bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic analysis of the highly complex OPN1LW/OPN1MW gene cluster using long-read sequencing and MLPA
Authors: Haer-Wigman Lonneke , den Ouden Amber , van Genderen Maria M. , Kroes Hester Y. , Verheij Joke , Smailhodzic Dzenita , Hoekstra Attje S. , Vijzelaar Raymon , Blom Jan , Derks Ronny , Tjon-Pon-Fong Menno , Yntema Helger G. , Nelen Marcel R. , Vissers Lisenka E.L.M. , Lugtenberg Dorien , Neveling Kornelia 
Published: November 2022

AbstractPathogenic variants in the OPN1LW/OPN1MW gene cluster are causal for a range of mild to severe visual impairments with color deficiencies. The widely utilized short-read next-generation sequencing (NGS) is inappropriate for the analysis of the OPN1LW/OPN1MW gene cluster and many patients with pathogenic variants stay underdiagnosed. A diagnostic genetic assay was developed for the OPN1LW/OPN1MW gene cluster, consisting of copy number analysis via multiplex ligation-dependent probe amplification and sequence analysis via long-read circular consensus sequencing. Performance was determined on 50 clinical samples referred for genetic confirmation of the clinical diagnosis (n = 43) or carrier status analysis (n = 7). A broad range of pathogenic haplotypes were detected, including deletions, hybrid genes, single variants and combinations of variants. The developed genetic assay for the OPN1LW/OPN1MW gene cluster is a diagnostic test that can detect both structural and nucleotide variants with a straightforward analysis, improving diagnostic care of patients with visual impairment.
Sentinel2GlobalLULC: A Sentinel-2 RGB image tile dataset for global land use/cover mapping with deep learning
Authors: Benhammou Yassir , Alcaraz-Segura Domingo , Guirado Emilio , Khaldi Rohaifa , Achchab Boujemâa , Herrera Francisco , Tabik Siham 
Published: November 2022

AbstractLand-Use and Land-Cover (LULC) mapping is relevant for many applications, from Earth system and climate modelling to territorial and urban planning. Global LULC products are continuously developing as remote sensing data and methods grow. However, there still exists low consistency among LULC products due to low accuracy in some regions and LULC types. Here, we introduce Sentinel2GlobalLULC, a Sentinel-2 RGB image dataset, built from the spatial-temporal consensus of up to 15 global LULC maps available in Google Earth Engine. Sentinel2GlobalLULC v2.1 contains 194877 single-class RGB image tiles organized into 29 LULC classes. Each image is a 224 × 224 pixels tile at 10 × 10 m resolution built as a cloud-free composite from Sentinel-2 images acquired between June 2015 and October 2020. Metadata includes a unique LULC annotation per image, together with level of consensus, reverse geo-referencing, global human modification index, and number of dates used in the composite. Sentinel2GlobalLULC is designed for training deep learning models aiming to build precise and robust global or regional LULC maps.
Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil
Authors: Bianco Kayo , de Farias Beatriz Oliveira , Gonçalves-Brito Andressa Silva , Alves do Nascimento Ana Paula , Magaldi Mariana , Montenegro Kaylanne , Flores Claudia , Oliveira Samara , Monteiro Mychelle Alves , Spisso Bernardete Ferraz , Pereira Mararlene Ulberg , Ferreira Rosana Gomes , Albano Rodolpho Mattos , Cardoso Alexander Machado , Clementino Maysa Mandetta 
Published: November 2022

