bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals
Authors: Kustin Talia , Harel Noam , Finkel Uriah , Perchik Shay , Harari Sheri , Tahor Maayan , Caspi Itamar , Levy Rachel , Leshchinsky Michael , Ken Dror Shifra , Bergerzon Galit , Gadban Hala , Gadban Faten , Eliassian Eti , Shimron Orit , Saleh Loulou , Ben-Zvi Haim , Keren Taraday Elena , Amichay Doron , Ben-Dor Anat , Sagas Dana , Strauss Merav , Shemer Avni Yonat , Huppert Amit , Kepten Eldad , Balicer Ran D. , Netzer Doron , Ben-Shachar Shay , Stern Adi 
Published: June 2021

AbstractThe BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vaccine sera in laboratory assays. We performed a matched cohort study to examine the distribution of VOCs in infections of BNT162b2 mRNA vaccinees from Clalit Health Services (Israel) using viral genomic sequencing, and hypothesized that if vaccine effectiveness against a VOC is reduced, its proportion among breakthrough cases would be higher than in unvaccinated controls. Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.
Statistical and sequence learning lead to persistent memory in children after a one-year offline period
Authors: Tóth-Fáber Eszter , Janacsek Karolina , Németh Dezső 
Published: June 2021

AbstractExtraction of environmental patterns underlies human learning throughout the lifespan and plays a crucial role not only in cognitive but also perceptual, motor, and social skills. At least two types of regularities contribute to acquiring skills: (1) statistical, probability-based regularities, and (2) serial order-based regularities. Memory performance of probability-based and/or serial order-based regularities over short periods (from minutes to weeks) has been widely investigated across the lifespan. However, long-term (months or year-long) memory performance of such knowledge has received relatively less attention and has not been assessed in children yet. Here, we aimed to test the long-term memory performance of probability-based and serial order-based regularities over a 1-year offline period in neurotypical children between the age of 9 and 15. Participants performed a visuomotor four-choice reaction time task designed to measure the acquisition of probability-based and serial order-based regularities simultaneously. Short-term consolidation effects were controlled by retesting their performance after a 5-h delay. They were then retested on the same task 1 year later without any practice between the sessions. Participants successfully acquired both probability-based and serial order-based regularities and retained both types of knowledge over the 1-year period. The successful retention was independent of age. Our study demonstrates that the representation of probability-based and serial order-based regularities remains stable over a long period of time. These findings offer indirect evidence for the developmental invariance model of skill consolidation.
Cyclotide host-defense tailored for species and environments in violets from the Canary Islands
Authors: Slazak Blazej , Kaltenböck Klara , Steffen Karin , Rogala Martyna , Rodríguez-Rodríguez Priscila , Nilsson Anna , Shariatgorji Reza , Andrén Per E. , Göransson Ulf 
Published: June 2021

AbstractCyclotides are cyclic peptides produced by plants. Due to their insecticidal properties, they are thought to be involved in host defense. Violets produce complex mixtures of cyclotides, that are characteristic for each species and variable in different environments. Herein, we utilized mass spectrometry (LC–MS, MALDI-MS), transcriptomics and biological assays to investigate the diversity, differences in cyclotide expression based on species and different environment, and antimicrobial activity of cyclotides found in violets from the Canary Islands. A wide range of different habitats can be found on these islands, from subtropical forests to dry volcano peaks at high altitudes. The islands are inhabited by the endemic Viola palmensis, V. cheiranthifolia, V. anagae and the common V. odorata. The number of cyclotides produced by a given species varied in plants from different environments. The highest diversity was noted in V. anagae which resides in subtropical forest and the lowest in V. cheiranthifolia from the Teide volcano. Transcriptome sequencing and LC–MS were used to identify 23 cyclotide sequences from V. anagae. Cyclotide extracts exhibited antifungal activities with the lowest minimal inhibitory concentrations noted for V. anagae (15.62 μg/ml against Fusarium culmorum). The analysis of the relative abundance of 30 selected cyclotides revealed patterns characteristic to both species and populations, which can be the result of genetic variability or environmental conditions in different habitats. The current study exemplifies how plants tailor their host defense peptides for various habitats, and the usefulness of cyclotides as markers for chemosystematics.
The joint involvement in adult onset Still's disease is characterised by a peculiar magnetic resonance imaging and a specific transcriptomic profile
Authors: Ruscitti Piero , Barile Antonio , Berardicurti Onorina , Iafrate Sonia , Di Benedetto Paola , Vitale Antonio , Caso Francesco , Costa Luisa , Bruno Federico , Ursini Francesco , Navarini Luca , Sensini Federica , Scarpa Raffaele , Frediani Bruno , Cantarini Luca , Masciocchi Carlo , Giacomelli Roberto , Cipriani Paola 
Published: June 2021

