bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and visualization of quantitative proteomics data using FragPipe-Analyst
Authors: Hsiao Yi , Zhang Haijian , Li Ginny Xiaohe , Deng Yamei , Yu Fengchao , Kahrood Hossein Valipour , Steele Joel R. , Schittenhelm Ralf B. , Nesvizhskii Alexey I. 
Published: March 2024

ABSTRACTThe FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.
A new group of LysM-RLKs involved in symbiotic signal perception and arbuscular mycorrhiza establishment
Authors: Ding Yi , Gasciolli Virginie , Medioni Lauréna , Gaston Mégane , de-Regibus Annélie , Rem-blière Céline , Bono Jean Jacques , Cullimore Julie , Dalmais Marion , Saffray Christine , Mazeau Solène , Bendahmane Abdelhafid , Sibout Richard , Vandenbussche Michiel , Rouster Jacques , Wang Tongming , He Guanghua , Masselin Arnaud , Cottaz Sylvain , Fort Sébastien , Lefebvre Benoit 
Published: March 2024

AbstractLipo-chitooligosaccharides (LCO) and short-chain chitooligosaccharides (CO) are produced by arbuscular mycorrhizal fungi (AMF) and activate the plant symbiosis signalling pathway, which is essential for mycorrhiza formation. High affinity LCO receptors belonging to the LysM receptor-like kinase (LysM-RLK) phylogenetic groupLYR-IAplay a role in AM establishment, but no plant high affinity short-chain CO receptors have yet been identified. Here we studied members of the uncharacterizedLYR-IBgroup, and found that they show high affinity for LCO, short- and long-chain CO, and play a complementary role with theLYR-IALCO receptors for AM establishment. WhileLYR-IBknock out mutants had a reduced AMF colonization in several species, constitutive/ectopic expression in wheat increased AMF colonization.LYR-IBfunction is conserved in all tested angiosperms, but in most japonica rice a deletion creates a frameshift in the gene, explaining differences in AM phenotypes between rice and other monocot singleLYR-IAmutants. In conclusion, we identified a class of LysM-RLK receptors in angiosperms with new biochemical properties and a role in both LCO and CO perception for AM establishment.
XopM, a FFAT motif containing type-III effector protein fromXanthomonas, suppresses PTI responses at the plant plasma membrane
Authors: Brinkmann Charlotte , Bortlik Jennifer , Raffeiner Margot , Üstün Suayib , Börnke Frederik 
Published: March 2024

AbstractMany Gram-negative pathogenic bacteria use type-III effector proteins (T3Es) as essential virulence factors to suppress host immunity and to cause disease. However, in many cases the molecular function of T3Es remains unknown. The plant pathogenXanthomonas campestrispv.vesicatoria(Xcv) is the causal agent of bacterial spot disease on tomato and pepper plants and is known to translocate around 30 T3Es into its host cell, which collectively suppress plant defense and promote infection. XopM is anXcvcore T3E with unknown function that has no similarity to any other known protein. We found that XopM interacts with vesicle-associated membrane protein (VAMP)-associated proteins (VAPs) in an isoform specific manner. The endoplasmic reticulum (ER) integral membrane protein VAP is a common component of membrane contact sites involved in both tethering and lipid transfer by binding directly to proteins containing a FFAT [two phenylalanines (FF) in an acidic tract (AT)] motif. Sequence analyses revealed that XopM displays two FFAT motifs that cooperatively mediated the interaction of XopM with VAP. When expressed in plants, XopM supports growth of a non-pathogenic bacterial strain and dampens the production of reactive oxygen species, indicating its ability to suppress plant immunity. Further analyses revealed that the interaction with VAP and the ability to suppress PTI are structurally and functionally separable. Although XopM requires localization to the host membrane system for full PTI suppression activity. We discuss a working model in which XopM uses FFAT-motifs to target the membrane in order to interfere with early PTI responses.
A six molecule nenonatal serum metabolite biosignature has high neonatal sepsis predictability and resolves upon treatment completion
Authors: Ahmed Riya , Behera Anil , Sarangi Adyasha , Debata Pradeep , Gaind Rajni , Kaushal GP , Gur Renu , Shrivastava Sushil , Nirmal Kirti , Kaur Ravinder , Nangia Sushma , Kumar Vivek , Sankar M Jeeva , Nanda Ranjan Kumar 
Published: March 2024

