bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing iNaturalist to quantify hotspots of urban biodiversity: the Los Angeles case study
Authors: Beninde Joscha , Delaney Tatum W. , Gonzalez Germar , Shaffer H. Bradley 
Published: June 2023

IntroductionA major goal for conservation planning is the prioritized protection and management of areas that harbor maximal biodiversity. However, such spatial prioritization often suffers from limited data availability, resulting in decisions driven by a handful of iconic or endangered species, with uncertain benefits for co-occurring taxa. We argue that multi-species habitat preferences based on field observations should guide conservation planning to optimize the long-term persistence of as many species as possible.MethodsUsing habitat suitability modeling techniques and data from the community-science platform iNaturalist, we provide a strategy to develop spatially explicit models of habitat suitability that enable better informed, place-based conservation prioritization. Our case study in Greater Los Angeles used Maxent and Random Forests to generate suitability models for 1,200 terrestrial species with at least 25 occurrence records, drawn from plants (45.5%), arthropods (27.45%), vertebrates (22.2%), fungi (3.2%), molluscs (1.3%), and other taxonomic groups (&lt; 0.3%). This modeling strategy further compared spatial thinning and taxonomic bias file corrections to account for the biases inherent to the iNaturalist dataset, modeling species jointly and separately in wildland and urban sub-regions and validated model performance using null models and a “test” dataset of species and occurrences that were not used to train models.ResultsMean models of habitat suitability of all species combined were similar across model settings, but the mean Random Forest model received the highest median AUCROC and AUCPRG scores in model evaluation. Taxonomic groups showed relatively modest differences in their response to the urbanization gradient, while native and non-native species showed contrasting patterns in the most urban and the most wildland habitats and both peaked in mean habitat suitability near the urban-wildland interface.DiscussionOur modeling framework is based entirely on open-source software and our code is provided for further use. Given the increasing availability of urban biodiversity data via platforms such as iNaturalist, this modeling framework can easily be applied to other regions. Quantifying habitat suitability for a large, representative subset of the locally occurring pool of species in this way provides a clear, data-driven basis for further ecological research and conservation decision-making, maximizing the impact of current and future conservation efforts.
Endothelial glycocalyx injury is involved in heatstroke-associated coagulopathy and protected by N-acetylcysteine
Authors: Peng Na , Geng Yan , Ouyang Jiafu , Liu Shuai , Yuan Fangfang , Wan Yantong , Chen Wenda , Yu Baojun , Tang Youqing , Su Lei , Liang Huaping , Wang Jiang Huai , Liu Jinghua 
Published: June 2023

IntroductionDamage to endothelial glycocalyx (EGCX) can lead to coagulation disorders in sepsis. Heat stroke (HS) resembles sepsis in many aspects; however, it is unclear whether EGCX injury is involved in its pathophysiology. The purpose of this study was to examine the relationship between the damage of EGCX and the development of coagulation disorders during HS.MethodsWe retrospectively collected 159 HS patients and analyzed coagulation characteristics and prognosis of HS patients with or without disseminated intravascular coagulation (DIC). We also replicated a rat HS model and measured coagulation indexes, pulmonary capillary EGCX injury in HS rats. Finally, we evaluated the effect of the antioxidant N-acetylcysteine (NAC) on HS-initiated EGCX injury and coagulation disorders.ResultsClinical data showed that HS patients complicated with DIC had a higher risk of death than HS patients without DIC. In a rat HS model, we found that rats subjected to heat stress developed hypercoagulability and platelet activation at the core body temperature of 43°C, just before the onset of HS. At 24 h of HS, the rats showed a consumptive hypo-coagulation state. The pulmonary capillary EGCX started to shed at 0 h of HS and became more severe at 24 h of HS. Importantly, pretreatment with NAC substantially alleviated EGCX damage and reversed the hypo-coagulation state in HS rats. Mechanically, HS initiated reactive oxidative species (ROS) generation, while ROS could directly cause EGCX damage. Critically, NAC protected against EGCX injury by attenuating ROS production in heat-stressed or hydrogen peroxide (H2O2)-stimulated endothelial cells.DiscussionOur results indicate that the poor prognosis of HS patients correlates with severe coagulation disorders, coagulation abnormalities in HS rats are associated with the damage of EGCX, and NAC improves HS-induced coagulopathy, probably through its protection against EGCX injury by preventing ROS generation.
The development of endoplasmic reticulum-related gene signatures and the immune infiltration analysis of sepsis
Authors: Zhou Yi , Chen Yifang , Li Jianbo , Fu Zailin , Chen Qian , Zhang Wei , Luo Huan , Xie Minghua 
Published: June 2023

