bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of image quality on color fundus retinal images using the automatic retinal image analysis
Authors: Shi Chuying , Lee Jack , Wang Gechun , Dou Xinyan , Yuan Fei , Zee Benny 
Published: June 2022

AbstractImage quality assessment is essential for retinopathy detection on color fundus retinal image. However, most studies focused on the classification of good and poor quality without considering the different types of poor quality. This study developed an automatic retinal image analysis (ARIA) method, incorporating transfer net ResNet50 deep network with the automatic features generation approach to automatically assess image quality, and distinguish eye-abnormality-associated-poor-quality from artefact-associated-poor-quality on color fundus retinal images. A total of 2434 retinal images, including 1439 good quality and 995 poor quality (483 eye-abnormality-associated-poor-quality and 512 artefact-associated-poor-quality), were used for training, testing, and 10-ford cross-validation. We also analyzed the external validation with the clinical diagnosis of eye abnormality as the reference standard to evaluate the performance of the method. The sensitivity, specificity, and accuracy for testing good quality against poor quality were 98.0%, 99.1%, and 98.6%, and for differentiating between eye-abnormality-associated-poor-quality and artefact-associated-poor-quality were 92.2%, 93.8%, and 93.0%, respectively. In external validation, our method achieved an area under the ROC curve of 0.997 for the overall quality classification and 0.915 for the classification of two types of poor quality. The proposed approach, ARIA, showed good performance in testing, 10-fold cross validation and external validation. This study provides a novel angle for image quality screening based on the different poor quality types and corresponding dealing methods. It suggested that the ARIA can be used as a screening tool in the preliminary stage of retinopathy grading by telemedicine or artificial intelligence analysis.
Multi-task learning to leverage partially annotated data for PPI interface prediction
Authors: Capel Henriette , Feenstra K. Anton , Abeln Sanne 
Published: June 2022

AbstractProtein protein interactions (PPI) are crucial for protein functioning, nevertheless predicting residues in PPI interfaces from the protein sequence remains a challenging problem. In addition, structure-based functional annotations, such as the PPI interface annotations, are scarce: only for about one-third of all protein structures residue-based PPI interface annotations are available. If we want to use a deep learning strategy, we have to overcome the problem of limited data availability. Here we use a multi-task learning strategy that can handle missing data. We start with the multi-task model architecture, and adapted it to carefully handle missing data in the cost function. As related learning tasks we include prediction of secondary structure, solvent accessibility, and buried residue. Our results show that the multi-task learning strategy significantly outperforms single task approaches. Moreover, only the multi-task strategy is able to effectively learn over a dataset extended with structural feature data, without additional PPI annotations. The multi-task setup becomes even more important, if the fraction of PPI annotations becomes very small: the multi-task learner trained on only one-eighth of the PPI annotations—with data extension—reaches the same performances as the single-task learner on all PPI annotations. Thus, we show that the multi-task learning strategy can be beneficial for a small training dataset where the protein’s functional properties of interest are only partially annotated.
Theoretical study of metal-free catalytic for catalyzing CO-oxidation with a synergistic effect on P and N co-doped graphene
Authors: Hadsadee Sarinya , Jungsuttiwong Siriporn , Zhang Rui-Qin , Rungrotmongkol Thanyada 
Published: June 2022

AbstractP and N co-doped graphene (PNxCy-G with x = 1, 2, 3 and y = 0, 1, 2) is designed to enhance graphene reactivity with a synergistic effect of the P and N atoms for the CO oxidation reaction, focusing on the influence of the N dopant concentration on graphene. The calculated results indicate that increasing two or three coordinated N to P can facilitate charge transfer from the surface onto O2 molecules. However, the adsorbed O2 molecule breaks apart on PN3-G surface, affecting CO oxidation performance. Furthermore, PN2C1-G exhibits excellent catalytic activity towards the oxidation of CO via the ER mechanism, which catalyzes CO oxidation with the rate-determining step of only 0.26 eV for the first and 0.25 eV for the second oxidation at 0 K. Additionally, the catalytic oxidation of PN2C1-G via Eley–Rideal mechanism prefers to occur at room temperature (298.15 K), with a rate-determining step of 0.77 eV. The reaction rates at 298.15 K is calculated to be 5.36 × 1016 mol s–1. The rate constants are obtained according to harmonic transition state theory, which could be supportive for catalytic oxidation of CO on the experiment.
Linking metabolites in eight bioactive forage species to their in vitro methane reduction potential across several cultivars and harvests
Authors: Verma Supriya , Wolffram Siegfried , Salminen Juha-Pekka , Hasler Mario , Susenbeth Andreas , Blank Ralf , Taube Friedhelm , Kluß Christof , Malisch Carsten Stefan 
Published: June 2022

