bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards the implementation and interpretation of masked ICA for identifying signatures of autonomic activation in the brainstem with resting-state BOLD fMRI
Authors: Miedema Mary , Pattinson Kyle T.S. , Mitsis Georgios D. 
Published: December 2024

AbstractThe brainstem is the site of key exchanges between the autonomic and central nervous systems but has historically presented a challenging target for study with BOLD fMRI. A potentially powerful although under-characterized approach to identifying nucleic activation within the brainstem is masked independent component analysis (mICA), which restricts signal decomposition to the brainstem itself, thus aiming to reduce the strong effect of physiological noise in nearby regions such as ventricles and large arteries. In this study, we systematically investigate the use of mICA to uncover signatures of autonomic activation in the brainstem at rest. We apply mICA on 40 subjects in a high-resolution resting state 7T dataset following different strategies for dimensionality selection, denoising, and component classification. We show that among the noise mitigation techniques investigated, cerebrospinal fluid denoising makes the largest impact in terms of mICA outcomes. We further demonstrate that across preprocessing pipelines and previously reported results the majority of components are spatially reproducible, but temporal outcomes differ widely depending on denoising strategy. Evaluating both hand-labelling and whole-brain specificity criteria, we develop an intuitive framework for mICA classifications. Finally, we make a comparison between mICA and atlas-based segmentations of brainstem nuclei, finding little consistency between these two approaches. Based on our evaluation of the effects of methodology on mICA and its relationship to other signals of interest in the brainstem, we provide recommendations for future uses of mICA to identify autonomically-relevant BOLD fluctuations in subcortical structures.
Postnatal Sensory Experience and Barrel Cortex Alterations Anticipate Autistic Traits in a Mouse Model of Cdkl5 Deficiency Disorder
Authors: Raspanti Alessandra , Pizzo Riccardo , Gurgone Antonia , Giraudo Cecilia , Sagona Giulia , Macioce Andrea , Battaglia Anthony , Katsanou Lamprini , Medici Giorgio , Ferrini Francesco , Pizzorusso Tommaso , Ciani Elisabetta , Giustetto Maurizio 
Published: December 2024

ABSTRACTAutistic traits may arise from atypical sensory experience during postnatal life, but whether there is a causal link between defects in cortical circuitry in the brain, altered sensory processing and social behavior remains unknown. Here, we studied tactile stimuli processing in the barrel cortex (BC) and social interactions in juvenile male mice lacking Cyclin-dependent kinase-like 5 (CDKL5), a model of a severe neurodevelopmental disease showing autistic traits and sensory impairments. We identified in these mice defects of whisker-dependent postnatal sensorimotor reflexes, NMDA receptors-dependent signaling, and dendritic orientation in thalamic inputs-receiving spiny stellate neurons. We also found that CDKL5 is required for mapping and processing whisker-derived tactile stimuli in the BC. Intriguingly, KO mice show autistic traits at p21 that are rescued by neonatal CDKL5 replacement in the BC. Our data suggest that CDKL5 is required to link tactile processing in the BC to the onset of social interaction abilities.
Identification of strain-specific cues that regulate biofilm formation inBacteroides thetaiotaomicron
Authors: Glowacki Robert W.P. , Engelhart Morgan J. , Till Jessica M. , Kadam Anagha , Nemet Ina , Sangwan Naseer , Ahern Philip P. 
Published: December 2024

