bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cenozoic evolution of the Yangjiang-Yitong’ansha fault zone in the northern South China Sea: Evidence from 3D seismic data
Authors: Zhan Huawang , Wang Guangzeng , Peng Guangrong , Suo Yanhui , Wang Pengcheng , Du Xiaodong , Zhou Jie , Li Sanzhong , Zhu Dingwei 
Published: January 2023

The Yanjiang-Yitong’ansha Fault Zone (YYFZ) traverses the Pearl River Mouth Basin (PRMB) and plays an essential role in basin formation and hydrocarbon accumulation in the PRMB. Because of the lack of seismic data, its distribution, evolution, and effect on the basin evolution in the Cenozoic are poorly known. Based on a detailed interpretation of 3D multi-channel seismic data and previous research results, the YYFZ was identified and characterized. It comprises a series of NW-trending strike-slip faults that exhibit horsetail and en echelon structures in the map view and flower-like or Y-shaped structures in the profile view. By comprehensively analyzing the Paleogene migration of depocenters, activity characteristics of the YYFZ-related faults, and the relationships between faults and sedimentary sequences along the YYFZ, we propose the sinistral motion of the YYFZ initiated at about 35 Ma. The YYFZ served as a transfer zone during the intense rifting in the PRMB from 65 to 35 Ma. Then due to the combined effect of the Indian-Eurasian collision to the west, the Pacific subduction to the east, and the proto-SCS slab-pull to the south, it became a sinistral transtensional fault from 35 Ma to 16.5 Ma. Our results highlight the significant role of the NW-trending fault systems in the basin formation and the regional tectonic evolution of the PRMB.
A novel non-destructive workflow for examining germanium and co-substituents in ZnS
Authors: Hayes Sarah M. , McAleer Ryan J. , Piatak Nadine M. , White Sarah Jane O. , Seal Robert R. 
Published: January 2023

A suite of complementary techniques was used to examine germanium (Ge), a byproduct critical element, and co-substituent trace elements in ZnS and mine wastes from four mineral districts where germanium is, or has been, produced within the United States. This contribution establishes a comprehensive workflow for characterizing Ge and other trace elements, which captures the full heterogeneity of samples through extensive pre-characterization. This process proceeded from optical microscopy, to scanning electron microscopy and cathodoluminescence (CL) imaging, to electron microprobe analysis, prior to synchrotron-based investigations. Utilizing non-destructive techniques enabled reanalysis, which proved essential for verifying observations and validating unexpected results. In cases where the Fe content was &lt;0.3 wt% in ZnS, cathodoluminescence imaging proved to be an efficient means to qualitatively identify trace element zonation that could then be further explored by other micro-focused techniques. Micro-focused X-ray diffraction was used to map the distribution of the non-cubic ZnS polymorph, whereas micro-focused X-ray fluorescence (μ-XRF) phase mapping distinguished between Ge4+ hosted in primary ZnS and a weathering product, hemimorphite [Zn4Si2O7(OH)2·H2O]. Microprobe data and μ-XRF maps identified spatial relationships among trace elements in ZnS and implied substitutional mechanisms, which were further explored using Ge and copper (Cu) X-ray absorption near-edge spectroscopy (XANES). Both oxidation states of Ge (4+ and 2+) were identified in ZnS along with, almost exclusively, monovalent Cu. However, the relative abundance of Ge oxidation states varied among mineral districts and, sometimes, within samples. Further, bulk XANES measurements typically agreed with micro-focused XANES (μ-XANES) spectra, but unique micro-environments were detected, highlighting the importance of complementary bulk and micro-focused measurements. Some Ge μ-XANES utilized a high energy resolution fluorescence detector, which improved spectral resolution and spectral signal-to-noise ratio. This detector opens new opportunities for exploring byproduct critical elements in complex matrices. Overall, the non-destructive workflow employed here can be extended to other byproduct critical elements to more fully understand fundamental ore enrichment processes, which have practical implications for critical element exploration, resource quantification, and extraction.
Effects of the therapy shift from cortisone acetate to modified-release hydrocortisone in a group of patients with adrenal insufficiency
Authors: Frigerio Sofia , Carosi Giulia , Ferrante Emanuele , Sala Elisa , Polledri Elisa , Fustinoni Silvia , Ambrosi Bruno , Chiodini Iacopo , Mantovani Giovanna , Morelli Valentina , Arosio Maura 
Published: January 2023

