bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced multi-class pathology lesion detection in gastric neoplasms using deep learning-based approach and validation
Authors: Kim Byeong Soo , Kim Bokyung , Cho Minwoo , Chung Hyunsoo , Ryu Ji Kon , Kim Sungwan 
Published: May 2024

AbstractThis study developed a new convolutional neural network model to detect and classify gastric lesions as malignant, premalignant, and benign. We used 10,181 white-light endoscopy images from 2606 patients in an 8:1:1 ratio. Lesions were categorized as early gastric cancer (EGC), advanced gastric cancer (AGC), gastric dysplasia, benign gastric ulcer (BGU), benign polyp, and benign erosion. We assessed the lesion detection and classification model using six-class, cancer versus non-cancer, and neoplasm versus non-neoplasm categories, as well as T-stage estimation in cancer lesions (T1, T2-T4). The lesion detection rate was 95.22% (219/230 patients) on a per-patient basis: 100% for EGC, 97.22% for AGC, 96.49% for dysplasia, 75.00% for BGU, 97.22% for benign polyps, and 80.49% for benign erosion. The six-class category exhibited an accuracy of 73.43%, sensitivity of 80.90%, specificity of 83.32%, positive predictive value (PPV) of 73.68%, and negative predictive value (NPV) of 88.53%. The sensitivity and NPV were 78.62% and 88.57% for the cancer versus non-cancer category, and 83.26% and 89.80% for the neoplasm versus non-neoplasm category, respectively. The T stage estimation model achieved an accuracy of 85.17%, sensitivity of 88.68%, specificity of 79.81%, PPV of 87.04%, and NPV of 82.18%. The novel CNN-based model remarkably detected and classified malignant, premalignant, and benign gastric lesions and accurately estimated gastric cancer T-stages.
Revealing novel biomarkers for diagnosing chronic kidney disease in pediatric patients
Authors: Benito Sandra , Unceta Nora , Maciejczyk Mateusz , Sánchez-Ortega Alicia , Taranta-Janusz Katarzyna , Szulimowska Julita , Zalewska Anna , Andrade Fernando , Gómez-Caballero Alberto , Dubiela Pawel , Barrio Ramón J. 
Published: May 2024

AbstractPediatric chronic kidney disease (CKD) is a clinical condition characterized by progressive renal function deterioration. CKD diagnosis is based on glomerular filtration rate, but its reliability is limited, especially at the early stages. New potential biomarkers (citrulline (CIT), symmetric dimethylarginine (SDMA), S-adenosylmethionine (SAM), n-butyrylcarnitine (nC4), cis-4-decenoylcarnitine, sphingosine-1-phosphate and bilirubin) in addition to creatinine (CNN) have been proposed for early diagnosis. To verify the clinical value of these biomarkers we performed a comprehensive targeted metabolomics study on a representative cohort of CKD and healthy pediatric patients. Sixty-seven children with CKD and forty-five healthy children have been enrolled in the study. Targeted metabolomics based on liquid chromatography-triple quadrupole mass spectrometry has been used for serum and plasma samples analysis. Univariate data analysis showed statistically significant differences (p < 0.05) in the concentration of CNN, CIT, SDMA, and nC4 among healthy and CKD pediatric patients. The predictive ability of the proposed biomarkers was also confirmed through specificity and sensitivity expressed in Receiver Operating Characteristic curves (AUC = 0.909). In the group of early CKD pediatric patients, AUC of 0.831 was obtained, improving the diagnostic reliability of CNN alone. Moreover, the models built on combined CIT, nC4, SDMA, and CNN allowed to distinguish CKD patients from healthy control regardless of blood matrix type (serum or plasma). Our data demonstrate potential biomarkers in the diagnosis of early CKD stages.
Py-CoMFA, docking, and molecular dynamics simulations of Leishmania (L.) amazonensis arginase inhibitors
Authors: Camargo Priscila Goes , dos Santos Carine Ribeiro , Girão Albuquerque Magaly , Rangel Rodrigues Carlos , Lima Camilo Henrique da Silva 
Published: May 2024

