bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of vision transformer and swin transformer models for lemon quality classification in fruit juice factories
Authors: Dümen Sezer , Kavalcı Yılmaz Esra , Adem Kemal , Avaroglu Erdinç 
Published: April 2024

AbstractAssessing the quality of agricultural products holds vital significance in enhancing production efficiency and market viability. The adoption of artificial intelligence (AI) has notably surged for this purpose, employing deep learning and machine learning techniques to process and classify agricultural product images, adhering to defined standards. This study focuses on the lemon dataset, encompassing ‘good’ and ‘bad’ quality classes, initiate by augmenting data through rescaling, random zoom, flip, and rotation methods. Subsequently, employing eight diverse deep learning approaches and two transformer methods for classification, the study culminated in the ViT method achieving an unprecedented 99.84% accuracy, 99.95% recall, and 99.66% precision, marking the highest accuracy documented. These findings strongly advocate for the efficacy of the ViT method in successfully classifying lemon quality, spotlighting its potential impact on agricultural quality assessment.
Structural characteristics of gut microbiota in longevity from Changshou town, Hubei, China
Authors: Ai Xu , Liu Yu , Shi Jinrong , Xie Xiongwei , Li Linzi , Duan Rui , Lv Yongling , Xiong Kai , Miao Yuanxin , Zhang Yonglian 
Published: April 2024

Abstract
The gut microbiota (GM) and its potential functions play a crucial role in maintaining host health and longevity. The aim of this study was to investigate the potential relationship between GM and longevity. We collected fecal samples from 92 healthy volunteers (middle-aged and elderly: 43–79 years old; longevity: ≥ 90 years old) from Changshou Town, Zhongxiang City, Hubei, China. In addition, we collected samples from 30 healthy middle-aged and elderly controls (aged 51–70 years) from Wuhan, Hubei. The 16S rDNA V3 + V4 region of the fecal samples was sequenced using high-throughput sequencing technology. Diversity analysis results showed that the elderly group with longevity and the elderly group with low body mass index (BMI) exhibited higher α diversity. However, no significant difference was observed in β diversity. The results of the microbiome composition indicate that Firmicutes, Proteobacteria, and Bacteroidota are the core phyla in all groups. Compared to younger elderly individuals, Akkermansia and Lactobacillus are significantly enriched in the long-lived elderly group, while Megamonas is significantly reduced. In addition, a high abundance of Akkermansia is a significant characteristic of elderly populations with low BMI values. Furthermore, the functional prediction results showed that the elderly longevity group had higher abilities in short-chain fatty acid metabolism, amino acid metabolism, and xenobiotic biodegradation. Taken together, our study provides characteristic information on GM in the long-lived elderly population in Changshou Town. This study can serve as a valuable addition to the current research on age-related GM.

Key points
• The gut microbiota of elderly individuals with longevity and low BMI exhibit higher alpha diversity
• Gut microbiota diversity did not differ significantly between genders in the elderly population
• Several potentially beneficial bacteria (e.g., Akkermansia and Lactobacillus) are enriched in long-lived individuals
Integrating bulk and single-cell sequencing data to construct a Scissor+ dendritic cells prognostic model for predicting prognosis and immune responses in ESCC
Authors: Cheng Maosheng , Xiong Jianqi , Liu Qianwen , Zhang Caihua , Li Kang , Wang Xinyuan , Chen Shuang 
Published: April 2024

