bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Federated Learning for distributed NeuroImaging Data
Authors: Thapaliya Bishal , Ohib Riyasat , Geenjar Eloy , Liu Jingyu , Calhoun Vince , Plis Sergey 
Published: May 2024

ABSTRACTRecent advancements in neuroimaging have led to greater data sharing among the scientific community. However, institutions frequently maintain control over their data, citing concerns related to research culture, privacy, and accountability. This creates a demand for innovative tools capable of analyzing amalgamated datasets without the need to transfer actual data between entities. To address this challenge, we propose a decentralized sparse federated learning (FL) strategy. This approach emphasizes local training of sparse models to facilitate efficient communication within such frameworks. By capitalizing on model sparsity and selectively sharing parameters between client sites during the training phase, our method significantly lowers communication overheads. This advantage becomes increasingly pronounced when dealing with larger models and accommodating the diverse resource capabilities of various sites. We demonstrate the effectiveness of our approach through the application to the Adolescent Brain Cognitive Development (ABCD) dataset.
Excitoprotective effects of conditional tau reduction in excitatory neurons and in adulthood
Authors: Voskobiynyk Yuliya , Li Zhiyong , Cochran J. Nicholas , Davis M. Natalie , Carullo Nancy V.N. , Creed Rose B. , Buckingham Susan C. , Hall Alicia M. , Wilson Scott M. , Roberson Erik D. 
Published: May 2024

ABSTRACTTau reduction is a promising therapeutic strategy for Alzheimer’s disease. In numerous models, tau reduction via genetic knockout is beneficial, at least in part due to protection against hyperexcitability and seizures, but the underlying mechanisms are unclear. Here we describe the generation and initial study of a new conditional Taufloxmodel to address these mechanisms. Given the protective effects of tau reduction against hyperexcitability, we compared the effects of selective tau reduction in excitatory or inhibitory neurons. Tau reduction in excitatory neurons mimicked the protective effects of global tau reduction, while tau reduction in inhibitory neurons had the opposite effect and increased seizure susceptibility. Since most prior studies used knockout mice lacking tau throughout development, we crossed Taufloxmice with inducible Cre mice and found beneficial effects of tau reduction in adulthood. Our findings support the effectiveness of tau reduction in adulthood and indicate that excitatory neurons may be a key site for its excitoprotective effects.SUMMARYA new conditional tau knockout model was generated to study the protective effects of tau reduction against hyperexcitability. Conditional tau reduction in excitatory, but not inhibitory, neurons was excitoprotective, and induced tau reduction in adulthood was excitoprotective without adverse effects.
A Generalized Signal Model for Dual-Module Velocity-Selective Arterial Spin Labeling
Authors: Liu Thomas T. , Chen Conan , Guo Jia , Wong Eric C. , Bolar Divya S. 
Published: May 2024

AbstractPurposeTo develop a generalized signal model for dual-module velocity-selective arterial spin labeling (dm-VSASL) that can integrate arbitrary saturation and inversion profiles.Theory and MethodsA recently developed mathematical framework for single-module VSASL is extended to address the increased complexity of dm-VSASL and to model the use of realistic velocity-selective profiles in the label-control and vascular crushing modules. Expressions for magnetization difference, arterial delivery functions, labeling efficiency, and cerebral blood flow (CBF) estimation error are presented. Sources of error are examined and timing requirements to minimize quantification errors are derived.ResultsFor ideal velocity-selective profiles, the predicted signals match those of prior work. With realistic profiles, a CBF-dependent estimation error can occur when velocity-selective inversion (VSI) is used for the labeling modules and velocity-selective saturation (VSS) is used for the vascular crushing module. The error reflects a mismatch between the leading and trailing edges of the delivery function for the second bolus and can be minimized by choosing a nominal labeling cutoff velocity that is lower than the nominal saturation cutoff velocity. In the presence ofB0andB1inhomogeneities, the labeling efficiency of dual-module VSI is more attenuated than that of dual-module VSS.ConclusionThe proposed signal model will enable researchers to more accurately assess and compare the performance of realistic dm-VSASL implementations and improve the quantification of dm-VSASL CBF measures.
The Role of Deep Learning in Diagnostic Imaging of Spondyloarthropathies: A Systematic Review
Authors: Omar Mahmud , Watad Abdulla , McGonagle Dennis , Soffer Shelly , Glicksberg Benjamin S , Nadkarni Girish N , Klang Eyal 
Published: May 2024

