bluuebunny/crossref_metadata_2025 huggingface dataset:
Sub-Sized Creep Specimen Testing for High Throughput and Post-Irradiation Testing
Authors: McMurtrey Michael D. , Mohale Ninad
Published: November 2023

Testing on small, sub-sized specimens is of interest in cases where material is limited, or where the material/specimens are difficult to handle, as is the case for irradiation experiments. However, it is known that sub-sized specimens are susceptible to error if the specimen size is too small to achieve bulk properties. It is critical that the test results be validated against standard specimens to ensure the results are reasonable and give the desired bulk properties. This will help continue to build a database of test results that can be used to further increase the understanding of applicability and limitations in using small specimen testing.

This paper covers the preliminary results of sub-sized creep testing performed at Idaho National Laboratory on Alloy 617 and compares the creep properties to prior data generated for use in the Alloy 617 Code Case. The goal of this testing is to allow for higher throughput generation of creep data that can be used in computational models, and ultimately for material qualification. The preliminary results generally show good agreement between the 1.0 mm thick sub-sized specimens and the standard sized specimen tests, though with larger variation in the results of the thinner specimens. Future work will continue generating creep tests, as well as include more detailed microscopy that will be used to better understand how these tests could be reliably used.
Evaluation of the Inherent LBB Behavior of Small-Diameter Class 1 and 2 Nuclear Piping Systems
Authors: Twombly Elizabeth , Hill Lance , Wilkowski Gery , Brust Frederick , Lin Bruce , Tregoning Robert
Published: November 2023

Traditional Leak-Before-Break (LBB) evaluations are generally easy to meet the acceptance criteria for large-diameter primary pipe loops but become more difficult to satisfy as the pipe diameter decreases. An advanced LBB method, the Engineering Mechanics Corporation of Columbus (Emc2) Robust LBB procedure, was implemented for representative 3-inch and 4-inch nominal pipe size pipe systems that are employed at a U.S. pressurized water reactor (PWR) and boiling water reactor (BWR), respectively. The Robust LBB procedure uses a finite element model of a piping system which accounts for plasticity from the applied forces and moments.

In the Robust LBB procedure, it is necessary to input the seismic loading time-history inputs due to the plasticity making the traditional design elastic response-spectrum analyses unusable. The inertial and seismic anchor motion (SAM) contribution can be based on the maximum allowable elastic stress limits for reaching Service Level D loading. The SAM stresses in a dynamic displacement-time stress analysis are dependent on the difference between the applied and natural frequencies of the pipe system, i.e., if there is an exciting frequency right at the natural frequency to reach the SL-D inertial stress limit, the displacement amplitudes are small and consequently the SAM stresses are small.

The analysis procedures were: first, the displacement-time input at the anchor points with different frequencies around the first natural frequency of the pipe system was done with elastic uncracked analyses to reach the moment corresponding to 3Sm inertial stresses. Second, the uncracked pipe analysis is performed with the nonlinear stress-strain curve to calculate the reduction of the applied moments compared to the design elastic limits with the same forcing function. A circumferential through-wall crack (TWC) of a small size was then inserted at the high stress location using a cracked-pipe-element (CPE) methodology. The crack size was increased until it was at least 75% around the circumference or pipe severance/rupture was reached.

The findings to date for the two pipe-system geometries involving 3-inch and 4-inch diameter A106B and TP304 stainless steel pipes, show that when doing the FE time-dependent analyses at the maximum SL-D inertial stress loading, the circumferential cracks were stable for TWC lengths greater than 75-percent of the circumference. Simply introducing plasticity into the piping system has a significant impact on the peak applied moment for the same displacement-time history. As the crack size is increased in the peak applied moment continues to decline due to flexibility changes in the pipe system. The decrease in moment as a function of crack size shows that the piping system under seismic inertial loading is acting more like it is under displacement-controlled loading rather than load-controlled loading.
Development of Seismic Response Analysis Method of Piping System: Proposal of the Nonlinear Spring Model for Piping Support Structures
Authors: Takito Kiyotaka , Okuda Yukihiko , Nishida Akemi , Li Yinsheng
Published: November 2023

In probabilistic risk assessment against earthquakes for nuclear power plants, developing a realistic response analysis method for the fragility assessment of piping systems considering input seismic motions exceeding the design assumptions is critical. Piping systems typically exhibit complex three-dimensional shapes, and the arrangement and stiffness of the piping support structures significantly affect the response characteristics of the entire piping system. Therefore, developing a realistic response analysis method for piping systems and support structures is necessary. This study proposes a method for modeling the elastoplastic hysteresis characteristics of piping support structures to establish a seismic response analysis method for piping systems and support structures. First, the authors propose an elastoplastic spring model that can express the elastoplastic hysteresis characteristics of a piping support structure. Subsequently, using this model, the authors perform a simulation analysis for the loading test of a piping support structure. The analysis and test results correlated well, confirming the effectiveness of the proportion of the model. The main contents, including the proportion of the elastoplastic spring model, the simulation analysis of the loading test, and the comparison between the analysis solutions and the test results, are reported in this paper.
A Qualitative Examination of Online Practices During the COVID-19 Pandemic and Observational Preferences Within Physical Education
Authors: Murfay Ken , Pyszczynski Sarah , Erwin Heather
Published: November 2023