BackgroundSepsis is a complex condition involving multiorgan failure, resulting from the hosts’ deleterious systemic immune response to infection. It is characterized by high mortality, with limited effective detection and treatment options. Dysregulated endoplasmic reticulum (ER) stress is directly involved in the pathophysiology of immune-mediated diseases.MethodsClinical samples were obtained from Gene Expression Omnibus datasets (i.e., GSE65682, GSE54514, and GSE95233) to perform the differential analysis in this study. A weighted gene co-expression network analysis algorithm combining multiple machine learning algorithms was used to identify the diagnostic biomarkers for sepsis. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and the single-sample gene set enrichment analysis algorithm were used to analyze immune infiltration characteristics in sepsis. PCR analysis and western blotting were used to demonstrate the potential role of TXN in sepsis.ResultsFour ERRGs, namely SET, LPIN1, TXN, and CD74, have been identified as characteristic diagnostic biomarkers for sepsis. Immune infiltration has been repeatedly proved to play a vital role both in sepsis and ER. Subsequently, the immune infiltration characteristics result indicated that the development of sepsis is mediated by immune-related function, as four diagnostic biomarkers were strongly associated with the immune infiltration landscape of sepsis. The biological experiments in vitro and vivo demonstrate TXN is emerging as crucial player in maintaining ER homeostasis in sepsis.ConclusionOur research identified novel potential biomarkers for sepsis diagnosis, which point toward a potential strategy for the diagnosis and treatment of sepsis.
Application of abdominal ultrasonography in surgical necrotizing enterocolitis: a retrospective study
Authors: Chen Qin , Yao Weiquan , Xu Fengdan , Liao Jinfeng , Li Jinfeng , Mai Minling , Xie Haoqiang , He Xiaoguang , Li Ning 
Published: June 2023

BackgroundNecrotizing enterocolitis (NEC) is a severe inflammatory bowel disease that may lead to perforation, causing high morbidity and mortality in preterm infants. Abdominal ultrasound (AUS) has been shown to provide benefits in diagnosing and managing NEC in recent years.ObjectiveThis study focused on the utility of AUS in the diagnosis and evaluation of surgical NEC.Patients and methodsIn this retrospective study, available data of the patients diagnosed from January 2019 to June 2022 were reviewed. The sensitivity and specificity of AUS in diagnosing a perforation were analyzed. Typical cases for the application of AUS in monitoring and evaluating the progression, complications, and sequela of NEC were described.ResultsThere were 69 neonates diagnosed with NEC and examined by AUS, of whom eight patients developed a perforation. AUS was used for diagnosing a perforation in eight patients with key features of pneumoperitoneum and/or complex ascites, allowing us to find four locations of perforation, with a sensitivity and specificity of 100%.ConclusionAUS plays an important role in diagnosing and evaluating surgical NEC in newborn infants, with good sensitivity and specificity.
Evidence of neuroplasticity with brain–computer interface in a randomized trial for post-stroke rehabilitation: a graph-theoretic study of subnetwork analysis
Authors: Ma Zhen-Zhen , Wu Jia-Jia , Hua Xu-Yun , Zheng Mou-Xiong , Xing Xiang-Xin , Ma Jie , Shan Chun-Lei , Xu Jian-Guang 
Published: June 2023