AbstractAimDiagnostic imaging is an integral part of identifying spondyloarthropathies (SpA), yet the interpretation of these images can be challenging. This review evaluated the use of deep learning models to enhance the diagnostic accuracy of SpA imaging.MethodsFollowing PRISMA guidelines, we systematically searched major databases up to February 2024, focusing on studies that applied deep learning to SpA imaging. Performance metrics, model types, and diagnostic tasks were extracted and analyzed. Study quality was assessed using QUADAS-2.ResultsWe included 22 studies demonstrating that deep learning aids in diagnosing and classifying SpA, differentiating arthritis forms, and estimating disease progression and structural changes. These models, particularly those using advanced U-Net architectures, consistently outperformed traditional diagnostic methods, showing a notable increase in diagnostic accuracy.ConclusionDeep learning models are excellent for augmenting the accuracy of SpA imaging diagnostics. Despite their potential, challenges in overcoming retrospective study biases and integrating these models into clinical practice remain. Future directions should aim to validate these models in real-world clinical settings.
Unmasking the determinants of knowledge, attitude and practice of Personal Protective Equipment use among Nepalese farmers using pesticides
Authors: Piya Reecha , G.C Krishna , Rajbhandari Ajay K. , Kakchapati Sampurna 
Published: May 2024

AbstractBackgroundFarmer using commercially available chemical pesticides are at high risk to develop various pesticide-related-illnesses. To mitigate the adverse effect of pesticides, it is crucial for famers to wear Personal Protective Equipment (PPE). This study aimed to assess the factors influencing knowledge, attitude, and practice (KAP) of PPE use among farmers using pesticides in mid-hills of Nepal.MethodsWe conducted a cross-sectional study among 256 farmers in Kirtipur Municipality. We collected data using structured questionnaire via telephone. Bi-variate and multivariate logistic regression was done to identify the association between individual, household and farming related characteristic with knowledge, attitude, and practice of PPE use.ResultsThe study found that the knowledge, attitude, and practice of PPE use was 53.75%, 55.11%, and 47.16%, respectively. The farmers with primary level schooling (AOR= 2.63; 95% CI 1.00-6.88) and secondary level schooling or higher (AOR= 4.19; 95% CI 1.64-0.68) had higher odds of having knowledge on PPE use rather than the farmers with no formal schooling. Farmers of upper lower socioeconomic status had higher odds (AOR=6.40; 95% CI 1.68-24.45) of having positive attitude towards PPE use compared to farmers of upper middle and upper socio-economic status. On the contrary, farmers with good knowledge (AOR=0.20; CI 0.09-0.48) and experience of pesticide-related-illness (AOR=0.29; 95% CI 0.13-0.65) had lower odds of having positive attitude towards PPE use. Married farmers (AOR=10.63; 95% CI 1.11-101.95), farmers using pesticides for more than 10 years (AOR=5.22; 95% CI 1.27-21.43), and farmers using pesticides for 10 hours or more in their lifetime (AOR=4.86; 95% CI 1.63-14.50) had higher odds of wearing basic set of PPE while handling pesticides. However, farmers who were involved in farming for more than 10 years (AOR=0.26; 95% CI 0.07-1.03), farmers who were using pesticide applying methods other than knapsack sprayer (AOR=0.03; 95% CI 0.00-0.34), and farmers having positive attitude towards PPE use (AOR=0.28; 95% CI 0.11-0.70) had lower odds of wearing basic set of PPE while handling pesticides.ConclusionFarmers in Nepal have a positive outlook on PPE use but multitude of factors including knowledge, farming related factors and socio-economic condition have acted as barrier to its use. Tailored educational programs that not only encompasses knowledge dissemination but also cultivation of positive safety attitudes towards PPE can help increase PPE use.
Physician burnout in the context of the COVID-19 pandemic: prevalence and associated factors among resident doctors and consultants in Delta State, Nigeria
Authors: Moeteke Nnamdi Stephen , Erhirhie Ezinneamaka 
Published: May 2024