Purpose: This qualitative case study examined students’ interpretations of their physical activity (PA) experiences within in-person and online physical education and how that influenced their PA self-efficacy. Method: The study participants were 40 (24 females) current high school students from three different schools who participated in focus group semistructured interviews. Results: Two themes were developed during analysis of the coded data: (a) online participation in PA within physical education was awkward and (b) students had a variety of observational preferences based on perceived and actual similarities/differences between students and their teachers, peers, and people within online videos. Discussion/Conclusion: The design of PA experiences should attempt to support or increase students’ PA self-efficacy by limiting students’ feelings of being uncomfortable or on display, increasing students’ opportunities to learn from each other in comfortable ways, and providing students with detailed demonstrations from teachers and peers with a variety of skill levels.
An injury-responsivemmp14benhancer is required for heart regeneration
Authors: Zlatanova Ivana , Sun Fei , Wu Roland S. , Chen Xiaoxin , Lau Bryan H. , Colombier Pauline , Sinha Tanvi , Celona Barbara , Xu Shan-Mei , Materna Stefan C. , Huang Guo N. , Black Brian L.
Published: November 2023

Mammals have limited capacity for heart regeneration, whereas zebrafish have extraordinary regeneration abilities. During zebrafish heart regeneration, endothelial cells promote cardiomyocyte cell cycle reentry and myocardial repair, but the mechanisms responsible for promoting an injury microenvironment conducive to regeneration remain incompletely defined. Here, we identify the matrix metalloproteinase Mmp14b as an essential regulator of heart regeneration. We identify a TEAD-dependentmmp14bendothelial enhancer induced by heart injury in zebrafish and mice, and we show that the enhancer is required for regeneration, supporting a role for Hippo signaling upstream ofmmp14b. Last, we show that MMP-14 function in mice is important for the accumulation of Agrin, an essential regulator of neonatal mouse heart regeneration. These findings reveal mechanisms for extracellular matrix remodeling that promote heart regeneration.
Storyline attribution of human influence on a record-breaking spatially compounding flood-heat event
Authors: Wang Jun , Chen Yang , Tett Simon F. B. , Stone Dáithí , Nie Ji , Feng Jinming , Yan Zhongwei , Zhai Panmao , Ge Quansheng
Published: November 2023

Attribution of compound events informs preparedness for emerging hazards with disproportionate impacts. However, the task remains challenging because space-time interactions among extremes and uncertain dynamic changes are not satisfactorily addressed in the well-established attribution framework. For attributing the 2020 record-breaking spatially compounding flood-heat event in China, we conduct a storyline attribution analysis by designing simulation experiments via a weather forecast model, quantifying component-based attributable changes, and comparing with historical flow analogs. We quantify that given the large-scale circulation, anthropogenic influence to date has exacerbated the extreme Mei-yu rainfall in the mid-lower reaches of the Yangtze River during June–July 2020 by ~6.5% and warmed the co-occurring seasonal extreme heat in South China by ~1°C. Our projections show a further intensification of the compound event by the end of this century, with moderate emissions making the rainfall totals ~14% larger and the season ~2.1°C warmer in South China than the 2020 status.
Callosal inputs generate side-invariant receptive fields in the barrel cortex
Authors: Montanari Roberto , Alegre-Cortés Javier , Alonso-Andrés Alicia , Cabrera-Moreno Jorge , Navarro Ismael , García-Frigola Cristina , Sáez María , Reig Ramón
Published: November 2023

Barrel cortex integrates contra- and ipsilateral whiskers’ inputs. While contralateral inputs depend on the thalamocortical innervation, ipsilateral ones are thought to rely on callosal axons. These are more abundant in the barrel cortex region bordering with S2 and containing the row A-whiskers representation, the row lying nearest to the facial midline. Here, we ask what role this callosal axonal arrangement plays in ipsilateral tactile signaling. We found that novel object exploration with ipsilateral whiskers confines c-Fos expression within the highly callosal subregion. Targeting this area with in vivo patch-clamp recordings revealed neurons with uniquely strong ipsilateral responses dependent on the corpus callosum, as assessed by tetrodotoxin silencing and by optogenetic activation of the contralateral hemisphere. Still, in this area, stimulation of contra- or ipsilateral row A-whiskers evoked an indistinguishable response in some neurons, mostly located in layers 5/6, indicating their involvement in the midline representation of the whiskers’ sensory space.
“Robots for good”: Ten defining questions
Authors: Šabanović Selma , Charisi Vicky , Belpaeme Tony , Bethel Cindy L. , Matarić Maja , Murphy Robin , Levy-Tzedek Shelly
Published: November 2023