ObjectivePatients with adrenal insufficiency (AI) may be exposed to supraphysiological glucocorticoids levels during standard treatment with cortisone acetate (CA) or immediate-release hydrocortisone (IR-HC). Recent studies, predominantly including patients in IR-HC treatment, suggested that modified-release hydrocortisone (MRH) provide a more physiological cortisol rhythm, improving metabolic control and quality of life. Our primary aim was to assess clinical and biochemical modifications in patients shifted from CA to MRH.Design/MethodsWe designed a retrospective longitudinal study, enrolling 45 AI patients (22 primary and 23 secondary AI) treated exclusively with CA thrice daily, shifted to MRH once daily; 29/45 patients concluded at least 18-months follow-up (MRH-group). We recruited 35 AI patients continuing CA as a control group (CA-group). Biochemical and clinical data, including metabolic parameters, bone quality, and symptoms of under- or overtreatment were collected. In 24 patients, a daily salivary cortisol curve (SCC) performed before and one month after shifting to MRH was compared to healthy subjects (HS).ResultsNo significant changes in glycometabolic and bone parameters were observed both in MRH and CA-groups during a median follow-up of 35 months. A more frequent decrease in blood pressure values (23.1% vs 2.8%, p=0.04) and improvement of under- or overtreatment symptoms were observed in MRH vs CA-group. The SCC showed a significant steroid overexposure in both CA and MRH-groups compared to HS [AUC (area under the curve) = 74.4 ± 38.1 nmol×hr/L and 94.6 ± 62.5 nmol×hr/L respectively, vs 44.1 ± 8.4 nmol×hr/L, p&lt;0.01 for both comparisons], although SCC profile was more similar to HS in MRH-group.ConclusionsIn our experience, patients shifted from CA to equivalent doses of MRH do not show significant glycometabolic modifications but blood pressure control and symptoms of over-or undertreatment may improve. The lack of amelioration in glucose metabolism and total cortisol daily exposure could suggest the need for a dose reduction when shifting from CA to MRH, due to their different pharmacokinetics.
Disrupted metabolic signatures in amniotic fluid associated with increased risk of intestinal inflammation in cesarean section offspring
Authors: Liu Yongjie , Zhang Jun , Feng Liping 
Published: January 2023

IntroductionChildren born by cesarean section (CS) are at a greater risk of inflammatory bowel disease (IBD). However, the mechanisms underlying the association are not yet well understood. Herein, we investigated the impact of CS delivery on colonic inflammation and mechanisms underlying these effects in offspring.MethodsCS mice model and dextran sulfate sodium (DSS)-induced colitis model were constructed and used to analyze the impact of CS on the development of colitis. Colonic tight junction markers and epithelium differentiation markers were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Levels of zonulin in serum were detected by enzyme-linked immunosorbent assay (ELISA). Immune cells in colon were analyzed by flow cytometry. Metabolic profiling between human vaginal delivery (VD) and CS AF were analyzed by using mass spectrometry. Transcriptome changes between VD AF- and CS AF-treated human intestine epithelial cells were analyzed by RNA-sequencing. A multi-omics approach that integrated transcriptomics with metabolomics to identify the pathways underlying colonic inflammation associated with delivery modes. Then, the identified pathways were confirmed by immunoblotting and ELISA.ResultsMice pups delivered by CS exhibited a defective intestinal homeostasis manifested by decreased expression of tight junction markers of ZO-1 and Occludin in the colons, increased levels of zonulin in serum and dysregulated expression of intestinal epithelium differentiation markers of Lysozyme, Mucin2, and Dipeptidyl peptidase-4. CS pups were more susceptible to DSS-induced colitis compared to VD pups. The proportion of macrophage, dendritic cells (DCs), and natural killer cells (NKs) in the colons were altered in an age-dependent manner compared with pups born naturally. The metabolites in AF differed between CS and VD cases, and the CS AF-induced differentially expressed genes (DEGs) were significantly enriched in pathways underlying IBD. Signal transducer and activator of transcription 3 (STAT3) signaling was downregulated in NCM460 intestinal epithelial cells by CS AF compared to VD AF and in colon of CS pups compared to VD pups. Deficiency in metabolites like vitamin D2 glucosiduronate in CS AF may attribute to the risk of inflammatory intestine through STAT3 signaling.ConclusionOur study provides a novel insight into the underlying mechanisms of CS-associated intestinal inflammation and potential prevention strategies.
Kinetics of SARS-CoV-2 neutralizing antibodies in Omicron breakthrough cases with inactivated vaccination: Role in inferring the history and duration of infection
Authors: Simayi Aidibai , Li Chuchu , Chen Cong , Wang Yin , Dong Chen , Tian Hua , Kong Xiaoxiao , Zhou Lu , Peng Jiefu , Zhang Shihan , Zhu Fengcai , Hu Jianli , Xu Ke , Jin Hui , Fan Huafeng , Bao Changjun , Zhu Liguo 
Published: January 2023

