bluuebunny/crossref_metadata_2025_split huggingface dataset:
The crucial role of bioimage analysts in scientific research and publication
Authors: Cimini Beth A. , Bankhead Peter , D'Antuono Rocco , Fazeli Elnaz , Fernandez-Rodriguez Julia , Fuster-Barceló Caterina , Haase Robert , Jambor Helena Klara , Jones Martin L. , Jug Florian , Klemm Anna H. , Kreshuk Anna , Marcotti Stefania , Martins Gabriel G. , McArdle Sara , Miura Kota , Muñoz-Barrutia Arrate , Murphy Laura C. , Nelson Michael S. , Nørrelykke Simon F. , Paul-Gilloteaux Perrine , Pengo Thomas , Pylvänäinen Joanna W. , Pytowski Lior , Ravera Arianna , Reinke Annika , Rekik Yousr , Strambio-De-Castillia Caterina , Thédié Daniel , Uhlmann Virginie , Umney Oliver , Wiggins Laura , Eliceiri Kevin W. 
Published: October 2024

ABSTRACT
Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality and efficiency and can significantly advance scientific discovery. However, a lack of training resources, limited career paths and insufficient recognition of the contributions made by bioimage analysts prevent the full realization of this potential. This Perspective – the result of the recent The Company of Biologists Workshop ‘Effectively Communicating Bioimage Analysis’, which aimed to summarize the global BIA landscape, categorize obstacles and offer possible solutions – proposes strategies to bring about a cultural shift towards recognizing the value of BIA by standardizing tools, improving training and encouraging formal credit for contributions. We also advocate for increased funding, standardized practices and enhanced collaboration, and we conclude with a call to action for all stakeholders to join efforts in advancing BIA.
Shift in distribution of division of labour in chronically stressed honeybee colonies after perturbation
Authors: Ulgezen Zeynep N. , van Dooremalen Coby , van Langevelde Frank 
Published: October 2024

ABSTRACT
Division of labour (DOL) in eusocial insects plays an important role in colony fitness. Honeybees face a variety of stressors that compromise the homeostasis of the colony and reduce survival and reproduction. Considering the significance of DOL in colony homeostasis, it is important to understand whether and how DOL may be altered as a result of chronic stress. Therefore, we tested whether honeybee colonies shift DOL in response to high infestation with the parasitic mite Varroa destructor. For this, we monitored chronically stressed and presumably low-stress colonies from April till December 2022. During the experiment, we applied a cold shock to test whether a perturbation resulted in a larger alteration in DOL in chronically stressed colonies. We found that after cold shock, there was a lower proportion of nurses in the chronically stressed colonies. For foragers, we found higher activity post-cold shock in chronically stressed colonies, but no difference between treatments in nectar inflow, suggesting less efficient foragers. Furthermore, we found that there was an accelerated task switch in chronically stressed colonies after the cold shock. The large changes after the perturbation may indicate inefficient task allocation due to chronic stress. Our study contributes to the understanding of social resilience and chronic stress responses in eusocial animals.
Safety and efficacy of posterior approach for resection of spinal meningioma: Impact of dural attachment location
Authors: Chen Hong , Fu Ya-Ni , Fu Chu-Di 
Published: October 2024

BACKGROUND
Spinal meningiomas (SMs) are common benign tumors that are typically treated with surgical resection. The choice of surgical approach may vary depending on the location of dural attachment of the SM, with a posterior approach being the traditional preference. However, there is limited research available on the impact of dural attachment location on outcomes following posterior approach for SM resection.
AIM
To investigate the outcomes of posterior approach for SM resection, and compare the results among different dural attachment location subgroups.
METHODS
Between January 2013 and February 2023, a total of 34 SM patients were included in the study. Various clinical and radiologic features, functional states before and after surgery, operating time, intraoperative blood loss, tumor recurrence, and perioperative complications were assessed and compared.
RESULTS
The average age of the included 34 patients’ (10 males and 24 females) age was 62.09 years. Mean follow-up duration was 22.65 months. The location of SM was the thoracic spine in 32 cases, with only 2 in the cervical spine. On average, intraoperative blood loss was 520.59 mL, and operating time was 176.76 minutes. Thirty three cases had successful outcomes while only 1 experienced an unexpected outcome. The tumor recurrence rate was 2.9%. After surgery, there were 3 cases of cerebral spinal fluid leakage, 1 case of pneumonia, and 1 case of urinary tract infection. Dural attachments were predominantly found dorsal or dorsolateral (13 cases), followed by ventral or ventrolateral (14 cases), and lateral (7 cases). The outcomes among these subgroups were similar.
CONCLUSION
The posterior approach for SM resection is safe and effective, yielding comparable surgical and neurological outcomes regardless of the dural attachment location.
An Improved Crop Yield Prediction Using CNN-BiLSTM Model with Attention Mechanism
Authors: Jia Zhaohong , Wu Kunming , Wang Haitao , Zeng Weihui , Guo YangYang , Liang Dong 
Published: October 2024

