bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease
Authors: Zhou Yanyan , Yang Zhen , Liu Jinguang , Li Xudong , Wang Xingxiang , Dai Chuanchao , Zhang Taolin , Carrión Víctor J. , Wei Zhong , Cao Fuliang , Delgado-Baquerizo Manuel , Li Xiaogang 
Published: December 2023

AbstractIt is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.
Electrical performance of a fully reconfigurable series-parallel photovoltaic module
Authors: Calcabrini Andres , Muttillo Mirco , Zeman Miro , Manganiello Patrizio , Isabella Olindo 
Published: December 2023

AbstractReconfigurable photovoltaic modules are a promising approach to improve the energy yield of partially shaded systems. So far, the feasibility of this concept has been evaluated through simulations or simplified experiments. In this work, we analyse the outdoor performance of a full-scale prototype of a series-parallel photovoltaic module with six reconfigurable blocks. Over a 4-month-long period, its performance was compared to a reference photovoltaic module with static interconnections and six bypass diodes. The results show that under partial shading, the reconfigurable module produced 10.2% more energy than the reference module. In contrast, under uniform illumination the energy yield of the reconfigurable PV module was 1.9% lower due to the additional losses introduced by its switching matrix. Finally, a modification in the reconfiguration algorithm is proposed to reduce the output current–voltage range of the module and simplify the design of module-level power converters while limiting the shading tolerance loss.
LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation
Authors: Zhu Yixiao , Huang Chengmei , Zhang Chao , Zhou Yi , Zhao Enen , Zhang Yaxin , Pan Xingyan , Huang Huilin , Liao Wenting , Wang Xin 
Published: December 2023

AbstractGastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subtype associated with a poor prognosis. Here, we apply integrated network analysis to uncover lncRNA heterogeneity between GC subtypes, and identify MIR200CHG as a master regulator mediating EMT specifically in MSS/EMT GC. The expression of MIR200CHG is silenced in MSS/EMT GC by promoter hypermethylation, associated with poor prognosis. MIR200CHG reverses the mesenchymal identity of GC cells in vitro and inhibits metastasis in vivo. Mechanistically, MIR200CHG not only facilitates the biogenesis of its intronic miRNAs miR-200c and miR-141, but also protects miR-200c from target-directed miRNA degradation (TDMD) through direct binding to miR-200c. Our studies reveal a landscape of a subtype-specific lncRNA regulatory network, providing clinically relevant biological insights towards MSS/EMT GC.
Nutrient deprivation alters the rate of COPII subunit recruitment at ER subdomains to tune secretory protein transport
Authors: Kasberg William , Luong Peter , Swift Kevin A. , Audhya Anjon 
Published: December 2023

AbstractCo-assembly of the multilayered coat protein complex II (COPII) with the Sar1 GTPase at subdomains of the endoplasmic reticulum (ER) enables secretory cargoes to be concentrated efficiently within nascent transport intermediates, which subsequently deliver their contents to ER-Golgi intermediate compartments. Here, we define the spatiotemporal accumulation of native COPII subunits and secretory cargoes at ER subdomains under differing nutrient availability conditions using a combination of CRISPR/Cas9-mediated genome editing and live cell imaging. Our findings demonstrate that the rate of inner COPII coat recruitment serves as a determinant for the pace of cargo export, irrespective of COPII subunit expression levels. Moreover, increasing inner COPII coat recruitment kinetics is sufficient to rescue cargo trafficking deficits caused by acute nutrient limitation. Our findings are consistent with a model in which the rate of inner COPII coat addition acts as an important control point to regulate cargo export from the ER.
BACH1 promotes tissue necrosis and Mycobacterium tuberculosis susceptibility
Authors: Amaral Eduardo P. , Namasivayam Sivaranjani , Queiroz Artur T. L. , Fukutani Eduardo , Hilligan Kerry L. , Aberman Kate , Fisher Logan , Bomfim Caio Cesar B. , Kauffman Keith , Buchanan Jay , Santuo Leslie , Gazzinelli-Guimaraes Pedro Henrique , Costa Diego L. , Teixeira Mariane Araujo , Barreto-Duarte Beatriz , Rocha Clarissa Gurgel , Santana Monique Freire , Cordeiro-Santos Marcelo , Barber Daniel L. , Wilkinson Robert J. , Kramnik Igor , Igarashi Kazuhiko , Scriba Thomas , Mayer-Barber Katrin D. , Andrade Bruno B. , Sher Alan 
Published: December 2023

