bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microcoleus (Cyanobacteria) form watershed‐wide populations without strong gradients in population structure
Authors: Bouma‐Gregson Keith , Crits‐Christoph Alexander , Olm Mathew R. , Power Mary E. , Banfield Jillian F. 
Published: October 2021

AbstractThe relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome‐resolved metagenomic analyses of benthic Microcoleus‐dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within‐mat genetic diversity does not appear to depend on the downstream accumulation of upstream‐derived strains. The four‐gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene‐flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.
The efficient physiological strategy of a novel tomato genotype to adapt to chronic combined water and heat stress
Authors: Francesca S. , Vitale L. , Arena C. , Raimondi G. , Olivieri F. , Cirillo V. , Paradiso A. , de Pinto M. C. , Maggio A. , Barone A. , Rigano M. M. 
Published: October 2021

ABSTRACT

Climate change is increasing the frequency of high temperature shocks and water shortages, pointing to the need to develop novel tolerant varieties and to understand the mechanisms employed to withstand combined abiotic stresses.

Two tomato genotypes, a heat‐tolerant Solanum lycopersicum accession (LA3120) and a novel genotype (E42), previously selected as a stable yielding genotype under high temperatures, were exposed to single and combined water and heat stress. Plant functional traits, pollen viability and physiological (leaf gas exchange and chlorophyll a fluorescence emission measurements) and biochemical (antioxidant content and antioxidant enzyme activity) measurements were carried out. A Reduced Representation Sequencing approach allowed exploration of the genetic variability of both genotypes to identify candidate genes that could regulate stress responses.

Both abiotic stresses had a severe impact on plant growth parameters and on the reproductive phase of development. Growth parameters and leaf gas exchange measurements revealed that the two genotypes used different physiological strategies to overcome individual and combined stresses, with E42 having a more efficient capacity to utilize the limiting water resources. Activation of antioxidant defence mechanisms seemed to be critical for both genotypes to counteract combined abiotic stresses. Candidate genes were identified that could explain the different physiological responses to stress observed in E42 compared with LA3120.

Results here obtained have shown how new tomato genetic resources can be a valuable source of traits for adaptation to combined abiotic stresses and should be used in breeding programmes to improve stress tolerance in commercial varieties.
Climate and sea‐level controlling internal architecture of a Quaternary carbonate ramp (Northwest Shelf of Australia)
Authors: Hallenberger Maximilian , Reuning Lars , Back Stefan , Gallagher Stephen J. , Iwatani Hokuto , Lindhorst Katja 
Published: October 2021

AbstractThe continental shelf of Northwest Australia hosts an extensive tropical carbonate ramp that forms an important template for the interpretation of similar systems in the sedimentary record. Yet, little is known about its development from the middle to late Quaternary, a period of high frequency glacioeustatic changes in sea‐level and climate. This research describes core and seismic‐reflection data from a mid‐ramp to outer ramp transect at the Northwest Shelf. Core material includes the upper 70 m of International Ocean Discovery Program Site U1461 (Expedition 356), which covers the last 500 kyr. During arid glacials, sedimentation is characterized by inorganically precipitated carbonates, including aragonite‐needle mud and ooids. Ooids developed under shallow marine conditions on small‐scale flat‐topped platforms. Seismic and sedimentological evidence indicates that these platforms developed locally on top of the present‐day mid‐ramp and were typically only active during a single glacial period. Aragonite‐needle mud precipitated (inorganically) in shallow‐water areas. Much of these fine sediments were subsequently exported into deeper water where they mixed with pelagic carbonates. Humid interglacials are generally characterized by reduced sedimentation across the Northwest Shelf of Australia, resulting in the amalgamation of glacial lowstand deposits. Yet, substantial amounts of skeletal carbonates were deposited at the studied location during the Holocene and Marine Isotope Stage 11. These sediment accumulations are interpreted as a local feature caused by a decline in current energy. The study presented highlights a ramp system where climate is as important as sea‐level in controlling carbonate deposition.
Repeatability and sensitivity of passive mechanical stiffness measurements in the triceps surae muscle‐tendon complex
Authors: Walker Josh , Bissas Athanassios , Wainwright Barney , Hanley Brian , Cronin Neil J. 
Published: October 2021

