Sink Kerry J. , Micheli Fiorenza , Cavanaugh Kyle C.
Published: May 2024

Kelp forests are one of the earth’s most productive ecosystems and are at the greatest risk from climate change, yet little is known regarding their future threats and current conservation status. By combining a global remote sensing dataset of floating kelp forests with climate data and projections, we find that exposure to projected marine heatwaves will increase ∼8 times compared to contemporary (2001-2020) exposure for intermediate climate scenarios. While exposure will intensify for all forests, climate refugia emerge for some southern hemisphere kelp forests, which have lower exposure to contemporary and projected marine heatwaves. Under these escalating threats, less than 3% of global kelp forests are currently within highly restrictive marine protected areas, the most effective conservation measure for providing climate resilience. Our findings emphasize the urgent need to increase the global protection of kelp forests and set bolder climate adaptation goals.
CREATION OF SAFE DOSE ZONES USING ISODOSE MAPS IN VIDEO FLUOROSCOPIC SWALLOWING STUDIES FOR PEDIATRIC PATIENTS
Authors: María Ignacia Gac P. , Sofía Moncada H. , Mathias Redenz R. , Marco Jiménez H. , Ricardo Castillo V.
Published: May 2024

Background

During video fluoroscopic procedures in pediatric patients, a considerable number of individuals, including occupationally exposed professionals (OEP) and patient companions, must be present, exposing themselves to radiation.

Objective

To determine safety areas for OEP to receive the lowest absorbed dose during the examination, as shown in isodose maps.

Method

Technical parameters used in the examination were obtained by reviewing exams conducted during the years 2021 and 2022. Subsequently, a procedure was conducted to simulate these data using an anthropomorphic phantom and taking measurements at different points and levels of the examination room to create a map with dose zones in three dimensions. A Geiger Müller ionization chamber was used to measure the doses.

Results

It was found that the points closest to the patient at pelvic level of the professional had the highest doses.

Conclusion

OEP who must remain close to the patient have an essential obligation to comply with the use of radiological protection elements, and the relocation of elements in the room could be considered.
The Health for Life in Singapore (HELIOS) Study: delivering Precision Medicine research for Asian populations
Authors: Wang Xiaoyan , Mina Theresia , Sadhu Nilanjana , Jain Pritesh R , Ng Hong Kiat , Low Dorrain Yanwen , Tay Darwin , Tong Terry Yoke Yin , Choo Wee-Lin , Kerk Swat Kim , Low Guo Liang ,   The HELIOS Study team, Lam Benjamin Chih Chiang , Dalan Rinkoo , Wanseicheong Gervais , Yew Yik Weng , Leow Ee-J , Brage Soren , Michelotti Gregory A , Wong Kari E , Sheridan Patricia A , Low Pin Yan , Yeo Zhen Xuan , Bertin Nicolas , Bellis Claire , Hebrard Maxime , Goy Pierre-Alexis , Tsilidis Kostas , Sanikini Harinakshi , Guan Xue Li , Lim Tock Han , Lee Lionel , Best James D , Tan Patrick , Elliott Paul , Lee Eng Sing , Lee Jimmy , Ngeow Joanne , Riboli Elio , Lam Max , Loh Marie , Chambers John C
Published: May 2024