AbstractMembers of the gut microbiome encounter a barrage of host- and microbe-derived microbiocidal factors that must be overcome to maintain fitness in the intestine. The long-term stability of many gut microbiome strains within the microbiome suggests the existence of strain-specific strategies that have evolved to foster resilience to such insults. Despite this, little is known about the mechanisms that mediate this resistance. Biofilm formation represents one commonly employed defense strategy against stressors like those found in the intestine. Here, we demonstrate strain-level variation in the capacity of the gut symbiontBacteroides thetaiotaomicronto form biofilms. Despite the potent induction of biofilm formation by purified bile in most strains, we show that the specific bile acid species driving biofilm formation differ among strains, and uncover that a secondary bile-acid, lithocholic acid, and its conjugated forms, potently induce biofilm formation in a strain-specific manner. Additionally, we found that the short-chain fatty acid, acetic acid, could suppress biofilm formation. Thus, our data defines the molecular components of bile that promote biofilm formation inB. thetaiotaomicronand reveals that distinct molecular cues trigger the induction or inhibition of this process. Moreover, we uncover strain-level variation in these responses, thus identifying that both shared and strain-specific determinants govern biofilm formation in this species.ImportanceIn order to thrive within the intestine, it is imperative that gut microbes resist the multitude of insults derived from the host immune system and other microbiome members. As such, they have evolved strategies that ensure their survival within the intestine. We investigated one such strategy, biofilm formation, inBacteroides thetaiotaomicron, a common member of the human microbiome. We uncovered significant variation in natural biofilm formation in the absence of an overt stimulus among differentBacteroides thetaiotaomicronstrains, and revealed that different strains adopted a biofilm lifestyle in response to distinct molecular stimuli. Thus our studies provide novel insights into factors mediating gut symbiont resiliency, revealing strain-specific and shared strategies in these responses. Collectively, our findings underscore the prevalence of strain-level differences that should be factored into our understanding of gut microbiome functions.
Circuit-Level Dynamics of Slow Wave Activity and Propagation During the Awakening Process
Authors: Pazienti Antonio , Müller Mariel , Bosman Conrado A. , Olcese Umberto , Mattia Maurizio 
Published: December 2024

SummarySlow-wave activity (SWA) is a hallmark of the loss of consciousness in non-REM sleep and anesthesia. The mechanistic underpinnings of SWA, and its evolution when transitioning towards the conscious brain state is poorly understood. We address this topic by recording multi-area and laminar activity in posterior parietal (PPC) and primary visual (V1) cortices of mice spontaneously awakening from isoflurane anesthesia. Spectral power is stronger in PPC (especially in superficial layers) during deep unconsciousness, but stronger in V1 when awakening. Rostro-caudal (feedback-like) propagation of SWA also shows state-dependent modulation, particularly in layer 5. The excitability of layer 2/3 neurons, hindered at high isoflurane, recovers during awakening, when V1 and the feedforward pathway reacquire a strong role. Detailing the hierarchical and laminar properties of spontaneous traveling oscillations, we provide evidence that SWA is a multiscale phenomenon. Explicating the functional role of these processes is critical to understand the neuronal mechanisms of consciousness.
Increased cerebrospinal fluid and plasma apoE glycosylation is associated with reduced levels of Alzheimer’s disease biomarkers
Authors: Nedelkov Dobrin , Tsokolas Zoe E. , Rodrigues Matheus Scarpatto , Sible Isabel , Han S. Duke , Kerman Bilal E. , Renteln Michael , Mack Wendy J. , Pascoal Tharick A. , Yassine Hussein N ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: December 2024

AbstractThe apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for Alzheimer’s disease (AD). ApoE is glycosylated with an O-linked Core-1 sialylated glycan at several sites, yet the impact and function of this glycosylation on AD biomarkers remains unclear. We examined apoE glycosylation in a cohort of cerebrospinal fluid (CSF, n=181) and plasma (n= 178) samples from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) stratified into 4 groups: cognitively normal (CN), Mild Cognitive Impairment (MCI), progressors and non-progressors based on delayed word recall performance over 4 years. We observed decreasing glycosylation from apoE2 > apoE3 > apoE4 in CSF, and in plasma (apoE3 > apoE4). ApoE glycosylation was reduced in the MCI compared with CN groups, and in progressors compared to non-progressors. In CSF, higher apoE glycosylation associated cross-sectionally with lower total tau (t-tau), p-tau181, and with higher Aβ1-42. Similar associations of apoE glycosylation with higher Aβ1-42were observed in plasma. In CSF, greater apoE4 glycosylation was associated with lower t-tau and p-tau181. Over a 6-year period, higher baseline levels of CSF apoE glycosylation predicted lower rates of increase in CSF t-tau and p-tau181 and lower rates of decrease in CSF Aβ1-42. These results indicate strong associations of apoE glycosylation with biomarkers of AD pathology independent of apoE genotype, warranting a deeper understanding of the functional role of apoE glycosylation on AD tau pathology.
Online interference of declarative memory on fast and slow adaptive processes in force field motor learning
Authors: Rudolph J. L. , Selen L. P. J. , Medendorp W. P. 
Published: December 2024

