bluuebunny/crossref_metadata_2025_split huggingface dataset:
When crayfish make news, headlines are correct but still misleading
Authors: Faulkes Zen 
Published: September 2024

ABSTRACTCrayfish are well known to many but not often newsworthy, so cases where crayfish are covered in international news provide an example of how science journalism covers a news story about basic research. Headlines have a disproportionately large influence on people’s factual knowledge and perceptions of stories covered in media. I tracked online media coverage of one scientific paper involving marbled crayfish and analyzed the headlines used by the articles. Articles were framed as “news,” but almost no headlines contained “new” facts that first appeared in the target scientific paper. The fact that appeared in the most headlines (that marbled crayfish reproduce by cloning) was over a decade old. Headlines misled readers into thinking a “breakthrough” was made by one team, rather than showing incremental advances by many teams of researchers over years.
Controlled retrieval relies on directed interactions between semantic control regions and visual cortex: MEG evidence from oscillatory dynamics
Authors: Eisenhauer Susanne , Zhang Meichao , Krieger-Redwood Katya , Aveyard Richard , Jackson Rebecca L. , Cornelissen Piers L. , Smallwood Jonathan , Jefferies Elizabeth 
Published: September 2024

AbstractTo navigate the world, we store knowledge about relationships between concepts and retrieve this information flexibly to suit our goals. The semantic control network, comprising left inferior frontal gyrus (IFG) and posterior middle temporal gyrus (pMTG), is thought to orchestrate this flexible retrieval by modulating sensory inputs. However, interactions between semantic control and input regions are not sufficiently understood. Moreover, pMTG’s well-formed structural connections to both IFG and visual cortex suggest it as a candidate region to integrate control and input processes. We used magnetoencephalography to investigate oscillatory dynamics during semantic decisions to pairs of words, when participants did or did not know the type of semantic relation between them. IFG showed early increases and decreases in oscillatory activity to prior task knowledge, while pMTG only showed positive effects of task knowledge at a later time window. Furthermore, both regions provided feedback to visual cortex when task goals were absent, while IFG also provided feedback when goals were known. This goal-dependent feedback coincided with an earlier onset of feedforward signalling from visual cortex to pMTG, indicating rapid retrieval of task-relevant features. Knowledge of task goals also enhanced simultaneous inputs to pMTG from both IFG and visual cortex, consistent with the view that pMTG integrates top-down control with bottom-up input. Our findings elucidate the separate roles of anterior and posterior components of the semantic control network and reveal the spectro-temporal cascade of interactions between semantic control and visual regions that underlie our ability to flexibly adapt cognition to the current goals.Significance StatementUsing magnetoencephalography, we characterize the spectro-temporal dynamics that underlie our ability to flexibly adapt semantic cognition to the current context and goals. We find that semantic goals increase oscillatory activity first in IFG and later in pMTG, and ultimately facilitate visual processing. Effective connectivity analyses confirm the proposed direct modulation of visual cortex by semantic control regions both in the presence and absence of goals, resulting in rapid retrieval when semantic goals are known. Moreover, our findings suggest differential roles for the two semantic control regions: while IFGcontrolsearly goal-dependent retrieval, pMTGintegratestop-down information from IFG with bottom-up visual input later.
Assessing Aral Sea residual lake system: impact of fluctuating salinity on phytoplankton communities
Authors: Malashenkov Dmitry V. , Vörös Lajos , Duisen Aiym , Dashkova Veronika , Abilkas Aidyn , Vorobjev Ivan A. , Barteneva Natasha S. 
Published: September 2024

AbstractThe Aral Sea was once the fourth-largest inland water body in the world. However, the lake rapidly shrank over the past six decades, mainly due to the loss of inflow from one of its tributaries, the Amu Darya River. Lakes and reservoirs are traditionally characterized by static chemical and morphological parameters, leaving untouched a dynamic impact of phytoplankton changes. We used an integrated approach combining traditional microscopy and FlowCam-based imaging flow cytometry to study phytoplankton communities during the 2018 and 2019 expeditions in the Aral Sea remnant lakes system. The residual Aral Sea water bodies experienced different environmental conditions, forming hypersaline South Aral, North Aral Sea that is constantly getting freshwater, and brackish Chernyshev Bay and Tushchybas Lake with 2-8 times amplitude of salinity changes attributed to the variability in the precipitation and periodical influx of freshwater. The salinity fluctuations had an impact on the phytoplankton communities in Chernyshev Bay, making it similar to the phytoplankton of North Aral in 2018 while resembling the hypersaline South Aral phytoplankton assemblages in 2019. Multivariate analysis revealed that salinity, water temperature, ammonium, and nitrates were major contributors to explaining the variance in the sampling data. We conclude that drastic phytoplankton fluctuations occur in the two brackish water bodies in the middle of the former Aral Sea, reflecting changes in salinity.
3D Molecular Pretraining via Localized Geometric Generation
Authors: Sun Yuancheng , Chen Kai , Liu Kang , Ye Qiwei 
Published: September 2024