ABSTRACTBackgroundSepsis, a life-threatening disorder with multi-organ dysfunction, is a leading cause of neonatal mortality. Current microbiology-based sepsis diagnosis is time-consuming, and identification of deregulated host serum metabolite signatures might be useful to develop early screening tools and host-directed therapeutics.MethodsIn this multi-institutional study, 500 neonates (41.2% female) were classified to culture-positive (CP) or negative sepsis (CN) cases and controls (no sepsis: NS, healthy control: HC) based on their microbial culture and mass spectrometry test results. The neonates were randomly grouped into two discovery sets (I:n=71; II:n=269), a validation set (n=60), and a longitudinally followed-up population (n=100). Serum samples of these neonates were processed and profiled using gas chromatography coupled to either quadrupole or time-of-flight mass spectrometry (GC-MS/-TOF-MS). Deregulated (log2case/control ≥±0.58, p<0.05) serum metabolites in sepsis cases were identified from the discovery sets and their predictive accuracy in the validation set was calculated using area under the receiving operator characteristic curve (AUC of ROC). The abundance of these deregulated metabolites was monitored in the longitudinally followed-up neonates (CP:n=29, CN:n=35, and NS:n=36) completing therapeutic intervention.ResultsMost of the CP cases wereKlebsiella pneumoniae(28.6%) orAcinetobacter baumannii(20.6%) positive. Gestational age (CP: 30.9±1.9 weeks, CN: 30.9±1.8 weeks, HC: 32.3±1.3 weeks, NS: 31.6±1.5 weeks) and birthweight (CP: 1.4±0.3 kg, CN: 1.4±0.4 kg, HC: 1.7±0.3 kg, NS: 1.6±0.3 kg) were lower in sepsis neonates compared to controls. Out of 57 identified serum metabolites, a set of six (1,5-Anhydro-D-sorbitol-Lactic-acid-Malic-acid-Myo-inositol-Phenylalanine-Lysine) were identified as sepsis biosignature. The AUC of ROC of the biosignature to predict CP or CN from HC was 0.97 and from NS was 0.84 and 0.64, respectively. Myo-inositol, malic acid, and 1,5-anhydro-D-sorbitol revert to the HC levels in neonates completing therapeutic intervention.ConclusionsA serum metabolite signature showed a >97% predictive accuracy for sepsis and could be further explored for its diagnostic and host-directed therapeutic potential.
Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains
Authors: Madaj Rafal , Martinez-Goikoetxea Mikel , Kaminski Kamil , Ludwiczak Jan , Dunin-Horkawicz Stanislaw 
Published: March 2024

AbstractCoiled coils are a common protein structural motif involved in cellular functions ranging from mediating protein-protein interactions to facilitating processes such as signal transduction or regulation of gene expression. They are formed by two or more alpha helices that wind around a central axis to form a buried hydrophobic core. Various forms of coiled-coil bundles have been reported, each characterized by the number, orientation, and degree of winding of the constituent helices. This variability is underpinned by short sequence repeats that form coiled coils and whose properties determine both their overall topology and the local geometry of the hydrophobic core. The strikingly repetitive sequence has enabled the development of accurate sequence-based coiled-coil prediction methods; however, the modeling of coiled-coil domains remains a challenging task. In this work, we evaluated the accuracy of AlphaFold2 in modeling coiled-coil domains, both in modeling local geometry and in predicting global topological properties. Furthermore, we show that the prediction of the oligomeric state of coiled-coil bundles can be achieved by using the internal representations of AlphaFold2, with a performance better than any previous state-of-the-art method (code available athttps://github.com/labstructbioinf/dc2_oligo).
Breaking the rule: An exceptional Y chromosome introgression between deeply divergent primate species
Authors: Jensen Axel , Horton Emma R. , Amboko Junior , Parke Stacy-Anne , Hart John A. , Tosi Anthony , Guschanski Katerina , Detwiler Kate M. 
Published: March 2024

