bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D reconstructions of brain from MRI scans using neural radiance fields
Authors: Iddrisu Khadija , Malec Sylwia , Crimi Alessandro 
Published: April 2023

AbstractThe advent of 3D Magnetic Resonance Imaging (MRI) has revolutionized medical imaging and diagnostic capabilities, allowing for more precise diagnosis, treatment planning, and improved patient outcomes. 3D MRI imaging enables the creation of detailed 3D reconstructions of anatomical structures that can be used for visualization, analysis, and surgical planning. However, these reconstructions often require many scan acquisitions, demanding a long session to use the machine and requiring the patient to remain still, with consequent possible motion artifacts. The development of neural radiance fields (NeRF) technology has shown promising results in generating highly accurate 3D reconstructions of MRI images with less user input. Our approach is based on neural radiance fields to reconstruct 3D projections from 2D slices of MRI scans. We do this by using 3D convolutional neural networks to address challenges posed by variable slice thickness; incorporating multiple MRI modalities to ensure robustness and extracting the shape and volumetric depth of both surface and internal anatomical structures with slice interpolation. This approach provides more comprehensive and robust 3D reconstructions of both surface and internal anatomical structures and has significant potential for clinical applications, allowing medical professionals to better visualize and analyze anatomical structures with less available data, potentially reducing times and motion-related issues.
A crucial role for dynamic expression of components encoding the negative arm of the circadian clock
Authors: Wang Bin , Zhou Xiaoying , Kettenbach Arminja N. , Mitchell Hugh D. , Markillie Lye Meng , Loros Jennifer J. , Dunlap Jay C. 
Published: April 2023

ABSTRACTIn theNeurosporacircadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm componentfrequency(frq). FRQ interacts with FRH (FRQ-interacting helicase) and CK-1 forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated asbrd-8, that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss ofbrd-8reduces H4 acetylation and RNA polymerase (Pol) II occupancy atfrqand other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression ofbrd-8, bye-1, histone hH2Az, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin.Taken together, our data identify new auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamicfrqexpression and thereby a normal and persistent circadian rhythm.
Risks of digestive diseases in long COVID: Evidence from a large-scale cohort study
Authors: Ma Yuying , Zhang Lijun , Wei Rui , Dai Weiyu , Zeng Ruijie , Luo Dongling , Jiang Rui , Wu Huihuan , Zhuo Zewei , Yang Qi , Li Jingwei , Leung Felix W , Duan Chongyang , Sha Weihong , Chen Hao 
Published: April 2023

AbstractObjectivesThis study aims to evaluate the effect of coronavirus disease 2019 (COVID-19) on the long-term risk of digestive diseases in the general population.DesignLarge-scale population-based cohort study based on a prospective cohort.SettingUK Biobank cohort linked to multiple nationwide electronic health records databases.ParticipantsThe cohort consisted of 112,311 individuals who survived the initial 30 days following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as well as two control groups: a contemporary group (n = 359,671) without any history of COVID-19, and a historical control group (n = 370,979) that predated the COVID-19 outbreak.Main outcome measuresMain outcomes were predefined digestive diseases. Hazard ratios and corresponding 95% confidence intervals (CI) were computed utilizing the Cox regression models after inverse probability weighting.ResultsCompared with the contemporary control group, patients with previous COVID-19 infection had higher risks of digestive diseases, including functional gastrointestinal disorders (hazard ratios [HR] 1.95 (95% CI 1.62 to 2.35)); peptic ulcer disease (HR 1.27 (1.04 to 1.56)); gastroesophageal reflux disease (GERD) (HR 1.46 (1.34 to 1.58)); inflammatory bowel diseases (HR 1.40 (1.02 to 1.90)); gallbladder disease (HR 1.28 (1.13 to 1.46)); severe liver disease (HR 1.46 (1.12 to 1.90)); non-alcoholic liver disease (HR 1.33 (1.15 to 1.55)); and pancreatic disease (HR 1.43 (1.17 to 1.74)). The risks of GERD were stepwise increased with severity of the acute phase of COVID-19 infection. The results were consistent when using the historical cohort as the control group.ConclusionsOur study provides important insights into the association between COVID-19 and the long-term risk of digestive system disorders. COVID-19 patients are at a higher risk of developing gastrointestinal disorders, with stepwise increased risk with the severity and persisting even after one year follow-up.
Epistasis between mutator alleles contributes to germline mutation spectra variability in laboratory mice
Authors: Sasani Thomas A. , Quinlan Aaron R. , Harris Kelley 
Published: April 2023

AbstractMaintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair [1],mutator alleleshave largely eluded detection in mammals.DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum ofde novomutations — the frequencies of C>T, A>G, etc. — will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair geneMutyhthat increased the C>A germline mutation rate in a family of inbred mice known as the BXDs [2,3].In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlapsOgg1, a DNA glycosylase involved in the same base-excision repair network asMutyh[4]. Its effect depended on the presence of a mutator allele nearMutyh, and BXDs with mutator alleles at both loci had greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
Optimized replication of arrayed bacterial mutant libraries increase access to biological resources
Authors: Willett Julia L. E. , Barnes Aaron M. T. , Brunson Debra N. , Lecomte Alexandre , Robertson Ethan B. , Dunny Gary M. 
Published: April 2023

AbstractBiological collections, including arrayed libraries of single transposon or deletion mutants, greatly accelerate the pace of bacterial genetics research. Despite the importance of these resources, few protocols exist for the replication and distribution of these materials. Here, we describe a protocol for creating multiple replicates of an arrayed bacterial Tn library consisting of approximately 6,800 mutants in 73 × 96-well plates. Our protocol provides multiple checkpoints to guard against contamination and minimize genetic drift caused by freeze/thaw cycles. This approach can also be scaled for arrayed culture collections of various sizes. Overall, this protocol is a valuable resource for other researchers considering the construction and distribution of arrayed culture collection resources for the benefit of the greater scientific community.ImportanceArrayed mutant collections drive robust genetic screens, yet few protocols exist for replication of these resources and subsequent quality control. Increasing distribution of arrayed biological collections will increase accessibility to and use of these resources. Developing standardized techniques for replication of these resources is essential for ensuring their quality and usefulness to the scientific community.
An energy costly architecture of neuromodulators for human brain evolution and cognition
Authors: Castrillon Gabriel , Epp Samira , Bose Antonia , Fraticelli Laura , Hechler André , Belenya Roman , Ranft Andreas , Yakushev Igor , Utz Lukas , Sundar Lalith , Rauschecker Josef P , Preibisch Christine , Kurcyus Katarzyna , Riedl Valentin 
Published: April 2023

AbstractHumans spend more energy on the brain than any other species. However, the high energy demand cannot be fully explained by brain size scaling alone. We hypothesized that energy-demanding signaling strategies may have contributed to human cognitive development. We measured the energy distribution along signaling pathways using multimodal brain imaging and found that evolutionarily novel connections have up to 67% higher energetic costs of signaling than sensory-motor pathways. Additionally, histology, transcriptomic data, and molecular imaging independently reveal an upregulation of signaling at G-protein coupled receptors in energy-demanding regions. We found that neuromodulators are predominantly involved in complex cognition such as reading or memory processing. Our study suggests that the upregulation of neuromodulator activity, alongside increased brain size, is a crucial aspect of human brain evolution.
Root branching in salt requires auxin-independent modulation of LBD16 function
Authors: Zhang Yanxia , Li Yiyun , de Zeeuw Thijs , Duijts Kilian , Kawa Dorota , Lamers Jasper , Munzert Kristina S. , Li Hongfei , Zou Yutao , Meyer A. Jessica , Yan Jinxuan , Verstappen Francel , Wang Yixuan , Gijsberts Tom , Wang Jielin , Gigli-Bisceglia Nora , Engelsdorf Timo , van Dijk Aalt D.J , Testerink Christa 
Published: April 2023

AbstractSalinity stress constrains lateral root (LR) growth and severely impacts plant growth. Auxin signaling is indispensable for the regulation of LR formation. Nevertheless, the molecular mechanism of how salinity affects root auxin signaling and whether salt would steer alternative pathway(s) to regulate LR development is unknown. Here we show that the auxin- regulated transcription factor LATERAL ORGAN BOUNDARY DOMAIN (LBD)16, known as an essential player for LR development under control conditions, is regulated by an alternative non-canonical pathway under salinity. Salt represses auxin signaling but in parallel activates an upstream transcriptional activator of LBD16, ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6). ZAT6 modulates the activity ofLBD16to contribute to downstream cell wall remodeling, and promotes LR development under salinity stress. Our study thus shows that root developmental plasticity in response to salt stress is achieved by integration of auxin- dependent repressive and salt-activated auxin-independent pathways converging on LBD16 to modulate root branching modulation under salinity.
Direction-dependent neural control of finger dexterity in humans
Authors: Rajchert Ohad , Ofir-Geva Shay , Melul Yoel , Khoury-Mireb Mona , Bar-Sela Orit Wonderman , Granot Osnat , Caspi Tom , Toledo Silvi Frenkel , Soroker Nachum , Mawase Firas 
Published: April 2023