ABSTRACTBackgroundResidents Doctors (RDs) and consultants carry out the most specialised medical care. The strain of their job predisposes them to the three domains of burnout: Emotional Exhaustion (EE), Depersonalisation (DP), and diminished Personal Accomplishment (PA). Globally, this public health crisis has worsened with the overwhelming effect of COVID-19 on health systems.AimThis study assessed the prevalence and associated factors of burnout among RDs and Consultants in tertiary hospitals in Delta State, Nigeria during the pandemic.MethodsA cross-sectional design was employed. Previously validated instruments were used to collect data via an online survey. The questionnaire was sent to physicians selected by multistage sampling. The proportion of participants with a high grade in each of the domains of burnout was obtained. Stepwise analyses from bivariate to multivariate were done to obtain adjusted odds ratios.ResultsThe prevalence of high-grade burnout in EE, DP, and PA was 35.1%, 13.2%, and 33.3% respectively. Relative to those ≤ 30 years, the age group 41 – 50 years had less likelihood of high EE (AOR 0.050; 95% CI 0.004 – 0.651). Other independent predictors of high EE were manageable workload (AOR 0.094; 95% CI 0.027 – 0.328), reward for work (AOR 0.427; 95% CI 0.205 – 0.892), and good leadership (AOR 0.525; 95% CI 0.113 – 0.929).Conclusion and ContributionThis study suggests that the determinants of burnout among RDs and consultants are mainly contextual factors in the work setting. Promoting an institutional culture of leadership, a manageable workload, and appropriate rewards could help control physician burnout.
Functional Magnetic Resonance Spectroscopy of Prolonged Motor Activation using Conventional and Spectral GLM Analyses
Authors: Morelli Maria , Dudzikowska Katarzyna , Deelchand Dinesh K. , Quinn Andrew J. , Mullins Paul G. , Apps Matthew A. J. , Wilson Martin 
Published: May 2024

AbstractBackgroundFunctional MRS (fMRS) is a technique used to measure metabolic changes in response to increased neuronal activity, providing unique insights into neurotransmitter dynamics and neuroenergetics. In this study we investigate the response of lactate and glutamate levels in the motor cortex during a sustained motor task using conventional spectral fitting and explore the use of a novel analysis approach based on the application of linear modelling directly to the spectro-temporal fMRS data.MethodsfMRS data were acquired at a field strength of 3 Tesla from 23 healthy participants using a short echo-time (28ms) semi-LASER sequence. The functional task involved rhythmic hand clenching over a duration of 8 minutes and standard MRS preprocessing steps, including frequency and phase alignment, were employed. Both conventional spectral fitting and direct linear modelling were applied, and results from participant-averaged spectra and metabolite-averaged individual analyses were compared.ResultsWe observed a 20% increase in lactate in response to the motor task, consistent with findings at higher magnetic field strengths. However, statistical testing showed some variability between the two averaging schemes and fitting algorithms. While lactate changes were supported by the direct spectral modelling approach, smaller increases in glutamate (2%) were inconsistent. Exploratory spectral modelling identified a 4% decrease in aspartate, aligning with conventional fitting and observations from prolonged visual stimulation.ConclusionWe demonstrate that lactate dynamics in response to a prolonged motor task are observed using short-echo time semi-LASER at 3 Tesla, and that direct linear modelling of fMRS data is a useful complement to conventional analysis. Future work includes mitigating spectral confounds, such as scalp lipid contamination and lineshape drift, and further validation of our novel direct linear modelling approach through experimental and simulated datasets.
Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life
Authors: Torruella Guifré , Galindo Luis Javier , Moreira David , López-García Purificación 
Published: May 2024