AbstractAdult onset Still's disease (AOSD) is a rare systemic autoinflammatory disease, characterised by fever, arthritis, and skin rash, and joint involvement is one of its clinical manifestations. The aims of this work were to assess joint involvement, to describe main patterns of involvement, and associated clinical characteristics. In this work, we aimed at assessing the joint involvement in AOSD by using MRI, to describe main patterns and associated clinical characteristics. In addition, we aimed at assessing the global transcriptomic profile of synovial tissues in AOSD to elucidate possible pathogenic pathways involved. We also evaluated the global transcriptomic profile of synovial tissues to elucidate possible pathogenic pathways involved in the disease. Thus, AOSD patients, who underwent to MRI exam on joints, were assessed to describe patterns of joint involvement and associated clinical characteristics. Some synovial tissues were collected for RNA-sequencing purposes. The most common MRI finding was the presence of synovitis on 60.5%, mainly in peripheral affected joints, with low to intermediate signal intensity on T1-weighted images and intermediate to high signal intensity on T2-fat-saturated weighted and STIR images. Bone oedema and MRI-bone erosions were reported on 34.9% and 25.6% MRI exams, respectively. Patients with MRI-bone erosions showed a higher prevalence of splenomegaly, a more frequent chronic disease course, lower levels of erythrocyte sedimentation rate, and ferritin. In AOSD synovial tissues, a hyper-expression of interleukin (IL)-1, IL-6, and TNF pathways was shown together with ferritin genes. In conclusion, in AOSD patients, the most common MRI-finding was the presence of synovitis, characterised by intermediate to high signal intensity on T2-fat-saturated weighted and STIR images. MRI-bone erosions and bone oedema were also observed. In AOSD synovial tissues, IL-1, IL-6, and TNF pathways together with ferritin genes resulted to be hyper-expressed.
Improved dynamic imaging of multiphase flow by constrained tomographic reconstruction
Authors: Rasmussen Peter Winkel , Sørensen Henning Osholm , Bruns Stefan , Dahl Anders Bjorholm , Christensen Anders Nymark 
Published: June 2021

AbstractDynamic tomography has become an important technique to study fluid flow processes in porous media. The use of laboratory X-ray tomography instruments is, however, limited by their low X-ray brilliance. The prolonged exposure times, in turn, greatly limit temporal resolution. We have developed a tomographic reconstruction algorithm that maintains high image quality, despite reducing the exposure time and the number of projections significantly. Our approach, based on the Simultaneous Iterative Reconstruction Technique, mitigates the problem of few and noisy exposures by utilising a high-quality scan of the system before the dynamic process is started. We use the high-quality scan to initialise the first time step of the dynamic reconstruction. We further constrain regions of the dynamic reconstruction with a segmentation of the static system. We test the performance of the algorithm by reconstructing the dynamics of fluid separation in a multiphase system. The algorithm is compared quantitatively and qualitatively with several other reconstruction algorithms and we show that it can maintain high image quality using only a fraction of the normally required number of projections and with a substantially larger noise level. By robustly allowing fewer projections and shorter exposure, our algorithm enables the study of faster flow processes using laboratory tomography instrumentation but it can also be used to improve the reconstruction quality of dynamic synchrotron experiments.
Changes in the geometry of modern daily disposable soft contact lenses during wear
Authors: Mlyniuk Patryk , Stachura Joanna , Jiménez-Villar Alfonso , Grulkowski Ireneusz , Kaluzny Bartlomiej J. 
Published: June 2021

