bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unconscious Neural Activity Predicts Overt Attention in Visual Search
Authors: Nadra John G. , Bengson Jesse J. , Mangun George R. 
Published: February 2025

AbstractUnconscious neural activity has been shown to precede both motor and cognitive acts. In the present study, we investigated the neural antecedents of overt attention during visual search, where subjects make voluntary saccadic eye movements to search a cluttered stimulus array for a target item. Building on studies of both overt self-generated motor actions (Lau et al., 2004, Soon et al., 2008) and self-generated cognitive actions (Bengson et al., 2014, Soon et al., 2013), we hypothesized that brain activity prior to the onset of a search array would predict the direction of the first saccade during unguided visual search. Because both spatial attention and gaze are coordinated during visual search, both cognition and motor actions are coupled during visual search. A well-established finding in fMRI studies of willed action is that neural antecedents of the intention to make a motor act (e.g., reaching) can be identified seconds before the action occurs. Studies of the volitional control ofcovertspatial attention in EEG have shown that predictive brain activity is limited to only a few hundred milliseconds before a voluntary shift of covert spatial attention. In the present study, the visual search task and stimuli were designed so that subjects could not predict the onset of the search array. Perceptual task difficulty was high, such that they could not locate the target using covert attention alone, thus requiring overt shifts of attention (saccades) to carry out the visual search. If the first saccade to the array onset in unguided visual search shares mechanisms with willed shifts of covert attention, we expected predictive EEG alpha-band activity (8-12 Hz) immediately prior to the array onset (within 1 sec) (Bengson et al., 2014; Nadra et al., 2023). Alternatively, if they follow the principles of willed motor actions, predictive neural signals should be reflected in broadband EEG activity (Libet et al., 1983) and would likely emerge earlier (Soon et al., 2008). Applying support vector machine decoding, we found that the direction of the first saccade in an unguided visual search could be predicted up to two seconds preceding the search array’s onset in the broadband but not alpha-band EEG. These findings suggest that self-directed eye movements in visual search emerge from early preparatory neural activity more akin to willed motor actions than to covert willed attention. This highlights a distinct role for unconscious neural dynamics in shaping visual search behavior.
Shared computational principles for mouse superior colliculus and primate population orientation selectivity
Authors: Kuo Austin , Gardner Justin L , Merriam Elisha P 
Published: February 2025

AbstractWhile the mouse visual system is known to differ substantially from the primate, if the two systems share computational principles, then generalization of results across species may still be possible. One prominent difference is that orientation selectivity is found in mouse superficial superior colliculus (SC), but is not commonly observed in primate SC. Nevertheless, there may be conservation of computational principles if orientation selectivity in mouse superficial SC displays similar properties to primate visual cortex (V1), such as invariance to differences in other stimulus dimensions. However, a recent calcium (Ca2+) imaging study revealed a population map for stimulus orientation in mouse superficial SC that changed with stimulus properties such as size, shape and spatial frequency, in apparent contradistinction to the computational principles for orientation selectivity in primates. To reconcile the mouse and primate mechanisms for orientation selectivity, we constructed computational models of mouse superficial SC populations with the fixed, stimulus-invariant receptive fields classically used to describe neural receptive fields in monkey lateral geniculate nucleus (LGN) and V1. We found that simulated neural responses reproduced the patterns of stimulus-dependent orientation selectivity from the imaging data. Our models provide a parsimonious explanation for stimulus-dependent orientation selectivity consistent with well-established results from sensory neurophysiology.
µFIX – Enabling Combinations of Concurrent Optogenetics and Lock-in Amplification Fiber Photometry via Removal of Optogenetic Stimulation Crosstalk
Authors: Breakstone Maxim , Chen Spencer C. , Vadapalli Sreya , Chavez Emmanuel , Parsonnet Lauren S. , Gross Robert E. , Tescarollo Fabio , Barker David J. , Sun Hai 
Published: February 2025