HighlightsA yield prediction model based on the CNN-BiLSTM fusion attention mechanism is constructed.The superiority of BiLSTM over the traditional LSTM model in the field of yield prediction is verified.The yield prediction effect of the proposed model is better than that of the existing yield prediction research.Abstract. Food is an important source of nutrients for people, and food production is an important basis for food reserves. In this study, a convolutional neural network-bidirectional long short-term memory (CNN-BiLSTM) model combined with an attention mechanism is proposed to predict crop yield. Firstly, the maximum temperature, minimum temperature, and rainfall data of 9 states in the rainfed corn belt of the United States are adopted as the original data, which are converted into cumulative climate parameters to reflect the growth process of corn. Then, the cumulative climate parameters are used as the input of the proposed model. The proposed model mainly consists of 4 parts: CNN module, BiLSTM module, attention module, and fully connected layer, which makes full use of the advantages of CNN in feature extraction and BiLSTM in processing time series. In addition, to ensure the relevance of time series data, the attention mechanism is used to allocate weights and calculate the correlation degrees between data. The experimental results show that BiLSTM exhibits better convergence ability than the standard one-way LSTM, and the crop yield prediction results obtained by the proposed model are better than those of the exponentially weighted average method, DeepCropNet, and CNN-RNN comparative algorithm. Keywords: Attention mechanism, Bidirectional long short memory network, Convolutional neural network, Crop yield prediction.
Short-Term Performance Evaluation of Real-Time Kinematic Global Navigation Satellite System Receivers in Unmanned Aircraft Systems
Authors: Ladino Karla S. , Sama Michael Patrick 
Published: October 2024

HighlightsAn evaluation of relative GNSS receiver accuracy was performed using a UAS-based GNSS accuracy testing system.RTK receivers displayed minimal mean error and consistent standard deviations across deployment strategies and error directions.Non-RTK receivers exhibited significantly greater mean error and variability across deployment strategies, particularly in elevation error.UAS deployment strategy did not have a meaningful impact on RTK receiver positioning performance.Abstract. Global navigation satellite system (GNSS) receivers commonly integrated into small unmanned aircraft systems (UAS) generally function in standard or differential fix configurations, providing horizontal and vertical accuracies of approximately ±5 meters and ±15 meters, respectively. The accuracy of GNSS positioning is an important factor with widespread implications, affecting domains such as precision agriculture, meteorology, and photogrammetry. In the context of atmospheric observations, spatial accuracy plays a critical role, particularly in applications related to barometric pressure and precipitable water vapor. Similarly, UAS-based photogrammetry applications rely on high geospatial precision for tasks including topographic mapping and environmental monitoring. As such, this study aimed to improve our understanding of GNSS positioning accuracy in UAS-based observations. The main objectives included (1) deploying a UAS-based GNSS accuracy testing system and (2) evaluating the static and dynamic short-term accuracy of L1 and L1/L2 GNSS receivers in RTK and non-RTK fix modes. Results indicated significant differences across receiver configurations and deployment strategies. RTK receivers displayed minimal mean error and consistent standard deviations, while non-RTK receivers exhibited greater mean error and variability, especially in elevation. Though the study did not conclusively confirm a consistent reduction in accuracy due to UAS deployment, findings suggest that RTK receivers substantially enhance accuracy by reducing position measurement error by two orders of magnitude (1–6 cm for RTK; 50–315 cm for non-RTK), thereby mitigating measurement variability attributable to timing or deployment strategy. In conclusion, this research contributed insights into GNSS accuracy for UAS-based observations and underscored the importance of considering receiver configurations and deployment strategies for position measurement during atmospheric and photogrammetric observations. Keywords: Global navigation satellite systems (GNSS), Meteorology, Photogrammetry, Positioning accuracy, Precision agriculture, Real-time kinematic (RTK), Unmanned aircraft systems (UAS).
Suspended nanophotonic waveguide for isotope-specific CO2 detection
Authors: Salaj Jehona , Vlk Marek , Zakoldaev Roman , Seton Ragnar , Čtyroký Jiří , Alberti Sebastián , Aksnes Astrid , Jágerská Jana 
Published: October 2024