Asian people are under-represented in population-based, clinical, and genomic research.1,2To address this gap, we have initiated the HELIOS longitudinal cohort study, comprising comprehensive behavioural, phenotypic, and genomic measurements from 10,004 Asian men and women of Chinese, Indian or Malay background. Phenotyping has been carried out using validated approaches, that are internationally interoperable. Health record linkage enriches both baseline phenotyping and evaluation of prospective outcomes. The integrated multi-omics data include whole-genome and RNA sequencing, quantification of DNA methylation, and metabolomic profiling. Our data reveal extensive lifestyle, physiological, genomic, and molecular diversity between the distinct Asian ethnic groups, and the biological interconnectivity between functional layers. This includes characterisation of divergent patterns of genome regulation between Asian individuals, that correlate with differences in educational attainment, dietary quality, and adiposity, and which overlap transcription factors and DNA methylation sites linked to the development of diabetes and other chronic diseases. Our unique HELIOS Asian Precision Medicine cohort study represents a state-of-the art platform to enable biomedical researchers to understand the aetiology and pathogenesis of diverse disease outcomes in Asia, and to generate insights that have the potential to improve health outcomes for Asian populations globally.
TILTomorrow today: dynamic factors predicting changes in intracranial pressure treatment intensity after traumatic brain injury
Authors: Bhattacharyay Shubhayu , van Leeuwen Florian D , Beqiri Erta , Åkerlund Cecilia , Wilson Lindsay , Steyerberg Ewout W , Nelson David W , Maas Andrew I R , Menon David K , Ercole Ari ,   the CENTER-TBI investigators and participants
Published: May 2024

Practices for controlling intracranial pressure (ICP) in traumatic brain injury (TBI) patients admitted to the intensive care unit (ICU) vary considerably between centres. To help understand the rational basis for such variance in care, this study aims to identify the patient-level predictors of changes in ICP management. We extracted all heterogeneous data (2,008 pre-ICU and ICU variables) collected from a prospective cohort (n=844, 51 ICUs) of ICP-monitored TBI patients in the Collaborative European NeuroTrauma Effectiveness Research in TBI (CENTER-TBI) study. We developed the TILTomorrow modelling strategy, which leverages recurrent neural networks to map a token-embedded time series representation of all variables (including missing values) to an ordinal, dynamic prediction of the following day’s five-category therapy intensity level (TIL(Basic)) score. With 20 repeats of 5-fold cross-validation, we trained TILTomorrow on different variable sets and applied the TimeSHAP (temporal extension of SHapley Additive exPlanations) algorithm to estimate variable contributions towards predictions of next-day changes in TIL(Basic). Based on Somers’Dxy, the full range of variables explained 68% (95% CI: 65–72%) of the ordinal variation in next-day changes in TIL(Basic)on day one and up to 51% (95% CI: 45–56%) thereafter, when changes in TIL(Basic)became less frequent. Up to 81% (95% CI: 78–85%) of this explanation could be derived from non-treatment variables (i.e., markers of pathophysiology and injury severity), but the prior trajectory of ICU management significantly improved prediction of future de-escalations in ICP-targeted treatment. Whilst there was no significant difference in the predictive discriminability (i.e., area under receiver operating characteristic curve [AUC]) between next-day escalations (0.80 [95% CI: 0.77–0.84]) and de-escalations (0.79 [95% CI: 0.76– 0.82]) in TIL(Basic)after day two, we found specific predictor effects to be more robust with de-escalations. The most important predictors of day-to-day changes in ICP management included preceding treatments, age, space-occupying lesions, ICP, metabolic derangements, and neurological function. Serial protein biomarkers were also important and may serve a useful role in the clinical armamentarium for assessing therapeutic needs. Approximately half of the ordinal variation in day-to-day changes in TIL(Basic)after day two remained unexplained, underscoring the significant contribution of unmeasured factors or clinicians’ personal preferences in ICP treatment. At the same time, specific dynamic markers of pathophysiology associated strongly with changes in treatment intensity and, upon mechanistic investigation, may improve the timing and personalised targeting of future care.
The triple combination of Remdesivir (GS-441524), Molnupiravir and Ribavirin is highly efficient in inhibiting coronavirus replication in human nasal airway epithelial cell cultures and in a hamster infection model
Authors: Do Thuc Nguyen Dan , Abdelnabi Rana , Boda Bernadett , Constant Samuel , Neyts Johan , Jochmans Dirk
Published: May 2024