Measurements of muscle‐tendon unit passive mechanical properties are often used to illustrate acute and chronic responses to a training stimulus. The purpose of this study was to quantify the inter‐session repeatability of triceps surae passive stiffness measurements in athletic and non‐athletic populations, with the view to discussing its usefulness both as a muscle‐tendon profiling tool and a control measure for studies with multiple data collection sessions. The study also aimed to observe the effects of quiet standing on passive stiffness parameters. Twenty‐nine men (10 cyclists, nine triathletes, 10 controls) visited the laboratory on three separate occasions, where passive stiffness tests were carried out using an isokinetic dynamometer and B‐mode ultrasound. Participants were fully rested on two of the sessions and subjected to 20 min of quiet standing in the other. The passive stiffness assessment generally showed only moderate inter‐session repeatability but was still able to detect inter‐group differences, with triathletes showing higher passive stiffness than cyclists (p < 0.05). Furthermore, quiet standing impacted passive stiffness by causing a reduction in ankle joint range of motion, although mechanical resistance to stretch in the muscle‐tendon unit at a given joint angle was relatively unaffected. These findings show that passive stiffness assessment is appropriate for detecting inter‐group differences in the triceps surae and even the effects of a low‐intensity task such as quiet standing, despite showing some inter‐session variation. However, the inter‐session variation suggests that passive stiffness testing might not be suitable as a control measure when testing participants on multiple sessions.
Screening of organic substrates for a permeable biobarrier to remediate nitrate contaminated groundwater
Authors: Özkaraova Emre Burcu , Aydın Sema , Gemechu Abdella Usman 
Published: October 2021

AbstractEasily available organic substrates (e.g., peanut, walnut and almond shells and luffa sponge) were evaluated as potential filter material for permeable biobarrier systems. Higher removal efficiencies and rate constants were observed for lower (20%) substrate (e.g., peanut, walnut and luffa sponge) percentages indicating to the importance of substrate percentage. Rate constants were higher for total inorganic nitrogen removal (≥0.137 mg N/L/d) than for nitrate removal (≥0.127 mg N/L/d) in the batch bioreactors promising the capability of microorganisms in consuming substrate released nitrogen compounds. Continuous flow biobarriers revealed greater removal efficiencies (<1 mg NO3−–N/L) and rate constants (≥2.38 mg NO3−–N/L/d) that were related to better microbial performance with increased substrate contact. Different dissolved oxygen levels observed for peanut shell (≤7.45 mg O2/L) and luffa sponge columns (<3 mg O2/L) were indicating to the existence of different mechanisms and microorganisms during simultaneous heterotrophic nitrification and aerobic or anoxic denitrification. Luffa sponge was found to be the best candidate as a biobarrier substrate for a longer timescale, although walnut and almond shells may be excellent materials both supporting the denitrification process and permeability of barrier system.
A finite-deformation constitutive model of particle-binder composites incorporating yield-surface-free plasticity
Authors: Agarwal Ankit , Gonzalez Marcial 
Published: October 2021

Abstract
We present a constitutive model for particle-binder composites that accounts for finite-deformation kinematics, nonlinear elasto-plasticity without apparent yield, cyclic hysteresis, and progressive stress-softening before the attainment of stable cyclic response. The model is based on deformation mechanisms experimentally observed during quasi-static monotonic and cyclic compression of mock Plastic-Bonded Explosives (PBX) at large strain. An additive decomposition of strain energy into elastic and inelastic parts is assumed, where the elastic response is modeled using Ogden hyperelasticity while the inelastic response is described using yield-surface-free endochronic plasticity based on the concepts of internal variables and of evolution or rate equations. Stress-softening is modeled using two approaches; a discontinuous isotropic damage model to appropriately describe the softening in the overall loading-unloading response, and a material scale function to describe the progressive cyclic softening until cyclic stabilization. A nonlinear multivariate optimization procedure is developed to estimate the elasto-plastic model parameters from nominal stress-strain experimental compression data. Finally, a correlation between model parameters and the unique stress-strain response of mock PBX specimens with differing concentrations of aluminum is identified, thus establishing a relationship between model parameters and material composition.
Tobacco industry strategies for flavour capsule cigarettes: analysis of patents and internal industry documents
Authors: van der Eijk Yvette , Teo Ken Wah , Tan Grace Ping Ping , Chua Wee Meng 
Published: October 2021