The spectroscopic detection of gases and their stable isotopes holds
significant value in bio-sciences and climate studies. However,
achieving high precision has long been confined to bulky and costly
equipment. In this work, we introduce a nanophotonic waveguide that is
capable of detecting CO2 gas down to 20 parts per billion, and
for the first time perform accurate stable isotope ratio measurements.
The waveguide leverages a suspended membrane design with
microstructured cladding, providing a high evanescent field
confinement factor of 102%, moderate loss of 3.4 dB/cm, and
effective suppression of etalons. The δ13C isotope ratio precision of 0.2‰ was
achieved, replicating the performance of high-end laser absorption
spectrometers. This marks the inaugural instance of on-chip,
isotope-specific gas detection with a compact and cost-efficient
system scalable to sensor networks.
High-speed three-dimensional random access scanning with a linear SLM
Authors: Berlage Caroline , Böhm Urs L. , Sanchez Moreno Ana , Ledderose Julia , Gidon Albert , Larkum Matthew E. , Plested Andrew , Judkewitz Benjamin 
Published: October 2024

High-speed volumetric imaging is crucial for observing fast and
distributed processes such as neuronal activity. Multiphoton
microscopy helps to mitigate scattering effects inside tissue, but the
standard raster scanning approach limits achievable volume rates.
Random access point scanning can lead to a considerable speed-up by
sampling only pre-selected locations, but existing techniques based on
acousto-optic deflectors are still limited to a point rate of up to . This limits the number of parallel
targets at the high acquisition rates necessary, for example, in
voltage imaging or imaging of fast synaptic events. Here, we introduce
SPARCLS, a method for 3D random access point scanning at up to
340 kHz using a single 1D phase modulator. We show the
potential of this method by imaging synaptic events with fluorescent
glutamate sensors in mammalian organotypic slices as well as in
zebrafish larvae.
Strong coupling between a quasi-two-dimensional perovskite and a honeycomb plasmonic nanocone array
Authors: Song Zixuan , Huang Xuexuan , Li Lingyao , Zhao Leyi , Xiao Jiamin , Yuan Jiazhi , Wang Zhihang , Bi Chenghao , Wang Wenxin 
Published: October 2024

Recently organic-inorganic perovskite has been established as a promising platform for achieving room temperature exciton-polaritons, attributable to its superior optical coherence and robust exciton binding energies. However, when interfaced with metallic surfaces, the rapid degradation and quenching effect in perovskite have presented significant challenges, which critically hinders the exploration of light-matter interactions within metallic plasmonic structures. In this study, we report a quasi-two-dimensional lead halide perovskite that demonstrates a pronounced strong coupling phenomenon within an array of aluminum nanocones. The investigated quasi-two-dimensional perovskite structure exhibits high photoluminescence quantum efficiency and improved stability against metallic-induced degradation. Interestingly, the periodical arraying in honeycomb formation of plasmonic structure has advantages in angle-dependent dispersions and the loss neutralizing effectively. Besides, the plasmonic cone lattice characterized by its collective surface lattice resonance, features an exceptionally small mode volume and high quality, enhancing its interaction with the perovskite. A significant Rabi splitting of 243 meV is observed at an incident angle of 30°. The dynamics of the Rabi oscillation is revealed by transient absorption spectra and theoretically analyzed by cavity quantum electrodynamics. This advancement in polariton research paves the way for novel applications, including quantum sources, enhanced photon-electron conversion efficiencies, and low-threshold lasing.
Polarization toward Tfh2 cell involved in development of MBC and antibody responses against Plasmodium vivax infection
Authors: Thawornpan Pongsakorn , Salsabila Zulfa Zahra , Kochayoo Piyawan , Khunsri Tipanan , Malee Chayapat , Wangriatisak Kittikorn , Leepiyasakulchai Chaniya , Ntumngia Francis Babila , Adams John H. , Chootong Patchanee 
Published: October 2024

