bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversifying crop rotation increases food production, reduces net greenhouse gas emissions and improves soil health
Authors: Yang Xiaolin , Xiong Jinran , Du Taisheng , Ju Xiaotang , Gan Yantai , Li Sien , Xia Longlong , Shen Yanjun , Pacenka Steven , Steenhuis Tammo S. , Siddique Kadambot H. M. , Kang Shaozhong , Butterbach-Bahl Klaus 
Published: January 2024

AbstractGlobal food production faces challenges in balancing the need for increased yields with environmental sustainability. This study presents a six-year field experiment in the North China Plain, demonstrating the benefits of diversifying traditional cereal monoculture (wheat–maize) with cash crops (sweet potato) and legumes (peanut and soybean). The diversified rotations increase equivalent yield by up to 38%, reduce N2O emissions by 39%, and improve the system’s greenhouse gas balance by 88%. Furthermore, including legumes in crop rotations stimulates soil microbial activities, increases soil organic carbon stocks by 8%, and enhances soil health (indexed with the selected soil physiochemical and biological properties) by 45%. The large-scale adoption of diversified cropping systems in the North China Plain could increase cereal production by 32% when wheat–maize follows alternative crops in rotation and farmer income by 20% while benefiting the environment. This study provides an example of sustainable food production practices, emphasizing the significance of crop diversification for long-term agricultural resilience and soil health.
Reorganization of intrinsic functional connectivity in early-stage Parkinson’s disease patients with probable REM sleep behavior disorder
Authors: Dan Xiao-Juan , Wang Yu-Wei , Sun Jun-Yan , Gao Lin-Lin , Chen Xiao , Yang Xue-Ying , Xu Er-He , Ma Jing-Hong , Yan Chao-Gan , Wu Tao , Chan Piu 
Published: January 2024

AbstractREM sleep behavior disorder (RBD) symptoms in Parkinson’s disease (PD) suggest both a clinically and pathologically malignant subtype. However, whether RBD symptoms are associated with alterations in the organization of whole-brain intrinsic functional networks in PD, especially at early disease stages, remains unclear. Here we use resting-state functional MRI, coupled with graph-theoretical approaches and network-based statistics analyses, and validated with large-scale network analyses, to characterize functional brain networks and their relationship with clinical measures in early PD patients with probable RBD (PD+pRBD), early PD patients without probable RBD (PD-pRBD) and healthy controls. Thirty-six PD+pRBD, 57 PD-pRBD and 71 healthy controls were included in the final analyses. The PD+pRBD group demonstrated decreased global efficiency (t = -2.036, P = 0.0432) compared to PD-pRBD, and decreased network efficiency, as well as comprehensively disrupted nodal efficiency and whole-brain networks (all eight networks, but especially in the sensorimotor, default mode and visual networks) compared to healthy controls. The PD-pRBD group showed decreased nodal degree in right ventral frontal cortex and more affected edges in the frontoparietal and ventral attention networks compared to healthy controls. Furthermore, the assortativity coefficient was negatively correlated with Montreal cognitive assessment scores in the PD+pRBD group (r = -0.365, P = 0.026, d = 0.154). The observation of altered whole-brain functional networks and its correlation with cognitive function in PD+pRBD suggest reorganization of the intrinsic functional connectivity to maintain the brain function in the early stage of the disease. Future longitudinal studies following these alterations along disease progression are warranted.
Transcriptomic profiling of early synucleinopathy in rats induced with preformed fibrils
Authors: Patterson Joseph R. , Kochmanski Joseph , Stoll Anna C. , Kubik Michael , Kemp Christopher J. , Duffy Megan F. , Thompson Kajene , Howe Jacob W. , Cole-Strauss Allyson , Kuhn Nathan C. , Miller Kathryn M. , Nelson Seth , Onyekpe Christopher U. , Beck John S. , Counts Scott E. , Bernstein Alison I. , Steece-Collier Kathy , Luk Kelvin C. , Sortwell Caryl E. 
Published: January 2024

