bluuebunny/crossref_metadata_2025_split huggingface dataset:
A network simplification approach to ease topological studies about the food-web architecture
Authors: Gini Andrea , Re Simona , Facchini Angelo 
Published: August 2022

AbstractFood webs studies are intrinsically complex and time-consuming. Network data about trophic interaction across different large locations and ecosystems are scarce in comparison with general ecological data, especially if we consider terrestrial habitats. Here we present a complex network strategy to ease the gathering of the information by simplifying the collection of data with a taxonomic key. We test how well the topology of three different food webs retain their structure at the resolution of the nodes across distinct levels of simplification, and we estimate how community detection could be impacted by this strategy. The first level of simplification retains most of the general topological indices; betweenness and trophic levels seem to be consistent and robust even at the higher levels of simplification. This result suggests that generalisation and standardisation, as a good practice in food webs science, could benefit the community, both increasing the amount of open data available and the comparison among them, thus providing support especially for scientists that are new in this field and for exploratory analysis.
An integrative pan cancer analysis of RET aberrations and their potential clinical implications
Authors: Zhou Lei , Li Juanni , Zhang Xiaofang , Xu Zhijie , Yan Yuanliang , Hu Kuan 
Published: August 2022

AbstractRET (rearranged during transfection), encoding a tyrosine kinase receptor, is a novel therapeutic target for cancers. The aberrations of RET are commonly found in cancers. Here, we profiled a comprehensive genomic landscape of RET mutations, copy number variants (CNVs), co-occurrence of RET and its mRNA expression and methylation levels in pan cancer, paving the way to the development of new RET-targeted therapies in clinic. Analysis of RET somatic mutations, CNVs, co-occurrence, mRNA expression and methylation were performed among 32 cancer types from The Cancer Genome Atlas (TCGA) dataset covering a total of 10,953 patients with 10,967 samples. RET aberrations were found in 3.0% of diverse cancers. The top two RET-altered tumors were skin cutaneous melanoma (SKCM) and uterine corpus endometrial carcinoma (UCEC) with dominant mutations in the other and PKinase_Tyr domains. RET-G823E and RET-S891L were most commonly found in SKCM and UCEC. Thyroid carcinoma (THCA) demonstrated the highest rate of coiled-coil domain containing 6 (CCDC6)-RET fusions, which constitutively activate RET kinase. Two FDA-approved RET inhibitors—pralsetinib and selpercatinib have been implied for the treatment of patients with RET S891L mutant UCEC and the treatment of patients with metastatic RET-fusion positive THCA and non-small cell lung cancer (NSCLC) at therapeutic level 1. We also identified four RET M918T-altered cases in patients with pheochromocytoma and paraganglioma (PCPG), which may induce drug resistance against multikinase inhibitors. Next, 273 co-occurring aberrations, most frequently in Notch signaling, TGF-β pathway, cell cycle, and Ras-Raf-MEK-Erk/JNK signaling, were uncovered among 311 RET altered cases. TP53 mutations (162 patients) leads to the most significant co-occurrence associated with RET aberrations. Furthermore, the RET expression was found most significantly increased in breast invasive carcinoma (BRCA) and neck squamous cell carcinoma (HNSC), as compared to their corresponding normal tissues. At last, patients with higher expression and sequence variant frequency have a worse prognosis, such as sarcoma patients. This work provided a profound and comprehensive analysis of RET and co-occurred alterations, RET mRNA expression and the clinical significance in pan cancer, offering new insights into targeted therapy for patients with RET anomalies.
Identification and characterization of a new family of long satellite DNA, specific of true toads (Anura, Amphibia, Bufonidae)
Authors: Guzmán Katerina , Roco Álvaro S. , Stöck Matthias , Ruiz-García Adrián , García-Muñoz Enrique , Bullejos Mónica 
Published: August 2022

