bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated simulation framework for flood risk mapping integrating aerial point clouds and deep learning
Authors: Fang Xin , Wu Jie , Jiang Peiqi , Liu Kang , Wang Xiaohua , Zhang Sherong , Wang Chao , Li Heng , Lai Yishu 
Published: October 2023

Abstract
In recent years, floods have brought renewed attention and requirement for real-time and city-scaled flood forecasting, due to climate change and urbanization. Flood risk mapping through traditional physics-based modeling methods is often unrealistic for rapid emergency response requirements, because of long model runtime, hydrological information lacking, and terrain change caused by human activity. In this study, an automated simulation framework is proposed by integrating aerial point clouds and deep learning technique that is capable of superior modeling efficiency and analysis accuracy for flood risk mapping. The framework includes four application modules, i.e., data acquisition and preprocessing, point clouds segmentation, digital elevation model (DEM) reconstruction, and hydrodynamics simulation. To more clearly demonstrate the advantages of the proposed automated simulation framework, a case study is conducted in a local area of the South-to-North Water Transfer Project in China. In addition, the efficiency and accuracy of the suggested point cloud segmentation network for large-scale 3D point clouds in basin scenes are discussed in detail by comparison with PointNet and PointNet + + networks.
Causal Relationships Between Myasthenia Gravis and Gut Microbiota by Mendelian Randomization Analysis
Authors: Wang Jiahui , Wang Jing , Wang Xihao , Yao Qifeng , Ying Jianghua , Huang Yueyu , Mao Weiming , Zhao An 
Published: October 2023

Abstract

OBJECTIVE
Evidence from observational studies suggests a possible association between gastrointestinal microbiota (GM) and myasthenia gravis (MG). The association between GM and MG remains to be determined because observational studies are confounded by external confounders and reverse causality. The present study determined the causal association between specific GM and MG by Mendelian randomization (MR).
METHODS
Genome-wide association studies (GWAS) explore the associations between complex diseases, shapes, and genes. Extraction of single nucleotide polymorphisms (SNPs) from GWAS as instrumental variables (IVs) for Mendelian randomization studies reveals causal associations between disease and exposure at the genetic level. We performed Mendelian randomization by performing a MibioGen consortium for 211 different species of gastrointestinal microbiota (from 18,340 individuals, 24 cohorts) with MG (ncase = 426, ncontrol = 373848) from the Finngen database. Inverse variance weighting (IVW) was used as the primary method of analysis to compare the causal association between the two after false discovery rate (FDR) correction, with P < 0.05 as the difference being significant.
RESULTS
A MR study identified eight gastrointestinal microbiota, weighted by inverse variance, that may be negatively associated with the MG family.Clostridiaceae1.id.1869 (OR:0.424, 95%CI:0.202–0.889, P = 0.023), family.Defluviitaleaceae.id.1924 (OR:0.537, 95%CI:0.290–0.995, P = 0.048), family.Enterobacteriaceae.id.3469 (OR:0.341, 95%CI:0.135–0.865, P = 0.023), genus.Actinomyces.id.423 (OR:0.520, 95%CI:0.271–0.999, P = 0.049), genus.Victivallis.id.2256 (OR:0.627, 95%CI:0.426–0.923, P = 0.018), genus.Unknown genus. id.826 (OR:0.407, 95%CI:0.209–0.793, P = 0.008), order.Enterobacteriales.id.3468 (OR:0.341, 95%CI:0.135–0.865, P = 0.023). Genus.Lachnoclostridium.id.11308 (OR:2.431, 95%CI:1.047–5.647, P = 0.039) showed a possible positive association with MG after inverse variance weighting. However, no GM showed a causal association with MG after FDR correction. Reverse MR likewise did not find a causal association between MG and GM.
CONCLUSION
Although the causal association of MG and GM was negative by MR Analysis, the extended database or new microbiome data needs to be further validated.
Characterizing movement and searching behavior of humpback whales along the North-Norwegian coast
Authors: Utengen Ingvild Ytterhus , Vogel Emma F , Biuw Martin , Ruiten Meghan Van , Rikardsen Audun 
Published: October 2023

