bluuebunny/crossref_metadata_2025_split huggingface dataset:
The chemokine landscape: one system multiple shades
Authors: Cecchinato Valentina , Martini Veronica , Pirani Edisa , Ghovehoud Elaheh , Uguccioni Mariagrazia 
Published: May 2023

Leukocyte trafficking is mainly governed by chemokines, chemotactic cytokines, which can be concomitantly produced in tissues during homeostatic conditions or inflammation. After the discovery and characterization of the individual chemokines, we and others have shown that they present additional properties. The first discoveries demonstrated that some chemokines act as natural antagonists on chemokine receptors, and prevent infiltration of leukocyte subsets in tissues. Later on it was shown that they can exert a repulsive effect on selective cell types, or synergize with other chemokines and inflammatory mediators to enhance chemokine receptors activities. The relevance of the fine-tuning modulation has been demonstrated in vivo in a multitude of processes, spanning from chronic inflammation to tissue regeneration, while its role in the tumor microenvironment needs further investigation. Moreover, naturally occurring autoantibodies targeting chemokines were found in tumors and autoimmune diseases. More recently in SARS-CoV-2 infection, the presence of several autoantibodies neutralizing chemokine activities distinguished disease severity, and they were shown to be beneficial, protecting from long-term sequelae. Here, we review the additional properties of chemokines that influence cell recruitment and activities. We believe these features need to be taken into account when designing novel therapeutic strategies targeting immunological disorders.
Outcome indicators for cross linking in pediatric keratoconus
Authors: Wajnsztajn Denise , Shmueli Or , Tarnovsky Yehuda , Frucht-Pery Joseph , Solomon Abraham 
Published: May 2023

PurposeTo evaluate the predictive factors for successful corneal collagen cross-linking (CXL) in pediatric patients with Keratoconus (KC).MethodsThis retrospective study was conducted using a prospectively built database. Patients (18 years old or younger) underwent CXL for KC between 2007 and 2017, with a 1-year follow-up period or longer. The outcomes included changes in Kmax (delta [Δ] Kmax = Kmaxlast − Kmaxpre) and LogMAR visual acuity (ΔLogMAR = LogMARlast − LogMARpre).The effects of CXL type (accelerated or non-accelerated), demographics (age, sex, background of ocular allergy, ethnicity), preoperative LogMAR visual acuity, maximal corneal power (Kmax), pachymetry (CCTpre), refractive cylinder, and follow-up (FU) time on the outcomes were analyzed.ResultsOne hundred thirty-one eyes of 110 children were included (mean age, 16 ± 2 years; range, 10–18 years). Kmax and LogMAR improved from baseline to last visit: from 53.81 D ± 6.39 D to 52.31 D ± 6.06 D (p &lt; 0.001) and from 0.27 ± 0.23 LogMAR units to 0.23 ± 0.19 LogMAR units (p = 0.005), respectively. A negative ΔKmax (meaning corneal flattening) was associated with a long FU, low CCTpre, high Kmaxpre, high LogMARpre, and non-accelerated CXL on univariate analysis. High Kmaxpre and non-accelerated CXL were associated with negative ΔKmax in the multivariate analysis.A negative ΔLogMAR (meaning vision improvement) was associated with a high LogMARpre in univariate analysis.ConclusionCXL is an effective treatment option in pediatric patients with KC. Our results showed that the non-accelerated treatment was more effective than the accelerated treatment. Corneas with advanced disease had a greater effect on CXL.
Explainable artificial intelligence (XAI) in radiology and nuclear medicine: a literature review
Authors: de Vries Bart M. , Zwezerijnen Gerben J. C. , Burchell George L. , van Velden Floris H. P. , Menke-van der Houven van Oordt Catharina Willemien , Boellaard Ronald 
Published: May 2023