Background
Plasmodium vivax is the dominant Plasmodium spp. causing malaria throughout tropical and sub-tropical countries. Humoral immunity is induced during P. vivax infection. However, data on longevity of antibody and memory B cell (MBC) responses is lacking. Follicular helper T cells (Tfh) are drivers of high-affinity and long-lived antibody responses. Understanding of Tfh-mediated immunity against malaria is valuable for vaccine development.

Methodology/Principal findings
We enrolled 31 acutely infected P. vivax patients in low malaria transmission areas of Thailand to detect frequencies, phenotypes and kinetics of different subsets of circulating Tfh (cTfh) and MBCs, and to evaluate their association with humoral immunity following natural P. vivax infection. Expansion of cTfh2 cells, activated and atypical MBCs were shown during acute malaria. To relate increased cTfh2 cells to humoral immunity, P. vivax-specific MBCs and antibodies were assessed. High anti-PvCSP and -PvDBPII seropositivity was detected and most subjects produced MBCs specific to these antigens. The increased cTfh2 cells were positively related to atypical MBCs, plasmablasts/plasma cells, and anti-PvDBPII IgM and IgG levels. Distributions of memory cTfh cell subsets were altered from central memory (CM) to effector memory (EM) during infection. The highest ratios of cTfh-EM/cTfh-CM were represented in cTfh2 cells. Positive correlation of cTfh17-EM with activated and atypical MBCs was observed, while cTfh2-CM and cTfh17-CM cells were positively related to PvDBPII-specific MBCs and IgM levels.

Conclusions/Significance
Present study demonstrated that P. vivax infection induced cTfh polarization into cTfh2 subset, and alteration of memory cTfh2 phenotype from CM to EM phase. These P. vivax-induced cTfh responses significantly associated with generation of MBCs and antibody responses. Therefore, cTfh2 cells might possibly influence humoral immunity by inducing expansion of activated and atypical MBCs, and by generating P. vivax-specific MBCs and antibody responses following natural infection.
Exploring common biomarkers of ischemic stroke and obstructive sleep apnea through bioinformatics analysis
Authors: Wu Zhe , Qian Yutong , Shang Yaxin , Zhang Yu , Wang Meilin , Jiao Mingyuan 
Published: October 2024

Background
Clinical observations have shown that many patients with ischemic stroke (IS) have a history of obstructive sleep apnea (OSA) both before and after the stroke’s onset, suggesting potential underlying connections and shared comorbid mechanisms between the two conditions. The aim of this study is to identify the genetic characteristics of OSA patients who develop IS and to establish a reliable disease diagnostic model to assess the risk of IS in OSA patients.

Methods
We selected IS and OSA datasets from the Gene Expression Omnibus (GEO) database as training sets. Core genes were identified using the Limma package, Weighted Gene Co-expression Network Analysis (WGCNA), and machine learning algorithms. Gene Set Variation Analysis (GSVA) was conducted for pathway enrichment analysis, while single-sample gene set enrichment analysis (ssGSEA) was employed for immune infiltration analysis. Finally, a diagnostic model was developed using Least Absolute Shrinkage and Selection Operator (LASSO) regression, with its diagnostic efficacy validated using receiver operating characteristic (ROC) curves across two independent validation sets.

Results
The results revealed that differential analysis and machine learning identified two common genes, TM9SF2 and CCL8, shared between IS and OSA. Additionally, seven signaling pathways were found to be commonly upregulated in both conditions. Immune infiltration analysis demonstrated a significant decrease in monocyte levels, with TM9SF2 showing a negative correlation and CCL8 showing a positive correlation with monocytes. The diagnostic model we developed exhibited excellent predictive value in the validation set.

