bluuebunny/crossref_metadata_2025_split huggingface dataset:
The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science
Authors: He Sike , Wei Jingwen , Feng Jiaming , Liu Dan , Wang Neng , Chen Liyu , Xiong Ying 
Published: August 2023

BackgroundInfectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis.MethodsThe literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3).ResultsIn total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections.ConclusionThis study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.
Multi-station volcano tectonic earthquake monitoring based on transfer learning
Authors: Titos Manuel , Gutiérrez Ligdamis , Benítez Carmen , Rey Devesa Pablo , Koulakov Ivan , Ibáñez Jesús M. 
Published: August 2023

Introduction: Developing reliable seismic catalogs for volcanoes is essential for investigating underlying volcanic structures. However, owing to the complexity and heterogeneity of volcanic environments, seismic signals are strongly affected by seismic attenuation, which modifies the seismic waveforms and their spectral content observed at different seismic stations. As a consequence, the ability to properly discriminate incoming information is compromised. To address this issue, multi-station operational frameworks that allow unequivocal real-time management of large volumes of volcano seismic data are needed.Methods: In this study, we developed a multi-station volcano tectonic earthquake monitoring approach based on transfer learning techniques. We applied two machine learning systems—a recurrent neural network based on long short-term memory cells (RNN–LSTM) and a temporal convolutional network (TCN)—both trained with a master dataset and catalogue belonging to Deception Island volcano (Antarctica), as blind-recognizers to a new volcanic environment (Mount Bezymianny, Kamchatka; 6 months of data collected from June to December 2017, including periods of quiescence and eruption).Results and discussion: When the systems were re-trained under a multi correlation-based approach (i.e., only seismic traces detected at the same time at different seismic stations were selected), the performances of the systems improved substantially. We found that the RNN-based system offered the most reliable recognition by excluding low confidence detections for seismic traces (i.e., those that were only partially similar to those of the baseline). In contrast, the TCN-based network was capable of detecting a greater number of events; however, many of those events were only partially similar to the master events of the baseline. Together, these two approaches offer complementary tools for volcano monitoring. Moreover, we found that our approach had a number of advantages over the classical short time average over long time-average (STA/LTA) algorithm. In particular, the systems automatically detect VTs in a seismic trace without searching for optimal parameter settings, which makes it a portable, scalable, and economical tool with relatively low computational cost. Moreover, besides obtaining a preliminary seismic catalog, it offers information on the confidence of the detected events. Finally, our approach provides a useful tentative label for subsequent analysis carried out by a human operator. Ultimately, this study contributes a new framework for rapid and easy volcano monitoring based on temporal changes in monitored seismic signals.
Easterly wave activity in the Intra Americas Seas region analyzed with vertically integrated moisture fluxes
Authors: Pazos Marni , Magaña Víctor , Herrera Eduardo 
Published: August 2023

Introduction: Easterly waves (EWs) are a dominant atmospheric phenomenon in the tropics. EWs in Mexico, Central America and the Caribbean region produce intense precipitation and significantly contribute to the summer rainy season, but some climatologies indicate their activity is weak or even null over the Intra-Americas Seas (IAS). As it is shown in the present study, EW activity over the IAS is not negligible but its variability is less than that off the western coast of Africa.Method: Given the well-known coupling of wind and atmospheric moisture in EWs, their characteristics may be described using vertically integrated moisture fluxes (VIMF) and their divergence. By means of Hovmöller diagrams, lagged correlations and composite analyses, the propagation and the meteorological effects of these waves across the Caribbean Sea and the Gulf of Mexico, particularly on moisture and rains, are examined.Results: It is observed that as EWs propagate, the VIMF convergence increases the level of precipitable water which frequently results in intense precipitation events. High frequency variability of the meridional component of the VIMF is used to estimate EW activity. Over the Caribbean Sea, EWs are less energetic than in the eastern tropical Atlantic even while the number of waves over these regions is comparable.Discussion: When the Caribbean Low-Level Jet (CLLJ) is strong, EW activity tends to diminish due to a decrease in precipitable water (PW), sea surface temperature (SST) over the Caribbean, and possibly to an intensified vertical wind shear. Therefore, years of a stronger than normal CLLJ tend to result in summer precipitation below normal over most of the IAS and southern Mexico.
The rise of bronze in Central Asia: new evidence for the origin of Bronze Age tin and copper from multi-analytical research
Authors: Berger Daniel , Kaniuth Kai , Boroffka Nikolaus , Brügmann Gerhard , Kraus Steffen , Lutz Joachim , Teufer Mike , Wittke Andreas , Pernicka Ernst 
Published: August 2023

