bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whitham modulation theory for the Zakharov–Kuznetsov equation and stability analysis of its periodic traveling wave solutions
Authors: Biondini Gino , Chernyavsky Alexander 
Published: November 2023

AbstractWe derive the Whitham modulation equations for the Zakharov–Kuznetsov equation via a multiple scales expansion and averaging two conservation laws over one oscillation period of its periodic traveling wave solutions. We then use the Whitham modulation equations to study the transverse stability of the periodic traveling wave solutions. We find that all periodic solutions traveling along the first spatial coordinate are linearly unstable with respect to purely transversal perturbations, and we obtain an explicit expression for the growth rate of perturbations in the long wave limit. We validate these predictions by linearizing the equation around its periodic solutions and solving the resulting eigenvalue problem numerically. We also calculate the growth rate of the solitary waves analytically. The predictions of Whitham modulation theory are in excellent agreement with both of these approaches. Finally, we generalize the stability analysis to periodic waves traveling in arbitrary directions and to perturbations that are not purely transversal, and we determine the resulting domains of stability and instability.
Preservice teachers’ errors in the creation and extension of sequences using color tiles: An exploratory study
Authors: Kurz Terri L. , Lee Mi Yeon 
Published: November 2023

AbstractRecognizing, building, describing, extending, and analyzing patterns are key components of algebraic reasoning. Oftentimes pattern‐based instruction is used to support the understanding of functions and variables. In this study, elementary preservice teachers (n = 23) were asked to explore, extend, explain, create equations for, and analyze linear, geometric, and quadratic integer patterns using color tiles. Then they created, extended, described, and analyzed their own patterns while working in groups (n = 8). The research question was: What algebraic errors do PSTs demonstrate in the process of constructing, explaining, and analyzing their own linear, geometric, and quadratic patterns using color tiles? The analysis, which focused on errors and misunderstandings preservice teachers demonstrated in their final unit, revealed three specific areas of difficulties: figural errors, explanation challenges, and improper use of algebraic language. Participants failed to connect their algebraic images in a coherent manner, there was confusion in articulating their algebraic thought processes, and algebraic terminology was improperly used. Implications for teaching and further research are described.
Teacher noticing: A literature review of mathematics and science teacher noticing conceptualizations
Authors: Weston Tracy L. , Amador Julie M. 
Published: November 2023

AbstractWe conducted a literature review to describe the conceptual use of noticing in pivotal mathematics and science education publications from 2002 to 2022 by tracing the language and ideas used to describe and study teacher noticing. Results from 12 highly cited or recently written publications indicated substantial differences in the assumptions and orientations of researchers which included: (a) differences in the primary theoretical construct, (b) differences in definitions of noticing and whether noticing is attending, making sense, both, or broader than cognition and includes context, culture, and/or perception, and (c) differences in researchers' beliefs about identifying what teachers should notice as compared to researchers who describe what teachers do notice. We propose directions for future writing practices in this field, including the need for researchers to explicitly state their definition of noticing. We conclude by reflecting on this project through some of Mason's foundational ideas about noticing.
Exploring perspectives of personal learning plans in a residency programme
Authors: Awad Sara , Turnnidge Jennifer , Cheung Jeffrey J. H. , Taylor David , Dalgarno Nancy , Schwartz Alan 
Published: November 2023

AbstractBackgroundPersonal learning plans (PLPs) have gained traction in postgraduate medical education as an avenue for enhancing resident learning. However, implementing PLPs in real‐world education settings presents unique challenges. To realise the potential of PLPs, we must understand the factors that influence the quality of PLP implementation. The purpose of this study was to explore the use and implementation of PLPs during residency training from the residents' and academic advisors' perspectives within a competency‐based residency programme.MethodsWe conducted semi‐structured interviews with residents (n = 18) and academic advisors (n = 9) in an Internal Medicine residency programme at a Canadian academic centre. Interviews were audio recorded, transcribed verbatim and analysed using open coding.FindingsThree higher order themes were developed to represent the participants' perceptions of implementing PLPs in a competency‐based residency programme: (a) setting the stage for learning, (b) fostering meaningful engagement and (c) learning through reflection. Results indicated that implementing PLPs requires collaboration between residents and academic advisors and supports from the broader programme and institution. PLP implementation is an iterative process that can provide a salient avenue for reflection and the development of self‐regulation skills.Discussion and ConclusionPLPs can be a useful tool to foster self‐regulated learning skills in residency education. It is imperative to consider how social and environmental supports can be enacted to facilitate engagement with, and implementation of, PLPs.
Successful treatment of sebaceous adenitis with oclacitinib and low‐dose prednisolone in a dog
Authors: Pérez‐Aranda María , Yotti César , Pérez Judith , Ginel Pedro J. 
Published: November 2023