BackgroundThe global market for flavour capsule variants (FCVs), cigarettes with a crushable flavour capsule, has grown exponentially. To inform further regulatory efforts, it is important to understand tobacco industry strategies for FCVs.MethodsAnalysis of data from 65 patents and 179 internal tobacco industry documents, retrieved via snowball searches in Patsnap and the Truth Tobacco Industry Documents Library, describing tobacco industry developments related to FCVs. We used an inductive coding method to identify themes relating to FCV features or developments.ResultsTobacco companies were developing FCVs since the 1960s, with little market success until the 2000s following the launch of Camel Crush, a brand which targeted millennials (in their teens or early 20s at the time). Tobacco companies have patented, but not yet marketed, FCVs with microcapsule surface coatings, adjustable or heat-triggered flavour release systems, airflow manipulation features, transparent filters to visualise flavour release, and various flavours and additives for capsules including nicotine/tobacco extracts for an on-demand nicotine hit. Tobacco companies developed FCVs purported to be reduced harm, although their own tests showed that FCVs have higher toxicant concentrations. They have also developed loose flavour capsule units designed to fit into cigarettes, packs, or recessed filters to enable users to customise cigarettes and circumvent tobacco flavour bans.ConclusionsTo prevent tobacco companies from targeting young people and exploiting regulatory loopholes, regulations on tobacco products should ban flavours and consider the broad variety of FCV designs, additives and loose products designed to impart flavour into tobacco products.
New pyrido[3′,2′:4,5]thieno[3,2-d]pyrimidin-4(3H)-one hybrids linked to arene units: synthesis of potential MRSA, VRE, and COX-2 inhibitors
Authors: Sanad Sherif M.H. , Mekky Ahmed E.M. 
Published: October 2021

In the current study, we reported the tandem synthesis of two series of arene-linked pyrimidinone hybrids with related fused thieno[2,3-b]pyridine moiety. The target hybrids were prepared, in moderate to excellent yields, by the reaction of a ternary mixture of the appropriate of 3-aminothieno[2,3-b]pyridine-2-carboxylate, DMF-DMA, and a series of aryl amines in dioxane at 110 °C for 8 h. The antibacterial activity of the new hybrids was estimated against six susceptible ATCC strains. Hybrids 5g and 7g, linked to a sulfonamide unit, showed the best efficacy against S. aureus and E. faecalis strains with minimum inhibitory concentration (MIC) values of 1.7–1.8 μM, which exceed ciprofloxacin. Furthermore, some of new hybrids were examined as potential inhibitors of four different MRSA and VRE strains. Hybrids 5g and 7g demonstrated more potent efficacy than linezolid against MRSA strains with MIC values of 3.6/3.4 and 1.8/1.7 μM against ATCC:33591 and ATCC:43300 strains, respectively. The prior hybrids displayed a comparable efficacy with linezolid against VRE strains with MIC values of 7.3/6.9 and 3.6/3.4 μM against ATCC:51299 and ATCC:51575 strains, respectively. Additionally, some of the new hybrids were examined as potential COX-2 inhibitors using the reference celecoxib (IC50 of 0.117 µM). Hybrid 7g revealed more potent inhibitory efficacy than celecoxib with IC50 of 0.112 µM, whereas hybrid 5g showed almost inhibitory activity equivalent to celecoxib with IC50 of 0.121 µM. Molecular docking was performed to predict the possible binding interactions between hybrids 5g and 7g with the target COX-2 enzyme.
AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations
Authors: Capponi Sara , Wang Shangying , Navarro Erik J. , Bianco Simone 
Published: October 2021

