bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localized states in passive and active phase-field-crystal models
Authors: Holl Max Philipp , Archer Andrew J , Gurevich Svetlana V , Knobloch Edgar , Ophaus Lukas , Thiele Uwe 
Published: June 2021

Abstract
The passive conserved Swift–Hohenberg equation (or phase-field-crystal [PFC] model) describes gradient dynamics of a single-order parameter field related to density. It provides a simple microscopic description of the thermodynamic transition between liquid and crystalline states. In addition to spatially extended periodic structures, the model describes a large variety of steady spatially localized structures. In appropriate bifurcation diagrams the corresponding solution branches exhibit characteristic slanted homoclinic snaking. In an active PFC model, encoding for instance the active motion of self-propelled colloidal particles, the gradient dynamics structure is broken by a coupling between density and an additional polarization field. Then, resting and traveling localized states are found with transitions characterized by parity-breaking drift bifurcations. Here, we briefly review the snaking behavior of localized states in passive and active PFC models before discussing the bifurcation behavior of localized states in systems of (i) two coupled passive PFC models with common gradient dynamics, (ii) two coupled passive PFC models where the coupling breaks the gradient dynamics structure and (iii) a passive PFC model coupled to an active PFC model.
Accelerated Dirichlet–Robin alternating algorithms for solving the Cauchy problem for the Helmholtz equation
Authors: Berntsson Fredrik , Chepkorir Jennifer , Kozlov Vladimir 
Published: June 2021

Abstract
The Cauchy problem for Helmholtz equation, for moderate wave number $k^{2}$, is considered. In the previous paper of Achieng et al. (2020, Analysis of Dirichlet–Robin iterations for solving the Cauchy problem for elliptic equations. Bull. Iran. Math. Soc.), a proof of convergence for the Dirichlet–Robin alternating algorithm was given for general elliptic operators of second order, provided that appropriate Robin parameters were used. Also, it has been noted that the rate of convergence for the alternating iterative algorithm is quite slow. Thus, we reformulate the Cauchy problem as an operator equation and implement iterative methods based on Krylov subspaces. The aim is to achieve faster convergence. In particular, we consider the Landweber method, the conjugate gradient method and the generalized minimal residual method. The numerical results show that all the methods work well. In this work, we discuss also how one can approach non-symmetric differential operators by using similar operator equations and model problems which are used for symmetric differential operators.
Secrecy and Subjectivity: Double Agents and the Dark Underside of the International System
Authors: Lundborg Tom 
Published: June 2021

AbstractDrawing on a wide range of material, from memoirs of former spy masters to the highly acclaimed TV series Le Bureau des Légendes, this article shows how documentary as well as fictional accounts of double agents cast light on a “dark underside” of the international system. This dark underside is made up of exceptional spaces of secrecy in which intelligence organizations and spies operate. The article's main point of entry when analyzing these spaces is the intimate connection between secrecy and subjectivity. While secrecy as a social practice has received increased attention in sociological accounts of secret intelligence, the constitutive role of secrecy in relation to subjectivity is a much less explored theme. This theme, it is argued, becomes especially valuable for thinking about the conflicting lines that constitute the life and becoming of the double agent. In particular, it can be drawn on to show how this subject both is captured by the transparent norms and limits of the international state system and effectively transgresses those limits. In this way, rather than upholding a dichotomy of secrecy and transparency as two separable sides of the international system, the double agent emerges as a disruptive figure calling for its deconstruction.
Anti-biofilm activity of murepavadin against cystic fibrosis Pseudomonas aeruginosa isolates
Authors: Díez-Aguilar María , Ekkelenkamp Miquel , Morosini María-Isabel , Huertas Natalia , del Campo Rosa , Zamora Javier , Fluit Ad C , Tunney Michael M , Obrecht Daniel , Bernardini Francesca , Cantón Rafael 
Published: June 2021

Abstract

Objectives
To determine the activity of murepavadin in comparison with tobramycin, colistin and aztreonam, against cystic fibrosis (CF) Pseudomonas aeruginosa isolates growing in biofilms. The biofilm-epidemiological cut-off (ECOFF) values that include intrinsic resistance mechanisms present in biofilms were estimated.

