bluuebunny/crossref_metadata_2025_split huggingface dataset:
Range expansion by avocado lace bug, Pseudacysta perseae (Hemiptera: Tingidae): a reassessment of population genetic structure reveals evidence for a second invasion into California
Authors: Dadlani Lakshmi Paloma , Gebiola Marco , Rugman-Jones Paul , Mauck Kerry E , Hoddle Mark S 
Published: January 2025

Abstract
Pseudacysta perseae (Heidemann 1908) (Hemiptera: Tingidae), a foliar pest of avocados, was first discovered in urban San Diego County, California U.S. in 2004. In 2017, damaging populations of P. perseae were discovered in commercial Hass avocado groves in San Diego and Riverside Counties. The unexpected and rapid spread of P. perseae raised the question of whether this range expansion was an extension of the original incursion or the result of a second invasion event. Using sequences of the mitochondrial COI gene, we found strong evidence that P. perseae populations in southern San Diego County are comprised almost entirely of the single haplotype (A) that was detected in 2004. In contrast, newly established (2017 onwards) populations of P. perseae infesting commercial orchards consisted exclusively of a second mitochondrial haplotype (G). This haplotype is found in Florida and the Caribbean and is conclusive evidence that California has been invaded a second time. Molecular analyses also confirmed that invasive P. perseae populations in Hawaiʻi are haplotype G, indicating that California and Hawaiʻi populations may have originated from the same source area (possibly Florida), or that California may have acted as an invasion bridgehead for the invasion of Hawaiʻi. Reproductive compatibility of the primary (haplotype A) and secondary (haplotype G) invasive populations in California was confirmed via a series of reciprocal laboratory crosses and results suggest that fertility of hybrid eggs is increased. The potential consequences of this second invasion into California by P. perseae are discussed.
The Elastic Wave Propagation in Lo's Three-Phase Porous Media Theory - Based Time-splitting Staggered-grid Finite-difference Method
Authors: Qi Yujuan , Zhang Xiumei , Liu Lin 
Published: January 2025

Abstract
Unsaturated porous media constitutes a prevalent scenario in underground formations, such as oil and gas reservoirs and CO2 geological storage. The two-fluids saturated porous media is a typical manifestation of unsaturated porous media. Understanding how the elastic waves propagate in such media is fundamental for geophysical detection and security monitoring. In this work, leveraging Lo's three-phase porous media theory, a numerical simulation algorithm is introduced to analyze the propagation characteristics through such media in the time-space domain. For this purpose, the constitutive equations and the equations of motion are reformulated into velocity-stress format. By merging the time-splitting scheme with the staggered-grid finite-difference algorithm, the acoustic responses within these porous media are efficiently simulated. Moreover, reference solutions for purely dilatational point and line sources are derived to corroborate the numerical simulation results. Based on these procedures, generation mechanisms of slow compressional waves, influencing factors, and wave conversion phenomena within the interface of porous media are analyzed in focus. The study identifies four distinct waves in two-fluids saturated porous media, encompassing three types of compressional waves (P1, P2, P3) and one type of shear wave (S). Slow compressional waves (P2, P3), attributed to the relative motion in solid-fluid and fluid-fluid, respectively, are significantly affected by the fluid viscosity and frequency. Although slow waves may not be directly observed in seismic frequencies, their energy distribution needs to be emphasized, especially considering the conversion of slow waves into normally propagating P1 and S waves at interfaces.
Randomized empirical likelihood test for ultra-high dimensional means under general covariances
Authors: Chen Yuexin , Zhu Lixing , Xu Wangli 
Published: January 2025

Abstract
This article proposes a calibrated empirical likelihood test for ultra-high dimensional means that incorporates multiple projections. Under weak moment conditions on the distributions of data, we analyse all possible asymptotic distributions of the proposed test statistic in different scenarios. To determine the critical value and enhance test power, we employ the random symmetrization method based on the group of sign flips and use multiple selected projections. The test can still maintain the significance level asymptotically, even in the presence of heterogeneity in the data distribution. Moreover, the proposed test procedure allows for general covariance structures and ultra-high dimensional regimes. Further, the power function reveals the relation with the projection term in an asymptotic sense such that we can select suitable projections to achieve good power in various scenarios. A quasi-Newton algorithm is introduced to reduce the computational cost arising from the intensive optimizations required for computing empirical likelihood. Numerical studies evidence the promising performance of the proposed test compared with existing tests.
Rapid Radiation of a Plant Lineage Sheds Light on the Assembly of Dry Valley Biomes
Authors: Chen Ya-Ping , Sunojkumar Purayidathkandy , Spicer Robert A , Hodel Richard G J , Soltis Douglas E , Soltis Pamela S , Paton Alan J , Sun Miao , Drew Bryan T , Xiang Chun-Lei 
Published: January 2025