Ten questions to guide reflection and assessment of the “good” in robotics projects are suggested.
Radiation-induced bone loss in mice is ameliorated by inhibition of HIF-2α in skeletal progenitor cells
Authors: Guo Wendi , Hoque Jiaul , Garcia Garcia Carolina J. , Spiller Kassandra V. , Leinroth Abigail P. , Puviindran Vijitha , Potnis Cahil K. , Gunn Kiana A. , Newman Hunter , Ishikawa Koji , Fujimoto Tara N. , Neill Denae W. , Delahoussaye Abagail M. , Williams Nerissa T. , Kirsch David G. , Hilton Matthew J. , Varghese Shyni , Taniguchi Cullen M. , Wu Colleen
Published: November 2023

Radiotherapy remains a common treatment modality for cancer despite skeletal complications. However, there are currently no effective treatments for radiation-induced bone loss, and the consequences of radiotherapy on skeletal progenitor cell (SPC) survival and function remain unclear. After radiation, leptin receptor–expressing cells, which include a population of SPCs, become localized to hypoxic regions of the bone and stabilize the transcription factor hypoxia-inducible factor-2α (HIF-2α), thus suggesting a role for HIF-2α in the skeletal response to radiation. Here, we conditionally knocked out HIF-2α in leptin receptor–expressing cells and their descendants in mice. Radiation therapy in littermate control mice reduced bone mass; however, HIF-2α conditional knockout mice maintained bone mass comparable to nonirradiated control animals. HIF-2α negatively regulated the number of SPCs, bone formation, and bone mineralization. To test whether blocking HIF-2α pharmacologically could reduce bone loss during radiation, we administered a selective HIF-2α inhibitor called PT2399 (a structural analog of which was recently FDA-approved) to wild-type mice before radiation exposure. Pharmacological inhibition of HIF-2α was sufficient to prevent radiation-induced bone loss in a single-limb irradiation mouse model. Given that ~90% of patients who receive a HIF-2α inhibitor develop anemia because of off-target effects, we developed a bone-targeting nanocarrier formulation to deliver the HIF-2α inhibitor to mouse bone, to increase on-target efficacy and reduce off-target toxicities. Nanocarrier-loaded PT2399 prevented radiation-induced bone loss in mice while reducing drug accumulation in the kidney. Targeted inhibition of HIF-2α may represent a therapeutic approach for protecting bone during radiation therapy.
Enhanced mTORC1 signaling and protein synthesis in pathologic α-synuclein cellular and animal models of Parkinson’s disease
Authors: Khan Mohammed Repon , Yin Xiling , Kang Sung-Ung , Mitra Jaba , Wang Hu , Ryu Taekyung , Brahmachari Saurav , Karuppagounder Senthilkumar S. , Kimura Yasuyoshi , Jhaldiyal Aanishaa , Kim Hyun Hee , Gu Hao , Chen Rong , Redding-Ochoa Javier , Troncoso Juan , Na Chan Hyun , Ha Taekjip , Dawson Valina L. , Dawson Ted M.
Published: November 2023

Pathologic α-synuclein plays an important role in the pathogenesis of α-synucleinopathies such as Parkinson’s disease (PD). Disruption of proteostasis is thought to be central to pathologic α-synuclein toxicity; however, the molecular mechanism of this deregulation is poorly understood. Complementary proteomic approaches in cellular and animal models of PD were used to identify and characterize the pathologic α-synuclein interactome. We report that the highest biological processes that interacted with pathologic α-synuclein in mice included RNA processing and translation initiation. Regulation of catabolic processes that include autophagy were also identified. Pathologic α-synuclein was found to bind with the tuberous sclerosis protein 2 (TSC2) and to trigger the activation of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1), which augmented mRNA translation and protein synthesis, leading to neurodegeneration. Genetic and pharmacologic inhibition of mTOR and protein synthesis rescued the dopamine neuron loss, behavioral deficits, and aberrant biochemical signaling in the α-synuclein preformed fibril mouse model and
Drosophila
transgenic models of pathologic α-synuclein–induced degeneration. Pathologic α-synuclein furthermore led to a destabilization of the TSC1-TSC2 complex, which plays an important role in mTORC1 activity. Constitutive overexpression of TSC2 rescued motor deficits and neuropathology in α-synuclein flies. Biochemical examination of PD postmortem brain tissues also suggested deregulated mTORC1 signaling. These findings establish a connection between mRNA translation deregulation and mTORC1 pathway activation that is induced by pathologic α-synuclein in cellular and animal models of PD.
EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance
Authors: Zhang Ruizhen , Wang Yan
Published: November 2023

Two-component systems (TCSs) widely exist in bacteria and assist bacteria in adjusting behaviors to adapt to environmental changes after sensing environmental signals and transducing information into cells. As a member of TCSs in
Escherichia coli
, after sensing signals, EvgS/EvgA mainly induces multiple resistances, such as acid and multidrug resistance, and increases bacterial adherence. Notably, the EvgS is one of the five unorthodox sensors in
E. coli
, which has an internal phosphorelay based on the structure with extra domains different from other orthodox sensors. Here, we summarize research on EvgS and EvgA published since 1994. This review includes comprehensive knowledge of EvgS/EvgA and focuses on the EvgS structure and the multiple resistance conferred by EvgS/EvgA. Furthermore, we discuss the unsolved questions of EvgS/EvgA and propose assumptions and inferences on the EvgS structure and the EvgS/EvgA function.

