bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predation and spatial connectivity interact to shape ecosystem resilience to an ongoing regime shift
Authors: Olin Agnes B. , Bergström Ulf , Bodin Örjan , Sundblad Göran , Eriksson Britas Klemens , Erlandsson Mårten , Fredriksson Ronny , Eklöf Johan S. 
Published: February 2024

AbstractEcosystem regime shifts can have severe ecological and economic consequences, making it a top priority to understand how to make systems more resilient. Theory predicts that spatial connectivity and the local environment interact to shape resilience, but empirical studies are scarce. Here, we use >7000 fish samplings from the Baltic Sea coast to test this prediction in an ongoing, spatially propagating shift in dominance from predatory fish to an opportunistic mesopredator, with cascading effects throughout the food web. After controlling for the influence of other drivers (including increasing mesopredator densities), we find that predatory fish habitat connectivity increases resilience to the shift, but only when densities of fish-eating top predators (seals, cormorants) are low. Resilience also increases with temperature, likely through boosted predatory fish growth and recruitment. These findings confirm theoretical predictions that spatial connectivity and the local environment can together shape resilience to regime shifts.
O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology
Authors: Balana Aaron T. , Mahul-Mellier Anne-Laure , Nguyen Binh A. , Horvath Mian , Javed Afraah , Hard Eldon R. , Jasiqi Yllza , Singh Preeti , Afrin Shumaila , Pedretti Rose , Singh Virender , Lee Virginia M.-Y. , Luk Kelvin C. , Saelices Lorena , Lashuel Hilal A. , Pratt Matthew R. 
Published: February 2024

AbstractAmyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer’s and Parkinson’s disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the determinants contributing to the formation of different amyloid features could open new avenues for developing disease-specific diagnostics and therapies. Here we report that O-GlcNAc modification of α-synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by cryogenic electron microscopy, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson’s disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc-modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the α-synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that posttranslational modifications, such as O-GlcNAc modification, of α-synuclein are key determinants of α-synuclein amyloid strains and pathogenicity.
A paintbrush for delivery of nanoparticles and molecules to live cells with precise spatiotemporal control
Authors: Holler Cornelia , Taylor Richard William , Schambony Alexandra , Möckl Leonhard , Sandoghdar Vahid 
Published: February 2024

AbstractDelivery of very small amounts of reagents to the near-field of cells with micrometer spatial precision and millisecond time resolution is currently out of reach. Here we present μkiss as a micropipette-based scheme for brushing a layer of small molecules and nanoparticles onto the live cell membrane from a subfemtoliter confined volume of a perfusion flow. We characterize our system through both experiments and modeling, and find excellent agreement. We demonstrate several applications that benefit from a controlled brush delivery, such as a direct means to quantify local and long-range membrane mobility and organization as well as dynamical probing of intercellular force signaling.
Morpho-molecular and nutritional profiling for yield improvement and value addition of indigenous aromatic Joha rice of Assam
Authors: Bordoloi Dibosh , Sarma Debojit , Sarma Barua Nagendra , Das Ranjan , Das Bikram Kishore 
Published: February 2024