Abstract
Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of diversification of the numerous dry valley plant lineages remain unknown. To address this knowledge gap, we investigated the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa. We reconstructed a robust phylogeny encompassing nearly 90% of the approximately 140 extant Isodon species using transcriptome and genome-resequencing data. Our results suggest a rapid radiation of Isodon during the Pliocene that coincided with a habit shift from herbs to shrubs and a habitat shift from humid areas to dry valleys. The shrubby growth form likely acted as a preadaptation allowing for the movement of Isodon species into these dry valleys. Ecological analyses highlight drought-related factors as key drivers influencing the niche preferences of different growth forms and species richness of Isodon. The interplay between topography and the development of the East Asian monsoon since the middle Miocene likely contributed to the formation of the dry valley biome in southwest China. This study enhances our understanding of evolutionary dynamics and ecological drivers shaping the distinctive flora of southwest China and reveals the strategies employed by montane plants in response to climate change and dryland expansion, thus facilitating conservation efforts globally.
2024 Update of the Japan College of Rheumatology Clinical Practice Guidelines for the Management of Rheumatoid Arthritis: Secondary publication
Authors: Harigai Masayoshi , Kaneko Yuko , Tanaka Eiichi , Hirata Shintaro , Kameda Hideto , Kaneko Kayoko , Kishimoto Mitsumasa , Kohno Masataka , Kojima Masayo , Kojima Toshihisa , Morinobu Akio , Nakajima Ayako , Sugihara Takahiko , Fusama Mie , Yajima Nobuyuki , Yanai Ryo , Kawahito Yutaka 
Published: January 2025

ABSTRACT

Objectives
The aim of this study is to update the Japan College of Rheumatology Clinical Practice Guidelines for the Management of Rheumatoid Arthritis (CPG for RA).

Methods
The recommendations were developed based on the evidence published until the end of June 2022 using the Grading of Recommendations Assessment, Development, and Evaluation. The steering committee, CPG panel, systematic review (SR) group, and SR support team were organised.

Results
The treatment goal and drug treatment algorithm required no modifications; however, the footnotes of the drug treatment algorithm were modified. SR of 21 new or updated recommendations for subcutaneous methotrexate (n = 1), biological disease-modifying antirheumatic drugs (n = 1), rituximab (n = 5), Janus kinase inhibitors (n = 6), biosimilars (n = 2), older patients (n = 4), and pregnancy and lactation (n = 2) was conducted. The recommendations for comorbidities and surgery and rehabilitation remained unchanged from the 2020 CPG for RA.

Conclusions
The 2024 CPG for RA, which provide recommendations that reflect the current healthcare environment for rheumatoid arthritis in Japan, can be used effectively as a tool for shared decision-making between rheumatologists and patients in the treatment of RA.
Prevalence and Correlates of Hepatitis C Viremia Among People With Human Immunodeficiency Virus in the Direct-Acting Antiviral Era
Authors: Ma Jimmy , Nance Robin M , Cachay Edward , Ruderman Stephanie A , Kitahata Mari , Falade-Nwulia Oluwaseun , Chander Geetanjali , Drumright Lydia N , Hurt Christopher B , Yendewa George A , Pettit April , Moore Richard D , Fredericksen Rob J , Lloyd Audrey , Bamford Laura , Napravnik Sonia , Fleming Julia , Christopoulos Katerina , Burkholder Greer , Keruly Jeanne , Delaney Joseph A C , Crane Heidi , Kim H Nina 
Published: January 2025

Abstract

Background
National US data on the burden and risks for hepatitis C virus (HCV) infection in people with human immunodeficiency virus (HIV) during the direct-acting antiviral (DAA) era are limited. These data are important to understand current progress and guide future efforts toward HCV microelimination.

