bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive divergence in the eyes ofHeliconiusbutterflies likely contributes to pre- and post-mating isolation
Authors: Wright Daniel Shane , Rodriguez-Fuentes Juliana , Ammer Lisa , Darragh Kathy , Kuo Chi-Yun , McMillan W. Owen , Jiggins Chris D. , Montgomery Stephen H. , Merrill Richard M. 
Published: November 2023

AbstractWhen populations experience different sensory conditions, natural selection may favor whole sensory system divergence, from the peripheral structures to the brain. We characterized the outer eye morphology of sympatricHeliconiusspecies from different forest types, and their first-generation reciprocal hybrids to test for adaptive visual system divergence and hybrid disruption. In Panama,Heliconius cydnooccurs in closed forests, whereasHeliconius melpomeneresides in more open areas. Previous work has shown that, among wild individuals,H. cydnohas larger eyes thanH. melpomene, and there are heritable, habitat-associated differences in the visual brain structures that exceed neutral divergence expectations. Notably, hybrids have intermediate neural phenotypes, suggesting disruption. To test for similar effects in the visual periphery, we reared both species and their hybrids in common garden conditions. We confirm thatH. cydnohas larger eyes and provide new evidence that this is driven by selection. Hybrid eye morphology is moreH. melpomene-like despite body size being intermediate, contrasting with neural trait intermediacy. Thus, eye morphology differences betweenH. cydnoandH. melpomeneare consistent with adaptive divergence, and when combined with previous neuroanatomy data, suggest hybrid visual system disruption due to mismatched patterns of intermediacy and dominance in the visual pathway.
Evaluation of chromosome structure modelling tools in bacteria
Authors: Liu Tong , Qiu Qin-Tian , Hua Kang-Jian , Ma Bin-Guang 
Published: November 2023

AbstractThe three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained fromEscherichia coliandCaulobacter crescentus, as well as simulating datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.
RNA activities of trans species: RNA from the sperm of the father of an autistic child programs glial cells and behavioral disorders in mice
Authors: Yilmaz Sukranli Zeynep , Korkmaz Bayram Keziban , Mehmetbeyoglu Ecmel , Doganyigit Zuleyha , Beyaz Feyzullah , Sener Elif Funda , Taheri Serpil , Ozkul Yusuf , Rassoulzadegan Minoo 
Published: November 2023

AbstractRecently, we described the alteration of six miRNAs in the serum of autistic children, their fathers, mothers, siblings and in the sperm of autistic mouse models. Studies in model organisms suggest that noncoding RNAs participate in transcriptional modulation pathways. Using mice, approaches to alter the amount of RNA in fertilized eggs enableinvivointervention at an early stage of development. Noncoding RNAs are very numerous in spermatozoa. Our study aims to address a fundamental question: Can the transfer of RNA content from sperm to eggs result in changes in phenotypic traits, such as autism? To explore this, we utilized RNA from the sperm of a father with autistic children and microinjected it into fertilized mouse eggs, thus creating mouse models for autism. Here, we induced in a single step by microinjection of sperm RNA into fertilized eggs the transformation of glial cells into cells capable of developing ‵autism-like‵ disorders in mice born from these alterations.
The role of task on the human brain’s responses to, and representation of, visual regularity defined by reflection and rotation
Authors: Zamboni E , Makin A.D.J. , Bertamini M. , Morland A.B. 
Published: November 2023

AbstractIdentifying and segmenting objects in an image is generally achieved effortlessly and is facilitated by the presence of symmetry: a principle of perceptual organisation used to interpret sensory inputs from the retina into meaningful representations. However, while imaging studies show evidence of symmetry selective responses across extrastriate visual areas in the human brain, whether symmetry is processed automatically is still under debate. We used functional Magnetic Resonance Imaging (fMRI) to study the response to and representation of two types of symmetry: reflection and rotation. Dot pattern stimuli were presented to 15 human participants (10 female) under stimulus-relevant (symmetry) and stimulus-irrelevant (luminance) task conditions. Our results show that symmetry-selective responses emerge from area V3 and extend throughout extrastriate visual areas. This response is largely maintained when participants engage in the stimulus irrelevant task, suggesting an automaticity to processing visual symmetry. Our multi-voxel pattern analysis (MVPA) results extend these findings by suggesting that not only spatial organisation of responses to symmetrical patterns can be distinguished from that of non-symmetrical (random) patterns, but also that representation of reflection and rotation symmetry can be differentiated in extrastriate and object-selective visual areas. Moreover, task demands did not affect the neural representation of the symmetry information. Intriguingly, our MVPA results show an interesting dissociation: representation of luminance (stimulus irrelevant feature) is maintained in visual cortex only when task relevant, while information of the spatial configuration of the stimuli is available across task conditions. This speaks in favour of the automaticity for processing perceptual organisation: extrastriate visual areas compute and represent global, spatial properties irrespective of the task at hand.Key PointsSymmetry selective responses observed in extrastriate visual cortex but not V1 whether stimulus spatial configuration is task relevant or irrelevant.Representation for reflection and rotation differ in extrastriate and object-selective areas, during both stimulus relevant and irrelevant tasks.Representation of luminance information is available only when task relevant.
Physical exercise restores adult neurogenesis deficits induced by simulated microgravity
Authors: Gros Alexandra , Furlan Fandilla Marie , Rouglan Vanessa , Favereaux Alexandre , Bontempi Bruno , Morel Jean-Luc 
Published: November 2023

