Miracle-dz/UniFAR-FTUs huggingface dataset:
Lifting the lid on impact and peer review

Brain and Neuroscience Advances has grown in tandem with the British Neuroscience Association’s campaign to build Credibility in Neuroscience, which encourages actions and initiatives aimed at improving reproducibility, reliability and openness. This commitment to credibility impacts not only what the Journal publishes, but also how it operates. With that in mind, the Editorial Board sought the views of the neuroscience community on the peer review process, and on how they should respond to the Journal Impact Factor that will be assigned to Brain and Neuroscience Advances. In this editorial, we present the results of a survey of neuroscience researchers conducted in the autumn of 2020 and discuss the broader implications of our findings for the Journal and the neuroscience community.
Effect of Three-Dimensional Detector Orientation on Small-Field Output Factors

The IAEA TRS 483 has recommended that the orientation for cylindrical ionization chambers be perpendicular to the beam for small-field output factor (OF) measurements. The recommendation was based on the unavailability of field output correction factor data for measurements using parallel orientation at the time of publication. Two three-dimensional (3D) air ionization chambers were used to perform measurements in parallel and perpendicular orientations and compared to data determined using a PTW 31018. The aim of the study was to establish whether the 3D detectors behaved as spherical or cylindrical devices. From the results, it was confirmed that the PTW 31016 and PTW 31021 detectors are suitable for OF measurements in both orientations for field sizes down to an equivalent square field of 1.8 cm and 0.96 cm, respectively, using the field output correction factor data published in the IAEA TRS 483. The preferred orientation is parallel to the beam to facilitate beam profile measurements and minimize the irradiation of the chamber stem and detector cable and decrease the volume averaging factor.
A quantitative comparison of towed-camera and diver-camera transects for monitoring coral reefs

Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.
Morpho-molecular characterization of Discosia ravennica sp. nov. and a new host record for Sporocadus rosigena

Abstract Collections of fungal samples from two dead leaf specimens from Italy were subjected to morphological examination and phylogenetic analyses. Two coelomycetous taxa belonging to two different genera in Xylariomycetidae, Sordariomycetes, namely Discosia and Sporocadus, were identified. The Discosia taxon is revealed as a new species and is herein introduced as Discosia ravennicasp. nov. while the Sporocadus taxon is identified as Sporocadus rosigena. Multi-locus phylogeny based on DNA sequence data of the large subunit (LSU) and internal transcribed spacer (ITS) of nuclear ribosomal genes, β-tubulin (β-tub) and RNA polymerase II second largest subunit (rpb2) showed that D. ravennica is related to D. neofraxinea but it forms an independent lineage that supports its new species status. The new taxon also differs from other Discosia species by its unilocular to bilocular, superficial and applanate conidiomata with basal stroma composed of cells of textura angularis, elongate-ampulliform conidiogenous cells and conidia smaller in size. Sporocadus rosigena is here reported as a new host record from Quercus ilex from Italy. Descriptions, illustrations and molecular data for both species are provided in this paper.
A case report: adenosine triggered myocardial infarction during myocardial perfusion stress test imaging in a diabetic patient

Abstract Background Myocardial perfusion imaging (MPI) using single-photon emission computed tomography (SPECT) can in general be used safely in daily clinical practice. However, under the right circumstances, it can lead to serious complications. Case summary A 68-year-old female patient with diabetes and a history of inferior ST-elevation myocardial infarction 8 years earlier, visited our outpatient clinic with atypical chest discomfort. In order to assess whether this is due to myocardial ischaemia, MPI-SPECT was ordered. As it was suspected she would not achieve sufficient exercise levels, pharmacologic stress using adenosine was arranged. During the scan, she developed acute myocardial infarction. Subsequent urgent coronary angiography demonstrated a subtotal stenosis in the proximal left anterior descending coronary artery which was successfully stented. She was still free from angina 4 months later. Discussion The combination of a reduced systemic and coronary perfusion pressure in the presence of an exhausted coronary autoregulation, may be a starting point for local geometrical changes that initiate the classic cascade of thrombus formation and acute occlusion of coronary arteries during MPI-SPECT. This illustrates the need for continuous patient and electrocardiogram monitoring.
Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2