SummaryEukaryotes evolved from prokaryotic predecessors in the early Proterozoic1,2and radiated from their already complex last common ancestor3, diversifying into several supergroups with unresolved deep evolutionary connections4. They evolved extremely diverse lifestyles, playing crucial roles in the carbon cycle5,6. Heterotrophic flagellates are arguably the most diverse eukaryotes4,7-9and often occupy basal positions in phylogenetic trees. However, many of them remain undersampled4,10and/orincertae sedis4,11-18. Progressive improvement of phylogenomic methods and a wider protist sampling have reshaped and consolidated major clades in the eukaryotic tree13-19. This is illustrated by the Opimoda14, one of the largest eukaryotic supergroups (Amoebozoa, Ancyromonadida, Apusomonadida, Breviatea, CRuMs, Malawimonadida, and Opisthokonta –including animals and fungi–)4,14,19-22. However, their deepest evolutionary relationships still remain uncertain. Here, we sequenced transcriptomes of poorly studied flagellates23,24(fourteen apusomonads25,26, seven ancyromonads27and one cultured Mediterranean strain ofMeteora sporadica17) and conducted comprehensive phylogenomics analyses with an expanded taxon sampling of early-branching protists. Our findings support the monophyly of Opimoda, with CRuMs being sister to the Amorphea (amoebozoans, breviates, apusomonads, and opisthokonts), and ancyromonads and malawimonads forming a moderately supported clade. By mapping key complex phenotypic traits onto this phylogenetic framework, we infer an opimodan biflagellate ancestor with an excavate-like feeding groove, which ancyromonads subsequently lost. While breviates and apusomonads retained the ancestral biflagellate state, some early-diverging Amorphea lost one or both flagella, facilitating the evolution of amoeboid morphologies, novel feeding modes, and palintomic cell division resulting in multinucleated cells. These innovations likely facilitated the subsequent evolution of fungal and metazoan multicellularity.
Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network
Authors: Kellman Benjamin P. , Mariethoz Julien , Zhang Yujie , Shaul Sigal , Alteri Mia , Sandoval Daniel , Jeffris Mia , Armingol Erick , Bao Bokan , Lisacek Frederique , Bojar Daniel , Lewis Nathan E. 
Published: May 2024

AbstractGlycosylation is described as a non-templated biosynthesis. Yet, the template-free premise is antithetical to the observation that different N-glycans are consistently placed at specific sites. It has been proposed that glycosite-proximal protein structures could constrain glycosylation and explain the observed microheterogeneity. Using site-specific glycosylation data, we trained a hybrid neural network to parse glycosites (recurrent neural network) and match them to feasible N-glycosylation events (graph neural network). From glycosite-flanking sequences, the algorithm predicts most human N-glycosylation events documented in the GlyConnect database and proposed structures corresponding to observed monosaccharide composition of the glycans at these sites. The algorithm also recapitulated glycosylation in Enhanced Aromatic Sequons, SARS-CoV-2 spike, and IgG3 variants, thus demonstrating the ability of the algorithm to predict both glycan structure and abundance. Thus, protein structure constrains glycosylation, and the neural network enables predictivein silicoglycosylation of uncharacterized or novel protein sequences and genetic variants.
Efficient Genetic Code Expansion Without Host Genome Modifications
Authors: Costello Alan , Peterson Alexander A. , Lanster David L. , Li Zhiyi , Carver Gavriela D. , Badran Ahmed H. 
Published: May 2024

AbstractSupplementing translation with non-canonical amino acids (ncAAs) can yield protein sequences with new-to-nature functions, but existing ncAA incorporation strategies suffer from low efficiency and context dependence. We uncover codon usage as a previously unrecognized contributor to efficient genetic code expansion using non-native codons. Relying only on conventionalE. colistrains with native ribosomes, we develop a novel plasmid-based codon compression strategy that minimizes context dependence and improves ncAA incorporation at quadruplet codons. We confirm that this strategy is compatible with all known genetic code expansion resources, which allows us to identify 12 mutually orthogonal tRNA–synthetase pairs. Enabled by these findings, we evolve and optimize five tRNA–synthetase pairs to incorporate a broad repertoire of ncAAs at orthogonal quadruplet codons. Finally, we extend these resources to anin vivobiosynthesis platform that can readily create >100 new-to-nature peptide macrocycles bearing up to three unique ncAAs. Given the generality of our approach and streamlined resources, our findings will accelerate innovations in multiplexed genetic code expansion and enable the discovery of chemically diverse biomolecules for researcher-defined applications.
Cortico-amygdala synaptic structural abnormalities produced by templated aggregation of α-synuclein
Authors: Gcwensa Nolwazi Z. , Russell Dreson L. , Long Khaliah Y. , Brzozowski Charlotte F. , Liu Xinran , Gamble Karen L. , Cowell Rita M. , Volpicelli-Daley Laura A. 
Published: May 2024