AbstractFinding an effective and well‐tolerated treatment for canine idiopathic sebaceous adenitis (ISA) can be challenging. This case report describes an 8‐year‐old male Rottweiler with ISA successfully treated with a combination of oclacitinib and low doses of prednisolone.
Antimicrobial Resistance Laboratory Network’s multisite evaluation of the ThermoFisher Sensititre GN7F broth microdilution panel for antimicrobial susceptibility testing
Authors: Bhatnagar Amelia S. , Machado María-José , Patterson Logan , Anderson Karen , Abelman Rebecca L. , Bateman Allen , Biggs Angela , Bumpus-White Porscha , Craft Bradley , Howard Mondraya , LaVoie Stephen P. , Lonsway David , Sabour Sarah , Schneider Annah , Snippes-Vagnone Paula , Tran Michael , Torpey David , Valley Ann , Elkins Christopher A. , Karlsson Maria , Brown Allison C. 
Published: November 2023

ABSTRACT

In 2017, the Centers for Disease Control and Prevention (CDC) established the Antimicrobial Resistance Laboratory Network to improve domestic detection of multidrug-resistant organisms. CDC and four laboratories evaluated a commercial broth microdilution panel. Antimicrobial susceptibility testing using the Sensititre GN7F (ThermoFisher Scientific, Lenexa, KS) was evaluated by testing 100 CDC and Food and Drug Administration AR Isolate Bank isolates [40 Enterobacterales (ENT), 30
Pseudomonas aeruginosa
(PSA), and 30
Acinetobacter baumannii
(ACB)]. We assessed multiple amounts of transfer volume (TV) between the inoculum and tubed 11-mL cation-adjusted Mueller-Hinton broth: 1 µL [tribe Proteeae (P-tribe) only] and 10, 30, and 50 µL, resulting in respective CFU per milliter of 1 × 10
4
, 1 × 10
5
, 3 × 10
5
, and 5 × 10
5
. Four TV combinations were analyzed: standard (STD) [1 µL (P-tribe) and 10 µL], enhanced standard (E-STD) [1 µL (P-tribe) and 30 µL], 30 µL, and 50 µL. Essential agreement (EA), categorical agreement, major error (ME), and very major error (VME) were analyzed by organism then TVs. For ENT, the average EA across laboratories was <90% for 7 of 15 β-lactams using STD and E-STD TVs. As TVs increased, EA increased (>90%), and VMEs decreased. For PSA, EA improved as TVs increased; however, MEs also increased. For ACB, increased TVs provided slight EA improvements; all TVs yielded multiple VMEs and MEs. For ENT and ACB, Minimum inhibitory concentrations (MICs) trended downward using a 1 or 10 µL TV; there were no obvious MIC trends by TV for PSA. The public health and clinical consequences of missing resistance warrant increased TV of 30 µL for the GN7F, particularly for P-tribe, despite being considered “off-label” use.
Viral and host factors drive a type 1 Epstein–Barr virus spontaneous lytic phenotype
Authors: Willard Katherine A. , Barry Ashley P. , Oduor Cliff I. , Ong'echa John Michael , Bailey Jeffrey A. , Moormann Ann M. , Luftig Micah A. 
Published: November 2023

