bluuebunny/crossref_metadata_2025_split huggingface dataset:
The double-edged sword of inducible defences: costs and benefits of maladaptive switching from the individual to the community level
Authors: Kath Nadja J. , Gaedke Ursula , van Velzen Ellen 
Published: June 2022

AbstractPhenotypic plasticity can increase individual fitness when environmental conditions change over time. Inducible defences are a striking example, allowing species to react to fluctuating predation pressure by only expressing their costly defended phenotype under high predation risk. Previous theoretical investigations have focused on how this affects predator–prey dynamics, but the impact on competitive outcomes and broader community dynamics has received less attention. Here we use a small food web model, consisting of two competing plastic autotrophic species exploited by a shared consumer, to study how the speed of inducible defences across three trade-off constellations affects autotroph coexistence, biomasses across trophic levels, and temporal variability. Contrary to the intuitive idea that faster adaptation increases autotroph fitness, we found that higher switching rates reduced individual fitness as it consistently provoked more maladaptive switching towards undefended phenotypes under high predation pressure. This had an unexpected positive impact on the consumer, increasing consumer biomass and lowering total autotroph biomass. Additionally, maladaptive switching strongly reduced autotroph coexistence through an emerging source-sink dynamic between defended and undefended phenotypes. The striking impact of maladaptive switching on species and food web dynamics indicates that this mechanism may be of more critical importance than previously recognized.
Deep embeddings to comprehend and visualize microbiome protein space
Authors: Odrzywolek Krzysztof , Karwowska Zuzanna , Majta Jan , Byrski Aleksander , Milanowska-Zabel Kaja , Kosciolek Tomasz 
Published: June 2022

AbstractUnderstanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited, which indicates the need for further research on alignment-free methods. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.
Origin and significance of the human DNase repertoire
Authors: Mori Giulia , Delfino Danila , Pibiri Paola , Rivetti Claudio , Percudani Riccardo 
Published: June 2022

AbstractThe human genome contains four DNase1 and two DNase2 genes. The origin and functional specialization of this repertoire are not fully understood. Here we use genomics and transcriptomics data to infer the evolutionary history of DNases and investigate their biological significance. Both DNase1 and DNase2 families have expanded in vertebrates since ~ 650 million years ago before the divergence of jawless and jawed vertebrates. DNase1, DNase1L1, and DNase1L3 co-existed in jawless fish, whereas DNase1L2 originated in amniotes by tandem duplication of DNase1. Among the non-human DNases, DNase1L4 and newly identified DNase1L5 derived from early duplications that were lost in terrestrial vertebrates. The ancestral gene of the DNase2 family, DNase2b, has been conserved in synteny with the Uox gene across 700 million years of animal evolution,while DNase2 originated in jawless fish. DNase1L1 acquired a GPI-anchor for plasma membrane attachment in bony fishes, and DNase1L3 acquired a C-terminal basic peptide for the degradation of microparticle DNA in jawed vertebrates. The appearance of DNase1L2, with a distinct low pH optimum and skin localization, is among the amniote adaptations to life on land. The expansion of the DNase repertoire in vertebrates meets the diversified demand for DNA debris removal in complex multicellular organisms.
Detection of HOCl-driven degradation of the pericardium scaffolds by label-free multiphoton fluorescence lifetime imaging
Authors: Yakimov B. P. , Vlasova I. I. , Efremov Y. M. , Maksimov E. G. , Shirshin E. A. , Kagan V. E. , Timashev P. S. 
Published: June 2022

