bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orientation-invariant autoencoders learn robust representations for shape profiling of cells and organelles
Authors: Burgess James , Nirschl Jeffrey J. , Zanellati Maria-Clara , Lozano Alejandro , Cohen Sarah , Yeung-Levy Serena 
Published: February 2024

AbstractCell and organelle shape are driven by diverse genetic and environmental factors and thus accurate quantification of cellular morphology is essential to experimental cell biology. Autoencoders are a popular tool for unsupervised biological image analysis because they learn a low-dimensional representation that maps images to feature vectors to generate a semantically meaningful embedding space of morphological variation. The learned feature vectors can also be used for clustering, dimensionality reduction, outlier detection, and supervised learning problems. Shape properties do not change with orientation, and thus we argue that representation learning methods should encode this orientation invariance. We show that conventional autoencoders are sensitive to orientation, which can lead to suboptimal performance on downstream tasks. To address this, we develop O2-variational autoencoder (O2-VAE), an unsupervised method that learns robust, orientation-invariant representations. We use O2-VAE to discover morphology subgroups in segmented cells and mitochondria, detect outlier cells, and rapidly characterise cellular shape and texture in large datasets, including in a newly generated synthetic benchmark.
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
Authors: Aguilar Robin , Camplisson Conor K. , Lin Qiaoyi , Miga Karen H. , Noble William S. , Beliveau Brian J. 
Published: February 2024

AbstractFluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA.
Printed smart devices for anti-counterfeiting allowing precise identification with household equipment
Authors: Zhang Junfang , Tan Rong , Liu Yuxin , Albino Matteo , Zhang Weinan , Stevens Molly M. , Loeffler Felix F. 
Published: February 2024

AbstractCounterfeiting has become a serious global problem, causing worldwide losses and disrupting the normal order of society. Physical unclonable functions are promising hardware-based cryptographic primitives, especially those generated by chemical processes showing a massive challenge-response pair space. However, current chemical-based physical unclonable function devices typically require complex fabrication processes or sophisticated characterization methods with only binary (bit) keys, limiting their practical applications and security properties. Here, we report a flexible laser printing method to synthesize unclonable electronics with high randomness, uniqueness, and repeatability. Hexadecimal resistive keys and binary optical keys can be obtained by the challenge with an ohmmeter and an optical microscope. These readout methods not only make the identification process available to general end users without professional expertise, but also guarantee device complexity and data capacity. An adopted open-source deep learning model guarantees precise identification with high reliability. The electrodes and connection wires are directly printed during laser writing, which allows electronics with different structures to be realized through free design. Meanwhile, the electronics exhibit excellent mechanical and thermal stability. The high physical unclonable function performance and the widely accessible readout methods, together with the flexibility and stability, make this synthesis strategy extremely attractive for practical applications.
Magnetotransport of Sm2Ir2O7 across the pressure-induced quantum-critical phase boundary
Authors: Coak M. J. , Götze K. , Northam De La Fuente T. , Castelnovo C. , Tidey J. P. , Singleton J. , Boothroyd A. T. , Prabhakaran D. , Goddard P. A. 
Published: February 2024

AbstractRare-earth pyrochlore iridates host two interlocking magnetic sublattices of corner-sharing tetrahedra and can harbour a unique combination of frustrated moments, exotic excitations and highly correlated electrons. They are also the first systems predicted to display both topological Weyl semimetal and axion insulator phases. We have measured the transport and magnetotransport properties of single-crystal Sm2Ir2O7 up to and beyond the pressure-induced quantum critical point for all-in-all-out (AIAO) Ir order at pc = 63 kbar previously identified by resonant X-ray scattering and close to which Weyl semimetallic behavior has been previously predicted. Our findings overturn the accepted expectation that the suppression of AIAO order should lead to metallic conduction persisting down to zero temperature. Instead, the resistivity-minimum temperature, which tracks the decrease in the AIAO ordering temperature for pressures up to 30 kbar, begins to increase under further application of pressure, pointing to the presence of a second as-yet unidentified mechanism leading to non-metallic behavior. The magnetotransport does track the suppression of Ir magnetism, however, with a strong hysteresis observed only within the AIAO phase boundary, similar to that found for Ho2Ir2O7 and attributed to plastic deformation of Ir domains. Around pc we find the emergence of a new type of electronic phase, characterized by a negative magnetoresistance with small hysteresis at the lowest temperatures, and hysteresis-free positive magnetoresistance above approximately 5 K. The temperature dependence of our low-temperature transport data are found to be best described by a model consistent with a Weyl semimetal across the entire pressure range.
Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and Hi-C technology
Authors: Zheng Jianbo , Jiang Jianhu , Rui Qianlong , Li Fei , Liu Shili , Cheng Shun , Chi Meili , Jiang Wenping 
Published: February 2024