AbstractAntibiotic resistance genes (ARGs) are widespread in the environment due to the overuse of antibiotics and other pollutants, posing a threat to human and animal health. In this study, we evaluated antimicrobial residues, bacterial diversity and ARGs in two important watersheds, Guandu and São João, that supply drinking water to Rio de Janeiro city, Brazil. In addition, tap water samples were collected from three different cities in Rio de Janeiro State, including the metropolitan area of Rio de Janeiro city. Clarithromycin, sulfamethoxazole and azithromycin were found in untreated water and drinking water in all samples. A greater abundance of Proteobacteria was observed in Guandu and São João watersheds, with most of the sequences belonging to the Gammaproteobacteria class. A plasmidome-focused metagenomics approach revealed 4881 (Guandu), 3705 (São João) and 3385 (drinking water) ARGs mainly associated with efflux systems. The genes encoding metallo-β-lactamase enzymes (blaAIM, blaGIM, blaIMP, and blaVIM) were detected in the two watersheds and in drinking water samples. Moreover, we demonstrated the presence of the colistin resistance genes mcr-3 and mcr-4 (both watersheds) and mcr-9 (drinking water and Guandu) for the first time in Brazil. Our data emphasize the importance of introducing measures to reduce the disposal of antibiotics and other pollutants capable of promoting the occurrence and spread of the microbial resistome on aquatic environments and predicting possible negative impacts on human health.
Cerebellum-dependent associative learning is not impaired in a mouse model of neurofibromatosis type 1
Authors: Ottenhoff M. J. , Dijkhuizen S. , Ypelaar A. C. H. , de Oude N. L. , Koekkoek S. K. E. , Wang S. S.-H. , De Zeeuw C. I. , Elgersma Y. , Boele H. J. 
Published: November 2022

AbstractIndividuals with Neurofibromatosis type 1 (NF1) experience a high degree of motor problems. The cerebellum plays a pivotal role in motor functioning and the NF1 gene is highly expressed in cerebellar Purkinje cells. However, it is not well understood to what extent NF1 affects cerebellar functioning and how this relates to NF1 motor functioning. Therefore, we subjected global Nf1+/− mice to a cerebellum-dependent associative learning task, called Pavlovian eyeblink conditioning. Additionally, we assessed general motor function and muscle strength in Nf1+/− mice. To our surprise, we found that Nf1+/− mice showed a moderately increased learning rate of conditioned eyeblink responses, as well as improved accuracy in the adaptive timing of the eyeblink responses. Locomotion, balance, general motor function, and muscle strength were not affected in Nf1+/− mice. Together, our results support the view that cerebellar function in Nf1+/− mice is unimpaired.
Differentiation of patients with mild cognitive impairment and healthy controls based on computer assisted hand movement analysis: a proof-of-concept study
Authors: Horvath Andras Attila , Berente Dalida Borbala , Vertes Balazs , Farkas David , Csukly Gabor , Werber Tom , Zsuffa Janos Andras , Kiss Mate , Kamondi Anita 
Published: November 2022

AbstractMild cognitive impairment (MCI) is the prodromal phase of dementia, and it is highly underdiagnosed in the community. We aimed to develop an automated, rapid (< 5 min), electronic screening tool for the recognition of MCI based on hand movement analysis. Sixty-eight individuals participated in our study, 46 healthy controls and 22 patients with clinically defined MCI. All participants underwent a detailed medical assessment including neuropsychology and brain MRI. Significant differences were found between controls and MCI groups in mouse movement characteristics. Patients showed higher level of entropy for both the left (F = 5.24; p = 0.001) and the right hand (F = 8.46; p < 0.001). Longer time was required in MCI to perform the fine motor task (p < 0.005). Furthermore, we also found significant correlations between mouse movement parameters and neuropsychological test scores. Correlation was the strongest between motor parameters and Clinical Dementia Rating scale (CDR) score (average r: − 0.36, all p’s < 0.001). Importantly, motor parameters were not influenced by age, gender, or anxiety effect (all p’s > 0.05). Our study draws attention to the utility of hand movement analysis, especially to the estimation of entropy in the early recognition of MCI. It also suggests that our system might provide a promising tool for the cognitive screening of large populations.
Single-dose pharmacokinetics, safety, and tolerability of the dual endothelin receptor antagonist aprocitentan in subjects with moderate hepatic impairment
Authors: Fontes Magda S. C. , Dingemanse Jasper , Halabi Atef , Tomaszewska-Kiecana Monika , Sidharta Patricia N. 
Published: November 2022