AbstractArtificial biomaterials can significantly increase the rate of tissue regeneration. However, implantation of scaffolds leads not only to accelerated tissue healing but also to an immune response of the organism, which results in the degradation of the biomaterial. The synergy of the immune response and scaffold degradation processes largely determines the efficiency of tissue regeneration. Still, methods suitable for fast, accurate and non-invasive characterization of the degradation degree of biomaterial are highly demandable. Here we show the possibility of monitoring the degradation of decellularized bovine pericardium scaffolds under conditions mimicking the immune response and oxidation processes using multiphoton tomography combined with fluorescence lifetime imaging (MPT-FLIM). We found that the fluorescence lifetimes of genipin-induced cross-links in collagen and oxidation products of collagen are prominent markers of oxidative degradation of scaffolds. This was verified in model experiments, where the oxidation was induced with hypochlorous acid or by exposure to activated neutrophils. The fluorescence decay parameters also correlated with the changes of micromechanical properties of the scaffolds as assessed using atomic force microscopy (AFM). Our results suggest that FLIM can be used for quantitative assessments of the properties and degradation of the scaffolds essential for the wound healing processes in vivo.
Evaluation of root lodging resistance during whole growth stage at the plant level in maize
Authors: Wang Xiaohu , Li Yinchang , Han Wei , Song Zhaoyu , Wang Shengjian , Yang Jinzhong 
Published: June 2022

AbstractRoot lodging due to strong storm wind is a common problem in maize (Zea mays) production, leading to reduced crop yield and quality and harvest efficiency. Little information is available on quantifying effects of vertical leaf area distribution on root lodging in crops such as maize. Anti-lodging index of root was computed by the formula: ALroot = Mroot / Mwind, where AL denotes anti-lodging index, and M moment of force. Mroot, root failure moment of force equals to moment arm times max root side-pulling force measured in situ by means of the digital pole dynamometer, and Mwind, wind resultant moment of force is estimated with vertical leaf area distribution and wind speed. Two maize cultivars were examined at 5 different growth stages from V8 to physiological maturity in 2019 and 2020, in Qingdao, China. Root anti-lodging index in tested cultivars fluctuated to a small extent within any year during whole growth period excluding at V8, while there was an inter-annual shift in index means (1.23 vs 0.84). Both root failure moment and wind resultant moment increased first and then decreased with the growth stage, and their influences on root anti-lodging index varied with the year. At wind grade 6, effect sizes, as contribution to root anti-lodging index, of root moment and wind moment were respectively 0.88 and 0.98. The difference in anti-lodging index between cultivars seemed to be disappearing as wind grade goes up. Root failure moment of force positively related to single root tensile resistance, root-soil ball volume, root number and total root length, whose correlation coefficient was the maximum of 0.94. Root anti-lodging index of maize proved stable from V8 on during whole growth period, and vertical leaf area distribution played a substantial role in maize root lodging in terms of wind resultant moment. Our findings provide the insights into root lodging events in crops such as maize, and would serve an approach to assessing crop root lodging resistance in breeding and cultivation programs.
Impact of Plasmodium vivax malaria on executive and cognitive functions in elderlies in the Brazilian Amazon
Authors: Pessoa Rockson C. , Oliveira-Pessoa Gabriela F. , Souza Brenda K. A. , Sampaio Vanderson S. , Pinto André Luiz C. B. , Barboza Larissa L. , Mouta Gabriel S. , Silva Emanuelle Lira , Melo Gisely C. , Monteiro Wuelton M. , Silva-Filho José H. , Lacerda Marcus V. G. , Baía-da-Silva Djane Clarys 
Published: June 2022

AbstractThe exact path leading to cognitive impairment that goes beyond malaria is unclear, but it appears to be the result of interactive factors. Time of exposure to disease and recurrences are potentially major determinant variables. Cognitive impairment is described mainly in children, rarely in adults. The disease in high endemic areas usually does not affect elderlies, because of acquired immunity over time. However, this population is relatively more frequently sick in lower endemic areas, such as in the Amazon. This study assessed the effect of Plasmodium vivax malaria on the executive and cognitive functions of elderlies, in the Brazilian Amazon. A cohort study was conducted to evaluate executive and cognitive functions one week (T0), two months (T2) and eight months (T8) after the malaria episode. Mini-Mental State Examination (MMSE), Beck Depression Inventory II (BDI-II), Clock Drawing Test (CDT), Wechsler adult intelligence scale (WAIS-III), and Wisconsin Card Sorting Test (WCST) were used to assess executive and cognitive functions. One hundred-forty elderlies were enrolled (70 with P. vivax malaria and 70 without malaria). P. vivax malaria was associated with impairment of the executive and cognitive functions in elderlies for up to 8 months after acute P. vivax malaria. Prior history of malaria, recurrences and higher parasitemia were independently associated with various surrogates of executive and cognitive impairment. With the increase in life expectancy, elderlies living in malaria endemic areas will deserve more attention from health authorities, to guarantee improvement of their quality of life in the tropics.
210Po and 210Pb content in the smoke of Heated Tobacco Products versus Conventional Cigarette smoking
Authors: Berthet Aurélie , Butty Audrey , Rossier Jérémie , Sadowski Isabelle Jacot , Froidevaux Pascal 
Published: June 2022