Methods
We evaluated (1) HCV prevalence (2011–2013, 2014–2017, 2018–2022) using a serial cross-sectional design and (2) correlates for HCV viremia (2018–2022) in adult people with HIV (PWH) within the Centers for AIDS Research Network of Integrated Clinic Systems (CNICS) cohort using multivariable adjusted relative risk regression. The most recent data from each time period were used for calculations and models.

Results
In the CNICS cohort, HCV viremia prevalence was 8.7% in 2011–2013, 10.5% in 2014–2017, and 4.8% in 2018–2022. Disparities in prevalence across demographic groups defined by age, gender, and race/ethnicity were smaller in 2018–2022 than earlier time periods. In relative risk regression, female gender, detectable HIV RNA, higher proportion of missed visits (last 18 months), higher FIB-4 score, higher depressive symptom severity, and current use of methamphetamine and illicit opioids were associated with HCV viremia in 2018–2022.

Conclusions
The prevalence of HCV viremia during the DAA era in this US-based national cohort of PWH improved over time and across demographic subgroups but remains higher than those without HIV. Our findings highlight the continued importance of prioritizing HCV care in all PWH, especially in certain key, less-reached groups. Proactive, comprehensive efforts to care engagement, substance use, mental health, and other social determinants will be crucial to improve reach, prevention, and treatment to achieve HCV elimination goals.
Predictors of Clinical Outcomes Among People With Human Immunodeficiency Virus and Tuberculosis Symptoms After Rapid Treatment Initiation in Haiti
Authors: Richterman Aaron , Dorvil Nancy , Rivera Vanessa , Bang Heejung , Severe Patrice , Lavoile Kerylyne , Pierre Samuel , Apollon Alexandra , Dumond Emelyne , Pierre Louis Forestal Guyrlaine , Rouzier Vanessa , Joseph Patrice , Cremieux Pierre-Yves , Pape Jean W , Koenig Serena P 
Published: January 2025

Abstract

Background
Few studies have evaluated baseline predictors of clinical outcomes among people with human immunodeficiency virus (HIV) starting antiretroviral therapy (ART) in the modern era of rapid ART initiation.

Methods
We conducted a secondary analysis of a previously reported open-label randomized controlled trial of 2 rapid treatment initiation strategies for people with treatment-naive HIV and tuberculosis symptoms at a large urban clinic in Haiti. We used logistic regression models to assess associations between baseline characteristics and (1) retention in care at 48 weeks, (2) HIV viral load suppression at 48 weeks (among participants who underwent viral load testing), and (3) all-cause mortality. For the viral load suppression outcome, we used inverse probability weighting to account for potential selection bias resulting from exclusion of participants who did not undergo viral load testing.

Results
A total of 500 participants were enrolled in the study from November 2017 to January 2020. Tuberculosis was diagnosed in 88 participants (18%), and ART was started in 494 (99%). After multivariable adjustment, less than secondary school education (adjusted odds ratio [AOR] 0.21 [95% confidence interval (CI), .10–.46]) was significantly associated with a reduced odds of retention in care. Dolutegravir initiation (AOR, 2.57 [95% CI, 1.22–5.43]), age (1.42 per 10-year increase [1.01–1.99]), and tuberculosis diagnosis (3.92 [1.36–11.28]) were significantly associated with increased odds of retention. Age (AOR, 1.36 [95% CI, 1.05–1.75]) and dolutegravir initiation (1.75 [1.07–2.85]) were positively associated with viral suppression, and tuberculosis diagnosis (0.50 [.28–.89) was negatively associated with viral suppression, with similar findings after incorporation of inverse probability weights. Higher CD4 cell count at enrollment was significantly associated with a lower odds of mortality (unadjusted odds ratio, 0.69 [95% CI, .55–.87]), and anemia was associated with a significantly greater odds of mortality (4.86 [1.71–13.81]).