BackgroundThe quantitative level and kinetics of neutralizing antibodies (NAbs) in individuals with Omicron breakthrough infections may differ from those of vaccinated individuals without infection. Therefore, we aimed to evaluate the difference in NAb levels to distinguish the breakthrough cases from the post-immunized population to identify early infected person in an outbreak epidemic when nasal and/or pharyngeal swab nucleic acid real-time PCR results were negative.MethodsWe collected 1077 serum samples from 877 individuals, including 189 with Omicron BA.2 breakthrough infection and 688 post-immunized participants. NAb titers were detected using the surrogate virus neutralization test, and were log(2)-transformed to normalize prior to analysis using Student’s unpaired t-tests. Geometric mean titers (GMT) were calculated with 95% confidence intervals (CI). Linear regression models were used to identify factors associated with NAb levels. We further conducted ROC curve analysis to evaluate the NAbs’ ability to identify breakthrough infected individuals in the vaccinated population.ResultsThe breakthrough infection group had a consistently higher NAb levels than the post-immunized group according to time since the last vaccination. NAb titers in the breakthrough infection group were 6.4-fold higher than those in the post-immunized group (GMT: 40.72 AU/mL and 6.38 AU/mL, respectively; p&lt;0.0001). In the breakthrough infection group, the NAbs in the convalescent phase were 10.9-fold higher than in the acute phase (GMT: 200.48 AU/mL and 18.46 AU/mL, respectively; p&lt;0.0001). In addition, the time since infection, booster vaccination, and the time since last vaccination were associated with log(2)-transformed NAb levels in the breakthrough infection group. ROC curve analysis showed that ROC area was largest (0.728) when the cut-off value of log(2)-transformed NAb was 6, which indicated that NAb levels could identify breakthrough infected individuals in the vaccinated population.ConclusionOur study demonstrates that the NAb titers of Omicron BA.2 variant breakthrough cases are higher than in the post-immunized group. The difference in NAb levels could be used to identify cases of breakthrough infection from the post-immunized population in an outbreak epidemic.
Heterogeneity on the abyssal plains: A case study in the Bering Sea
Authors: Sigwart Julia D. , Brandt Angelika , Di Franco Davide , Briones Elva Escobar , Gerken Sarah , Gooday Andrew J. , Grimes Candace J. , Głuchowska Kamila , Hoffmann Sven , Jażdżewska Anna Maria , Kamyab Elham , Kelch Andreas , Knauber Henry , Kohlenbach Katharina , Miguez-Salas Olmo , Moreau Camille , Ogawa Akito , Poliseno Angelo , Santín Muriel Andreu , Tandberg Anne Helene S. , Theising Franziska I. , Walter Thomas , Wölfl Anne-Cathrin , Chen Chong 
Published: January 2023