ABSTRACT

Epstein–Barr virus (EBV) is a cancer and autoimmune disease-associated gamma-herpesvirus that infects the majority of adults worldwide. After initial infection, EBV generally maintains a latent state in the host with minimal viral gene expression. However, aberrations in this prototypical latent viral state leading to increased lytic replication can cause upregulation of oncogenic factors, promoting EBV-associated diseases. For example, nasopharyngeal carcinoma and post-transplant lymphoproliferative disease have strong associations with EBV lytic replication. Another EBV-associated disease, endemic Burkitt lymphoma (BL), is an extremely fast-growing cancer found primarily in children in malaria-endemic regions of Sub-Saharan Africa. Nearly all endemic BL tumors are infected with EBV and the hallmark of the disease is high levels of oncogenic c-Myc expression due to an immunoglobulin/
Myc
translocation. In this study, we describe spontaneous lytic phenotypes in EBV strains isolated from Kenyan BL patient tumors. We specifically focus on a novel Type 1 spontaneously lytic EBV strain and describe viral and host factors that could contribute to this phenotype. We found that cells infected with spontaneous lytic strains have lower c-Myc protein stability and express high levels of the plasma cell marker SLAMF7. Additionally, spontaneous lytic strains have altered latency states, which appear to further promote their lytic phenotypes. The isolation of spontaneously lytic EBV strains from endemic BL tumors provides more evidence that EBV may not maintain a prototypically latent state in patients with EBV-associated diseases and raises the possibility that promiscuous lytic activity may contribute to the formation of these diseases.

IMPORTANCE
Epstein–Barr virus (EBV) infects over 95% of adults worldwide. Given its connection to various cancers and autoimmune disorders, it is important to understand the mechanisms by which infection with EBV can lead to these diseases. In this study, we describe an unusual spontaneous lytic phenotype in EBV strains isolated from Kenyan endemic Burkitt lymphoma patients. Because lytic replication of EBV has been linked to the pathogenesis of various diseases, these data could illuminate viral and host factors involved in this process.
Genome sequences of isolates from high-touch surfaces in washrooms at a post-secondary institution
Authors: Holman Devin B. , James-Gzyl Katherine E. , Rieberger Rachael L. , Keim Kiya S. , Carson Michael J. , Norris Sean G. , Esmaeili Taheri Ahmad 
Published: November 2023

ABSTRACT

We report here the draft genome sequences of
Brevibacterium casei
(
n
= 1),
Heyndrickxia oleronia
(
n
= 1),
Kocuria palustris
(
n
=1),
Microbacterium
spp. (
n
= 5),
Staphylococcus cohnii
(
n
= 3), and
Staphylococcus epidermidis
isolated from high-touch surfaces in washrooms at a post-secondary institution.
Colonization of larval zebrafish (
Danio rerio
) with adherent-invasive
Escherichia coli
prevents recovery of the intestinal mucosa from drug-induced enterocolitis
Authors: Flores Erika , Dutta Soumita , Bosserman Rachel , van Hoof Ambro , Krachler Anne-Marie 
Published: November 2023

ABSTRACT

Inflammatory bowel disease (IBD) is a broad term for a range of chronic intestinal disorders, including Crohn’s disease and ulcerative colitis. The global prevalence of IBD is rising, with over one million patients affected in the United States alone. Adherent-invasive
Escherichia coli
(AIEC) is a pathobiont frequently found in IBD biopsies. AIEC adhere to and invade epithelial cells, and can survive inside phagocytes
in vitro
. However, how AIEC contribute to IBD
in vivo
remains unclear. Here, we established a larval zebrafish (
Danio rerio
) model to study the interplay between pre-existing intestinal inflammation and AIEC colonization of the gut. We used the pro-inflammatory drug dextran sulfate sodium (DSS) to induce intestinal inflammation. This was followed by food-borne infection of larvae with AIEC using the protozoan
Paramecium caudatum
, a natural prey, as a vehicle. We show that AIEC more robustly colonize the zebrafish gut and are cleared slower than non-pathogenic
E. coli
. In addition, DSS-induced enterocolitis increases bacterial burden and decreases bacterial clearance in the larval gut. We benchmark our model against existing rodent models using two mutants deficient in the known AIEC virulence factors FimH and IbeA, which have virulence defects in both rodent and the larval zebrafish model. Finally, we show that AIEC colonization exacerbates DSS-induced enterocolitis and prevents recovery from inflammation-induced damage. In conclusion, we established a high-throughput, genetically tractable model to study AIEC-host interactions in the context of pre-existing inflammation.