AbstractWe present a novel technique to predict binding affinity trends between two molecules from atomistic molecular dynamics simulations. The technique uses a neural network algorithm applied to a series of images encoding the distance between two molecules in time. We demonstrate that our algorithm is capable of separating with high accuracy non-hydrophobic mutations with low binding affinity from those with high binding affinity. Moreover, we show high accuracy in prediction using a small subset of the simulation, therefore requiring a much shorter simulation time. We apply our algorithm to the binding between several variants of the SARS-CoV-2 spike protein and the human receptor ACE2.Graphic abstract
Model theory of differential fields with finite group actions
Authors: Hoffmann Daniel Max , Sánchez Omar León 
Published: October 2021

Let [Formula: see text] be a finite group. We explore the model-theoretic properties of the class of differential fields of characteristic zero in [Formula: see text] commuting derivations equipped with a [Formula: see text]-action by differential field automorphisms. In the language of [Formula: see text]-differential rings (i.e. the language of rings with added symbols for derivations and automorphisms), we prove that this class has a model-companion — denoted [Formula: see text]. We then deploy the model-theoretic tools developed in the first author’s paper [D. M. Hoffmann, Model theoretic dynamics in a Galois fashion, Ann. Pure Appl. Logic 170(7) (2019) 755–804] to show that any model of [Formula: see text] is supersimple (but unstable when [Formula: see text] is nontrivial), a PAC-differential field (and hence differentially large in the sense of the second author and Tressl [Differentially large fields, preprint (2020), arXiv:2005.00888, available at https://arxiv.org/abs/2005.00888 ]), and admits elimination of imaginaries after adding a tuple of parameters. We also address model-completeness and supersimplicity of theories of bounded PAC-differential fields (extending the results of Chatzidakis and Pillay [Generic structures and simple theories, Ann. Pure Appl. Logic 95 (1998) 71–92] on bounded PAC-fields).
IQ Motif-Containing GTPase-Activating Protein 2 Inhibits Breast Cancer Angiogenesis by Suppressing VEGFR2–AKT Signaling
Authors: Kumar Dinesh , Patel Saket Awadhesbhai , Khan Rehan , Chawla Saurabh , Mohapatra Nachiketa , Dixit Manjusha 
Published: October 2021

Abstract

Antiangiogenesis cancer therapies are facing setbacks due to side effects and resistance. Parallel targeting of multiple pathways can help in the development of more effective therapies. This requires the discovery of new molecules that can regulate multiple cellular processes. Our study has recently established the association of reduced IQGAP2 expression in breast cancer with EMT and poor prognosis of the patient. Existing literature indirectly suggests the role of IQGAP2 in angiogenesis that is still unexplored. In this study, we searched the role of IQGAP2 in tumor angiogenesis in a comprehensive manner using cell culture, patients, and animal models. Depletion of IQGAP2 in breast cancer cells increased proliferation, migration, and tubulogenesis of HUVECs. Findings were validated in ex ovo CAM, Matrigel plug and skin wound-healing assays in mouse model, showing that the reduction of IQGAP2 significantly increased angiogenesis. As a confirmation, IHC analysis of the patient's tissues showed a negative correlation of IQGAP2 expression with the microvessel density. Mechanistically, loss of IQGAP2 appeared to activate VEGF-A via ERK activation in tumor cells, which activated the VEGFR2–AKT axis in HUVECs.

Implications:
The findings of this study suggest the antiangiogenic properties of IQGAP2 in breast cancer. The Dual effect of IQGAP2 on EMT and angiogenesis makes it a potential target for anticancer therapy.
Clinical Characteristics, Management Strategies, and Outcomes of Non–ST‐Segment–Elevation Myocardial Infarction Patients With and Without Prior Coronary Artery Bypass Grafting
Authors: Shoaib Ahmad , Rashid Muhammad , Berry Colin , Curzen Nick , Kontopantelis Evangelos , Timmis Adam , Ahmad Ayesha , Kinnaird Tim , Mamas Mamas A. 
Published: October 2021

Background
There are limited data on the management strategies, temporal trends and clinical outcomes of patients who present with non–ST‐segment–elevation myocardial infarction and have a prior history of CABG.