AbstractExamination of early phases of synucleinopathy when inclusions are present, but long before neurodegeneration occurs, is critical to both understanding disease progression and the development of disease modifying therapies. The rat alpha-synuclein (α-syn) preformed fibril (PFF) model induces synchronized synucleinopathy that recapitulates the pathological features of Parkinson’s disease (PD) and can be used to study synucleinopathy progression. In this model, phosphorylated α-syn (pSyn) inclusion-containing neurons and reactive microglia (major histocompatibility complex-II immunoreactive) peak in the substantia nigra pars compacta (SNpc) months before appreciable neurodegeneration. However, it remains unclear which specific genes are driving these phenotypic changes. To identify transcriptional changes associated with early synucleinopathy, we used laser capture microdissection of the SNpc paired with RNA sequencing (RNASeq). Precision collection of the SNpc allowed for the assessment of differential transcript expression in the nigral dopamine neurons and proximal glia. Transcripts upregulated in early synucleinopathy were mainly associated with an immune response, whereas transcripts downregulated were associated with neurotransmission and the dopamine pathway. A subset of 29 transcripts associated with neurotransmission/vesicular release and the dopamine pathway were verified in a separate cohort of males and females to confirm reproducibility. Within this subset, fluorescent in situ hybridization (FISH) was used to localize decreases in the Syt1 and Slc6a3 transcripts to pSyn inclusion-containing neurons. Identification of transcriptional changes in early synucleinopathy provides insight into the molecular mechanisms driving neurodegeneration.
Different effect of hypo- and hypermetabolism on cognition in dementia with Lewy bodies: are they coupled or independent?
Authors: Jeong Seong Ho , Cha Jungho , Yoo Han Soo , Chung Seok Jong , Jung Jin Ho , Sohn Young H. , Lee Phil Hyu 
Published: January 2024

AbstractPatients with dementia with Lewy bodies (DLB) show widespread brain metabolic changes. This study investigated whether brain hypo- and hypermetabolism in DLB have differential effects on cognition. We enrolled 55 patients with DLB (15 prodromal DLB [MCI-LB] and 40 probable DLB) and 13 healthy controls who underwent 18F-fluorodeoxyglucose positron emission tomography and detailed neuropsychological tests. Metabolic indices reflecting associated changes in regional cerebral glucose metabolism were calculated as follows: index(-) for hypometabolism [DLB-hypo] and index(+) for hypermetabolism [DLB-hyper]. The effects of DLB-hypo or DLB-hyper on cognitive function were assessed using a multivariate linear regression model. Additionally, a linear mixed model was used to investigate the association between each index and the longitudinal cognitive decline. There was no correlation between DLB-hypo and DLB-hyper in the disease group. The multivariate linear regression model showed that DLB-hypo was associated with language, visuospatial, visual memory, and frontal/executive functions; whereas DLB-hyper was responsible for attention and verbal memory. There was significant interaction between DLB-hypo and DLB-hyper for verbal and visual memory, which was substantially affected by DLB-hyper in relatively preserved DLB-hypo status. A linear mixed model showed that DLB-hypo was associated with longitudinal cognitive outcomes, regardless of cognitive status, and DLB-hyper contributed to cognitive decline only in the MCI-LB group. The present study suggests that DLB-hypo and DLB-hyper may be independent of each other and differentially affect the baseline and longitudinal cognitive function in patients with DLB.
Periodicity staircase in a centrosymmetric Fe/Gd magnetic thin film system
Authors: Singh Arnab , Li Junli , Montoya Sergio A. , Morley Sophie , Fischer Peter , Kevan Steve D. , Fullerton Eric E. , Yao Dao-Xin , Datta Trinanjan , Roy Sujoy 
Published: January 2024

AbstractThe presence of multiple competing periodicities may result in a system to go through states with modulated periodicities, an example of which is the self-similar staircase-like structure called the Devil’s Staircase. Herein we report on a novel staircase structure of domain periodicity in an amorphous and centrosymmetric Fe/Gd magnetic thin film system wherein the reciprocal space wavevector Q due to the ordered stripe domains does not evolve continuously, rather exhibits a staircase structure. Resonant X-ray scattering experiments show jumps in the periodicity of the stripe domains as a function of an external magnetic field. When resolved in components, the length-scale step change along Qx was found to be an integral multiple of a minimum step height of 7 nm, which resembles closely to the exchange length of the system. Modeling the magnetic texture in the Fe/Gd system as an achiral spin arrangement, we have been able to reproduce the steps in the magnetization using a Landau-Lifshitz spin dynamics calculation. Our results indicate that anisotropy and not the dipolar interaction is the dominant cause for the staircase pattern, thereby revealing the effect of achiral magnetism.
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens
Authors: Pfeilmeier Sebastian , Werz Anja , Ote Marine , Bortfeld-Miller Miriam , Kirner Pascal , Keppler Andreas , Hemmerle Lucas , Gäbelein Christoph G. , Petti Gabriella C. , Wolf Sarah , Pestalozzi Christine M. , Vorholt Julia A. 
Published: January 2024