AbstractCognitive impairments have been reported in astronauts during spaceflights and documented in ground-based models of simulated microgravity (SMG) in animals. However, the neuronal causes of these behavioral effects remain largely unknown. We explored whether adult neurogenesis, known to be a crucial plasticity mechanism supporting memory processes, is altered by SMG. Adult male Long-Evans rats were submitted to the hindlimb unloading model of SMG. We studied the proliferation, survival and maturation of newborn cells in the following neurogenic niches: the subventricular zone (SVZ)/olfactory bulb (OB) and the dentate gyrus (DG) of the hippocampus, at different delays following various periods of SMG. SMG exposure for 7 days, but not shorter periods of 6 or 24 hours, resulted in a decrease of newborn cell proliferation restricted to the DG. SMG also induced a decrease in short-term (7 days), but not long-term (21 days), survival of newborn cells in the SVZ/OB and DG. Physical exercise, used as a countermeasure, was able to reverse the decrease in newborn cell survival observed in the SVZ and DG. In addition, depending on the duration of SMG periods, transcriptomic analysis revealed modifications in gene expression involved in neurogenesis. These findings highlight the sensitivity of adult neurogenesis to gravitational environmental factors during a transient period, suggesting that there is a period of adaptation of physiological systems to this new environment.
Neutrophil-derived complement factor P induces cytotoxicity in basal-like cells via caspase 3/7 activation in pancreatic cancer
Authors: Kishore Uday , Varghese Praveen M , Mangogna Alessandro , Klein Lukas , Tu Mengyu , Urbach Laura , Qiu Mengjie , Nicolle Remy , Murugaiah Valarmathy , Beirag Nazar , Roth Susanne , Pedersen Dennis , Sim Robert B. , Ellenrieder Volker , Andersen Gregers Rom , Bulla Roberta , Singh Shiv K. 
Published: November 2023

ABSTRACTDue to profound heterogeneity within stromal immune tumor microenvironment (TME), pancreatic ductal adenocarcinoma (PDAC) remains a hard to treat disease, with the lowest 5-year survival below 10%. Large-scale transcriptomic analysis has revealed two main, clinically relevant PDAC signatures: therapy responsive ‘Classical’ subtype with better prognosis, and poorly-differentiated Basal-like with poor prognosis. It has also become evident that the cellular and humoral components in the immune TME considerably influence the outcome of tumorigenesis. Complement system, a potent humoral innate immune mechanism, also forms a part of this immune TME. In addition to the regular production of various complement components in the liver, certain infiltrating immune cells such as macrophages, dendritic cells and neutrophils, can produce a few complement components locally at the site of infection and inflammation including TME, and modulate tumorigenic outcomes. Neutrophils are the most prevalent innate immune cells in the PDAC TME; however, its role has been attributed as either pro-tumorigenic or anti-tumorigenic. Neutrophils, when stimulated or under stress, are capable of releasing their secretory granules that also contain the only known up-regulator of the complement alternative pathway, Complement Factor P (CFP) or properdin. Properdin can not only facilitate alternative pathway activation by stabilising the C3 convertase, but also act as a pattern recognition receptor on its own and modify inflammatory response. Here, by combining multicenter transcriptome analysis of PDAC patient tumors, single-cell-RNA-seq analysis, preclinical mouse models and human PDAC specimens, we show that properdin expression and neutrophil surveillance are linked to better prognosis in PDAC patients. Furthermore, properdin expression is substantially higher in well-to-moderately differentiated Classical subtype compared to the highly aggressive basal-like PDAC tumours. Mechanistically, exogenous properdin binds to the cell membrane and activates caspase 3/7 to induce apoptosis in basal-like PDAC cells. Together, these findings suggest that the complement protein, properdin, could be a favorable prognostic factor and exhibit anti-tumorigenic functions in PDAC.
Excessive cortical beta oscillations are associated with slow-wave sleep dysfunction in mild parkinsonism
Authors: Verma Ajay K. , Nandakumar Bharadwaj , Acedillo Kit , Yu Ying , Marshall Ethan , Schneck David , Fiecas Mark , Wang Jing , MacKinnon Colum D. , Howell Michael J. , Vitek Jerrold L. , Johnson Luke A. 
Published: November 2023