AbstractSimultaneous fiber photometry and optogenetics is a powerful emerging technique for precisely studying the interactions of neuronal brain networks. However, spectral overlap between photometry and optogenetic components has severely limited the application of an all-optical approach. Due to spectral overlap, light from optogenetic stimulation saturates the photosensor and occludes photometry fluorescence, which is especially problematic in physically smaller model organism brains like mice. Here, we demonstrate the Multi-Frequency Interpolation X- talk removal algorithm (MuFIX, or µFIX) for recovering crosstalk-contaminated photometry responses recorded with lock-in amplification. µFIX exploits multi-frequency lock-in amplification by modeling the remaining uncontaminated data to interpolate across crosstalk- affected segments (R2∼ 1.0); we found that this approach accurately recovers the original photometry response after demodulation (Pearson’sr∼ 1.0). When applied to crosstalk- contaminated data, µFIX recovered a photometry response closely resembling the dynamics of non-crosstalk photometry recorded simultaneously. Upon further verification using simulated and empirical data, we demonstrated that µFIX reproduces any signal that underwent simulated crosstalk contamination (r∼ 1.0). We believe adopting µFIX will enable experimental designs using simultaneous fiber photometry and optogenetics that were previously not feasible due to crosstalk.
Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion
Authors: Sanath-Kumar Ram , Rahman Arafat , Ren Zhongqing , Reynolds Ian P. , Augusta Lauren , Fuqua Clay , Weisberg Alexandra J. , Wang Xindan 
Published: February 2025

SummaryMultipartite bacterial genome organization can confer advantages including coordinated gene regulation and faster genome replication but is challenging to maintain.Agrobacterium tumefacienslineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the lab model strain C58, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzedAgrobacteriumnatural isolates from the French Collection for Plant-Associated Bacteria (CFBP) and identified two strains with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed both replication origins remain active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres are essential. Importantly, the site-specific recombinases XerCD are required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains.ImportanceMost bacterial genomes are monopartite with a single, circular chromosome. But some species, likeAgrobacterium tumefaciens,carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches including pathogenesis or symbiosis. Multipartite genomes confer certain advantages, however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage ofA. tumefaciensstrain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two environmental isolates ofA. tumefacienscontaining fused chromosomes derived from a different route, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings help us better understand how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification.
Pattern-triggered immunity in blue and white seed cultivars ofPapaver somniferum
Authors: Hernandéz Orozco Jhonny Stalyn , Iakovenko Oksana , Zeiner Adam , Hronková Marie , Kubásek Jiří , Kučerová Bára , Vachová Iveta , Pop Serban , Maršík Petr , Macho Markéta , Fojtíková Pavla , Rychlá Andrea , Hejna Ondřej , Kulich Ivan , Wrzaczek Michael , Janda Martin 
Published: February 2025

ABSTRACTPapaver somniferum(poppy) is a traditional component of Central and Eastern European cuisine and an important oilseed crop in the region. The crucial thread for poppy stable yield is pathogen infection. Thus, we need to understand poppy defence mechanisms in detail. The first robust layer of plant immunity, which plays a crucial role in combat against pathogens, is pattern-triggered immunity (PTI). Here, we provide the first insights into PTI in poppy. We selected four poppy varieties used in the food industry. We investigated poppy response to various peptide elicitors acting as microbe-associated molecular patterns (MAMPs) and damage-associated molecular patterns (DAMPs). Flg22 induced the most robust reactive oxygen species (ROS) burst among all tested peptides. Flg22 also triggered putative mitogen-activated protein kinase (MAPK) phosphorylation and seedling growth inhibition in all tested cultivars. We identifiedPsWRKY22andPsPR2as candidate marker genes suitable for monitoring poppy PTI responses. The tested poppy cultivars have low levels of salicylic acid. Callose accumulation was triggered by wounding but not by flg22. For studying PTI in poppy, wounding is a challenge that needs to be considered as it can obscure potential PTI responses. Our findings highlight conserved aspects of poppy immunity and challenges in studying poppy PTI. The established pipeline facilitates improving our understanding of poppy immunity and has the potential for widespread application in poppy breeding and improving selection for broad-spectrum disease resistance provided by enhanced PTI.GRAPHICAL ABSTRACTGraphical abstractThe establishment of the methods for studying pattern-triggered immunity (PTI) inPapaver somniferumL. (poppy) was inspired by the knowledge of the model plantArabidopsis thaliana. The study showed a similarity between Arabidopsis and poppy in response to flg22 but also pointed out the obstacles for PTI analysis in poppy and the differences compared to the model plant.Created with BioRender.com.
The Effect of Arsenic on Mitochondrial Fatty Acid Metabolism via Inhibition of Carnitine Palmitoyltransferase 1B and Choline Kinase Beta in C2C12 Cells
Authors: Yu Fu-Lin , Zhang Ming-Yan , Song Gang-Wei , Ning Yang-Shan , Wu Xian , Gao Yan 
Published: February 2025