AbstractThe effect of moderate hepatic impairment on the pharmacokinetics (PK), safety, and tolerability of the dual endothelin receptor antagonist aprocitentan was clinically investigated as 25% of aprocitentan is cleared through the liver. Aprocitentan is in clinical development for the treatment of resistant hypertension. This was an open-label, Phase 1 study. Subjects were recruited in two groups (i.e., moderate hepatic impairment (Child–Pugh B; n = 8) and matched healthy subjects (n = 9) and received a single oral dose of 25 mg aprocitentan. Thereafter, they were observed for 14 days. Due to personal reasons one healthy subject discontinued the study. The PK of aprocitentan were similar between subjects with moderate hepatic impairment and healthy subjects, with maximum plasma concentrations (Cmax) reached at 4.0 h. There was no difference in Cmax, indicated by the geometric means ratio (90% confidence interval) of 1.03 (0.86–1.24). There was a lower apparent clearance, a similar apparent volume of distribution, a longer terminal half-life (56.4 h vs 48.3 h in healthy subjects), and an increase in area under the curve from zero to infinity of 23% in moderate hepatically impaired subjects compared to healthy subjects. There were no differences observed in plasma protein binding (range 98.7–99.0%). Aprocitentan was well tolerated, and headache was the only adverse event reported by one subject. In conclusion, there were no clinically relevant differences in PK between subjects with moderate hepatic impairment and healthy subjects. Based on these results, aprocitentan can be administered in subjects with mild and moderate hepatic impairment and dose adjustment is not required.Clinical Trial Registration ClinicalTrials.gov NCT04252495.
Mechanical investigations supported by DIC of structural components intended for operation
Authors: Szymczak T. , Brodecki A. , Kowalewski Z. L. , Rudnik D. 
Published: November 2022

AbstractThe paper deals with experimental attempts for determination of the mechanical resistance of various components subjected to static loading by analysis of displacement values in a 3D coordinate system using a non-contact testing method. The problem is studied on the basis of results from tests of the wheelchair and SUV’s wheel, supported by means of a PONTOS 5M Digital Image Correlation (DIC) system enabling determination of the patterns deflection at discretised facet measuring zones of an element. The objects tested extend a knowledge on the components’ behaviour under static loading within their loading capacity. Data collected in the experiments are expressed by variations of the resultant vector of deflection in the 3D coordinate system and images under loading and unloading stages as well. The results enabled to indicate the weakest zone in the wheelchair and to express an influence of the foot tire on the rim edge, giving necessary knowledge on the mechanical resistance of tested components. In case of the wheelchair a rear side and axle represent the weakest regions, while for the wheel a rim edge is the most loading sensitive region on the tire guard with respect to safety of the operational process. All data captured by DIC system as a function of time can be directly used for modelling and improving a suitability of the selected components since they can be employed as the limit levels during determination of safety factor. The experimental approach applied to the SUV wheel investigation can be also used as a procedure for wheels of other type vehicles tested either in laboratories of research institutions or technical universities.
Prey localization in spider orb webs using modal vibration analysis
Authors: Lott Martin , Poggetto Vinicius F. Dal , Greco Gabriele , Pugno Nicola M. , Bosia Federico 
Published: November 2022

AbstractSpider webs are finely tuned multifunctional structures, widely studied for their prey capture functionalities such as impact strength and stickiness. However, they are also sophisticated sensing tools that enable the spider to precisely determine the location of impact and capture the prey before it escapes. In this paper, we suggest a new mechanism for this detection process, based on potential modal analysis capabilities of the spider, using its legs as distinct distributed point sensors. To do this, we consider a numerical model of the web structure, including asymmetry in the design, prestress, and geometrical nonlinearity effects. We show how vibration signals deriving from impacts can be decomposed into web eigenmode components, through which the spider can efficiently trace the source location. Based on this numerical analysis, we discuss the role of the web structure, asymmetry, and prestress in the imaging mechanism, confirming the role of the latter in tuning the web response to achieve an efficient prey detection instrument. The results can be relevant for efficient distributed impact sensing applications.
Understanding action concepts from videos and brain activity through subjects’ consensus
Authors: Cavazza Jacopo , Ahmed Waqar , Volpi Riccardo , Morerio Pietro , Bossi Francesco , Willemse Cesco , Wykowska Agnieszka , Murino Vittorio 
Published: November 2022