Abstract

Background: Studying movement patterns of individual animals over time can give insight into how they interact with the environment and optimize foraging strategies. Humpback whales (Megaptera novaeangliae) undertake long seasonal migrations between feeding areas in polar regions and breeding grounds in tropical areas. During the last decade, several individuals have had up to a three month stop-over period around specific fjord-areas in Northern Norway to feed on Norwegian spring-spawning (NSS -) herring (Culpea harengus L.). Their behavioral patterns during this period are not well understood, including why some whales seemingly leave the fjords and then later return within the same season.
Methods: Here we for the first-time classified humpback whale tracks into five distinct movement modes; ranging, encamped, nomadic, roundtrip and semi-roundtrip. A behavioral change point analysis (BCPA) was used to select homogeneous segments based on persistence velocity. Then, net squared displacement (NSD) over time was modeled to differentiate movement modes. This study also visually identified longer roundtrips away from the fjords that lasted several days and examined movement modes within these.
Results: Inside the fjord systems, encamped mode was most prevalent in December-January, suggesting the whales were mainly foraging on overwintering NSS-herring in this area. During the same winter seasons, half of the whales left the fjords and then returned. We hypothesize that these trips serve as 'searching trips' during which the whales seek better feeding opportunities outside the fjords. If better foraging conditions are not found, they return to the fjords to continue their feeding. The overall most common mode was ranging (54%), particularly seen during the start of their southwards migration and in areas outside the fjord systems, indicating that the whales mainly moved over larger distances in the offshore habitat.
Conclusion: This study serves as a baseline for future studies investigating both the searching trip theory and humpback whale behavior in general, and confirms that this method is useful to analyze smaller scale movement patterns of satellite tagged whales.
Human-bird interactions in the Levant during the Late Pleistocene to Early Holocene: Multi-scalar analysis of avifaunal remains
Authors: Yeomans Lisa , Mazzucato Camilla 
Published: October 2023

Abstract

This paper describes analyses of avifauna from Levantine Late Pleistocene and Early Holocene sites at contrasting scales. Firstly, we present avian osteological data from a sequence of occupation at Shubayqa, in northeast Jordan, illustrating changing human-bird-environment interactions over 4000 years offering interpretations of environmental change on avifaunal communities and nature of multi-species relationships at this wetland environment. Secondly, we compare published avifaunal assemblages to investigate the nature of bird-human relationships across a broader temporal and geographical span. During the Late Pleistocene and Early Holocene our species gradually transitioned to an agricultural mode of subsistence. Whilst explanations of long-term human behavioural dynamics are frequently sought, disparity between correlation and causation obscures interpretation of trajectories in the human past. People hunted birds for subsistence but extensive evidence for the symbolic importance of birds suggests complex relationships between species. Avifaunal evidence, therefore, presents insights into two commonly suggested primary causes for the shift from hunter-foragers to agriculturalists – resource pressure and symbolic expression. Here we argue that actions of humans gradually modified the landscape and ecological system but this was not a reactionary response to resource stress. Nevertheless, this resulted in the productivity of the landscape increasing and allowed further intensification. Feathers and talons of birds were used for millennia preceding the shift to agriculture and the increase in bird hunting towards the end of the Pleistocene cannot be explained by the increased role of birds in the symbolic realm.
Characteristics of small bowel lesions and disease evaluation in Crohn’s disease by Capsule endoscopy
Authors: Qiu Donghao , Wang Chunlian , Li Xiaojun , Zhang Jie , Wang Xuehong , Ouyang Chunhui 
Published: October 2023

Abstract
Purpose
Early endoscopic diagnosis and evaluation of small bowel Crohn’s disease (CD) have been important and challenging. This study aimed to investigate features of small bowel lesion in CD detected by capsule endoscopy (CE) as well as mucosal evaluation performance compared to clinical activity.
Methods
In this retrospective study, we collected baseline CE data of 60 small bowel CD patients. Characteristics of lesions location and features were summarized. Lesions of location difference were compared by McNemar's test. Lewis score (LS) and Crohn’s Disease Activity Index (CDAI) were used to evaluate disease activity independently, correlation was analyzed by Spearman's rank correlation test.
Results
Under CE, ulceration shape presented by irregular (76.7%), longitudinal (66.7%), oval (40%) and circular (8.3%). Some lesions were arranged by longitudinally (36.7%) and circumferentially (23.3%). Prevalence of cobblestone appearance and longitudinal arrangement in jejunum was higher than in ileum (P < 0.05). In small bowel and colon involvement, LS was weakly connected with CDAI (r = 0.367, P༜0.05), while in isolated small bowel CD, no significant correlation was found (P > 0.05).
Conclusion
Ulcer shape of small bowel CD is diverse. Cobblestone appearance tends to occur in jejunum and may result in poor prognosis. Multi-segment small oval or irregular ulcer arranged by longitudinally in jejunum may be a clue for CD early diagnosis. CDAI may underestimate mucosal inflammation. LS is necessary for small bowel CD for accurate evaluation.
A putative ormycovirus potentially associating with the yellow leaf disease of areca palm
Authors: Niu Xiaoqing , Xu Zhongtian , Tian Yujing , Xiao Siyun , Xie Yuan , Du Zhenguo , Qin Weiquan , Gao Fangluan 
Published: October 2023