AbstractAmphibians have some of the most variable genome sizes among vertebrates. Genome size variation has been attributed to repetitive and noncoding DNA, including satellite repeats, transposable elements, introns, and nuclear insertions of viral and organelle DNA. In vertebrates, satellite DNAs have been widely described in mammals, but few molecular studies have been carried out in amphibians. Here, we provide a detailed characterization of a new family of satellite DNA, present in all 15 examined species of the family Bufonidae. Southern-blot analysis and PCR reveal that this satellite is formed by monomers of 807 bp, is organized in tandem arrays, and has an AT-content of 57.4%. Phylogenetic analyses show that most clades exhibit species-specific variances, indicating that this satellite DNA has evolved by concerted evolution. The homogenization/fixation process is heterogeneous in Bufonidae, where the genera Bufo and Bufotes do not show species-specific differences, while populations from Rhinella marina exhibit population-specific changes. Additionally, variants of this satellite DNA have been identified in Duttaphrynus melanostictus and R. marina, supporting the ‘library hypothesis’ (a set, ‘library’, of satellite DNAs is shared by a species group). Physical mapping in Bufo bufo, Bufo spinosus, Epidalea calamita and Bufotes viridis provides evidence that this repetitive DNA is not dispersed in the karyotype, but accumulated in pericentromeric regions of some chromosomal pairs. This location, together with its presence in the transcriptomes of bufonids, could indicate a role in centromere function or heterochromatin formation and maintenance.
Hot dense silica glass with ultrahigh elastic moduli
Authors: Sun Ningyu , Mao Zhu , Zhang Xinyue , Tkachev Sergey N. , Lin Jung-Fu 
Published: August 2022

AbstractSilicate and oxide glasses are often chemically doped with a variety of cations to tune for desirable properties in technological applications, but their performances are often limited by relatively lower mechanical and elastic properties. Finding a new route to synthesize silica-based glasses with high elastic and mechanical properties needs to be explored. Here, we report a dense SiO2-glass with ultra-high elastic moduli using sound velocity measurements by Brillouin scattering up to 72 GPa at 300 K. High-temperature measurements were performed up to 63 GPa at 750 K and 59 GPa at 1000 K. Compared to compression at 300 K, elevated temperature helps compressed SiO2-glass effectively overcome the kinetic barrier to undergo permanent densification with enhanced coordination number and connectivity. This hot compressed SiO2-glass exhibits a substantially high bulk modulus of 361–429 GPa which is at least 2–3 times greater than the metallic, oxide, and silicate glasses at ambient conditions. Its Poisson’s ratio, an indicator for the packing efficiency, is comparable to the metallic glasses. Even after temperature quench and decompression to ambient conditions, the SiO2-glass retains some of its unique properties at compression and possesses a Poisson’s ratio of 0.248(11). In addition to chemical alternatives in glass syntheses, coupled compression and heating treatments can be an effective means to enhance mechanical and elastic properties in high-performance glasses.
Identifying potential training factors in a vibrotactile P300-BCI
Authors: Eidel M. , Kübler A. 
Published: August 2022

AbstractBrain–computer interfaces (BCI) often rely on visual stimulation and feedback. Potential end-users with impaired vision, however, cannot use these BCIs efficiently and require a non-visual alternative. Both auditory and tactile paradigms have been developed but are often not sufficiently fast or accurate. Thus, it is particularly relevant to investigate if and how users can train and improve performance. We report data from 29 healthy participants who trained with a 4-choice tactile P300-BCI during five sessions. To identify potential training factors, we pre-post assessed the robustness of the BCI performance against increased workload in a dual task condition and determined the participants’ somatosensory sensitivity thresholds with a forced-choice intensity discrimination task. Accuracy (M = 79.2% to 92.0%) and tactually evoked P300 amplitudes increased significantly, confirming successful training. Pre-post somatosensory sensitivity increased, and workload decreased significantly, but results of the dual task condition remained inconclusive. The present study confirmed the previously reported feasibility and trainability of our tactile BCI paradigm within a multi-session design. Importantly, we provide first evidence of improvement in the somatosensory system as a potential mediator for the observed training effects.
The influence of thyroid hormone medication on intra-therapeutic half-life of 131I during radioiodine therapy of solitary toxic thyroid nodules
Authors: Happel Christian , Kranert Wolfgang Tilman , Bockisch Benjamin , Sabet Amir , Grünwald Frank , Groener Daniel 
Published: August 2022