AbstractThe geometry of contact lenses can be altered by wear but determining the changes that occur in soft contact lenses (SCLs) is challenging. This study aimed to investigate the shape alterations of daily disposable SCLs after wear using swept-source optical coherence tomography (SS-OCT). Forty-five eyes with myopia of − 3.00 diopters (D) were enrolled. The participants wore three types of SCLs: hydrogel lens (nesofilcon A) and silicone hydrogel lenses (delefilcon A and stenfilcon A). The SCLs were scanned 3–6 min after lens removal. We found a significant decrease in the SCL anterior curvature: 0.24 ± 0.17 mm for nesofilcon A, 0.44 ± 0.21 mm for delefilcon A, and 0.53 ± 0.29 mm for stenfilcon A. The changes in the anterior curvature of SCLs correlated moderately with the mean corneal keratometry; Pearson’s correlation coefficients for nesofilcon A and delefilcon A were 0.57 and 0.52, respectively (P < 0.001). A statistically significant change in the total diameter was observed in SCL made of stenfilcon A (0.39 mm, P < 0.001). To conclude, the central radii of curvature decreased after a wearing period for all three types of daily disposable SCLs to imitate the anterior corneal surface, however, the changes in other geometrical parameters measured with SS-OCT were lens-specific.
Heat transfer intensification of nanomaterial with involve of swirl flow device concerning entropy generation
Authors: Shah Zahir , Jafaryar M. , Sheikholeslami M. , Ikramullah  , Kumam Poom 
Published: June 2021

AbstractThe thermal features of hybrid nano-powder turbulent motion through a pipe employing helical turbulator is numerically simulated via Finite Volume Method (FVM). The hybrid nanofluid (MWCNTs + Fe3O4 + H2O) is obtained by uniformly dispersing MWCNTs + Fe3O4 nanomaterials in H2O. The characteristics features of thermal energy transfer of hybrid nanofluid are investigated by varying the pitch ratio (P) of the helical turbulator and Reynolds number (Re) of the fluid. The outputs of the study are depicted in terms of contour plots of temperature, velocity, frictional irreversibility Sgen,f, and thermal irreversibility Sgen,th. The variation of Sgen,f, and Sgen,th with changing P and Re are also displayed by 3D plots. It is found that making the fluid more turbulent by increasing Re, the temperature of the fluid drops whereas the fluid velocity augments. The frictional irreversibility enhances, whereas the thermal irreversibility drops with the increasing turbulent motion. The decreasing P causes to drop the temperature of the higher turbulent fluid flow, while opposite effect is observed for smaller Re. The decreasing P causes to enhance the fluid mixing and thus augments the fluid velocity. Sgen,f and Sgen,th both augment with decreasing P. The comparison of current outputs with the older article shows an acceptable accuracy. The results of the present investigation will be useful in modelling of efficient thermal energy transfer systems.
A feasibility study of dual-task strategy training to improve gait performance in patients with Parkinson’s disease
Authors: Wollesen Bettina , Rudnik Silvan , Gulberti Alessandro , Cordes Thomas , Gerloff Christian , Poetter-Nerger Monika 
Published: June 2021

AbstractGait disorders in patients with Parkinson’s disease (PD) impact their mobility and self-dependence. Gait training and dual-task (DT)-training improve gait quality. This study aims to assess the feasibility of a specific, gradually intensified DT-training for PD patients with a special focus on gait performance under single task (ST) and DT conditions. Correlations to Freezing of Gait (FoG) were examined. 17 PD patients (70.1 ± 7.4 years, H&Y Stadium 2–3, FoG-Q 9.0 ± 5.5) participated in a four-week DT-training (1x/week, 60 min) with progressively increasing task difficulty and number of tasks. Gait performance (spatiotemporal parameters) was assessed during ST and DT conditions. The training improved DT gait performance, especially gait velocity + 0.11 m/s; (F(2,16) = 7.163; p = .0171; η2part = .309) and step length (+ 5.73 cm). Also, physical well-being and absolved walking distance improved significantly. Correlation analyses of the FoG score at baseline with relative change of gait metrics post-training revealed significant correlations with training-induced changes of step length and improvement of gait velocity. Overall, the developed DT-training was feasible and effective. Further studies should examine the long-term benefits and the optimal setting to achieve the highest impact. The study was registered in the DRKS (ID DRKS00018084, 23.1.20).
Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML
Authors: Modarres Parastoo , Mohamadi Farsani Farzaneh , Nekouie Amir Abas , Vallian Sadeq 
Published: June 2021