AbstractAn in vitro Hohenheim gas test was conducted to analyze the fermentation end-products from 17 cultivars of eight polyphenol containing forage species. The polyphenol composition and proanthocyanidin (PA) structural features of all the cultivars were analyzed with UPLC-MS/MS in leaves of vegetative or generative plants. The samples were incubated with and without polyethylene glycol (PEG, a tannin-binding agent) to separate the tannin-effect on methane (CH4, ml/200 mg DM) production from that of forage quality. Sulla and big trefoil, two particularly PA rich species, were found to have the highest CH4 reduction potential of up to 47% when compared to the samples without PEG. However, concomitant reduction in gas production (GP, ml/200 mg DM) of up to 44% was also observed. An increase in both GP and CH4 production under PEG treatments, confirms the role of tannins in CH4 reduction. Moreover, PA structural features and concentration were found to be an important source of variation for CH4 production from PA containing species. Despite having low polyphenol concentrations, chicory and plantain were found to reduce CH4 production without reducing GP. Additionally, interspecies variability was found to be higher than intraspecies variability, and these results were consistent across growth stages, indicating the findings’ representativeness.
Selectively biased tri-terminal vertically-integrated memristor configuration
Authors: Manouras Vasileios , Stathopoulos Spyros , Serb Alex , Prodromakis Themis 
Published: June 2022

AbstractMemristors, when utilized as electronic components in circuits, can offer opportunities for the implementation of novel reconfigurable electronics. While they have been used in large arrays, studies in ensembles of devices are comparatively limited. Here we propose a vertically stacked memristor configuration with a shared middle electrode. We study the compound resistive states presented by the combined in-series devices and we alter them either by controlling each device separately, or by altering the full configuration, which depends on selective usage of the middle floating electrode. The shared middle electrode enables a rare look into the combined system, which is not normally available in vertically stacked devices. In the course of this study, it was found that separate switching of individual devices carries over its effects to the Complete device (albeit non-linearly), enabling increased resistive state range, which leads to a larger number of distinguishable states (above SNR variance limits) and hence enhanced device memory. Additionally, by applying a switching stimulus to the external electrodes it is possible to switch both devices simultaneously, making the entire configuration a voltage divider with individual memristive components. Through usage of this type of configuration and by taking advantage of the voltage division, it is possible to surge-protect fragile devices, while it was also found that simultaneous reset of stacked devices is possible, significantly reducing the required reset time in larger arrays.
Worsening hearing was associated with higher β-amyloid and tau burden in age-related hearing loss
Authors: Zheng Mengmeng , Yan Jiangyu , Hao Wenjuan , Ren Yuan , Zhou Ming , Wang Yunzhi , Wang Kai 
Published: June 2022