AbstractAcrossocheilus fasciatus (Cypriniformes, Cyprinidae) is emerged as a newly commercial stream fish in the south of China with high economic and ornamental value. In this study, a chromosome-level reference genome of A. fasciatus was assembled using PacBio, Illumina and Hi-C sequencing technologies. As a result, a high-quality genome was generated with a size of 879.52 Mb (accession number: JAVLVS000000000), scaffold N50 of 32.7 Mb, and contig N50 of 32.7 Mb. The largest and smallest scafford was 60.57 Mb and 16 kb, respectively. BUSCO analysis showed a completeness score of 98.3%. Meanwhile, the assembled sequences were anchored to 25 pseudo-chromosomes with an integration efficiency of 96.95%. Additionally, we found approximately 390.91 Mb of repetitive sequences that accounting for 44.45% of the assembled genome, and predicted 24,900 protein-coding genes. The available genome reported in the present study provided a crucial resource to further investigate the regulation mechanism of genetic diversity, sexual dimorphism and evolutionary histories.
ArcTiCA: Arctic tidal constituents atlas
Authors: Hart-Davis M. G. , Howard S. L. , Ray R. D. , Andersen O. B. , Padman L. , Nilsen F. , Dettmering D. 
Published: February 2024

AbstractTides in the Arctic Ocean affect ocean circulation and mixing, and sea ice dynamics and thermodynamics. However, there is a limited network of available in situ tidal coefficient data for understanding tidal variability in the Arctic Ocean; e.g., the global TICON-3 database contains only 111 sites above 60°N and 21 above 70°N. At the same time, the presence of sea ice and latitude limits of satellite altimetry complicate altimetry-based retrievals of Arctic tidal coefficients. This leads to a reliance on ocean tide models whose accuracy depend on having sufficient in situ data for validation and assimilation. Here, we present a comprehensive new dataset of tidal constituents in the Arctic region, combining analyses of in situ measurements from tide gauges, ocean bottom pressure sensors and GNSS interferometric reflectometry. The new dataset contains 914 measurement sites above 60°N and 399 above 70°N, with each site being quality-assessed and expert guidance provided to help maximise the usage of the dataset. We also compare the dataset to recent tide models.
Ultra-restrictive red blood cell transfusion strategies in extensively burned patients
Authors: Wang Yiran , Zhu Zhikang , Duan Deqing , Xu Wanting , Chen Zexin , Shen Tao , Wang Xingang , Xu Qinglian , Zhang Hongyan , Han Chunmao 
Published: February 2024