AbstractError-based motor adaptation is currently understood as a dual-rate process involving a fast adaptive process that learns quickly but also decays rapidly and a slow process that learns slowly but has good retention. While the fast process is typically categorized as procedural learning, recent evidence suggests that it relies on the declarative memory system. To test this hypothesis, we investigated in what manner a declarative memory task interferes with two processes that supposedly underly force field adaptation in reaching. This declarative memory task, which involved learning of a list of words, was assessed through either recognition or recall, and was compared to a non-declarative, vowel counting task, using a within-subject design (n=32). We employed a Bayesian hierarchical dual-rate process model to capture the observed force compensation across trials, expecting that the parameters of the fast process would be affected by the declarative memory task. We examined the 95% highest density interval of the posterior distribution of the difference between the experimental and control condition for each parameter. While most parameters remained unaffected by the declarative memory task, the retention rate of the fast process showed a hint of reduction, suggesting a complex interplay between declarative memory and ongoing motor adaptation processes.
Use of Genome Scale Metabolic Reconstructions of Avian PathogenicEscherichia coli(APEC) phylogroups for the identification of lineage-specific metabolic pathways
Authors: Long Huijun , Mehat Jai W. , Wu HuiHai , van Vliet Arnoud H. M. , La Ragione Roberto M. 
Published: December 2024

ABSTRACTAvian PathogenicEscherichia coli(APEC) are a genetically diverse pathotype primarily associated with extra-intestinal infections in birds. APEC lineages are predicted to have unique metabolic capabilities contributing to virulence and survival in the host environment. Here we present a genome-scale metabolic model for the APEC pathotype based on 114 APEC genome sequences, and lineage-specific models for the phylogroups B2, C and G based on a representative isolate for each phylogroup. A total of 1,848 metabolic reactions were predicted in the 114 APEC isolates before gap filling and manual correction. Of these, 89% represented core reactions, whilst the 11% accessory reactions were mostly associated with carbon and nitrogen metabolism. Predictions of auxotrophy were confirmed by inactivation of the conditionally essentiallysAand the non-essentialpotEgenes. The APEC metabolic model outperformed theE. coliK-12iJO1366 model in the Biolog Phenotypic Array platform. Sub-models specific for phylogroups B2, C and G predicted differences in the metabolism of 3-hydroxyphenylacetate (3-HPAA), a phenolic acid derived from the flavonoid quercetin, which is commonly added to poultry feed. Two 3-HPAA associated reactions/genes distinguished APEC phylogroup C from APEC phylogroups B2 and G, and 3-HPAA supported the growth of APEC phylogroup C in minimal media, but not phylogroups B2 and G. In conclusion, we have constructed genome-scale metabolic models for the three major APEC phylogroups B2, C and G, and have identified a metabolic pathway distinguishing phylogroup C APEC. This demonstrates the importance of lineage- and pathotype-specific metabolic models when investigating genetically diverse microbial pathogens.IMPACT STATEMENTAvian PathogenicEscherichia coli(APEC) are the cause of colibacillosis in poultry, which results in a significant economic burden to the poultry industry, and strongly affects the health and welfare of flocks. APEC isolates show a high level of genetic diversity, which complicates diagnostics, epidemiology and the design of prevention and treatment strategies. In this study we have used genome sequences derived from 114 APEC isolates to investigate their metabolic capabilities, and define the metabolic diversity of APEC within a generalised APEC metabolic model, and lineage-specific metabolic models. These models have been interrogated to find unique pathways that can be targeted for the development of anti-APEC treatments, and one such metabolic pathway was identified as a proof of principle. This approach shows great promise for the design of future strategies to prevent and deal with APEC infections, and can be adapted to other genetically diverse microbial pathogens.
Proteome-scale quantification of the interactions driving condensate formation of intrinsically disordered proteins
Authors: Norrild Rasmus K. , von Bülow Sören , Halldórsson Einar , Lindorff-Larsen Kresten , Rogers Joseph M. , Buell Alexander K. 
Published: December 2024