AbstractHumans, more than all other species, skillfully flex and extend their fingers to perform delicate motor tasks. This unique dexterous ability is a product of the complex anatomical properties of the human hand and the neural mechanisms that control it. Yet, the neural basis that underlies human dexterous hand movement remains unclear. Here we characterizedindividuation(fine control) andstrength(gross control) during flexion and extension finger movements, isolated the peripheral passive mechanical coupling component from the central neuromuscular activity involved in dexterity and then applied voxel-based lesion mapping in first-event sub-acute stroke patients to investigate the causal link between the neural substrates and the behavioral aspects of finger dexterity. We found substantial differences in dexterous behavior, favoring finger flexion over extension. These differences were not caused by peripheral factors but were rather driven by central origins. Lesion-symptom mapping identified a critical brain region for finger individuation within the primary sensory-motor cortex (M1, S1), the premotor cortex (PMC), and the corticospinal (CST) fibers that descend from them. Although there was a great deal of overlap between individuated flexion and extension, we were able to identify distinct areas within this region that were associated exclusively with finger flexion. This flexion-biased differential premotor and motor cortical organization was associated with the finger individuation component, but not with finger strength. Conversely, lesion mapping revealed slight extension-biases in finger strength within descending tracts of M1. From these results we propose a model that summarizes the distinctions between individuation and strength and between finger movement in flexion and extension, revealed in human manual dexterity.
Inhibitory neurons control the consolidation of neural assemblies via adaptation to selective stimuli
Authors: Bergoin Raphaël , Torcini Alessandro , Deco Gustavo , Quoy Mathias , Zamora-López Gorka 
Published: April 2023

ABSTRACTBrain circuits display modular architecture at different scales of organization. Such neural assemblies are typically associated to functional specialization but the mechanisms leading to their emergence and consolidation still remain elusive. In this paper we investigate the role of inhibition in structuring new neural assemblies driven by the entrainment to various inputs. In particular, we focus on the role of partially synchronized dynamics for the creation and maintenance of structural modules in neural circuits by considering a network of excitatory and inhibitoryθ-neurons with plastic Hebbian synapses. The learning process consists of an entrainment to temporally alternating stimuli that are applied to separate regions of the network. This entrainment leads to the emergence of modular structures. Contrary to common practice in artificial neural networks – where the acquired weights are typically frozen after the learning session – we allow for synaptic adaptation even after the learning phase. We find that the presence of inhibitory neurons in the network is crucial for the emergence and the post-learning consolidation of the modular structures. Indeed networks made of purely excitatory neurons or of neurons not respecting Dale’s principle are unable to form or maintain the modular architecture induced by the entrained stimuli. We also demonstrate that the number of inhibitory neurons in the network is directly related to the maximal number of neural assemblies that can be consolidated, supporting the idea that inhibition has a direct impact on the memory capacity of the neural network.
The A domain of clonal complex 1-type fibronectin binding protein B promotes adherence and biofilm formation inStaphylococcus aureus
Authors: Henderson Sara R. , Geoghegan Joan A. 
Published: April 2023

AbstractAdhesive interactions betweenStaphylococcus aureusand the host rely on cell wall-anchored proteins such as fibronectin binding protein B (FnBPB). Recently we showed that the FnBPB protein expressed by clonal complex (CC) 1 isolates ofS. aureusmediates bacterial adhesion to corneodesmosin. The proposed ligand binding region of CC1-type FnBPB shares just 60% amino acid identity with the archetypal FnBPB protein from CC8. Here we investigated ligand binding and biofilm formation by CC1-type FnBPB. We found that the A domain of FnBPB binds to fibrinogen and corneodesmosin and identified residues within the hydrophobic ligand trench in the A domain that are essential for the binding of CC1-type FnBPB to ligands and during biofilm formation. We further investigated the interplay between different ligands and the influence of ligand binding on biofilm formation. Overall, our study provides new insights into the requirements for CC1-type FnBPB-mediated adhesion to host proteins and FnBPB-mediated biofilm formation inS. aureus.
Individual word representations dissociate from linguistic context along a cortical unimodal to heteromodal gradient
Authors: Eisenhauer Susanne , Gonzalez Alam Tirso Rene del Jesus , Cornelissen Piers L. , Smallwood Jonathan , Jefferies Elizabeth 
Published: April 2023