AbstractOxidative stress triggers ferroptosis, a form of cellular necrosis characterized by iron-dependent lipid peroxidation, and has been implicated in Mycobacterium tuberculosis (Mtb) pathogenesis. We investigated whether Bach1, a transcription factor that represses multiple antioxidant genes, regulates host resistance to Mtb. We found that BACH1 expression is associated clinically with active pulmonary tuberculosis. Bach1 deletion in Mtb-infected mice increased glutathione levels and Gpx4 expression that inhibit lipid peroxidation. Bach1−/− macrophages exhibited increased resistance to Mtb-induced cell death, while Mtb-infected Bach1-deficient mice displayed reduced bacterial loads, pulmonary necrosis and lipid peroxidation concurrent with increased survival. Single-cell RNA-seq analysis of lungs from Mtb-infected Bach1−/− mice revealed an enrichment of genes associated with ferroptosis suppression. Bach1 depletion in Mtb-infected B6.Sst1S mice that display human-like necrotic lung pathology also markedly reduced necrosis and increased host resistance. These findings identify Bach1 as a key regulator of cellular and tissue necrosis and host resistance in Mtb infection.
RNAseq of diverse spring wheat cultivars released during last 110 years
Authors: Maqbool Saman , Naseer Samar , Zahra Nageen , Rasool Fatima , Qayyum Humaira , Majeed Khawar , Jahanzaib Muhammad , Sajjad Muhammad , Fayyaz Muhammad , Naeem Muhammad Kashif , Khan Muhammad Ramzan , Zhang Hao , Rasheed Awais , Li Huihui 
Published: December 2023

AbstractHere, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson’s correlation coefficients between root phenotypes and expression of root-specific genes varied from −0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.
Selective digestive tract decontamination to prevent healthcare associated infections in critically ill children: the PICNIC multicentre randomised pilot clinical trial
Authors: Pathan Nazima , Woolfall Kerry , Popa Mariana , de la Fuente Gema Milla , Ferrando-Vivas Paloma , Brown Alanna , Gouliouris Theodore , Tume Lyvonne N. , Shulman Robert , Cuthbertson Brian H. , Sale Isobel , Feltbower Richard G. , Myburgh John , Pappachan John , Harrison David , Mouncey Paul , Rowan Kathryn ,   the PICNIC study investigators, Fulham Charlotte , James Melanie , Beadon Kirsten , Postlethwaite Cat , Pond Jenny , Hargadon-Lowe Antonia , Cassidy Jane , Robbins Ceri , Milner Phil , Dwarakanathan Buvana , De Queiroz Joana Gomes , Daubney Esther , White Deborah , Davis Peter , Dodge Laura , Moody Francesca 
Published: December 2023