AbstractAge-related hearing loss (ARHL) represents the frequently occurring disability that affects the elderly worldwide. The recent evidence has calculated ARHL to be most potential risk factor to predict dementia. β-amyloid plaques and tau accumulation in brain are hallmarks pathologic feature of Alzheimer’s disease (AD), which is a leading cause resulting in dementia. However, the potential mechanistic associations between ARHL and dementia remains unknown. We performed the present cross-sectional cohort study by enrolling 72 patients from research on hearing as well as the pathologic hallmarks of AD in brain. The exposure of hearing was measured by either word recognition score or mean pure-tone of the superior ear. The brain β-amyloid and tau standardized uptake value ratio (SUVR) were measured by positron emission tomography (PET). The covariates included gender, age, cardiovascular disease, education and hearing aid use. To analyze the association between hearing and β-amyloid/tau, linear regression was used and adjusted for potentially confounding covariates. Our data showed that the mean age was 67.1 ± 2.9 years. After adjusted for all the covariates, SUVR of β-amyloid showed an increase of 0.028 [95% confidence interval (CI) 0.004–0.061; P = 0.026], while that of tau exhibited an increase of 0.026 (95% CI 0.003–0.056; P = 0.033) per mean pure-tone increase by 10 dB (worsening). Likewise, per mean word-recognition score increase by 10%, the SUVR of β-amyloid showed an increase of 0.060 (95% CI 0.008–0.113; P = 0.023), while that of tau exhibited an increase of 0.059 (95% CI 0.009–0.111; P = 0.031). Taken together, our data demonstrates that hearing worsening was related to the increased burdens of β-amyloid as well as tau detected by PET, which were the AD pathological markers.
The impact of alternative energy technology investment on environment and food security in northern Ethiopia
Authors: Tofu Daniel Assefa , Wolka Kebede , Woldeamanuel Teshale 
Published: June 2022

AbstractEnergy is a key factor in the economic development. Currently, however, millions of people across the world suffer from energy poverty, having little or no access to energy for cooking, lighting, heating, cooling, or using information and communication technologies. Objective of this study was to investigate the domestic energy sources for households and the impact of biomass use as a source of energy on the environment and food insecurity in the drought-affected northern highlands of Ethiopia. A total of 398 household heads were interviewed using a structured questionnaire, whereas 16 focus group discussions and 12 key informant interviews were conducted. Descriptive data analysis techniques were used to analyze quantitative data while content analysis methods were used to analyze qualitative data. The use of traditional biomass fuels such as firewood, charcoal, crop residue, animal dung, and biomass residue that can be combusted were prevalent in the area, which aggravated the degradation of agricultural lands. As commented by the majority of respondents, the move towards the adoption of modern energy sources was not common due to finance (98%), access (97%), durability (97%) and lack of awareness (93%). The findings showed that land degradation has been severe to the extent that no grain yield can be collected from crop production. As a result, people were exposed to both chronic and transitory food insecurity, and hence the majority of people make their living on food aid. In food-insecure areas, relying on biomass energy could increase land degradation or retard the speed of land restoration, which adversely affects agricultural production and food security. Investing in alternative energy technologies can improve the environment, food security, and people’s health.
Utility of targeted next generation sequencing for inborn errors of immunity at a tertiary care centre in North India
Authors: Rawat Amit , Sharma Madhubala , Vignesh Pandiarajan , Jindal Ankur Kumar , Suri Deepti , Das Jhumki , Joshi Vibhu , Tyagi Rahul , Sharma Jyoti , Kaur Gurjit , Lau Yu-Lung , Imai Kohsuke , Nonoyama Shigeaki , Lenardo Michael , Singh Surjit 
Published: June 2022

AbstractInborn errors of immunity (IEI) are a heterogeneous group of monogenic disorders that include primary immunodeficiency’s and other disorders affecting different aspects of the immune system. Next-Generation Sequencing (NGS) is an essential tool to diagnose IEI. We report our 3-year experience in setting up facilities for NGS for diagnosis of IEI in Chandigarh, North India. We used a targeted, customized gene panel of 44 genes known to result in IEI. Variant analysis was done using Ion Reporter software. The in-house NGS has enabled us to offer genetic diagnoses to patients with IEI at minimal costs. Of 121 patients who were included pathogenic variants were identified in 77 patients. These included patients with Chronic Granulomatous Disease, Severe Combined Immune Deficiency, leukocyte adhesion defect, X-linked agammaglobulinemia, Ataxia Telangiectasia, Hyper-IgE syndrome, Wiskott Aldrich syndrome, Mendelian susceptibility to mycobacterial diseases, Hyper-IgM syndrome, autoimmune lymphoproliferative syndrome, and GATA-2 deficiency. This manuscript discusses the challenges encountered while setting up and running targeted NGS for IEI in our unit. Genetic diagnosis has helped our patients with IEI in genetic counselling, prenatal diagnosis, and accessing appropriate therapeutic options.
Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings
Authors: Rocha Jaqueline , Henriques Isabel , Gomila Margarita , Manaia Célia M. 
Published: June 2022