Methods and Results

We identified 287 658 patients with non–ST‐segment–elevation myocardial infarction between 2010 and 2017 in the United Kingdom Myocardial Infarction National Audit Project database. Clinical and outcome data were analyzed by dividing into 2 groups by prior history of coronary artery bypass grafting (CABG): group 1, no prior CABG (n=262 362); and group 2, prior CABG (n=25 296). Patients in group 2 were older, had higher GRACE (Global Registry of Acute Coronary Events) risk scores and burden of comorbid illnesses. More patients underwent coronary angiography (69% versus 63%) and revascularization (53% versus 40%) in group 1 compared with group 2. Adjusted odds of receiving inpatient coronary angiogram (odds ratio [OR], 0.91; 95% CI, 0.88–0.95;
P
<0.001) and revascularization (OR, 0.73; 95% CI, 0.70–0.76;
P
<0.001) were lower in group 2 compared with group 1. Following multivariable logistic regression analyses, the OR of in‐hospital major adverse cardiovascular events (composite of inpatient death and reinfarction; OR, 0.97; 95% CI, 0.90–1.04;
P
=0.44), all‐cause mortality (OR, 0.96; 95% CI, 0.88–1.04;
P
=0.31), reinfarction (OR, 1.02; 95% CI, 0.89–1.17;
P
=0.78), and major bleeding (OR, 1.01; 95% CI, 0.90–1.11;
P
=0.98) were similar across groups. Lower adjusted risk of inpatient mortality (OR, 0.67; 95% CI, 0.46–0.98;
P
=0.04) but similar risk of bleeding (OR,1.07; CI, 0.79–1.44;
P
=0.68) and reinfarction (OR, 1.13; 95% CI, 0.81–1.57;
P
=0.47) were observed in group 2 patients who underwent percutaneous coronary intervention compared with those managed medically.

Conclusions
In this national cohort, patients with non–ST‐segment–elevation myocardial infarction with prior CABG had a higher risk profile, but similar risk‐adjusted in‐hospital adverse outcomes compared with patients without prior CABG. Patients with prior CABG who received percutaneous coronary intervention had lower in‐hospital mortality compared with those who received medical management.
Favorable Atrial Remodeling After Percutaneous Pulmonary Valve Implantation and Its Association With Changes in Exercise Capacity and Right Ventricular Function
Authors: Latus Heiner , Born Danik , Shehu Nerejda , Stern Heiko , Hager Alfred , Georgiev Stainimir , Tanase Daniel , Meierhofer Christian , Ewert Peter , Eicken Andreas , Tutarel Oktay 
Published: October 2021

Background
Right atrial (RA) dilatation and impaired right ventricular (RV) filling are common in patients with RV outflow tract dysfunction. We aimed to study potential correlations between atrial function with clinically relevant hemodynamic parameters and to assess the predictive impact of atrial performance on the recovery of exercise capacity and RV pump function after percutaneous pulmonary valve implantation (PPVI).

Methods and Results
Altogether, 105 patients with right ventricular outflow tract dysfunction (median age at PPVI, 19.2 years; range, 6.2–53.4 years) who underwent cardiac magnetic resonance imaging before and 6 months after PPVI were included. RA and left atrial maximal and minimal volumes as well as atrial passive and active emptying function were assessed from axial cine slices. RA emptying function was inversely related to invasive RV end‐diastolic pressure, and RA passive emptying correlated significantly with peak oxygen uptake. After PPVI, a significant decrease in RA minimum volume was observed, whereas RA passive emptying function improved, and RA active emptying function decreased significantly. Patients with predominant right ventricular outflow tract stenosis showed more favorable changes in RA active and left atrial passive emptying than those with primary volume overload. None of the RA and left atrial emptying parameters was predictive for recovery of peak oxygen uptake or RV ejection fraction.

Conclusions
In patients with right ventricular outflow tract dysfunction, impaired RA emptying assessed by cardiac magnetic resonance imaging was associated with increased RV filling pressures and lower exercise capacity. PPVI leads to a reduction in RA size and improved passive RA emptying function. However, RA function was not associated with improved exercise performance and RV pump function.