RationalDeep learning (DL) has demonstrated a remarkable performance in diagnostic imaging for various diseases and modalities and therefore has a high potential to be used as a clinical tool. However, current practice shows low deployment of these algorithms in clinical practice, because DL algorithms lack transparency and trust due to their underlying black-box mechanism. For successful employment, explainable artificial intelligence (XAI) could be introduced to close the gap between the medical professionals and the DL algorithms. In this literature review, XAI methods available for magnetic resonance (MR), computed tomography (CT), and positron emission tomography (PET) imaging are discussed and future suggestions are made.MethodsPubMed, Embase.com and Clarivate Analytics/Web of Science Core Collection were screened. Articles were considered eligible for inclusion if XAI was used (and well described) to describe the behavior of a DL model used in MR, CT and PET imaging.ResultsA total of 75 articles were included of which 54 and 17 articles described post and ad hoc XAI methods, respectively, and 4 articles described both XAI methods. Major variations in performance is seen between the methods. Overall, post hoc XAI lacks the ability to provide class-discriminative and target-specific explanation. Ad hoc XAI seems to tackle this because of its intrinsic ability to explain. However, quality control of the XAI methods is rarely applied and therefore systematic comparison between the methods is difficult.ConclusionThere is currently no clear consensus on how XAI should be deployed in order to close the gap between medical professionals and DL algorithms for clinical implementation. We advocate for systematic technical and clinical quality assessment of XAI methods. Also, to ensure end-to-end unbiased and safe integration of XAI in clinical workflow, (anatomical) data minimization and quality control methods should be included.
Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli
Authors: Vorimore Fabien , Jaudou Sandra , Tran Mai-Lan , Richard Hugues , Fach Patrick , Delannoy Sabine 
Published: May 2023

IntroductionThe objective of this study was to develop, using a genome wide machine learning approach, an unambiguous model to predict the presence of highly pathogenic STEC in E. coli reads assemblies derived from complex samples containing potentially multiple E. coli strains. Our approach has taken into account the high genomic plasticity of E. coli and utilized the stratification of STEC and E. coli pathogroups classification based on the serotype and virulence factors to identify specific combinations of biomarkers for improved characterization of eae-positive STEC (also named EHEC for enterohemorrhagic E.coli) which are associated with bloody diarrhea and hemolytic uremic syndrome (HUS) in human.MethodsThe Machine Learning (ML) approach was used in this study on a large curated dataset composed of 1,493 E. coli genome sequences and 1,178 Coding Sequences (CDS). Feature selection has been performed using eight classification algorithms, resulting in a reduction of the number of CDS to six. From this reduced dataset, the eight ML models were trained with hyper-parameter tuning and cross-validation steps.Results and discussionIt is remarkable that only using these six genes, EHEC can be clearly identified from E. coli read assemblies obtained from in silico mixtures and complex samples such as milk metagenomes. These various combinations of discriminative biomarkers can be implemented as novel marker genes for the unambiguous EHEC characterization from different E. coli strains mixtures as well as from raw milk metagenomes.
A bibliometric review on vitamins and Alzheimer’s disease between 1996 and 2023
Authors: Sun Xiaoyu , Xu Haichun , Qu Huiling , Dong Wenwu 
Published: May 2023

ObjectiveAlzheimer’s disease (AD) is a major disease that affects the elderly worldwide. Several studies have revealed that vitamins may influence the risk of developing AD. However, information in this field remains ambiguous. Therefore, this study aimed to examine the relationship between AD and vitamins, identify journal publications and collaborators, and analyze keywords and research trends using a bibliometric method.MethodsWe systematically searched the Web of Science (WOS) Core Collection for papers published on AD and vitamins. Retrieved data regarding institutions, journals, countries, authors, journal distribution, keywords, and so on. SPSS 25 software was used for the statistical analysis, and CiteSpace V.6.1.R6 was used to visualize the information through collaborative networks.ResultsA total of 2,838 publications were ultimately included in accordance with the specified inclusion criteria. The number of publications gradually increased from 1996 to 2023, with papers published in 87 countries/regions and 329 institutions. China (centrality: 0.02) and the University of Kentucky (centrality: 0.09) were the major research countries and institutions, respectively. NEUROLOGY was cited most frequently, reaching 1,573, and had the greatest impact. The cited keywords show that “Alzheimer’s disease,” “oxidative stress,” “vitamin E,” and “dementia” have been research hotspots in recent years. Beta-carotene emerged in 2023 and was identified as a developmental trend in this field.ConclusionThis is the first bibliometric analysis of vitamins associated with AD. We identified 2,838 articles in the field of vitamins and AD, analyzed the information of major countries/regions, institutions, and core journals in this field, and summarized the research hotspots and frontiers. These findings provide useful information for researchers to explore the role of vitamins in AD further.
Empirically validated theoretical analysis of visual-spatial perception under change of nervous system arousal
Authors: Purohit Pratik , Dutta Prasun , Roy Prasun K. 
Published: May 2023