AbstractLeishmaniasis is a disease caused by a protozoan of the genus Leishmania, affecting millions of people, mainly in tropical countries, due to poor social conditions and low economic development. First-line chemotherapeutic agents involve highly toxic pentavalent antimonials, while treatment failure is mainly due to the emergence of drug-resistant strains. Leishmania arginase (ARG) enzyme is vital in pathogenicity and contributes to a higher infection rate, thus representing a potential drug target. This study helps in designing ARG inhibitors for the treatment of leishmaniasis. Py-CoMFA (3D-QSAR) models were constructed using 34 inhibitors from different chemical classes against ARG from L. (L.) amazonensis (LaARG). The 3D-QSAR predictions showed an excellent correlation between experimental and calculated pIC50 values. The molecular docking study identified the favorable hydrophobicity contribution of phenyl and cyclohexyl groups as substituents in the enzyme allosteric site. Molecular dynamics simulations of selected protein–ligand complexes were conducted to understand derivatives’ interaction modes and affinity in both active and allosteric sites. Two cinnamide compounds, 7g and 7k, were identified, with similar structures to the reference 4h allosteric site inhibitor. These compounds can guide the development of more effective arginase inhibitors as potential antileishmanial drugs.
Influence of relatively short-term culture on adult porcine islets for xenotransplantation
Authors: Sakata Naoaki , Yoshimatsu Gumpei , Kawakami Ryo , Kodama Shohta 
Published: May 2024

AbstractPorcine islet xenotransplantation is a promising therapy for severe diabetes mellitus. Maintenance of the quality and quantity of porcine islets is important for the success of this treatment. Here, we aimed to elucidate the influence of relatively short-term (14 days) culture on adult porcine islets isolated from three micro-minipigs (P111, P112 and P121). Morphological characteristics of islets changed little after 14 days of culture. The viability of cultured islets was also maintained at a high level (> 80%). Furthermore, cultured islets exhibited similar glucose-stimulated insulin secretion and insulin content at Day 14 were preserved comparing with Day 1, while the expressions of Ins, Gcg and Sst were attenuated at Day 14. Xenotransplantation using diabetic nude mice showed no normalization of blood glucose but increased levels of plasma porcine C-peptide after the transplantation of 14 day cultured porcine islets. Histological assessment revealed that relatively short-term cultured porcine islets were successfully engrafted 56 days following transplantation. These data show that relatively short-term culture did not impair the quality of adult porcine islets in regard to function, morphology, and viability. Prevention of impairment of gene correlated with endocrine hormone is warranted for further improvement.
Escalating tropical cyclone precipitation extremes and landslide hazards in South China under global warming
Authors: Shi Xiaoming , Liu Yang , Chen Jianan , Chen Haoming , Wang Yueya , Lu Zhongming , Wang Ruo-Qian , Fung Jimmy C.-H. , Ng Charles W. W. 
Published: May 2024

AbstractTropical cyclones (TCs) are expected to produce more intense precipitation under global warming. However, substantial uncertainties exist in the projection of coarse-resolution global climate models. Here, we use deep learning to aid targeted cloud-resolving simulations of extreme TCs. Contrary to the Clausius-Clapeyron (CC) scaling, which indicates a 7% moisture increase per K warming, our simulations reveal more complex responses of TC rainfall. TCs will not intensify via strengthened updrafts but through the expansion of deep convective cores with suppression of shallow cumulus and congestus. Consequently, while localized hourly rainfall may adhere to the CC scaling, precipitation accumulation over city-sized areas could surge by 18%K-1. This super-CC intensification due to changing TC structure has profound implications for floods and landslides. Estimations using Hong Kong’s slope data confirm this concern and suggest an up to 215% increase in landslide risks with 4-K warming, highlighting amplified threats from compound disasters under climate change.
Extratropical storms induce carbon outgassing over the Southern Ocean
Authors: Carranza Magdalena M. , Long Matthew. C. , Di Luca Alejandro , Fassbender Andrea J. , Johnson Kenneth S. , Takeshita Yui , Mongwe Precious , Turner Katherine E. 
Published: May 2024