Abstract
Yellow leaf disease (YLD) is a significant limiting factor in Areca palm cultivation, yet its etiology remains uncertain. In our investigation of YLD-affected Areca palm plants, transcriptome sequencing revealed an RNA contig with the RNA-dependent RNA polymerase (RdRp) of ormycoviruses as its top BLASTx matches. Subsequent gene cloning techniques yielded the full-length sequence of this RNA, potentially representing the genome or partial genome of a previously unknown ormycovirus, tentatively named areca palm yellow leaf-associated ormycovirus (APYLaOMV). RT-PCR detection found that APYLaOMV is present in more than 69% of YLD-affected areca palm samples but not in healthy ones, suggesting a potential link between APYLaOMV and YLD. Overall, these data may be valuable in understanding the etiology of YLD in Areca palms.
Clinical Implications and Outcomes of Bone Marrow Granulomas
Authors: Lin Ting-An , Lee Wan-Ching , Sun Yi-Syuan , Yang Ching-Fen , Hsiao Liang‑Tsai , Gau Jyh-Pyng , Liu Jin-Hwang , Chang Yuan-I 
Published: October 2023

Abstract
Background
Bone marrow granuloma is an uncommon finding that is associated with diverse underlying etiologies. Its clinical significance and impact on patient prognosis remain poorly understood.
Methods
We reviewed bone marrow biopsies from a tertiary medical center in Taiwan between 2005 and 2020. Cases with bone marrow granuloma were included and analyzed retrospectively.
Results
A total of 81 cases were evaluated. The primary cause of bone marrow granuloma was mycobacterial infection (38.3%), followed by hematologic malignancies (25.9%). The diagnosis of mycobacterial infection in these patients was often delayed due to low positivity rates of mycobacteria cultures (9.5%), acid-fast bacilli smears (13.3%), and nucleic acid amplification tests (6.3%) from bone marrow aspirates. We identified splenomegaly, severe hypoalbuminemia, and high C-reactive protein levels as potential diagnostic indicators for mycobacterial infections in patients with bone marrow granulomas. The one-year and two-year mortality rates for patients with bone marrow granuloma were 24.7% and 29.6%, respectively. Male gender (HR, 5.70; p = 0.021), age ≥ 65 years (HR, 3.83; p = 0.008), and pre-existing malignancy (HR, 2.72; p = 0.038) were identified as independent risk factors for 1-year mortality. Interestingly, the underlying cause of bone marrow granulomas did not affect the prognosis.
Conclusion
Bone marrow granuloma is often a diagnostic challenge and requires extensive investigation, mainly to identify mycobacterial infection. The presence of bone marrow granuloma is associated with poor prognosis, especially in male and elderly patients. Our study highlights the diagnostic and prognostic importance of bone marrow granulomas in clinical practice.
Evaluation of genetic diversity and population structure of reticulate iris genotypes in the Iraqi Kurdistan region using SCoT and SRAP markers
Authors: Majeed Hoshman Omar , Faraj Jamal Mahmood , Rasul Kamaran Salh , Lateef Djshwar Dhahir , Tahir Nawroz Abdul-razzak 
Published: October 2023

