bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments
Authors: Cote D , McClenaghan B , Desforges J , Fahner N A , Hajibabaei M , Chawarski J , Roul S , Singer G , Aubry C , Geoffroy M 
Published: November 2023

Abstract
The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located conventional methods, oblique midwater trawls and vertical multinets, to compare regional and sample-level diversity. We then assessed the concordance of ecological patterns across water column habitats and evaluated how DNA markers and the level of sampling effort influenced the inferred community. We found eDNA metabarcoding characterized regional diversity well, detecting more taxa while identifying similar ecological patterns as conventional samples. Within sampling locations, eDNA metabarcoding rarely detected taxa across more than one replicate. While more taxa were found in eDNA than oblique midwater trawls within sample stations, fewer were found compared to vertical multinets. Our simulations show greater eDNA sampling effort would improve concordance with conventional methods. We also observed that using taxonomic data from multiple markers generated ecological patterns most similar to those observed with conventional methods. Patterns observed with Exact Sequence Variants were more stable across markers suggesting they are more powerful for detecting change. eDNA metabarcoding is a valuable tool for identifying and monitoring biological hotspots but some methodological adjustments are recommended for deep ocean environments.
Two-scale methods for the normalized infinity Laplacian: rates of convergence
Authors: Li Wenbo , Salgado Abner J 
Published: November 2023

Abstract
We propose a monotone and consistent numerical scheme for the approximation of the Dirichlet problem for the normalized infinity Laplacian, which could be related to the family of the so-called two-scale methods. We show that this method is convergent and prove rates of convergence. These rates depend not only on the regularity of the solution, but also on whether or not the right-hand side vanishes. Some extensions to this approach, like obstacle problems and symmetric Finsler norms, are also considered.
Weak error analysis for strong approximation schemes of SDEs with super-linear coefficients
Authors: Wang Xiaojie , Zhao Yuying , Zhang Zhongqiang 
Published: November 2023

Abstract
We present an error analysis of weak convergence of one-step numerical schemes for stochastic differential equations (SDEs) with super-linearly growing coefficients. Following Milstein’s weak error analysis on the one-step approximation of SDEs, we prove a general result on weak convergence of the one-step discretization of the SDEs mentioned above. As applications, we show the weak convergence rates for several numerical schemes of half-order strong convergence, such as tamed and balanced schemes. Numerical examples are presented to verify our theoretical analysis.
Strategies to reduce antimicrobials in livestock and aquaculture, and their impact under field conditions: a structured scoping literature review
Authors: Sucena Afonso João , El Tholth Mahmoud , Mcintyre K Marie , Carmo Luís Pedro , Coyne Lucy , Manriquez Diego , Raboisson Didier , Lhermie Guillaume , Rushton Jonathan 
Published: November 2023

Abstract
Antimicrobial resistance is a pandemic problem, causing substantial health and economic burdens. Antimicrobials are extensively used in livestock and aquaculture, exacerbating this global threat. Fostering the prudent use of antimicrobials will safeguard animal and human health. A lack of knowledge about alternatives to replace antimicrobials, and their effectiveness under field conditions, hampers changes in farming practices.
This work aimed to understand the impact of strategies to reduce antimicrobial usage (AMU) in livestock and aquaculture, under field conditions, using a structured scoping literature review. The Extension for Scoping Reviews of the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines (PRISMA-ScR) were followed and the Patient, Intervention, Comparison, Outcome, Time and Setting (PICOTS) framework used. Articles were identified from CAB Abstracts, MEDLINE and Scopus. A total of 7505 unique research articles were identified, 926 of which were eligible for full-text assessment; 203 articles were included in data extraction. Given heterogeneity across articles in the way alternatives to antimicrobials or interventions against their usage were described, there was a need to standardize these by grouping them in categories.
There were differences in the impacts of the strategies between and within species; this highlights the absence of a ‘one-size-fits-all’ solution. Nevertheless, some options seem more promising than others, as their impacts were consistently equivalent or positive when compared with animal performance using antimicrobials. This was particularly the case for bioactive protein and peptides, and feed/water management. The outcomes of this work provide data to inform cost-effectiveness assessments of strategies to reduce AMU.
Free vibration analysis of Timoshenko pipes conveying fluid with gravity and different boundary conditions
Authors: Shui Bo , Li Yun-dong , Luo Yu-mei , Luo Fei 
Published: November 2023