AbstractThe strength and variability of the Southern Ocean carbon sink is a significant source of uncertainty in the global carbon budget. One barrier to reconciling observations and models is understanding how synoptic weather patterns modulate air-sea carbon exchange. Here, we identify and track storms using atmospheric sea level pressure fields from reanalysis data to assess the role that storms play in driving air-sea CO2exchange. We examine the main drivers of CO2fluxes under storm forcing and quantify their contribution to Southern Ocean annual air-sea CO2fluxes. Our analysis relies on a forced ocean-ice simulation from the Community Earth System Model, as well as CO2fluxes estimated from Biogeochemical Argo floats. We find that extratropical storms in the Southern Hemisphere induce CO2outgassing, driven by CO2disequilibrium. However, this effect is an order of magnitude larger in observations compared to the model and caused by different reasons. Despite large uncertainties in CO2fluxes and storm statistics, observations suggest a pivotal role of storms in driving Southern Ocean air-sea CO2outgassing that remains to be well represented in climate models, and needs to be further investigated in observations.
Precision immuno-oncology approach for four malignant tumors in siblings with constitutional mismatch repair deficiency syndrome
Authors: Palova Hana , Das Anirban , Pokorna Petra , Bajciova Viera , Pavelka Zdenek , Jezova Marta , Pal Karol , Dimayacyac Jose R. , Negm Logine , Stengs Lucie , Bianchi Vanessa , Vejmelkova Klara , Noskova Kristyna , Jarosova Marie , Mejstrikova Sona , Mudry Peter , Kyr Michal , Merta Tomas , Tinka Pavel , Drabova Klara , Aulicka Stefania , Jugas Robin , Tabori Uri , Slaby Ondrej , Sterba Jaroslav 
Published: May 2024

AbstractConstitutional mismatch repair deficiency (CMMRD) is a rare syndrome characterized by an increased incidence of cancer. It is caused by biallelic germline mutations in one of the four mismatch repair genes (MMR) genes: MLH1, MSH2, MSH6, or PMS2. Accurate diagnosis accompanied by a proper molecular genetic examination plays a crucial role in cancer management and also has implications for other family members. In this report, we share the impact of the diagnosis and challenges during the clinical management of two brothers with CMMRD from a non-consanguineous family harbouring compound heterozygous variants in the PMS2 gene. Both brothers presented with different phenotypic manifestations and cancer spectrum. Treatment involving immune checkpoint inhibitors significantly contributed to prolonged survival in both patients affected by lethal gliomas. The uniform hypermutation also allowed immune-directed treatment using nivolumab for the B-cell lymphoma, thereby limiting the intensive chemotherapy exposure in this young patient who remains at risk for subsequent malignancies.
A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean
Authors: Wang Wanpeng , Zhang Tianxu , Liu Chunyu , Liu Chunyan , Jiang Zhenfeng , Zhang Zhaohan , Ali Shahid , Li Zhuozheng , Wang Jiang , Sun Shanwen , Chen Qingshan , Zhang Qingzhu , Xie Linan 
Published: May 2024

AbstractUnderstanding how to increase soybean yield is crucial for global food security. The genetic and epigenetic factors influencing seed size, a major crop yield determinant, are not fully understood. We explore the role of DNA demethylase GmDMEa in soybean seed size. Our research indicates that GmDMEa negatively correlates with soybean seed size. Using CRISPR-Cas9, we edited GmDMEa in the Dongnong soybean cultivar, known for small seeds. Modified plants had larger seeds and greater yields without altering plant architecture or seed nutrition. GmDMEa preferentially demethylates AT-rich transposable elements, thus activating genes and transcription factors associated with the abscisic acid pathway, which typically decreases seed size. Chromosomal substitution lines confirm that these modifications are inheritable, suggesting a stable epigenetic method to boost seed size in future breeding. Our findings provide insights into epigenetic seed size control and suggest a strategy for improving crop yields through the epigenetic regulation of crucial genes. This work implies that targeted epigenetic modification has practical agricultural applications, potentially enhancing food production without compromising crop quality.
Long term declines in the functional diversity of sharks in the coastal oceans of eastern Australia
Authors: Henderson Christopher J. , Gilby Ben L. , Turschwell Mischa P. , Goodridge Gaines Lucy A. , Mosman Jesse D. , Schlacher Thomas A. , Borland Hayden P. , Olds Andrew D. 
Published: May 2024

AbstractHuman impacts lead to widespread changes in the abundance, diversity and traits of shark assemblages, altering the functioning of coastal ecosystems. The functional consequences of shark declines are often poorly understood due to the absence of empirical data describing long-term change. We use data from the Queensland Shark Control Program in eastern Australia, which has deployed mesh nets and baited hooks across 80 beaches using standardised methodologies since 1962. We illustrate consistent declines in shark functional richness quantified using both ecological (e.g., feeding, habitat and movement) and morphological (e.g., size, morphology) traits, and this corresponds with declining ecological functioning. We demonstrate a community shift from targeted apex sharks to a greater functional richness of non-target species. Declines in apex shark functional richness and corresponding changes in non-target species may lead to an anthropogenically induced trophic cascade. We suggest that repairing diminished shark populations is crucial for the stability of coastal ecosystems.
Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain
Authors: Hegarty Brianna E. , Gruenhagen George W. , Johnson Zachary V. , Baker Cristina M. , Streelman Jeffrey T. 
Published: May 2024