Methods
Fifty-three CF P. aeruginosa isolates from respiratory samples were tested using the Calgary (closed system) device, while 4 [2 clinical (one smooth, one mucoid) and 2 reference strains] were tested using the BioFlux, a microfluidic open model of biofilm testing. Biofilm was stained with SYTO9® and propidium iodide. The minimal biofilm inhibitory concentration (MBIC) and the minimal biofilm eradication concentration (MBEC) were determined. The MBIC-ECOFF and the MBEC-ECOFF were calculated.

Results
Colistin, tobramycin and murepavadin presented similar MBIC50/MBIC90 values (4/32, 8/64 and 2/32, respectively). Murepavadin exhibited the lowest MBEC90 (64 mg/L). Aztreonam MBIC and MBEC values were higher than those of the other antibiotics tested. Tobramycin and murepavadin had the lowest MBEC-ECOFF (64 and 128 mg/L, respectively), while those of aztreonam and colistin exceeded 512 mg/L. Using the BioFlux, for the PAO1, PAO mutS and the smooth clinical strain, a significant difference (P &lt; 0.0125) was observed when comparing the fluorescence of treated and untreated biofilms. For the mucoid strain, only the biofilm treated with aztreonam (MBIC and MBEC) and tobramycin (MBEC) showed differences with respect to the untreated biofilm.

Conclusions
Murepavadin demonstrated good activity against P. aeruginosa biofilms both in open and closed systems. The MBIC-ECOFF and the MBEC-ECOFF are proposed as new parameters to estimate the activity of antibiotics on biofilms.
Modulation of jejunal mucosa-associated microbiota in relation to intestinal health and nutrient digestibility in pigs by supplementation of β-glucanase to corn–soybean meal-based diets with xylanase
Authors: Duarte Marcos Elias , Sparks Chris , Kim Sung Woo 
Published: June 2021

Abstract
This study aimed to evaluate the effects of increasing levels of β-glucanase on the modulation of jejunal mucosa-associated microbiota in relation to nutrient digestibility and intestinal health of pigs fed diets with 30% corn distiller’s dried grains with solubles and xylanase. Forty pigs at 12.4 ± 0.5 kg body weight (BW) were allotted in a randomized complete block design with initial BW and sex as blocks. Dietary treatments consisted of a basal diet with xylanase (1,500 endo-pentosanase units [EPU]/kg) and increasing levels of β-glucanase (0, 200, 400, and 600 U/kg) meeting nutrient requirements and fed to pigs for 21 d. Blood samples were collected on day 19. On day 21, all pigs were euthanized to collect intestinal tissues and digesta. Tumor necrosis factor-alpha, interleukin (IL)-6, and malondialdehyde were measured in the plasma and mid-jejunal mucosa. Viscosity was determined using digesta from the distal jejunum. Ileal and rectal digesta were evaluated to determine apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of nutrients. Mucosa samples from the mid-jejunum were utilized for microbiota sequencing. Data were analyzed using the MIXED procedure on SAS 9.4. Overall, increasing dietary β-glucanase tended to increase (linear; P = 0.077) the average daily gain of pigs. Increasing dietary β-glucanase affected (quadratic; P &lt; 0.05) the relative abundance of Bacteroidetes, reduced (linear; P &lt; 0.05) Helicobacter rappini, and increased (linear, P &lt; 0.05) Faecalibacterium prausnitzii. β-Glucanase supplementation (0 vs. others) tended to increase (P = 0.096) the AID of crude protein in the diet, whereas increasing dietary β-glucanase tended to increase (linear; P = 0.097) the ATTD of gross energy in the diet and increased (linear; P &lt; 0.05) the concentration of IL-6 in the plasma of pigs. In conclusion, increasing β-glucanase up to 600 U/kg feed in a diet containing xylanase (1,500 EPU/kg) modulated mucosa-associated microbiota by increasing the relative abundance of beneficial bacteria and reducing potentially harmful bacteria. Furthermore, increasing β-glucanase up to 600 U/kg feed in a diet containing xylanase (1,500 EPU/kg feed) enhanced the status of the intestinal environment and nutrient utilization, as well as reduced systemic inflammation of pigs, collectively resulting in moderate improvement of growth performance. Supplementing β-glucanase at a range of 312 to 410 U/kg with xylanase at 1,500 EPU/kg feed showed the most benefit on jejunal mucosa-associated microbiota and reduced systemic inflammation of pigs.
Beef production from cull dairy cows: a review from culling to consumption
Authors: Moreira Ligia C , Rosa Guilherme J M , Schaefer Daniel M 
Published: June 2021

