bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species
Authors: Xu Wu‐Qin , Ren Chao‐Qian , Zhang Xin‐Yi , Comes Hans‐Peter , Liu Xin‐Hong , Li Yin‐Gang , Kettle Christopher J. , Jalonen Riina , Gaisberger Hannes , Ma Ya‐Zhen , Qiu Ying‐Xiong 
Published: February 2024

SUMMARYUnderstanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non‐model tree species are not yet fully understood. To address this issue, we generated whole‐genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long‐term refugial isolation and recent differential introgression in low‐recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.
Long-Term Prediction of Large-Scale and Sporadic COVID-19 Epidemics Induced by the Original Strain in China Based on the Improved Nonautonomous Delayed Susceptible-Infected-Recovered-Dead and Susceptible-Infected-Removed Models
Authors: Xie Xin , Pei Lijun 
Published: February 2024

Abstract
The COVID-19 virus emerged abruptly in early 2020 and disseminated swiftly, resulting in a substantial impact on public health. This paper aims to forecast the evolution of large-scale and sporadic COVID-19 outbreaks, stemming from the original strain, within the context of stringent quarantine measures in China. In order to accomplish our objective, we introduce a time-delay factor into the conventional susceptible-infected-removed/susceptible-infected-recovered-dead (SIR/SIRD) model. In the nonautonomous delayed SIRD model, the finite difference method is employed to determine that the transmission rate in a large-scale epidemic area exhibits an approximately exponential decay, the cure rate demonstrates a linear increase, and the death rate is approximately piecewise constant with a downward trend. We employ an improved delayed SIR model for sporadic epidemic regions characterized by extremely low or nearly zero mortality rates. In these regions, the transmission rate is estimated through a two-stage exponential decay function with variable coefficients, while the rate of removal aligns with the recovery rate in the previously mentioned SIRD model. The results of this study demonstrate a high level of concordance with the actual evolution of COVID-19, and the predictive precision can be consistently maintained within a margin of 3%. From the perspective of our model parameters, it is observed that under strict isolation policies, the transmission rate of COVID-19 in China is relatively low and has been significantly reduced. This suggests that government intervention has had a positive effect on epidemic prevention in the country. Moreover, our model has been successfully utilized to forecast the outbreaks caused by the SARS virus in 2003 and the COVID-19 outbreak induced by the Omicron virus in 2022, showcasing its broad applicability and efficacy. This study enables the prompt implementation of measures and allocation of medical resources in different regions, ultimately contributing to the mitigation of economic and social losses.
Introduction of Local Resonators to a Nonlinear Metamaterial With Topological Features
Authors: LeGrande Joshua , Malla Arun , Bukhari Mohammad , Barry Oumar 
Published: February 2024

Abstract
Recent work in nonlinear topological metamaterials has revealed many useful properties such as amplitude dependent localized vibration modes and nonreciprocal wave propagation. However, thus far, there have not been any studies to include the use of local resonators in these systems. This work seeks to fill that gap through investigating a nonlinear quasi-periodic metamaterial with periodic local resonator attachments. We model a one-dimensional metamaterial lattice as a spring-mass chain with coupled local resonators. Quasi-periodic modulation in the nonlinear connecting springs is utilized to achieve topological features. For comparison, a similar system without local resonators is also modeled. Both analytical and numerical methods are used to study this system. The dispersion relation of the infinite chain of the proposed system is determined analytically through the perturbation method of multiple scales. This analytical solution is compared to the finite chain response, estimated using the method of harmonic balance and solved numerically. The resulting band structures and mode shapes are used to study the effects of quasi-periodic parameters and excitation amplitude on the system behavior both with and without the presence of local resonators. Specifically, the impact of local resonators on topological features such as edge modes is established, demonstrating the appearance of a trivial bandgap and multiple localized edge states for both main cells and local resonators. These results highlight the interplay between local resonance and nonlinearity in a topological metamaterial demonstrating for the first time the presence of an amplitude invariant bandgap alongside amplitude dependent topological bandgaps.
Design of a Simple Valveless Micropump Using Piezoelectric Actuators
Authors: Yu Tai-Ho , Lai Chun-Hung , Chen Yuan-Hsin 
Published: February 2024