AbstractIncreasing evidence associates slow-wave sleep (SWS) dysfunction with neurodegeneration. Using a within-subject design in the nonhuman primate model of Parkinson’s disease (PD), we found that reduced SWS quantity in mild parkinsonism was accompanied by elevated beta and reduced delta power during SWS in the motor cortex. Our findings support excessive beta oscillations as a mechanism for SWS dysfunction and will inform development of neuromodulation therapies for enhancing SWS in PD.
The saccade-induced temporal attentional gradient: Duration compression of the post-saccadic second event
Authors: Chen Lingyue , Grzeczkowski Lukasz , Müller Hermann J. , Shi Zhuanghua 
Published: November 2023

AbstractRapid eye movements can distort our perception of time, as evidenced by the phenomenon of Chronostasis, where the first event following a saccade appears to last longer than it actually does. Despite extensive research on this phenomenon, the effect of saccades on sequential post-saccadic events, beyond the first one, has never been investigated. To address this, in the present study we compared the subjective estimates of the time of first and second post-saccadic events (with fixation conditions as controls). We found saccadic eye movements not only to affect the perceived duration of the first post-saccadic event (Chronostasis), but also that of the second event. Specifically, when the second event immediately following the first event, it was subjectively compressed. When the second event was used as the (constant) reference interval, Chronostasis was enhanced. Remarkably, the compression effect persisted even when potential “attentional-blink”-induced processes, that might affect timing at the transition from the first to the second event, were eliminated. To explain our findings, we propose that saccades induce a transient temporal attentional gradient that results in an overestimation of the first and an underestimation of the second interval when the two intervals are temporally (near-) contiguous.
Evolution of sex-biased genes inDrosophilaspecies with neo-sex chromosomes: potential contribution to reducing sexual conflict
Authors: Minovic Anika , Nozawa Masafumi 
Published: November 2023

ABSTRACTAn advantage of sex chromosomes is the potential to reduce sexual conflict because they provide a basis for selection to operate separately on females and males. However, evaluating the relationship between sex chromosomes and sexual conflict is challenging owing to the difficulty in measuring sexual conflict and substantial divergence between species with and without sex chromosomes. We therefore examined sex-biased gene expression as a proxy for sexual conflict in three sets ofDrosophilaspecies with and without young sex chromosomes, the so-called neo-sex chromosomes. In all sets, we detected more sex-biased genes in the species with neo-sex chromosomes than in the species without neo-sex chromosomes in larvae, pupae, and adult somatic tissues but not in gonads. In particular, many unbiased genes became either female- or male-biased after linkage to the neo-sex chromosomes in larvae, despite the low sexual dimorphism in larvae. However, sexual dimorphism at the adult stage can be a consequence of sexual conflict at the larval stage. For example, larval body size and rate of development are likely targets of sexually antagonistic selection (i.e., large size and rapid development are selected for in females but selected against in males). Indeed, genes involved in metabolism, a key determinant of the rate of development in many animals, were enriched in the genes that acquired sex-biased expression on the neo-sex chromosomes at the larval stage. These results indicate that acquiring neo-sex chromosomes may have contributed to a reduction in sexual conflict, particularly at the larval stage, inDrosophila. (247/250 words)
Perilipin membrane-integration determines lipid droplet heterogeneity in differentiating adipocytes
Authors: Majchrzak Mario , Stojanović Ozren , Ajjaji Dalila , M’barek Kalthoum Ben , Omrane Mohyeddine , Thiam Abdou Rachid , Klemm Robin W. 
Published: November 2023

SummaryThe storage of fat within lipid droplets (LDs) of adipocytes is critical for whole-body health. Acute fatty acid (FA) uptake by differentiating adipocytes leads to the formation of at least two LD-classes marked by distinct perilipins (PLINs). How this LD-heterogeneity arises is an important yet unresolved cell biological problem. Here, we show that an unconventional integral membrane-segment (iMS) targets the adipocyte specific LD-surface factor PLIN1 to the endoplasmic reticulum (ER) and facilitates high affinity binding to the first LD-class. The other PLINs remain largely excluded from these LDs until FA-influx recruits them to a second LD-population. Preventing ER-targeting turns PLIN1 into a soluble, cytoplasmic LD-protein, reduces its LD-affinity and switches its LD-class specificity. Conversely, moving the iMS to PLIN2 leads to ER-insertion and formation of a separate LD-class. Our results shed light on how differences in organelle targeting and disparities in lipid-affinity of LD-surface factors contribute to formation of LD-heterogeneity.HighlightsPLIN1 is an integral membrane protein behaving as a class I LD protein.An unconventional integral membrane segment (iMS) mediates ER insertion.The iMS is required for LD-heterogeneity in differentiating adipocytes.High affinity LD-targeting from the ER is likely a gated process.eTOC blurbMajchrzak et al. use biochemistry, imaging andin vitroexperiments to identify molecular features in PLIN1 that determine ER insertion and high lipid droplet affinity which are both important in the generation of LD-heterogeneity within differentiating adipocytes.
Body Mass Index Asian Populations category and stroke and heart disease in the adult population: A longitudinal study of The Indonesia Family Life Survey (IFLS) 2007 and 2014
Authors: Latief Kamaluddin , Nurrika Dieta , Tsai Min-Kuang , Gao Wayne 
Published: November 2023

