bluuebunny/crossref_metadata_2025 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

Food 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

RET (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

Amphibians 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

Silicate 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

Brain–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

Despite 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

Rill 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

Microaneurysms (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

Water 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

Laryngeal 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

SobraliaandBrasoliaform 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

Long 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

An 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.
Polyimide aerogels for ballistic impact protection
Authors: Malakooti Sadeq , Vivod Stephanie L. , Pereira Michael , Ruggeri Charles R. , Revilock Duane M. , Zhang Runyu , Guo Haiquan , Scheiman Daniel A. , McCorkle Linda S. , Lu Hongbing
Published: August 2022

The ballistic performance of edge-clamped monolithic polyimide aerogel blocks (12 mm thickness) has been studied through a series of impact tests using a helium-filled gas gun connected to a vacuum chamber and a spherical steel projectile (approximately 3 mm diameter) with an impact velocity range of 150–1300 m s−1. The aerogels had an average bulk density of 0.17 g cm−3 with high porosity of approximately 88%. The ballistic limit velocity of the aerogels was estimated to be in the range of 175–179 m s−1. Moreover, the aerogels showed a robust ballistic energy absorption performance (e.g., at the impact velocity of 1283 m s−1 at least 18% of the impact energy was absorbed). At low impact velocities, the aerogels failed by ductile hole enlargement followed by a tensile failure. By contrast, at high impact velocities, the aerogels failed through an adiabatic shearing process. Given the substantially robust ballistic performance, the polyimide aerogels have a potential to combat multiple constraints such as cost, weight, and volume restrictions in aeronautical and aerospace applications with high blast resistance and ballistic performance requirements such as in stuffed Whipple shields for orbital debris containment application.
Protective effect of rosiglitazone on microscopic and oxidative stress parameters of ram sperm after freeze-thawing
Authors: Mehdipour Mahdieh , Daghigh-Kia Hossein , Najafi Abouzar , Mehdipour Zohreh , Mohammadi Hossein
Published: August 2022

The purpose of this study was to investigate the effects of rosiglitazone on ram semen after cryopreservation on the quality of thawed sperm. Sperm motility, membrane functionality, viability, total abnormality, acrosome membrane integrity, mitochondrial activity, reactive oxygen species production, ATP content and apoptotic features were assessed after thawing. Rosiglitazone at concentration of 60 µM resulted in the highest (P < 0.05) total motility, progressive motility and straight-line velocity. The percentages of average path velocity and curvilinear velocity were greater in the 60 µM group. Different concentrations of rosiglitazone did not have significant effects on amplitude of the lateral head displacement, linearity and straightness. The highest amounts of membrane functionality and mitochondrial activity after freeze-thawing were observed in groups containing 60 µM. By increasing the rosiglitazone level to 80 µM, no positive effect was observed in most of the evaluated parameters. The lowest ROS concentration was recorded in 60 µM rosiglitazone group (P < 0.05). The group containing 60 µM rosiglitazone also produced the lowest significant percentage of apoptosis-like changes and dead sperm. A greater (P < 0.05) percentage of acrosome integrity in frozen-thawed spermatozoa was observed in the 60 µM rosiglitazone group. There was no significant difference between 40 and 60 µM rosiglitazone in intact acrosome of ram thawed semen. The result showed that supplementation in ram semen extender with rosiglitazone had a positive role in the regulation of ram sperm motility and had strong protective effect on the sperm membrane and acrosome integrity.
A pretraining domain decomposition method using artificial neural networks to solve elliptic PDE boundary value problems
Authors: Seo Jeong-Kweon
Published: August 2022

Developing methods of domain decomposition (DDM) has been widely studied in the field of numerical computation to estimate solutions of partial differential equations (PDEs). Several case studies have also reported that it is feasible to use the domain decomposition approach for the application of artificial neural networks (ANNs) to solve PDEs. In this study, we devised a pretraining scheme called smoothing with a basis reconstruction process on the structure of ANNs and then implemented the classic concept of DDM. The pretraining process that is engaged at the beginning of the training epochs can make the approximation basis become well-posed on the domain so that the quality of the estimated solution is enhanced. We report that such a well-organized pretraining scheme may affect any NN-based PDE solvers as we can speed up the approximation, improve the solution’s smoothness, and so on. Numerical experiments were performed to verify the effectiveness of the proposed DDM method on ANN for estimating solutions of PDEs. Results revealed that this method could be used as a tool for tasks in general machine learning.
Alhagi maurorum extract modulates quorum sensing genes and biofilm formation in Proteus mirabilis
Authors: Mirzaei Arezoo , Nasr Esfahani Bahram , Ghanadian Mustafa , Moghim Sharareh
Published: August 2022