AbstractSelf-supervised learning on 3D molecular structures is gaining importance in data-driven scientific research and applications due to the high costs of annotating bio-chemical data. However, the strategic selection of semantic units for modeling 3D molecular structures remains underexplored, despite its crucial role in effective pre-training—a concept well-established in language processing and computer vision. We introduce Localized Geometric Generation (LEGO), a novel approach that treats tetrahedrons within 3D molecular structures as fundamental building blocks, leveraging their geometric simplicity and widespread presence across chemical functional patterns. Inspired by masked modeling, LEGO perturbs tetrahedral local structures and learns to reconstruct them in a self-supervised manner. Experimental results demonstrate LEGO consistently enhances molecular representations across biochemistry and quantum property prediction benchmarks. Additionally, the tetrahedral modeling and pretraining generalize from small molecules to larger molecular systems, validating by protein-ligand affinity prediction. Our results highlight the potential of selecting semantic units to build more expressive and interpretable neural networks for scientific AI applications.
Mesenchymal stem cell-derived extracellular vesicles alleviate imiquimod-induced psoriasis symptoms in a mouse disease model
Authors: Yi Yuan , Yan Yu , Liu Guowu , Cui Chuang , Zhai Yanhua , He Xinjun , Xu Ke 
Published: September 2024

AbstractPsoriasis is an immune mediated, chronic inflammatory skin disease. Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have inherent immunomodulatory potency from their parental cells, the mesenchymal stem cells (MSCs). In this study, we revealed the application potential of MSC-EVs to alleviate psoriatic symptoms in imiquimod-induced psoriasis mouse model.
Evaluation of stress tolerance in IR64 rice near-isogenic lines carryingSUB1andDRO1genes
Authors: Soe Ibrahim , Thu Hang Nguyen Thi , Odama Emmanuel , Chepkoech Rael , Ookawa Taiichiro , Ismail Abdelbagi M , Sakagami Jun-Ichi 
Published: September 2024

AbstractFlooding and drought significantly reduce rice yield in rainfed environments. Rice varieties that tolerate complete inundation for up to two weeks carry theSUB1Agene, while those enduring deeper water conditions for weeks or months have theSK1andSK2genes. Conversely, theDRO1gene, responsible for deep-rooting, helps in water acquisition under drought. In this study, we compared the growth of NIL-SUB1DRO1 a novel rice genotype with an IR64 background regarding its dual tolerance to submergence and drought. Additionally, we assessed its recovery capacity after exposure to stress. Sixteen and thirteen-days old seedlings of three genotypes (Experiment 1-1 and 2-1) and fourteen-days old seedlings of the two genotypes (Experiment 1-2 and 2-2) were tested under submergence and drought stress in a greenhouse experimental condition respectively. Seedlings were submerged for 10 and 7 days and then allowed to recover for 10 and 7 days respectively. In the drought experiment, seedlings underwent 29 days of drought (Experiment 2-1) and 18 days of drought, followed by 10 days of rewatering (Experiment 2-2). Growth parameters were measured before and after treatment, 4 days after submergence in experiment 1-1 and after the recovery periods. Submergence and drought adversely affected growth and performance. Shoot elongation in submerged plants was reduced by 29.2% for NIL-SUB1DRO1 compared to IR64. Accelerated shoot elongation of IR64 negatively affected its recovery. Chlorophyll content and maximum fluorescence of IR64 were significantly lower than other genotypes after 10 and 7 days of complete submergence. Ten days after recovery in experiment 1-1 the Chlorophyll content and maximum fluorescence of IR64 were not significantly different compared to other genotypes. Seven days after of recovery in experiment 1-2, NIL-SUB1DRO1 had significantly higher chlorophyll content and maximum fluorescence than IR64. After 29 days of drought the tiller number and leaf area of IR64 was lower than other genotypes (Experiment 2-1), while in Experiment 2-2 during drought treatment and recovery, NIL-SUB1DRO1 had greater relative water content, leaf water potential, leaf area, SPAD value, dry weights of shoots and roots, root length, surface area and volume compared to IR64. stomatal conductance of IR64 was higher than NIL-SUB1DRO1 during drought, leading to greater water loss and reduced growth during recovery. NIL-SUB1DRO1 absorbed and retained water more effectively under dry conditions. NIL-SUB1DRO1 and NIL-SUB1 is tolerant to submergence and NIL-SUB1DRO1 and NIL-DRO1 to drought, with no negative effects from combining these genes in modern rice varieties for rainfed lowlands.
Ndufs4 inactivation in glutamatergic neurons reveals swallow-breathing discoordination in a mouse model of Leigh Syndrome
Authors: Huff Alyssa , Oliveira Luiz Marcelo , Karlen-Amarante Marlusa , Ebiala Favour , Ramirez Jan Marino , Kalume Franck 
Published: September 2024