The rapid spread of COVID-19, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a worldwide health emergency. Unfortunately, to date, a very small number of remedies have been to be found effective against SARS-CoV-2 infection. Therefore, further research is required to achieve a lasting solution against this deadly disease. Repurposing available drugs and evaluating natural product inhibitors against target proteins of SARS-CoV-2 could be an effective approach to accelerate drug discovery and development. With this strategy in mind, we derived Marine Natural Products (MNP)-based drug-like small molecules and evaluated them against three major target proteins of the SARS-CoV-2 virus replication cycle. A drug-like database from MNP library was generated using Lipinski’s rule of five and ADMET descriptors. A total of 2,033 compounds were obtained and were subsequently subjected to molecular docking with 3CLpro, PLpro, and RdRp. The docking analyses revealed that a total of 14 compounds displayed better docking scores than the reference compounds and have significant molecular interactions with the active site residues of SARS-CoV-2 virus targeted proteins. Furthermore, the stability of docking-derived complexes was analyzed using molecular dynamics simulations and binding free energy calculations. The analyses revealed two hit compounds against each targeted protein displaying stable behavior, binding affinity, and molecular interactions. Our investigation identified two hit compounds against each targeted proteins displaying stable behavior, higher binding affinity and key residual molecular interactions, with good in silico pharmacokinetic properties, therefore can be considered for further in vitro studies.
Delay minimization based uplink resource allocation for device-to-device communications considering mmWave propagation

This paper addresses the resource allocation problem in multi-sharing uplink for device-to-device (D2D) communication, one aspect of 5G communication networks. The main advantage and motivation in relation to the use of D2D communication is the significant improvement in the spectral efficiency of the system when exploiting the proximity of communication pairs and reusing idle resources of the network, mainly in the uplink mode, where there are more idle available resources. An approach is proposed for allocating resources to D2D and cellular user equipments (CUE) users in the uplink of a 5G based network which considers the estimation of delay bound value. The proposed algorithm considers minimization of total delay for users in the uplink and solves the problem by forming conflict graph and by finding the maximal weight independent set. For the user delay estimation, an approach is proposed that considers the multifractal traffic envelope process and service curve for the uplink. The performance of the algorithm is evaluated through computer simulations in comparison with those of other algorithms in the literature in terms of throughput, delay, fairness and computational complexity in a scenario with channel modeling that describes the propagation of millimeter waves at frequencies above 6 GHz. Simulation results show that the proposed allocation algorithm outperforms other algorithms in the literature, being highly efficient to 5G systems.
Forsythoside A Alleviates High Glucose-Induced Oxidative Stress and Inflammation in Podocytes by Inactivating MAPK Signaling via MMP12 Inhibition