AbstractShort-grain aromatic Joha rice of Assam is a unique class of specialty rice having tremendous potential in domestic and international markets. The poor yielding ability of Assam's Joha rice demands its systematic characterization for an effective breeding program. This study investigates the morphological, molecular and biochemical profiles of twenty popular Joha (aromatic) rice cultivars indigenous to Assam. Distinctiveness, Uniformity and Stability (DUS) characterization of the cultivars revealed polymorphism in thirty-seven traits, establishing distinctiveness for their utilization in breeding programs. Unweighted Neighbor Joining (UNJ) clustering based on usual Euclidean distances for the polymorphic morphological markers grouped the cultivars into three clusters with eight, eleven, and one genotypes. The Joha rice cultivars showed significant differences for all the quantitative traits except for panicle length. The genotypic and phenotypic coefficients of variability (GCV & PCV) were high for grain yield ha−1 (24.62 & 24.85%) and filled grains panicle−1 (23.69 & 25.02%). Mahalanobis D2 analysis revealed three multi-genotypic and four mono-genotypic clusters of the cultivars. The first five principal components explain 85.87% of the variation among the cultivars for the traits under study; filled grain panicle−1 (0.91) and stem thickness (0.55) positively contributed to the first PC. The cultivars' average polyunsaturated fatty acids were 37.9% oleic acid, 39.22% linoleic acid, and 0.5% linolenic acid. Kon Joha 4 and Ronga Joha contained the highest iron (82.88 mg kg−1) and zinc (47.39 mg kg−1), respectively. Kalijeera, Kunkuni Joha, Kon Joha-5, Manimuni Joha and Kon Joha-2 accorded a strong aroma. PCR amplified 174 alleles with a mean value 2.64 across the 66 polymorphic SSR markers. PIC values ranged from 0.091 to 0.698, with an average of 0.326. The highly informative (PIC > 0.50) markers were RM316, RM283, RM585, RM1388, RM3562, RM171, R1M30, RM118, RM11and RM29 for identification of the twenty aromatic rice cultivars. PCR amplification of 27 SSR markers identified 28 unique alleles (97–362 bp) in 13 Joha rice cultivars, which can help their identification/DNA fingerprinting. The UNJ clustering based on Jaccard's coefficients classified the cultivars into three distinct clusters with eight, ten, and two genotypes. Our study revealed the nutritional richness of these specialty Joha rice cultivars and sufficient scope for yield enhancement through their interbreeding to keep quality intact.
Risk factors affecting patients survival with colorectal cancer in Morocco: survival analysis using an interpretable machine learning approach
Authors: El Badisy Imad , BenBrahim Zineb , Khalis Mohamed , Elansari Soukaina , ElHitmi Youssef , Abbass Fouad , Mellas Nawfal , EL Rhazi Karima 
Published: February 2024

AbstractThe aim of our study was to assess the overall survival rates for colorectal cancer at 3 years and to identify associated strong prognostic factors among patients in Morocco through an interpretable machine learning approach. This approach is based on a fully non-parametric survival random forest (RSF), incorporating variable importance and partial dependence effects. The data was povided from a retrospective study of 343 patients diagnosed and followed at Hassan II University Hospital. Covariate selection was performed using the variable importance based on permutation and partial dependence plots were displayed to explore in depth the relationship between the estimated partial effect of a given predictor and survival rates. The predictive performance was measured by two metrics, the Concordance Index (C-index) and the Brier Score (BS). Overall survival rates at 1, 2 and 3 years were, respectively, 87% (SE = 0.02; CI-95% 0.84–0.91), 77% (SE = 0.02; CI-95% 0.73–0.82) and 60% (SE = 0.03; CI-95% 0.54–0.66). In the Cox model after adjustment for all covariates, sex, tumor differentiation had no significant effect on prognosis, but rather tumor site had a significant effect. The variable importance obtained from RSF strengthens that surgery, stage, insurance, residency, and age were the most important prognostic factors. The discriminative capacity of the Cox PH and RSF was, respectively, 0.771 and 0.798 for the C-index while the accuracy of the Cox PH and RSF was, respectively, 0.257 and 0.207 for the BS. This shows that RSF had both better discriminative capacity and predictive accuracy. Our results show that patients who are older than 70, living in rural areas, without health insurance, at a distant stage and who have not had surgery constitute a subgroup of patients with poor prognosis.
Real-time study of spatio-temporal dynamics (4D) of physiological activities in alive biological specimens with different FOVs and resolutions simultaneously
Authors: K. S. Aiswarya , Sarkar Sohela , Vishnu Smitha , S. R. Rinsa , Negi Simran , Narendradev Nikhil Dev , Arora Rishica Harish , Sanam Sreelakshmi , P. V. Anu , Sharma Rahul , Khurana Satish , Varghese Jishy , Srinivasula Srinivasa Murty , Singh Mayanglambam Suheshkumar 
Published: February 2024