AbstractIn healthy plants, the innate immune system contributes to maintenance of microbiota homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis, and enrichment of opportunistic plant pathogens like Xanthomonas. It is currently unclear whether the microbiota change occurs independently of the opportunistic pathogens or is caused by the latter. Here we tested if protein export through the type-2 secretion system (T2SS) by Xanthomonas causes microbiome dysbiosis in Arabidopsis thaliana in immunocompromised plants. We found that Xanthomonas strains secrete a cocktail of plant cell wall-degrading enzymes that promote Xanthomonas growth during infection. Disease severity and leaf tissue degradation were increased in A. thaliana mutants lacking the NADPH oxidase RBOHD. Experiments with gnotobiotic plants, synthetic bacterial communities and wild-type or T2SS-mutant Xanthomonas revealed that virulence and leaf microbiome composition are controlled by the T2SS. Overall, a compromised immune system in plants can enrich opportunistic pathogens, which damage leaf tissues and ultimately cause microbiome dysbiosis by facilitating growth of specific commensal bacteria.
3D nanofabricated soft microrobots with super-compliant picoforce springs as onboard sensors and actuators
Authors: Xu Haifeng , Wu Song , Liu Yuan , Wang Xiaopu , Efremov Artem K. , Wang Lei , McCaskill John S. , Medina-Sánchez Mariana , Schmidt Oliver G. 
Published: January 2024

AbstractMicroscale organisms and specialized motile cells use protein-based spring-like responsive structures to sense, grasp and move. Rendering this biomechanical transduction functionality in an artificial micromachine for applications in single-cell manipulations is challenging due to the need for a bio-applicable nanoscale spring system with a large and programmable strain response to piconewton-scale forces. Here we present three-dimensional nanofabrication and monolithic integration, based on an acrylic elastomer photoresist, of a magnetic spring system with quantifiable compliance sensitive to 0.5 pN, constructed with customized elasticity and magnetization distributions at the nanoscale. We demonstrate the effective design programmability of these ‘picospring’ ensembles as energy transduction mechanisms for the integrated construction of customized soft micromachines, with onboard sensing and actuation functions at the single-cell scale for microrobotic grasping and locomotion. The integration of active soft springs into three-dimensional nanofabrication offers an avenue to create biocompatible soft microrobots for non-disruptive interactions with biological entities.
Inferring neural activity before plasticity as a foundation for learning beyond backpropagation
Authors: Song Yuhang , Millidge Beren , Salvatori Tommaso , Lukasiewicz Thomas , Xu Zhenghua , Bogacz Rafal 
Published: January 2024

AbstractFor both humans and machines, the essence of learning is to pinpoint which components in its information processing pipeline are responsible for an error in its output, a challenge that is known as ‘credit assignment’. It has long been assumed that credit assignment is best solved by backpropagation, which is also the foundation of modern machine learning. Here, we set out a fundamentally different principle on credit assignment called ‘prospective configuration’. In prospective configuration, the network first infers the pattern of neural activity that should result from learning, and then the synaptic weights are modified to consolidate the change in neural activity. We demonstrate that this distinct mechanism, in contrast to backpropagation, (1) underlies learning in a well-established family of models of cortical circuits, (2) enables learning that is more efficient and effective in many contexts faced by biological organisms and (3) reproduces surprising patterns of neural activity and behavior observed in diverse human and rat learning experiments.
PRMT5 inhibition shows in vitro efficacy against H3K27M-altered diffuse midline glioma, but does not extend survival in vivo
Authors: Brown Elizabeth J. , Balaguer-Lluna Leire , Cribbs Adam P. , Philpott Martin , Campo Leticia , Browne Molly , Wong Jong Fu , Oppermann Udo , Carcaboso Ángel M. , Bullock Alex N. , Farnie Gillian 
Published: January 2024