Conclusions
We identified sociodemographic, treatment-related, clinical, and laboratory-based predictors of clinical outcomes. These characteristics may serve as markers of subpopulations that could benefit from additional interventions to support treatment success after rapid treatment initiation.
SmERF6 promotes the expression of terpenoid pathway in Salvia officinalis and improves the production of high-value abietane diterpenes, carnosol and carnosic acid
Authors: Revuru Bharadwaj , Thashanamoorthi Gayathri , Demiwal Prathiba , Sircar Debabrata , Ramalingam Sathishkumar 
Published: January 2025

Abstract
Carnosol (CO) and carnosic acid (CA) are pharmaceutically important diterpenes predominantly produced in members of Lamiaceae, Salvia officinalis (garden sage), Salvia fruticosa, and Rosmarinus officinalis. Nevertheless, the availability of these compounds in plant systems is very low. In an effort to improve the in planta content of these diterpenes in garden sage, SmERF6 (Salvia miltiorrhiza Ethylene Responsive Factor 6) transcription factor was expressed heterologously. Bai et al. (The ethylene response factor SmERF6 co-regulates the transcription of SmCPS1 and SmKSL1 and is involved in tanshinone biosynthesis in Salvia miltiorrhiza hairy roots. Planta 2018; 248:243–55.) proved that SmERF6 binds to the promoter regions of Copalyl pyrophosphate synthase and Kaurene synthase-like genes and improves transcription, thereby augmenting ferruginol levels, a common precursor for abietane diterpenes in Salvia genus; moreover, transgenic hairy roots of S. miltiorrhiza displayed 4-fold improved tanshinone content. In our study, heterologous transient expression of SmERF6 in S. officinalis exhibited inter-specific activity in promoting differential accumulation of diterpenes. Overexpression studies showed elevation in the levels of CO (2-fold) and CA (5-fold). Furthermore, in infiltrated leaves levels of ferruginol (50%) and CA derivatives (rosmanol, epirosmanol, and methyl CA) were significantly upregulated along with the other signature terpenes. Finally, stable transgenic lines of S. officinalis developed through Agrobacterium-mediated in planta genetic transformation accumulated significant amounts of CO (4-folds) and CA (3-folds), as compared to wild plants. Overall, the present study is the first report on improving the content of pharmaceutically important diterpenes in S. officinalis by overexpressing pathway-specific transcription factors. The current findings showed convincing evidence for the concept of improving specialized metabolite(s) content in medicinal plants by manipulating the expression of transcriptional regulators.
An epiallele of a gene encoding a PfkB-type carbohydrate kinase affects plant architecture in maize
Authors: Li Ruonan , Xu Yue , Xu Qiang , Tang Jing , Chen Wenqing , Luo Zhixiang , Liu Hongbo , Li Wenqiang , Yan Jianbing , Springer Nathan M , Li Lin , Li Qing 
Published: January 2025

Abstract
Plant architecture greatly contributes to grain yield, but the epigenetic regulation of plant architecture remains elusive. Here, we identified the maize (Zea mays L.) mutant plant architecture 1 (par1), which shows reduced plant height, shorter and narrower leaves, and larger leaf angles than the wild type. Interestingly, par1 is an epiallele harbouring a de novo CACTA insertion in the intron of the Par1 gene. High DNA methylation levels of the CACTA insertion are associated with strong Par1 expression and normal phenotypes. In contrast, low DNA methylation levels of this insertion are associated with weak Par1 expression and a mutant-like phenotype. The Par1 gene encodes a PfkB-type carbohydrate kinase that converts nucleosides to nucleoside monophosphates both in vitro and in vivo. Additional analyses showed that genes differentially expressed in the par1 mutant are enriched in jasmonic acid (JA) metabolism, and levels of JA metabolites were significantly higher in the mutant than in the wild type. Treatment with either nucleoside monophosphates or a synthetic inhibitor of JA biosynthesis reduced JA levels and partially rescued the mutant phenotype. In summary, we identified an epiallele of a gene encoding a PfkB-type carbohydrate kinase that might affect nucleoside monophosphate and JA levels, thus affecting maize growth.
The vacuolar phosphatases purple acid phosphatase 26 and haloacid dehalogenase IIA2.1 hydrolyze 5′-, 3′-, and 2′-nucleotides derived from RNA degradation
Authors: Firdoos Nabila , Krumwiede Lukas , Medina-Escobar Nieves , Treichel Leonie , Fischer Lisa , Herde Marco , Witte Claus-Peter 
Published: January 2025

