bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mixoplankton interferences in dilution grazing experiments
Authors: Duarte Ferreira Guilherme , Romano Filomena , Medić Nikola , Pitta Paraskevi , Hansen Per Juel , Flynn Kevin J. , Mitra Aditee , Calbet Albert 
Published: December 2021

AbstractIt remains unclear as to how mixoplankton (coupled phototrophy and phagotrophy in one cell) affects the estimation of grazing rates obtained from the widely used dilution grazing technique. To address this issue, we prepared laboratory-controlled dilution experiments with known mixtures of phyto-, protozoo-, and mixoplankton, operated under different light regimes and species combinations. Our results evidenced that chlorophyll is an inadequate proxy for phytoplankton when mixoplankton are present. Conversely, species-specific cellular counts could assist (although not fully solve) in the integration of mixoplanktonic activity in a dilution experiment. Moreover, cell counts can expose prey selectivity patterns and intraguild interactions among grazers. Our results also demonstrated that whole community approaches mimic reality better than single-species laboratory experiments. We also confirmed that light is required for protozoo- and mixoplankton to correctly express their feeding activity, and that overall diurnal grazing is higher than nocturnal. Thus, we recommend that a detailed examination of initial and final plankton communities should become routine in dilution experiments, and that incubations should preferably be started at the beginning of both day and night periods. Finally, we hypothesize that in silico approaches may help disentangle the contribution of mixoplankton to the community grazing of a given system.
Transgenic refractory Aedes aegypti lines are resistant to multiple serotypes of dengue virus
Authors: Liu Wei-Liang , Hsu Chia-Wei , Chan Shih-Peng , Yen Pei-Shi , Su Matthew P. , Li Jian-Chiuan , Li Hsing-Han , Cheng Lie , Tang Cheng-Kang , Ko Shih-Hsun , Tsai Huai-Kuang , Tsai Zing Tsung-Yeh , Akbari Omar S. , Failloux Anna-Bella , Chen Chun-Hong 
Published: December 2021

AbstractThe areas where dengue virus (DENV) is endemic have expanded rapidly, driven in part by the global spread ofAedesspecies, which act as disease vectors. DENV replicates in the mosquito midgut and is disseminated to the mosquito’s salivary glands for amplification. Thus, blocking virus infection or replication in the tissues of the mosquito may be a viable strategy for reducing the incidence of DENV transmission to humans. Here we used the marinerMos1 transposase to create anAedes aegyptiline that expresses virus-specific miRNA hairpins capable of blocking DENV replication. These microRNA are driven by the blood-meal-inducible carboxypeptidase A promoter or by the polyubiquitin promoter. The transgenic mosquitoes exhibited significantly lower infection rates and viral titers for most DENV serotypes 7 days after receiving an infectious blood meal. The treatment was also effective at day 14 post infection after a second blood meal had been administered. In viral transmission assay, we found there was significantly reduced transmission in these lines. These transgenic mosquitoes were effective in silencing most of the DENV genome; such an approach may be employed to control a dengue fever epidemic.
Artefactual depiction of predator–prey trophic linkages in global soils
Authors: Wyckhuys Kris A. G. , Nguyen Ha , Fonte Steven J. 
Published: December 2021

AbstractSoil invertebrates contribute to multiple ecosystem services, including pest control, nutrient cycling, and soil structural regulation, yet trophic interactions that determine their diversity and activity in soils remain critically understudied. Here, we systematically review literature (1966–2020) on feeding habits of soil arthropods and macrofauna and summarize empirically studied predator–prey linkages across ecosystem types, geographies and taxa. Out of 522 unique predators and 372 prey organisms (constituting 1947 predator–prey linkages), the vast majority (> 75%) are only covered in a single study. We report a mean of just 3.0 ± 4.7 documented linkages per organism, with pronounced taxonomic biases. In general, model organisms and crop pests (generally Insecta) are well-studied, while important soil-dwelling predators, fungivores and detritivores (e.g., Collembola, Chilopoda and Malacostraca) remain largely ignored. We argue that broader food-web based research approaches, considering multiple linkages per organism and targeting neglected taxa, are needed to inform science-driven management of soil communities and associated ecosystem services.
A prospective study of the relationships between movement and glycemic control during day and night in pregnancy
Authors: Behravesh Masoud , Fernandez-Tajes Juan , Estampador Angela C. , Varga Tibor V. , Gunnarsson Ómar S. , Strevens Helena , Timpka Simon , Franks Paul W. 
Published: December 2021