AbstractH3K27-altered Diffuse Midline Glioma (DMG) is a universally fatal paediatric brainstem tumour. The prevalent driver mutation H3K27M creates a unique epigenetic landscape that may also establish therapeutic vulnerabilities to epigenetic inhibitors. However, while HDAC, EZH2 and BET inhibitors have proven somewhat effective in pre-clinical models, none have translated into clinical benefit due to either poor blood–brain barrier penetration, lack of efficacy or toxicity. Thus, there remains an urgent need for new DMG treatments. Here, we performed wider screening of an epigenetic inhibitor library and identified inhibitors of protein arginine methyltransferases (PRMTs) among the top hits reducing DMG cell viability. Two of the most effective inhibitors, LLY-283 and GSK591, were targeted against PRMT5 using distinct binding mechanisms and reduced the viability of a subset of DMG cells expressing wild-type TP53 and mutant ACVR1. RNA-sequencing and phenotypic analyses revealed that LLY-283 could reduce the viability, clonogenicity and invasion of DMG cells in vitro, representing three clinically important phenotypes, but failed to prolong survival in an orthotopic xenograft model. Together, these data show the challenges of DMG treatment and highlight PRMT5 inhibitors for consideration in future studies of combination treatments.
Assessing hypo-arousal during reward anticipation with pupillometry in patients with major depressive disorder: replication and correlations with anhedonia
Authors: Brendler Andy , Schneider Max , Elbau Immanuel G. , Sun Rui , Nantawisarakul Taechawidd , Pöhlchen Dorothee , Brückl Tanja ,   BeCOME Working Group, Brem A. K. , Binder E. B. , Erhardt A. , Fietz J. , Grandi N. C. , Kim Y. , Ilić-Ćoćić S. , Leuchs L. , Lucae S. , Namendorf T. , Pape J. , Schilbach L. , von Mücke-Heim I. , Ziebula J. , Czisch Michael , Sämann Philipp G. , Lee Michael D. , Spoormaker Victor I. 
Published: January 2024

AbstractMajor depressive disorder (MDD) is a devastating and heterogenous disorder for which there are no approved biomarkers in clinical practice. We recently identified anticipatory hypo-arousal indexed by pupil responses as a candidate mechanism subserving depression symptomatology. Here, we conducted a replication and extension study of these findings. We analyzed a replication sample of 40 unmedicated patients with a diagnosis of depression and 30 healthy control participants, who performed a reward anticipation task while pupil responses were measured. Using a Bayesian modelling approach taking measurement uncertainty into account, we could show that the negative correlation between pupil dilation and symptom load during reward anticipation is replicable within MDD patients, albeit with a lower effect size. Furthermore, with the combined sample of 136 participants (81 unmedicated depressed and 55 healthy control participants), we further showed that reduced pupil dilation in anticipation of reward is inversely associated with anhedonia items of the Beck Depression Inventory in particular. Moreover, using simultaneous fMRI, particularly the right anterior insula as part of the salience network was negatively correlated with depressive symptom load in general and anhedonia items specifically. The present study supports the utility of pupillometry in assessing noradrenergically mediated hypo-arousal during reward anticipation in MDD, a physiological process that appears to subserve anhedonia.
Diagnostic performance of wide-field optical coherence tomography angiography for high myopic glaucoma
Authors: Hong Rim Kyung , Kim Ji Hong , Toh Gyungmin , Na Kyeong Ik , Seong Mincheol , Lee Won June 
Published: January 2024

AbstractDiagnosing and monitoring glaucoma in high myopic (HM) eyes are becoming very important; however, it is challenging to diagnose this condition. This study aimed to evaluate the diagnostic ability of wide-field optical coherence tomography angiography (WF-OCTA) maps for the detection of glaucomatous damage in eyes with HM and to compare the diagnostic ability of WF-OCTA maps with that of conventional imaging approaches, including swept-source optical coherence tomography (SS-OCT) wide-field maps. In this retrospective observational study, a total 62 HM-healthy eyes and 140 HM eyes with open-angle glaucoma were included. Patients underwent a comprehensive ocular examination, including SS-OCT wide-field and 12 × 12 WF-OCTA scans. The WF-OCTA map represents the peripapillary and macular superficial vascular density maps. Glaucoma specialists determined the presence of glaucomatous damage in HM eyes by reading the WF-OCTA map and comparing its sensitivity and specificity with those of conventional SS-OCT images. The sensitivity and specificity of 12 × 12 WF-OCTA scans for HM-glaucoma diagnosis were 87.28% and 86.94%, respectively, while, the sensitivity and specificity of SS-OCT wide-field maps for HM-glaucoma diagnosis were 87.49% and 80.51%, respectively. The specificity of the WF-OCTA map was significantly higher than that of the SS-OCT wide-field map (p < 0.05). The sensitivity of the WF-OCTA map was comparable with that of the SS-OCT wide-field map (p = 0.078). The WF-OCTA map showed good diagnostic ability for discriminating HM-glaucomatous eyes from HM-healthy eyes. As a complementary method to an alternative imaging modality, WF-OCTA mapping can be a useful tool for the detection of HM glaucoma.
Deep learning-based prediction of in-hospital mortality for sepsis
Authors: Yong Li , Zhenzhou Liu 
Published: January 2024