AbstractEsophageal squamous cell carcinoma (ESCC) is characterized by molecular heterogeneity with various immune cell infiltration patterns, which have been associated with therapeutic sensitivity and resistance. In particular, dendritic cells (DCs) are recently discovered to be associated with prognosis and survival in cancer. However, how DCs differ among ESCC patients has not been fully comprehended. Recently, the advance of single-cell RNA sequencing (scRNA-seq) enables us to profile the cell types, states, and lineages in the heterogeneous ESCC tissues. Here, we dissect the ESCC tumor microenvironment at high resolution by integrating 192,078 single cells from 60 patients, including 4379 DCs. We then used Scissor, a method that identifies cell subpopulations from single-cell data that are associated bulk samples with genomic and clinical information, to stratify DCs into Scissorhi and Scissorlow subtypes. We applied the Scissorhi gene signature to stratify ESCC scRNAseq patient, and we found that PD-L1, TIGIT, PVR and IL6 ligand-receptor-mediated cell interactions existed mainly in Scissorhi patients. Finally, based on the Scissor results, we successfully developed a validated prognostic risk model for ESCC and further validated the reliability of the risk prediction model by recruiting 40 ESCC clinical patients. This information highlights the importance of these genes in assessing patient prognosis and may help in the development of targeted or personalized therapies for ESCC.
T-cell subsets and cytokines are indicative of neoadjuvant chemoimmunotherapy responses in NSCLC
Authors: Yi Ling , Xu Ziwei , Ma Tianyu , Wang Chong , Wei Panjian , Xiao Bo , Zhang Hongtao , Che Nanying , Liu Zhidong , Han Yi 
Published: April 2024

Abstract
Purpose
Neoadjuvant PD-1 blockade combined with chemotherapy is a promising treatment for resectable non-small cell lung cancer (NSCLC), yet the immunological mechanisms contributing to tumor regression and biomarkers corresponding to different pathological responses remain unclear.

Methods
Using dynamic and paired blood samples from NSCLC patients receiving neoadjuvant chemoimmunotherapy, we analyzed the frequencies of CD8 + T-cell and Treg subsets and their dynamic changes during neoadjuvant treatment through flow cytometry. Cytokine profiles and function-related gene expression of CD8 + T cells and Tregs were analyzed through flow cytometry and mRNA-seq. Infiltrating T-cell subsets in resected tissues from patients with different pathological responses were analyzed through multiplex immunofluorescence.

Results
Forty-two NSCLC patients receiving neoadjuvant chemoimmunotherapy were enrolled and then underwent surgical resection and pathological evaluation. Nineteen patients had pCR (45%), 7 patients had MPR (17%), and 16 patients had non-MPR (38%). In patients with pCR, the frequencies of CD137 + CD8 + T cells (P = 0.0475), PD-1 + Ki-67 + CD8 + T cells (P = 0.0261) and Tregs (P = 0.0317) were significantly different from those of non-pCR patients before treatment. pCR patients usually had low frequencies of CD137 + CD8 + T cells, PD-1 + Ki-67 + CD8 + T cells and Tregs, and their AUCs were higher than that of tissue PD-L1 expression. Neoadjuvant chemoimmunotherapy markedly improved CD8 + T-cell proliferation and activation, especially in pCR patients, as the frequencies of CD137 + CD8 + (P = 0.0136) and Ki-67 + CD8 + (P = 0.0391) T cells were significantly increased. The blood levels of cytokines such as IL-2 (P = 0.0391) and CXCL10 (P = 0.0195) were also significantly increased in the pCR group, which is consistent with the high density of activated cytotoxic T cells at the tumor site (P < 0.0001).

Conclusion
Neoadjuvant chemoimmunotherapy drives CD8 + T cells toward a proliferative and active profile. The frequencies of CD137 + CD8 + T cells, PD-1 + Ki-67 + CD8 + T cells and Tregs at baseline might predict the response to neoadjuvant chemoimmunotherapy in NSCLC patients. The increase in IL-2 and CXCL10 might reflect the chemotaxis and enrichment of cytotoxic T cells at the tumor site and a better response to neoadjuvant chemoimmunotherapy.
High sensitivity of hop plants (Humulus lupulus L.) to limited soil water availability: the role of stomata regulation and xylem vulnerability to embolism
Authors: Gloser Vít , Baláž Milan , Svoboda Petr , Jupa Radek , Gloser Jan 
Published: April 2024