The Bronze Age in Central Asia was dominated by the Andronovo Culture and the Bactria-Margiana Archaeological Complex (BMAC). Both cultural entities produced bronze, however, the extent of bronze production and use varied considerably in space and time across their territories. The introduction and spread of bronze metallurgy in the region is commonly associated with the Andronovo Culture, but comparatively little is known about the copper and tin sources that were exploited to make the bronze. To shed light on this aspect, this paper examines 91 bronze artefacts from the Middle Bronze Age (MBA) and the Late Bronze Age (LBA) recovered from twenty sites of Andronovo and the BMAC through a combined evaluation of chemical and isotopic analyses. Trace element patterns and isotopic compositions of lead, tin, and copper are determined for the objects complemented by tin isotope analysis of Central Asian tin ores. The data shows a clear separation of two source areas in the MBA and LBA I: the BMAC obtained copper from polymetallic (tin-bearing) deposits in Iran (Deh Hosein, Nakhlak/Bagh Gorogh) and possibly Afghanistan, while the Andronovo Culture mainly used copper from the Tian Shan Mountains. With the transition to the LBA II, a change in the material basis can be recognised, in which the BMAC increasingly relied on metal deposits from the Andronovo territory. The most important result in this context is the analytical proof of the coextraction of copper and tin from the copper-tin mine at Mushiston, Tajikistan, and the first direct link of tin in bronze objects with a tin deposit. Mushiston apparently supplied both cultural macro regions with a “natural” bronze, which accounted for about one third of all objects analysed, but there is no indication yet that metal or ores from Mushiston were traded or used at a distance of more than 500 km. Moreover, the artefact data indicates a decline in the exploitation of the mine in the course of the developed LBA, while other copper and tin sources in the Tian Shan and probably the Hindukush were exploited. This testifies to the intensive use of the rich mineral resources of Central Asia and beyond, as well as the intensification of cultural and trade contacts between Andronovo and the BMAC.
Study on the consolidation behavior of horizontal drainage foundation under complex aquifer formation conditions in karst regions
Authors: Xu Yunbo , Zhang Jiachao , Liu Zhongyu , Cui Penglu 
Published: August 2023

Introduction: The consolidation behavior of horizontal drainage foundation under complex aquifer conditions in karst areas is a hot topic in the field of geotechnical engineering.Methods: This paper presents a modified piecewise-linear model for plane-strain consolidation. In this model, the distributed drainage boundary was used to describe the drainage performance of soil layer boundaries, and the UH model considering the time effect was selected to reflect soil’s rheological property. Through comparison with existing research, the validity of the calculation model in this paper was verified. Then several examples were used to analyze the consolidation behavior of the foundation under the combined action of rheological effect and distributed drainage boundaries.Results and discussion: Numerical studies show that the phenomenon of the increase of excess pore pressure exists in the foundation of the distributed drainage boundary after considering the rheology in the early stage of consolidation. Moreover, the larger the secondary consolidation coefficient and the initial over-consolidation parameter, or the smaller the pave rate and the thickness-width ratio, the above phenomenon is more obvious. In terms of the dissipation of the pore water pressure, the larger the secondary consolidation coefficient and the initial over-consolidation parameter, the slower the pore pressure dissipation, and the smaller the pave rate or the thickness-width ratio can achieve the above effects. In terms of the impact on settlement, the above-mentioned parameters are consistent, that is, the larger the corresponding parameter, the larger the corresponding settlement value.
Identifying cancer-associated leukocyte profiles using high-resolution flow cytometry screening and machine learning
Authors: Simon Davis David A. , Ritchie Melissa , Hammill Dillon , Garrett Jessica , Slater Robert O. , Otoo Naomi , Orlov Anna , Gosling Katharine , Price Jason , Yip Desmond , Jung Kylie , Syed Farhan M. , Atmosukarto Ines I. , Quah Ben J. C. 
Published: August 2023