Abstract210Po is a radioactive component of conventional cigarette tobacco smoke and is a recognized carcinogen. Despite the expanding market of heated tobacco products, no data are available on the activity of 210Po in the smoke of IQOS Heets cigarette. We determined the 210Po activity in the mainstream smoke of thirteen cigarette brands available on the Swiss market using a smoking machine and compared the results to the 210Po activity measured in the mainstream smoke of the IQOS system. In addition, we measured the 210Po and 210Pb loss on heating after uniform heating from 50 to 600 °C for several cigarette brands and the Heets cigarettes. 13.6 ± 4.1% of 210Po activity was found in the mainstream smoke in conventional cigarette smoking (7% for 210Pb). This dropped to 1.8 ± 0.3% in the mainstream smoke of IQOS Heets. Conversely, when the tobacco was heated uniformly at 330 °C, a loss of 210Po of more than 80% was observed for all type of cigarettes. Apparently, IQOS significantly reduced the 210Po and 210Pb activities in the mainstream smoke. However, our results show that only 15% of the Heets tobacco reaches 330 °C with IQOS. While IQOS reduces the 210Po and 210Pb activities in the mainstream smoke compared to conventional cigarettes, it only heats a marginal fraction of the tobacco present in the Heets cigarette. Because smoking is an addiction (mostly due to nicotine), IQOS could possibly deliver an unsatisfactory dose of nicotine to a Heets cigarette smoker, as most of the tobacco is left unaltered.
Effect of different types of exercise in adult subjects with fibromyalgia: a systematic review and meta-analysis of randomised clinical trials
Authors: Couto Nuno , Monteiro Diogo , Cid Luís , Bento Teresa 
Published: June 2022

AbstractExercise has been recommended for fibromyalgia treatment. However, doubts related to exercise benefits remain unclear. The objective of this study was to summarise, through a systematic review with meta-analysis, the available evidence on the effects of aerobic, resistance and stretching exercise on pain, depression, and quality of life. Search was performed using electronic databases Pubmed and Cochrane Library. Studies with interventions based on aerobic exercise, resistance exercise and stretching exercise published until July 2020 and updated in December 2021, were identified. Randomized controlled trials and meta-analyses involving adults with fibromyalgia were also included. Eighteen studies were selected, including a total of 1184 subjects. The effects were summarised using standardised mean differences (95% confidence intervals) by random effect models. In general, aerobic exercise seems to reduce pain perception, depression and improves quality of life; it also improves mental and physical health-related quality of life. Resistance exercise decreases pain perception and improves quality of life and moreover improves the physical dimension of health-related quality of life. It was also observed that resistance exercise appears to have a non-significant positive effect on depression and the mental dimension of health-related quality of life. Studies revealed that stretching exercise reduces the perception and additionally improves quality of life and health-related quality of life. However, a non-significant effect was observed on depression. We conclude that exercise may be a way to reduce depression, and pain and improve the quality of life in adult subjects with fibromyalgia and should be part of the treatment for this pathology.
Development and internal validation of a model to predict type 2 diabetic complications after gestational diabetes
Authors: Ukah Ugochinyere Vivian , Platt Robert W. , Auger Nathalie , Dasgupta Kaberi , Dayan Natalie 
Published: June 2022