AbstractHybridization between distinct lineages is widespread in nature, with important implications for adaptation and speciation. If hybrids are fertile, alleles can introgress across species boundaries. Hybrid fitness is often sex dependent, with heterogametic hybrids showing lower fitness than homogametic individuals, a phenomenon known as Haldane’s rule. Consequently, loci inherited strictly through the heterogametic sex rarely introgress. We focus on the Y-chromosomal history of guenons (tribe Cercopithecini), a group of African primates that hybridized extensively throughout their evolutionary history. Although our inferences suggest that Haldane’s rule is generally in place, we uncover a remarkable Y chromosome introgression event fromCercopithecus mitisintoC. denti, which occurred ca. six million years after their initial divergence. Only a weak signal of autosomal gene flow is present, suggesting that the introgressing Y chromosome reached fixation inC. dentifrom a very low initial frequency. We use simulations to explore the evolutionary mechanisms at play, and find that selection is needed to achieve fixation of the novel Y chromosome. We identify a number of fixed protein differences between the introgressed and ancestral Y, with meiotic drive being an alternative mechanism to adaptive introgression. Our results show that the ability to produce viable and fertile heterogametic hybrids persisted for six million years in guenons, providing a remarkable exception to Haldane’s rule.
Normative models combining fetal and postnatal MRI data to characterize neurodevelopmental trajectories during the transition from in- to ex-utero
Authors: Mihailov A. , Pron A. , Lefèvre J. , Deruelle C. , Desnous B. , Bretelle F. , Manchon A. , Milh M. , Rousseau F. , Auzias G. , Girard N. 
Published: March 2024

ABSTRACTThe perinatal period involves transitioning from an intra- to an extrauterine environment, which requires a complex adaptation of the brain. This period is marked with dynamic and multifaceted cortical changes in both structure and function. Most studies to date have focused either on the fetal or postnatal period, independently. To the best of our knowledge, this is the first neurodevelopmental study targeting the cortical trajectory of typically developing perinatal subjects, combining MRIs from both fetal and postnatal participants. Prior to analysis, preprocessing and segmentation parameters were harmonized across all subjects in order to overcome methodological limitations that arise when studying such different populations. We conducted a normative modeling analysis on a sample of 607 subjects, age ranged 24 to 45 weeks post-conception, to observe changes that arise as participants traverse the birth barrier. We observed that the trajectories of global surface area and several volumetric features, including total gray matter, white matter, brainstem, cerebellum and hippocampi, follow distinct but continuous patterns during this transition. We further report three features presenting a discontinuity in their neurodevelopmental trajectories as participants traverse from a fetal to a postnatal environment: the extra-cerebrospinal fluid volume, the ventricular volume and global gyrification. The current study demonstrates the presence of unique neurodevelopmental patterns for several structural features during the perinatal period, and confirms that not all features are affected in the same way as they cross the birth barrier.SIGNIFICANCE STATEMENTThe perinatal phase comprises the fetal and immediate postnatal period, and is generally described as the time surrounding birth. Comprehensively understanding this period is crucial due to the presence of dynamic and multifaceted brain changes. What makes this investigation unique is that it is the first neurodevelopmental study, to the best of our knowledge, focused on the cortical trajectory of typically developing perinatal subjects through the combination of both fetal and postnatal participants into one analysis. We report that certain brain feature trajectories change drastically as fetuses become newborns, while other features remain continuous. These observations are relevant in both the isolation of biomarkers for later cognitive and physiological disorders and in the understanding of typical cerebral development.
UrbanCepaea nemoralissnails are less likely to have nematodes trapped within their shells
Authors: Dahirel Maxime , Reyné Hannah , De Wolf Katrien , Bonte Dries 
Published: March 2024