BackgroundMachine learning (ML) is a valuable tool with the potential to aid clinical decision making. Adoption of ML to this end requires data that reliably correlates with the clinical outcome of interest; the advantage of ML is that it can model these correlations from complex multiparameter data sets that can be difficult to interpret conventionally. While currently available clinical data can be used in ML for this purpose, there exists the potential to discover new “biomarkers” that will enhance the effectiveness of ML in clinical decision making. Since the interaction of the immune system and cancer is a hallmark of tumor establishment and progression, one potential area for cancer biomarker discovery is through the investigation of cancer-related immune cell signatures. Hence, we hypothesize that blood immune cell signatures can act as a biomarker for cancer progression.MethodsTo probe this, we have developed and tested a multiparameter cell-surface marker screening pipeline, using flow cytometry to obtain high-resolution systemic leukocyte population profiles that correlate with detection and characterization of several cancers in murine syngeneic tumor models.ResultsWe discovered a signature of several blood leukocyte subsets, the most notable of which were monocyte subsets, that could be used to train CATboost ML models to predict the presence and type of cancer present in the animals.ConclusionsOur findings highlight the potential utility of a screening approach to identify robust leukocyte biomarkers for cancer detection and characterization. This pipeline can easily be adapted to screen for cancer specific leukocyte markers from the blood of cancer patient.
Real world validation of an AI-based CT hemorrhage detection tool
Authors: Wang Dongang , Jin Ruilin , Shieh Chun-Chien , Ng Adrian Y. , Pham Hiep , Dugal Tej , Barnett Michael , Winoto Luis , Wang Chenyu , Barnett Yael 
Published: August 2023

IntroductionIntracranial hemorrhage (ICH) is a potentially life-threatening medical event that requires expedited diagnosis with computed tomography (CT). Automated medical imaging triaging tools can rapidly bring scans containing critical abnormalities, such as ICH, to the attention of radiologists and clinicians. Here, we retrospectively investigated the real-world performance of VeriScout™, an artificial intelligence-based CT hemorrhage detection and triage tool.MethodsGround truth for the presence or absence of ICH was iteratively determined by expert consensus in an unselected dataset of 527 consecutively acquired non-contrast head CT scans, which were sub-grouped according to the presence of artefact, post-operative features and referral source. The performance of VeriScout™ was compared with the ground truths for all groups.ResultsVeriScout™ detected hemorrhage with a sensitivity of 0.92 (CI 0.84–0.96) and a specificity of 0.96 (CI 0.94–0.98) in the global dataset, exceeding the sensitivity of general radiologists (0.88) with only a minor relative decrement in specificity (0.98). Crucially, the AI tool detected 13/14 cases of subarachnoid hemorrhage, a potentially fatal condition that is often missed in emergency department settings. There was no decrement in the performance of VeriScout™ in scans containing artefact or postoperative change. Using an integrated informatics platform, VeriScout™ was deployed into the existing radiology workflow. Detected hemorrhage cases were flagged in the hospital radiology information system (RIS) and relevant, annotated, preview images made available in the picture archiving and communications system (PACS) within 10 min.ConclusionAI-based radiology worklist prioritization for critical abnormalities, such as ICH, may enhance patient care without adding to radiologist or clinician burden.
Machine learning in the prediction of post-stroke cognitive impairment: a systematic review and meta-analysis
Authors: Li XiaoSheng , Chen Zongning , Jiao Hexian , Wang BinYang , Yin Hui , Chen LuJia , Shi Hongling , Yin Yong , Qin Dongdong 
Published: August 2023

