bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulated confluence on micropatterned substrates correlates responses regulating cellular differentiation
Authors: Berent Zachary T. , Jain Ishita , Underhill Gregory H. , Wagoner Johnson Amy J. 
Published: February 2022

AbstractWhile cells are known to behave differently based on the size of micropatterned islands, and this behavior is thought to be related to cell size and cell−cell contacts, the exact threshold for this difference between small and large islands is unknown. Furthermore, while cell size and cell−cell contacts can be easily manipulated on small islands, they are harder to measure and continually monitor on larger islands. To investigate this size threshold, and to explore cell size, cell−cell contacts, and differentiation, we use a previously established simulation to plan experiments and explain results that we could not explain from experiments alone. We use five seeding densities covering three orders of magnitude over 25−500 µm diameter islands to examine markers of proliferation and differentiation in bone marrow‐derived mesenchymal cells (cell line). We show that osteogenic markers are most accurately described as a function of confluence for larger islands, but a function of time for smaller islands. We further show, using results of the simulation, that cell size and cell‐cell contacts are also related to confluence on larger islands, but only cell−cell contacts are related to confluence on small islands. This study uses simulations to explain experimental results that could not be explained from experiments alone. Together, the simulations and experiments in this study show different differentiation patterns on large and small islands, and this simulation may be useful in planning future studies related to this study.
Synthesis, Antimicrobial Evaluation, and Molecular Modeling Studies of New Thiosemicarbazide‐Triazole Hybrid Derivatives of (S)‐Naproxen
Authors: Han M. İhsan , Ince Ufuk , Gündüz Miyase Gözde , Küçükgüzel Ş. Güniz 
Published: February 2022

AbstractThe discovery of new antimicrobial molecules is crucial for combating drug‐resistant bacterial and fungal infections that pose a dangerous threat to human health. In the current research, we applied a molecular hybridization approach to synthesize original thiosemicarbazide‐triazole derivatives starting from (S)‐naproxen (7a–7k). After structural characterization using FT‐IR, 1H‐NMR, 13C‐NMR, and HR‐MS, the obtained compounds were screened for their antimicrobial activities against Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 25922, Candida albicans ATCC 10231 and their isolates, as well. Although all compounds were found to be moderate antimicrobial agents, in general, their antibacterial activities were better than antifungal effects. Among the tested compounds, 7j carrying nitrophenyl group on the thiosemicarbazide functionality represented the best MIC value against S. aureus isolate. Finally, molecular docking studies were performed in the active pocket of S. aureus flavohemoglobin to rationalize the obtained biological data.
Principles of Amino‐Acid‐Nucleotide Interactions Revealed by Binding Affinities between Homogeneous Oligopeptides and Single‐Stranded DNA Molecules
Authors: Wang Pengyu , Fang Xiaocui , Du Rong , Wang Jiali , Liu Mingpeng , Xu Peng , Li Shiqi , Zhang Kaiyue , Ye Siyuan , You Qing , Yang Yanlian , Wang Chen 
Published: February 2022

AbstractWe have determined the binding strengths between nucleotides of adenine, thymine, guanine and cytosine in homogeneous single stranded DNAs and homo‐octapeptides consisting of 20 common amino acids. We use a bead‐based fluorescence assay for these measurements in which octapeptides are immobilized on the bead surface and ssDNAs are in solutions. Comparative analyses of the distribution of the binding energies reveal unique binding strength patterns assignable to each DNA nucleotide and amino acid originating from the chemical structures. Pronounced favorable (such as Arg‐G, etc.) and unfavorable (such as Ile‐T, etc.) binding interactions can be identified in selected groups of amino acid and nucleotide pairs that could provide basis to elucidate energetics of amino‐acid‐nucleotide interactions. Such interaction selectivity, specificity and polymorphism establish the contributions from DNA backbone, DNA bases, as well as main chain and side chain of the amino acids.
The effect of all‐trans retinoic acid on the mitochondrial function and survival of cardiomyoblasts exposed to local photodamage
Authors: Kurekova Simona , Sevcikova Tomaskova Zuzana , Andelova Natalia , Macejova Dana , Cervienkova Michaela , Brtko Julius , Ferko Miroslav , Grman Marian , Mackova Katarina 
Published: February 2022