IMPORTANCE

EvgS/EvgA, one of the five unorthodox two-component systems in
Escherichia coli
, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
Impact of surface receptors TLR2, CR3, and FcγRIII on
Rhodococcus equi
phagocytosis and intracellular survival in macrophages
Authors: da Silveira Bibiana Petri , Barhoumi Rola , Bray Jocelyne M. , Cole-Pfeiffer Hannah M. , Mabry Cory J. , Burghardt Robert C. , Cohen Noah D. , Bordin Angela I.
Published: November 2023

The virulence-associated protein A (VapA) produced by virulent
Rhodococcus equi
allows it to replicate in macrophages and cause pneumonia in foals. It is unknown how VapA interacts with mammalian cell receptors, but intracellular replication of avirulent
R. equi
lacking
vapA
can be restored by supplementation with recombinant VapA (rVapA). Our objectives were to determine whether the absence of the surface receptors Toll-like receptor 2 (TLR2), complement receptor 3 (CR3), or Fc gamma receptor III (FcγRIII) impacts
R. equi
phagocytosis and intracellular replication in macrophages, and whether rVapA restoration of virulence in
R. equi
is dependent upon these receptors. Wild-type (WT) murine macrophages with TLR2, CR3, or FcγRIII blocked or knocked out (KO) were infected with virulent or avirulent
R. equi
, with or without rVapA supplementation. Quantitative bacterial culture and immunofluorescence imaging were performed. Phagocytosis of
R. equi
was not affected by blockade or KO of TLR2 or CR3. Intracellular replication of virulent
R. equi
was not affected by TLR2, CR3, or FcγRIII blockade or KO; however, avirulent
R. equi
replicated in TLR2
-/-
and CR3
-/-
macrophages but not in WT and FcγRIII
-/-
. rVapA supplementation did not affect avirulent
R. equi
phagocytosis but promoted intracellular replication in WT and all KO cells. By demonstrating that TLR2 and CR3 limit replication of avirulent but not virulent
R. equi
and that VapA-mediated virulence is independent of TLR2, CR3, or FcγRIII, our study provides novel insights into the role of these specific surface receptors in determining the entry and intracellular fate of
R. equi
.
Identification of
recG
genetic interactions in
Escherichia coli
by transposon sequencing
Authors: Bonde Nina J. , Wood Elizabeth A. , Myers Kevin S. , Place Michael , Keck James L. , Cox Michael M.
Published: November 2023

Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In
Escherichia coli
, the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing to identify
recG
genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the
dam
,
uvrD
,
rnhA
,
radA
, and
rep
genes. The conditional importance of these five genes in cells lacking
recG
was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with
uvrD, rep,
and
radA
, but not
rnhA
or
dam
) were suppressed by deletion of
recF
or
recO
, indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a
recG
deletion when combined with
dam
,
uvrD
,
radA
, or
rnhA
deletions but not with
rep
. The results reinforce the idea of RecG as a general genome guardian. RecG has at least two functions. It plays an important role in the resolution of joint molecules behind the fork, formed during post-replication gap repair. RecG is also required to suppress genome over-replication caused by unscheduled replication initiation at R-loops, at double-strand breaks caused by
dam
inactivation, and during replication termination.

IMPORTANCE

DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the
recG
gene, which renders
Escherichia coli
cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported
recG
genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.
Igniting children’s enthusiasm for microbes with an origami paper microscope
Authors: Gardner Joshua , Perry Cynthia , Cervantes Jorge
Published: November 2023

The COVID-19 pandemic has underscored the urgent need for microbiology literacy in society. Microbiology knowledge, and its dissemination, can help inform and increase the objectivity of important decisions, such as treatment or vaccination. A microbiology learning experience titled “What you can’t see can hurt you” was delivered as part of a larger outreach event where children were exposed to various aspects of medicine and health care fields. The activity involved an introduction to and a discussion of bacteria of clinical importance and the use of a smartphone-attachable paper-based foldable microscope. To explore the impact of this activity on participants’ interest in science and microbiology, a pre- and post-activity survey of five questions on an emoji-based Likert scale was completed by the participants. A statistically significant increase in their interest in microbes and where to find them, as well as in microscopy, was observed after the event. Making microbes visible to children and allowing them to capture images of microbes exposes them directly and personally to microscopy and microbiology. An affordable low-cost paper-based microscope can become an alternative approach to teaching and learning to deliver clinical microbiology information to a wide audience range.
Diversity of short linear interaction motifs in SARS-CoV-2 nucleocapsid protein
Authors: Schuck Peter , Zhao Huaying
Published: November 2023