AbstractThe telencephalon has undergone remarkable diversification and expansion throughout vertebrate evolution, exhibiting striking variations in structural and functional complexity. Nevertheless, fundamental features are shared across vertebrate taxa, such as the presence of distinct regions including the pallium, subpallium, and olfactory structures. Teleost fishes have a uniquely “everted” telencephalon, which has confounded comparisons of their brain regions to other vertebrates. Here we combine spatial transcriptomics and single nucleus RNA-sequencing to generate a spatially-resolved transcriptional atlas of the Mchenga conophorus cichlid fish telencephalon. We then compare cell-types and anatomical regions in the cichlid telencephalon with those in amphibians, reptiles, birds, and mammals. We uncover striking transcriptional similarities between cell-types in the fish telencephalon and subpallial, hippocampal, and cortical cell-types in tetrapods, and find support for partial eversion of the teleost telencephalon. Ultimately, our work lends new insights into the organization and evolution of conserved cell-types and regions in the vertebrate forebrain.
Large anomalous Hall conductivity induced by spin chirality fluctuation in an ultraclean frustrated antiferromagnet PdCrO2
Authors: Jeon Hoseong , Seo Hyeongwoo , Seo Junho , Kim Yong Hyun , Choi Eun Sang , Jo Younjung , Lee Ho Nyung , Ok Jong Mok , Kim Jun Sung 
Published: May 2024

AbstractMagnetic frustration, realized in the special geometrical arrangement of localized spins, often promotes topologically nontrivial spin textures in the real space and induces significantly large unconventional Hall responses. This spin Berry curvature effect in itinerant frustrated magnets mainly works with a static spin order, limiting the effective temperature range below the magnetic transition temperature and yielding the typical anomalous Hall conductivity below ~ 103 Ω−1cm−1. Here we show that an ultraclean triangular-lattice antiferromagnet PdCrO2 exhibits a large anomalous Hall conductivity up to ~ 106 Ω−1cm−1 in the paramagnetic state, which is maintained far above the Neel temperature (TN) up to ~ 4TN. The reported enhancement of anomalous Hall response above TN is attributed to the skew scattering of highly mobile Pd electrons to fluctuating but locally-correlated Cr spins with a finite spin chirality. Our findings point at an alternative route to realizing high-temperature giant anomalous Hall responses, exploiting magnetic frustration in the ultraclean regime.
3D skyrmion strings and their melting dynamics revealed via scalar-field electron tomography
Authors: Yu Xiuzhen , Nakanishi Nobuto , Chiew Yi-Ling , Liu Yizhou , Nakajima Kiyomi , Kanazawa Naoya , Karube Kosuke , Taguchi Yasujiro , Nagaosa Naoto , Tokura Yoshinori 
Published: May 2024

AbstractTwo-dimensional skyrmion, a topological spin texture, has been extensively investigated in non-centrosymmetric magnets. It is thermodynamically stable in bulk materials and can extend perpendicularly to the spin-rotating plane, forming the three-dimensional (3D) skyrmion string that occasionally terminates inside the bulk or at its surfaces, thereby producing spin (anti)hedgehogs. While magnetically manipulated skyrmion strings have been demonstrated thus far, an understanding of metastable skyrmion strings and their melting dynamics remain elusive. The challenge arises from the absence of a suitable 3D magnetic imaging technique that is capable of tracking their dynamics while varying the temperature. Here, we show a high-resolution 3D phase imaging to show the metastable skyrmions and their melting dynamics accompanied by the emergence of (anti)hedgehogs over a temperature range from 95 K to room temperature in helimagnets.
Multiple carbonate system parameters independently govern shell formation in a marine mussel
Authors: Ninokawa Aaron T. , Saley Alisha M. , Shalchi Roya , Gaylord Brian 
Published: May 2024