Abstract
The vacuole is an important site for RNA degradation. Autophagy delivers RNA to the vacuole, where the vacuolar T2 RNase ribonuclease 2 (RNS2) plays a major role in RNA catabolism. The presumed products of RNS2 activity are 3′-nucleoside monophosphates (3′-NMPs). Vacuolar phosphatases that carry out 3′-NMP hydrolysis are required to metabolize 3′-NMPs, but the specific players remain unknown. Using a mutant of RNS2 and mutants of the autophagy-related genes 5 and 9 (atg5 and atg9), we confirmed that 3′-NMPs are products of vacuolar RNS2-mediated RNA degradation in Arabidopsis (Arabidopsis thaliana). Moreover, we identified purple acid phosphatase 26 (PAP26) and haloacid dehalogenase IIA2.1 (HIIA2.1) as vacuolar 3′-NMP phosphatases. Based on phylogenetic analysis, we propose systematic nomenclature for HADIIA enzymes, some of which were previously named vegetative storage proteins, which we critically discuss. PAP26 and HIIA2.1 differ in their NMP specificity and activity in vitro. However, hiia2.1 pap26 double mutant plants, but generally not the respective single mutants, accumulate 3′-NMPs in addition to 5′-NMPs and, surprisingly, also 2′-NMPs. These findings suggest that PAP26 and HIIA2.1 have overlapping NMP substrate spectra in vivo. Excess 3′- and 2′-NMPs accumulate in plants exposed to a prolonged night, presumably because carbon limitation enhances autophagy-mediated vacuolar RNA degradation. We conclude that vacuolar RNA catabolism releases 3′-NMPs and 2′-NMPs through RNS2 and other RNases that also generate 5′-NMPs. PAP26 and HIIA2.1 are required to dephosphorylate these NMPs, so that they can enter general nucleotide metabolism outside the vacuole.
From relief to resistance: implications of self-medication practice for malaria elimination in India
Authors: Verma Kanika , Nitika Nitika , Bharti Praveen Kumar 
Published: January 2025

Abstract
The self-medication practices in India may pose challenges to malaria elimination efforts. While individuals often seek immediate relief from symptoms, the indiscriminate use of antimalarial medications can lead to increased resistance among malaria parasites. This study highlights the implications of self-medication on public health, exploring their impact on malaria elimination. Public awareness campaigns highlighting the risks of self-treatment, necessity of professional medical consultation and the need for malaria diagnosis prior to initiating treatment should be carried out. Addressing self-treatment practices will improve patient outcomes, mitigate the development of drug resistance in parasites and contribute to the goal of a malaria-free India.
The Lipo-DIEP Flap Breast Reconstruction: A Valuable Innovation for Maximizing Abdominal Tissue Volume
Authors: Longo Benedetto , D’Orsi Gennaro , Farcomeni Alessio , Giacalone Martina , Gagliano Elettra , Vannucchi Lisa , Catenacci Maximilian , Vanni Gianluca , Buonomo Claudio Oreste , Cervelli Valerio 
Published: January 2025

Background:
The deep inferior epigastric perforator (DIEP) flap is universally considered the gold standard technique for breast reconstruction (BR), though it cannot always be proposed to patients with insufficient donor-site volume. We explore the efficacy of autologous fat transfer (AFT) of the Holm abdomen zone IV in the retropectoral plane during DIEP flap reconstruction (lipo-DIEP flap), to enhance the volume provided by the abdominal donor site in patients with low body mass index (BMI).

Methods:
We prospectively enrolled patients with BMI less than 25 kg/m2 and candidates for lipo-DIEP flap BR (group A) comparing them with a control group (group B) undergoing traditional DIEP flap BR with the same characteristics of the first group (BMI < 25 kg/m2). Patients belonging to group A underwent magnetic resonance imaging preoperatively and 6 months after the BR, evaluating the adipose tissue volume retained in the retropectoral space.

Results:
A total of 40 breasts were included in the study. The 2 groups were homogeneous regarding the collected variables, except for mean delayed AFT sessions (0.25 versus 0.95; P= 0.00094). The average volume of retropectoral AFT was 116.25 mL (SD 31.36). Six months after the procedure, the mean retropectoral fat volume calculated through magnetic resonance imaging was 48.64 mL (SD 14.15), whereas the mean graft integration rate was 45.98% (range, 30.7%–64.2%).

Conclusions:
The lipo-DIEP flap is a valuable technique for patients with insufficient donor-site volume. Immediate retropectoral fat grafting from the Holm zone IV has proven to be safe in terms of complications, reducing the need for further AFT sessions.