BackgroundBrain–computer interface (BCI) has been widely used for functional recovery after stroke. Understanding the brain mechanisms following BCI intervention to optimize BCI strategies is crucial for the benefit of stroke patients.MethodsForty-six patients with upper limb motor dysfunction after stroke were recruited and randomly divided into the control group or the BCI group. The primary outcome was measured by the assessment of Fugl–Meyer Assessment of Upper Extremity (FMA-UE). Meanwhile, we performed resting-state functional magnetic resonance imaging (rs-fMRI) in all patients, followed by independent component analysis (ICA) to identify functionally connected brain networks. Finally, we assessed the topological efficiency of both groups using graph-theoretic analysis in these brain subnetworks.ResultsThe FMA-UE score of the BCI group was significantly higher than that of the control group after treatment (p = 0.035). From the network topology analysis, we first identified seven subnetworks from the rs-fMRI data. In the following analysis of subnetwork properties, small-world properties including γ (p = 0.035) and σ (p = 0.031) within the visual network (VN) decreased in the BCI group. For the analysis of the dorsal attention network (DAN), significant differences were found in assortativity (p = 0.045) between the groups. Additionally, the improvement in FMA-UE was positively correlated with the assortativity of the dorsal attention network (R = 0.498, p = 0.011).ConclusionBrain–computer interface can promote the recovery of upper limbs after stroke by regulating VN and DAN. The correlation trend of weak intensity proves that functional recovery in stroke patients is likely to be related to the brain’s visuospatial processing ability, which can be used to optimize BCI strategies.Clinical Trial RegistrationThe trial is registered in the Chinese Clinical Trial Registry, number ChiCTR2000034848. Registered 21 July 2020.
Gait characteristics related to fall risk in patients with cerebral small vessel disease
Authors: Wang Yajing , Li Yanna , Liu Shoufeng , Liu Peipei , Zhu Zhizhong , Wu Jialing 
Published: June 2023

BackgroundFalls and gait disturbance are significant clinical manifestations of cerebral small vessel disease (CSVD). However, few relevant studies are reported at present. We aimed to investigate gait characteristics and fall risk in patients with CSVD.MethodsA total of 119 patients with CSVD admitted to the Department of Neurology at Tianjin Huanhu Hospital between 17 August 2018 and 7 November 2018 were enrolled in this study. All patients underwent cerebral magnetic resonance imaging scanning and a 2-min walking test using an OPAL wearable sensor and Mobility Lab software. Relevant data were collected using the gait analyzer test system to further analyze the time-space and kinematic parameters of gait. All patients were followed up, and univariate and multivariate logistic regression analyses were conducted to analyze the gait characteristics and relevant risk factors in patients with CSVD at an increased risk of falling.ResultsAll patients were grouped according to the presence or absence of falling and fear of falling and were divided into a high-fall risk group (n = 35) and a low-fall risk group (n = 72). Logistic multivariate regression analysis showed that the toe-off angle [odds ratio (OR) = 0.742, 95% confidence interval (CI) 0.584–0.942, p &lt; 0.05], toe-off angle coefficient of variation (CV) (OR = 0.717, 95% CI: 0.535–0.962, p &lt; 0.05), stride length CV (OR = 1.256, 95% CI: 1.017–1.552, p &lt; 0.05), and terminal double support CV (OR = 1.735, 95% CI: 1.271–2.369, p &lt; 0.05) were statistically significant (p &lt; 0.05) and were independent risk factors for high-fall risk in patients with CSVD.ConclusionCSVD patients with seemingly normal gait and ambulation independently still have a high risk of falling, and gait spatiotemporal-kinematic parameters, gait symmetry, and gait variability are important indicators to assess the high-fall risk. The decrease in toe-off angle, in particular, and an increase in related parameters of CV, can increase the fall risk of CSVD patients.
Development of a prognostic model based on ferroptosis-related genes for colorectal cancer patients and exploration of the biological functions of NOS2 in vivo and in vitro
Authors: Li Hongming , Feng Xiaochuang , Hu Yong , Wang Junjiang , Huang Chengzhi , Yao Xueqing 
Published: June 2023

BackgroundFerroptosis is involved in many malignant tumors and has been implicated in important mechanisms of colorectal cancer (CRC) suppression. However, the prognostic and predictive values of the ferroptosis activation pattern in CRC patients have not been noted. Here, we aimed to construct and validate a prediction model based on ferroptosis-related genes (FRGs) for CRC patients and investigated the expression pattern and biological function of the most significantly altered gene.MethodsA total of 112 FRGs were obtained from the FerrDb website, and the clinical characteristics of 545 CRC patients and their global gene expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database. Survival-related FRGs were identified by Cox proportional hazards regression analysis. Finally, the expression pattern and biological function of NOS2, the most implicated gene was explored in vitro and in vivo.ResultsThe prediction model was established based on 8 FRGs. Patients in the high- or low-risk group were stratified based on the median risk value calculated by our model, and patients in the high-risk group experienced poor overall survival (p&lt;0.01). Further validation demonstrated that the FRG model acted as an independent prognostic indicator for CRC patients (HR=1.428, 95% CI, 1.341-1.627; p&lt;0.001). The area under the receiver operating characteristic (ROC) curve (AUC) for 5-year survival was 0.741. NOS2 was one of the most significantly affected FRGs and was highly expressed in malignant tissue, but it inhibited tumor growth and induced tumor cell death in vitro and in vivo, possibly by repressing the NF-κB pathway.ConclusionOur study revealed that FRGs have potential prognostic value in CRC patients and that NOS2 suppresses tumor progression, providing a novel therapeutic target for CRC treatment based on ferroptosis.
A report of a pedigree with compound heterozygous mutations in the SLC22A5 gene
Authors: Zhou Yunguo , Liu Yucai , Shen Yang , Xu Fang , Xu Fei , Huang Hui , Duan Junkai 
Published: June 2023