AbstractThe pathways and robust deregulated gene signatures involved in AML chemo-resistance are not fully understood. Multiple subgroups of AMLs which are under treatment of various regimens seem to have similar regulatory gene(s) or pathway(s) related to their chemo-resistance phenotype. In this study using gene set enrichment approach, deregulated genes and pathways associated with relapse after chemotherapy were investigated in AML samples. Five AML libraries compiled from GEO and ArrayExpress repositories were used to identify significantly differentially expressed genes between chemo-resistance and chemo-sensitive groups. Functional and pathway enrichment analysis of differentially expressed genes was performed to assess molecular mechanisms related to AML chemotherapeutic resistance. A total of 34 genes selected to be differentially expressed in the chemo-resistance compared to the chemo-sensitive group. Among the genes selected, c-Jun, AKT3, ARAP3, GABBR1, PELI2 and SORT1 are involved in neurotrophin, estrogen, cAMP and Toll-like receptor signaling pathways. All these pathways are located upstream and regulate JNK signaling pathway which functions as a key regulator of cellular apoptosis. Our expression data are in favor of suppression of JNK pathway, which could induce pro-apoptotic gene expression as well as down regulation of survival factors, introducing this pathway as a key regulator of drug-resistance development in AML.
Facile fabrication of antibacterial and antiviral perhydrolase-polydopamine composite coatings
Authors: Wang Li-Sheng , Xu Shirley , Gopal Sneha , Kim Eunsol , Kim Domyoung , Brier Matthew , Solanki Kusum , Dordick Jonathan S. 
Published: June 2021

AbstractIn situ generation of antibacterial and antiviral agents by harnessing the catalytic activity of enzymes on surfaces provides an effective eco-friendly approach for disinfection. The perhydrolase (AcT) from Mycobacterium smegmatis catalyzes the perhydrolysis of acetate esters to generate the potent disinfectant, peracetic acid (PAA). In the presence of AcT and its two substrates, propylene glycol diacetate and H2O2, sufficient and continuous PAA is generated over an extended time to kill a wide range of bacteria with the enzyme dissolved in aqueous buffer. For extended self-disinfection, however, active and stable AcT bound onto or incorporated into a surface coating is necessary. In the current study, an active, stable and reusable AcT-based coating was developed by incorporating AcT into a polydopamine (PDA) matrix in a single step, thereby forming a biocatalytic composite onto a variety of surfaces. The resulting AcT-PDA composite coatings on glass, metal and epoxy surfaces yielded up to 7-log reduction of Gram-positive and Gram-negative bacteria when in contact with the biocatalytic coating. This composite coating also possessed potent antiviral activity, and dramatically reduced the infectivity of a SARS-CoV-2 pseudovirus within minutes. The single-step approach enables rapid and facile fabrication of enzyme-based disinfectant composite coatings with high activity and stability, which enables reuse following surface washing. As a result, this enzyme-polymer composite technique may serve as a general strategy for preparing antibacterial and antiviral surfaces for applications in health care and common infrastructure safety, such as in schools, the workplace, transportation, etc.
Vaccination with BCGΔBCG1419c protects against pulmonary and extrapulmonary TB and is safer than BCG
Authors: Aceves-Sánchez Michel de Jesús , Flores-Valdez Mario Alberto , Pedroza-Roldán César , Creissen Elizabeth , Izzo Linda , Silva-Angulo Fabiola , Dawson Clinton , Izzo Angelo , Bielefeldt-Ohmann Helle , Segura-Cerda Cristian Alfredo , López-Romero Wendy , Bravo-Madrigal Jorge , Barrios-Payán Jorge Alberto , de la Cruz Miguel Ángel , Ares Miguel , Jorge-Espinoza María Guadalupe 
Published: June 2021