AbstractGestational diabetes mellitus (GDM) increases the risk of early-onset type 2 diabetes, which further exacerbates the risk of developing diabetic complications such as kidney, circulatory, and neurological complications. Yet, existing models have solely focused on the prediction of type 2 diabetes, and not of its complications, which are arguably the most clinically relevant outcomes. Our aim was to develop a prediction model for type 2 diabetic complications in patients with GDM. Using provincial administrative data from Quebec, Canada, we developed a model to predict type 2 diabetic complications within 10 years among 90,143 women with GDM. The model was internally validated and assessed for discrimination, calibration, and risk stratification accuracy. The incidence of diabetic complications was 3.8 (95% confidence interval (CI) 3.4–4.3) per 10,000 person-years. The final prediction model included maternal age, socioeconomic deprivation, substance use disorder, gestational age at delivery, severe maternal morbidity, previous pregnancy complications, and hypertensive disorders of pregnancy. The model had good discrimination [area under the curve (AUROC) 0.72 (95% CI 0.69–0.74)] and calibration (slope ≥ 0.9) to predict diabetic complications. In the highest category of the risk stratification table, the positive likelihood ratio was 8.68 (95% CI 4.14–18.23), thereby showing a moderate ability to identify women at highest risk of developing type 2 diabetic complications. Our model predicts the risk of type 2 diabetic complications with moderate accuracy and, once externally validated, may prove to be a useful tool in the management of women after GDM.
Open-source, low-cost, in-situ turbidity sensor for river network monitoring
Authors: Droujko Jessica , Molnar Peter 
Published: June 2022

AbstractFine sediment transport in rivers is important for catchment nutrient fluxes, global biogeochemical cycles, water quality and pollution in riverine, coastal and marine ecosystems. Monitoring of suspended sediment in rivers with current sensors is challenging and expensive and most monitoring setups are restricted to few single site measurements. To better understand the spatial heterogeneity of fine sediment sources and transport in river networks there is a need for new smart water turbidity sensing that is multi-site, accurate and affordable. In this work, we have created such a sensor, which detects scattered light from an LED source using two detectors in a control volume, and can be placed in a river. We compare several replicates of our sensor to different commercial turbidity probes in a mixing tank experiment using two sediment types over a wide range of typical concentrations observed in rivers. Our results show that we can achieve precise and reproducible turbidity measurements in the 0–4000 NTU or 0–16g/L range. Our sensor can also be used directly as a suspended sediment sensor and bypass an unnecessary calibration to Formazin. The developed turbidity sensor is much cheaper than existing options of comparable quality and is especially intended for distributed sensing across river networks.
On the caveats of a multiplex test for SARS-CoV-2 to detect seroconversion after infection or vaccination
Authors: Fernandes-Siqueira Lorena O. , Ferreira Fabiana A. P. , Sousa Bruna G. , Mebus-Antunes Nathane C. , Neves-Martins Thais C. , Almeida Fabio C. L. , Ferreira Gustavo C. , Salmon Didier , Wermelinger Luciana S. , Da Poian Andrea T. 
Published: June 2022

AbstractThe Covid-19 pandemic, caused by SARS-CoV-2, has resulted in over 6 million reported deaths worldwide being one of the biggest challenges the world faces today. Here we present optimizations of all steps of an enzyme-linked immunosorbent assay (ELISA)-based test to detect IgG, IgA and IgM against the trimeric spike (S) protein, receptor binding domain (RBD), and N terminal domain of the nucleocapsid (N-NTD) protein of SARS-CoV-2. We discuss how to determine specific thresholds for antibody positivity and its limitations according to the antigen used. We applied the assay to a cohort of 126 individuals from Rio de Janeiro, Brazil, consisting of 23 PCR-positive individuals and 103 individuals without a confirmed diagnosis for SARS-CoV-2 infection. To illustrate the differences in serological responses to vaccinal immunization, we applied the test in 18 individuals from our cohort before and after receiving ChAdOx-1 nCoV-19 or CoronaVac vaccines. Taken together, our results show that the test can be customized at different stages depending on its application, enabling the user to analyze different cohorts, saving time, reagents, or samples. It is also a valuable tool for elucidating the immunological consequences of new viral strains and monitoring vaccination coverage and duration of response to different immunization regimens.
Calpain cleavage of Junctophilin-2 generates a spectrum of calcium-dependent cleavage products and DNA-rich NT1-fragment domains in cardiomyocytes
Authors: Weninger Gunnar , Pochechueva Tatiana , El Chami Dana , Luo Xiaojing , Kohl Tobias , Brandenburg Sören , Urlaub Henning , Guan Kaomei , Lenz Christof , Lehnart Stephan E. 
Published: June 2022