AbstractArsenic can enter the human body through environmental exposure via food, drinking water, and chemotherapy for cancer. Prolonged and excessive exposure to arsenic causes various toxic reactions, leading to diseases that significantly impact health and lifespan. Increasing evidence suggests that arsenic damages skeletal muscle tissue by reducing muscle mass and causing atrophy, thereby contributing to conditions such as respiratory and cardiovascular diseases, as well as diabetes. Fatty acid β-oxidation is the most efficient mechanism for ATP production and serves as a primary energy source for tissues, including the heart and skeletal muscles. However, the metabolic mechanisms underlying arsenic’s effects on muscle function and pathogenesis remain incompletely understood. In this study, we investigated the role of mitochondrial fatty acid oxidation in arsenic-induced muscular damage using mouse skeletal muscle C2C12 cells. Our results demonstrated a dose-dependent inhibitory effect of sodium arsenite (0-2 µM, 72 hours) on C2C12 cells proliferation, viability, and differentiation (indicated by reduction of myogenic differentiation 1 mRNA expression). Arsenic exposure disrupted mitochondria through increasing reactive oxygen species production, reducing mitochondrial membrane potential, downregulating mitochondrial fatty acid metabolism-related enzymes (carnitine palmitoyltransferase 1B and choline kinase beta mRNA), and decreasing mitochondrial DNA copy number. These findings suggest that arsenic-induced pathological changes in skeletal muscle are associated with impaired mitochondrial membrane function, disrupted fatty acid metabolism, and reduced mitochondrial DNA content in muscle cells.
De novobiosynthesis of cannabinoid and its analogs inYarrowia lipolytica
Authors: Hong Yuxiang , Gu Yang , Lin Dewei , Wu Zizhao , Chen Wenhao , Lu Tianjian , Lertphadungkit Pornpatsorn , Ma Jingbo , Wang Haili , Zhou Bo , Bar-Sela Gil , Cohen Idan , Xu Peng 
Published: February 2025

AbstractCannabis sativahas long been a cornerstone of both medicinal and cultural practices, with its therapeutic use spanning over 2,700 years. Central to its therapeutic effects are cannabinoids, which interact with the endocannabinoid system to influence various physiological processes such as anxiety, pain, and inflammation. Despite its benefits, cannabinoid production faces challenges and scarcity from plant extraction. This work leveragesYarrowia lipolyticaas a platform for cannabinoid biosynthesis. By optimizing precursor supply, engineering biomolecular condensate-like dual prenyltransferase expression and expanding endogenous metabolism with a noncanonical polyketide synthase, we achieved thede novobiosynthesis of various cannabinoid and its analogs. Our engineeredY. lipolyticaproduced ∼3.5 mg/L of cannabigerolic acid, 18.8 mg/L of orsellinic acid, and 0.5 mg/L of cannabigerorcinic acid. Additionally, CBGA titer reached 15.7 mg/L with olivetolic acid supplement. This work demonstratesY. lipolytica’s versatility as a promising host for cannabinoid and its analogs production, which opens avenues for further research and medicinal applications.
Noncommunicable diseases associated with hemorrhagic disorders, hospitalization and mortality in patients with dengue in Mexico: a national analysis of confirmed cases in 2024
Authors: Hernández Galdamez Diego Rolando , González-Block Miguel Ángel , Romo-Dueñas Daniela Karola , Osorio López Erick Antonio , Cerón-Meza Rosalba , Méndez-Hernández Pablo 
Published: February 2025