IntroductionVisual-spatial perception is a process for extracting the spatial relationship between objects in the environment. The changes in visual-spatial perception due to factors such as the activity of the sympathetic nervous system (hyperactivation) or parasympathetic nervous system (hypoactivation) can affect the internal representation of the external visual-spatial world. We formulated a quantitative model of the modulation of visual-perceptual space under action by hyperactivation or hypoactivation-inducing neuromodulating agents. We showed a Hill equation based relationship between neuromodulator agent concentration and alteration of visual-spatial perception utilizing the metric tensor to quantify the visual space.MethodsWe computed the dynamics of the psilocybin (hyperactivation-inducing agent) and chlorpromazine (hypoactivation-inducing agent) in brain tissue. Then, we validated our quantitative model by analyzing the findings of different independent behavioral studies where subjects were assessed for alterations in visual-spatial perception under the action of psilocybin and under chlorpromazine. To validate the neuronal correlates, we simulated the effect of the neuromodulating agent on the computational model of the grid-cell network, and also performed diffusion MRI-based tractography to find the neural tracts between the cortical areas involved: V2 and the entorhinal cortex.ResultsWe applied our computational model to an experiment (where perceptual alterations were measured under psilocybin) and found that for n (Hill-coefficient) = 14.8 and k = 1.39, the theoretical prediction followed experimental observations very well (χ2 test robustly satisfied, p &gt; 0.99). We predicted the outcome of another psilocybin-based experiment using these values (n = 14.8 and k = 1.39), whereby our prediction and experimental outcomes were well corroborated. Furthermore, we found that also under hypoactivation (chlorpromazine), the modulation of the visual-spatial perception follows our model. Moreover, we found neural tracts between the area V2 and entorhinal cortex, thus providing a possible brain network responsible for encoding visual-spatial perception. Thence, we simulated the altered grid-cell network activity, which was also found to follow the Hill equation.ConclusionWe developed a computational model of visuospatial perceptual alterations under altered neural sympathetic/parasympathetic tone. We validated our model using analysis of behavioral studies, neuroimaging assessment, and neurocomputational evaluation. Our quantitative approach may be probed as a potential behavioral screening and monitoring methodology in neuropsychology to analyze perceptual misjudgment and mishaps by highly stressed workers.
CT-based thrombus radiomics nomogram for predicting secondary embolization during mechanical thrombectomy for large vessel occlusion
Authors: Yusuying Shadamu , Lu Yao , Zhang Shun , Wang Junjie , Chen Juan , Wang Daming , Lu Jun , Qi Peng 
Published: May 2023

Background and aimsSecondary embolization (SE) during mechanical thrombectomy (MT) for cerebral large vessel occlusion (LVO) could reduce the anterior blood flow and worsen clinical outcomes. The current SE prediction tools have limited accuracy. In this study, we aimed to develop a nomogram to predict SE following MT for LVO based on clinical features and radiomics extracted from computed tomography (CT) images.Materials and methodsA total of 61 patients with LVO stroke treated by MT at Beijing Hospital were included in this retrospective study, of whom 27 developed SE during the MT procedure. The patients were randomly divided (7:3) into training (n = 42) and testing (n = 19) cohorts. The thrombus radiomics features were extracted from the pre-interventional thin-slice CT images, and the conventional clinical and radiological indicators associated with SE were recorded. A support vector machine (SVM) learning model with 5-fold cross-verification was used to obtain the radiomics and clinical signatures. For both signatures, a prediction nomogram for SE was constructed. The signatures were then combined using the logistic regression analysis to construct a combined clinical radiomics nomogram.ResultsIn the training cohort, the area under the receiver operating characteristic curve (AUC) of the nomograms was 0.963 for the combined model, 0.911 for the radiomics, and 0.891 for the clinical model. Following validation, the AUCs were 0.762 for the combined model, 0.714 for the radiomics model, and 0.637 for the clinical model. The combined clinical and radiomics nomogram had the best prediction accuracy in both the training and test cohort.ConclusionThis nomogram could be used to optimize the surgical MT procedure for LVO based on the risk of developing SE.
Therapeutic effects of repetitive transcranial magnetic stimulation on cognitive impairment in stroke patients: a systematic review and meta-analysis
Authors: Gong Cheng , Hu Hao , Peng Xu-Miao , Li Hai , Xiao Li , Liu Zhen , Zhong Yan-Biao , Wang Mao-Yuan , Luo Yun 
Published: May 2023