AbstractSwallowing, both nutritive and non-nutritive, is highly dysfunctional in children with Leigh Syndrome (LS) and contributes to the need for both gastrostomy and tracheostomy tube placement. Without these interventions aspiration of food, liquid, and mucus occur resulting in repeated bouts of respiratory infection. No study has investigated whether mouse models of LS, a neurometabolic disorder, exhibit dysfunctions in neuromuscular activity of swallow and breathing integration. We used a genetic mouse model of LS in which the NDUFS4 gene is knocked out (KO) specifically in Vglut2 or Gad2 neurons. We found increased variability of the swallow motor pattern, disruption in breathing regeneration post swallow, and water-induced apneas only in Vglut2 KO mice. These physiological changes likely contribute to weight loss and premature death seen in this mouse model. Following chronic hypoxia (CH) exposure, swallow motor pattern, breathing regeneration, weight, and life expectancy were not changed in the Vglut2-Ndufs4-KO CH mice compared to control, indicating a rescue of phenotypes. These findings show that like patients with LS, Ndufs4 mouse models of LS exhibit swallow impairments as well as swallow-breathing dyscoordination alongside the other phenotypic traits described in previous studies. Understanding this aspect of LS will open roads for the development of future more efficacious therapeutic intervention for this illness.
High-content microscopy and machine learning characterize a cell morphology signature ofNF1genotype in Schwann cells
Authors: Tomkinson Jenna , Mattson Cameron , Mattson-Hoss Michelle , Sarnoff Herb , Bouley Stephanie J. , Walker James A. , Way Gregory P. 
Published: September 2024

AbstractNeurofibromatosis type 1 (NF1) is a multi-system, autosomal dominant genetic disorder driven by the systemic loss of the NF1 protein neurofibromin. Loss of neurofibromin in Schwann cells is particularly detrimental, as the acquisition of a ‘second-hit’ (e.g., complete loss of NF1) can lead to the development of plexiform neurofibroma tumors. Plexiform neurofibromas are painful, disfiguring tumors with an approximately 1 in 5 chance of sarcoma transition. Selumetinib is currently the only medicine approved by the U.S. Food and Drug Administration (FDA) for the treatment of plexiform neurofibromas in a subset of patients. This motivates the need to develop new therapies, either derived to treatNF1haploinsufficiency or complete loss ofNF1function. To identify new therapies, we need to understand the impact neurofibromin has on Schwann cells. Here, we aimed to characterize differences in high-content microscopy imaging in neurofibromin-deficient Schwann cells. We applied a fluorescence microscopy assay (called Cell Painting) to two isogenic Schwann cell lines, one of wildtype genotype (NF1+/+) and one ofNF1null genotype (NF1-/-). We modified the canonical Cell Painting assay to mark four organelles/subcellular compartments: nuclei, endoplasmic reticulum, mitochondria, and F-actin. We utilized CellProfiler pipelines to perform quality control, illumination correction, segmentation, and cell morphology feature extraction. We segmented 22,585NF1wildtype and null cells, utilized 907 significant cell morphology features representing various organelle shapes and intensity patterns, and trained a logistic regression machine learning model to predict theNF1genotype of single Schwann cells. The machine learning model had high performance, with training and testing data yielding a balanced accuracy of 0.85 and 0.80, respectively. All of our data processing and analyses are freely available on GitHub. We look to improve upon this preliminary model in the future by applying it to large-scale drug screens of NF1 deficient cells to identify candidate drugs that return NF1 patient Schwann cells to phenocopy NF1 wildtype and healthier phenotype.
Impact of early postoperative ambulation on gait recovery after hip fracture surgery: A multicenter cohort study
Authors: Nakamura Keisuke , Kurobe Yasushi , Sue Keita , Sakurai Shinichi , Sasaki Tomohiro , Yamamoto Shuhei , Ushiyama Naoko , Taga Masahito , Momose Kimito 
Published: September 2024