AbstractParkinson’s disease (PD) and Dementia with Lewy bodies (DLB) are characterized by neuronal α-synuclein (α-syn) inclusions termed Lewy Pathology, which are abundant in the amygdala. The basolateral amygdala (BLA), in particular, receives projections from the thalamus and cortex. These projections play a role in cognition and emotional processing, behaviors which are impaired in α-synucleinopathies. To understand if and how pathologic α-syn impacts the BLA requires animal models of α-syn aggregation. Injection of α-synuclein pre-formed fibrils (PFFs) into the striatum induces robust α-synuclein aggregation in excitatory neurons in the BLA that corresponds with reduced contextual fear conditioning. At early time points after aggregate formation, cortico-amygdala excitatory transmission is abolished. The goal of this project was to determine if α-syn inclusions in the BLA induce synaptic degeneration and/or morphological changes. In this study, we used C57BL/6J mice injected bilaterally with PFFs in the dorsal striatum to induce α-syn aggregate formation in the BLA. A method was developed using immunofluorescence and three-dimensional reconstruction to analyze excitatory cortico-amygdala and thalamo-amygdala presynaptic terminals closely juxtaposed to postsynaptic densities. The abundance and morphology of synapses were analyzed at 6- or 12-weeks post-injection of PFFs. α-Syn aggregate formation in the BLA did not cause a significant loss of synapses, but cortico-amygdala and thalamo-amygdala presynaptic terminals and postsynaptic densities with aggregates of α-synuclein show increased volumes, similar to previous findings in human DLB cortex, and in non-human primate models of PD. Transmission electron microscopy showed that PFF-injected mice showed reduced intervesicular distances similar to a recent study showing phospho-serine-129 α-synuclein increases synaptic vesicle clustering. Thus, pathologic α-synuclein causes major alterations to synaptic architecture in the BLA, potentially contributing to behavioral impairment and amygdala dysfunction observed in synucleinopathies.
Clostridium ablates tumors by degrading collagen mesh and inducing ferroptosis
Authors: Yang Fengmin , Meng Lu , Chen Huan , Wang Xinyue , Zhang Mengmeng , Cao Zhenping , Pang Yan , Liu Jinyao 
Published: May 2024

AbstractThe supportive role of extracellular matrix in tumor growth and the drug resistance of tumor cells stand the major challenges in treating cancer. Here, we report the discovery of an oncolytic Clostridium strain, named RJ-1, which simultaneously expresses collagenases and produces iron-containing particles through intrabacterial mineralization. The secreted collagenases degrade pre-existing collagen mesh and show a collagen concentration-dependent degradation feature. Iron-containing particles released from RJ-1 by autolysis generate ferrous ions in the lysosomal acid environment following cell uptake and subsequently induce ferroptosis via the Fenton reaction. Due to selective germination in tumor sites, systemic administration of RJ-1 spores synchronously destructs dense tumor extracellular matrix and causes non-apoptotic tumor cell death. In collagen-dense tumor-bearing mice, a single intravenous injection achieves a favorable tolerance and rapid oncolysis of giant tumors with a size of ∼1000 mm3. This work finds a dual collagenase-expressing and iron-concentrating bacterium, proposing an alternative strategy to combat tumors.
A positive feedback loop between germ cells and gonads induces and maintains cnidarian sexual reproduction
Authors: Curantz Camille , Doody Ciara , Horkan Helen R , Krasovec Gabriel , Weavers Paris K , DuBuc Timothy Q , Frank Uri 
Published: May 2024

AbstractThe fertile gonad includes cells of two distinct developmental origins: the somatic mesoderm and the germline. How somatic and germ cells interact to develop and maintain fertility is not well understood. Here, using grafting experiments and transgenic reporter animals, we find that a specific part of the gonad–the germinal zone–acts as a sexual organizer to induce and maintainde novogerm cells and somatic gonads in non-sexual tissue in the cnidarianHydractinia symbiolongicarpus. We further show that germ cells express a novel member of the TGF-β family (Gonadless,Gls) that induces somatic gonad morphogenesis. Loss ofGlsresulted in animals lacking somatic gonadal structures but having few, non-proliferative germ cells. We propose a model according to which a small number of primary germ cells drive gonad development though Gls morphogen secretion. The germinal zone in the newly formed gonad, in turn, provides positive feedback to induce secondary germ cells by activatingTfap2(the master regulator of germ cell fate) in resident pluripotent stem cells.De novoinduction of germ cells by gonads in adult life is absent in bilaterians with a sequestered germline. However, the contribution of germ cell signaling to the patterning of somatic gonadal tissue, as observed inHydractinia, may be a general animal feature.