BackgroundIn recent years, repetitive transcranial magnetic stimulation (rTMS) has emerged as a noninvasive and painless treatment for post-stroke cognitive impairment (PSCI). However, few studies have analyzed the intervention parameters of cognitive function and the effectiveness and safety of rTMS for treating patients with PSCI. Thus, this meta-analysis aimed to analyze the interventional parameters of rTMS and evaluate the safety and effectiveness of rTMS for treating patients with PSCI.MethodsAccording to the PRISMA guidelines, we searched the Web of Science, PubMed, EBSCO, Cochrane Library, PEDro, and Embase to retrieve randomized controlled trials (RCTs) of rTMS for the treatment of patients with PSCI. Studies were screened according to the inclusion and exclusion criteria, and two reviewers independently performed literature screening, data extraction, and quality assessment. RevMan 5.40 software was used for data analysis.Results12 RCTs involving 497 patients with PSCI met the inclusion criteria. In our analysis, rTMS had a positive therapeutic effect on cognitive rehabilitation in patients with PSCI (P &lt; 0.05). Both high-frequency rTMS and low-frequency rTMS were effective in improving the cognitive function of patients with PSCI by stimulating the dorsolateral prefrontal cortex (DLPFC), but their efficacy was not statistically different (P &gt; 0.05).ConclusionsrTMS treatment on the DLPFC can improve cognitive function in patients with PSCI. There is no significant difference in the treatment effect of high-frequency rTMS and low-frequency rTMS in patients with PSCI between high-frequency and low-frequency rTMS.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=323720, identifier CRD 42022323720.
Factors influencing the relationship between cochlear health measures and speech recognition in cochlear implant users
Authors: Zamaninezhad Ladan , Mert Berkutay , Benav Heval , Tillein Jochen , Garnham Carolyn , Baumann Uwe 
Published: May 2023

BackgroundOne factor which influences the speech intelligibility of cochlear implant (CI) users is the number and the extent of the functionality of spiral ganglion neurons (SGNs), referred to as “cochlear health.” To explain the interindividual variability in speech perception of CI users, a clinically applicable estimate of cochlear health could be insightful. The change in the slope of the electrically evoked compound action potentials (eCAP), amplitude growth function (AGF) as a response to increased interphase gap (IPG) (IPGEslope) has been introduced as a potential measure of cochlear health. Although this measure has been widely used in research, its relationship to other parameters requires further investigation.MethodsThis study investigated the relationship between IPGEslope, demographics and speech intelligibility by (1) considering the relative importance of each frequency band to speech perception, and (2) investigating the effect of the stimulus polarity of the stimulating pulse. The eCAPs were measured in three different conditions: (1) Forward masking with anodic-leading (FMA) pulse, (2) Forward masking with cathodic-leading (FMC) pulse, and (3) with alternating polarity (AP). This allowed the investigation of the effect of polarity on the diagnosis of cochlear health. For an accurate investigation of the correlation between IPGEslope and speech intelligibility, a weighting function was applied to the measured IPGEslopes on each electrode in the array to consider the relative importance of each frequency band for speech perception. A weighted Pearson correlation analysis was also applied to compensate for the effect of missing data by giving higher weights to the ears with more successful IPGEslope measurements.ResultsA significant correlation was observed between IPGEslope and speech perception in both quiet and noise for between-subject data especially when the relative importance of frequency bands was considered. A strong and significant correlation was also observed between IPGEslope and age when stimulation was performed with cathodic-leading pulses but not for the anodic-leading pulse condition.ConclusionBased on the outcome of this study it can be concluded that IPGEslope has potential as a relevant clinical measure indicative of cochlear health and its relationship to speech intelligibility. The polarity of the stimulating pulse could influence the diagnostic potential of IPGEslope.
Derivation and validation of a nutrition-covered prognostic scoring system for extranodal NK/T-cell lymphoma
Authors: Lu Tiange , Shi Xue , Ge Xueling , Li Ying , Cai Yiqing , Chen Xiaomin , Hu Shunfeng , Ding Mei , Fang Xiaosheng , Liu Fang , Zhou Xiangxiang , Wang Xin 
Published: May 2023