AbstractA single intradermal vaccination with an antibiotic-less version of BCGΔBCG1419c given to guinea pigs conferred a significant improvement in outcome following a low dose aerosol exposure to M. tuberculosis compared to that provided by a single dose of BCG Pasteur. BCGΔBCG1419c was more attenuated than BCG in murine macrophages, athymic, BALB/c, and C57BL/6 mice. In guinea pigs, BCGΔBCG1419c was at least as attenuated as BCG and induced similar dermal reactivity to that of BCG. Vaccination of guinea pigs with BCGΔBCG1419c resulted in increased anti-PPD IgG compared with those receiving BCG. Guinea pigs vaccinated with BCGΔBCG1419c showed a significant reduction of M. tuberculosis replication in lungs and spleens compared with BCG, as well as a significant reduction of pulmonary and extrapulmonary tuberculosis (TB) pathology measured using pathology scores recorded at necropsy. Evaluation of cytokines produced in lungs of infected guinea pigs showed that BCGΔBCG1419c significantly reduced TNF-α and IL-17 compared with BCG-vaccinated animals, with no changes in IL-10. This work demonstrates a significantly improved protection against pulmonary and extrapulmonary TB provided by BCGΔBCG1419c in susceptible guinea pigs together with an increased safety compared with BCG in several models. These results support the continued development of BCGΔBCG1419c as an effective vaccine for TB.
Spectral-domain optical coherence tomography for evaluating palisades of Vogt in ocular surface disorders with limbal involvement
Authors: Chen Ying-Yi , Sun Yi-Chen , Tsai Chia-Ying , Chu Hsiao-Sang , Wu Jo-Hsuan , Chang Huai-Wen , Chen Wei-Li 
Published: June 2021

AbstractSpectral-domain optical coherence tomography (SD-OCT) has been used to observe the morphology of the palisades of Vogt (POV) with satisfactory resolutions. In this study, we used SD-OCT to examine the microstructure of the POV in ocular surface disorders with limbal involvement. We detect subclinical limbal pathologies based on five parameters, including (1) decreased epithelial thickness, (2) loss of the sharp stromal tip, (3) loss of the smooth epithelial-stromal interface, (4) dilated stromal vessels, and (5) decreased POV density. Eighteen eyes of 10 patients with advancing wavelike epitheliopathy (AWE) and 15 eyes of 9 patients with phlyctenular keratitis/ocular rosacea were recruited. SD-OCT could detect abnormal changes in the POV in 100% of the lesion sites. In presumed-healthy areas of the diseased eyes diagnosed by slit-lamp biomicroscopy, SD-OCT detected abnormal changes in the POV in 100% of the eyes in both groups. In patients with unilateral disease, abnormal changes in the POV were detected by SD-OCT in 50% and 100% of presumed-healthy eyes diagnosed by slit-lamp biomicroscopy in the AWE group and phlyctenular keratitis/ocular rosacea group, respectively. SD-OCT is powerful in detecting POV changes in ocular surface disorders and can provide useful information that cannot be provided by slit-lamp biomicroscopy.
Biomolecular changes and subsequent time-dependent recovery in hippocampal tissue after experimental mild traumatic brain injury
Authors: Ustaoglu Sebnem Garip , Ali Mohamed H. M. , Rakib Fazle , Blezer Erwin L. A. , Van Heijningen Caroline L. , Dijkhuizen Rick M. , Severcan Feride 
Published: June 2021

AbstractTraumatic brain injury (TBI) is the main cause of disability and mortality in individuals under the age of 45 years. Elucidation of the molecular and structural alterations in brain tissue due to TBI is crucial to understand secondary and long-term effects after traumatic brain injury, and to develop and apply the correct therapies. In the current study, the molecular effects of TBI were investigated in rat brain at 24 h and 1 month after the injury to determine acute and chronic effects, respectively by Fourier transform infrared imaging. This study reports the time-dependent contextual and structural effects of TBI on hippocampal brain tissue. A mild form of TBI was induced in 11-week old male Sprague Dawley rats by weight drop. Band area and intensity ratios, band frequency and bandwidth values of specific spectral bands showed that TBI causes significant structural and contextual global changes including decrease in carbonyl content, unsaturated lipid content, lipid acyl chain length, membrane lipid order, total protein content, lipid/protein ratio, besides increase in membrane fluidity with an altered protein secondary structure and metabolic activity in hippocampus 24 h after injury. However, improvement and/or recovery effects in these parameters were observed at one month after TBI.