The use of fixed dose-combinations of antivirals with different mechanisms of action has proven a key in the successful treatment of infections with HIV and HCV. For the treatment of infections with SARS-CoV-2 and possible future epi-/pandemic coronaviruses, it will be important to explore the efficacy of combinations of different drugs, in particular to avoid resistance development, such as in patients with immunodeficiencies. As a first effort, we studied the antiviral potency of combinations of antivirals. To that end, we made use of primary human airway epithelial cell (HAEC) cultures grown at the air-liquid interface that were infected with the beta coronavirus OC43. We found that the triple combination of GS-441524 (parent nucleoside of remdesivir), molnupiravir, and ribavirin resulted in a more pronounced antiviral efficacy than what could be expected from a purely additive antiviral effect. The potency of this triple combination was next tested in SARS-CoV-2 infected hamsters. To that end, for each of the drugs, intentionally suboptimal or even ineffective doses were selected. Yet, in the lungs of all hamsters that received triple prophylactic therapy with suboptimal/inactive doses of GS-441524, molnupiravir, and ribavirin, no infectious virus was detectable. Our finding indicate that co-administration of approved drugs for the treatment of coronavirus infections should be further explored but also against other families of viruses with epidemic and pandemic potential for which no effective antiviral treatment is available.
An acylated N-terminus and a conserved loop regulate the activity of the ABHD17 de-acylase
Authors: Holme Sydney , Sapia Jennifer , Davey Michael , Vanni Stefano , Conibear Elizabeth
Published: May 2024

The dynamic addition and removal of long chain fatty acids modulates protein function and localization. The alpha/beta hydrolase domain-containing (ABHD) 17 enzymes remove acyl chains from membrane localized proteins such as the oncoprotein NRas, but how the ABHD17 proteins are regulated is unknown. Here, we used cell-based studies and molecular dynamics simulations to show that ABHD17 activity is controlled by two mobile elements – an S-acylated N-terminal helix and a loop – that flank the substrate-binding pocket. S-acylation at multiple sites buries the helix in the membrane, which allows hydrophobic residues in the loop to interact with the bilayer. This stabilizes the conformation of both helix and loop, alters the conformation of the binding pocket and optimally positions the enzyme for substrate engagement. S-acylation may be a general feature of acyl-protein thioesterases. By providing a mechanistic understanding of how the lipid modification of a lipid-removing enzyme promotes its enzymatic activity, this work contributes to our understanding of cellular S-acylation cycles.
Computational Phenomapping of Randomized Clinical Trials to Enable Assessment of their Real-world Representativeness and Personalized Inference
Authors: Thangaraj Phyllis M , Oikonomou Evangelos K , Dhingra Lovedeep Singh , Aminorroaya Arya , Jayaram Rahul , Suchard Marc A , Khera Rohan
Published: May 2024

BACKGROUND: Randomized clinical trials (RCTs) define evidence-based medicine, but quantifying their generalizability to real-world patients remains challenging. We propose a multidimensional approach to compare individuals in RCT and electronic health record (EHR) cohorts by quantifying their representativeness and estimating real-world effects based on individualized treatment effects (ITE) observed in RCTs. METHODS: We identified 65 pre-randomization characteristics of an RCT of heart failure with preserved ejection fraction (HFpEF), the Treatment of Preserved Cardiac Function Heart Failure with an Aldosterone Antagonist Trial (TOPCAT), and extracted those features from patients with HFpEF from the EHR within the Yale New Haven Health System. We then assessed the real-world generalizability of TOPCAT by developing a multidimensional machine learning-based phenotypic distance metric between TOPCAT stratified by region including the United States (US) and Eastern Europe (EE) and EHR cohorts. Finally, from the ITE identified in TOPCAT participants, we assessed spironolactone benefit within the EHR cohorts. RESULTS: There were 3,445 patients in TOPCAT and 8,121 patients with HFpEF across 4 hospitals. Across covariates, the EHR patient populations were more similar to each other than the TOPCAT-US participants (median SMD 0.065, IQR 0.011-0.144 vs median SMD 0.186, IQR 0.040-0.479). At the multi-variate level using the phenotypic distance metric, our multidimensional similarity score found a higher generalizability of the TOPCAT-US participants to the EHR cohorts than the TOPCAT-EE participants. By phenotypic distance, a 47% of TOPCAT-US participants were closer to each other than any individual EHR patient. Using a TOPCAT-US-derived model of ITE from spironolactone, all patients were predicted to derive benefit from spironolactone treatment in the EHR cohort, while a TOPCAT-EE-derived model predicted 13% of patients to derive benefit. CONCLUSIONS: This novel multidimensional approach evaluates the real-world representativeness of RCT participants against corresponding patients in the EHR, enabling the evaluation of an RCT's implication for real-world patients.
Experiences of breastfeeding peer support: views from current, past and trainee breastfeeding peer support volunteers in Wales, UK
Authors: Jones H , Davies R , Williams F , Evans R , Bath R , Embling R , Brophy S
Published: May 2024