AbstractThis article reports the development of a microscopy imaging system that gives feasibility for studying spatio-temporal dynamics of physiological activities of alive biological specimens (over entire volume not only for a particular section, i.e., in 4D). The imaging technology facilitates to obtain two image frames of a section of the larger specimen ($$\sim \text {mm}$$

∼
mm

) with different FOVs at different resolutions or magnifications simultaneously in real-time (in addition to recovery of 3D (volume) information). Again, this imaging system addresses the longstanding challenges of housing multiple light sources (6 at the maximum till date) in microscopy (in general) and light sheet fluorescence microscopy (LSFM) (in particular), by using a tuneable pulsed laser source (with an operating wavelength in the range $$\sim 420$$

∼
420

–670 nm) in contrast to the conventional CW laser source being adopted for inducing photo-excitation of tagged fluorophores. In the present study, we employ four wavelengths ($$\sim$$
∼
488 nm, 585 nm, 590 nm, and 594 nm). Our study also demonstrates quantitative characterization of spatio-temporal dynamics (velocity—both amplitude and direction) of organelles (mitochondria) and their mutual correlationships. Mitochondria close to the nucleus (or in clustered cells) are observed to possess a lower degree of freedom in comparison to that at the cellular periphery (or isolated cells). In addition, the study demonstrates real-time observation and recording of the development and growth of all tracheal branches during the entire period ($$\sim 95$$

∼
95

min) of embryonic development (Drosophila). The experimental results—with experiments being conducted in various and diversified biological specimens (Drosophila melanogaster, mouse embryo, and HeLa cells)—demonstrate that the study is of great scientific impact both from the aspects of technology and biological sciences.
Lytic activity of phages against bacterial pathogens infecting diabetic foot ulcers
Authors: Kifelew Legesse Garedew , Warner Morgyn S. , Morales Sandra , Gordon David L. , Thomas Nicky , Mitchell James G. , Speck Peter G. 
Published: February 2024

AbstractComplications of diabetes, such as diabetic foot ulcers (DFUs), are common, multifactorial in origin, and costly to treat. DFUs are the cause of nearly 90% of limb amputations among persons with diabetes. In most chronic infections such as DFU, biofilms are involved. Bacteria in biofilms are 100–1000 times more resistant to antibiotics than their planktonic counterparts. Multidrug-resistant (MDR) Staphylococcus aureus and Pseudomonas aeruginosa infections in DFUs may require alternative therapeutic agents such as bacteriophages ("phages"). This study describes the lytic activity of phage cocktails AB-SA01 (3-phage cocktail) and AB-PA01 (4-phage cocktail), which target S. aureus and P. aeruginosa, respectively. The host range and lytic effect of AB-SA01 and AB-PA01 on a planktonic culture, single-species biofilm, and mixed-species biofilm were evaluated. In vitro testing showed that 88.7% of S. aureus and 92.7% of P. aeruginosa isolates were susceptible to AB-SA01 and AB-PA01, respectively, in the planktonic state. The component phages of AB-SA01 and AB-PA01 infected 66% to 94.3% of the bacterial isolates tested. Furthermore, AB-SA01 and AB-PA01 treatment significantly (p < 0.05) reduced the biofilm biomass of their hosts, regardless of the antibiotic-resistant characteristics of the isolates and the presence of a non-susceptible host. In conclusion, the strong lytic activity, broad host range, and significant biofilm biomass reduction of AB-SA01 and AB-PA01 suggest the considerable potential of phages in treating antibiotic-resistant S. aureus and P. aeruginosa infections alone or as coinfections in DFUs.
A transcriptomic time-series reveals differing trajectories during pre-floral development in the apex and leaf in winter and spring varieties of Brassica napus
Authors: Jones D. Marc , Hepworth Jo , Wells Rachel , Pullen Nick , Trick Martin , Morris Richard J. 
Published: February 2024