AbstractLanguage comprehension involves multiple hierarchical processing stages across time, space, and levels of representation. When processing a word, the sensory input is transformed into increasingly abstract representations that need to be integrated with the linguistic context. Thus, language comprehension involves both input-driven as well as context-dependent processes. While neuroimaging research has traditionally focused on mapping individual brain regions to the distinct underlying processes, recent studies indicate that whole-brain distributed patterns of cortical activation might be highly relevant for cognitive functions, including language. One such pattern, based on resting-state connectivity, is the ‘principal cortical gradient’, which dissociates sensory from heteromodal brain regions. The present study investigated the extent to which this gradient provides an organizational principle underlying language function, using a multimodal neuroimaging dataset of functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) recordings from 102 participants during sentence reading. We found that the brain response to individual representations of a word (word length, orthographic distance and word frequency), which reflect visual, orthographic, and lexical properties, gradually increases towards the sensory end of the gradient. Although these properties showed opposite effect directions in fMRI and MEG, their association with the sensory end of the gradient was consistent across both neuroimaging modalities. In contrast, MEG revealed that properties reflecting a word’s relation to its linguistic context (semantic similarity and position within the sentence) involve the heteromodal end of the gradient to a stronger extent. This dissociation between individual word and contextual properties was stable across earlier and later time windows during word presentation, indicating interactive processing of word representations and linguistic context at opposing ends of the principal gradient. To conclude, our findings indicate that the principal gradient underlies the organization of a range of linguistic representations while supporting a gradual distinction between context-independent and context-dependent representations. Furthermore, the gradient reveals convergent patterns across neuroimaging modalities (similar location along the gradient) in the presence of divergent responses (opposite effect directions).
Mycobacterium tuberculosisemploys atypical and different classes of B12switches to control separate operons
Authors: Kipkorir Terry , Polgar Peter , Barker Declan , D’Halluin Alexandre , Patel Zaynah , Arnvig Kristine B. 
Published: April 2023

AbstractVitamin B12(B12), an essential cofactor in all domains of life, is producedde novoby only a small subset of prokaryotes, but B12-sensing riboswitches are some of the most widely distributed riboswitches in bacteria.Mycobacterium tuberculosis, the causative agent of the ongoing tuberculosis pandemic, encodes two distinct vitamin B12riboswitches. One controls the expression ofmetE, encoding a B12-independent methionine synthase, while the other is located upstream ofppe2,a PE/PPE family gene whose function is still unresolved. Here, we analyse ligand sensing, secondary structure architecture, and gene expression control mechanisms of these two riboswitches. Our results provide the first evidence of direct ligand binding bymetEandppe2riboswitches and show that the two switches exhibit different preferences for natural isoforms of B12, use distinct regulatory and structural elements, and act as translational OFF switches. Based on our results, we propose that theppe2switch represents a new Class IIc of B12-sensing riboswitches. Moreover, we have identified small translated open reading frames (uORFs) upstream of bothmetEandppe2, which modulate the expression of the respective downstream genes in opposite directions. Translation of themetEriboswitch uORF suppresses MetE expression, while translation of the uORF in theppe2switch is essential for PPE2 expression via the synthesis of a uORF-PPE2 fusion protein. In summary, our findings reveal an unexpected diversity and complexity of B12-dependentcis-regulation inM. tuberculosis, with potential implications for host-pathogen interactions.
When the leader carries your career: a serial mediation testing on the role of servant leadership in career competencies and career adaptability of followers
Authors: Samo Asif Hussain , Bughio Moomal Baig , Ahmed Quratulain Nazeer , Shah Muzafar Ali , Ahmed Shafique 
Published: April 2023

PurposeThe literature on leadership is quite extensive; however, this study explains the impact of leadership styles on career success, career competence and career adaptability in the health sector. It explains the impact of servant leadership on career competence and career adaptability with a serial mediating impact of psychological safety and proactive behavior as well as self-efficacy and proactive behavior.Design/methodology/approachIt is a quantitative study, and it tested the suggested model in hospitals in Pakistan. The data were collected from 310 health practitioners from the hospitals, and it was analyzed with partial least square structural equation modeling.FindingsThe findings suggest that psychological safety and proactive behavior serially mediate the impact of servant leaders on career competence and career adaptability; hence, servant leadership tends to increase career competence and career adaptability of individuals. One more serial mediation has been tested with positive results between servant leadership and career competence and career adaptability.Originality/valueThe study takes a very well theoretically linked model which tests the serial mediating path of servant leadership to career competencies and career adaptability.