Abstract

The reticulate iris is one of the most attractive wild ornamentals, bulbous irises, widely distributed throughout the mountains of the Iraqi Kurdistan region. Due to a lack of information available about the genetic variability and population structure of this group of plants in Iraq. Thus, ten start codon targeted (SCoT) polymorphic and ten sequence-related amplified polymorphisms (SRAP) markers were used in the present study to evaluate genetic diversity and population structure in 50 wild reticulate iris genotypes from five different sites in Iraqi Kurdistan region. Over all, SCoT and SRAP markers produced 135 and 87 polymorphic bands, respectively. The average of number of polymorphic bands (TPB), number of observed alleles (Na), Shannon’s information index (I), effective number of alleles (Ne), expected heterozygosity or gene diversity (He), polymorphic information content (PIC), and unbiased expected heterozygosity (uHe), of SCoT primers were (13.7, 1.54, 0.35, 1.40, 0.23, 0.31, and 0.25) and of SRAP primers were 8.7, 1.54, 0.36, 1.40, 0.24, 0.32, and 0.25, respectively. According to the UPGMA dendrogram and structure analysis, SCoT markers grouped 50 reticulate iris genotypes into two main clades with some sub-clades, while SRAP markers separated these genotypes into four main clades. The analysis of molecular variance revealed 80 and 76% variability among populations with SCoT and SRAP markers, respectively, which indicated gene exchange between populations. Except for the number of private bands index in SCoT and SRAP markers, populations 3 and 1 had the highest diversity indices (Na, Ne, I, H uHe, and percentage of polymorphic loci (PPL)). The highest distance between populations was revealed by SCoT markers between population 1 and both population 2 and population 4, with 13% dissimilarity, while the maximum dissimilarity was observed by SRAP markers between population 1 and population 4, with 17% dissimilarity. The study's findings revealed the efficacy of these markers for genetic variation in iris genotypes, in addition to their ability for germplasm conservation and genome diversity.
Identification of candidate mechanisms for dystonic traits from an analysis of a complete system neurological / biomechanical model
Authors: Kuznik Michael 
Published: October 2023

Abstract
The research goal is to construct a complete system model for human head movement integrating skeletal, muscular, biomechanical and neurological aspects; verifying the model by simulating ‘normal’ volitional movement. Thereafter the model was used to explore pathological scenarios by variations to model components some of which resulted in dystonic traits, including tremor and abnormal twisting. This enabled identification and analysis of the underlying mechanisms.
Once research commenced it was soon apparent that a purely analytical model (a collection of mutually dependent components each mathematically expressed) was not realisable nor mathematically tractable and so a computer simulation configured for the specific case of head movement (targeting the condition of cervical dystonia but in principle generic) was constructed to allow the study to proceed. The resulting model was exercised to verify a reasonable approximation to normal volitional control of head positioning. With the model operating well in this context, a series of variations were made to see if these might induce dystonic traits. Whilst most of the variations investigated did not cause significant behavioural changes, those relating to the transmission of information to the brain for proprioception were found to be very influential on the system behaviour.
Simulated behaviours of pathological interest included: movement of the head to an orientation of maximum lateral twist and locking in that state, oscillations that evidenced themselves as repetitive movement of the head and finally a ‘self healing’ capability in the case of defective proprioception which is a well established characteristic of the temporal progression of cervical dystonia.
This research identifies candidate mechanisms for the dystonic traits of tremor and excess muscle tone.
Evaluation of Molecular Receptors Status in Breast Cancer Using an mpMRI-based Feature Fusion Radiomics Model: Mimicking Radiologists’ Diagnosis
Authors: Lai Shengsheng , Liang Fangrong , Zhang Wanli , Zhao Yue , Li Jiamin , Zhao Yandong , Xu Yongzhou , Ding Wenshuang , Zhan Jie , Zhen Xin , Yang Ruimeng 
Published: October 2023