AbstractOilseed rape (Brassica napus) is an important global oil crop, with spring and winter varieties grown commercially. To understand the transcriptomic differences between these varieties, we collected transcriptomes from apex and leaf tissue from a spring variety, Westar, and a winter variety, Tapidor, before, during, and after vernalisation treatment, until the plants flowered. Large transcriptomic differences were noted in both varieties during the vernalisation treatment because of temperature and day length changes. Transcriptomic alignment revealed that the apex transcriptome reflects developmental state, whereas the leaf transcriptome is more closely aligned to the age of the plant. Similar numbers of copies of genes were expressed in both varieties during the time series, although key flowering time genes exhibited expression pattern differences.BnaFLCcopies on A2 and A10 are the best candidates for the increased vernalisation requirement of Tapidor. OtherBnaFLCcopies show tissue-dependent reactivation of expression post-cold, with these dynamics suggesting some copies have retained or acquired a perennial nature.BnaSOC1genes, also related to the vernalisation pathway, have expression profiles which suggest tissue subfunctionalisation. This understanding may help to breed varieties with more consistent or robust vernalisation responses, of special importance due to the milder winters resulting from climate change.
Navigating the nuances: comparative analysis and hyperparameter optimisation of neural architectures on contrast-enhanced MRI for liver and liver tumour segmentation
Authors: Quinton Felix , Presles Benoit , Leclerc Sarah , Nodari Guillaume , Lopez Olivier , Chevallier Olivier , Pellegrinelli Julie , Vrigneaud Jean-Marc , Popoff Romain , Meriaudeau Fabrice , Alberini Jean-Louis 
Published: February 2024

AbstractIn medical imaging, accurate segmentation is crucial to improving diagnosis, treatment, or both. However, navigating the multitude of available architectures for automatic segmentation can be overwhelming, making it challenging to determine the appropriate type of architecture and tune the most crucial parameters during dataset optimisation. To address this problem, we examined and refined seven distinct architectures for segmenting the liver, as well as liver tumours, with a restricted training collection of 60 3D contrast-enhanced magnetic resonance images (CE-MRI) from the ATLAS dataset. Included in these architectures are convolutional neural networks (CNNs), transformers, and hybrid CNN/transformer architectures. Bayesian search techniques were used for hyperparameter tuning to hasten convergence to the optimal parameter mixes while also minimising the number of trained models. It was unexpected that hybrid models, which typically exhibit superior performance on larger datasets, would exhibit comparable performance to CNNs. The optimisation of parameters contributed to better segmentations, resulting in an average increase of 1.7% and 5.0% in liver and tumour segmentation Dice coefficients, respectively. In conclusion, the findings of this study indicate that hybrid CNN/transformer architectures may serve as a practical substitute for CNNs even in small datasets. This underscores the significance of hyperparameter optimisation.
The metabolism-related lncRNA signature predicts the prognosis of breast cancer patients
Authors: Ge Xin , Lei Shu , Wang Panliang , Wang Wenkang , Wang Wendong 
Published: February 2024

AbstractLong non-coding RNAs (lncRNAs) involved in metabolism are recognized as significant factors in breast cancer (BC) progression. We constructed a novel prognostic signature for BC using metabolism-related lncRNAs and investigated their underlying mechanisms. The training and validation cohorts were established from BC patients acquired from two public sources: The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The prognostic signature of metabolism-related lncRNAs was constructed using the least absolute shrinkage and selection operator (LASSO) cox regression analysis. We developed and validated a new prognostic risk model for BC using the signature of metabolism-related lncRNAs (SIRLNT, SIAH2-AS1, MIR205HG, USP30-AS1, MIR200CHG, TFAP2A-AS1, AP005131.2, AL031316.1, C6orf99). The risk score obtained from this signature was proven to be an independent prognostic factor for BC patients, resulting in a poor overall survival (OS) for individuals in the high-risk group. The area under the curve (AUC) for OS at three and five years were 0.67 and 0.65 in the TCGA cohort, and 0.697 and 0.68 in the GEO validation cohort, respectively. The prognostic signature demonstrated a robust association with the immunological state of BC patients. Conventional chemotherapeutics, such as docetaxel and paclitaxel, showed greater efficacy in BC patients classified as high-risk. A nomogram with a c-index of 0.764 was developed to forecast the survival time of BC patients, considering their risk score and age. The silencing of C6orf99 markedly decreased the proliferation, migration, and invasion capacities in MCF-7 cells. Our study identified a signature of metabolism-related lncRNAs that predicts outcomes in BC patients and could assist in tailoring personalized prevention and treatment plans.
Early maladaptive schemas in female patients with migraine and tension-type headache
Authors: Yontar Gözde , Ozgan Esen 
Published: February 2024