AbstractDrought poses a serious threat to the productivity of hop, an important perennial crop. However, the precise physiological mechanisms that make it highly susceptible to drought are not yet fully understood. In this study, we investigated stomatal regulation and xylem vulnerability to embolism, which are important traits closely associated with plant drought resistance. In a glasshouse cultivation experiment, we monitored changes in leaf water potential, stem elongation rates, and leaf gas exchange, including net photosynthetic rates, stomatal conductance, and intrinsic water use efficiency, on relatively young hop plants (traditional Saaz - Osvald’s clone 31) exposed to declining soil water availability. The transpiration rate and stem elongation of plants decreased significantly with a small decline in substrate water potential (ΨSUB), indicating a highly sensitive stomata response during early phases of soil dehydration. The stem elongation was completely halted, and the transpiration rate dropped to less than 50% of its maximum at ΨSUB levels below − 0.8 MPa. In well-watered hop plants, xylem in stems operates near the initial point of embolization and is highly vulnerable to embolism, with a water potential corresponding to a 50% loss of xylem conductivity at -1.6 MPa. The sensitive stomatal response to declining ΨSUB likely helps to mitigate the risk of hydraulic failure, albeit at the cost of impaired growth. Scheduled irrigation, particularly during the sensitive stem elongation stage, may be a promising approach to mitigate the detrimental effects of reduced soil water availability on hop growth and yield while also conserving water resources.
StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
Authors: Bonthala Venkata Suresh , Stich Benjamin 
Published: April 2024

Abstract
Key message
We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research.

Abstract
Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de. This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
Phytoliths from modern plants in the Canary Islands as a reference for the reconstruction of long-term vegetation change and culture-environment interactions
Authors: Castilla-Beltrán Alvaro , Fernández-Palacios Enrique , Vrydaghs Luc , Mallol Carolina , Fernández-Palacios José María , de Nascimento Lea 
Published: April 2024

AbstractThe Canary Islands were the first part of the Macaronesian archipelago to have been settled by humans. The various ways in which the indigenous inhabitants and later European colonisers interacted with the native and endemic flora is a central topic for archaeologists, geographers and ecologists. Floristic changes can be studied from phytoliths which are plant microfossils with a high potential for preservation in sediment deposits and they can help reconstruct past ways of life and vegetation changes through time. However, there is no comprehensive and systematic study and reference collection of phytoliths produced by the flora of the Canary Islands, so far. To make a start with a first phytolith reference collection of a selection of plants relevant for the study of past socio-ecological interactions there, we processed over a hundred modern plant specimens collected on the islands of Tenerife, Gran Canaria and La Palma to obtain the phytoliths from them, using the dry-ashing method. We then described the phytolith morphologies, and counted the numbers of morphotypes for each species. We have categorised taxa according to their phytolith concentration and production of morphotypes with diagnostic potential. Our results suggest that among the selected taxa, species within the Arecaceae, Boraginaceae, Cyperaceae, Poaceae and Urticaceae families are the main native producers of phytoliths in the archipelago. We also identified phytoliths with diagnostic potential in particular species within the Asteraceae, Brassicaceae, Cistaceae, Euphorbiaceae, Lamiaceae, Lauraceae, Ranunculaceae and Rubiaceae. We discuss how phytolith assemblages can be interpreted in archaeological sites and sediment records. Our growing reference collection is a significant step towards the application of phytolith analysis to disentangle the long-term climatic and human-driven transformation of this biodiversity hotspot, as well as the cultural use of plant resources.
Mortality and rehospitalization in patients with pre-existing implantable pacemakers undergoing catheter ablation are related to increased comorbidity burden—data from the German Ablation Registry
Authors: Frommeyer Gerrit , Reinke Florian , Brachmann Johannes , Lewalter Thorsten , Tilz Roland Richard , Willems Stephan , Straube Florian , Akin Ibrahim , Lugenbiel Patrick , Hochadel Matthias , Senges Jochen , Eckardt Lars 
Published: April 2024

Abstract
Background
Catheter ablation of atrial fibrillation and atrial flutter is routinely performed in patients with implantable devices. The aim of the present study was to assess success rates and potential complications in a large registry cohort of patients with cardiac pacemakers.