AbstractBoth disturbed sleep and lack of exercise can disrupt metabolism in pregnancy. Accelerometery was used to objectively assess movement during waking (physical activity) and movement during sleeping (sleep disturbance) periods and evaluated relationships with continuous blood glucose variation during pregnancy. Data was analysed prospectively. 15-women without pre-existing diabetes mellitus wore continuous glucose monitors and triaxial accelerometers from February through June 2018 in Sweden. The relationships between physical activity and sleep disturbance with blood glucose rate of change were assessed. An interaction term was fitted to determine difference in the relationship between movement and glucose variation, conditional on waking/sleeping. Total movement was inversely related to glucose rate of change (p < 0.001, 95% CI (− 0.037, − 0.026)). Stratified analyses showed total physical activity was inversely related to glucose rate of change (p < 0.001, 95% CI (− 0.040, − 0.028)), whereas sleep disturbance was not related to glucose rate of change (p = 0.07, 95% CI (< − 0.001, 0.013)). The interaction term was positively related to glucose rate of change (p < 0.001, 95% CI (0.029, 0.047)). This study provides temporal evidence of a relationship between total movement and glycemic control in pregnancy, which is conditional on time of day. Movement is beneficially related with glycemic control while awake, but not during sleep.
Fusion of multi-scale bag of deep visual words features of chest X-ray images to detect COVID-19 infection
Authors: Sitaula Chiranjibi , Shahi Tej Bahadur , Aryal Sunil , Marzbanrad Faezeh 
Published: December 2021

AbstractChest X-ray (CXR) images have been one of the important diagnosis tools used in the COVID-19 disease diagnosis. Deep learning (DL)-based methods have been used heavily to analyze these images. Compared to other DL-based methods, the bag of deep visual words-based method (BoDVW) proposed recently is shown to be a prominent representation of CXR images for their better discriminability. However, single-scale BoDVW features are insufficient to capture the detailed semantic information of the infected regions in the lungs as the resolution of such images varies in real application. In this paper, we propose a new multi-scale bag of deep visual words (MBoDVW) features, which exploits three different scales of the 4thpooling layer’s output feature map achieved from VGG-16 model. For MBoDVW-based features, we perform the Convolution with Max pooling operation over the 4thpooling layer using three different kernels:$$1 \times 1$$1×1,$$2 \times 2$$2×2, and$$3 \times 3$$3×3. We evaluate our proposed features with the Support Vector Machine (SVM) classification algorithm on four CXR public datasets (CD1, CD2, CD3, and CD4) with over 5000 CXR images. Experimental results show that our method produces stable and prominent classification accuracy (84.37%, 88.88%, 90.29%, and 83.65% on CD1, CD2, CD3, and CD4, respectively).
Impact of different renal function equations on direct oral anticoagulant concentrations
Authors: Lin Shin-Yi , Kuo Ching-Hua , Huang Tao-Min , Peng Yu-Fong , Huang Chih-Fen , Tang Sung-Chun , Jeng Jiann-Shing 
Published: December 2021

AbstractThe purpose of this study is to investigate the correlation between glomerular filtration rate (GFR) estimated by different renal function equations and non-vitamin K antagonist oral anticoagulant concentration. Atrial fibrillation patients who aged ≥ 20 years and used dabigatran, rivaroxaban, or apixaban for thromboembolism prevention were enrolled to collect blood samples and measure drug concentrations using ultra-high-performance liquid chromatography with tandem mass spectrometry. The GFR was estimated using the Cockroft–Gault formula (abbreviated as creatinine clearance, CrCL), Chronic Kidney Disease Epidemiology Collaboration formula (CKD-EPI) featuring both creatinine and cystatin C, and the Modification of Diet in Renal Disease Study equation (MDRD). Multivariate regression was used to investigate the associations of different renal function estimates with drug concentrations. A total of 511 participants were enrolled, including 146 dabigatran users, 164 rivaroxaban users and 201 apixaban users. Compared to clinical trials, 35.4% of dabigatran, 4.9% of rivaroxaban, and 5.5% of apixaban concentrations were higher than the expected range (p < 0.001). CKD-EPI and MDRD estimates classified fewer patients as having GFR < 50 mL/min than CrCL in all 3 groups. Both CrCL and CKD-EPI were associated with higher-than-expected ranges of dabigatran or rivaroxaban concentrations. Nevertheless, none of the renal function equations was associated with higher-than-expected apixaban concentrations. For participants aged ≥ 75 years, CKD-EPI may be associated with higher-than-expected trough concentration of dabigatran. In conclusion, CrCL and CKD-EPI both can be used to identify patients with high trough concentrations of dabigatran or rivaroxaban. Among elderly patients who used dabigatran, CKD-EPI may be associated with increased drug concentration.
Changes of plasma nitric oxide, endothelin-1, and blood coagulation following intravitreal conbercept
Authors: Yi Quan-Yong , Chen Li-Shuang , Shen Yu , Liao Yan-Hong , Wang Yan-Yan , Yang Jie , Jin Yuanhui , Cheng Lingyun 
Published: December 2021