Abstract
In this paper, the free vibration of Timoshenko pipes conveying fluid with gravity and different boundary conditions is analyzed by using the weak form quadrature element method. The dimensionless frequency and critical flow velocity have been calculated considering various parameters such as the mass ratio of pipe to fluid, slenderness ratio and gravity. The numerical results with different numbers of discrete points are tested, and the results show that the method has a fast convergence speed. Some numerical results are compared with the existing literature, which proves that the weak form quadrature element method has high accuracy and computational efficiency. This paper shows that the weak form quadrature element method is a preferred method for analyzing fluid-conveying pipes with various boundary conditions.
Development and feasibility of an educational module on medication reconciliation for hospital pharmacists in the United Arab Emirates: a pilot study
Authors: Farajallah Alaa , Zainal Hadzliana , Palaian Subish 
Published: November 2023

Abstract

Background
The practice of medication reconciliation by pharmacists is minimal in United Arab Emirates hospitals.

Objectives
To design an educational module for pharmacists on medication reconciliation and assess its feasibility.

Methods
The study consisted of three parts: A pre-educational module survey using a validated knowledge, perception, practice, and barriers questionnaire (Cronbach’s α = 0.78), delivery of the educational module, and participants’ feedback. An educational module (general introduction to medication reconciliation, what is medication reconciliation, how to do medication reconciliation, and practicing medication reconciliation) was developed based on Miller’s pyramid and validated by three experts and pilot-tested. The knowledge and perceptions of pharmacists were evaluated by comparing pre-post educational module survey results.

Results
The module influenced the participants’ knowledge and perception of medication reconciliation. All of the participants gave ‘positive’ feedback on the intervention and the methodology applied, and they agreed on the need for training and workshops related to medication reconciliation. In addition, all ‘agreed’ that a lack of knowledge about medication reconciliation is the biggest barrier to medication reconciliation practices. The results further illustrated that all pharmacists had a ‘positive’ experience and ‘agreed strongly’ on understanding the majority of the content.

Conclusion
This study was successful in answering the research question by enrolling suitable participants, managing the timeline, and possessing resources for completing the study and hence considered feasible. This module can be utilized in continuous professional development programs to improve pharmacists’ knowledge, perceptions, and practice toward the medication reconciliation process aiming to reduce drug therapy-related problems in hospital settings.
Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers?
Authors: Kimotho Roy Njoroge , Maina Solomon 
Published: November 2023

Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant–microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop–microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant–microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
ROS and RNS production, subcellular localization, and signaling triggered by immunogenic danger signals
Authors: Giulietti Sarah , Bigini Valentina , Savatin Daniel V 
Published: November 2023

Abstract
Plants continuously monitor the environment to detect changing conditions and to properly respond, avoiding deleterious effects on their fitness and survival. An enormous number of cell surface and intracellular immune receptors are deployed to perceive danger signals associated with microbial infections. Ligand binding by cognate receptors represents the first essential event in triggering plant immunity and determining the outcome of the tissue invasion attempt. Reactive oxygen and nitrogen species (ROS/RNS) are secondary messengers rapidly produced in different subcellular localizations upon the perception of immunogenic signals. Danger signal transduction inside the plant cells involves cytoskeletal rearrangements as well as several organelles and interactions between them to activate key immune signaling modules. Such immune processes depend on ROS and RNS accumulation, highlighting their role as key regulators in the execution of the immune cellular program. In fact, ROS and RNS are synergic and interdependent intracellular signals required for decoding danger signals and for the modulation of defense-related responses. Here we summarize current knowledge on ROS/RNS production, compartmentalization, and signaling in plant cells that have perceived immunogenic danger signals.
Accommodations of private and family life and non-traditional families: the limits of deference in cases of cross-border surrogacy before the European Court of Human Rights
Authors: Bracken Lydia 
Published: November 2023

Abstract
The European Court of Human Rights (ECtHR) case law on cross-border surrogacy establishes that a ‘general and absolute impossibility’ of obtaining recognition of the relationship, legally established in another country, between a surrogate-born child and their intended parents will violate the child’s right to respect for private life. This approach requires States to accommodate familial bonds created through cross-border surrogacy and limits the margin of appreciation available to States to determine their national response. In recent case law, the ECtHR has adopted an interventionist approach in respect of national decision-making and has gone further than might be expected under the principle of subsidiarity. Examination of the emerging body of jurisprudence on cross-border surrogacy, however, reveals a preference for ‘traditional’ family formations, with the ECtHR tending to adopt a less interventionist and more deferential approach to national decision-making where the family at the centre of the case deviates from the structure of the family reflected in the seminal cross-border surrogacy case of Mennesson v France App no 65192/11 (ECtHR, 26 June 2014). This approach leads to inconsistency in the cross-border surrogacy case law as it creates something of a moving target for the vindication of children’s rights in ‘less traditional’ family forms.
Quantification of Unsupported Thin-Film X-ray Spectra Using Bulk Standards
Authors: Ritchie Nicholas W M , Herzing Andrew , Oleshko Vladimir P 
Published: November 2023