AbstractDespite a significantly improved dietary iodine supply, solitary toxic thyroid nodules (STN) are still a common clinical problem in former iodine deficient areas. Radioiodine treatment (RIT) is a well-established therapeutic option with few side effects and high success rates. As radioiodine biokinetics are individual for every patient, the necessary activity has to be calculated individually by a pre-therapeutic measurement of the intra-therapeutic effective half-life (EHL) in a radioiodine uptake test (RIUT). A suppressive medication with triiodothyronine (T3) or tetraiodothyronine (T4) is often needed to suppress uptake in normal thyroid tissue. Therefore, the aim of this study was to quantify the possible influence of this medication on intra-therapeutic radioiodine biokinetics. A cohort of 928 patients with STN undergoing RIUT and RIT was analysed. Patients were subdivided into 3 groups. Group T3: medication with T3 (n = 274), group T4: medication with T4 (n = 184) and group NM: no additional medication (n = 470). The T3 and T4 subgroups were further subdivided depending on the dose of thyroid hormone medication. In order to analyse the influence of thyroid hormone medication on individual intra-thyroidal biokinetics, the variance of the determined individual EHL between RIUT and RIT within the single groups and within the subgroups was investigated. EHL was significantly decreased between RIUT and RIT in the T3 and T4 subgroups (EHL: T3: 5.9 ± 1.1 d in RIUT and 3.3 ± 1.4 d in RIT (− 43%) (p < 0.05); T4: 5.9 ± 1.2 d in RIUT and 3.4 ± 1.5 d in RIT (− 42%) (p < 0.05). The decrease of EHL did not differ statistically between T3 or T4. However, both showed a highly significant difference compared to the NM group (p < < 0.05). A further subgroup analysis showed a significant dependence of the decrease in EHL related to the dose of thyroid hormone medication of 35–58% (T3) and 15–67% (T4) (p < 0.05). A significantly reduced EHL compared to RIUT in patients receiving thyroid hormone medication was detected. Moreover, a significant correlation between the dose of thyroid hormone medication (T3 or T4) and the decrease of EHL was found. Therefore, an adaption of the calculated activity should be considered in RIUT to obtain the required radiation dose in RIT of patients suffering from STN.
Influence of topography on the asymmetry of rill cross-sections in the Yuanmou dry-hot valley
Authors: Gu Xingli , Luo Jun , Zhang Bin , Wang Lei , Wu Qiangjianzhong 
Published: August 2022

AbstractRill erosion is one of the most common types of erosion, and the development conditions of the asymmetric characteristics of rill cross-sections are still relatively poorly understood. To explore the relationship between rill topography and rill cross-sectional asymmetry, we used the microtopographic profiler method to measure 712 groups of rill cross-sections in the Yuanmou dry-hot valley area. The results of correlation analysis and principal component analysis to investigate the topographical conditions of rill development show that: (1) asymmetry is the main feature in rill cross-sections; 53% of rill cross-sections are right-biased and 47% are left-biased. (2) There is an extremely significant positive correlation between the slope difference and the rill cross-section asymmetry ratio (p < 0.01); the asymmetry ratio increases as the slope difference on both sides (B) increases, and the directionality of the asymmetry ratio is affected by B. The difference between the catchment areas on both sides has a significant linear correlation with the asymmetry ratio of the width (r = 0.07, p < 0.05). (3) Seven topographic factors were divided into two types of principal components: the first represents the rill slope surface shape and the rill shape, and the second represents the difference between the two sides of the rill.
Automatic detection of microaneurysms in optical coherence tomography images of retina using convolutional neural networks and transfer learning
Authors: Almasi Ramin , Vafaei Abbas , Kazeminasab Elahe , Rabbani Hossein 
Published: August 2022