AbstractBackgroundIn Mexico, some of the most prevalent non-communicable diseases (NCDs) among adults are diabetes, hypertension, and chronic kidney disease (CKD). Mexico could be going through a syndemic of dengue and NCDs. This study aims to describe and analyze the association between the prevalence of NCDs and hospitalization, the presence of hemorrhagic disorders, and death in all officially confirmed cases of dengue in Mexico during 2024.Methodology/Principal FindingsThis cross-sectional study is carried out through a secondary analysis of the confirmed cases of dengue reported in 2024. The likelihood of hospitalization, hemorrhagic disorders, and death were assessed according to NCDs, estimating odds ratios (ORs). A multivariate logistic regression model was used, adjusting by age, sex, and for each of the NCDs (diabetes, hypertension, chronic kidney disease, immunosuppression, cirrhosis, and peptic ulcer disease). The most co-prevalent non-communicable diseases were diabetes, hypertension, CKD, and immunosuppression. For hospitalization, CKD has the highest risk of hospitalization (OR 5.73), followed by immunosuppression (OR 2.84), peptic ulcer disease (OR 2.35), and diabetes (OR 2.09). We found higher probabilities for having bleeding disorders in people with diabetes (OR 19.51), peptic ulcer disease (OR 7.85), immunosuppression (OR 4.75), cirrhosis (OR 3.37), and hypertension (OR 2.99) compared to people who did not have these diseases. The highest risk for death was observed in the cases with CKD (OR 6.54), followed by peptic ulcer disease (OR 3.09) and diabetes (OR 2.87).Conclusions/SignificancePatients with dengue and some comorbidities were more likely to have worse clinical outcomes, such as being hospitalized, having bleeding disorders, or dying. The syndemic of NCDs and dengue in Mexico has been rapidly increasing, and this problem needs to be addressed. This work demonstrates that patients with these comorbidities have worse clinical outcomes.
Meta-analysis identifies the patient classification major impact on the ACPA association with rheumatoid arthritis-associated interstitial lung disease (RA-ILD)
Authors: Kaczmarczyk Bartosz , Conde Carmen , Gonzalez Antonio 
Published: February 2025

ABSTRACTBackgroundWe need screening for RA patients at high risk of RA-ILD to prevent the associated decrease in life quality and survival. The proposed screenings disagree regarding the anti-citrullinated protein antibodies (ACPA) because of their inconsistent association across recent studies. Therefore, we hypothesized that meta-analysis of the published reports should reveal clues explaining the heterogeneity of results and that knowing them could help us progress in RA-ILD early detection.ObjectivesWe aimed to discover the factors accounting for the variability of the ACPA association in the published reports.MethodsWe searched the Web of Science and PubMed databases for studies reporting ACPA in RA-ILD and RA-control groups. The identified studies were analyzed using meta-analysis and meta-regression to identify moderators of the ACPA association.ResultsWe found 513 unique records, containing 31 eligible data sets. The meta-analysis preceding the search for moderators showed a remarkable heterogeneity (pQ= 5.7 x 10-7). Appropriate tests showed that it was largely attributable (58.1 %) to an outlier study, which had recruited cases and controls in different place and time contexts. The exclusion of this outlier from subsequent analyses did not completely remove heterogeneity (pQ= 0.004). However, it permitted the identification of the patient classification method as a significant moderator: The 14 studies using chest CT showed stronger ACPA association with RA-ILD (OR = 3.05 [95%CI: 2.12-4.38]) than the 16 employing multifactorial criteria (1.55 [95%CI: 1.18-2.03]; p = 0.0047 for the contrast). This moderator accounted for the significant heterogeneity (pQ= 0.079), was robust in sensitivity analyses, and was the only one found.ConclusionsOur results validate the ACPA association with RA-ILD, reinforce the importance of study design, and suggest the need to consider if studies relying on chest CT for classification could be more fruitful in the search for RA-ILD biomarkers.
Does immersive VR improve diagnostic accuracy of post-stroke spatial neglect relative to conventional and digital tests?
Authors: Palmans Elise , Tuts Nora , Michiels Karla , Note Eline , Van den Bussche Eva , Gillebert Céline R. , Huygelier Hanne 
Published: February 2025