Background

Breastfeeding peer support involves mothers with personal experience of breastfeeding providing support, information, and encouragement to other breastfeeding mothers. The Unicef UK Baby Friendly Initiative standards require that additional support for new mothers, such as peer support, is provided and that services work together to ensure that mothers can get additional help as needed. As work begins on a national framework for feeding support, we wanted to explore the current activity of breastfeeding supporters in Wales, UK. We aimed to explore the experiences of current, past and trainee breastfeeding peer support volunteers to understand what they need from a refreshed All Wales Breastfeeding Action Plan and how they could benefit.

Methods

Current, past and trainee breastfeeding peer support volunteers were invited by Public Health Wales to complete an online survey about their experiences of providing breastfeeding peer support including both open and closed questions. Codebook thematic analysis was used to generate key themes arising from qualitative data.

Results

81 volunteers completed the online survey between 21/12/23 and 22/1/24. Their experiences were described as ’rewarding’ (50% (44/81)) and ‘empowering’ (12%, 10/81), but also ’frustrating’ (19%, 15/81) and ’challenging’ (8%, 7/81). Peer supporters supported basic positioning and latching, challenges with milk supply, frequency of feeds, weaning, and poor weight gain. Three key themes were developed from the open-ended question ‘why did you decide to undertake peer support training?’ (1) Paying it forward (2) Limited peer support in local areas and (3) The need for more support. Funding was noted as a barrier to continuing to provide breastfeeding peer support.

Conclusions

Breastfeeding peer support was associated with benefits for the peer supporters themselves and recognised as beneficial for the mothers they helped. Investment in training future breastfeeding peer supporters is essential to ensure the continued success of these important initiatives.
Precision fMRI reveals that the language network exhibits adult-like left-hemispheric lateralization by 4 years of age
Authors: Ozernov-Palchik Ola , O’Brien Amanda M. , Lee Elizabeth Jiachen , Richardson Hilary , Romeo Rachel , Lipkin Benjamin , Small Hannah , Capella Jimmy , Nieto-Castañón Alfonso , Saxe Rebecca , Gabrieli John D. E. , Fedorenko Evelina
Published: May 2024

Left hemisphere damage in adulthood often leads to linguistic deficits, but many cases of early damage leave linguistic processing preserved, and a functional language system can develop in the right hemisphere. To explain this early apparent equipotentiality of the two hemispheres for language, some have proposed that the language system is bilateral during early development and only becomes left-lateralized with age. We examined language lateralization using functional magnetic resonance imaging with two large pediatric cohorts (total n=273 children ages 4-16; n=107 adults). Strong, adult-level left-hemispheric lateralization (in activation volume and response magnitude) was evident by age 4. Thus, although the right hemisphere can take over language function in some cases of early brain damage, and although some features of the language system do show protracted development (magnitude of language response and strength of inter-regional correlations in the language network), the left-hemisphere bias for language is robustly present by 4 years of age. These results call for alternative accounts of early equipotentiality of the two hemispheres for language.