ObjectiveCognitive impairment is a detrimental complication of stroke that compromises the quality of life of the patients and poses a huge burden on society. Due to the lack of effective early prediction tools in clinical practice, many researchers have introduced machine learning (ML) into the prediction of post-stroke cognitive impairment (PSCI). However, the mathematical models for ML are diverse, and their accuracy remains highly contentious. Therefore, this study aimed to examine the efficiency of ML in the prediction of PSCI.MethodsRelevant articles were retrieved from Cochrane, Embase, PubMed, and Web of Science from the inception of each database to 5 December 2022. Study quality was evaluated by PROBAST, and c-index, sensitivity, specificity, and overall accuracy of the prediction models were meta-analyzed.ResultsA total of 21 articles involving 7,822 stroke patients (2,876 with PSCI) were included. The main modeling variables comprised age, gender, education level, stroke history, stroke severity, lesion volume, lesion site, stroke subtype, white matter hyperintensity (WMH), and vascular risk factors. The prediction models used were prediction nomograms constructed based on logistic regression. The pooled c-index, sensitivity, and specificity were 0.82 (95% CI 0.77–0.87), 0.77 (95% CI 0.72–0.80), and 0.80 (95% CI 0.71–0.86) in the training set, and 0.82 (95% CI 0.77–0.87), 0.82 (95% CI 0.70–0.90), and 0.80 (95% CI 0.68–0.82) in the validation set, respectively.ConclusionML is a potential tool for predicting PSCI and may be used to develop simple clinical scoring scales for subsequent clinical use.Systematic Review Registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=383476.
Quantitative interocular suppression in children with intermittent exotropia
Authors: Chen Hui , Jiang Xiaohui , Liu Weijie , Zhou Jiawei , Chen Jie , Sun Qianqian , Liang Lin , Lou Jiangtao , Yu Xinping , Qu Jia 
Published: August 2023

PurposeWe have demonstrated that the depth of unbalanced interocular suppression can be quantified by balancing the interocular luminance differences required when both eyes are viewing simultaneously. In this study, we aimed to investigate the applicability of this method in children with intermittent exotropia (IXT), offering a quantitative assessment of interocular suppression in individuals with binocular imbalance. Additionally, we evaluated its association with the clinical characteristics of IXT.MethodsInterocular suppression in IXT was quantitatively measured using a polarizer and neutral-density (ND) filters. The density of the ND filter was adjusted incrementally from 0.3ND to 3ND, with a step size of 0.3ND (a total of 10 levels). Our prospective study involved 46 patients with IXT (mean age: 10.12 ± 4.89 years; mean ± SD) and 24 normal observers (mean age: 7.88 ± 1.83 years).ResultsThe suppression test exhibited good test–retest reliability, supported by statistical analysis. We observed more pronounced interocular suppression in individuals with IXT compared to controls. Notably, the magnitude of suppression during distant and near viewing significantly differed in IXT (1.55 ± 0.93 vs. 0.57 ± 0.64; Z = 4.764, p &lt; 0.001). Furthermore, we identified a positive correlation between interocular suppression and data obtained from the Worth-4-Dot test. Additionally, interocular suppression showed a significant association with distance control scores.ConclusionOur novel test offers a convenient and reliable means to quantify interocular suppression in patients with IXT. The quantitative assessment of interocular suppression provides a sensitive tool to evaluate the clinical characteristics of IXT.
A monocentric, randomized, double-blind, controlled crossover trial of nasturtium (Tropaeolum majus) on the lipid regulator prostaglandin E2
Authors: Herz Corinna , Frei Linda , Tran Hoai T. T. , Claßen Sophie , Spöttel Jenny , Krell Mareike , Hanschen Franziska S. , Arvandi Marjan , Binder Nadine , Schreiner Monika , Rohn Sascha , Lamy Evelyn 
Published: August 2023