AbstractObjectiveAssessing post-stroke spatial neglect in immersive Virtual Reality (iVR) may improve diagnostic accuracy due to its ability to combine experimental control with increased ecological validity. This study investigated the diagnostic accuracy of an iVR assessment relative to conventional and non-iVR digital tests. Additionally, feasibility was evaluated.MethodStroke patients performed an iVR assessment, conventional pen-and-paper tests (3 Cancellation tests and a line bisection test), and non-iVR digital tests (Digital Cancellation and Posner test). A new Bayesian statistical method was developed to address the absence of a gold standard for neglect. Instead of conventional diagnostic cut-offs, we quantified the uncertainty of classifying patients as having neglect or not and incorporated this into estimating diagnostic accuracy. Feasibility was evaluated using recruitment and drop-out rates, sample characteristics, cybersickness and user experience.Results54 stroke patients and 56 healthy controls completed the study. Both iVR and non-iVR digital tests had higher diagnostic accuracies than pen-and-paper tests, although differences were not statistically significant due to high diagnostic uncertainty (resulting from inconsistencies across tests). For 6 patients, the iVR assessment and Posner test indicated neglect, while pen-and-paper tests did not. The iVR assessment was feasible for most patients, with low cybersickness and positive evaluations.ConclusionThe iVR assessment and Posner test identified spatial biases missed by conventional tests. Inconsistencies across tests highlight the complexity of neglect assessment, suggesting that future studies should explore crucial test characteristics needed for a precise and sensitive evaluation. Furthermore, results established good feasibility of iVR neglect assessment.
Chronic Traumatic Encephalopathy Neuropathologic Change is Infrequent Following Isolated Moderate-Severe Traumatic Brain Injury
Authors: Selmanovic E. , Pruyser A. , Seifert A.C. , Delman B.N. , Thorn E.L. , Folkerth R. , Dams-O’Connor K. 
Published: February 2025

ABSTRACTChronic traumatic encephalopathy-neuropathologic change (CTE-NC) has been primarily studied in contact sport athletes with repetitive head impacts (RHI). An association with isolated traumatic brain injury (TBI) is less clear. We systematically reviewed the autopsied cohort of Late Effects of TBI (LETBI), characterized primarily by isolated TBI but also including RHI, for features of CTE-NC. A consecutive series of 44 brains underwent comprehensive neuropathologic evaluation, exceeding recommended CTE consensus protocols. Of the 44, 6 (13.6%) (age range, 3rd-7thdecades; median, 6thdecade) had CTE-NC, forming the basis for this exploratory analysis. Ex vivo neuroimaging (in 4 of 6) highlighted traumatic and white matter microvascular lesions, facilitating histological sampling of subtle neuropathologies that might otherwise have been missed by conventional sectioning. Macroscopically, 5 had cortical (contusional) and white matter (torsional) volume loss, with septal lesions and hydrocephalus ex vacuo (i.e., structural lesions of moderate-severe TBI). Microscopically, tau-immunopositive neuronal and astrocytic pathology in a perivascular arrangement within sulcal depths met current pathognomonic criteria for CTE-NC in 5 (3 “low” and 2 “high” burden); 1 had more limited findings considered “suspicious” for CTE-NC. Five of 6 cases with any CTE-NC reported substantial exposure to RHI, through contact sport ranging over at least 16 years. One case had no known exposure to RHI: this case (death: 6th decade) had 2 isolated severe TBIs (sustained 30y and 3y prior to death). Of note, one case with “high” CTE also had Alzheimer Disease Neuropathologic Change (high stage), Lewy Body Disease (limbic), and TDP43 accumulation (“polyproteinopathy”). Aging-related tau astrogliopathy, mostly subpial, was seen in 4 cases. Glial tau was also noted around old cavitary contusions in 2. These findings converge with prior studies demonstrating that CTE is largely associated with RHI and is infrequent among individuals with isolated TBI.