AbstractCalcification is vital to marine organisms that produce calcium carbonate shells and skeletons. However, how calcification is impacted by ongoing environmental changes, including ocean acidification, remains incompletely understood due to complex relationships among the carbonate system variables hypothesized to drive calcification. Here, we experimentally decouple these drivers in an exploration of shell formation in adult marine mussels, Mytilus californianus. In contrast to models that focus on single parameters like calcium carbonate saturation state, our results implicate two independent factors, bicarbonate concentration and seawater pH, in governing calcification. While qualitatively similar to ideas embodied in the related substrate-inhibitor ratio (bicarbonate divided by hydrogen ion concentration), our data highlight that merging bicarbonate ion and hydrogen ion concentrations into a simple quotient obscures important features of calcification. Considering a dual-parameter framework improves mechanistic understanding of how calcifiers interact with complex and changing chemical conditions.
Deep imaging reveals dynamics and signaling in one-to-one pollen tube guidance
Authors: Mizuta Yoko , Sakakibara Daigo , Nagahara Shiori , Kaneshiro Ikuma , Nagae Takuya T , Kurihara Daisuke , Higashiyama Tetsuya 
Published: May 2024

AbstractIn the pistil of flowering plants, each ovule usually associates with a single pollen tube for fertilization. This one-to-one pollen tube guidance, which contributes to polyspermy blocking and efficient seed production, is largely different from animal chemotaxis of many sperms to one egg. However, the functional mechanisms underlying the directional cues and polytubey blocks in the depths of the pistil remain unknown. Here, we develop a two-photon live imaging method to directly observe pollen tube guidance in the pistil of Arabidopsis thaliana, clarifying signaling and cellular behaviors in the one-to-one guidance. Ovules are suggested to emit multiple signals for pollen tubes, including an integument-dependent directional signal that reaches the inner surface of the septum and adhesion signals for emerged pollen tubes on the septum. Not only FERONIA in the septum but ovular gametophytic FERONIA and LORELEI, as well as FERONIA- and LORELEI-independent repulsion signal, are involved in polytubey blocks on the ovular funiculus. However, these funicular blocks are not strictly maintained in the first 45 min, explaining previous reports of polyspermy in flowering plants.
Epsilon tubulin is an essential determinant of microtubule-based structures in male germ cells
Authors: Stathatos G Gemma , Merriner D Jo , O’Connor Anne E , Zenker Jennifer , Dunleavy Jessica EM , O’Bryan Moira K 
Published: May 2024

AbstractAlpha, beta, and gamma tubulins are essential building blocks for all eukaryotic cells. The functions of the non-canonical tubulins, delta, epsilon, and zeta, however, remain poorly understood and their requirement in mammalian development untested. Herein we have used a spermatogenesis model to define epsilon tubulin (TUBE1) function in mice. We show that TUBE1 is essential for the function of multiple complex microtubule arrays, including the meiotic spindle, axoneme and manchette and in its absence, there is a dramatic loss of germ cells and male sterility. Moreover, we provide evidence for the interplay between TUBE1 and katanin-mediated microtubule severing, and for the sub-specialization of individual katanin paralogs in the regulation of specific microtubule arrays.
Improvement in non‐linear electrical conductivity of silicone rubber by incorporating zinc oxide fillers and grafting small polar molecules
Authors: Chi Qingguo , Zhang Huiyang , Meng Zhaotong , Zhang Changhai , Zhang Yongquan , Zhang Yue , Yin Chao , Zhang Tiandong 
Published: May 2024

AbstractSilicone rubber (SiR) is commonly used in reinforced insulation parts for high‐voltage direct current (HVDC) cable accessories due to its excellent insulation, elasticity, and high‐temperature resistance. HVDC cable accessories always suffer from the local electric field concentration due to the electrical conductivity mismatch between reinforced insulation and main insulation, which can ultimately lead to electric breakdown. The non‐linear conductive composites based on SiR have the ability to adaptively adjust the distribution of the electric field in cable accessories. This is expected to solve the problem of localised electric field concentration. The zinc oxide (ZnO) and glycidyl methacrylate (GMA) are used as fillers and grafted modifier respectively to improve the non‐linear electrical conductivity of ZnO/SiR‐GMA composites. The results indicate that grafting GMA can increase electrical conductivity of SiR, while doping ZnO filler enables SiR to have non‐linear conductivity characteristics. The combination of doping and grafting modification of the composites achieves excellent non‐linear conductive properties at lower ZnO filler content. Additionally, the mechanical properties of the modified composites are enhanced. The simulation results indicate that ZnO/SiR‐GMA is the most effective material for homogenising the electric field when used as reinforced insulation for cable intermediate joints.