AbstractUrbanization is a major human-induced environmental change which can impact not only individual species, but also the way these species interact with each other. As a group, terrestrial molluscs interact frequently with a wide diversity of parasites, yet the way these interactions vary across space and in response to environmental pressures is poorly documented. In this study we leveraged a recently discovered defence mechanism, by which snails trap parasitic nematodes in their shells, to explore how snail-nematodes interactions may vary in response to city life. We examined shells from the generalist snailCepaea nemoralissampled in three urban areas in Belgium for trapped nematodes, and attempted to link this to urbanization and shell phenotypic traits. We found that even a small degree of urbanization led to large decreases in the rates of shell encapsulation, and that larger snails were more likely to contain trapped nematodes. However, we found no evidence that shell colour, which had been previously linked to immune function, was correlated to encapsulation rates. We discuss how between-population variation in encapsulation rates can result from urbanization-induced changes on the nematodes side, the snail side, or both, and suggest potential tests for future studies aiming to disentangle these mechanisms.
Role of the right middle occipital gyrus in egocentric spatial orientation in reference to gravitational information: Evidence from a pre-registered rTMS study
Authors: Tani Keisuke , Naito Eiichi , Mizobe Koji , Hirose Satoshi 
Published: March 2024

AbstractAccurate perception of the orientation of external objects relative to the body, known asegocentric spatial orientation, is fundamental to action. Previously, we found via behavioral and magnetic resonance imaging voxel-based morphometry studies that egocentric spatial orientation is distorted when the whole body is tilted with respect to gravity, and that the magnitude of this perceptual distortion is correlated with grey matter volume in the right middle occipital gyrus (rMOG). In the present pre-registered study, we demonstrated that neural processing in the rMOG is indeed a cause of the perceptual distortion. We transiently suppressed neural activity in the rMOG by applying low-frequency repetitive transcranial magnetic stimulation (rTMS) and evaluated the consequent effect on perceptual distortion. Our results showed that while rTMS over the rMOG significantly reduced perceptual distortion when the body was tilted with respect to gravity, it did not affect egocentric spatial orientation when in the upright position. No changes in perceptual distortion were observed when rTMS was applied to a control site (right temporoparietal junction) or to air (sham TMS). These results indicate that neural processing in the rMOG during body tilt is an essential cause of perceptual distortion, suggesting that the rMOG is engaged in egocentric spatial orientation concerning gravitational information.Significance statementThe findings of this pre-registered study support a causal role of neural activity in the right middle occipital gyrus (rMOG) in the perceptual distortion of egocentric spatial orientation induced by whole-body tilt relative to gravity. We suppressed neural activity in the rMOG using low-frequency repetitive transcranial magnetic stimulation (rTMS) and measured perceptual distortion. We observed a significant reduction in perceptual distortion after rTMS over the rMOG, but not after control or sham rTMS. These results provide, for the first time, direct evidence of the engagement of the rMOG in egocentric spatial orientation in reference to gravitational information.
Cognitive modeling of the Mnemonic Similarity Task as a digital biomarker for Alzheimer’s Disease
Authors: Vanderlip Casey , Lee Michael D. , Stark Craig E.L. 
Published: March 2024

AbstractAD related pathologies, such as beta-amyloid (Aβ) and phosphorylated tau (pTau), are evident decades before any noticeable decline in memory occurs. Identifying individuals during this asymptomatic phase is crucial for timely intervention. The Mnemonic Similarity Task (MST), a modified recognition memory task, is especially relevant for early AD screening, as it assesses hippocampal integrity, a region affected (both directly and indirectly) early in the progression of the disease. Further, strong inferences on the underlying cognitive mechanisms that support performance on this task can be made using Bayesian cognitive modeling. We assessed whether analyzing MST performance using a cognitive model could detect subtle changes in cognitive function and AD biomarker status prior to overt cognitive decline. We analyzed MST data from >200 individuals (young, cognitively healthy older adults, and individuals with MCI), a subset of which also had existing CSF Aβ and pTau data. Traditional performance scores and cognitive modeling using multinomial processing trees was applied to each participants MST data using Bayesian approaches. We assessed how well each could predict age group, memory ability, MCI status, Aβ/pTau status using ROC analyses. Both approaches predicted age group membership equally, but cognitive modeling approaches exceeded traditional metrics in all other comparisons. This work establishes that cognitive modeling of the MST can detect individuals with AD prior to cognitive decline, making it a potentially useful tool for both screening and monitoring older adults during the asymptomatic phase of AD.
Planning and adjusting the COVID-19 booster vaccination campaign to reduce disease burden
Authors: Domenico Laura Di , Goldberg Yair , Colizza Vittoria 
Published: March 2024