IMPORTANCE
Although inflammatory bowel diseases are on the rise, what factors influence IBD risk and severity, and the underlying mechanisms remain to be fully understood. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible to pro-inflammatory stimuli. It is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host in order to develop successful therapeutics. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models and can be utilized to address these gaps in knowledge.
The versatility of the putative transient receptor potential ion channels in regulating the calcium signaling in
Aspergillus nidulans
Authors: Wang Hongchen , Gao Renwei , Zhang Yuanwei , Lu Ling 
Published: November 2023

ABSTRACT

Transient receptor potential (TRP) channels are evolutionarily conserved integral membrane proteins. They serve as crucial mediators of sensory signals and have profound effects on cellular functions. However, many functions of the TRP family remain to be explored. In this study, the biological functions of three potential TRP channels, TrpA, TrpB, and TrpC, in
Aspergillus nidulans
have been verified. Green fluorescent protein labeling indicated that these TRP channels have distinct localization patterns. TrpA was primarily located at hyphal tips, TrpB showed a localization pattern resembling the Golgi apparatus, and TrpC displayed a possible ER-like localization pattern. Findings suggested that these TRP channels may be involved in different physiological processes. Deletion or reduced expression of TrpA resulted in severe growth defects and abolished conidiation. Moreover, TrpA may have multiple roles during fungal development, as TrpA mutants caused significant changes in gene expression. The lack of TrpB resulted in colony defects in a calcium-dependent manner, especially under high-temperature conditions. These defects in Δ
trpB
can be largely rescued by adding calcium, indicating that TrpB is required in low-calcium conditions. The deletion of TrpC did not exhibit any detectable phenotypes under tested cultural conditions. However, when major calcium channels MidA/CchA or PmrA were absent, the lack of TrpC further exacerbated the colony defects, implying that TrpC serves as a supplementary function. In conclusion, TRP channels are involved in a wide range of physiological processes and findings provide a valuable reference for investigating the functions of TRP proteins in other fungal or eukaryotic species.

IMPORTANCE

Transient receptor potential (TRP) ion channels are evolutionarily conserved integral membrane proteins with non-selective ion permeability, and they are widely distributed in mammals and single-cell yeast and serve as crucial mediators of sensory signals. However, the relevant information concerning TRP channels in
Aspergillus nidulans
remains inadequately understood. In this study, by gene deletion, green fluorescent protein tagging, and cytosolic Ca
2+
transient monitoring techniques, the biological functions of three potential TRP channels (TrpA, TrpB, and TrpC) have been explored for which they play distinct and multiple roles in hyphal growth, conidiation, responsiveness to external stress, and regulation of intracellular Ca
2+
homeostasis. The findings of this study on the functions of potential TRP channels in
A. nidulans
may serve as a valuable reference for understanding the roles of TRP homologs in industrial or medical strains of
Aspergillus
, as well as in other filamentous fungi.
Distinct mode of action of a highly stable, engineered phage lysin killing Gram-negative bacteria
Authors: Gerstmans Hans , Duyvejonck Lisa , Vázquez Roberto , Staes Ines , Borloo Jimmy , Abdelkader Karim , Leroy Jeroen , Cremelie Emma , Gutiérrez Diana , Tamés-Caunedo Héctor , Ruas-Madiedo Patricia , Rodríguez Ana , Aertsen Abram , Lammertyn Jeroen , Lavigne Rob , Briers Yves 
Published: November 2023

ABSTRACT

Therapeutic options to treat bacterial infections caused by Gram-negative pathogens are limited due to the spread of multidrug resistance. Protein engineering of phage-derived lysins can play a key role in the search for new antimicrobial compounds targeting Gram-negative pathogens. A previous high-throughput screen of a combinatorial lysin library identified lysin 1D10 active against
Acinetobacter baumannii
under elevated human serum concentrations. The engineered lysin consists of four modules: cecropin A, a linker, cell wall-binding domain, and an enzymatic active domain. Using time-lapse microscopy, we show that 1D10 has a distinct antibacterial mode of action resulting in local cell wall bulging at the septum instead of cell-wide lysis, as observed for previously reported engineered lysins that target Gram-negative bacteria. Our results indicate that the activity of 1D10 relies on the antibacterial activity of both cecropin A (CecA) and the enzymatically active domain. Based on a truncation analysis, the role of each of the four modules of 1D10 was dissected. We further compared the antibacterial spectrum, thermostability, and cytotoxicity of cecropin A alone and lysin 1D10. Both lysin 1D10 and CecA are most active against
A. baumannii
and are not cytotoxic toward human keratinocytes. Lysin 1D10 unfolds at 57°C and has a remarkable refolding capacity, as it regains its activity even after exposure to 90°C and sterilization conditions, whereas CecA is inactivated at 70°C. Overall, the present study shows that an improved understanding of the killing mechanism and the protein properties will further support lysin engineering designs in the future.