AbstractCalpains are calcium-activated neutral proteases involved in the regulation of key signaling pathways. Junctophilin-2 (JP2) is a Calpain-specific proteolytic target and essential structural protein inside Ca2+ release units required for excitation-contraction coupling in cardiomyocytes. While downregulation of JP2 by Calpain cleavage in heart failure has been reported, the precise molecular identity of the Calpain cleavage sites and the (patho-)physiological roles of the JP2 proteolytic products remain controversial. We systematically analyzed the JP2 cleavage fragments as function of Calpain-1 versus Calpain-2 proteolytic activities, revealing that both Calpain isoforms preferentially cleave mouse JP2 at R565, but subsequently at three additional secondary Calpain cleavage sites. Moreover, we identified the Calpain-specific primary cleavage products for the first time in human iPSC-derived cardiomyocytes. Knockout of RyR2 in hiPSC-cardiomyocytes destabilized JP2 resulting in an increase of the Calpain-specific cleavage fragments. The primary N-terminal cleavage product NT1 accumulated in the nucleus of mouse and human cardiomyocytes in a Ca2+-dependent manner, closely associated with euchromatic chromosomal regions, where NT1 is proposed to function as a cardio-protective transcriptional regulator in heart failure. Taken together, our data suggest that stabilizing NT1 by preventing secondary cleavage events by Calpain and other proteases could be an important therapeutic target for future studies.
High precision robust control design of piezoelectric nanopositioning platform
Authors: Feng Huan , Pang Aiping , Zhou Hongbo 
Published: June 2022

AbstractThe piezoelectric nanopositioning platform requires extremely accurate tracking during the task, while the model uncertainty caused by load variations requires strong robustness of the system. The high accuracy and robustness in the control design are coupled to each other, making it difficult to achieve both optimally at the same time. In addition, the system itself has a weakly damped resonant mode, which makes it extremely difficult to control the piezoelectric nanopositioning platform while suppressing the inherent resonance of the system as well as meeting the requirements for robustness and high accuracy. For the multi-performance integrated control problem of piezoelectric nanopositioning platform, this paper gives two kinds of control designs (integral resonance control (IRC) and H∞ control) satisfying accuracy requirements and robustness, and carries out simulation study and comparative analysis with positive position feedback control (PPF). Simulation results show that the H∞ control strategy given in this paper has the smallest tracking error compared to PPF and IRC under 5, 10 and 20 Hz input grating scan signals, though it has a higher order, with better robustness to mechanical load variations and high frequency signal perturbations in the 0–1000 g load range.
Efficient biodiesel production from oleic and palmitic acid using a novel molybdenum metal–organic framework as efficient and reusable catalyst
Authors: Ghorbani-Choghamarani Arash , Taherinia Zahra , Tyula Yunes Abbasi 
Published: June 2022

AbstractIn this study, metal–organic framework based on molybdenum and piperidine-4-carboxylic acid, was synthesized through a simple solvothermal method and employed as an effective catalyst for biodiesel production from oleic acid and palmitic acid via esterification reaction. The prepared catalyst was characterized by XRD, FTIR, TGA, DSC, BET, SEM, TEM, ICP-OES, X-ray mapping and EDX analysis. The resulting Mo–MOF catalyst exhibit a rod-like morphology, specific surface area of 56 m2/g, and thermal stability up to 300 °C. The solid catalyst exhibited high activities for esterification of oleic acid and palmitic acid. Moreover, the catalyst could be simply recovered and efficiently reutilized for several times without significant loss in its activity, also obtained results revealed that metal–organic framework could be used for the appropriate and rapid biodiesel production.