AbstractChronic headache is a serious clinical problem in women which psychological factors play major role and requires an approach with bio-psycho-social integrity. Psychiatric comorbidities such as anxiety disorder and major depression are frequent. Young described Early Maladaptive Schemas (EMS) as maladaptive and dysfunctional patterns that appear due to unpleasant situations occurred between patient and people who were important to him. EMS affect perception, emotions, thoughts and behaviors that makes a basis for many disorders. EMS are found to be related with depression, anxiety and somatization within recent literature. In literature, chronic pain and migraine’s relationship with EMS were studied before in a few separate articles. However, there is a lack of data that compares the relationship between EMS and clearly distinguished headache types: migraine (MH) and tension-type headache (TTH) especially in female patients who are more prone to somatic complaints/findings. Our study directly compared three groups, migraine and tension type headache and healthy controls. 150 female patients with chronic headache were enrolled for study in consecutive fashion. Exclusion criteria were as follows: age < 18 or > 60 years, male gender, existence of comorbidity affecting central nervous system, headache due to drug/substance abuse, previous diagnosis of migraine with aura, previous diagnosis of psychotic disease, mental retardation, cognitive disorders, being in delirium state. Patients were grouped into two categories according to type of headache and a third control group. All patients were evaluated with Young Schema Questionnaire (YSQ) and their scores were noted and categorized in related schema domains. Sociodemographic data were comparable among groups. However, there were significant differences in terms of previous psychiatric diagnosis and psychiatric drug usage. When we compared YSQ scores, groups differed in many schema categories. MH group showed significantly higher scores in dependency/incompetency, unrelenting standards and punitiveness schemas when compared to remaining two groups. TTH group had significantly more points in emotional deprivation, vulnerability to harm or illness schemas among all groups. On the other hand, control group had significantly higher scores in insufficient self-discipline and entitlement/grandiosity schemas when compared to both MH and TTH groups. Presence of EMS in female patients with headache significantly differed from control group. Types of EMS were also significantly different between patients with MH and TTH among this whole headache group. We suggest that a comprehensive psychotherapeutic approach that targets to improve coping methods for distinct EMS in distinct headache types would provide critical aid to general treatment of headaches especially in resistant cases.
Effects of radiofrequency field from 5G communication on fecal microbiome and metabolome profiles in mice
Authors: Wang Xing , Zhou Guiqiang , Lin Jiajin , Qin Tongzhou , Du Junze , Guo Ling , Lai Panpan , jing Yuntao , Zhang Zhaowen , Zhou Yan , Ding Guirong 
Published: February 2024

AbstractWith the rapid development of 5G networks, the influence of the radiofrequency field (RF) generated from 5G communication equipment on human health is drawing increasing attention in public. The study aimed at assessing the effects of long-term exposure to 4.9 GHz (one of the working frequencies of 5G communication) RF field on fecal microbiome and metabolome profiles in adult male C57BL/6 mice. The animals were divided into Sham group and radiofrequency group (RF group). For RF group, the mice were whole body exposed to 4.9 GHz RF field for three weeks, 1 h/d, at average power density (PD) of 50 W/m2. After RF exposure, the mice fecal samples were collected to detect gut microorganisms and metabolites by 16S rRNA gene sequencing and LC–MS method, respectively. The results showed that intestinal microbial compositions were altered in RF group, as evidenced by reduced microbial diversity and changed microbial community distribution. Metabolomics profiling identified 258 significantly differentially abundant metabolites in RF group, 57 of which can be classified to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Besides, functional correlation analysis showed that changes in gut microbiota genera were significantly correlated with changes in fecal metabolites. In summary, the results suggested that altered gut microbiota and metabolic profile are associated with 4.9 GHz radiofrequency exposure.