Molecular mimicry of short linear interaction motifs has emerged as a key mechanism for viral proteins binding host domains and hijacking host cell processes. Here, we examine the role of RNA virus sequence diversity in the dynamics of the virus-host interface by analyzing the uniquely vast sequence record of viable SARS-CoV-2 species with focus on the multi-functional nucleocapsid protein. We observe the abundant presentation of motifs encoding several essential host protein interactions, alongside a majority of possibly non-functional and randomly occurring motif sequences absent in subsets of viable virus species. A large number of motifs emerge
ex nihilo
through transient mutations relative to the ancestral consensus sequence. The observed mutational landscape implies an accessible motif space that spans at least 25% of known eukaryotic motifs. This reveals motif mimicry as a highly dynamic process with the capacity to broadly explore host motifs, allowing the virus to rapidly evolve the virus-host interface.

IMPORTANCE

Short linear motifs (SLiMs) are 3–10 amino acid long binding motifs in intrinsically disordered protein regions (IDRs) that serve as ubiquitous protein-protein interaction modules in eukaryotic cells. Through molecular mimicry, viruses hijack these sequence motifs to control host cellular processes. It is thought that the small size of SLiMs and the high mutation frequencies of viral IDRs allow rapid host adaptation. However, a salient characteristic of RNA viruses, due to high replication errors, is their obligate existence as mutant swarms. Taking advantage of the uniquely large genomic database of SARS-CoV-2, here, we analyze the role of sequence diversity in the presentation of SLiMs, focusing on the highly abundant, multi-functional nucleocapsid protein. We find that motif mimicry is a highly dynamic process that produces an abundance of motifs transiently present in subsets of mutant species. This diversity allows the virus to efficiently explore eukaryotic motifs and evolve the host-virus interface.
On the origin of the nucleus: a hypothesis
Authors: Baum Buzz , Spang Anja
Published: November 2023

In this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions—emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
Complete genome sequence of
Escherichia
phage iGC_PHA_EC001
Authors: Khan Tahsin , Haider Arefeen , Rahman Sezanur , Moon Shovan Basak , Mahamud Imtiaz , Mondal Shakhinur Islam , Begum Anowara , Biswas Sudhangshu Kumar , Jubair Mohammad , Rahman Mustafizur
Published: November 2023

Antimicrobial resistance (AMR) in bacteria poses a global health emergency due to limited treatment options. Here, we report a lytic bacteriophage belonging to
Stephanstirmvirinae
family against an AMR
Escherichia coli
(ST2089).
Escherichia
phage iGC_PHA_EC001 is of genus
Phapecoctavirus
and 148,445 bp in length, encoding 269 predicted protein-coding sequences and 10 tRNAs. The phage encodes two lytic proteins containing phage_lysozyme (PF00959.22) and cell wall hydrolase_2 (PF07486.15) as catalytic domains, respectively.
Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting
Authors: Ottesen Andrea , Kocurek Brandon , Deaver Christine , Chiesa Oscar , Cohen Rachael , Reed Elizabeth , Commichaux Seth , Mammel Mark , McDermott Patrick , Strain Errol , Myers Michael
Published: November 2023

Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast
in vivo
versus
in vitro
bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.
Complete genome sequence of
Bordetella parapertussis
strain 400431-b, isolated from a protracted course of whooping cough in Austria, 2023
Authors: Cardoso Maria João , Rouhani David , Cabal Rosel Adriana , Daza Prieto Beatriz , Hopfgartner Miriam , Stöger Anna , Hasenberger Petra , Stadlbauer Silke , Moesenbacher Tobias , Hyden Patrick , Wiedermann Ursula , Schmid Daniela , Ruppitsch Werner
Published: November 2023

Here, we report the complete genome of
Bordetella parapertussis
strain 400431-b isolated from a nasopharyngeal swab from a 4-year-old patient presenting with a protracted course of whooping cough, vaccinated with three doses of diphtheria-tetanus-acellular pertussis-hepatitis B-poliomyelitis-
Haemophilus influenzae
type b vaccine.
Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system
Authors: Freeman Claire N. , Russell Jennifer N. , Yost Chris K.
Published: November 2023

The biological removal of nitrogen using natural microbial metabolic processes can be a valuable component of wastewater treatment that helps reduce downstream eutrophication of receiving water ecosystems. Biological nutrient removal (BNR) is a well-established component of wastewater treatment due to its recognized environmental benefits. The composition and diversity of these microbial communities are an important consideration, as disruptions to or instability in the microbial community can negatively impact N cycling and reduce treatment efficiency. To characterize the bacterial community and associated nitrogen cycling genes within a cold-acclimated BNR facility, metagenomic sequencing combined with a read-based quantification strategy and metagenomic assembled genome (MAG) generation was used on samples collected from a Canadian prairie wastewater treatment plant. Generally, this system had a high abundance of Proteobacteria and Actinobacteria throughout the year, including the genera
Thiomonas, Tetrasphaera, Afipia,
and
Hyphomicrobium
. Communities remained stable throughout the different bioreactors in this system, while diversity varied between sampling months, demonstrating seasonal effects on the population dynamics. Genes involved in the denitrification pathway were abundant and distributed widely across different MAGs, while genes involved in nitrification were absent. Additionally, these genes remained stable across all sampling months, suggesting that the efficacy and robustness of this system rely on more than the taxonomic composition of the microbial community.