AbstractThe formation of biomolecular condensates is involved in compartmentalisation, regulation, and signalling across most living organisms. Condensation can be driven by phase separation of proteins, and involves highly dynamic, multivalent, and weak interactions of their intrinsically disordered regions (IDRs). Understanding these interactions has been limited by the lack of large-scale experimental methods capable of generating thermodynamic data. Here, we develop and use Condensate Partitioning by mRNA-Display (CPmD) to directly measure the energetics of the partitioning of almost 100,000 peptides of 14 to 40 amino acid length into condensates formed by an IDR, that of the germ granule protein Dead-box helicase 4 (DDX4). This large set of peptides contained many that were derived from DDX4 itself, as well as a tiling library of a significant fraction of all experimentally characterised IDRs. We show that the results of such large scale partitioning studies yield a uniquely quantitative picture of the driving forces that govern IDR condensate formation of DDX4, as well as partitioning of other sequences into its condensates. Furthermore, we demonstrate that the derived set of interactions is also able to quantitatively explain condensate formation of unrelated sequences.
Do career competencies optimize individual work performance? Evidence from Indian HR professionals
Authors: Shrivastava Neha , Mishra Pavan 
Published: December 2024

PurposeThis paper aims to synergize the Job Demands-Resources (JD-R) theory with the Intelligent Career theory (ICT) to identify the potential influence of career competencies (CCs) on individual work performance.Design/methodology/approachWe explore a motivational process within JD-R theory, where CCs such as knowing-why, knowing-how, and knowing-whom serve as personal resources to optimize contextual performance (CP), task performance (TP), and reduce counterproductive work behavior (CWB). The study comprises two phases with samples of human resource (HR) professionals in India. Phase-1 (N = 107) involves adapting measurement instruments through exploratory factor analysis, while phase-2 (N = 396) tests the model using structural equation modeling. We applied the confirmatory factor analysis marker technique, with “conflict avoidance” as the non-ideal marker variable.FindingsOur research indicates that CCs positively influence TP based on statistical and substantive significance. However, their influence on CP and CWB lacks substantive significance.Research limitations/implicationsThis study enhances the JD-R theory by highlighting individual performance as a key outcome of personal resources, like CCs, within the theory’s motivational process.Practical implicationsOrganizations can structure skill development programs to align with specific CCs and desired outcomes, using them as benchmarks to assess effectiveness.Originality/valueTo our knowledge, this is the first attempt to apply both JD-R theory and ICT in a work context, specifically among Indian HR professionals, which remains an unexplored area. Additionally, we assume that CCs may initiate motivation independently, even in the absence of job resources.
Dynamic capabilities and firm performance: moderated mediation model with product innovation as mediator and technology uncertainty as moderator
Authors: Zehir Cemal , Vural Sümeyye Çiçek 
Published: December 2024