AbstractUsing H9C2 cardiomyoblasts, we have shown that all‐trans retinoic acid (ATRA), the biologically active metabolite of vitamin A, affects mitochondrial dynamics and functions. The low dose (10 nM) ATRA stimulates the expression of nuclear retinoid receptors and induces mechanisms that are protective against severe local damage caused by laser irradiation at the mitochondrial level. These changes include increased density of the mitochondrial network, higher number of mitochondrial junctions, and enhanced mitochondrial velocity. Moreover, the treated cells had lower basal level of reactive oxygen species (ROS) and could maintain mitochondrial potential (ΔΨm) after photodamage. Cells treated with 10 nM ATRA had significantly better survival rate after photodamage in comparison to control cells. Cells treated with pharmacological concentration of ATRA (1 µM) expressed higher mitochondrial connectivity without increased motility, which did not lead to better survival or decreased ROS level as was in the case of low‐dose ATRA. The proteomics analysis showed changes in proteins related to cellular metabolism (glycolysis) and respiration in ATRA‐treated cells. The l‐lactate assay confirmed the shift to anaerobic glycolysis in cells treated with 1 µm ATRA, whereas the 10 nM ATRA decreased the level of lactate in medium. The increased levels of cytochrome c or peroxiredoxins 5 level and also lower expression of retinoid and rexinoid receptors were observed in cells treated with 1 µM ATRA. The effect of ATRA is concentration‐dependent; the increased mitochondrial dynamics and slower metabolism at 10 nM ATRA contributed significantly to the chance of survival of the cells after photodamage whereas the higher concentration of ATRA overrode the protective effect and led to the unfavorable ones.
Modified safety techniques for transcatheter repair of superior sinus venosus defects with partial anomalous pulmonary venous drainage using a 100‐mm Optimus‐CVS® covered XXL stent
Authors: Haddad Raymond N. , Bonnet Damien , Gewillig Marc , Malekzadeh‐Milani Sophie 
Published: February 2022

AbstractWe report the first use of a single 100‐mm long custom‐made version of the Optimus‐CVS® balloon‐expandable PTFE‐covered XXL (15‐Zig) stent (AndraTec, GmbH) to eliminate sinus venosus defect left‐to‐right shunt and redirect anomalous right pulmonary veins blood flow through a new walled channel to the left atrium. Anatomical feasibility and strategy decision were guided by ex‐vivo procedure simulation on the patient‐specific 3D printed heart model and in‐vivo balloon interrogation. Modified procedural and implantation techniques are detailed. Immediate and one‐month follow‐up showed excellent outcomes.
Probing the Potential of Hitherto Unexplored Base‐Stabilized Borylenes in Dinitrogen Binding
Authors: Fantuzzi Felipe , Moral Rubi , Dewhurst Rian D. , Braunschweig Holger , Phukan Ashwini K. 
Published: February 2022

AbstractComputational investigations were carried out to probe the potential of several dicoordinate, singly base‐stabilized borylenes of the form [L→BR] (L=neutral Lewis base) in dinitrogen binding. The calculated reaction free energies and activation barriers associated with the formation of mono‐ and diborylene‐N2 adducts suggest the presence of thermally surmountable kinetic barriers towards their possible isolation. Our results show that the exergonicity of dinitrogen activation and fixation is linearly dependent on the natural charge at the boron center, which can be tuned to design novel boron‐based compounds with potential applications to small‐molecule activation. EDA‐NOCV analysis reveals strong binding of dinitrogen to these base‐stabilized borylenes.
Biological applications of chiral inorganic nanomaterials
Authors: Fan Yuan , Ou‐yang Shaobo , Zhou Dong , Wei Junchao , Liao Lan 
Published: February 2022

AbstractChirality is common in nature and plays the essential role in maintaining physiological process. Chiral inorganic nanomaterials with intense optical activity have attracted more attention due to amazing properties in recent years. Over the past decades, many efforts have been paid to the preparation and chirality origin of chiral nanomaterials; furthermore, emerging biological applications have been investigated widely. This review mainly summarizes recent advances in chiral nanomaterials. The top‐down and bottom‐up preparation methods and chirality origin of chiral nanomaterials are introduced; besides, the biological applications, such as sensing, therapy, and catalysis, will be introduced comprehensively. Finally, we also provide a perspective on the biomedical applications of chiral nanomaterials.
Non‐vitamin K oral anticoagulants versus vitamin K antagonists in post transcatheter aortic valve replacement patients with clinical indication for oral anticoagulation: A meta‐analysis
Authors: Chen Yi‐feng , Liu Fei , Li Xi‐wen , Zhang Hou‐jing , Liu Yi‐ge , Lin Lu 
Published: February 2022