The abyssal plains are vast areas without large scale relief that occupy much of the ocean floor. Although long considered relatively featureless, they are now known to display substantial biological heterogeneity across different spatial scales. Ecological research in these regions benefits increasingly from non-destructive visual sampling of epifaunal organisms with imaging technology. We analysed images from ultra-high-definition towed camera transects at depths of around 3500 m across three stations (100–130 km apart) in the Bering Sea, to ask whether the density and distribution of visible epifauna indicated any substantial heterogeneity. We identified 71 different megafaunal taxa, of which 24 occurred at only one station. Measurements of the two most abundant faunal elements, the holothurian Elpidia minutissima and two xenophyophores morphotypes (the more common identifiable as Syringammina limosa), indicated significant differences in local densities and patchy aggregations that were strikingly dissimilar among stations. One station was dominated by xenophyophores, one was relatively depauperate in both target taxa as well as other identified megafauna, and the third station was dominated by Elpidia. This is an unexpected level of variation within comparable transects in a well-mixed oceanic basin, reinforcing the emerging view that abyssal habitats encompass biological heterogeneity at similar spatial scales to terrestrial continental realms.
EBHI-Seg: A novel enteroscope biopsy histopathological hematoxylin and eosin image dataset for image segmentation tasks
Authors: Shi Liyu , Li Xiaoyan , Hu Weiming , Chen Haoyuan , Chen Jing , Fan Zizhen , Gao Minghe , Jing Yujie , Lu Guotao , Ma Deguo , Ma Zhiyu , Meng Qingtao , Tang Dechao , Sun Hongzan , Grzegorzek Marcin , Qi Shouliang , Teng Yueyang , Li Chen 
Published: January 2023

Background and purposeColorectal cancer is a common fatal malignancy, the fourth most common cancer in men, and the third most common cancer in women worldwide. Timely detection of cancer in its early stages is essential for treating the disease. Currently, there is a lack of datasets for histopathological image segmentation of colorectal cancer, which often hampers the assessment accuracy when computer technology is used to aid in diagnosis.MethodsThis present study provided a new publicly available Enteroscope Biopsy Histopathological Hematoxylin and Eosin Image Dataset for Image Segmentation Tasks (EBHI-Seg). To demonstrate the validity and extensiveness of EBHI-Seg, the experimental results for EBHI-Seg are evaluated using classical machine learning methods and deep learning methods.ResultsThe experimental results showed that deep learning methods had a better image segmentation performance when utilizing EBHI-Seg. The maximum accuracy of the Dice evaluation metric for the classical machine learning method is 0.948, while the Dice evaluation metric for the deep learning method is 0.965.ConclusionThis publicly available dataset contained 4,456 images of six types of tumor differentiation stages and the corresponding ground truth images. The dataset can provide researchers with new segmentation algorithms for medical diagnosis of colorectal cancer, which can be used in the clinical setting to help doctors and patients. EBHI-Seg is publicly available at: https://figshare.com/articles/dataset/EBHI-SEG/21540159/1.
Evaluation of computational phage detection tools for metagenomic datasets
Authors: Schackart Kenneth E. , Graham Jessica B. , Ponsero Alise J. , Hurwitz Bonnie L. 
Published: January 2023

IntroductionAs new computational tools for detecting phage in metagenomes are being rapidly developed, a critical need has emerged to develop systematic benchmarks.MethodsIn this study, we surveyed 19 metagenomic phage detection tools, 9 of which could be installed and run at scale. Those 9 tools were assessed on several benchmark challenges. Fragmented reference genomes are used to assess the effects of fragment length, low viral content, phage taxonomy, robustness to eukaryotic contamination, and computational resource usage. Simulated metagenomes are used to assess the effects of sequencing and assembly quality on the tool performances. Finally, real human gut metagenomes and viromes are used to assess the differences and similarities in the phage communities predicted by the tools.ResultsWe find that the various tools yield strikingly different results. Generally, tools that use a homology approach (VirSorter, MARVEL, viralVerify, VIBRANT, and VirSorter2) demonstrate low false positive rates and robustness to eukaryotic contamination. Conversely, tools that use a sequence composition approach (VirFinder, DeepVirFinder, Seeker), and MetaPhinder, have higher sensitivity, including to phages with less representation in reference databases. These differences led to widely differing predicted phage communities in human gut metagenomes, with nearly 80% of contigs being marked as phage by at least one tool and a maximum overlap of 38.8% between any two tools. While the results were more consistent among the tools on viromes, the differences in results were still significant, with a maximum overlap of 60.65%. Discussion: Importantly, the benchmark datasets developed in this study are publicly available and reusable to enable the future comparability of new tools developed.
Ultra-processed foods consumption is associated with multiple sclerosis severity
Authors: Guglielmetti Monica , Grosso Giuseppe , Ferraris Cinzia , Bergamaschi Roberto , Tavazzi Eleonora , La Malfa Alessandro , Wahidah H. Al-Qahtani , Tagliabue Anna 
Published: January 2023