Proteus mirabilis (P. mirabilis) is a frequent cause of catheter-associated urinary tract infections. This study aims to investigate the anti-infective effect of Alhagi maurorum extract (AME), the traditional medicinal plant in the middle east, on the biofilm-forming P. mirabilis isolates. Hydroalcoholic extract and oil of A. maurorum were characterized by HPLC and GC–MS. The antiproliferative, anti-biofilm, and bactericidal activity of AME at various concentrations were assessed by turbidity, crystal violet binding, and agar well diffusion assays, respectively. The AME’s effect on adhesion and quorum sensing (QS) were investigated by in vitro adhesion assay on cell culture and agar overlay assay using Janthinobacterium lividum (ATCC 12472) as a biosensor strain. In addition, the expression level of selected genes involved in QS and biofilm regulation were determined by quantitative Real-Time PCR. Furthermore, the bladder phantom model was created to evaluate the assays and investigate the catheter’s calcium deposition. The most effective chemical compounds found in AME were tamarixetin, quercetin, and trans-anethole. Although AME did not inhibit swarming motility, it reduced biofilm production and exerted a concentration-dependent anti-adhesive and anti-QS activity against P. mirabilis. AME also downregulated the expression level of selected genes involved in biofilm formation and QS. This study showed that AME as a natural compound reduced biofilm formation of P. mirabilis by targeting virulence factor genes, quorum sensing, and other strategies that include preventing the adhesion of P. mirabilis to the cells. The results suggest that A. maurorum extract might have the potential to be considered for preventing UTIs caused by P. mirabilis.
Repeatability of radiographic assessments for feline hip dysplasia suggest consensus scores in radiology are more uncertain than commonly assumed
Authors: Ball Elisabeth , Uhlhorn Margareta , Eksell Per , Olsson Ulrika , Ohlsson Åsa , Low Matthew
Published: August 2022

Variation in the diagnostic interpretation of radiographs is a well-recognised problem in human and veterinary medicine. One common solution is to create a ‘consensus’ score based on a majority or unanimous decision from multiple observers. While consensus approaches are generally assumed to improve diagnostic repeatability, the extent to which consensus scores are themselves repeatable has rarely been examined. Here we use repeated assessments by three radiologists of 196 hip radiographs from 98 cats within a health-screening programme to examine intra-observer, inter-observer, majority-consensus and unanimous-consensus repeatability scores for feline hip dysplasia. In line with other studies, intra-observer and inter-observer repeatability was moderate (63–71%), and related to the reference assessment and time taken to reach a decision. Consensus scores did show reduced variation between assessments compared to individuals, but consensus repeatability was far from perfect. Only 75% of majority consensus scores were in agreement between assessments, and based on Bayesian multinomial modelling we estimate that unanimous consensus scores can have repeatabilities as low as 83%. These results clearly show that consensus scores in radiology can have large uncertainties, and that future studies in both human and veterinary medicine need to include consensus-uncertainty estimates if we are to properly interpret radiological diagnoses and the extent to which consensus scores improve diagnostic accuracy.
Deep learning-based fully automatic segmentation of the maxillary sinus on cone-beam computed tomographic images
Authors: Choi Hanseung , Jeon Kug Jin , Kim Young Hyun , Ha Eun-Gyu , Lee Chena , Han Sang-Sun
Published: August 2022

The detection of maxillary sinus wall is important in dental fields such as implant surgery, tooth extraction, and odontogenic disease diagnosis. The accurate segmentation of the maxillary sinus is required as a cornerstone for diagnosis and treatment planning. This study proposes a deep learning-based method for fully automatic segmentation of the maxillary sinus, including clear or hazy states, on cone-beam computed tomographic (CBCT) images. A model for segmentation of the maxillary sinuses was developed using U-Net, a convolutional neural network, and a total of 19,350 CBCT images were used from 90 maxillary sinuses (34 clear sinuses, 56 hazy sinuses). Post-processing to eliminate prediction errors of the U-Net segmentation results increased the accuracy. The average prediction results of U-Net were a dice similarity coefficient (DSC) of 0.9090 ± 0.1921 and a Hausdorff distance (HD) of 2.7013 ± 4.6154. After post-processing, the average results improved to a DSC of 0.9099 ± 0.1914 and an HD of 2.1470 ± 2.2790. The proposed deep learning model with post-processing showed good performance for clear and hazy maxillary sinus segmentation. This model has the potential to help dental clinicians with maxillary sinus segmentation, yielding equivalent accuracy in a variety of cases.
The diagnostic and triage accuracy of digital and online symptom checker tools: a systematic review
Authors: Wallace William , Chan Calvin , Chidambaram Swathikan , Hanna Lydia , Iqbal Fahad Mujtaba , Acharya Amish , Normahani Pasha , Ashrafian Hutan , Markar Sheraz R. , Sounderajah Viknesh , Darzi Ara
Published: August 2022