PurposeThis study aims to explain the relationships between dynamic capabilities, product innovation, firm performance and technology uncertainty.Design/methodology/approachThe quantitative research method was the preferred approach. Data were collected through a questionnaire from managers working in different sectors. The study’s sample consists of 619 managers from 226 different firms.FindingsThe findings show that there is a positive relationship between dynamic capabilities and product innovation and that dynamic capabilities have a positive relationship with firm performance. In addition, the findings indicate a significant positive mediating effect of product innovation on the relationship between dynamic capabilities and firm performance. Another key finding is the positive moderation effect of technology uncertainty on the relationship between product innovation and firm performance.Research limitations/implicationsUsing a single sample (country) limits generalizability due to differences in economic structure and market dynamics. Furthermore, by focusing only on product innovation, the role of other types of innovation is not considered.Practical implicationsThis study emphasizes that, especially in environments with high technology uncertainty, it is important to develop dynamic capabilities for better firm performance as well as turn these capabilities into tangible outputs such as product innovation.Originality/valueThis study examines the relationship between dynamic capabilities and firm performance, which is frequently discussed and extremely important for the literature, from different perspectives within the context of an emerging economy. In addition to the direct relationship between dynamic capabilities and firm performance, the contribution of dynamic capabilities to performance through product innovation, which is an ordinary capability, (together with the moderating effect of technological uncertainty) was investigated.
A Geometric Morphometric Study on the Rat Mandible
Authors: Gürbüz İftar , Demiraslan Yasin 
Published: December 2024

ABSTRACTThe aim of the study was to investigate the shape of the mandible in Wistar albino rats using the geometric morphometric method. However, ‘Is the shape of the mandible different in rats depending on gender?’ the question formed the hypothesis of the study. For this purpose, a total of 52 rat mandibles, 31 female and 21 male rats, were used in the study. The right mandible was photographed from the lateral aspect. A total of 16 landmarks were marked on the photographs. In the study, principal component analysis (PCA) and discriminant function analysis were performed with the MorphoJ program. As a result of the study, 28 principal components (PC) were calculated. The values of variance of the first three PC were explained as 54.887% of the total shape difference. Principal component analysis showed the shape changes were more in mandibular ramus. However, no shape change was observed, especially the most top point of the ventral edge of the mandible at the rostral side. In the graph of PCA, the groups according to gender did not show a clear distinction. According to cross‐validation scores, 24 females and 17 males showed correct grouping. In the study, the shape characteristics of the rat mandible from the lateral aspect were revealed. However, it was determined that the most difference in shape by gender was in the condylar process, coronoid process and angular process. As a result, despite the formal differences, when all the data were evaluated, it was concluded that gender discrimination could be made mostly (77% female, 80% male) according to shape of the rat mandible.
Examining the Effects of Different Exertion Levels and Reference Standards on the Diagnostic Accuracy of Exercise ECG for Detecting Coronary Artery Disease — A Pilot Study
Authors: Heimann Julius , Schramm Thomas , Grauduszus Martin , Joisten Christine 
Published: December 2024

ABSTRACTBackgroundExercise electrocardiogram (ECG) is frequently used for evaluating patients with suspected coronary artery disease (CAD). However, it has been downgraded in international guidelines due to a limited sensitivity and specificity, compared with other non‐invasive tests.MethodsWe hypothesized, that a sufficient exertion going beyond 85% of the age predicted maximal heart rate (APMHR), by considering the achieved level of workload can improve sensitivity and specificity of the exercise ECG. Secondly, the performance of exercise ECG, when evaluated against a functional reference standard has barely been investigated, although an improved diagnostic accuracy has been reported for other non‐invasive tests in this case. Therefore, in this pilot study, a total of 147 patients without known CAD who underwent exercise ECG followed by coronary angiography within 90 days were retrospectively evaluated.ResultsThe combined end point of 85% of APMHR and 75% of the predicted workload showed a slight but not statistically significant benefit over APMHR alone (66.7% vs. 58.1%; p = 0.545). The sensitivity of ST‐segment depression was 51.3% for detecting anatomically defined CAD and 62.5% for functionally relevant CAD (p = 0.378).ConclusionsAlthough the results of this pilot study lack statistical significance, the numeric differences clearly justify further research on this topic.