BackgroundMS is a chronic inflammatory neurological and immune-mediated disease of multifactorial etiology. Ultra-processed foods (UPFs) have been generally considered unhealthy due to their poor nutritional value. Emerging evidence suggests that factors other than their nutritional content may play an additional role toward chronic inflammation.AimTo investigate the potential association of UPF consumption and MS severity in a group of MS Italian consecutive patients.MethodsDemographic (age, sex, marital status, educational level), neurological (EDSS, MSSS), and nutritional (anthropometric measures, dietary habits) information were collected. Physical activity and smoking habits were also investigated. Food items were grouped according to the NOVA classification. Patients were classified in two groups based on MS severity (“mild” and “moderate to high”).ResultsHigher UPF consumption was associated with moderate-to-high MS severity compared to lower consumption in both the unadjusted model (OR = 2.28, 95% CI: 1.04–5.01) and after adjustment for potential background (OR = 2.46, 95% CI: 1.04–5.83) and clinical confounding factors (OR = 2.97, 95% CI: 1.13–7.77).ConclusionsAlthough these results are only preliminary and hypothesis generating, it is important to explore how various aspects of the diet may relate to MS severity in order to identify the best strategy to support MS patients over the disease course.
Association between urinary levels of 8-hydroxy-2-deoxyguanosine and F2a-isoprostane in male football players and healthy non-athlete controls with dietary inflammatory and antioxidant indices
Authors: Zare Mahsa , Shateri Zainab , Nouri Mehran , Sarbakhsh Parvin , Eftekhari Mohammad Hasan , Pourghassem Gargari Bahram 
Published: January 2023

PurposeThe relationship between the inflammatory and antioxidant potential of an athlete's diet and their oxidative biomarkers is an important area of investigation. Therefore, this study aimed to assess the excretion of 8-hydroxy-2-deoxyguanosine (8-OHdG) and F2alpha-isoprostane (F2a-IP) in the urine of male football players and healthy non-athlete controls. This study also aimed to examine the associations among the dietary inflammatory index (DII), the dietary total antioxidant capacity (DTAC), and the dietary phytochemical index (PI) with 8-OHdG and F2a-IP.MethodsIn this descriptive-analytical study, 45 male football players and 45 healthy non-athletes, who were individually matched based on age and body mass index (BMI), were recruited from Shiraz City, Iran. Fasted urine samples were analyzed for 8-OHdG and F2a-IP levels. Anthropometric measurements were performed, and body composition was assessed using a body composition analyzer. A valid food frequency questionnaire (FFQ) was used to calculate DII, DTAC, and PI scores. Data analysis was conducted using a generalized estimating equation (GEE) model.ResultsWe found that 8-OHdG (β = −6.96), F2a-IP (β = −82.58), and DII (β = −2.06) were significantly lower, while DTAC (β = 2.37) and PI (β = 0.084) were significantly higher in the football player group compared with the non-athlete group (P &lt; 0.001 for all variables). In all participants, dietary indices were significantly associated with oxidative biomarkers. DII was positively associated with 8-OHdG (β = 2.25; P &lt; 0.001) and F2a-IP (β = 38.34; P &lt; 0.001). Furthermore, negative associations between DTAC (β = −1.42; P &lt; 0.001) and PI (β = −35.37; P &lt; 0.001) with 8-OHdG were found. Moreover, DTAC (β = −17.34; P &lt; 0.001) and PI (β = −428.11; P = 0.003) were negatively associated with F2a-IP.ConclusionThe results of this study highlighted the importance of a healthy diet in reducing oxidative stress among football athletes. The levels of urinary biomarkers for DNA and lipid oxidation were found to be lower in football players compared to non-athletes. This suggests that following an anti-inflammatory and antioxidant-rich diet may help reduce oxidative stress in these individuals.