IntroductionPatients with aggressive lymphomas are at high risk of losing body resources, resulting in malnutrition, immunodeficiency and inferior outcomes. Nutritional status is closely associated with survival, but often neglected in the prognostic assessment. This study aimed to explore the significance of nutritional status in extranodal NK/T-cell lymphoma (ENKTL).MethodsUnivariate and multivariate Cox regression analyses were conducted to examine the significance of nutritional index on overall survival (OS) and progression-free survival (PFS). A nutrition-incorporated score system was constructed based on the multivariate results, and its calibration, discrimination and clinical utility were tested in the training and validation cohort.ResultsMultivariate analysis revealed controlling nutritional status (CONUT) score could independently predict OS (HR 10.247, P=0.001) and PFS (HR 5.587, P=0.001) in addition to prognostic index of natural killer lymphoma plus EBV (PINK-E). Herein, a reformative model, CONUT-PINK-E, was developed and further verified in external validation cohort. CONUT-PINK-E classified patients into three risk grades with significant survival differences (P &lt; 0.001). Compared with the current models, CONUT-PINK-E presented superior discrimination, calibration and clinical benefit.DiscussionIn this study, we firstly verified that CONUT score was efficient to screen prognosis-related malnutrition in ENKTL. Moreover, we developed the first nutritional assessment-covered scoring system, CONUT-PINK-E, which might be a promising tool to provide references for clinical decision-making of ENKTL patients.
Serum vitamin C levels and risk of non-alcoholic fatty liver disease: results from a cross-sectional study and Mendelian randomization analysis
Authors: Wu Hui , Guo Jiang-Long , Yao Jing-Jiong , Yu Jia-Jun , Xia Run-Yu , Huang Wei-Qing , Tang Xuan , He Guang-Ming 
Published: May 2023

Background and aimsVitamin C, as an antioxidant, may play a role in the treatment of NAFLD. This research aimed to investigate the association of serum vitamin C levels with the risk of NAFLD and to further examine the causal relationship by Mendelian randomization (MR) method.MethodsThe cross-sectional study selected 5,578 participants of the National Health and Nutrition Examination Survey (NHANES), 2005–2006 and 2017–2018. The association of serum vitamin C levels with NAFLD risk was evaluated under a multivariable logistic regression model. A two-sample MR study, using genetic data from large-scale genome-wide association studies (GWAS) of serum vitamin C levels (52,014 individuals) and NAFLD (primary analysis: 1,483 cases /17,781 controls; secondary analysis: 1,908 cases/340,591 controls), was conducted to infer causality between them. The inverse-variance-weighted (IVW) was applied as the main method of MR analysis. A series of sensitivity analyzes were used to evaluate the pleiotropy.ResultsIn the cross-sectional study, results showed that Tertile 3 group (Tertile 3: ≥1.06 mg/dl) had a significantly lower risk (OR = 0.59, 95% CI: 0.48 ~ 0.74, p &lt; 0.001) of NAFLD than Tertile 1 group (Tertile 1: ≤0.69 mg/dl) after full adjustments. In regard to gender, serum vitamin C was protective against NAFLD in both women (OR = 0.63, 95% CI: 0.49 ~ 0.80, p &lt; 0.001) and men (OR = 0.73, 95% CI: 0.55 ~ 0.97, p = 0.029) but was stronger among women. However, in the IVW of MR analyzes, no causal relationship between serum vitamin C levels and NAFLD risk was observed in the primary analysis (OR = 0.82, 95% CI: 0.47 ~ 1.45, p = 0.502) and secondary analysis (OR = 0.80, 95% CI: 0.53 ~ 1.22, p = 0.308). MR sensitivity analyzes yielded consistent results.ConclusionOur MR study did not support a causal association between serum vitamin C levels and NAFLD risk. Further studies with greater cases are warranted to confirm our findings.