Digital and online symptom checkers are an increasingly adopted class of health technologies that enable patients to input their symptoms and biodata to produce a set of likely diagnoses and associated triage advice. However, concerns regarding the accuracy and safety of these symptom checkers have been raised. This systematic review evaluates the accuracy of symptom checkers in providing diagnoses and appropriate triage advice. MEDLINE and Web of Science were searched for studies that used either real or simulated patients to evaluate online or digital symptom checkers. The primary outcomes were the diagnostic and triage accuracy of the symptom checkers. The QUADAS-2 tool was used to assess study quality. Of the 177 studies retrieved, 10 studies met the inclusion criteria. Researchers evaluated the accuracy of symptom checkers using a variety of medical conditions, including ophthalmological conditions, inflammatory arthritides and HIV. A total of 50% of the studies recruited real patients, while the remainder used simulated cases. The diagnostic accuracy of the primary diagnosis was low across included studies (range: 19–37.9%) and varied between individual symptom checkers, despite consistent symptom data input. Triage accuracy (range: 48.8–90.1%) was typically higher than diagnostic accuracy. Overall, the diagnostic and triage accuracy of symptom checkers are variable and of low accuracy. Given the increasing push towards adopting this class of technologies across numerous health systems, this study demonstrates that reliance upon symptom checkers could pose significant patient safety hazards. Large-scale primary studies, based upon real-world data, are warranted to demonstrate the adequate performance of these technologies in a manner that is non-inferior to current best practices. Moreover, an urgent assessment of how these systems are regulated and implemented is required.
Multistate Structures and Dynamics at Atomic Resolution Using Exact Nuclear Overhauser Enhancements (eNOEs)
Authors: Kadavath Harindranath , Riek Roland
Published: August 2022

Biomolecules are highly dynamic systems comprising a complex interplay between motions covering several orders of magnitude in time that can be local or distant, and can be anticorrelated, random, or of concerted type. Understanding the relationship between motion and functions requires knowledge of the structure and dynamics at atomic resolution. However, the determined 3D structures of biomolecules are usually averaged snapshots of their conformational space or restricted to crystal packing and dynamics investigations mainly focusing on the time scale of motion. The recent advances in exact nuclear Overhauser enhancements (eNOEs) open an avenue for the ensemble-based structure determination of proteins on the basis of highly accurate quantitative ensemble-averaged distance restraints. In this chapter, the authors briefly describe the most recent progress in the applications of eNOEs for the calculation of multistate structural ensembles toward revealing the molecular mechanism of their activities. Among others, the implications of the exact NOEs to dissect protein allostery at atomic resolution and regulation of enzymatic activities are discussed. It appears that the eNOE methodology is a versatile tool in NMR-based structural biology to study the structure–dynamics–function relationship of biomacromolecules.
Lineshape Analysis as a Tool for Probing Functional Motions at Biological Interfaces
Authors: De Soumya , Greenwood Alexander I. , Acevedo L. Andrea , Korson Nathan E. , Nicholson Linda K.
Published: August 2022

The analysis of peak lineshapes in two-dimensional NMR spectra acquired during titration experiments is a powerful technique for quantitative studies of biological interfaces. The theoretical basis for how the thermodynamics (equilibrium populations) and kinetics (rate constants) of a multi-state equilibrium are encoded in the lineshape of an NMR peak is presented. Insights on how an exchange process influences the observed magnetization, how to construct the rate matrix for a given reaction scheme, and the origins of the governing lineshape equation are included. Applications of lineshape analysis to two-state binding and to four-state peptidyl prolyl cis–trans isomerization reactions involved in Alzheimer's disease and lateral root development in rice are presented. These studies illustrate how lineshape analysis of NMR titration experiments provides key mechanistic details for understanding the role of biological interfaces. Importantly, the quantitative model obtained from observations of an exchange reaction in the NMR tube enables predictions of activity to be scaled to cellular concentrations. This method is highly complementary to more recently developed NMR relaxation techniques. The application of lineshape analysis and relaxation methods to the same samples could enable quantitative characterization of even more complex multi-state systems.
Monitoring Interfaces of Thermo- and pH-responsive Polymers Using Solvent Relaxation
Authors: Chakraborty Ipsita , Bhattacharyya Rangeet
Published: August 2022