AbstractIn recent years, due to the shortage of blood products, some extensive burn patients were forced to adopt an “ultra-restrictive” transfusion strategy, in which the hemoglobin levels of RBC transfusion thresholds were < 7 g/dl or even < 6 g/dl. This study investigated the prognostic impacts of ultra-restrictive RBC transfusion in extensive burn patients. This retrospective multicenter cohort study recruited extensive burns (total body surface area ≥ 50%) from three hospitals in Eastern China between 1 January 2016 and 30 June 2022. Patients were divided into an ultra-restrictive transfusion group and a restrictive transfusion group depending on whether they received timely RBC transfusion at a hemoglobin level < 7 g/dl. 1:1 ratio propensity score matching (PSM) was performed to balance selection bias. Modified Poisson regression and linear regression were conducted for sensitive analysis. Subsequently, according to whether they received timely RBC transfusion at a hemoglobin level < 6 g/dl, patients in the ultra-restrictive transfusion group were divided into < 6 g/dl group and 6–7 g/dl group to further compare the prognostic outcomes. 271 eligible patients with extensive burns were included, of whom 107 patients were in the ultra-restrictive transfusion group and 164 patients were in the restrictive transfusion group. The ultra-restrictive transfusion group had a significantly lower RBC transfusion volume than the restrictive transfusion group (11.5 [5.5, 21.5] vs 17.3 [9.0, 32.5] units, p = 0.004). There were no significant differences between the two groups in terms of in-hospital mortality, risk of infection, hospital length of stay, and wound healing time after PSM or multivariate adjustment (p > 0.05). Among the ultra-restrictive transfusion group, patients with RBC transfusion threshold < 6 g/dl had a significantly higher hospital mortality than 6–7 g/dl (53.1% vs 21.3%, p = 0.001). For extensive burn patients, no significant adverse effects of ultra-restrictive RBC transfusion were found in this study. When the blood supply is tight, it is acceptable to adopt an RBC transfusion threshold of < 7 g/dL but not < 6 g/dL.
Potential anthelmintic effect of chitosan on Syphacia muris infecting Wistar rats: biochemical, immunological, and histopathological studies
Authors: Mostafa Nesma A. , Hamdi Salwa A. H. , Fol Mona F. 
Published: February 2024

AbstractNatural products extracted from animal sources have many biological activities, such as chitosan, which is being researched for its medicinal or therapeutic potential. Syphacia muris is the most well-known intestinal nematode, infecting laboratory rats and influencing their immune systems. In this study, we looked at the anthelminthic activity of chitosan particles against S. muris infection using biochemical, immunological, and histopathological methods. Chitosan particles were characterized using Fourier-transform infrared spectroscopy (FTIR). Rats were separated into four groups, each consisting of seven individuals (n = 7). The first group was the control (non-infected), the second group was infected, and both groups received 0.5 ml of 1% glacial acetic acid orally. The third group was the infected group (treated), and the fourth group (normal) received 0.5 ml of 30 mg/kg/day chitosan dissolved in 1% glacial acetic acid for 14 days using gavage. Liver and kidney parameters, oxidative stress markers, serum levels of cytokines (IFN-γ, IL-5, IL-13, IL-33, and IL-10), as well as immunoglobulins (total IgE and IgG), were assessed. Histological examinations of host tissues (intestine, liver, kidney, and spleen) were also performed. Following chitosan treatment, a significant decrease in worm count (P < 0.05) was indicated; this was associated with an enhancement of biochemical and oxidative stress biomarkers, which were altered due to infection. Moreover, immunological analysis revealed a significant drop in INF-γ, IL-5, IL-13, and IL-33 levels and total immunoglobulins (IgE and IgG) as well as an improvement in rat tissues. Conclusively, this study showed the anthelminthic effect of chitosan against S. muris infection.
AI models for automated segmentation of engineered polycystic kidney tubules
Authors: Monaco Simone , Bussola Nicole , Buttò Sara , Sona Diego , Giobergia Flavio , Jurman Giuseppe , Xinaris Christodoulos , Apiletti Daniele 
Published: February 2024