IntroductionTo investigate the clinical characteristics and disease outcomes of a pedigree with compound heterozygous mutations in the SLC22A5 gene.MethodsSerum acylcarnitine profiles of patients were analyzed using tandem mass spectrometry. DNA samples isolated from patients and their first-degree relatives were subjected to high-throughput sequencing, and mutations were validated using Sanger sequencing.ResultsThe proband, a 4-month-old girl, presented with seizure episodes and mild cardiac hypertrophy and was diagnosed with primary carnitine deficiency (PCD), with carnitine levels of 5.165 mol/L. Her brother, a 6-year-and 4-month-old boy, was also diagnosed with PCD with serum-free carnitine levels of 1.014 mol/L (reference values 10–60 mol/L). Compound heterozygous mutations (c.760C &gt; T [p.R254X] and c.825G &gt; A [p.W275X]) were detected in the SLC22A5 gene in both patients and were inherited from the mother and father, respectively. Oral L-carnitine significantly improved or resolved the clinical symptoms.ConclusionChildren with compound mutations in SLC22A5 may present different clinical manifestations, particularly at different ages. Early clinical manifestations have a greater impact on the organs and may cause irreversible damage. PCD can cause epilepsy and dilated cardiomyopathy. Tandem mass spectrometry and high-throughput sequencing are recommended to confirm the diagnosis. Early L-carnitine supplementation can improve symptoms and reverse organ damage in some children. Tandem mass spectrometry should be used to screen for newborns with a family history of PCD.
Bibliometric analysis of real-time PCR-based pathogen detection in plant protection research: a comprehensive study
Authors: Lal Priyanka , Tiwari Rahul Kumar , Kumar Awadhesh , Altaf Muhammad Ahsan , Alsahli Abdulaziz Abdullah , Lal Milan Kumar , Kumar Ravinder 
Published: June 2023

IntroductionThe discovery of RT-PCR-based pathogen detection and gene expression analysis has had a transformative impact on the field of plant protection. This study aims to analyze the global research conducted between 2001 and 2021, focusing on the utilization of RT-PCR techniques for diagnostic assays and gene expression level studies. By retrieving data from the 'Dimensions' database and employing bibliometric visualization software, this analysis provides insights into the major publishing journals, institutions involved, leading journals, influential authors, most cited articles, and common keywords.MethodsThe 'Dimensions' database was utilized to retrieve relevant literature on RT-PCR-based pathogen detection. Fourteen distinct search queries were employed, and the resulting dataset was analyzed for trends in scholarly publications over time. The bibliometric visualization software facilitated the identification of major publishing journals, institutions, leading journals, influential authors, most cited articles, and common keywords. The study's search query was based on the conjunction 'AND', ensuring a comprehensive analysis of the literature.ResultsThe analysis revealed a significant increase in the number of scholarly publications on RT-PCR-based pathogen detection over the years, indicating a growing interest and investment in research within the field. This finding emphasizes the importance of ongoing investigation and development, highlighting the potential for further advancements in knowledge and understanding. In terms of publishing journals, Plos One emerged as the leading journal, closely followed by BMC Genomics and Phytopathology. Among the highly cited journals were the European Journal of Plant Pathology, BMC Genomics, and Fungal Genetics and Biology. The publications with the highest number of citations and publications were associated with the United Nations and China. Furthermore, a network visualization map of co-authorship analysis provided intriguing insights into the collaborative nature of the research. Out of 2,636 authors analyzed, 50 surpassed the level threshold, suggesting active collaboration among researchers in the field.DiscussionOverall, this bibliometric analysis demonstrates that the research on RT-PCR-based pathogen detection is thriving. However, there is a need for further strengthening using modern diagnostic tools and promoting collaboration among well-equipped laboratories. The findings underscore the significance of RT-PCR-based pathogen detection in plant protection and highlight the potential for continued advancements in this field. Continued research and collaboration are vital for enhancing knowledge, developing innovative diagnostic tools, and effectively protecting plants from pathogens.
Talkitt: toward a new instrument based on artificial intelligence for augmentative and alternative communication in children with down syndrome
Authors: Costanzo Floriana , Fucà Elisa , Caciolo Cristina , Ruà Deborah , Smolley Sara , Weissberg Danny , Vicari Stefano 
Published: June 2023