AbstractBackgroundStroke and heart disease are included in the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) concerns. Body Mass Index (BMI) is a modifiable risk factor for stroke and heart disease alike. Most studies classify BMI according to the WHO BMI cut-off point in stroke and heart disease studies. However, there is a limited understanding of the association between the BMI cut-off point in the Asian population category and stroke and heart disease. This study aimed to investigate the incidence rate ratio of stroke and heart disease by BMI categories for Asian population.MethodsA 7-year prospective longitudinal study (2007-2014) was conducted on 6,688 adult Indonesian individuals (≥ 35 years) living in 13 different provinces in Indonesia during the survey periods. Data on BMI were collected in 2007. Information on stroke and heart disease was obtained in both 2007 and in 2014. A multivariate-adjusted Poisson regression model was used to estimate the incidence rate ratio (IRR) and 95% confidence intervals (CIs) of either stroke or heart disease or both stroke and heart disease by BMI.ResultsOut of 6,688 eligible participants, 334 (5%) were judged as stroke and heart disease in 2014. The IRR (95% CI) of stroke and heart disease for participants with obesity was 2.57 (1.64-4.04) compared with those within normal weight. This incidence rate ratio remained among middle-aged adults (<55 years) rather than the older adults (≥55 years); the IRR of stroke and heart disease among obese middle-aged adults was 4.18 (95% CI 2.10–8.31).ConclusionsThe association was observed between obesity and the risk of stroke and heart disease, especially in middle-aged adults. These findings suggest that lowering BMI through healthy dietary habits and increasing physical activity, especially among middle-aged adults with high education, who are employees, and who live in urban or rural areas may be beneficial for preventing stroke and heart disease.
Development of meta-prompts for Large Language Models to screen titles and abstracts for diagnostic test accuracy reviews
Authors: Kataoka Yuki , So Ryuhei , Banno Masahiro , Kumasawa Junji , Someko Hidehiro , Taito Shunsuke , Terasawa Teruhiko , Tsujimoto Yasushi , Tsutsumi Yusuke , Wada Yoshitaka , Furukawa Toshi A. 
Published: November 2023

AbstractSystematic reviews (SRs) are a critical component of evidence-based medicine, but the process of screening titles and abstracts is time-consuming. This study aimed to develop and externally validate a method using large language models to classify abstracts for diagnostic test accuracy (DTA) systematic reviews, thereby reducing the human workload. We used a previously collected dataset for developing DTA abstract classifiers and applied prompt engineering. We developed an optimized meta-prompt for Generative Pre-trained Transformer (GPT)-3.5-turbo and GPT-4 to classify abstracts. In the external validation dataset 1, the prompt with GPT-3.5 turbo showed a sensitivity of 0.988, and a specificity of 0.298. GPT-4 showed a sensitivity of 0.982, and a specificity of 0.677. In the external validation dataset 2, GPT-3.5 turbo showed a sensitivity of 0.919, and a specificity of 0.434. GPT-4 showed a sensitivity of 0.806, and a specificity of 0.740. If we included eligible studies from among the references of the identified studies, GPT-3.5 turbo had no critical misses, while GPT-4 had some misses. Our study indicates that GPT-3.5 turbo can be effectively used to classify abstracts for DTA systematic reviews. Further studies using other dataset are warranted to confirm our results. Additionally, we encourage the use of our framework and publicly available dataset for further exploration of more effective classifiers using other LLMs and prompts (https://github.com/youkiti/ARE/).HightlightsWhat is already known- Title and abstract screening in systematic reviews (SRs) consumes significant time.- Several attempts using machine learning to reduce this process in diagnostic test accuracy (DTA) SRs exist, but they have not yielded positive results in external validation.What is new- We aimed to develop and externally validate optimized meta-prompt for GPT-3.5-turbo and GPT-4 to classify abstracts for DTA SRs.- Through an iterative approach across three training datasets, an optimal meta-prompt capable of identifying DTA studies with remarkable sensitivity and specificity was developed.- The accuracy reproduced in the external validation datasets.Potential Impact for Readers- The developed meta-prompt can lessen the need for humans to read abstracts for DTA SRs, saving significant time and resources.