AbstractHealthcare-associated infections (HCAIs) are a major cause of morbidity and mortality in critically ill children. Data from adult studies suggest Selective Decontamination of the Digestive tract (SDD) may reduce the incidence of HCAIs and improve survival. There are no data from randomised clinical trials in the paediatric setting. An open label, parallel group pilot cRCT and mixed-methods perspectives study was conducted in six paediatric intensive care units (PICUs) in England. Participants were children (> 37 weeks corrected gestational age, up to 16 years) requiring mechanical ventilation expected to last for at least 48 h. Sites undertook standard care for a period of 9 weeks and were randomised into 3 sites which continued standard care and 3 where SDD was incorporated into infection control practice for eligible children. Interviews and focus groups were conducted for parents and staff working in PICU. 434 children fulfilled eligibility criteria, of whom 368 (85%) were enrolled. This included 207 in the baseline phase (Period One) and 161 in the intervention period (Period Two). In sites delivering SDD, the majority (98%) of children received at least one dose of SDD and of these, 68% commenced within the first 6 h. Whilst admission swabs were collected in 91% of enrolled children, consent for the collection of additional swabs was low (44%). Recruited children were representative of the wider PICU population. Overall, 3.6 children/site/week were recruited compared with the potential recruitment rate for a definitive cRCT of 3 children/site/week, based on data from all UK PICUs. Parents (n = 65) and staff (n = 44) were supportive of the aims of the study, suggesting adaptations for a larger definitive trial including formulation and administration of SDD paste, approaches to consent and ecology monitoring. Stakeholders identified preferred clinical outcomes, focusing on complications of critical illness and quality-of-life. A definitive cRCT in SDD to prevent HCAIs in critically ill children is feasible but should include adaptations to ecology monitoring along with the dosing schedule and packaging into a paediatric specific format. A definitive study is supported by the findings with adaptations to ecology monitoring and SDD administration.Trial Registration: ISRCTN40310490 Registered 30/10/2020.
Phenotyping EMT and MET cellular states in lung cancer patient liquid biopsies at a personalized level using mass cytometry
Authors: Karacosta Loukia G. , Pancirer Danny , Preiss Jordan S. , Benson Jalen A. , Trope Winston , Shrager Joseph B. , Sung Arthur Wai , Neal Joel W. , Bendall Sean C. , Wakelee Heather , Plevritis Sylvia K. 
Published: December 2023

AbstractMalignant pleural effusions (MPEs) can be utilized as liquid biopsy for phenotyping malignant cells and for precision immunotherapy, yet MPEs are inadequately studied at the single-cell proteomic level. Here we leverage mass cytometry to interrogate immune and epithelial cellular profiles of primary tumors and pleural effusions (PEs) from early and late-stage non-small cell lung cancer (NSCLC) patients, with the goal of assessing epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) states in patient specimens. By using the EMT–MET reference map PHENOSTAMP, we observe a variety of EMT states in cytokeratin positive (CK+) cells, and report for the first time MET-enriched CK+ cells in MPEs. We show that these states may be relevant to disease stage and therapy response. Furthermore, we found that the fraction of CD33+ myeloid cells in PEs was positively correlated to the fraction of CK+ cells. Longitudinal analysis of MPEs drawn 2 months apart from a patient undergoing therapy, revealed that CK+ cells acquired heterogeneous EMT features during treatment. We present this work as a feasibility study that justifies deeper characterization of EMT and MET states in malignant cells found in PEs as a promising clinical platform to better evaluate disease progression and treatment response at a personalized level.
Influenza activity and regional mortality for non-small cell lung cancer
Authors: Kinslow Connor J. , Wang Yuankun , Liu Yi , Zuev Konstantin M. , Chaudhary Kunal R. , Wang Tony J. C. , Donalek Ciro , Amori Michael , Cheng Simon K. 
Published: December 2023

AbstractLung cancer is the leading cause of cancer deaths in the United States and worldwide. While influenza illness is known to be particularly dangerous for frail and elderly patients, the relationship between influenza illness and outcomes in patients with cancer remains largely unknown. The Surveillance, Epidemiology, and End Results (SEER) database was queried to identify patients with non-small cell lung cancer (NSCLC) diagnosed between 2009 and 2015. Influenza-like illness (ILI) activity, provided by the Outpatient Influenza-like Illness Surveillance Network of the Center of Disease for Control and Prevention, was merged with the SEER dataset on the state-month level. Regional monthly mortality rates were compared during low versus high flu months in this ecological cohort study. 202,485 patients with NSCLC from 13 SEER-reporting states were included in the analysis. 53 of 1049 state-months (5.1%) had high flu activity. Monthly mortality rates during low and high flu months were 0.041 (95% CI 0.041–0.042) and 0.051 (95% CI 0.050–0.053), respectively (RR 1.24 [95% CI 1.21–1.27]). The association between ILI activity and mortality was observed at the individual state level and in all clinical and regional subgroups. Increased regional influenza activity is associated with higher mortality rates for patients with NSCLC. Vaccine-directed initiatives and increased awareness amongst providers will be necessary to address the growing but potentially preventable burden of influenza-related lung cancer deaths in the U.S.
Complexity and 1/f slope jointly reflect brain states
Authors: Medel Vicente , Irani Martín , Crossley Nicolás , Ossandón Tomás , Boncompte Gonzalo 
Published: December 2023