Background Podocyte injury serves an important role during the progression of diabetic nephropathy (DN). The aim of this study was to investigate the effects of forsythoside A (FA) on high glucose (HG)-induced podocyte injury and to identify the possible mechanisms. Methods MPC-5 podocytes were cultured under HG conditions. After exposure to different doses of FA, cell viability and apoptosis were respectively evaluated with CCK-8 assay and flow cytometry. Then, the levels of oxidative stress-related markers and inflammatory factors were examined by corresponding kits. Western blot analysis was employed to detect the expression of Nox2, Nox4, COX-2, iNOS and matrix metalloproteinases 12 (MMP12). Subsequently, MMP12 was overexpressed to assess whether the effects of FA on HG-stimulated podocyte injury were mediated by MMP12 and MAPK signaling. Results Results indicated that FA dose-dependently elevated cell viability, reduced cell apoptosis in HG-induced MPC-5 cells. Additionally, FA significantly inhibited oxidative stress, which could be certified by decreased content of malondialdehyde (MDA), enhanced activities of superoxide dismutase (SOD) and catalase (CAT), and downregulated expression of Nox2 and Nox4. Moreover, notably reduced levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1β and IL-6 were observed in FA-treated MPC-5 cells under HG conditions, accompanied by decreased COX-2 and iNOS expression. Remarkably, FA suppressed MMP12 expression in a dose-dependent manner, and the effects of FA on MPC-5 cells exposed to HG were partially counteracted by MMP12 overexpression. Mechanically, FA inactivated the expression of phospho-ERK (p-ERK), p-p38 and p-JNK, which was restored after MMP12 overexpression. Conclusion These findings demonstrate a protective mechanism of FA by inactivating MAPK signaling via MMP12 inhibition in HG-induced podocyte injury, providing a promising therapeutic candidate for the treatment of DN.
A new species of Viola (Violaceae) from Guangdong Province, China

Abstract Viola huizhouensis (Violaceae), a new species from Xiangtoushan National Nature Reserve of Guangdong Province in China, is described and illustrated. The new species is most similar to V. guangzhouensis, but it can be easily distinguished by its much stouter rhizome, lack of aerial stem, dense pubescence of the basal pedicel and the whole plant. Our phylogenetic analysis, based on ITS sequences, confirms that the new species belongs to V. sect. Diffusae.
A computer vision-based approach for behavior recognition of gestating sows fed different fiber levels during high ambient temperature

Abstract The objectives of this study were to evaluate convolutional neural network models and computer vision techniques for the classification of swine posture with high accuracy and to use the derived result in the investigation of the effect of dietary fiber level on the behavioral characteristics of the pregnant sow under low and high ambient temperatures during the last stage of gestation. A total of 27 crossbred sows (Yorkshire × Landrace; average body weight, 192.2 ± 4.8 kg) were assigned to three treatments in a randomized complete block design during the last stage of gestation (days 90 to 114). The sows in group 1 were fed a 3% fiber diet under neutral ambient temperature; the sows in group 2 were fed a diet with 3% fiber under high ambient temperature (HT); the sows in group 3 were fed a 6% fiber diet under HT. Eight popular deep learning-based feature extraction frameworks (DenseNet121, DenseNet201, InceptionResNetV2, InceptionV3, MobileNet, VGG16, VGG19, and Xception) used for automatic swine posture classification were selected and compared using the swine posture image dataset that was constructed under real swine farm conditions. The neural network models showed excellent performance on previously unseen data (ability to generalize). The DenseNet121 feature extractor achieved the best performance with 99.83% accuracy, and both DenseNet201 and MobileNet showed an accuracy of 99.77% for the classification of the image dataset. The behavior of sows classified by the DenseNet121 feature extractor showed that the HT in our study reduced (p < 0.05) the standing behavior of sows and also has a tendency to increase (p = 0.082) lying behavior. High dietary fiber treatment tended to increase (p = 0.064) lying and decrease (p < 0.05) the standing behavior of sows, but there was no change in sitting under HT conditions.
Assessment of Single-and Double-Strand Breaks in DNA Induced by Auger Electrons of Radioisotopes Used in Diagnostic and Therapeutic Applications