AbstractIntravitreal anti-VEGF (anti-vascular endothelial growth factor) biologics have revolutionized the pharmacological management of chorioretinal diseases. However, the systemic adverse events such as stroke or bleeding are the concerns for many patients and physicians. The mechanism to develop these side effects are poorly understood. Consecutive 95 patients with retinal diseases were studied for their blood activated partial thromboplastin time (APTT), prothrombin time (PT), international normalized ratio (INR), and concentration of fibrinogen before and after intravitreal conbercept. Additionally, plasma nitric oxide (NO) and endothelin-1 (ET-1) were investigated on 38 of the 95 patients. Compared with the pre-injection, 4-week post-injection values of APTT and PT were increased by 0.582 s (p = 0.038, paired t test) and by 0.086 s (p = 0.080, paired t test; p = 0.0475, Sign test), respectively. At the same time, fibrinogen decreased by 0.048 g/L. Plasma levels of NO or ET-1 or VEGF did not significantly change from pre-injection levels. Our findings advanced the understanding of mechanism for systemic side effects associated with intravitreal anti-VEGF and emphasized paying more attention to higher risk of possible bleedings for patients following intravitreal conbercept.
Increased resting state connectivity in the anterior default mode network of idiopathic epileptic dogs
Authors: Beckmann Katrin M. , Wang-Leandro Adriano , Richter Henning , Bektas Rima N. , Steffen Frank , Dennler Matthias , Carrera Ines , Haller Sven 
Published: December 2021

AbstractEpilepsy is one of the most common chronic, neurological diseases in humans and dogs and considered to be a network disease. In human epilepsy altered functional connectivity in different large-scale networks have been identified with functional resting state magnetic resonance imaging. Since large-scale resting state networks have been consistently identified in anesthetised dogs’ application of this technique became promising in canine epilepsy research. The aim of the present study was to investigate differences in large-scale resting state networks in epileptic dogs compared to healthy controls. Our hypothesis was, that large-scale networks differ between epileptic dogs and healthy control dogs. A group of 17 dogs (Border Collies and Greater Swiss Mountain Dogs) with idiopathic epilepsy was compared to 20 healthy control dogs under a standardized sevoflurane anaesthesia protocol. Group level independent component analysis with dimensionality of 20 components, dual regression and two-sample t test were performed and revealed significantly increased functional connectivity in the anterior default mode network of idiopathic epileptic dogs compared to healthy control dogs (p = 0.00060). This group level differences between epileptic dogs and healthy control dogs identified using a rather simple data driven approach could serve as a starting point for more advanced resting state network analysis in epileptic dogs.
Recent trends in global insecticide use for disease vector control and potential implications for resistance management
Authors: van den Berg Henk , da Silva Bezerra Haroldo Sergio , Al-Eryani Samira , Chanda Emmanuel , Nagpal Bhupender N. , Knox Tessa B. , Velayudhan Raman , Yadav Rajpal S. 
Published: December 2021

AbstractInsecticides have played a major role in the prevention, control, and elimination of vector-borne diseases, but insecticide resistance threatens the efficacy of available vector control tools. A global survey was conducted to investigate vector control insecticide use from 2010 to 2019. Out of 140 countries selected as sample for the study, 87 countries responded. Also, data on ex-factory deliveries of insecticide-treated nets (ITNs) were analyzed. Insecticide operational use was highest for control of malaria, followed by dengue, leishmaniasis and Chagas disease. Vector control relied on few insecticide classes with pyrethroids the most used overall. Results indicated that IRS programs have been slow to react to detection of pyrethroid resistance, while proactive resistance management using insecticides with unrelated modes of action was generally weak. The intensive use of recently introduced insecticide products raised concern about product stewardship regarding the preservation of insecticide susceptibility in vector populations. Resistance management was weakest for control of dengue, leishmaniasis or Chagas disease. Therefore, it will be vital that vector control programs coordinate on insecticide procurement, planning, implementation, resistance monitoring, and capacity building. Moreover, increased consideration should be given to alternative vector control tools that prevent the development of insecticide resistance.
Protein embeddings and deep learning predict binding residues for various ligand classes
Authors: Littmann Maria , Heinzinger Michael , Dallago Christian , Weissenow Konstantin , Rost Burkhard 
Published: December 2021