AbstractCharacterization of brain states is essential for understanding its functioning in the absence of external stimuli. Brain states differ on their balance between excitation and inhibition, and on the diversity of their activity patterns. These can be respectively indexed by 1/f slope and Lempel–Ziv complexity (LZc). However, whether and how these two brain state properties relate remain elusive. Here we analyzed the relation between 1/f slope and LZc with two in-silico approaches and in both rat EEG and monkey ECoG data. We contrasted resting state with propofol anesthesia, which directly modulates the excitation-inhibition balance. We found convergent results among simulated and empirical data, showing a strong, inverse and non trivial monotonic relation between 1/f slope and complexity, consistent at both ECoG and EEG scales. We hypothesize that differentially entropic regimes could underlie the link between the excitation-inhibition balance and the vastness of the repertoire of brain systems.
Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets
Authors: Fyles Martyn , Vihta Karina-Doris , Sudre Carole H , Long Harry , Das Rajenki , Jay Caroline , Wingfield Tom , Cumming Fergus , Green William , Hadjipantelis Pantelis , Kirk Joni , Steves Claire J , Ourselin Sebastien , Medley Graham F , Fearon Elizabeth , House Thomas 
Published: December 2023

AbstractVariability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt upon which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance, in balancing the sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases and syndromes.
Model-based deep learning framework for accelerated optical projection tomography
Authors: Obando Marcos , Bassi Andrea , Ducros Nicolas , Mato Germán , Correia Teresa M. 
Published: December 2023

AbstractIn this work, we propose a model-based deep learning reconstruction algorithm for optical projection tomography (ToMoDL), to greatly reduce acquisition and reconstruction times. The proposed method iterates over a data consistency step and an image domain artefact removal step achieved by a convolutional neural network. A preprocessing stage is also included to avoid potential misalignments between the sample center of rotation and the detector. The algorithm is trained using a database of wild-type zebrafish (Danio rerio) at different stages of development to minimise the mean square error for a fixed number of iterations. Using a cross-validation scheme, we compare the results to other reconstruction methods, such as filtered backprojection, compressed sensing and a direct deep learning method where the pseudo-inverse solution is corrected by a U-Net. The proposed method performs equally well or better than the alternatives. For a highly reduced number of projections, only the U-Net method provides images comparable to those obtained with ToMoDL. However, ToMoDL has a much better performance if the amount of data available for training is limited, given that the number of network trainable parameters is smaller.
Sex-specific effects of a high fat diet on aortic inflammation and dysfunction
Authors: Tran Vivian , Brettle Holly , Diep Henry , Dinh Quynh Nhu , O’Keeffe Maeve , Fanson Kerry V. , Sobey Christopher G. , Lim Kyungjoon , Drummond Grant R. , Vinh Antony , Jelinic Maria 
Published: December 2023

AbstractObesity and vascular dysfunction are independent and sexually dimorphic risk factors for cardiovascular disease. A high fat diet (HFD) is often used to model obesity in mice, but the sex-specific effects of this diet on aortic inflammation and function are unclear. Therefore, we characterized the aortic immune cell profile and function in 6-week-old male and female C57BL/6 mice fed a normal chow diet (NCD) or HFD for 10 weeks. Metabolic parameters were measured weekly and fortnightly. At end point, aortic immune cell populations and endothelial function were characterized using flow cytometry and wire myography. HFD-male mice had higher bodyweight, blood cholesterol, fasting blood glucose and plasma insulin levels than NCD mice (P < 0.05). HFD did not alter systolic blood pressure (SBP), glycated hemoglobin or blood triglycerides in either sex. HFD-females had delayed increases in bodyweight with a transient increase in fasting blood glucose at week 8 (P < 0.05). Flow cytometry revealed fewer proinflammatory aortic monocytes in females fed a HFD compared to NCD. HFD did not affect aortic leukocyte populations in males. Conversely, HFD impaired endothelium-dependent vasorelaxation, but only in males. Overall, this highlights biological sex as a key factor determining vascular disease severity in HFD-fed mice.