IMPORTANCE

Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.
CRISPR-Cas9-mediated IncF plasmid curing in extraintestinal pathogenic
Escherichia coli
Authors: Chen Liang , Peirano Gisele , Yen Kelly , Wang Bingjie , Terlecky Austin , DeVinney Rebekah , Kreiswirth Barry N. , Pitout Johann D. D.
Published: November 2023

IncF plasmids are commonly found in extra-intestinal pathogenic
Escherichia coli
(ExPEC) strains, serving as reservoirs for antimicrobial resistance (AMR) genes and virulence factors, persistently coexisting with ExPEC lineages. Multidrug-resistant (MDR) high-risk ExPEC clones, particularly ST131, ST1193, and ST410, have acquired diverse IncF plasmids over time, containing various AMR determinants, contributing significantly to their global success. However, the broader roles of these IncF plasmids in the success of MDR ExPEC clones, beyond AMR, remain elusive. In this study, we employed a novel clustered regularly interspaced short palindromic repeats–CRISPR-associated protein-9 nuclease (CRISPR-Cas9)-mediated pCasCure plasmid-curing system to precisely remove specific IncF plasmids among ExPEC clones (ST1193, ST131, and ST410). Antibiotic-resistant parent strains reverted to antibiotic-susceptible states post-curing; however, IncF plasmid curing did not show significant impact on bacterial
in vitro
growth and had little impact on other
in vitro
phenotypes, including survival in water, dry environment and biofilm production. In addition, IncF plasmid curing did not affect the conjugation frequency of KPC-producing pKpQIL plasmid. This study represents a pivotal initial step in understanding the precise roles of IncF plasmids in the success of ExPEC. Future research will be crucial in investigating their influence on cell invasion and
in vivo
fitness, thereby providing a more comprehensive perspective on the functions of IncF plasmids in MDR ExPEC clones.

IMPORTANCE

Understanding the role of IncF plasmids in the success of drug-resistant bacteria has far-reaching implications for tackling antibiotic resistance. The study's use of a novel CRISPR-Cas9-mediated plasmid-curing system provides a precision tool for dissecting the specific impact of IncF plasmids on ExPEC clones, especially high-risk, multidrug-resistant strains like ST131, ST1193, and ST410. The study offers a crucial stepping stone for future research into understanding how these plasmids influence more complex aspects of bacterial behavior, such as cell invasion and
in vivo
fitness.
Late Miocene to present synchronous extension and contraction in the eastern Pamir: Insights from inversion of thermochronologic data across the southern Muztaghata dome
Authors: Chen Shenqiang , Fellin Maria Giuditta , Willett Sean D. , Maden Colin , Guillong Marcel , Chen Hanlin , Chen Yaguang
Published: November 2023

Late Cenozoic gneiss domes cover ~30% of the surface of the Pamir salient in the northwestern end of the India–Asia collision zone. The highest peaks of the Pamir are in the east, where the ~250-km-long, ~N–S-trending Kongur Shan extensional system controls the topography. We combined 115 new apatite (U-Th-Sm)/He and zircon (U-Th)/He single-grain dates from 18 samples and previous thermochronologic data with three-dimensional thermokinematic models to constrain the thermo-tectonic history of the southern portion of the Muztaghata dome, one of the largest gneiss domes in the eastern Pamir. The new cooling dates from the western boundary of the southern Muztaghata dome generally increase with distance from the southern Kongur Shan fault and are related to normal faulting along the fault at near-surface levels over the last 6.5 m.y. The new dates across the central–eastern portion of the dome outline the previously recorded U-shaped date pattern at a higher spatial resolution. The modeling indicates that this pattern is most likely the result of uplift and erosion above a flat-ramp-flat thrust fault at depth over the last 7 m.y. Modeling does not resolve how topographic changes may have affected the observed distribution of cooling dates, but it indicates a faster thrust-slip rate associated with an increase in relief and a slower one associated with steady-state topography. Our results suggest that the modern topography along the southern Muztaghata dome, similar to the rest of the eastern Pamir salient, is shaped by normal faulting at shallow depth, but its growth may still be governed by contraction and crustal thickening at depth.
Effectiveness of prevention programmes on the rate of burn injuries in children: a systematic review
Authors: van Balen Nina I M , Simon Myrthe H , Botman Matthijs , Bloemers Frank W , Schoonmade Linda J , Meij-de Vries Annebeth
Published: November 2023

Introduction

Burns are a frequent injury in children and can cause great physical and psychological impairment. Studies have identified positive effects of prevention measures based on increase in knowledge or reduction in hazards. The main goal of burn prevention campaigns, however, is to prevent burns. Therefore, this review is focused on the effectiveness of prevention programmes on the rates of burns in children.