AbstractBackgroundCurrent guidelines recommend oral anticoagulation (OAC) following transcatheter aortic valve replacement (TAVR) in patients with clinical indication, but the optimal antithrombotic regimen remains uncertain. We aimed to compare the efficacy and safety of non‐vitamin K oral anticoagulants (NOACs) versus vitamin K antagonists (VKAs) in patients undergoing TAVR with concomitant indication of OAC.HypothesisComparing with VKAs therapy, NOACs are similar in reducing the all‐cause mortality and major bleeding in post‐TAVR patients requiring OAC medication.MethodsWe searched the databases of PubMed, Embase, and Cochrane library databases to identify studies that investigated NOACs versus VKAs after TAVR in patients with another indication of OAC, which were published before 28th September 28, 2021. The effectiveness of outcomes was all‐cause mortality and stroke or systemic embolism, while the main safety outcome was major and/or life‐threatening bleeding. The hazard ratio (HR) with 95% confidence interval (CI) was used as a measure of treatment effect.ResultsOur search identified eight studies. We included 4947 post‐TAVR patients with another indication of OAC allocated to the NOAC (n = 2146) or VKA groups (n = 2801). There were no significant differences in the all‐cause mortality (HR: 0.91, 95% CI: 0.77–1.08, p = .29, I2 = 47%), stroke or systemic embolism (HR: 0.96, 95% CI: 0.68–1.37, p = .84, I2 = 0%), and major and/or life‐threatening bleeding (HR: 1.09, 95% CI: 0.89–1.32, p = .40, I2 = 30%) in both groups.ConclusionAmong post‐TAVR patients who required OAC therapy, NOACs therapy compared to VKAs is similar in reducing the all‐cause mortality, stroke or systemic embolism, and major and/or life‐threatening bleeding events.
Substituent Effects in π‐Hole Regium Bonding Interactions Between Au(p‐X‐Py)2Complexes and Lewis Bases: Anab initioStudy
Authors: De las Nieves Piña María , Burguera Sergi , Buils Jordi , Àngel Crespí Miquel , Ernesto Morales Julian , Pons Jordi , Bauzá Antonio , Frontera Antonio 
Published: February 2022

AbstractLong range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated for the first time. The Au(I) atom is coordinated to twopara‐substituted pyridine ligands. The interaction energy (RI‐MP2/def2‐TZVP level of theory) of the π‐hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energiesvs. Hammett's σ parameter). The Bader's theory of “atoms‐in‐molecules” has been used to evidence that the electron density computed at the bond critical point that connects the Au‐atom to the electron donor can be used as a measure of bond order in regium bonding. Several X‐ray structures retrieved from the Cambridge Structural Database (CSD) provide experimental support to the existence of π‐hole regium bonding in [Au(Py)2]+derivatives.
Selective Catalytic Transfer Hydrogenation of Lignin to Alkyl Guaiacols Over NiMo/Al‐MCM‐41
Authors: Lu Xinyu , Guo Haoquan , Chen Jiajia , Wang Duoying , Lee Adam F. , Gu Xiaoli 
Published: February 2022

AbstractEfficient deoxygenation of lignin‐derived bio‐oils is central to their adoption as precursors to sustainable liquid fuels in place of current fossil resources. In‐situ catalytic transfer hydrogenation (CTH), using isopropanol and formic acid as solvent and in‐situ hydrogen sources, was demonstrated over metal‐doped and promoted MCM‐41 for the depolymerization of oxygen‐rich (35.85 wt%) lignin from Chinese fir sawdust (termed O‐lignin). A NiMo/Al‐MCM‐41 catalyst conferred an optimal lignin‐derived oil yield of 61.6 wt% with a comparatively low molecular weight (Mw=542 g mol−1, Mn=290 g mol−1) and H/C ratio of 1.39. High selectivity to alkyl guaiacols was attributed to efficient in‐situ hydrogen transfer from isopropanol/formic acid donors, and a synergy between surface acid sites in the Al‐doped MCM‐41 support and reducible Ni/Mo species, which improved the chemical stability and quality of the resulting lignin‐derived bio‐oils.
Ecosystem restoration and belowground multifunctionality: A network view
Authors: Tian Dashuan , Xiang Yangzhou , Seabloom Eric , Chen Han Y. H. , Wang Jinsong , Yu Guirui , Deng Ye , Li Zhaolei , Niu Shuli 
Published: February 2022

AbstractEcological restoration is essential to reverse land degradation worldwide. Most studies have assessed the restoration of ecosystem functions individually, as opposed to a holistic view. Here we developed a network‐based ecosystem multifunctionality (EMF) framework to identify key functions in evaluating EMF restoration. Through synthesizing 293 restoration studies (2900 observations) following cropland abandonment, we found that individual soil functions played different roles in determining the restoration of belowground EMF. Soil carbon, total nitrogen, and phosphatase were key functions to predict the recovery of belowground EMF. On average, abandoned cropland recovered ~19% of EMF during 18 years. The restoration of EMF became larger with longer recovery time and higher humidity index, but lower with increasing soil depth and initial soil carbon. Overall, this study presents a network‐based EMF framework, effectively helping to evaluate the success of ecosystem restoration and identify the key functions.
Functional differences in scavenger communities and the speed of carcass decomposition
Authors: Wenting Elke , Rinzema Salomé C. Y. , van Langevelde Frank 
Published: February 2022