AbstractOne important aspect of protein function is the binding of proteins to ligands, including small molecules, metal ions, and macromolecules such as DNA or RNA. Despite decades of experimental progress many binding sites remain obscure. Here, we proposed bindEmbed21, a method predicting whether a protein residue binds to metal ions, nucleic acids, or small molecules. The Artificial Intelligence (AI)-based method exclusively uses embeddings from the Transformer-based protein Language Model (pLM) ProtT5 as input. Using only single sequences without creating multiple sequence alignments (MSAs), bindEmbed21DL outperformed MSA-based predictions. Combination with homology-based inference increased performance to F1 = 48 ± 3% (95% CI) and MCC = 0.46 ± 0.04 when merging all three ligand classes into one. All results were confirmed by three independent data sets. Focusing on very reliably predicted residues could complement experimental evidence: For the 25% most strongly predicted binding residues, at least 73% were correctly predicted even when ignoring the problem of missing experimental annotations. The new method bindEmbed21 is fast, simple, and broadly applicable—neither using structure nor MSAs. Thereby, it found binding residues in over 42% of all human proteins not otherwise implied in binding and predicted about 6% of all residues as binding to metal ions, nucleic acids, or small molecules.
Salivary gland dysfunction and salivary redox imbalance in patients with Alzheimer’s disease
Authors: Zalewska Anna , Klimiuk Anna , Zięba Sara , Wnorowska Olga , Rusak Małgorzata , Waszkiewicz Napoleon , Szarmach Izabela , Dzierżanowski Krzysztof , Maciejczyk Mateusz 
Published: December 2021

AbstractAlzheimer’s disease (AD) is associated with the deposition of β-amyloid in the brain. AD accounts for over 50% of cases of dementia which results from disturbances in redox homeostasis. Indeed, increased intensity of protein oxidation and nitration as well as lipid peroxidation is observed in brain areas with considerable amounts of amyloid plaques and neurofibrillary tangles. However, little is known about the oxidoreductive balance of salivary glands in AD patients. Therefore, the aim of this study was to evaluate the antioxidant barrier and oxidative/nitrosative stress biomarkers in stimulated saliva and blood of AD patients. The study was participated by 25 AD patients and 25 non-demented controls without neurological diseases or cognitive impairment, matched by age and gender to the study group. The number of patients was determined based on a previous pilot study (test power = 0.9). We found a significant decrease in the activity of erythrocyte superoxide dismutase (SOD) and glutathione peroxidase (GPx), increased activity of catalase (CAT) and reduced concentration of plasma non-enzymatic antioxidants (uric acid, UA and reduced glutathione, GSH). In contrast, in the stimulated saliva of AD patients we observed significantly decreased activity of all antioxidant enzymes (SOD, CAT and GPx) as well as concentration of GSH compared to the control group. The content of lipid (malondialdehyde, MDA) and protein (advanced oxidation protein products, AOPP; advanced glycation end-products, AGE) oxidation products as well as biomarkers of nitrosative stress (peroxynitrite, nitrotyrosine) was significantly higher in both saliva and plasma of AD patients compared to the controls. In AD patients, we also observed a considerable decrease in stimulated saliva secretion and salivary total protein content, and an increase in salivary β-amyloid concentration. In conclusion, AD results in redox imbalance towards oxidative reactions, both at the level of the oral cavity and the entire body. General redox balance disturbances do not coincide with salivary redox balance disturbances. Reduction in stimulated saliva secretion in AD patients reflects secretory dysfunction of the parotid glands.
Long-term repeatability of peripapillary optical coherence tomography angiography measurements in healthy eyes
Authors: Lee Woo Hyuk , Lee Min-Woo , Kim Min-Su , Ryu Cheon Kuk , Kim Jung-Yeul 
Published: December 2021