AbstractAutosomal dominant polycystic kidney disease (ADPKD) is a monogenic, rare disease, characterized by the formation of multiple cysts that grow out of the renal tubules. Despite intensive attempts to develop new drugs or repurpose existing ones, there is currently no definitive cure for ADPKD. This is primarily due to the complex and variable pathogenesis of the disease and the lack of models that can faithfully reproduce the human phenotype. Therefore, the development of models that allow automated detection of cysts’ growth directly on human kidney tissue is a crucial step in the search for efficient therapeutic solutions. Artificial Intelligence methods, and deep learning algorithms in particular, can provide powerful and effective solutions to such tasks, and indeed various architectures have been proposed in the literature in recent years. Here, we comparatively review state-of-the-art deep learning segmentation models, using as a testbed a set of sequential RGB immunofluorescence images from 4 in vitro experiments with 32 engineered polycystic kidney tubules. To gain a deeper understanding of the detection process, we implemented both pixel-wise and cyst-wise performance metrics to evaluate the algorithms. Overall, two models stand out as the best performing, namely UNet++ and UACANet: the latter uses a self-attention mechanism introducing some explainability aspects that can be further exploited in future developments, thus making it the most promising algorithm to build upon towards a more refined cyst-detection platform. UACANet model achieves a cyst-wise Intersection over Union of 0.83, 0.91 for Recall, and 0.92 for Precision when applied to detect large-size cysts. On all-size cysts, UACANet averages at 0.624 pixel-wise Intersection over Union. The code to reproduce all results is freely available in a public GitHub repository.
Electric field simulation and appropriate electrode positioning for optimized transcranial direct current stimulation of stroke patients: an in Silico model
Authors: Yoon Mi-Jeong , Park Hye Jung , Yoo Yeun Jie , Oh Hyun Mi , Im Sun , Kim Tae-Woo , Lim Seong Hoon 
Published: February 2024

AbstractTranscranial Direct Current Stimulation (tDCS) has benefits for motor rehabilitation in stroke patients, but its clinical application is limited due to inter-individual heterogeneous effects. Recently, optimized tDCS that considers individual brain structure has been proposed, but the utility thereof has not been studied in detail. We explored whether optimized tDCS provides unique electrode positions for each patient and creates a higher target electric field than the conventional approach. A comparative within-subject simulation study was conducted using data collected for a randomized controlled study evaluating the effect of optimized tDCS on upper extremity function in stroke patients. Using Neurophet tES LAB 3.0 software, individual brain models were created based on magnetic resonance images and tDCS simulations were performed for each of the conventional and optimized configurations. A comparison of electrode positions between conventional tDCS and optimized tDCS was quantified by calculation of Euclidean distances. A total of 21 stroke patients were studied. Optimized tDCS produced a higher electric field in the hand motor region than conventional tDCS, with an average improvement of 20% and a maximum of 52%. The electrode montage for optimized tDCS was unique to each patient and exhibited various configurations that differed from electrode placement of conventional tDCS. Optimized tDCS afforded a higher electric field in the target of a stroke patient compared to conventional tDCS, which was made possible by appropriately positioning the electrodes. Our findings may encourage further trials on optimized tDCS for motor rehabilitation after stroke.
Intersectional strategy to study cortical inhibitory parvalbumin-expressing interneurons
Authors: Palicz Rebeka , Pater Bettina , Truschow Pavel , Witte Mirko , Staiger Jochen F. 
Published: February 2024

AbstractParvalbumin-expressing (PV) interneurons are key neuronal elements to a global excitatory-inhibitory balance in normal cortical functioning. To better understand the circuit functions of PV interneurons, reliable animal models are needed. This study investigated the sensitivity and specificity of the most frequently used PV-Cre/tdTomato mouse line in this regard. The colocalization of the transgene (tdTomato) with the parvalbumin protein, with GAD1 (a conclusive inhibitory cell marker) and Vglut1 (a conclusive excitatory cell marker) as well as with a marker for perineuronal nets (WFA) was assessed and a substantial proportion of layer 5 PV neurons was found to be excitatory and not inhibitory in the PV-Cre/tdTomato mouse. The intersectional transgenic mouse line Vgat-Cre/PV-Flp/tdTomato provided a solution, since no colocalization of tdTomato with the Vglut1 probe was found there. In conclusion, the Vgat-Cre/PV-Flp/tdTomato mouse line seems to be a more reliable animal model for functional studies of GABAergic PV interneurons.
Exposure to arsenic and other potentially toxic elements: health risk assessment and source analysis in the Wuming Basin, Guangxi Province, China
Authors: Hu Bo , Li Jie , Liu Rui , Lei Guoxin , Wang Xinyu , Wang Lei 
Published: February 2024