Conclusions
In summary, two immune-related core genes, TM9SF2 and CCL8, were identified as common to both IS and OSA. The diagnostic model developed based on these genes may be used to predict the risk of IS in OSA patients.
Glimpse: An Anthology of Black British Speculative Fiction, Leone Ross (ed.) (2022)
Authors: March-Russell Paul 
Published: October 2024

Review of: Glimpse: An Anthology of Black British Speculative Fiction, Leone Ross (ed.) (2022)
Leeds: Peepal Tree Press, 247 pp.,
ISBN 978-1-84523-542-0, p/bk, £10.99
Spinal pain prevalence and associated determinants: A population‐based study using the National Survey for Wales
Authors: Byfield David C. , Stacey Benjamin S. , Evans Hywel T. , Farr Ian W. , Yandle Leon , Roberts Lora , Filipponi Teresa , Bailey Damian M. 
Published: October 2024

AbstractSpinal pain (SP) remains the leading cause of disability worldwide. The present study aimed to establish a current prevalence of SP and associated determinants in Wales by retrospectively analyzing data from the National Survey for Wales Dataset (NSWD). The NSWD is a large‐scale cross‐sectional, representative sample of adults across Wales, UK. A univariable and multivariable regression analysis was carried out on self‐reported answers to health and well‐being questions contained within the NSWD (2016–2020) to determine the strength of association of various determinants and comorbidities related to spinal pain. A total population of 38,954 of adults were included in the analysis. The study population included interview responses of 21,735 females and 17,219 males. The prevalence of SP in Wales was 4.95% (95% CI: 4.74%–5.15%) with a total of 847 males (4.92%, CI: 4.60%–5.24%) and 1082 females (4.98%, CI: 4.69%–5.27%) reporting spinal pain. The age group with the highest prevalence of SP was in the 70+ years age group for both males (5.44%, CI: 4.82%–6.07%) and females (5.95%, CI: 5.37%–6.54%). The strength of association between age and SP reaches its peak at 50–59 years with an adjusted Odds Ratio (aOR) of 3.74 (p = <0.001), that decreases slightly at 60–69 years and 70+ years. For various comorbidities included in the NSWD, significant associations with SP were confirmed for: mental illness (aOR = 1.42, p = <0.001), migraine (aOR = 2.73, p = <0.001), nervous system issues (aOR = 1.61, p = <0.001), arthritis (aOR = 1.30, p = <0.001) and issues with bones/joints/muscles (aOR = 1.93, p = <0.001). For lifestyle factors, associations were confirmed for current smokers (aOR = 1.41, p = <0.001) and ex‐smokers (aOR = 1.23, p = 0.003). This study demonstrates a low prevalence of SP in Wales when compared to global estimates and strong associations to a variety of determinants. This still represents a significant societal burden and these findings may help inform public health initiatives to encourage prevention and evidence‐based interventional strategies and ultimately, improve the quality of life for those suffering with SP in Wales.
Reverse epidemiology of obesity paradox: Fact or fiction?
Authors: Kishore Bellamkonda K. 
Published: October 2024

AbstractObesity paradox refers to the clinical observation that when acute cardiovascular decompensation occurs, patients with obesity may have a survival benefit. This apparently runs counter to the epidemiology of obesity, which may increase the risk for non‐communicable diseases (NCDs). The scientific community is split on obesity paradox, with some supporting it, while others call it BMI paradox. This review: (a) defines the obesity paradox, and its proposed role in overall mortality in NCDs; (b) delineates evidence for and against obesity paradox; (c) presents the importance of using different indices of body mass to assess the risk in NCDs; (d) examines the role of metabolically healthy obesity in obesity paradox, and emerging importance of cardio‐respiratory fitness (CRF) as an independent predictor of CVD risk and all‐cause mortality in patients with/without obesity. Evidence suggests that the development of obesity and insulin resistance are influenced by genetic (or ethnic) make up and dietary habits (culture) of the individuals. Hence, this review presents lean diabetes, which has higher total CVD and non‐CVD mortality as compared to diabetics with obesity and the possibility of maternal factors programming cardiometabolic risk during fetal development, which may lead to a paradigm shift in our understanding of obesity.