Abstract
Although more than 3 million head of dairy cows enter the food supply chain in the U.S. every year, research on this topic remains limited and scarce. Meat production from dairy cows is a significant component of beef production, accounting for almost 10% of U.S. commercial beef production. Thus, the purpose of this review is to demonstrate the importance of dairy cows as a beef source, and to provide an overview on topics from farm to meat product—culling, marketing, transportation, welfare, body composition and its relationship with lactation particularities, carcass characteristics, meat quality, and traceability. Current scientific evidence has shown that culling a dairy cow at an appropriate time has beneficial effects on cow welfare and, consequently, cow value. During marketing the dairy cow is visually evaluated for health and factors associated with its expected carcass value; thus, marketing a well-conditioned cow will ensure that the animal is fit for transportation and provides high carcass yield. However, limitations such as low body condition score, lameness or mobility problems, and visual defects remain persistent. Even though beef harvest plants accommodate cows in all body composition states, the current carcass grade system does not reflect the mature cow industry needs. Therefore, improvement of the grading system could maximize carcass utilization and increase cow carcass value by recognizing subprimal cuts that could be merchandised as whole muscle cuts. Lastly, implementation of a traceability system would unify information from the farm to harvest assisting the industry in making further advancements.
The Effect of Summer Cover Crops and Strawberry Cultivars on the Twospotted Spider Mite,Tetranychus urticae(Acari: Tetranychidae) and the Predatory Mite,Neoseiulus californicus(Acari: Phytoseidae) in Organic Strawberry Production Systems in Florida
Authors: Olaniyi Omotola G , Rhodes Elena M , Chase Carlene A , Liburd Oscar E 
Published: June 2021

AbstractThe twospotted spider mite, Tetranychus urticae (Koch) (Acari: Tetranychidae), is a key pest of strawberries and many other crops worldwide. Cover cropping, selecting tolerant or resistant cultivars, and biological control are important strategies of an organic management plan. In this study, we examined the effect of summer cover crops and strawberry cultivars on populations of T. urticae and a commercially available predatory mite, Neoseiulus californicus McGregor (Acari: Phytoseiidae), commonly used for T. urticae management in Florida. In the 2013–2014 season, four cover crops and eight strawberry cultivars were screened at the research station and on a commercial organic strawberry farm. The following season, the most promising cover crops (sunn hemp and hairy indigo) and cultivars, ‘Sensation’, ‘Strawberry Festival’, and ‘Winterstar’ were tested at the research station and on two small organic farms. In the 2016–2017, 2017–2018, and 2018–2019 seasons, a 4-way mix of cover crops was compared to sunn hemp and hairy indigo. In 2016–2017, ‘Florida Radiance’ was added to the three previously selected cultivars. ‘Florida Beauty’ replaced ‘Strawberry Festival’ in 2017–2018 and 2018–2019, and ‘Florida Brilliance’ replaced ‘Winterstar’ in 2018–2019. The effects of summer cover crops on both T. urticae and N. californicus were minimal. ‘Florida Brilliance’, ‘Florida Radiance’, ‘Sensation’, ‘Strawberry Festival’, and ‘Winterstar’ had lower T. urticae populations and higher yields in most seasons at most locations. The establishment and abundance of N. californicus was similar on these cultivars and was generally higher where T. urticae populations were higher. Implications for organic strawberry production in Florida are discussed.
Nitric oxide signalling in roots is required for MYB72-dependent systemic resistance induced by Trichoderma volatile compounds in Arabidopsis
Authors: Pescador Leyre , Fernandez Iván , Pozo María J , Romero-Puertas María C , Pieterse Corné M J , Martínez-Medina Ainhoa 
Published: June 2021