Methods and results
The German Ablation Registry is a nationwide, prospective registry with a 1-year follow-up investigating patients who underwent catheter ablation of supraventricular arrhythmias in 51 German centers. The present analysis focussed on the presence of cardiac pacemakers in 591 patients undergoing catheter ablation of atrial fibrillation or atrial flutter. These were compared to 7393 patients without a pacemaker. Patients with pacemakers were significantly older and presented more comorbidities like diabetes, renal failure, cardiovascular disease, or previous stroke. One-year mortality (2.4% vs. 1.3%, p = 0.022) and a combined endpoint of death, myocardial infarction, and stroke (3.6% vs. 2.1%, p = 0.014) were significantly elevated in patients with pacemakers. Re-hospitalization was also more common in patients with a pacemaker (53.3% vs. 45.0%, p < 0.01). After adjustment for important comorbidities, pre-existing pacemaker systems did not show any negative effect. Procedural success was reported in 98.8% vs. 98.4% (p = 0.93). Device-related complications were only observed in 0.4% of patients with pacemakers.

Conclusion
Patients with pacemaker systems undergoing catheter ablation of atrial fibrillation or atrial flutter demonstrate an increased risk of death, cardiovascular events, and re-hospitalization. This observation can be largely attributed to an older patient population and an increased rate of comorbidities.
Testing in-situ apatite Lu–Hf dating in polymetamorphic mafic rocks: a case study from Palaeoproterozoic southern Australia
Authors: Brown Dillon A. , Reid Anthony , Jagodzinski Elizabeth A. , Williams Megan , Simpson Alex , Pawley Mark , Kirkland Christopher L. , Wade Claire , De Vries Van Leeuwen Alexander T. , Glorie Stijn 
Published: April 2024

AbstractIn mafic systems where primary mineral assemblages have witnessed moderate- to high-temperature hydrous overprinting and deformation, little is known about the retentivity of the Lu–Hf isotopic system in apatite. This study presents apatite laser-ablation Lu–Hf and U–Pb geochronology, zircon geochronology, and detailed petrological information from polymetamorphic mafic intrusions located in the central-western Gawler Craton in southern Australia, which records an extensive tectonometamorphic history spanning the Neoarchaean to the Mesoproterozoic. Zircon records magmatic crystallisation ages of c. 2479–2467 Ma, coinciding with the onset of the c. 2475–2410 Ma granulite-facies Sleafordian Orogeny. The amphibole-dominant hydrous assemblages which extensively overprint the primary magmatic assemblages are hypothesised to post-date the Sleafordian Orogeny. The Lu–Hf and U–Pb isotopic systems in apatite are used to test this hypothesis, with both isotopic systems recording significantly younger ages correlating with the c. 1730–1690 Ma Kimban Orogeny and the c. 1590–1575 Ma Hiltaba magmatic event, respectively. While the early Mesoproterozoic apatite U–Pb ages are attributed to thermal re-equilibration, the older Lu–Hf ages are interpreted to reflect re-equilibration facilitated primarily by dissolution-reprecipitation, but also thermally activated volume diffusion. The mechanisms of Lu–Hf isotopic resetting are distinguished based on microscale textures and trace element abundances in apatite and the integration of apatite-amphibole textural relationships and temperatures determined from the Ti content in amphibole. More broadly, the results indicate that at low to moderate temperatures, apatite hosted in mafic rocks is susceptible to complete recrystallisation in rocks that have weak to moderate foliations. In contrast, at higher temperatures in the absence of strain, the Lu–Hf system in apatite is comparatively robust. Ultimately, the findings from this study advance our understanding of the complex role that both metamorphism and deformation play on the ability of mafic-hosted apatite to retain primary Lu–Hf isotopic signatures.
Effectiveness of low dose computed tomography to detect fractures in paediatric suspected physical abuse: a systematic review
Authors: Doyle Edel , Bugeja Lyndal , Dimmock Matthew R. , Lee Kam L. , Ng Jessica , Bassed Richard B. 
Published: April 2024

Abstract
Purpose
The skeletal survey X-ray series is the current ‘gold standard’ when investigating suspected physical abuse (SPA) of children, in addition to a non-contrast computed tomography (CT) brain scan. This systematic literature review synthesised findings of published research to determine if low dose computed tomography (LDCT) could detect subtle fractures and therefore replace the skeletal survey X-ray series in the investigation of SPA in children aged under 3 years.