AbstractIn this paper, we investigate brain activity associated with complex visual tasks, showing that electroencephalography (EEG) data can help computer vision in reliably recognizing actions from video footage that is used to stimulate human observers. Notably, we consider not only typical “explicit” video action benchmarks, but also more complex data sequences in which action concepts are only referred to, implicitly. To this end, we consider a challenging action recognition benchmark dataset—Moments in Time—whose video sequences do not explicitly visualize actions, but only implicitly refer to them (e.g., fireworks in the sky as an extreme example of “flying”). We employ such videos as stimuli and involve a large sample of subjects to collect a high-definition, multi-modal EEG and video data, designed for understanding action concepts. We discover an agreement among brain activities of different subjects stimulated by the same video footage. We name it as subjects consensus, and we design a computational pipeline to transfer knowledge from EEG to video, sharply boosting the recognition performance.
WARS1, TYMP and GBP1 display a distinctive microcirculation pattern by immunohistochemistry during antibody-mediated rejection in kidney transplantation
Authors: Chauveau Bertrand , Garric Antoine , Di Tommaso Sylvaine , Raymond Anne-Aurélie , Visentin Jonathan , Vermorel Agathe , Dugot-Senant Nathalie , Déchanet-Merville Julie , Duong Van Huyen Jean-Paul , Rabant Marion , Couzi Lionel , Saltel Frédéric , Merville Pierre 
Published: November 2022

AbstractAntibody-mediated rejection (ABMR) is the leading cause of allograft failure in kidney transplantation. Defined by the Banff classification, its gold standard diagnosis remains a challenge, with limited inter-observer reproducibility of the histological scores and efficient immunomarker availability. We performed an immunohistochemical analysis of 3 interferon-related proteins, WARS1, TYMP and GBP1 in a cohort of kidney allograft biopsies including 17 ABMR cases and 37 other common graft injuries. Slides were interpreted, for an ABMR diagnosis, by four blinded nephropathologists and by a deep learning framework using convolutional neural networks. Pathologists identified a distinctive microcirculation staining pattern in ABMR with all three antibodies, displaying promising diagnostic performances and a substantial reproducibility. The deep learning analysis supported the microcirculation staining pattern and achieved similar diagnostic performance from internal validation, with a mean area under the receiver operating characteristic curve of 0.89 (± 0.02) for WARS1, 0.80 (± 0.04) for TYMP and 0.89 (± 0.04) for GBP1. The glomerulitis and peritubular capillaritis scores, the hallmarks of histological ABMR, were the most highly correlated Banff scores with the deep learning output, whatever the C4d status. These novel immunomarkers combined with a CNN framework could help mitigate current challenges in ABMR diagnosis and should be assessed in larger cohorts.
Behavioral signatures of Y-like neuronal responses in human vision
Authors: Ramirez Ana L. , Thompson Lowell W. , Rosenberg Ari , Baker Curtis L. 
Published: November 2022

AbstractRetinal ganglion cells initiating the magnocellular/Y-cell visual pathways respond nonlinearly to high spatial frequencies (SFs) and temporal frequencies (TFs). This nonlinearity is implicated in the processing of contrast modulation (CM) stimuli in cats and monkeys, but its contribution to human visual perception is not well understood. Here, we evaluate human psychophysical performance for CM stimuli, consisting of a high SF grating carrier whose contrast is modulated by a low SF sinewave envelope. Subjects reported the direction of motion of CM envelopes or luminance modulation (LM) gratings at different eccentricities. The performance on SF (for LMs) or carrier SF (for CMs) was measured for different TFs (LMs) or carrier TFs (CMs). The best performance for LMs was at lower TFs and SFs, decreasing systematically with eccentricity. However, performance with CMs was bandpass with carrier SF, largely independent of carrier TF, and at the highest carrier TF (20 Hz) decreased minimally with eccentricity. Since the nonlinear subunits of Y-cells respond better at higher TFs compared to the linear response components and respond best at higher SFs that are relatively independent of eccentricity, these results suggest that behavioral tasks employing CM stimuli might reveal nonlinear contributions of retinal Y-like cells to human perception.
Bioinformatics approach for the construction of multiple epitope vaccine against omicron variant of SARS-CoV-2
Authors: Zaib Sumera , Akram Fatima , Liaqat Syed Talha , Altaf Muhammad Zain , Khan Imtiaz , Dera Ayed A. , Uddin Jalal , Khan Ajmal , Al-Harrasi Ahmed 
Published: November 2022