Introduction: Most of the radionuclides that are used for diagnostic purposes emit Auger electrons and can thus cause damage to the DNA molecule on a nanometer scale. Therefore, the nanodosimetric calculation of these radioisotopes is necessary to achieve better understanding on their effects. Aim: The aim of this study was to calculate the mean number of DNA strand breaks (single-strand breaks and double-strand breaks) caused by direct and indirect effects for six widely used Auger electron-emitting diagnostic radioisotopes, including 123I, 125I, 99mTc, 67Ga, 201Tl, 111In and two therapeutic radioisotopes of 131I(beta + Auger + CK emitter) and 211At(alpha + Auger + CK emitter). Materials and Methods: Geant4-DNA simulation tool was used to evaluate the effects of Auger electrons, beta and alpha particles of these radioisotopes on DNA molecules. Two different DNA molecule geometric models were simulated and the results of these two models were compared with each other as well as with the results of previous studies. Results and Conclusion: The results showed that the geometric shape of the sugar-phosphate groups may have a significant effect on the number of single-strand breaks (SSBs) and double-strand breaks (DSBs) of the DNA molecule. Among the most widely used diagnostic radioisotopes, 201Tl and 125I, had the greatest impact on the number of SSBs and DSBs, respectively, while therapeutic radioisotope of 131I almost had no effect, therapeutic radioisotope of 211At had the moderate effect on the number of breaks in the DNA chain.
Downregulation of miR-497-5p Improves Sepsis-Induced Acute Lung Injury by Targeting IL2RB

Introduction Acute lung injury (ALI) induced by sepsis is a process related to inflammatory reactions, which involves lung cell apoptosis and production of inflammatory cytokine. Here, lipopolysaccharide (LPS) was applied to stimulate the mouse or human normal lung epithelial cell line (BEAS-2B) to construct a sepsis model in vivo and in vitro, and we also investigated the effect of miR-497-5p on sepsis-induced ALI. Material and Methods. Before LPS treatment, miR-497-5p antagomir was injected intravenously into mice to inhibit miR-497-5p expression in vivo. Similarly, miR-497-5p was knocked down in BEAS-2B cells. Luciferase reporter assay was applied to predict and confirm the miR-497-5p target gene. Cell viability, apoptosis, the levels of miR-497-5p, IL2RB, SP1, inflammatory cytokine, and lung injury were assessed. Results In BEAS-2B cells, a significant increase of apoptosis and inflammatory cytokine was shown after LPS stimulation. In septic mice, increased inflammatory cytokine production and apoptosis in lung cells and pulmonary morphological abnormalities were shown. The miR-497-5p inhibitor transfection showed antiapoptotic and anti-inflammatory effects on BEAS-2B cells upon LPS stimulation. In septic mice, the miR-497-5p antagomir injection also alleviated ALI, apoptosis, and inflammation caused by sepsis. The downregulation of IL2RB in BEAS-2B cells reversed the protective effects of the miR-497-5p inhibitor against ALI. Conclusion In conclusion, downregulation of miR-497-5p reduced ALI caused by sepsis through targeting IL2RB, indicating the potential effect of miR-497-5p for improving ALI caused by sepsis.
Computational Model-Based Estimation of Mouse Eyeball Structure From Two-Dimensional Flatmount Microscopy Images

Purpose Retinal pigment epithelial (RPE) cells serve as a supporter for the metabolism and visual function of photoreceptors and a barrier for photoreceptor protection. Morphology dynamics, spatial organization, distribution density, and growth patterns of RPE cells are important for further research on these RPE main functions. To enable such investigations within the authentic eyeball structure, a new method for estimating the three-dimensional (3D) eyeball sphere from two-dimensional tissue flatmount microscopy images was investigated. Methods An error-correction term was formulated to compensate for the reconstruction error as a result of tissue distortions. The effect of the tissue-distortion error was evaluated by excluding partial data points from the low- and high-latitude zones. The error-correction parameter was learned automatically using a set of samples with the ground truth eyeball diameters measured with noncontact light-emitting diode micrometry at submicron accuracy and precision. Results The analysis showed that the error-correction term in the reconstruction model is a valid method for modeling tissue distortions in the tissue flatmount preparation steps. With the error-correction model, the average relative error of the estimated eyeball diameter was reduced from 14% to 5%, and the absolute error was reduced from 0.22 to 0.03 mm. Conclusions A new method for enabling RPE morphometry analysis with respect to locations on an eyeball sphere was created, an important step in increasing RPE research and eye disease diagnosis. Translational Relevance This method enables one to derive RPE cell information from the 3D eyeball surface and helps characterize eyeball volume growth patterns under diseased conditions.
Atorvastatin and growth, rupture of small unruptured intracranial aneurysm: results of a prospective cohort study