AbstractCarcass decomposition largely depends on vertebrate scavengers. However, how behavioral differences between vertebrate scavenger species, the dominance of certain species, and the diversity of the vertebrate scavenger community affect the speed of carcass decomposition is poorly understood. As scavenging is an overlooked trophic interaction, studying the different functional roles of vertebrate species in the scavenging process increases our understanding about the effect of the vertebrate scavenger community on carcass decomposition. We used motion‐triggered infrared camera trap footages to profile the behavior and activity of vertebrate scavengers visiting carcasses in Dutch nature areas. We grouped vertebrate scavengers with similar functional roles. We found a clear distinction between occasional scavengers and more specialized scavengers, and we found wild boar (Sus scrofa) to be the dominant scavenger species in our study system. We showed that these groups are functionally different within the scavenger community. We found that overall vertebrate scavenger diversity was positively correlated with carcass decomposition speed. With these findings, our study contributes to the understanding about the different functional roles scavengers can have in ecological communities.
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing
Authors: Lizano Apollo Marco , Smolina Irina , Choquet Marvin , Kopp Martina , Hoarau Galice 
Published: February 2022

AbstractCopepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole‐genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis, C. hyperboreus, C. marshallae, C. pacificus, and C. helgolandicus. Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein‐coding genes mined from RNA‐seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein‐coding genes support a separation between three groups: the C. finmarchicus group (including C. finmarchicus, C. glacialis, and C. marshallae), the C. helgolandicus group (including C. helgolandicus, C. sinicus, and C. pacificus) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species.
Dung beetle community composition affects dung turnover in subtropical US grasslands
Authors: Stanbrook Roisin , King Joshua R. 
Published: February 2022

Abstract

An important service in many ecosystems is the turnover and degradation of dung deposited by cattle. Dung beetles are the primary group of insects responsible for dung turnover, and factors affecting their abundance and distribution thus impact dung degradation. Lands lost to grazing due to dung buildup and pasture contamination total millions of acres per year in US pastures.

We evaluated the structural differences in dung beetle assemblages in natural grasslands versus a managed agroecosystem in subtropical southeastern Florida (USA). We measured the direct effect of dung longevity when dung beetle fauna normally inhabiting dung pats were excluded.

Our results indicate dung beetle abundance, functional diversity, and species richness have a substantial impact on the rate of dung turnover in subtropical pastoral lands with ~70% of dung removed from the soil surface after three months. Functional diversity and evenness did not have a significant positive effect on dung removal in managed, versus natural grasslands demonstrating a strong relationship between dung beetle assemblage composition and delivery of a key ecological process, dung degradation.

We suggest the importance of trees, which provide a thermal refuge for beetles, should be dispersed within matrixes of open pasture areas and within proximity to adjacent closed‐canopy hammocks to facilitate the exchange of dung beetles between habitats and therefore maintain the provisioning of dung degradation services by dung beetle assemblages.
Sex and habitat drive hantavirus prevalence in marsh rice rat populations impacted by the Deepwater Horizon oil spill
Authors: Pérez‐Umphrey Anna A. , Jonsson Colleen B. , Bonisoli‐Alquati Andrea , Snider Allison M. , Stouffer Philip C. , Taylor Sabrina S. 
Published: February 2022

AbstractBayou orthohantavirus (BAYV) is one of several hantaviruses in the United States that cause hantavirus pulmonary syndrome in humans. Its host reservoir, the marsh rice rat (Oryzomys palustris), inhabits coastal saltmarshes of Louisiana, a region extensively impacted by anthropogenic disturbances, such as the 2010 Deepwater Horizon (DWH) oil spill. The oil spill presents an opportunity to investigate how a large‐scale ecological disturbance can influence the hantavirus host–pathogen dynamic by examining BAYV presence in its reservoir host species in areas with different oiling histories. Here, we: (1) quantify BAYV prevalence in the rice rat in coastal saltmarshes of Louisiana; (2) assess whether prevalence is driven by rice rat demographics, seasonality, or association with habitat characteristics; and (3) determine whether these factors differ by marsh oiling history. We collected mark–recapture data and blood and tissue samples over 5 years (2013–2017) at oiled, unoiled, and reference sites. Testing of the samples for BAYV revealed an antibody and RNA prevalence of 13.7%. Logistic regression analysis found that prevalence varied seasonally and inter‐annually, and in July of 2016 reached 30.8%. Sex (male) and increasing cover of Sporobolus alterniflorus and open water compared to Juncus roemerianus and bare ground were the strongest predictors of hantavirus prevalence. Abundance estimates derived from Huggins closed‐capture models were greatest at oiled sites, but oiling treatment had no residual influence on BAYV prevalence, and abundance and prevalence were not correlated. This study supports the hypothesis that habitat is a main driver of hantavirus prevalence in the host and implies that continued and future disturbances in the region will likely impact the rice rat–BAYV dynamic by altering plant communities and landscape structure.