Abstract
An open valveless micropump pumped by a disk-shaped piezo-electric actuator was developed, and its working principles were investigated. The electrode of the pump buzzer was divided into two semicircles as piezo-electric actuators, and single-phase or dual-phase AC driving potential was applied. The flowrate of the pump was analyzed when actuated in basic symmetric (W00) and antisymmetric (W01) modes. The finite element package software ANSYS was used to analyze the resonant frequency and mode of the buzzer under fluid loading, and the vibration displacement generated by the single-phase and dual-phase time-harmonic actuation was both simulated by using an additional mass method and experimentally investigated. The experimental results show that the resonant frequency of the disk-shaped actuator decreased due to the fluid loading effect and as the gap distance between the conduit and the actuator decreased. The maximum flow rates of the W00 and W01 mode actuated pumps were 133.13 and 9.63 mL/min, respectively. The driving frequency with the highest pump efficiency was slightly lower than the resonance frequency of the fluid-loaded buzzer. Applying a hydrophobic treatment to the back of the buzzer decreased the resonance frequency under fluid loading. The results show that simulating the structural resonance frequency for various fluid loads by the additional mass method is feasible. The flow direction could be controlled by activating the W01 mode.
GCRV-II invades monocytes/macrophages and induces macrophage polarization and apoptosis in tissues to facilitate viral replication and dissemination
Authors: Xia Ning , Zhang Yanqi , Zhu Wentao , Su Jianguo 
Published: February 2024

ABSTRACT

Grass carp reovirus (GCRV), particularly the highly prevalent type II GCRV (GCRV-II), causes huge losses in the aquaculture industry. However, little is known about the mechanisms by which GCRV-II invades grass carp and further disseminates among tissues. In the present study, monocytes/macrophages (Mo/Mφs) were isolated from the peripheral blood of grass carp and infected with GCRV-II. The results of indirect immunofluorescent microscopy, transmission electron microscopy, real-time quantitative RT-PCR (qRT-PCR), western blot (WB), and flow cytometry analysis collectively demonstrated that GCRV-II invaded Mo/Mφs and replicated in them. Additionally, we observed that GCRV-II induced different types (M1 and M2) of polarization of Mo/Mφs in multiple tissues, especially in the brain, head kidney, and intestine. To assess the impact of different types of polarization on GCRV-II replication, we recombinantly expressed and purified the intact cytokines CiIFN-γ2, CiIL-4/13A, and CiIL-4/13B and successfully induced M1 and M2 type polarization of macrophages using these cytokines through
in vitro
experiments. qRT-PCR, WB, and flow cytometry analyses showed that M2 macrophages had higher susceptibility to GCRV-II infection than other types of Mo/Mφs. In addition, we found GCRV-II induced apoptosis of Mo/Mφs to facilitate virus replication and dissemination and also detected the presence of GCRV-II virus in plasma. Collectively, our findings indicated that GCRV-II could invade immune cells Mo/Mφs and induce apoptosis and polarization of Mo/Mφs for efficient infection and dissemination, emphasizing the crucial role of Mo/Mφs as a vector for GCRV-II infection.

IMPORTANCE
Type II grass carp reovirus (GCRV) is a prevalent viral strain and causes huge losses in aquaculture. However, the related dissemination pathway and mechanism remain largely unclear. Here, our study focused on phagocytic immune cells, monocytes/macrophages (Mo/Mφs) in blood and tissues, and explored whether GCRV-II can invade Mo/Mφs and replicate and disseminate via Mo/Mφs with their differentiated type M1 and M2 macrophages. Our findings demonstrated that GCRV-II infected Mo/Mφs and replicated in them. Furthermore, GCRV-II infection induces an increased number of M1 and M2 macrophages in grass carp tissues and a higher viral load in M2 macrophages. Furthermore, GCRV-II induced Mo/Mφs apoptosis to release viruses, eventually infecting more cells. Our study identified Mo/Mφs as crucial components in the pathway of GCRV-II dissemination and provides a solid foundation for the development of treatment strategies for GCRV-II infection.
Pseudomonas aeruginosa
MipA-MipB envelope proteins act as new sensors of polymyxins
Authors: Janet-Maitre Manon , Job Viviana , Bour Maxime , Robert-Genthon Mylène , Brugière Sabine , Triponney Pauline , Cobessi David , Couté Yohann , Jeannot Katy , Attrée Ina 
Published: February 2024

ABSTRACT

Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic pathogen
Pseudomonas aeruginosa
develops resistance to colistin/polymyxin B by distinct molecular mechanisms, mostly through modification of the lipid A component of the LPS by proteins encoded within the
arnBCDATEF-ugd
(
arn
) operon. In this work, we characterized a polymyxin-induced operon named
mipBA
, present in
P. aeruginosa
strains devoid of the
arn
operon. We showed that
mipBA
is activated by the ParR/ParS two-component regulatory system in response to polymyxins. Structural modeling revealed that MipA folds as an outer-membrane β-barrel, harboring an internal negatively charged channel, able to host a polymyxin molecule, while the lipoprotein MipB adopts a β-lactamase fold with two additional C-terminal domains. Experimental work confirmed that MipA and MipB localize to the bacterial envelope, and they co-purify
in vitro
. Nano differential scanning fluorimetry showed that polymyxins stabilized MipA in a specific and dose-dependent manner. Mass spectrometry-based quantitative proteomics on
P. aeruginosa
membranes demonstrated that ∆
mipBA
synthesized fourfold less MexXY-OprA proteins in response to polymyxin B compared to the wild-type strain. The decrease was a direct consequence of impaired transcriptional activation of the
mex
operon operated by ParR/ParS. We propose MipA/MipB to act as membrane (co)sensors working in concert to activate ParS histidine kinase and help the bacterium to cope with polymyxin-mediated envelope stress through synthesis of the efflux pump, MexXY-OprA.