AbstractObjectiveThis study aimed to investigate the effect of early postoperative ambulation on gait recovery at the initial postoperative week and at discharge after hip fracture surgery in older patients.DesignMulticenter prospective cohort study.Setting and ParticipantsThe study included 882 patients aged ≥65 years from 10 acute hospitals in Japan.MethodsPatients were divided into two groups according to the interval between surgery and first ambulation: early-ambulation (EA) group (initiation of ambulation on postoperative day 1 or 2) and late-ambulation (LA) group (initiation of ambulation on postoperative day 3 or later). The Functional Independence Measure (FIM) was assessed 1 day postoperatively, 1 week postoperatively, and at discharge. Independent walking regardless of use of walking aids was defined as walking FIM ≥5. Confounding variables were age, mobility and cognitive function before injury, medical history, fracture type, and waiting days for surgery.Multivariate logistic regression analysis was conducted to determine whether EA affected independent walking at 1 week postoperatively and at discharge.ResultsThe number of patients in the EA and LA groups was 292 (33.1%) and 590 (66.9%), respectively. The number of patients walking independently 1 week postoperatively and at discharge was 156 (17.7%) and 292 (33.1%), respectively. Multivariate logistic regression analysis revealed that EA was associated with independent walking at 1 week postoperatively (odds ratio [OR], 3.27; 95% confidence interval [CI], 2.17-4.94;P< .0001) and at discharge after adjusting for confounders (OR, 3.33; 95% CI, 2.38-4.69;P< .0001). EA was associated with the recovery to pre-injury walking status at discharge after adjusting for confounders (OR, 3.05; 95% CI, 1.59–5.93;P=.0009).Conclusion and ImplicationsEarly ambulation after hip fracture surgery has an impact on independent walking and recovery of pre-injury walking status at 1 week postoperatively and at discharge from acute hospitals in older patients.
Patterns and functional consequences of antibody speciation in maternal-fetal transfer of coronavirus-specific humoral immunity
Authors: Hederman Andrew P. , Brookes Hannah M. , Natarajan Harini , Heyndrickx Leo , Ariën Kevin K. , Weiner Joshua A. , Rottenstreich Amihai , Zarbiv Gila , Wolf Dana , Goetghebuer Tessa , Marchant Arnaud , Ackerman Margaret E. 
Published: September 2024

AbstractMaternal antibodies serve as a temporary form of inherited immunity, providing humoral protection to vulnerable neonates. Whereas IgG is actively transferred up a concentration gradient via the neonatal Fc Receptor (FcRn), maternal IgA and IgM are typically excluded from fetal circulation. Further, not all IgG molecules exhibit the same transfer efficiency, being influenced by subclass, Fab and Fc domain glycosylation, antigen-specificity, and the temporal dynamics of maternal antibody responses. Here, we investigate the phenotypes and functions of maternal and cord blood antibodies induced by SARS-CoV-2 infection and compare them to those induced by mRNA vaccination, focusing on breadth of antigen recognition and antiviral functions including neutralization and effector function. While cord blood coronavirus-specific antibody functional breadth and potency appeared to be more compromised than binding breadth and potency in both groups, vaccination induced substantially greater function and breadth in cord blood than did natural infection. These functional phenotypes were associated with speciation of the maternal serum repertoires, as some IgG subpopulations were enriched while others were relatively depleted. Relevant to the continued protection of vulnerable populations in the context of a diversifying pathogen, greater breadth was observed for antibody effector functions than for neutralization, and these activities were associated with greater affinity for antigen. This work provides insights into the functional breadth of maternal-fetal antibody responses in the context of novel mRNA vaccines and a recently emerged pathogen that is likely to be a public health burden for the foreseeable future.
Repetitive magnetic stimuli over the motor cortex impair consolidation of a balance task by suppressing up-regulation of intracortical inhibition
Authors: Egger Sven , Wälchli Michael , Meyer Samuel , Taube Wolfgang 
Published: September 2024