Abstract
A quantification model which uses standard X-ray spectra collected from bulk materials to determine the composition and mass thickness of single-layer and multilayer unsupported thin films is presented. The multivariate model can be iteratively solved for single layers in which each element produces at least one visible characteristic X-ray line. The model can be extended to multilayer thin films in which each element is associated with only one layer. The model may sometimes be solved when an element is present in multiple layers if additional information is added in the form of independent k-ratios or model assumptions. While the algorithm is suitable for any measured k-ratios, it is particularly well suited to energy-dispersive X-ray spectrometry where the bulk standard spectra can be used to deconvolve peak interferences in the thin-film spectra. The algorithm has been implemented and made available in the Open Source application National Institute of Standards and Technology DTSA-II. We present experimental data and Monte Carlo simulations supporting the quantification model.
Quasar feedback survey: molecular gas affected by central outflows and by ∼10-kpc radio lobes reveal dual feedback effects in ‘radio quiet’ quasars
Authors: Girdhar A , Harrison C M , Mainieri V , Fernández Aranda R , Alexander D M , Arrigoni Battaia F , Bianchin M , Calistro Rivera G , Circosta C , Costa T , Edge A C , Farina E P , Kakkad D , Kharb P , Molyneux S J , Mukherjee D , Njeri A , S. Silpa , Venturi G , Ward S R 
Published: November 2023

ABSTRACT
We present a study of molecular gas, traced via CO (3–2) from Atacama Large Millimeter/submillimeter Array data, of four z &lt; 0.2, ‘radio quiet’, type 2 quasars (Lbol ∼ 1045.3–1046.2 erg s−1; L$_{\mathrm{1.4\, GHz}}\sim 10^{23.7}\!-\!10^{24.3}$ W Hz−1). Targets were selected to have extended radio lobes (≥ 10 kpc), and compact, moderate-power jets (1–10 kpc; Pjet ∼ 1043.2–1043.7 erg s−1). All targets show evidence of central molecular outflows, or injected turbulence, within the gas discs (traced via high-velocity wing components in CO emission-line profiles). The inferred velocities (Vout = 250–440 km s−1) and spatial scales (0.6–1.6 kpc), are consistent with those of other samples of luminous low-redshift active galactic nuclei. In two targets, we observe extended molecular gas structures beyond the central discs, containing 9–53 per cent of the total molecular gas mass. These structures tend to be elongated, extending from the core, and wrap-around (or along) the radio lobes. Their properties are similar to the molecular gas filaments observed around radio lobes of, mostly ‘radio loud’, brightest cluster galaxies. They have the following: projected distances of 5–13 kpc; bulk velocities of 100–340 km s−1; velocity dispersion of 30–130 km s−1; inferred mass outflow rates of 4–20 M⊙ yr−1; and estimated kinetic powers of 1040.3–1041.7 erg s−1. Our observations are consistent with simulations that suggest moderate-power jets can have a direct (but modest) impact on molecular gas on small scales, through direct jet–cloud interactions. Then, on larger scales, jet-cocoons can push gas aside. Both processes could contribute to the long-term regulation of star formation.
Main belt asteroids taxonomical information from dark energy survey data
Authors: Carruba V , Camargo J I B , Aljbaae S , Ferreira F S , Lin E , Figueiredo-Peixoto V , Banda-Huarca M V , Pieres A , Boufleur R C , da Costa L N , Abbott T M C , Aguena M , Allam Sahar S , Alves O , Bernardinelli P H , Bertin E , Brooks D , Carnero Rosell A , Carretero J , Pereira M E S , Davis T M , De Vicente J , Desai S , Doel P , Ferrero I , Friedel D , Frieman J , García-Bellido J , Gatti M , Giannini G , Gruen D , Gruendl R A , Herner K , Hinton S R , Hollowood D L , James D J , Kent S , Kuehn K , Lahav O , Marshall J L , Mena-Fernández J , Miquel R , Palmese A , Plazas Malagón A A , Rodríguez-Monroy M , Sanchez E , Santiago B , Schubnell M , Smith M , Suchyta E , Swanson M E C , Tarle G , Walker A R , Weaverdyck N , Wiseman P ,   (DES Collaboration)
Published: November 2023