IntroductionIndividuals with Down syndrome (DS) often exhibit a severe speech impairment, with important consequences on language intelligibility. For these cases, the use of Augmentative Alternative Communication instruments, that increase an individual’s communication abilities, becomes crucial. Talkitt is a mobile application created by Voiceitt Company, exploiting speech recognition technology and artificial intelligence models to translate in real-time unintelligible sounds into clear words, allowing individuals with language production impairment to verbally communicate in real-time.MethodsThe study evaluated the usability and satisfaction related to the Talkitt application use, as well as effects on adapted behavior and communication, of participants with DS. A final number of 23 individuals with DS, aged 5.54 to 28.9 years, participated in this study and completed 6 months of training. The application was trained to consistently recognize at least 20 different unintelligible words (e.g., nouns and/or short phrases)/person.ResultsResults revealed good usability and high levels of satisfaction related to the application use. Moreover, we registered improvement in linguistic abilities, particularly naming.DiscussionThese results paves the road for a potential role of Talkitt application as a supportive and rehabilitative tool for DS.
Comprehensive evaluation of machine learning algorithms for predicting sleep–wake conditions and differentiating between the wake conditions before and after sleep during pregnancy based on heart rate variability
Authors: Li Xue , Ono Chiaki , Warita Noriko , Shoji Tomoka , Nakagawa Takashi , Usukura Hitomi , Yu Zhiqian , Takahashi Yuta , Ichiji Kei , Sugita Norihiro , Kobayashi Natsuko , Kikuchi Saya , Kimura Ryoko , Hamaie Yumiko , Hino Mizuki , Kunii Yasuto , Murakami Keiko , Ishikuro Mami , Obara Taku , Nakamura Tomohiro , Nagami Fuji , Takai Takako , Ogishima Soichi , Sugawara Junichi , Hoshiai Tetsuro , Saito Masatoshi , Tamiya Gen , Fuse Nobuo , Fujii Susumu , Nakayama Masaharu , Kuriyama Shinichi , Yamamoto Masayuki , Yaegashi Nobuo , Homma Noriyasu , Tomita Hiroaki 
Published: June 2023

IntroductionPerinatal women tend to have difficulties with sleep along with autonomic characteristics. This study aimed to identify a machine learning algorithm capable of achieving high accuracy in predicting sleep–wake conditions and differentiating between the wake conditions before and after sleep during pregnancy based on heart rate variability (HRV).MethodsNine HRV indicators (features) and sleep–wake conditions of 154 pregnant women were measured for 1 week, from the 23rd to the 32nd weeks of pregnancy. Ten machine learning and three deep learning methods were applied to predict three types of sleep–wake conditions (wake, shallow sleep, and deep sleep). In addition, the prediction of four conditions, in which the wake conditions before and after sleep were differentiated—shallow sleep, deep sleep, and the two types of wake conditions—was also tested.Results and DiscussionIn the test for predicting three types of sleep–wake conditions, most of the algorithms, except for Naïve Bayes, showed higher areas under the curve (AUCs; 0.82–0.88) and accuracy (0.78–0.81). The test using four types of sleep–wake conditions with differentiation between the wake conditions before and after sleep also resulted in successful prediction by the gated recurrent unit with the highest AUC (0.86) and accuracy (0.79). Among the nine features, seven made major contributions to predicting sleep–wake conditions. Among the seven features, “the number of interval differences of successive RR intervals greater than 50 ms (NN50)” and “the proportion dividing NN50 by the total number of RR intervals (pNN50)” were useful to predict sleep–wake conditions unique to pregnancy. These findings suggest alterations in the vagal tone system specific to pregnancy.