We discuss here some of the recent developments of NMR methods which rely on solvent relaxation and yield valuable information about the interface of smart polymers in aqueous solutions. Smart polymers, such as pH-responsive or thermotropic, form structures in the form of micelles or globules in solutions. Such structures could be controlled by varying parameters which control the behavior of the smart polymer, such as the pH or temperature of the solution. These structures have interfaces where proton exchange with the solvent takes place. This proton exchange affects the relaxation of the solvent. As such, by monitoring the changes in the relaxation of the solvent with respect to the pH or temperature of the solvent, one can monitor the interface. This chapter provides simple explanations of the principles involved in the solvent relaxation method.
Structural Insight into the Slowly Exchanging Dark States at the Functional Interaction Interface
Authors: Bhattacharyya Dipita , Krishnamoorthy Janarthanan , Bhunia Anirban
Published: August 2022

Protein dynamics at biomolecular binding interfaces yield essential functional information. However, owing to their transient nature and relatively high–molecular–weight, these dynamic conformers have remained invisible or dark to spectroscopic intervention. Recent advances in solution-state NMR has enabled the development of Dark State Exchange Saturation Transfer (DEST) experiments to gain atomic-resolution insight into these “dark” conformers through radio-frequency saturation. DEST is particularly efficient at probing slow biomolecular chemical exchange, which provides invaluable information on the dynamic aspect of the interactions.
NMR Structures, Dynamics and Interactions of Protein Complexes in β2 Integrins
Authors: Bhattacharjya Surajit
Published: August 2022

Integrins are type I transmembrane heterodimeric, α and β subunit, signal transducers. Integrins are key proteins in regulating cell adhesion and migration. Leucocyte-specific β2 integrins are comprised of four members, αLβ2, αMβ2, αXβ2 and αDβ2, which are crucial for the maintenance of immune functions. The cytosolic tail or domain of the β subunit of β2 integrins interacts with the cytosolic tail of the α subunits in the resting state of the receptors. Also, a number of soluble proteins are known to interact with the β cytosolic tail. NMR methods are providing atomic-resolution information of the structures, dynamics and binding interactions of cytosolic tails and with cognate proteins. This chapter describes an overview of various models of allosteric structural changes of integrins and applications of NMR in revealing critical structures and transient interactions of β2 integrins.
Describing Dynamic Chaperone–Client Complexes by Solution NMR Spectroscopy
Authors: Hiller S. , Burmann B. M.
Published: August 2022

Chaperone–client interactions are highly dynamic in their nature and result in transient, multi-conformational complexes that are challenging to characterize at the atomic level. Solution NMR spectroscopy has the power to resolve structure and dynamics even for large molecular systems in aqueous solution and is therefore a method of choice for chaperone–client systems. Here, we categorize the NMR techniques suitable for the characterization of dynamic complexes, assess their particular usefulness for chaperone–client complexes and describe how the resulting data can be fruitfully interpreted toward structural models.
Methyl-TROSY NMR Spectroscopy in the Investigation of Allosteric Cooperativity in Large Biomolecular Complexes
Authors: Huang Rui
Published: August 2022

Allosteric cooperativity plays a critical role in the function of biological complexes. Methyl-TROSY NMR spectroscopy is a powerful technique to probe the structure and dynamics of large molecular complexes and is well suited to investigating allostery and cooperativity in such systems. In this chapter, we discuss the general concepts and models of cooperativity and introduce strategies to probe cooperativity in high-molecular-weight complexes by methyl-TROSY NMR. We include an overview of the methyl-TROSY technique, focusing on the practical aspects of isotope labeling of the methyl groups and current approaches for methyl resonance assignment. We present a few case studies that exemplify the unique advantages of the methyl-TROSY approach in providing insights into cooperativity and allostery in functionally important molecular machines.
New Concepts for the Mechanisms of Action of Antimicrobial Peptides from Solid-state NMR Investigations
Authors: Salnikov E. S. , Glattard E. , Lointier M. , Raya J. , Juhl D. W. , Saad A. , Bechinger B.
Published: August 2022