Abstract
Volatile compounds (VCs) of Trichoderma fungi trigger induced systemic resistance (ISR) in Arabidopsis that is effective against a broad spectrum of pathogens. The root-specific transcription factor MYB72 is an early regulator of ISR and also controls the activation of iron-deficiency responses. Nitric oxide (NO) is involved in the regulation of MYB72-dependent iron-deficiency responses in Arabidopsis roots, but the role of NO in the regulation of MYB72 and ISR by Trichoderma VCs remains unexplored. Using in vitro bioassays, we applied Trichoderma VCs to Arabidopsis seedlings. Plant perception of Trichoderma VCs triggered a burst of NO in Arabidopsis roots. By suppressing this burst using an NO scavenger, we show the involvement of NO in Trichoderma VCs-mediated regulation of MYB72 expression. Using an NO scavenger and the Arabidopsis lines myb72 and nia1nia2 in in planta bioassays, we demonstrate that NO signalling is required in the roots for activation of Trichoderma VCs-mediated ISR against the leaf pathogen Botrytis cinerea. Analysis of the defence-related genes PR1 and PDF1.2 points to the involvement of root NO in priming leaves for enhanced defence. Our results support a key role of root NO signalling in the regulation of MYB72 expression during the activation of ISR by Trichoderma VCs.
Dust in the central parsecs of unobscured AGN: more challenges to the torus
Authors: Prieto M Almudena , Nadolny Jakub , Fernández-Ontiveros Juan A , Mezcua Mar 
Published: June 2021

ABSTRACT
A parsec-scale dusty torus is thought to be the cause of active galactic nuclei (AGN) dichotomy in the 1/2 types, narrow/broad emission lines. In a previous work, on the basis of parsec-scale resolution infrared/optical dust maps, it was found that dust filaments, few parsecs wide and several hundred parsecs long, were ubiquitous features crossing the centre of type 2 AGN, their optical thickness being sufficient to fully obscure the optical nucleus. This work presents the complementary view for type 1 and intermediate-type AGN. The same type of narrow, collimated, dust filaments are equally found at the centre of these AGN. The difference now resides in their location with respect to the nucleus, next to it but not crossing it, as it is the case in type 2, and their reduced optical thickness towards the centre, $A_V \lesssim 1.5\, \rm {mag}$, insufficient to obscure at ultraviolet nucleus wavelengths. It is concluded that large-scale, hundred parsecs to kiloparsecs long, dust filaments and lanes, reminiscent of those seen in the Milky Way, are a common ingredient to the central parsec of galaxies. Their optical thickness changes along their structure in type 2 reaching optical depths high enough to obscure the nucleus in full. Their location with respect to the nucleus and increasing gradient in optical depth towards the centre could naturally lead to the canonical type 1/2 AGN classification, making these filaments to play the role of the torus. Dust filaments and lanes show equivalent morphologies in molecular gas. Gas kinematic in the filaments indicates mass inflows at rates ${\lt}1 \, \mathrm{M}_{\odot }~ \mathrm{yr}^{-1}$.
Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies
Authors: Speidel Leo , Cassidy Lara , Davies Robert W , Hellenthal Garrett , Skoglund Pontus , Myers Simon R 
Published: June 2021

Abstract
Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of &gt;0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k−15k years ago, but is not observed in samples &gt;30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.
Selenium-deficient diet induces inflammatory response in the pig adrenal glands by activating TLR4/NF-κB pathway via miR-30d-R_1
Authors: Kaixin Zhang , Xuedie Gu , Jing Lan , Yiming Zhang , Khoso Pervez Ahmed , Zhaoyi Liu , Shu Li 
Published: June 2021