AbstractAs public health policies shifted in 2023 from emergency response to long-term COVID-19 disease management, immunization programs started to face the challenge of formulating routine booster campaigns in a still highly uncertain seasonal behavior of the COVID-19 epidemic. Mathematical models assessing past booster campaigns and integrating knowledge on waning of immunity can help better inform current and future vaccination programs. Focusing on the first booster campaign in the 2021/2022 winter in France, we used a multi-strain age-stratified transmission model to assess the effectiveness of the observed booster vaccination in controlling the succession of Delta, Omicron BA.1 and BA.2 waves. We explored counterfactual scenarios altering the eligibility criteria and inter-dose delay. Our study showed that the success of the immunization program in curtailing the Omicron BA.1 and BA.2 waves was largely dependent on the inclusion of adults among the eligible groups, and was highly sensitive to the inter-dose delay, which was changed over time. Shortening or prolonging this delay, even by only one month, would have required substantial social distancing interventions to curtail the hospitalization peak. Also, the time window for adjusting the delay was very short. Our findings highlight the importance of readiness and adaptation in the formulation of routine booster campaign in the current level of epidemiological uncertainty.
Brief psychological interventions to improve mental health outcomes in refugee populations: A systematic review
Authors: Daniel Nadia A. , Liu Xin , Thomas Elizabeth T. , Eraneva-Dibb Emily , Ahmad Al-Maz , Heneghan Carl 
Published: March 2024

AbstractBackgroundRefugees, asylum seekers, and internally displaced people experience a high burden of mental health problems owing to their experiencing traumas and stressful events.ObjectiveTo summarise the available evidence and analyse the efficacy of brief psychological interventions (< 3 months) on improving mental health outcomes, including depression, anxiety, and post-traumatic stress disorder (PTSD)-related symptoms in refugees.MethodWe searched Medline, EMBASE, PsycINFO, CINAHL, and Global Index Medicus from inception to 19 December 2023. We included controlled studies using any cognitive behavioural therapy (CBT) or CBT-based therapies delivered over a short time (< 3 months), which reported mental health outcomes pre-and post-intervention. We conducted meta-analyses using random effects to derive pooled summary statistics.Results34 eligible studies across 36 publications were retrieved for analysis, and 33 studies were included in the meta-analysis. There was an overall improvement in immediate mental health outcomes for all three domains, with analysis of 13 studies on anxiety outcomes (SMD −1.12, 95% CI −1.72 to −0.52), 20 studies on depression (SMD −1.04, 95% CI −1.97 to −0.11), and 24 studies on PTSD (SMD −0.82, 95% CI −1.20 to −0.45). At 3 to 6-month follow-up, however, analysis of mental health outcomes shows no significant change from baseline, with standard mean differences of 0.24 (95% CI −0.94 to 1.42) across 4 studies, −0.73 (95% CI −2.14 to 0.68) across 9 studies, and 0.29 (95% CI −0.94 to 1.53) across 12 studies for anxiety, depression, and PTSD respectively.ConclusionLow-level evidence shows brief psychological interventions positively affect refugees and internally displaced people’s mental well-being. Heterogeneity was high, even among subgroups, impacting our findings’ generalisability.HIGHLIGHTS-We analysed the evidence on the use of brief CBT-based psychological interventions to improve mental health outcomes in forcibly displaced persons.-These interventions had a positive effect on anxiety, depression, and PTSD, though there was high heterogeneity between studies.-Positive effects on mental health disappeared at long-term follow-up.