AbstractThe World Health Organization categorized SARS-CoV-2 as a variant of concern, having numerous mutations in spike protein, which have been found to evade the effect of antibodies stimulated by the COVID-19 vaccine. The susceptibility to omicron variant by immunization-induced antibodies are direly required for risk evaluation. To avoid the risk of arising viral illness, the construction of a specific vaccine that triggers the production of targeted antibodies to combat infection remains highly imperative. The aim of the present study is to develop a particular vaccine exploiting bioinformatics approaches which can target B- and T-cells epitopes. Through this approach, novel epitopes of the S protein-SARS-CoV-2 were predicted for the development of a multiple epitope vaccine. Multiple epitopes were selected on the basis of toxicity, immunogenicity and antigenicity, and vaccine subunit was constructed having potential immunogenic properties. The epitopes were linked with 3 types of linker EAAAK, AAY and GPGPG for vaccine construction. Subsequently, vaccine structure was docked with the receptor and cloned in a pET-28a (+) vector. The constructed vaccine was ligated in pET-28a (+) vector in E. coli using the SnapGene tool for the expression study and a good immune response was observed. Several computational tools were used to predict and analyze the vaccine constructed by using spike protein sequence of omicrons. The current study identified a Multi-Epitope Vaccine (MEV) as a significant vaccine candidate that could potentially help the global world to combat SARS-CoV-2 infections.
Numerical investigation on the aerodynamic efficiency of bio-inspired corrugated and cambered airfoils in ground effect
Authors: Abdizadeh G. R. , Farokhinejad M. , Ghasemloo S. 
Published: November 2022

AbstractThis research numerically investigates the flapping motion effect on the flow around two subsonic airfoils near a ground wall. Thus far, the aerodynamic efficiency of the dragonfly-inspired flapping airfoil has not been challenged by an asymmetric cambered airfoil considering the ground effect phenomenon, especially in the MAV flight range. The analysis is carried out on the basis of an unsteady Reynolds-averaged Navier-stokes (URANS) simulation, whereby the Transition SST turbulence model simulates the flow characteristics. Dragonfly-inspired and NACA4412 airfoils are selected in this research to assess the geometry effect on aerodynamic efficiency. Moreover, the impacts of Reynolds number (Re), Strouhal number (St), and average ground clearance of the flapping airfoil are investigated. The results indicate a direct relationship between the airfoil’s aerodynamic performance ($$C_l$$Cl/$$C_d$$Cd) and the ground effect. The$$C_l$$Cl/$$C_d$$Cdincreases by reducing the airfoil and ground distance, especially at$$h_{0}=c$$h0=c. At$$Re=5\times 10^4$$Re=5×104, by increasing the St from 0.2 to 0.6, the values of$$C_l$$Cl/$$C_d$$Cddecrease from 10.34 to 2.1 and 3.22 to 1.8 for NACA4412 and dragonfly airfoils, respectively. As a result, the$$C_l$$Cl/$$C_d$$Cdof the NACA4412 airfoil is better than that of the dragonfly airfoil, especially at low oscillation frequency. The efficiency difference between the two airfoils atSt=0.6 is approximately 14%, indicating that the$$C_l$$Cl/$$C_d$$Cddifference decreases substantially with increasing frequency. For$$Re=5\times 10^3$$Re=5×103, the results show the dragonfly airfoil to have better$$C_l$$Cl/$$C_d$$Cdin all frequencies than the NACA4412 airfoil.
Frequency response characteristics and failure model of single-layered thin plate rock mass under dynamic loading
Authors: Li Feng , Wang Chenchen , Sun Runchuan , Xiang Guangyou , Ren Baorui , Zhang Zhao 
Published: November 2022

AbstractIn underground engineering, disturbance of dynamic load can change layered rock mass stress state and induce accidents. Traditional elastic mechanics can’t effectively solve the complex deformation problem. However, Hamiltonian mechanics system can overcome this problem. Dual variables are introduced in symplectic space to solve the deflection equations of single-layered thin plate rock mass. Comparing vibration parameters, it’s found the 1st, 5th and 6th order are effective vibration modes. The resonance characteristics of thin plate are obtained with three dynamic loads. It’s found the thin plate is most likely to resonate and damage due to the smallest resonance frequency interval and the largest vibration amplitude by impact wave and rectangular wave respectively. Then, the vibration mode of multi-layered rock mass is analyzed through Multiple Reference Impact Testing. The failure of fine sandstone is caused by the resonance of effective vibration modes by hammer excitation. Finally, the failure mechanism of thin plate is obtained by the failure theory and LS-DYNA. It’s found the four sides and corners suffer tensile shear failure and shear failure respectively. When tensile failure occurs in central, the main crack and secondary crack propagate along long axis and short axis to form “O-十” failure mode.