ScopeAs prostaglandin E2 (PGE2) has important roles in physiological and inflammatory functions, a double-blind randomized controlled crossover study to investigate the potential of nasturtium (Tropaeolum majus) for modulating PGE2 was conducted, aiming at clarifying the role of benzyl isothiocyanate (BITC). As secondary parameters leukotriene 4 (LTB4), and cytokine release (tumor necrosis factor alpha, TNF-α; interleukins IL-1β, IL-10, and IL-12) were quantified.Methods and resultsThirty-four healthy female participants consumed 1.5 g nasturtium containing BITC, (verum) or no BITC (control) twice a day for 2 weeks each. Nasturtium intervention resulted in an increase in mean PGE2 levels in serum samples (verum: 1.76-fold, p ≤ 0.05; control: 1.78-fold, p ≤ 0.01), and ex vivo stimulated peripheral blood mononuclear cells (PBMC) (verum: 1.71-fold, p ≤ 0.01; control: 1.43-fold). Using a pre-to-post responder analysis approach, 18 of 34 subjects showed a &gt; 25% PGE2 increase in serum, while it was &gt;25% decreased for 9 subjects (stimulated PBMC: 14 and 8 of 28, respectively). Under the selected conditions, the BITC content of nasturtium did not affect the observed changes in PGE2. Verum intervention also increased mean LTB4 serum level (1.24-fold, p ≤ 0.01), but not in LPS stimulated PBMC, and significantly increased TNF-α release in stimulated PBMC after 3 h (verum: 1.65-fold, p = 0.0032; control: 1.22-fold, p = 0.7818). No change was seen in the anti-inflammatory cytokine IL-10, or the pro-inflammatory cytokines IL-1β, and IL-12.ConclusionIn contrast to the previously reported in vitro results, on average, LPS activated PBMC and serum from both groups showed increased PGE2 levels. Further analyses suggest that PGE2 release after intervention could possibly depend on the baseline PGE2 level. Identification of phenotypes that respond differently to the nasturtium intervention could be useful to establish personalized approaches for dosing phytopharmaceuticals medicines.
Burden and geographic distribution of oral cavity and oropharyngeal cancers in the Russian Federation
Authors: Muntyanu Anastasiya , Nechaev Vladimir , Pastukhova Elena , Logan James , Rahme Elham , Zubarev Andrei , Netchiporouk Elena , Litvinov Ivan V. 
Published: August 2023

BackgroundThe global incidence of lip and oral cavity cancers (OCCs) and oropharyngeal cancers (OPCs) is steadily increasing. While tobacco and alcohol consumption are established risk factors, a considerable proportion of these cancers has become attributed to human papilloma virus (HPV) infection. We aimed to describe the occurrence and identify potential risk factors of OCCs and OPCs across the Russian Federation during 2007-2018.MethodsWe conducted an ecological analysis using publicly accessible data from the P.A. Herzen Moscow Oncology Research Institute. Incidence and mortality rates by jurisdiction were mapped for geospatial analysis. We pre-defined 11 potential contributing risk factors and used univariable and multivariable Poisson regression model with backwards stepwise variable selection to identify associated factors with OCC and OPC.ResultsA total of 190,585 individuals were diagnosed with OCCs and OPCs in Russia between 2007-2018. Non-uniform geographic distribution of cancer cases was noted where the Far Eastern Federal District had the highest rate of OCC and the Central Federal District of OPCs. Districts with high weekly alcohol consumption had significantly higher incidence and mortality rates in both sexes. Districts with high rates of daily smoking had higher incidence of OCC among females, and those with low smoking trends had lower mortality rates for OCCs and OPCs.ConclusionWe detail the burden of OCCs and OPCs across Russia, with the aim of elucidating modifiable risk factors and proposing evidence-based prevention strategies. Tobacco/alcohol sales control measures and smoking/drinking cessation programs should continue to be prioritized as public health measures, especially for females.