AbstractThe Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans’ opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola, n = 6; and K. quasipneumoniae, n = 7), of clinical (n = 78) and environmental (n = 61) origin from 21 countries were accessed from the GenBank. These genomes were compared based on phylogeny, pangenome and selected clinically relevant traits. Phylogenetic analysis based on 2704 genes of the core genome showed close relatedness between clinical and environmental strains, in agreement with the multi-locus sequence typing. Eight out of the 62 sequence types (STs) identified, included both clinical and environmental genomes (ST11, ST14, ST15, ST37, ST45, ST147, ST348, ST437). Pangenome-wide association studies did not evidence significant differences between clinical and environmental genomes. However, the genomes of clinical isolates presented significantly more exclusive genes related to antibiotic resistance/plasmids, while the environmental isolates yielded significantly higher allelic diversity of genes related with functions such as efflux or oxidative stress. The study suggests that K. pneumoniae can circulate among the natural environment and clinical settings, probably under distinct adaptation pressures.
A functional definition to distinguish ponds from lakes and wetlands
Authors: Richardson David C. , Holgerson Meredith A. , Farragher Matthew J. , Hoffman Kathryn K. , King Katelyn B. S. , Alfonso María B. , Andersen Mikkel R. , Cheruveil Kendra Spence , Coleman Kristen A. , Farruggia Mary Jade , Fernandez Rocio Luz , Hondula Kelly L. , López Moreira Mazacotte Gregorio A. , Paul Katherine , Peierls Benjamin L. , Rabaey Joseph S. , Sadro Steven , Sánchez María Laura , Smyth Robyn L. , Sweetman Jon N. 
Published: June 2022

AbstractPonds are often identified by their small size and shallow depths, but the lack of a universal evidence-based definition hampers science and weakens legal protection. Here, we compile existing pond definitions, compare ecosystem metrics (e.g., metabolism, nutrient concentrations, and gas fluxes) among ponds, wetlands, and lakes, and propose an evidence-based pond definition. Compiled definitions often mentioned surface area and depth, but were largely qualitative and variable. Government legislation rarely defined ponds, despite commonly using the term. Ponds, as defined in published studies, varied in origin and hydroperiod and were often distinct from lakes and wetlands in water chemistry. We also compared how ecosystem metrics related to three variables often seen in waterbody definitions: waterbody size, maximum depth, and emergent vegetation cover. Most ecosystem metrics (e.g., water chemistry, gas fluxes, and metabolism) exhibited nonlinear relationships with these variables, with average threshold changes at 3.7 ± 1.8 ha (median: 1.5 ha) in surface area, 5.8 ± 2.5 m (median: 5.2 m) in depth, and 13.4 ± 6.3% (median: 8.2%) emergent vegetation cover. We use this evidence and prior definitions to define ponds as waterbodies that are small (< 5 ha), shallow (< 5 m), with < 30% emergent vegetation and we highlight areas for further study near these boundaries. This definition will inform the science, policy, and management of globally abundant and ecologically significant pond ecosystems.
A comparison of Chinese multicenter breast cancer database and SEER database
Authors: Niu Yingjie , Zhang Fan , Chen Dong , Ye Guolin , Li Yong , Zha Yong , Chen Wenlin , Liu Dequan , Liao Xiaoming , Huang Qinghua , Tang Wei , Cai Gengxi , Guo Rong , Li Hongyang , Tang Shicong 
Published: June 2022