AbstractThis is a prospective observational study to establish the short- and long-term repeatability of measurements of peripapillary optical coherence tomography angiography (OCTA) parameters in healthy eyes and identify factors affecting long-term repeatability. We enrolled 84 healthy eyes. Participants with a history of any ophthalmic disease (except high myopia) or intraocular surgery were excluded from the study. An experienced examiner performed OCTA using disc-centered 6 × 6 mm scans. All examinations were conducted twice at 5-min intervals at the initial visit and repeated at least 6 months later. For short-term repeatability, the coefficient of variation (CV) was 2.94–4.22% and the intraclass correlation coefficient (ICC) was 0.840–0.934. For long-term repeatability, the CV was 2.73–3.84% and the ICC was 0.737–0.934. Multivariate analyses showed that the axial length (AL) (B = 0.970; p = 0.002) and mean signal strength (SS) (B = − 2.028; p < 0.001) significantly affected long-term repeatability. Measurements of peripapillary OCTA parameters exhibited excellent short-term and good long-term repeatability in healthy individuals. The mean SS and AL affected long-term repeatability and should be considered while interpreting peripapillary OCTA images.
Intermetallic PdZn nanoparticles catalyze the continuous-flow hydrogenation of alkynols to cis-enols
Authors: Chen Xiao , Shi Chuang , Wang Xing-Bao , Li Wen-Ying , Liang Changhai 
Published: December 2021

AbstractDesigning highly active and stable lead-free palladium-based catalysts without introducing surfactants and stabilizers is vital for large-scale and high-efficiency manufacturing of cis-enols via continuous-flow semi-hydrogenation of alkynols. Herein, we report an intermetallic PdZn/ZnO catalyst, designed by using the coupling strategy of strong electrostatic adsorption and reactive metal-support interaction, which can be used as a credible alternative to the commercial PdAg/Al2O3 and Lindlar catalysts. Intermetallic PdZn nanoparticles with electron-poor active sites on a Pd/ZnO catalyst significantly boost the thermodynamic selectivity with respect to the mechanistic selectivity and therefore enhance the selectivity towards cis-enols. Based on in situ diffuse reflectance infrared Fourier-transform spectra as well as simulations, we identify that the preferential adsorption of alkynol over enol on PdZn nanoparticles suppresses the over-hydrogenation of enols. These results suggest the application of fine surface engineering technology in oxide-supported metal (particles) could tune the ensemble and ligand effects of metallic active sites and achieve directional hydrogenation in fine chemical synthesis.
NADH inhibition of SIRT1 links energy state to transcription during time-restricted feeding
Authors: Levine Daniel C. , Kuo Hsin-Yu , Hong Hee-Kyung , Cedernaes Jonathan , Hepler Chelsea , Wright Alexandra G. , Sommars Meredith A. , Kobayashi Yumiko , Marcheva Biliana , Gao Peng , Ilkayeva Olga R. , Omura Chiaki , Ramsey Kathryn M. , Newgard Christopher B. , Barish Grant D. , Peek Clara Bien , Chandel Navdeep S. , Mrksich Milan , Bass Joseph 
Published: December 2021

AbstractIn mammals, circadian rhythms are entrained to the light cycle and drive daily oscillations in levels of NAD+, a cosubstrate of the class III histone deacetylase sirtuin 1 (SIRT1) that associates with clock transcription factors. Although NAD+ also participates in redox reactions, the extent to which NAD(H) couples nutrient state with circadian transcriptional cycles remains unknown. Here we show that nocturnal animals subjected to time-restricted feeding of a calorie-restricted diet (TRF-CR) only during night-time display reduced body temperature and elevated hepatic NADH during daytime. Genetic uncoupling of nutrient state from NADH redox state through transduction of the water-forming NADH oxidase from Lactobacillus brevis (LbNOX) increases daytime body temperature and blood and liver acyl-carnitines. LbNOX expression in TRF-CR mice induces oxidative gene networks controlled by brain and muscle Arnt-like protein 1 (BMAL1) and peroxisome proliferator-activated receptor alpha (PPARα) and suppresses amino acid catabolic pathways. Enzymatic analyses reveal that NADH inhibits SIRT1 in vitro, corresponding with reduced deacetylation of SIRT1 substrates during TRF-CR in vivo. Remarkably, Sirt1 liver nullizygous animals subjected to TRF-CR display persistent hypothermia even when NADH is oxidized by LbNOX. Our findings reveal that the hepatic NADH cycle links nutrient state to whole-body energetics through the rhythmic regulation of SIRT1.