IMPORTANCE

Due to the emergence of multidrug-resistant isolates, antibiotic options may be limited to polymyxins to eradicate Gram-negative infections.
Pseudomonas aeruginosa
, a leading opportunistic pathogen, has the ability to develop resistance to these cationic lipopeptides by modifying its lipopolysaccharide through proteins encoded within the
arn
operon. Herein, we describe a sub-group of
P. aeruginosa
strains lacking the
arn
operon yet exhibiting adaptability to polymyxins. Exposition to sub-lethal polymyxin concentrations induced the expression and production of two envelope-associated proteins. Among those, MipA, an outer-membrane barrel, is able to specifically bind polymyxins with an affinity in the 10-µM range. Using membrane proteomics and phenotypic assays, we showed that MipA and MipB participate in the adaptive response to polymyxins via ParR/ParS regulatory signaling. We propose a new model wherein the MipA-MipB module functions as a novel polymyxin sensing mechanism.
Whole genome sequencing of nine
Vibrio parahaemolyticus
strains encoding (
Pir
) toxin-like genes from shrimp cultures in northern Peru using Oxford Nanopore technology
Authors: Tapia-Chirinos Stephanie , Salcedo-Mejia Luis Alberto , Domínguez-Mendoza Luz , Nuñure-Ortega Jeferson , Ramos-Espinoza Fernando , Gómez-Sánchez Muriel , Tataje-Lavanda Luis , Velazco-Peña Rodolfo 
Published: February 2024

ABSTRACT

Nine Peruvian isolates of
Vibrio parahaemolyticus
were characterized through sequencing, revealing the presence of simple sequence repeat, Pir toxin-like genes, and genes associated with antibiotic resistance, toxic components, and transposable elements. These findings expand our understanding of the genetic diversity, disease resistance, and virulence in cultivated shrimp populations in Peru.
Alcohol-induced gut microbiome dysbiosis enhances the colonization of
Klebsiella pneumoniae
on the mouse intestinal tract
Authors: Shen Mengke , Zhao Huajie , Han Meiqing , Su Lin , Cui Xiaojian , Li Duan , Liu Liang , Wang Chuansheng , Yang Fan 
Published: February 2024

ABSTRACT

Chronic alcohol consumption, an important risk factor for diseases and deaths, can cause intestinal microbiota dysbiosis and increase the infection of some opportunistic pathogens. However, the current studies on the effects of alcohol-induced intestinal microbiota dysbiosis on gut colonization of
Klebsiella pneumoniae
are still scarce. In the present study, we established a binge-on-chronic alcohol model in mice to identify the characteristics of alcohol-induced intestinal microbiome and metabolite dysbiosis using multi-omics and explored the effects and potential mechanisms of these dysbioses on the intestinal colonization of
K. pneumoniae
. The results show that chronic alcohol consumption alters the diversity and composition of gut microbiota (including bacteria and fungi), decreases the complexity of the interaction between intestinal bacteria and fungi, disturbs the gut metabolites, and promotes the colonization of
K. pneumoniae
on the gut of mice. The relevance analyses find that alcohol-induced gut microbiome dysbiosis has a strong correlation with the alteration of secondary bile acids.
In vitro
results suggest that the high concentration of lithocholic acid, a secondary bile acid, could significantly inhibit the proliferation of
K. pneumoniae
, and the adhesion of
K. pneumoniae
to Caco-2 cells. Our results indicate that alcohol-induced microbiome dysbiosis contributes to decreased levels of secondary bile acids, which was one of the main reasons affecting the colonization of
K. pneumoniae
in mice’s intestines. Some secondary bile acids (e.g., lithocholic acid) might be a potential drug to prevent the colonization and spread of
K. pneumoniae
.