AbstractMicroaneurysms (MAs) are pathognomonic signs that help clinicians to detect diabetic retinopathy (DR) in the early stages. Automatic detection of MA in retinal images is an active area of research due to its application in screening processes for DR which is one of the main reasons of blindness amongst the working-age population. The focus of these works is on the automatic detection of MAs in en face retinal images like fundus color and Fluorescein Angiography (FA). On the other hand, detection of MAs from Optical Coherence Tomography (OCT) images has 2 main advantages: first, OCT is a non-invasive imaging technique that does not require injection, therefore is safer. Secondly, because of the proven application of OCT in detection of Age-Related Macular Degeneration, Diabetic Macular Edema, and normal cases, thanks to detecting MAs in OCT, extensive information is obtained by using this imaging technique. In this research, the concentration is on the diagnosis of MAs using deep learning in the OCT images which represent in-depth structure of retinal layers. To this end, OCT B-scans should be divided into strips and MA patterns should be searched in the resulted strips. Since we need a dataset comprising OCT image strips with suitable labels and such large labelled datasets are not yet available, we have created it. For this purpose, an exact registration method is utilized to align OCT images with FA photographs. Then, with the help of corresponding FA images, OCT image strips are created from OCT B-scans in four labels, namely MA, normal, abnormal, and vessel. Once the dataset of image strips is prepared, a stacked generalization (stacking) ensemble of four fine-tuned, pre-trained convolutional neural networks is trained to classify the strips of OCT images into the mentioned classes. FA images are used once to create OCT strips for training process and they are no longer needed for subsequent steps. Once the stacking ensemble model is obtained, it will be used to classify the OCT strips in the test process. The results demonstrate that the proposed framework classifies overall OCT image strips and OCT strips containing MAs with accuracy scores of 0.982 and 0.987, respectively.
Designing water vapor fuelled brine-silk cocoon protein bio-battery for a self-lighting kettle and water-vapor panels
Authors: Jangir Himanshi , Das Mainak 
Published: August 2022

AbstractWater vapor increases the electrical conductivity of silk cocoons, human hair, jute, and corn silk. This phenomenon is unclear. In the present study, XPS analysis of cocoons showed that water vapor reduces the surface presence of low-energy carbon species (C–C, C–H). In contrast, electron-dense, high-energy carbon species (C–N, C=C, C=O) remained unchanged, possibly enhancing surface charge hopping. While water vapor improves the conduction, the deficiency of charge carrier diminishes the effect. We increase the charge carrier by soaking the cocoon in an aqueous solution of common salt (NaCl) to amplify the current. Salt treatment followed by 2-min exposure to water vapor results in a sharp upward spike in the current (3.6 ± 1.07 mA, n = 12; mean ± SE) from the baseline (0.06 ± 0.02 mA, n = 12). After 1 h, it maintains an average value of 0.39 ± 0.12 mA; n = 12, indicating an upward shift in the baseline. Every time the cocoon charges with water vapor, the next charging cycle initiates after the cocoon dries up. Inspired by the cocoon ecology, we demonstrate an alternating 'water vapor–dry air' cycle for rapid charging and discharging of the cocoon battery. Finally, we designed a prototype of a self-lighting kettle and water–vapor panels for futuristic homes using a 'brine-silk cocoon protein bio-battery,' where moist waste heat generates electricity.
Hierarchical dynamic convolutional neural network for laryngeal disease classification
Authors: Wang Shaoli , Chen Yingying , Chen Siying , Zhong Qionglei , Zhang Kaiyan 
Published: August 2022

AbstractLaryngeal disease classification is a relatively hard task in medical image processing resulting from its complex structures and varying viewpoints in data collection. Some existing methods try to tackle this task via the convolutional neural network, but they more or less ignore the intrinsic difficulty differences among different input samples and suffer from high training complexity. In order to better resolve these problems, an end-to-end Hierarchical Dynamic Convolutional Network (HDCNet) is proposed, which can dynamically process the input samples based on their difficulty. For the easy-classified samples, the HDCNet processes them with a smaller resolution and a relatively small network, while the difficult samples are passed to a large network with a larger resolution for more accurate classification results. Furthermore, a Feature Reuse Module (FRM) is designed to transfer the features learned by the small network to the corresponding block in the deep network to enhance the overall performance of some rather complicated samples. To validate the effectiveness of the proposed HDCNet, comprehensive experiments are conducted on the public available laryngeal disease classification dataset and HDCNet provides superior performances compared with other current state-of-the-art methods.
Niche conservatism and evolution of climatic tolerance in the Neotropical orchid genera Sobralia and Brasolia (Orchidaceae)
Authors: Kolanowska Marta , Tsiftsis Spyros , Dudek Magdalena , Konowalik Kamil , Baranow Przemysław 
Published: August 2022