Background and aims: The role of statins in unruptured intracranial aneurysm (UIA) growth and rupture remains ambiguous. This study sought to determine whether atorvastatin is associated with aneurysm growth and rupture in patients harboring UIA <7 mm. Methods: This prospective, multicenter cohort study consecutively enrolled patients with concurrent UIA <7 mm and ischemic cerebrovascular disease from four hospitals between 2016 and 2019. Baseline and follow-up patient information was recorded. Because of the strong anti-inflammatory effect of aspirin, patients using aspirin were excluded. Patients taking atorvastatin 20 mg daily were atorvastatin users. The primary and exploratory endpoints were aneurysm rupture and growth, respectively. Results: Among the 1087 enrolled patients, 489 (45.0%) took atorvastatin, and 598 (55%) took no atorvastatin. After a mean follow-up duration of 33.0 ± 12.5 months, six (1.2%) and five (0.8%) aneurysms ruptured in atorvastatin and non-atorvastatin groups, respectively. In the adjusted multivariate Cox analysis, UIA sized 5 to <7 mm, current smoker, and uncontrolled hypertension were associated with aneurysm rupture, whereas atorvastatin [adjusted hazard ratio (HR) 1.495, 95% confidence interval (CI) 0.417–5.356, p = 0.537] was not. Of 159 patients who had follow-up imaging, 34 (21.4%) took atorvastatin and 125 (78.6%) took no atorvastatin. Aneurysm growth occurred in five (14.7%) and 21 (16.8%) patients in atorvastatin and non-atorvastatin groups (mean follow-up: 20.2 ± 12.9 months), respectively. In the adjusted multivariate Cox analysis, UIAs sized 5 to <7 mm and uncontrolled hypertension were associated with a high growth rate; atorvastatin (adjusted HR 0.151, 95% CI 0.031–0.729, p = 0.019) was associated with a reduced growth rate. Conclusions: We conclude atorvastatin use is associated with a reduced risk of UIA growth, whereas atorvastatin is not associated with UIA rupture. The trial registry name: The Clinic Benefit and Risk of Oral Aspirin for Unruptured Intracranial Aneurysm Combined With Cerebral Ischemia Clinical Trial Registration-URL: http://www.clinicaltrials. gov Unique identifier: NCT02846259
Evaluating spatial patterns of seasonal ozone exposure and incidence of respiratory emergency room visits in Dallas-Fort Worth

Background In urban environments, environmental air pollution poses significant risks to respiratory health. Moreover, the seasonal spatial variability of the air pollutant ozone, and respiratory illness within Dallas-Fort Worth (DFW) is not well understood. We examine the relationships between spatial patterns of long-term ozone exposure and respiratory illness to better understand impacts on health outcomes. We propose that this study will establish an enhanced understanding of the spatio-temporal characteristics of ozone concentrations and respiratory emergency room visits (ERV) incidence. Methods Air pollution data (ozone) and ERV incidence data from DFW was used to evaluate the relationships between exposures and outcomes using three steps: (1) develop a geostatistical model to produce quarterly maps of ozone exposure for the DFW area; (2) use spatial analysis techniques to identify clusters of zip codes with high or low values of ozone exposure and respiratory ERV incidence; and (3) use concentration-response curves to evaluate the relationships between respiratory ERV incidence and ozone exposure. Results Respiratory ERV incidence was highest in quarters 1 and 4, while ozone exposure was highest in quarters 2 and 3. Extensive statistically significant spatial clusters of ozone regions were identified. Although the maps revealed that there was no regional association between the spatial patterns of high respiratory ERV incidence and ozone exposure, the concentration-response analysis suggests that lower levels of ozone exposure may still contribute to adverse respiratory outcomes.