Methods
Five electronic databases and grey literature were systematically searched from their inception to 28 April 2022. Primary studies were included where the population comprised paediatric patients up to 16 years and LDCT was used to detect fractures associated with SPA. Studies involving imaging investigations of the head, standard dose CT examinations or accidental trauma were excluded.

Results
Three studies met the inclusion criteria, all of which were case series. These studies did not report many of the criteria required to compare the accuracy of LDCT to X-ray, i.e. they did not meet the criteria for a diagnostic accuracy test. Therefore, it is difficult to conclude from the case series if LDCT is accurate enough to replace X-rays.

Conclusion
Due to the gap in current literature, a phantom study and subsequent post-mortem CT study are recommended as the primary investigative methods to assess the ability of low-dose CT to identify the subtle fractures associated with SPA and to calculate how low the achievable CT dose can be.
The overall fractions of coronary heart diseases and depression attributable to multiple dependent psychosocial work factors in Europe
Authors: Niedhammer Isabelle , Sultan-Taïeb Hélène , Chastang Jean-François 
Published: April 2024

Abstract
Objectives
The literature is nonexistent on the assessment of overall fractions of diseases attributable to multiple dependent psychosocial work factors. The objectives of the study were to calculate the overall fractions of coronary heart diseases (CHD) and depression attributable to multiple dependent psychosocial work factors in 35 European countries.

Methods
We used already published fractions of CHD and depression attributable to each of the following psychosocial work factors: job strain, effort-reward imbalance, job insecurity, long working hours, and workplace bullying. We took all exposures and their correlations into account to calculate overall attributable fractions. Wald tests were performed to test differences in these overall attributable fractions between genders and between countries.

Results
The overall fractions of CHD and depression attributable to all studied psychosocial work factors together were found to be 8.1% [95% CI: 2.0-13.9] and 26.3% [95% CI: 16.2–35.5] respectively in the 35 European countries. There was no difference between genders and between countries.

Conclusion
Our study showed that the overall fractions attributable to all studied psychosocial work factors were substantial especially for depression. These overall attributable fractions may be particularly useful to evaluate the burden and costs attributable to psychosocial work factors, and also to inform policies makers at European level.
Impact of the $$\hbox {N}^4\hbox {LO}$$ Short-Range Three-Nucleon Force Components on the Nucleon-Deuteron Spin Correlation Coefficients
Authors: Skibiński Roman , Witała Henryk , Golak Jacek 
Published: April 2024

AbstractThe spin correlation coefficients in the neutron-deuteron elastic scattering process at incoming neutron laboratory energies $$\hbox {E}=10$$

E
=
10

, 135, 190, and 250 MeV are determined by solving the momentum space three-nucleon (3N) Faddeev equations. The chiral two-nucleon (2N) interaction with momentum-space semi-local (SMS) regularization up to the fifth order of chiral expansion ($$\hbox {N}^4\hbox {LO}$$

N
4

LO

), supplemented by the F-waves terms from the sixth order ($$\hbox {N}^5\hbox {LO}$$

N
5

LO

), is used. Additionally, the consistent 3N force (3NF) at the third order of chiral expansion, supplemented by the short-range contributions from $$\hbox {N}^4\hbox {LO}$$

N
4

LO

is applied. As a results, we give predictions for the complete set of spin correlation coefficients $$C_{\alpha ,\beta }$$

C

α
,
β

. We find that the effect of the investigated three-nucleon $$\hbox {N}^4\hbox {LO}$$

N
4

LO

components amounts up to several dozen percent, depending on reaction energy, scattering angle and type of spin correlation coefficient itself. Our results can serve as a guide for future measurements of the spin correlation coefficients.