AbstractSobraliaandBrasoliaform a large complex of Neotropical Orchidaceae. Although the molecular and morphological studies allowed to increase the rate of work on the modern classification of the taxa, they still require the attention as remaining without complete revision. The niche similarity analysis between representatives ofSobraliaand recently segregated from this taxon—genusBrasoliais presented. The ecological tolerance evolution within the group was investigated with molecular clock analysis and phylogeny as the background. The phylogenetic analysis has confirmed the previous results and placedBrasoliarepresentatives in a single clade withElleanthusandSobraliacore as a separated group. The molecular clock analysis suggests thatSobraliaandBrasoliaare relatively young groups that evolved between 8.5 and 8 million years ago. Distribution of suitable niches of studied species is generally congruent with the known geographical ranges of particular taxa. The calculated niche overlap did not indicate any correlation between niche overlap and species phylogenetic relationships and remains low for both intra- and intergeneric relationships. The reconstruction of climatic tolerance evolution indicated that the studied species ofBrasoliaandSobraliaare characterized by generally similar ecological tolerance for most of the analyzed variables.
LINE-1 and Alu methylation signatures in autism spectrum disorder and their associations with the expression of autism-related genes
Authors: Saeliw Thanit , Permpoon Tiravut , Iadsee Nutta , Tencomnao Tewin , Hu Valerie W. , Sarachana Tewarit , Green Daniel , Sae-Lee Chanachai 
Published: August 2022

AbstractLong interspersed nucleotide element-1 (LINE-1) andAluelements are retrotransposons whose abilities cause abnormal gene expression and genomic instability. Several studies have focused on DNA methylation profiling of gene regions, but the locus-specific methylation of LINE-1 andAluelements has not been identified in autism spectrum disorder (ASD). Here we interrogated locus- and family-specific methylation profiles of LINE-1 andAluelements in ASD whole blood using publicly-available Illumina Infinium 450 K methylation datasets from heterogeneous ASD and ASD variants (Chromodomain Helicase DNA-binding 8(CHD8) and 16p11.2del). Total DNA methylation of repetitive elements were notably hypomethylated exclusively in ASD withCHD8variants. Methylation alteration in a family-specific manner including L1P, L1H, HAL,AluJ, andAluSfamilies were observed in the heterogeneous ASD and ASD withCHD8variants. Moreover, LINE-1 andAlumethylation within target genes is inversely related to the expression level in each ASD variant. The DNA methylation signatures of the LINE-1 andAluelements in ASD whole blood, as well as their associations with the expression of ASD-related genes, have been identified. If confirmed in future larger studies, these findings may contribute to the identification of epigenomic biomarkers of ASD.
Platelet-to-lymphocyte ratio predicts short-term mortality in patients with moderate to severe traumatic brain injury
Authors: Li Wenjuan , Deng Wenjing 
Published: August 2022

AbstractAn easily accessible biomarker with good diagnostic power for patients with traumatic brain injury (TBI) was needed to predict the short-term mortality. Studies have shown that platelet-to-lymphocyte ratio (PLR) is a biomarker for patients with tumor. This study aimed to identify the relationship between PLR and short-term mortality in patients with moderate to severe TBI. This is a retrospective cohort study. We selected patients with moderate to severe TBI who were admitted to the emergency department of The First Affiliated Hospital of Zhengzhou University. Biomarkers were collected within 24 h after admission. To investigate their relationship with short-term mortality, Cox proportional hazards regression and ROC curve analysis were performed. A total number of 170 patients was included. 47 (27.6%) patients had died and 123 (72.4%) patients were survived by the end of the study. Patients with different Rotterdam CT score (HR = 1.571, 95%CI 1.232–2.002, p < 0.001) or PLR levels (HR = 1.523, 95%CI 1.110–2.090, p = 0.009) had significant different mortality rates. The AUC curve analysis showed that the AUC of Rotterdam CT score and PLR groups were 0.729 (95%CI 0.638–0.821, p < 0.001) and 0.711 (95%CI 0.618–0.803 p < 0.001), respectively. PLR level is an independent biomarker with great diagnostic power for short-term mortality in patients with moderate to severe brain injury.