Methods

A literature search was performed on PubMed, Embase, CINAHL, Web of Science, Google Scholar and Scopus, including a reference-check. Included were studies which evaluated burn prevention programmes in terms of burn injury rate in children up to 19 years old. Studies specifically focused on non-accidental burns were excluded as well as studies with only outcomes such as safety knowledge or number of hazards.

Results

The search led to 1783 articles that were screened on title and abstract. 85 articles were screened in full text, which led to 14 relevant studies. Nine of them reported a significant reduction in burn injury rate. Five others showed no effect on the number of burn injuries. In particular, studies that focused on high-risk populations and combined active with passive preventive strategies were successful.

Conclusion

Some prevention programmes appear to be an effective manner to reduce the number of burn injuries in children. However, it is essential to interpret the results of the included studies cautiously, as several forms of biases may have influenced the observed outcomes. The research and evidence on this subject is still very limited. Therefore, it is of great importance that future studies will be evaluated on a decrease in burns and bias will be prevented. Especially in low-income countries, where most of the burns in children occur and the need for effective prevention campaigns is vital.
Ancestry, race and ethnicity: the role and relevance of language in clinical genetics practice
Authors: Redman Melody Grace , Horton Rachel Helen , Carley Helena , Lucassen Anneke
Published: November 2023

Background

The terms ancestry, race and ethnicity are used variably within the medical literature and within society and clinical care. Biological lineage can provide an important context for the interpretation of genomic data, but the language used, and practices around when to ascertain this, vary.

Methods

Using a fictional case scenario we explore the relevance of questions around ancestry, race and ethnicity in clinical genetic practice.

Results

In the UK, data on ‘ethnicity’ are routinely collected by those using genomic medicine, as well as within the wider UK National Health Service, although the reasons for this are not always clear to practitioners and patients. Sometimes it is requested as a proxy for biological lineage to aid variant interpretation, refine estimations of carrier frequency and guide decisions around the need for pharmacogenetic testing.

Conclusion

There are many challenges around the use and utility of these terms. Currently, genomic databases are populated primarily with data from people of European descent, and this can lead to health disparities and poorer service for minoritised or underserved populations. Sensitivity and consideration are needed when communicating with patients around these areas. We explore the role and relevance of language around biological lineage in clinical genetics practice.
Tobacco industry accountability for marine pollution: country and global estimates
Authors: Sy Deborah K
Published: November 2023

Background

Commercial cigarette filters are single-use plastics and the main component of cigarette butts, the most common trash item collected worldwide. Governments bear the economic burden of managing the waste and the environmental pollution due to discarded filters and packages. Using available data sources, we estimate the economic burden of plastic tobacco waste on country economic groups.

Methods

We reviewed available public data sources that could inform estimates of the economic environmental burden of butt waste for countries. We estimated total weight of plastic cigarette filters and packaging based on cigarette consumption and applied World Bank waste management cost estimates per ton to this total. We then applied estimates of ecosystem losses per ton of plastic waste provided by the World Wildlife Fund to establish losses attributable to tobacco’s plastics.

Results

We estimate that US$25.7 billion is lost annually (waste management and marine ecosystem service losses) due to cigarette plastic sources. We estimate US$186 billion in such losses over a 10-year period, adjusted for inflation. Countries are making progress in developing plastics policies, particularly banning single-use ones, but the costs of tobacco’s plastic pollution are overlooked.

Conclusion

Efforts to reduce plastic pollution should address cigarette filters as toxic, widespread and preventable sources of marine pollution. Countries may develop specific estimates of waste management and ecosystem costs in order to assign tobacco industry accountability for this pollution. These results indicate minimum estimates for a majority of countries.
A two-dimensional effective stress framework for modelling whole-life soil strength changes due to pore pressure generation and dissipation, Part 1: Formulation
Authors: Wang Y. , O'Loughlin C. D. , Zhou Z. , Gaudin C.
Published: November 2023

The undrained shear strength of contractive fine-grained soils changes with time, reducing due to pore pressure generation and increasing during consolidation. There is an increasing appetite to recognise these temporal soil strength changes in offshore geotechnical design, as it provides a basis for potentially less conservative designs. Contributions to this endeavour are reported across two companion papers. This first paper extends an existing effective stress framework that relates the generation of pore pressure to accumulated plastic shear strain, allowing undrained shear strength to be calculated within the context of critical-state soil mechanics. The main development is the extension of the computational domain to two dimensions, allowing calculations to be made for boundary value problems that cannot be satisfactorily simplified to one-dimensional conditions. The magnitude and distribution of accumulated shear strain surrounding objects buried in soil are quantified through a series of large deformation finite element analyses. These spatial distributions are described using a strain influence function in the new 2D framework to calculate the extent and magnitude of excess pore pressure, and in turn the mobilised soil strength around the buried object. The performance of the 2D framework is examined in the companion paper through retrospective simulations of experimental and numerical data.
A Verifiable Multi-Secret Sharing Scheme Based on ℓ-Intersection Pair of Cyclic Codes
Authors: Hossain Md Ajaharul , Bandi Ramakrishna
Published: November 2023