ABSTRACT
While proper orbital elements are currently available for more than 1 million asteroids, taxonomical information is still lagging behind. Surveys like SDSS-MOC4 provided preliminary information for more than 100 000 objects, but many asteroids still lack even a basic taxonomy. In this study, we use Dark Energy Survey (DES) data to provide new information on asteroid physical properties. By cross-correlating the new DES data base with other data bases, we investigate how asteroid taxonomy is reflected in DES data. While the resolution of DES data is not sufficient to distinguish between different asteroid taxonomies within the complexes, except for V-type objects, it can provide information on whether an asteroid belongs to the C- or S-complex. Here, machine learning methods optimized through the use of genetic algorithms were used to predict the labels of more than 68 000 asteroids with no prior taxonomic information. Using a high-quality, limited set of asteroids with data on gri slopes and i − z colours, we detected 409 new possible V-type asteroids. Their orbital distribution is highly consistent with that of other known V-type objects.
The translational oscillation in oocyte and early embryo development
Authors: Iyyappan Rajan , Aleshkina Daria , Ming Hao , Dvoran Michal , Kakavand Kianoush , Jansova Denisa , del Llano Edgar , Gahurova Lenka , Bruce Alexander W , Masek Tomas , Pospisek Martin , Horvat Filip , Kubelka Michal , Jiang Zongliang , Susor Andrej 
Published: November 2023

AbstractTranslation is critical for development as transcription in the oocyte and early embryo is silenced. To illustrate the translational changes during meiosis and consecutive two mitoses of the oocyte and early embryo, we performed a genome-wide translatome analysis. Acquired data showed significant and uniform activation of key translational initiation and elongation axes specific to M-phases. Although global protein synthesis decreases in M-phases, translation initiation and elongation activity increases in a uniformly fluctuating manner, leading to qualitative changes in translation regulation via the mTOR1/4F/eEF2 axis. Overall, we have uncovered a highly dynamic and oscillatory pattern of translational reprogramming that contributes to the translational regulation of specific mRNAs with different modes of polysomal occupancy/translation that are important for oocyte and embryo developmental competence. Our results provide new insights into the regulation of gene expression during oocyte meiosis as well as the first two embryonic mitoses and show how temporal translation can be optimized. This study is the first step towards a comprehensive analysis of the molecular mechanisms that not only control translation during early development, but also regulate translation-related networks employed in the oocyte-to-embryo transition and embryonic genome activation.
ANGI-05. CDKN2A/B HOMOZYGOUS DELETION IN IDH-MUTANT ASTROCYTOMA ALTERS TUMOR CELL INVASION AND VASCULAR FORMATION
Authors: Grief Dustin , D'Angelo Fulvio , Caruso Francesca , Sereduk Christopher , Ceccarelli Michele , Hu Leland , Loftus Joseph , Tran Nhan , Ensign Shannon Fortin 
Published: November 2023

Abstract
High-grade gliomas represent the most common type of primary adult malignant brain tumor historically diagnosed and graded from histologic criteria alone. Gliomas harboring isocitrate dehydrogenase (IDH) 1 or 2 mutations are associated with lower grade tumors and portend a favorable prognosis relative to IDH-wildtype glioma. However, molecular profiling has identified additional alterations in lower grade gliomas that confer an aggressive high-grade phenotype and a worse clinical prognosis. Of these, the loss of CDKN2A/B in IDH-mutant astrocytoma is the strongest implicated alteration and is sufficient to define a grade 4 tumor regardless of histologic grade. However, there remain no effective therapies targeted at molecular subgroups in aggressive gliomas to date. Here, we sought to elucidate the biologic pathways and functional outcomes associated with the acquisition of high-grade behavior under loss of CDKN2A/B in IDH-mutant astrocytoma to inform future therapeutic strategies. We analyzed a cohort of patient IDH-mutant astrocytomas with whole exome and RNA sequencing data and found several candidate genes/pathways regulated concurrent with CDKN2A/B loss, including regulators of embryonic development, extracellular matrix organization and regulation of vascular processes. Moreover, we identified 1 tumor that displayed intratumoral heterogeneity of CDKN2A/B expression across biopsies. Using grade 4 IDH-mutant astrocytoma patient-derived (PDX) and established cell-lines harboring CDKN2A/B homozygous deletion, we then stably re-expressed cell cycle regulators p14, p15, and p16 using a Tet-inducible lentiviral system and confirmed their decreased proliferation as compared to parental lines. IDH-mutant cell lines with re-expression of p14, p15 or p16 were characterized by differential transcription factor activation and distinct vascular formation patterns as compared to parental lines. These lines also displayed an increased cell migration and invasive potential and were associated with enhanced integrin signaling through integrin beta-3. Together, our work supports a hypothesis of regional tumor evolution with distinct biologic phenotypes across IDH-mutant gliomas.