AbstractThere are different characteristics of BC in developing countries and developed countries. We intended to study the factors which influence the survival and prognosis of BC between southern China and the United States. (a) To study the two groups BC patients in southern China from 2001 to 2016 and SEER database from 1975 to 2016. (b) To register, collect and analyze the clinicopathological features and treatment information. Our study found that there are significant differences in tumor size, positive lymph node status and KI-67 between southern China and SEER cohort (P < 0.000). The positive lymph node status may be one of the causes of difference of morbidity and mortality of BC patients in China. Furthermore, the differences in treatment methods may also account for the differences between China and seer databases.
Rice straw structure changes following green pretreatment with petha wastewater for economically viable bioethanol production
Authors: Kumari Dolly , Singh Radhika 
Published: June 2022

AbstractEnergy efficient and environment friendly pretreatment processes for the production of biofuel have remained elusive and the research is further compounded by the high cost of processing lignocellulosic biomass—an essential factor for producing sustainable biofuels. In the last few decades, a number of pretreatment methods have been proposed, specifically chemical pretreatments but are either expensive or harmful to the environment. To address this urgent need, we propose a green pretreatment method that utilises the highly alkaline by-product, petha wastewater to pretreat the lignocellulosic waste rice straw (RS). The effectiveness of the pretreatment was analysed by monitoring both enhanced cellulose content and reducing sugar yield along with removal of hemicellulose and lignin. We found that PWW pretreatment yielded five times more reducing sugar than native RS with 10.12% increment in cellulose content. SEM and EDX studies further revealed that our process enhanced surface roughness and carbon content (from 32.19% increased to 41.59% and 41.66% for A and D, respectively) along with reduction in silica content (from 8.68% in RS to 4.30% and 7.72% for A and D, respectively). XRD and FTIR analyses indicate crystallinity index (CI) and alteration in lignocellulosic structure of RS, respectively. Decrease in CI was about 43.4% in A whereas only 4.5% in D as compared to native RS (CI 54.55%). Thereby we found PWW to be better substitute of an alkali for pretreatment of RS with negligible environmental impacts.
Single-scan volumetric imaging throughout thick tissue specimens by one-touch installable light-needle creating device
Authors: Chang Ching-Pu , Otomo Kohei , Kozawa Yuichi , Ishii Hirokazu , Yamasaki Miwako , Watanabe Masahiko , Sato Shunichi , Enoki Ryosuke , Nemoto Tomomi 
Published: June 2022

AbstractBiological tissues and their networks frequently change dynamically across large volumes. Understanding network operations requires monitoring their activities in three dimensions (3D) with single-cell resolution. Several researchers have proposed various volumetric imaging technologies. However, most technologies require large-scale and complicated optical setups, as well as deep expertise for microscopic technologies, resulting in a high threshold for biologists. In this study, we propose an easy-to-use light-needle creating device for conventional two-photon microscopy systems. By only installing the device in one position for a filter cube that conventional fluorescent microscopes have, single scanning of the excitation laser light beam excited fluorophores throughout over 200 μm thickness specimens simultaneously. Furthermore, the developed microscopy system successfully demonstrated single-scan visualization of the 3D structure of transparent YFP-expressing brain slices. Finally, in acute mouse cortical slices with a thickness of approximately 250 μm, we detected calcium activities with 7.5 Hz temporal resolution in the neuronal population.
Malleability of time through progress bars and throbbers
Authors: Ziat Mounia , Saoud Wafa , Prychitko Sonja , Servos Philip , Grondin Simon 
Published: June 2022

AbstractCompared to a stationary pattern, a moving pattern dilates the perception of time. However, when it comes to comparing only moving stimulus, the exact dilation effects are less clear. The time dilation may be attributed to either speed of motion, temporal and spatial frequency, stimulus complexity, or the number of changes in the stimulus pattern. In the present study, we used progress bars and throbbers for inducing impressions of fast and slow “apparent” motions while the speed of motion and distance covered was actually equivalent across all conditions. The results indicate that higher number of steps produced the impression of a faster progression leading to an underestimation of time, whereas a progression in large fewer steps, produced slower apparent progression, creating the illusion of dilated time. We suggest that the perception of time depends on the nature of the stimulus rather than the speed of motion or the distance covered by the stimulus.