AbstractGuangxi, China, is one of the world's largest karst regions where potential toxic elements tend to accumulate, resulting in high soil background values. This study explores the ecological risk, elemental baseline values, and sources of potential toxic elements in karst regions, expanding the research to include 21 common elements. The significance of this research lies in its implications for the management of potential toxic element pollution, the formulation of environmental quality standards, and soil remediation in karst areas. In this study, 12,547 topsoil samples (0–20 cm) were collected in the study area. Pollution assessment and ecological risk evaluation of eight potential toxic elements (Zn, Ni, Cu, Pb, Cd, Hg, Cr, and As) were conducted using the geo-accumulation index method and potential ecological risk index method. Multivariate statistical analysis was applied to analyze the total content of 21 common elements (Zn, Ni, Cu, Pb, P, Cd, Hg, Co, Mn, Cr, V, I, S, As, pH, Se, N, CaO, Corg, Mo, and F). Additionally, the potential sources of 21 soil elements were preliminarily quantitatively analyzed using the principal component analysis-absolute principal component scores-multiple linear regression receptor model. The results showed that (1) Zn, Ni, Cu, Pb, Cd, Cr, V, and As were enriched in the research area and Ca, Cd, Mn, Mo, Hg, As, and Cu might have been influenced by human activities; (2) Cr, Pb, As, and Zn were generally lightly polluted, with Hg having a moderate potential ecological risk level; and (3) Ni and Zn have contributions of 37.99% and 35.07% from geological sources, agricultural fertilization, and pesticides. Mo, V, Cr, Se, Hg, and As exhibit contributions ranging from 39.44 to 59.22% originating from geological backgrounds and human activities. Corg, S, N, and P show contributions of 45.39% to 80.33% from surface vegetation. F, Co, Mn, and Pb have contributions ranging from 31.63 to 47.93% from acidic rocks in the soil parent material, mining activities, and transportation. Cd and CaO derive 31.67% and 40.23%, respectively, from soil parent material and industrial sources. I has 31.94% from geological background and human activities, and 31.95% from soil parent material and atmospheric sources. Cu has 30.56% from geological sources. The study results can serve as a scientific basis for element research in karst areas domestically and internationally.
Prognosis prediction and risk stratification of breast cancer patients based on a mitochondria-related gene signature
Authors: Wang Yang , Wang Ding-yuan , Bu Ke-na , Gao Ji-dong , Zhang Bai-lin 
Published: February 2024

AbstractAs the malignancy with the highest global incidence, breast cancer represents a significant threat to women’s health. Recent advances have shed light on the importance of mitochondrial function in cancer, particularly in metabolic reprogramming within tumors. Recognizing this, we developed a novel risk signature based on mitochondrial-related genes to improve prognosis prediction and risk stratification in breast cancer patients. In this study, transcriptome data and clinical features of breast cancer samples were extracted from two sources: the TCGA, serving as the training set, and the METABRIC, used as the independent validation set. We developed the signature using LASSO-Cox regression and assessed its prognostic efficacy via ROC curves. Furthermore, the signature was integrated with clinical features to create a Nomogram model, whose accuracy was validated through clinical calibration curves and decision curve analysis. To further elucidate prognostic variations between high and low-risk groups, we conducted functional enrichment and immune infiltration analyses. Additionally, the study encompassed a comparison of mutation landscapes and drug sensitivity, providing a comprehensive understanding of the differing characteristics in these groups. Conclusively, we established a risk signature comprising 8 mitochondrial-related genes—ACSL1, ALDH2, MTHFD2, MRPL13, TP53AIP1, SLC1A1, ME3, and BCL2A1. This signature was identified as an independent risk predictor for breast cancer patient survival, exhibiting a significant high hazard ratio (HR = 3.028, 95%CI 2.038–4.499, P < 0.001). Patients in the low-risk group showed a more favorable prognosis, with enhanced immune infiltration, distinct mutation landscapes, and greater sensitivity to anti-tumor drugs. In contrast, the high-risk group exhibited an adverse trend in these aspects. This risk signature represents a novel and effective prognostic indicator, suggesting valuable insights for patient stratification in breast cancer.