AbstractAs a serious blood infection disease, sepsis is characterized by a high mortality risk and many complications. Accurate assessment of mortality risk of patients with sepsis can help physicians in Intensive Care Unit make optimal clinical decisions, which in turn can effectively save patients’ lives. However, most of the current clinical models used for assessing mortality risk in sepsis patients are based on conventional indicators. Unfortunately, some of the conventional indicators have been shown to be inapplicable in the accurate clinical diagnosis nowadays. Meanwhile, traditional evaluation models only focus on a small amount of personal data, causing misdiagnosis of sepsis patients. We refine the core indicators for mortality risk assessment of sepsis from massive clinical electronic medical records with machine learning, and propose a new mortality risk assessment model, DGFSD, for sepsis patients based on deep learning. The DGFSD model can not only learn individual clinical information about unassessed patients, but also obtain information about the structure of the similarity graph between diagnosed patients and patients to be assessed. Numerous experiments have shown that the accuracy of the DGFSD model is superior to baseline methods, and can significantly improve the efficiency of clinical auxiliary diagnosis.
HMGB1 mediates microbiome-immune axis dysregulation underlying reduced neutralization capacity in obesity-related post-acute sequelae of SARS-CoV-2
Authors: Rubas Noelle C. , Peres Rafael , Kunihiro Braden P. , Allan Nina P. , Phankitnirundorn Krit , Wells Riley K. , McCracken Trevor , Lee Rosa H. , Umeda Lesley , Conching Andie , Juarez Ruben , Maunakea Alika K. 
Published: January 2024

AbstractWhile obesity is a risk factor for post-acute sequelae of SARS-CoV-2 infection (PASC, "long-COVID"), the mechanism(s) underlying this phenomenon remains poorly understood. To address this gap in knowledge, we performed a 6-week longitudinal study to examine immune activity and gut microbiome dysbiosis in post-acute stage patients recovering from SARS-CoV-2 infection. Self-reported symptom frequencies and blood samples were collected weekly, with plasma assessed by ELISA and Luminex for multiple biomarkers and immune cell profiling. DNA from stool samples were collected at the early stage of recovery for baseline assessments of gut microbial composition and diversity using 16S-based metagenomic sequencing. Multiple regression analyses revealed obesity-related PASC linked to a sustained proinflammatory immune profile and reduced adaptive immunity, corresponding with reduced gut microbial diversity. In particular, enhanced signaling of the high mobility group box 1 (HMGB1) protein was found to associate with this dysregulation, with its upregulated levels in plasma associated with significantly impaired viral neutralization that was exacerbated with obesity. These findings implicate HMGB1 as a candidate biomarker of PASC, with potential applications for risk assessment and targeted therapies.
Rapid artefact removal and H&E-stained tissue segmentation
Authors: Schreiber B. A. , Denholm J. , Jaeckle F. , Arends M. J. , Branson K. M. , Schönlieb C.-B. , Soilleux E. J. 
Published: January 2024

AbstractWe present an innovative method for rapidly segmenting haematoxylin and eosin (H&E)-stained tissue in whole-slide images (WSIs) that eliminates a wide range of undesirable artefacts such as pen marks and scanning artefacts. Our method involves taking a single-channel representation of a low-magnification RGB overview of the WSI in which the pixel values are bimodally distributed such that H&E-stained tissue is easily distinguished from both background and a wide variety of artefacts. We demonstrate our method on 30 WSIs prepared from a wide range of institutions and WSI digital scanners, each containing substantial artefacts, and compare it to segmentations provided by Otsu thresholding and Histolab tissue segmentation and pen filtering tools. We found that our method segmented the tissue and fully removed all artefacts in 29 out of 30 WSIs, whereas Otsu thresholding failed to remove any artefacts, and the Histolab pen filtering tools only partially removed the pen marks. The beauty of our approach lies in its simplicity: manipulating RGB colour space and using Otsu thresholding allows for the segmentation of H&E-stained tissue and the rapid removal of artefacts without the need for machine learning or parameter tuning.