Abstract
Purpose: To investigate the performance of a novel feature fusion radiomics (RFF) model that incorporates features from multiparametric MRIs (mpMRI) in distinguishing different statuses of molecular receptors in breast cancer (BC) preoperatively.
Methods: 460 patients with 466 pathology-confirmed BCs who underwent breast mpMRI at 1.5T in our center were retrospectively included hormone receptor (HR) positive (HR+) (n=336) and HR negative (HR-) (n=130). The HR- patients were further categorized into human epidermal growth factor receptor 2 (HER-2) enriched BC (HEBC) (n=76) and triple negative BC (TNBC) (n=54). All lesions were divided into a training/validation cohort (n=337) and a test cohort (n=129). Volumes of interest (VOIs) delineation, followed by radiomics feature extraction, was performed on T2WI, DWI600 (b=600 s/mm2), DWI800 (b=800 s/mm2), ADC map, and DCE1-6 (six continuous DCE-MRI) images of each lesion. Simulating a radiologist’s work pattern, 150 classification base models were constructed and analyzed to determine the top four optimum sequences for classifying HR+ vs. HR-, TNBC vs. HEBC, TNBC vs. non-TNBC in a random selected training cohort (n=337). Building upon these findings, the optimal single sequence models (Rss) and combined sequences models (RFF) were developed. The AUC, sensitivity, accuracy and specificity of each model for subtype differentiation were evaluated. The paired samples Wilcoxon signed rank test was used for performance comparison.
Results: During the three classification tasks, the optimal single sequence for classifying HR+ vs. HR- was DWI600, while the ADC map, derived from DWI800 performed the best in distinguishing TNBC vs. HEBC, as well as identifying TNBC vs. non-TNBC, with corresponding training AUC values of 0.787, 0.788, and 0.809, respectively. Furthermore, the integration of the top four sequences in RFF models yielded improved performance, achieving AUC values of 0.809, 0.805 and 0.847, respectively. Consistent results was observed in both the training/validation and testing cohorts, with AUC values of 0.778，0.787, 0.818 and 0.726, 0.773, 0.773, respectively (all p < 0.05 except HR+ vs. HR-).
Conclusion: The RFF model, integrating mpMRI radiomics features, demonstrated promising ability to mimic radiologists’ diagnosis for preoperative identification of molecular receptors of BC.
Exploring the Molecular and Immune Landscape of Lung Cancer Associated with Cystic Airspaces: Implications for Prognosis and Therapeutic Strategies
Authors: Zheng Xiang , Qiu Li , Huang Ying , Cheng Ran , Huang Si , Xu Ke , Cai Wei , Deng Yu , Wang Wei , Zhong Xi , Cui Fei , Hao Zhexue , Liu Jun 
Published: October 2023

Abstract
Objective: To explore the molecular biological characteristics of lung cancer associated with cystic airspaces (LCCA) and its potential roles on prognosis.
Methods: A total of 165 LCCAs and 201 non-LCCAs were enrolled in this study. Bulk RNA sequencing was implemented in eight LCCAs and nine non-LCCAs to explore the differentially expressed genes. TCGA data were used to analyze LCCA-specific genes that associated with overall survival.
Results: The median age was 60 (IQR 53 to 65) years in LCCA cohort. We found LCCA were predominant in men and had less visceral pleura invasion (VPI) or lympho-vascular invasion (LVI). Moreover, LCCA presented with higher histological heterogeneity. Kaplan-Meier analysis showed that patients of age more than 60 and positive VPI had significantly less PFS in LCCA. Cox regression suggested that LCCA, micropapillary subtype proportion and VPI were the independent risk factors for PFS. LCCA had up-regulated pathways associated with EMT, angiogenesis and cell migration. In addition, LCCA displayed higher levels of immunosuppressor infiltration (M2 macrophages, CAFs and MDSCs) and distinct cell death and metabolic patterns. BCR/TCR repertoire analysis revealed less BCR richness, clonality and high-abundance shared clonotypes in LCCA. Finally, Cox regression analysis identified that four cystic-specific genes, KCNK3, NRN1, PARVB and TRHDE-AS1, were associated with OS of LUAD. And cystic-specific risk scores (CSRSs) were calculated to construct a nomogram, which performance well.
Conclusions: Our study for the first time indicated significantly distinct molecular biological and immune characteristics between LCCA and non-LCCA, which provide complementary prognostic values in early-stage NSCLC.
Exploring Pauli Configurations in Quantum Kernels for Enhanced Binary Classification
Authors: Bertel Luis Gerardo Ayala , Patel Ashish , Vaithiyashankar Jayakumar 
Published: October 2023

Abstract
This study pretends to set one’s sights on advancing the understanding of quantum machine learning’s applicability in binary tasks. By systematically assessing quantum kernels and their performance, the primary objective is to determine and evaluate how different Pauli configurations—precisely, ZZ, ZY, and a custom configuration (Z, YY, ZXZ)—impact execution accuracy running in simulator and 7-qubits IBM quantum hardware. The paper encompasses a robust methodology, including data preprocessing, quantum kernel creation, and integration into classical SVMs. It provides essential guidance for discussing the strengths and limitations of quantum methods, highlighting their potential as a valuable tool for developing accurate diagnostic models.