The development and application of solid-state NMR techniques during the investigation of the functional mechanisms of membrane-active peptides is presented with a focus on the antimicrobial sequences magainin 2, PGLa and designed derivatives. Important insights have been obtained from MAS and oriented solid-state NMR approaches. In the latter case the peptides are reconstituted into supported lipid bilayers and aligned with the membrane normal parallel to the magnetic field direction. This approach provides information about the structure, topology and dynamics of the peptide, as well as the orientational and conformational order of the lipids. A strong dependence of the interaction modes was observed on both the lipid head group and fatty acyl chain composition, which underlines the importance of a careful choice of experimental conditions. Together, solid-state NMR of peptides and lipids provides a comprehensive view of the peptide–lipid interactions, which has resulted in conceptionally new models for their antimicrobial action and the synergistic enhancement observed for combinations of magainin 2 and PGLa. Furthermore, a detailed analysis of the membrane topology of the antimicrobial designer peptide LAH4 reconstituted into supported lipid bilayers at pH 5.3 is presented illustrating the protocol and its limitations.
A novel quinoline-based fluorescent probe for real-time monitoring of Cys in glioma
Authors: Zeng Shang-Ming-Zhu , Zhang Qing , Li Qin , Yuan Liang-Chao , Abbas Muhammad , He Zhen-Xiang , Zhu Hai-Liang , Wang Zhong-Chang
Published: August 2022

The highly selective fluorescent probe ZS-C1 for imaging Cys in living cells and 3D tumor cell sphere.
Modulating SEI formation via tuning the solvation sheath for lithium metal batteries
Authors: Sun Seho , Kim Gaeun , Lee Dongsoo , Park Eunkyung , Myeong Seungcheol , Son Byoungkuk , Lee Kangchun , Jang Minchul , Paik Ungyu , Song Taeseup
Published: August 2022

Water-induced solvation sheath control enables higher efficiency of Li metal usage, resulting from novel anion-derived SEI layer formation.
Introducing competitive adsorption species in sulfonimide salt-based electrolytes for inhibiting aluminium corrosion
Authors: Xue Weiran , Wang Qiuchen , Sun Guochen , Li Quan , Yu Xiqian , Li Hong
Published: August 2022

The inhibition of aluminium corrosion for 4 V-class cathodes within LiTFSI-based electrolytes by introducing competitive adsorption species.
Platinum-like HER onset in a GNR/MoS2 quantum dot heterostructure through curvature-dependent electron density reconfiguration
Authors: Nair Aruna Narayanan , Sanad Mohamed F. , Chava Venkata S. N. , Sreenivasan Sreeprasad T.
Published: August 2022

Curvature-directed lattice strain, electron density modulation and enhanced interfacial charge transfer in a graphene nanoribbon-MoS2 quantum dot heterostructure for superior hydrogen evolution reaction.
Chemical design of homochiral heterocyclic organic ferroelectric crystals
Authors: Song Xian-Jiang , Tang Shu-Yu , Chen Xiao-Gang , Ai Yong
Published: August 2022

Single component organic ferroelectrics possess well-defined ferroelectric and a low acoustic impedance value that well-matches with the human body tissues, which is important for future wearable smart materials and biocompatible materials.
Materials discovery and design limits in MDABCO perovskites
Authors: Gale Samuel D. , Lloyd Harry J. , Male Louise , Warren Mark R. , Saunders Lucy K. , Anderson Paul A. , Yeung Hamish H.-M.
Published: August 2022

Three new structures in the MDABCO perovskite family of ferroelectrics define new design rules for ferroelectric phase discovery.
Accurate experimental characterization of the labile N–Cl bond inN-chloro-N′-(p-fluorophenyl)-benzamidine crystal at 17.5 K
Authors: Destro Riccardo , Barzaghi Mario , Soave Raffaella , Roversi Pietro , Lo Presti Leonardo
Published: August 2022

Very low temperature can preserve the photolabile N–Cl bond in aN-chloro-N-benzamidine derivative long enough to carry on an accurate experimental X-ray charge density study.
First principles study of thermoelectric performance in pristine and binary alloyed monolayers of noble metals
Authors: Kumar Sushil , Moudgil R. K.
Published: August 2022

The half-metallic like feature in the conduction band of a Pt monolayer gives excellent Seebeck coefficient and thermoelectric figure of merit.
Accurate core excitation and ionization energies from a state-specific coupled-cluster singles and doubles approach
Authors: Arias-Martinez Juan E. , Cunha Leonardo A. , Oosterbaan Katherine J. , Lee Joonho , Head-Gordon Martin
Published: August 2022

A proper treatment of orbital relaxation and correlation, while addressing spin contamination and the shortcomings of the CVS, allows ΔCCSD to reach errors smaller than 0.5 eV compared to experimental X-ray absorption excitation energies.