AbstractLow-frequency repetitive transcranial magnetic stimulation (rTMS) over the primary motor cortex (M1) was shown to impair short-term consolidation of a balance task, emphasizing the importance of M1 in balance skill consolidation. However, the disruptive mechanisms of rTMS on neural consolidation processes and their persistence across multiple balance acquisition sessions remain unclear. GABAergic processes are crucial for motor consolidation and, at the same time, are up-regulated when learning balance skills. Therefore, this study investigated the impact of rTMS on GABA-mediated short-interval intracortical inhibition (SICI) and consolidation of balance performance. Participants (n=31) underwent six balance acquisition sessions on a rocker board, each followed by rTMS (n=15) or sham-rTMS (n=16). In the PRE-measurement, SICI was assessed at baseline and after balance acquisition with subsequent rTMS/sham-rTMS. In the POST-measurement, this procedure was repeated to assess the influence of motor memory reactivation on SICI. In addition, SICI-PRE and SICI-POST were compared to assess long-term processes. Both groups achieved similar improvements within the balance acquisition sessions. However, they did not consolidate equally well indicated by significant declines in performance for the rTMS group (p= 0.006) in the subsequent sessions. Both short-(p= 0.014) and long-term (p= 0.038) adaptations in SICI were affected by rTMS: while the sham-rTMS group up-regulated SICI, rTMS led to reductions in inhibition. The interfering effect of rTMS on both balance consolidation and up-regulation of SICI suggests that increased intracortical inhibition is an important factor to protect and consolidate the newly acquired motor memory.
Different behaviourally relevant stimuli evoke different forms of adaptation in the olfactory system
Authors: Birkett Elliot , Nikolaev Anton 
Published: September 2024

AbstractSensory neurons are continuously exposed to a large diversity of stimuli and adjust their response according to the recent stimulation history, in a process called adaptation. Recent studies have demonstrated that many sensory neurons not only depress (decrease their response to repetitive sensory stimulation) but some neurons exhibit facilitation: a small initial response followed by increase in response amplitude. Adaptation has been mainly studied with neutral stimuli and it is not known whether different behaviourally relevant stimuli evoke adaptation with similar or different properties. Here we used ethologically relevant stimuli to study adaptation in the zebrafish olfactory system. We found that repetitive presentation of food odour caused a variety of adaptations ranging from very strong depression to facilitation, but depression was the predominant dynamic. On the other hand, a different behaviourally-relevant stimulus, alarm substance, evoked much stronger facilitation and also decreased the amplitude of responses to food presentation. Other sensory modalities, aversive mechanosensory and attractive visual stimuli, also caused adaptation with different properties in the same brain area. Different forms of adaptation may therefore be used for processing sensory stimuli evoking different behavioural reactions.Graphical abstractHighlightsFood odour evokes a diversity of adaptations ranging from extreme depression to facilitationAlarm substance evokes much stronger facilitation than food odourAlarm substance inhibits responses to food odourMechanosensory stimulation evokes both depression and facilitationVisual stimuli evoke responses in the olfactory bulbs that strongly and quickly depress
Human NLRP3 inflammasome activation leads to formation of condensate at the microtubule organizing center
Authors: Wang Jue , Wu Man , Magupalli Venkat G. , Dahlberg Peter D. , Wu Hao , Jensen Grant J. 
Published: September 2024

AbstractThe NLRP3 inflammasome is a multi-protein molecular machine that mediates inflammatory responses in innate immunity. Its dysregulation has been linked to a large number of human diseases. Using cryogenic fluorescence-guided focused-ion-beam (cryo-FIB) milling and electron cryo-tomography (cryo-ET), we obtained 3-D images of the NLRP3 inflammasomein situat various stages of its activation at macromolecular resolution. The cryo-tomograms unexpectedly reveal dense condensates of the human macrophage NLRP3 inflammasome that form within and around the microtubule organizing center (MTOC). We also find that following activation, the trans-Golgi network disperses and 50-nm NLRP3-associated vesicles appear which likely ferry NLRP3 to the MTOC. At later time points after activation, the electron-dense condensates progressively solidify and the cells undergo pyroptosis with widespread damaged mitochondria and autophagasomal structures.