IMPORTANCE

Alcohol is one of the most commonly misused substances in our lives. However, long-term heavy drinking will increase the colonization of some opportunistic pathogens (e.g.,
Klebsiella pneumoniae
) in the body. Here, we revealed that binge-on-chronic alcohol consumption disrupted the balance between gut bacteria and fungi, induced the gut microbiome and metabolites dysbiosis, and promoted the colonization of
K. pneumoniae
in the intestine of mice. In particular, alcohol-taking disrupted intestinal bile acid metabolism and reduced the lithocholic acid concentration. However, a high concentration of lithocholic acid can protect against intestinal colonization of
K. pneumoniae
by inhabiting the bacterial growth and adhesion to the host cell. Hence, regulating the balance of gut microbiota and intestinal bile acid metabolism may be a potential strategy for reducing the risk of
K. pneumoniae
infection and spread.
Comparison of definitive approaches for conotruncal defects following bidirectional Glenn procedure
Authors: Liu Yuze , He Qiyu , Dou Zheng , Ma Kai , Lin Xinjie , Li Shoujun 
Published: February 2024

BackgroundStaged repair is common for complex conotruncal defects, often involving bidirectional Glenn (BDG) procedure. Following the cavopulmonary shunt, both Fontan completion and biventricular conversion (BiVC) serve as definitive approaches. The optimal strategy remains controversial.MethodsThe baseline, perioperative and follow-up data were obtained for all paediatric patients with conotruncal defects who underwent BDG procedure as palliation in Fuwai Hospital from 2013 to 2022. Patients with single ventricle were excluded. The primary outcome was mortality. The secondary outcome was reintervention, including any cardiovascular surgeries and non-diagnostic catheterisations.ResultsA total of 232 patients were included in the cohort, with 142 underwent Fontan (61.2%) and 90 underwent BiVC (38.8%). The median interstage period from BDG to the definitive procedure was 3.83 years (IQR: 2.72–5.42) in the overall cohort, 3.62 years (IQR: 2.57–5.15) in the Fontan group and 4.15 years (IQR: 3.05–6.13) in the BiVC group (p=0.03). The in-hospital outcomes favoured the Fontan group, including duration of cardiopulmonary bypass, aortic cross-clamp, mechanical ventilation and intensive care unit stay. Postoperative mortality was generally low and comparable, as was the reintervention rate (HR=1.42, 95% CI: 0.708 to 2.85, p=0.32). The left ventricular size was smaller at baseline and within the normal range at follow-up for both Fontan and BiVC groups; however, it was significantly larger with BiVC at follow-up.ConclusionIn paediatric patients with conotruncal heart defects who underwent BDG procedure, BiVC is a feasible option, especially for patients with certain Fontan risk factors, and are not ideal candidates for successful Fontan completion.
Validation of the Prognostic Performance of Breast Cancer Index in Hormone Receptor–Positive Postmenopausal Breast Cancer Patients in the TEAM Trial
Authors: Bartlett John M.S. , Xu Keying , Wong Jenna , Pond Gregory , Zhang Yi , Spears Melanie , Salunga Ranelle , Mallon Elizabeth , Taylor Karen J. , Hasenburg Annette , Markopoulos Christos , Dirix Luc , van de Velde Cornelis J.H. , Rea Daniel , Schnabel Catherine A. , Treuner Kai , Bayani Jane 
Published: February 2024

Abstract

Purpose:
Patients with early-stage hormone receptor–positive (HR+) breast cancer face a prolonged risk of recurrence even after adjuvant endocrine therapy. The Breast Cancer Index (BCI) is significantly prognostic for overall (0–10 years) and late (5–10 years) distant recurrence (DR) risk in N0 and N1 patients. Here, BCI prognostic performance was evaluated in HR+ postmenopausal women from the Tamoxifen and Exemestane Adjuvant Multinational (TEAM) trial.

Experimental Design:
3,544 patients were included in the analysis (N = 1,519 N0, N = 2,025 N+). BCI risk groups were calculated using pre-specified cutoff points. Kaplan–Meier analyses and log-rank tests were used to assess the prognostic significance of BCI risk groups based on DR. Hazard ratios (HR) and confidence intervals (CI) were calculated using Cox models with and without clinical covariates.

Results:
For overall 10-year DR, BCI was significantly prognostic in Ni0 (N = 1,196) and N1 (N = 1,234) patients who did not receive prior chemotherapy (P &lt; 0.001). In patients who were DR-free for 5 years, 10-year late DR rates for low- and high-risk groups were 5.4% and 9.3% (N0 cohort, N = 1,285) and 4.8% and 12.2% (N1 cohort, N = 1,625) with multivariate HRs of 2.25 (95% CI, 1.30–3.88; P = 0.004) and 2.67 (95% CI, 1.53–4.63; P &lt; 0.001), respectively. Late DR performance was substantially improved using previously optimized cutoff points, identifying BCI low-risk groups with even lower 10-year late DR rates of 3.8% and 2.7% in N0 and N1 patients, respectively.

Conclusions:
The TEAM trial represents the largest prognostic validation study for BCI to date and provides a more representative assessment of late DR risk to guide individualized treatment decision-making for HR+ patients with early-stage breast cancer.