Significance Statement

Language is the most canonical function that shows a strong hemispheric asymmetry in adult brains. However, whether the language system is already lateralized to the left hemisphere early in development has long been debated, given that early left-hemisphere damage often leaves language processing unimpaired. We examined the developmental trajectory of language lateralization in two large-scale pediatric datasets using robust individual-subject fMRI approaches. We found that the language system exhibits adult-like left-hemispheric lateralization by age 4, although other aspects of the neural infrastructure for language show a clear change between age 4 and late childhood. These findings challengethe claim that the language system is bilateral during early development and call for alternative accounts of early hemispheric equipotentiality for language.
Transition to chaos separates learning regimes and relates to measure of consciousness in recurrent neural networks
Authors: Mastrovito Dana , Liu Yuhan Helena , Kusmierz Lukasz , Shea-Brown Eric , Koch Christof , Mihalas Stefan
Published: May 2024

Abstract

Recurrent neural networks exhibit chaotic dynamics when the variance in their connection strengths exceed a critical value. Recent work indicates connection variance also modulates learning strategies; networks learn ”rich” representations when initialized with low coupling and ”lazier”solutions with larger variance. Using Watts-Strogatz networks of varying sparsity, structure, and hidden weight variance, we find that the critical coupling strength dividing chaotic from ordered dynamics also differentiates rich and lazy learning strategies. Training moves both stable and chaotic networks closer to the edge of chaos, with networks learning richer representations before the transition to chaos. In contrast, biologically realistic connectivity structures foster stability over a wide range of variances. The transition to chaos is also reflected in a measure that clinically discriminates levels of consciousness, the perturbational complexity index (PCIst). Networks with high values of PCIst exhibit stable dynamics and rich learning, suggesting a consciousness prior may promote rich learning. The results suggest a clear relationship between critical dynamics, learning regimes and complexity-based measures of consciousness.
Meta-analyses reveal support for the Social Intelligence Hypothesis
Authors: Speechley Elizabeth M. , Ashton Benjamin J. , Foo Yong Zhi , Simmons Leigh W. , Ridley Amanda R.
Published: May 2024

The Social Intelligence Hypothesis (SIH) is one of the leading explanations for the evolution of cognition. Since its inception a vast body of literature investigating the predictions of the SIH has accumulated, using a variety of methodologies and species. However, the generalisability of the hypothesis remains unclear. To gain an understanding of the robustness of the SIH as an explanation for the evolution of cognition, we systematically searched the literature for studies investigating the predictions of the SIH. Accordingly, we compiled 103 studies with 584 effect sizes from 17 taxonomic orders. We present the results of four meta-analyses which reveal support for the SIH across interspecific, intraspecific and developmental studies. However, effect sizes did not differ significantly between the cognitive or sociality metrics used, taxonomy or testing conditions. Thus, support for the SIH is similar across studies using neuroanatomy and cognitive performance, those using broad categories of sociality, group size and social interactions, across taxonomic groups, and for tests conducted in captivity or the wild. Overall, our meta-analyses support the SIH as an evolutionary and developmental explanation for cognitive variation.
Dissociable encoding of evolving beliefs and momentary belief updates in distinct neural decision signals
Authors: Parés-Pujolràs Elisabet , Kelly Simon P. , Murphy Peter R.
Published: May 2024