IMPORTANCE

Engineered lysins are considered as highly promising alternatives for antibiotics. Our previous screening study using VersaTile technology identified 1D10 as a possible lead compound with activity against
Acinetobacter baumannii
strains under elevated human serum concentrations. In this manuscript, we reveal an unexpected mode of action and exceptional thermoresistance for lysin 1D10. Our findings shed new light on the development of engineered lysins, providing valuable insights for future research in this field.
Origin of Archean Pb isotope variability through open-system Paleoarchean crustal anatexis
Authors: Hartnady M.I.H. , Kirkand C.L. , Johnson S.P. , Smithies R.H. , Doucet L.S. , Mole D.R. 
Published: November 2023

Abstract
Lead isotopic data imply that thorium and uranium were fractionated from one another in Earth’s early history; however, the origin of this fractionation is poorly understood. We report new in situ Pb isotope data from orthoclase in 144 granites sampled across the Archean Yilgarn craton (Western Australia) to characterize its Pb isotope variability and evolution. Granite Pb isotope compositions reveal three Pb sources, a mantle-derived Pb reservoir and two crustal Pb reservoirs, distinguished by their implied source 232Th/238U (κPb). High-κPb granites reflect sources with high 232Th/238U (~4.7) and are largely co-located with Eoarchean–Paleoarchean crust. The Pb isotope compositions of most granites, and those of volcanic-hosted massive sulfide (VHMS) and gold ores, define a mixing array between a mantle Pb source and a Th-rich Eoarchean–Paleoarchean source. Pb isotope modeling indicates that the high-κPb source rocks experienced Th/U fractionation at ca. 3.3 Ga. As Th/U fractionation in the Yilgarn craton must have occurred before Earth’s atmosphere was oxygenated, subaerial weathering cannot explain the apparent differences in their geochemical behavior. Instead, the high Th/U source reflects Eoarchean–Paleoarchean rocks that experienced prior high-temperature metamorphism, partial melting, and melt loss in the presence of a Th-sequestering mineral like monazite. Archean Pb isotope variability thus has its origins in open-system high-temperature metamorphic processes responsible for the differentiation and stabilization of Earth’s continental crust.
Giant Planar Hall Effect in an Ultra-Pure Mercury Selenide Single Crystal Sample
Authors: Bobin S. B. , Lonchakov A. T. 
Published: November 2023

A giant planar Hall effect with an amplitude of about 50 mΩ cm at a temperature of T = 80 K in a magnetic field of 10 T has been detected in an ultra-pure HgSe single crystal sample with an electron density of 5.5 × 1015 cm–3. Its oscillating dependence on the rotation angle of the sample in various magnetic fields has been determined. Attributes (oscillation period, positions of extrema, correlation between the amplitudes of planar Hall and planar longitudinal magnetoresistance) indicate that the planar Hall effect in this nonmagnetic gapless semimetal with an isotropic Fermi surface originates from the chiral anomaly. This is a solid argument for the topological nature of the electronic spectrum of HgSe.
Diagnosing quantum phase transitions via holographic entanglement entropy at finite temperature
Authors: Gong Huajie , Fu Guoyang , Liu Peng , Chen Chongye , Kuang Xiao-Mei , Wu Jian-Pin 
Published: November 2023

AbstractWe investigate the behavior of the holographic entanglement entropy (HEE) in proximity to the quantum critical points (QCPs) of the metal-insulator transition (MIT) in the Einstein–Maxwell-dilaton-axions (EMDA) model. Since both the metallic phase and the insulating phase are characterized by distinct IR geometries, we used to expect that the HEE itself characterizes the QCPs. This expectation is validated for certain cases, however, we make a noteworthy observation: for a specific scenario where $$-1<\gamma \le -1/3$$

-
1
<
γ
≤
-
1
/
3

, with $$\gamma $$
γ
as a coupling parameter, it is not the HEE itself but rather the second-order derivative of HEE with respect to the lattice wave number that effectively characterizes quantum phase transitions (QPTs). This distinction arises due to the influence of thermal effects. These findings present novel insights into the interplay between HEE and QPTs in the context of the MIT, and have significant implications for studying QPTs at finite temperatures.