Abstract
Selenium (Se) is an important trace element to maintain the body's dynamic balance. Lack of Se can cause inflammation. Studies have shown that inflammation often leads to disorders of the hypothalamic–pituitary–adrenal axis, but the mechanism by which Se deficiency causes inflammation of the porcine adrenal glands is still unclear. In order to study the effect of Se deficiency on the adrenal glands of pigs, we obtained Se-deficient pig adrenal glands through a low-Se diet. The results of mass spectrometry showed that the Se content in the Se-deficient group was only one-tenth of the control group. We detected the expression of the toll-like receptor 4 (TLR4) and downstream factors by qRT-PCR and Western blotting, and found that the lack of Se affected the TLR4/NF-κB pathway. It is known that miR-155-3p, miR-30d-R_1, and miR-146b have all been verified for targeting relationship with TLR4. We confirmed by qRT-PCR that miR-30d-R_1 decreased most significantly in the Se-deficient pig model. Then we tested 25 selenoproteins and some indicators of oxidative stress. It is confirmed that Se deficiency reduces the antioxidant capacity and induces oxidative stress in pig adrenal tissue. In short, a diet lacking Se induces oxidative stress in pig adrenal tissues and leads to inflammation through the miR-30d-R_1/TLR4 pathway. This study provides a reference for the prevention of adrenal inflammation in pigs from a nutritional point of view.
Evidence for a chromosome origin unwinding system broadly conserved in bacteria
Authors: Pelliciari Simone , Dong Mei-Jing , Gao Feng , Murray Heath 
Published: June 2021

Abstract
Genome replication is a fundamental requirement for the proliferation of all cells. Throughout the domains of life, conserved DNA replication initiation proteins assemble at specific chromosomal loci termed replication origins and direct loading of replicative helicases (1). Despite decades of study on bacterial replication, the diversity of bacterial chromosome origin architecture has confounded the search for molecular mechanisms directing the initiation process. Recently a basal system for opening a bacterial chromosome origin (oriC) was proposed (2). In the model organism Bacillus subtilis, a pair of double-stranded DNA (dsDNA) binding sites (DnaA-boxes) guide the replication initiator DnaA onto adjacent single-stranded DNA (ssDNA) binding motifs (DnaA-trios) where the protein assembles into an oligomer that stretches DNA to promote origin unwinding. We report here that these core elements are predicted to be present in the majority of bacterial chromosome origins. Moreover, we find that the principle activities of the origin unwinding system are conserved in vitro and in vivo. The results suggest that this basal mechanism for oriC unwinding is broadly functionally conserved and therefore may represent an ancestral system to open bacterial chromosome origins.
External Validation and Modification of Nationwide Inpatient Sample Subarachnoid Hemorrhage Severity Score
Authors: Rawal Sapna , Rinkel Gabriel J E , Fang Jiming , Washington Chad W , Macdonald R Loch , Victor J Charles , Krings Timo , Kapral Moira K , Laupacis Andreas 
Published: June 2021

Abstract

BACKGROUND
The Nationwide Inpatient Sample Subarachnoid Hemorrhage (SAH) Severity Score (NIS-SSS) was developed as a measure of SAH severity for use in administrative databases. The NIS-SSS consists of International Classification of Diseases Ninth Revision (ICD-9) diagnostic and procedure codes derived from the SAH inpatient course and has been validated against the Hunt-Hess score (HH).

OBJECTIVE
To externally validate both the NIS-SSS and a modified version of the NIS-SSS (m-NIS-SSS) consisting of codes present only on admission, against the HH in a Canadian province-wide registry and administrative database of SAH patients.

METHODS
A total of 1467 SAH patients admitted to Ontario stroke centers between 2003 and 2013 with recorded HH were included. The NIS-SSS and m-NIS-SSS were validated against the HH by testing correlation between the NIS-SSS/m-NIS-SSS and HH, comparing discriminative ability of the NIS-SSS/m-NIS-SSS vs HH for poor outcome by calculating area under the curve (AUC), and comparing calibration of the NIS-SSS, m-NIS-SSS, and HH by plotting predicted vs observed outcome.

RESULTS
Correlation with HH was 0.417 (P ≤ .001) for NIS-SSS, and 0.403 (P ≤ .001) for m-NIS-SSS. AUC for prediction of poor outcome was 0.786 (0.764-0.808) for HH, 0.771 (0.748-0.793) for NIS-SSS, and 0.744 (0.721-0.767) for m-NIS-SSS. Calibration plots demonstrated that HH had the most accurate prediction of outcome, whereas the NIS-SSS and m-NIS-SSS did not accurately predict low risk of poor outcome.

CONCLUSION
The NIS-SSS and m-NIS-SSS have good external validity, and therefore, may be suitable to approximate traditional clinical scores of disease severity in SAH research using administrative data.