Making accurate decisions in noisy or otherwise uncertain environments requires integrating evidence over time. Using simple tasks requiring rapid evaluation of a stationary sensory feature, two human neurophysiological signals have been found to evolve with similar integration dynamics, with one (centroparietal positivity; CPP) appearing to compute the running integral and continuously feed it to the other (motor beta lateralisation; MBL). However, it remains unknown whether and how these signals serve more distinct functional roles in more complex scenarios where information arrives discontinuously and requires more computational steps to form appropriate belief updates. We employed a volatile expanded judgement task that permits dissociation of the encoding of raw sensory information in each of a series of discrete stimuli (‘objective evidence’), the appropriately transformed belief updates from that information (‘effective evidence’), and the evolving belief itself (accumulated evidence). Whereas MBL traced the evolving belief across stimuli, the CPP was found only to locally encode the effective evidence associated with each individual stimulus. Furthermore, fluctuations in CPP amplitude after each single stimulus could account for variability in the encoding of accumulated evidence in MBL. These results suggest a flexible computational hierarchy in which effective evidence can be computed sample-by-sample at an intermediate processing level to drive downstream belief updates for protracted decisions about discrete stimuli.
A Genetically Encoded System to Quantify and Evolve RuBisCO-Catalyzed Carbon Fixation
Authors: Lanster David L. , Li Zhiyi , Badran Ahmed H.
Published: May 2024

Strategies to study and alter the biochemical properties of RuBisCO often couple CO2fixation to bacterial growth. However, these viability-coupled strategies are not quantitative and are limited by toxicity of the RuBisCO substrate RuBP, the slow kinetics of RuBisCO, and differences in RuBisCO expression. We report the development of the first genetically encoded system capable of accurately quantifying RuBisCO-dependent CO2fixationin cellulousing a tripartite approach that combines bacterial strains which insulate RuBisCO-derived products, an engineered pathway that eliminates RuBP toxicity, and biosensors to concurrently monitor RuBisCO abundance and catalysis. We extended this biosensing strategy to 43 Form II and II/III RuBisCO homologs, finding strong agreement within vitro-derived enzyme kinetics in living cells for the first time. Finally, we show how this system can be used to rapidly evolve functional RuBisCO enzymes. Our approach overcomes prior limitations by streamlining intracellular RuBisCO analyses and will enable the development of enzymes with improved CO2fixation capabilities.
Assessing pH-dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 spike glycoprotein
Authors: Stepanenko Darya , Wang Yuzhang , Simmerling Carlos
Published: May 2024

One of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions the Fusion Peptide Proximal Region (FPPR) of the SARS-CoV-2 spike glycoprotein acts as a pH-dependent switch, modulating immune response accessibility by influencing the positioning of the Receptor Binding Domain (RBD). This would provide an indirect coupling of RBD opening to environmental pH. Here, we explored this possible pH-dependent conformational equilibrium of the FPPR within the SARS-CoV-2 spike glycoprotein. We analyzed hundreds of experimentally determined spike structures from the Protein Data Bank, and carry out pH-Replica Exchange Molecular Dynamics, exploring the extent to which the FPPR conformation depends on pH and the positioning of the RBD. Meta-analysis of experimental structures identified alternate conformations of the FPPR among structures in which this flexible regions was resolved. However, the results did not support a correlation between the FPPR conformation and either RBD position or the reported pH of the cryo-EM experiment. We calculated pKa values for titratable side chains in the FPPR region using PDB structures, but these pKa values showed large differences between alternate PDB structures that otherwise adopt the same FPPR conformation type. This hampers comparison of pKa values in different FPPR conformations to rationalize a pH-dependent conformational change. We supplemented these PDB-based analyses with all-atom simulations, using constant pH-Replica Exchange Molecular Dynamics to estimate pKa values in the context of flexibility and explicit water. The resulting titration curves show good reproducibility between simulations, but also suggest that the titration curves of the different FPPR conformations are the same within error bars. In summary, we were unable to find evidence supporting the previously published hypothesis of FPPR pH-dependent equilibrium, either from existing experimental data, or from constant pH MD simulations. The study underscores the complexity of the spike system and opens avenues for further exploration into the interplay between pH and SARS-CoV-2 viral entry mechanisms.
S100A9 interacts with a dynamic region on CD14 to activate Toll-like receptor 4
Authors: Chisholm Lauren O. , Jaeger Natalie M. , Murawsky Hannah E. , Harms Michael J.
Published: May 2024