A verifiable multi-secret sharing (VMSS) scheme addresses various security issues, helping in cheating detection and cheater identification. The dimension of the intersection of a given pair of cyclic codes over a finite field [Formula: see text] is represented by [Formula: see text]. In this paper, we propose a VMSS scheme based on an [Formula: see text]-intersection pair of cyclic codes. The proposed scheme is very useful for sharing a large number of secrets. If [Formula: see text] is the number of secrets in a threshold [Formula: see text] scheme, then for [Formula: see text], the computational complexity and the public values required in the reconstruction phase are much less compared to many existing schemes in the literature. Overall, the proposed scheme comprises nearly all the features, like being verifiable, testing participants’ integrity, checking Verifier frauds, and most importantly, it is of multi-use type.
Absence of Slc39a14/Zip14 in mouse pancreatic beta cells results in hyperinsulinemia
Authors: Hung Yu-Han , Kim Yongeun , Mitchell Samuel Blake , Thorn Trista Lee , Aydemir Tolunay Beker
Published: November 2023

Metal transporter SLC39A14/ZIP14 is downregulated in pancreatic islets of patients with T2D and mouse models of HFD- or db/db-induced obesity. However, the function of ZIP14-mediated intracellular zinc trafficking in β cells is unknown. Our analyses revealed that SLC39A14 is the only Zn transporter expressed abundantly in human β cells besides SLC30A8. Within the β cells, ZIP14 is localized on the endoplasmic reticulum and serves as a negative regulator of insulin secretion, providing a potential therapeutic target for T2D.
Influence of Guluronic and Mannuronic Groups in Sodium Alginate Blends with Silk Fibroin: Phase Equilibrium and Thermodynamic Modeling
Authors: Lopes Laise Maia , de Moraes Mariana Agostini , Beppu Marisa Masumi
Published: November 2023

Silk fibroin (SF) and sodium alginate (SA) are natural polymers with interesting properties to produce biomaterials. Blends of these polymers form a complex protein–polysaccharide system where phase separation can be observed. Therefore, the thermodynamic analysis of this system is important to understand the interaction between the polymers and predict the final state and composition of the phases found in these blends. This study explored blends with a different initial composition of SF, SA, and water at 25°C and neutral pH. The influence of the proportion between mannuronic and guluronic acids on SA composition was investigated. After phase separation, two phases were identified, and the equilibrium data were fitted on three different thermodynamic models: Flory–Huggins, non-random two-liquids, and universal quasichemical. Cohn equation was also used to investigate the potential of SA to precipitate the SF in solution. The results show that the proportion of mannuronic and guluronic acids on the SA can significantly influence on equilibrium data and on the SF/SA interaction parameter, hence, becoming a variability factor if this parameter is not under control in formulations.
Effect of Sonication and Edible Coating on Total Phenolic Content, Antioxidant Capacity, and Physical Characteristics of Infrared-Dried Sweet Cherries
Authors: Salehi Fakhreddin , Inanloodoghouz Moein , Amiri Mostafa
Published: November 2023

This research studied the influence of combined ultrasonic (40 kHz, 150 W, for 3 min) and 0.2% xanthan gum (XG), guar gum (GG), and wild sage seed gum (WG) coating pretreatments on total phenolic content, antioxidant activity, drying time, effective water diffusivity coefficient (

D

eff

), rehydration ratio (RR), total color difference (

Δ
E

), and surface shrinkage (SS) of infrared-dried sweet cherries. The ultrasonic pretreatment increased the water transfer rate and water diffusivity during infrared drying and decreased the drying time of fresh sweet cherries. The edible coating enhanced the total phenolic content, antioxidant activity, dehydration time, and RR and decreased the

D

eff

,

Δ
E

, and SS values of infrared-dried sweet cherries. The highest value of total phenolic content (3469.7 μg galic acid/g dry) was recorded for pretreated sweet cherry samples by GG. The mean antioxidant activities for uncoated, XG-coated, GG-coated, and WG-coated sweet cherries were 35.64, 59.88, 54.38, and 61.19%, respectively. In this study, the sweet cherry

D

eff

varied from

2.23
×

10

−
9

 m2/s (for untreated cherries) to

5.00
×

10

−
9

 m2/s (for sonicated and uncoated cherries). The experimental data for the drying curves were fitted to various single-layer equations, and the Page equation using the experimental constants best described the drying rate of sweet cherries. The mean

Δ
E

values for uncoated, XG-coated, GG-coated, and WG-coated sweet cherries were 15.11, 9.91, 8.74, and 10.69, respectively.