S100A9 is a Damage Associated Molecular Pattern (DAMP) that activates inflammatory pathways via Toll-like receptor 4 (TLR4). This activity plays important homeostatic roles in tissue repair, but can also contribute to inflammatory diseases. The mechanism of activation is unknown. Here, we follow up on a previous observation that the protein CD14 is an important co-receptor that enables S100A9 to activate TLR4. Using cell-based functional assays and a combination of mutations and pharmocological perturbations, we found that CD14 must be membrane bound to potentiate TLR4 activation by S100A9. Additionally, S100A9 is sensitive to inhibitors of pathways downstream of TLR4 internalization. Together, this suggests that S100A9 induces activity via CD14-dependent internalization of TLR4. We then used mutagenesis, structural modeling, andin vitrobinding experiments to establish that S100A9 binds to CD14’s N-terminus in a region that overlaps with, but is not identical to, the region where CD14 binds its canonical ligand, lipopolysaccharide (LPS). In molecular dynamics simulations, this region of the protein is dynamic, allowing it to reorganize to recognize both S100A9 (a soluble protein) and LPS (a small hydrophobic molecule). Our work is the first attempt at a molecular characterization of the S100A9/CD14 interaction, bringing us one step closer to unraveling the full mechanism by which S100A9 activates TLR4/MD-2.
Engineering Bacterial Biomanufacturing: Characterization and Manipulation ofSphingomonas sp.LM7 Extracellular Polymers
Authors: van Wijngaarden Ellen W. , Goetsch Alexandra G. , Brito Ilana L. , Hershey David M. , Silberstein Meredith N.
Published: May 2024

Biologically produced materials are an attractive alternative to traditional materials such as metals and plastics and offer improved functionalities such as better biodegradability and biocompatibility. Polysaccharides are an example of a biologically produced materials that can have a range of chemical and physical properties including high stiffness to weight ratios and thermal stability. Biomanufactured bacterial polysaccharides can come with many advantages such as being non-toxic and are mechanically robust relative to proteins and lipids, which are also secreted by bacteria to generate a biofilm. One major goal in biomanufacturing is to produce quality material quickly and cost-effectively. Biomanufacturing offers additional benefits compared to traditional manufacturing including low resource investment and equipment requirements, providing an alternative to sourcing fossil fuel byproducts, and relatively low temperatures needed for production. However, many biologically produced materials require complex and lengthy purification processes before use. This paper 1) identifies the material properties of a novel polysaccharide, dubbed promonan, isolated from the extracellular polymeric substances ofSphingomonas sp.LM7; 2) demonstrates that these properties can be manipulated to suit specific applications; and 3) presents two alternative methods of processing to shorten purification time by more than 50% while maintaining comparable material.
Computational structural prediction and chemical inhibition of the human mitochondrial pyruvate carrier protein heterodimer complex
Authors: Hadfield Christy M. , Walker John K. , Arnatt Chris , McCommis Kyle S.
Published: May 2024

The mitochondrial pyruvate carrier (MPC) plays a role in numerous diseases including neurodegeneration, metabolically dependent cancers, and the development of insulin resistance. Several previous studies in genetic mouse models or with existing inhibitors suggest that inhibition of the MPC could be used as a viable therapeutic strategy in these diseases. However, the MPC’s structure is unknown, making it difficult to screen for and develop therapeutically viable inhibitors. Currently known MPC inhibitors would make for poor drugs due to their poor pharmacokinetic properties, or in the case of the thiazolidinediones (TZDs), off-target specificity for peroxisome-proliferator activated receptor gamma (PPARγ) leads to unwanted side effects. In this study, we develop several structural models for the MPC heterodimer complex and investigate the chemical interactions required for the binding of these known inhibitors to MPC and PPARγ. Based on these models, the MPC most likely takes on outward-facing (OF) and inward-facing (IF) conformations during pyruvate transport, and inhibitors likely plug the carrier to inhibit pyruvate transport. Although some chemical interactions are similar between MPC and PPARγ binding, there is likely enough difference to reduce PPARγ specificity for future development of novel, more specific MPC inhibitors.