bluuebunny/crossref_metadata_2025_split huggingface dataset:
A real‐life experience of long‐term use of pilocarpine in irradiated head and neck cancer patients
Authors: Kittichet Rungarun , Chitapanarux Imjai , Kittidachanan Kittikun , Sripan Patumrat 
Published: February 2024

AbstractAimsTo assess long‐term efficacy and side effects of pilocarpine on irradiated head and neck cancer (HNC) patients in both for prevention and treatment of radiation‐induced xerostomia (RIX).MethodsRetrospective observational study was conducted. Eligibility criteria included irradiated HNC patients who received pilocarpine at least 12 weeks either for prevention (group A) or for treatment (group B) of RIX. We collected the documented Late Effect Normal Tissue Task Force‐Subjective, Objective, Management, Analytics subjective/objective grades of RIX before (only group B) and the latest visit for pilocarpine prescription, dosage, side effects, duration of treatment, and the cause of discontinuation.ResultsBetween December 2007 and June 2022, 182 patients were enrolled including 95 patients (52%) in group A and 87 patients (48%) in group B. Group A patients reported grades 1, 2, 3, and 4 objective RIX in 0%, 7%, 93%, and 0%. Grade 1, 2, and 3 subjective RIX were 57%, 28%, and 15%. All patients in group B had grade 3 both objective/subjective RIX. The overall improvement of objective/subjective RIX was found in 40%/83%. Discontinuation was found in 51% of patients due to tolerable symptoms or deterioration of the patient's status.ConclusionsBased on this retrospective analysis, long‐term use of pilocarpine in irradiated HNC appears feasible for both prevention and treatment of RIX.
Revisiting growth–defence trade‐offs and breeding strategies in crops
Authors: Gao Mingjun , Hao Zeyun , Ning Yuese , He Zuhua 
Published: February 2024

SummaryPlants have evolved a multi‐layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade‐offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth–defence trade‐offs to breed future crops with desirable disease resistance and high yield.
Amniotic membrane dressings for treatment of aplasia cutis in newborns
Authors: Kadivar Maliheh , Sangsari Razieh , Rostamli Somayeh , Sotoudeh Soheila , Mirnia Kayvan 
Published: February 2024

AbstractBackgroundAplasia cutis congenita (ACC) is a rare congenital skin defect characterized by a focal or extensive absence of the epidermis, dermis, and occasionally, subcutaneous tissue. When the wound caused by this defect is wide or deep, various treatments are used, including skin grafting. The amniotic membrane (AM) is a biological dressing that facilitates re‐epithelialization as it contains mesenchymal cells and numerous growth factors.ObjectiveTo report the efficacy of AM dressings in treating the skin defects of ACC.MethodThis study was conducted on five neonates diagnosed with ACC born between 2018 and 2022, referred to the Children's Medical Center in Tehran, Iran. AM dressings were applied on wounds larger than 1 cm2. The wounds were assessed weekly and, if required, an additional AM dressing was applied.ResultsThe skin defects gradually re‐epithelialized after application of the AM. The complete healing process took around 3.5 weeks on average. No hypertrophic scarring was observed.ConclusionThe application of AM dressing resulted in satisfactory cosmetic outcomes, with no hypertrophic scar formation. Complete healing occurred in all cases except one. The length of the hospital stay ranged from 2 to 6 weeks, depending on the size of the wound.
Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture
Authors: Charagh Sidra , Hui Suozhen , Wang Jingxin , Raza Ali , Zhou Liang , Xu Bo , Zhang Yuanyuan , Sheng Zhonghua , Tang Shaoqing , Hu Shikai , Hu Peisong 
Published: February 2024

AbstractDue to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM‐contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho‐physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting‐edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs‐tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.
Transcriptomic and proteomic analyses of distinct Arabidopsis organs reveal high PSI‐NDH complex accumulation in stems
Authors: Laihonen Laura , Rantala Marjaana , Ranasinghe Umanga , Tyystjärvi Esa , Mulo Paula 
Published: February 2024

AbstractIn addition to leaves, the main site of photosynthetic reactions, active photosynthesis also takes place in stems, siliques and tree trunks. Although non‐foliar photosynthesis has a marked effect on plant growth and yield, only limited information on the expression patterns of photosynthesis‐related genes and the structure of photosynthetic machinery in different plant organs has been available. Here, we report the results of transcriptomic analysis of various organs of Arabidopsis thaliana and compare the gene expression profiles of young and mature leaves with a special focus on photosynthetic genes. Further, we analyzed the composition and organization of the photosynthetic electron transfer machinery in leaves, stems and green siliques at the protein level using BN‐PAGE. RNA‐Seq analysis revealed unique gene expression profiles in different plant organs and showed major differences in the expression of photosynthesis‐related genes in young as compared to mature rosettes. Gel‐based proteomic analysis of the thylakoid protein complex organization further showed that all studied plant organs contain the necessary components of the photosynthetic electron transfer chain. Intriguingly, stems accumulate high amounts of PSI‐NDH complex, which has previously been implicated in cyclic electron transfer.
Performance Analysis of Waste Biomass Gasification and Renewable Hydrogen Production by Neural Network Algorithm
Authors: Vargas Gabriel Gomes , Ortiz Pablo Silva , de Oliveira Silvio 
Published: February 2024

Abstract
This study assesses renewable hydrogen production via gasification of residual biomass, using artificial neural networks (ANNs) for predictive modeling. The process uses residues from sugarcane and orange harvests, sewage sludge, corn byproducts, coffee remnants, eucalyptus remains, and urban waste. Simulation data from aspen plus® software predict hydrogen conversion from each biomass type, with a three-layer feedforward neural network algorithm used for model construction. The model showed high accuracy, with R2 values exceeding 0.9941 and 0.9931 in training and testing datasets, respectively. Performance metrics revealed a maximum higher heating value (HHV) of 18.1 MJ/kg for sewage sludge, the highest cold gas efficiency for urban and orange waste (82.2% and 80.6%), and the highest carbon conversion efficiency for sugarcane bagasse and orange residue (92.8% and 91.2%). Corn waste and sewage sludge yielded the highest hydrogen mole fractions (0.55 and 0.52). The system can reach relative exergy efficiencies from 24.4% for sugarcane straw residues to 42.6% for sugarcane bagasse. Rational exergy efficiencies reached from 23.7% (coffee waste) to 39.0% (sugarcane bagasse). This research highlights the potential of ANNs in forecasting hydrogen conversion and assessing the performance of gasification-based renewable hydrogen procedures using biomass wastes.
Oil Film Formation and Delamination Process on Nanostructured Surfaces in Boundary Lubrication: A Coarse-Grained Molecular Dynamics Study
Authors: Deng Shizhe , Kubo Atsushi , Todaka Yoshikazu , Shiihara Yoshinori , Mitsuhara Masatoshi , Umeno Yoshitaka 
Published: February 2024

Abstract
A series of coarse-grained molecular dynamics simulations were conducted to investigate the temporal evolution of frictional behaviors of lubricants between sliding nanostructured iron surfaces. Grain boundary atoms were given a stronger interaction with the lubricant molecules. We varied the surface distance and interaction strength between grain boundary atoms and lubricants. It was found that, below the critical compressive stress, the oil film detached from the surface at first and then attached to it after several nanoseconds due to the localized molecular rearrangement within lubricants and the enhancement of interaction between lubricants and iron surfaces. The transition times required for oil film formation and de-lamination both increased as it approached the critical compressive stress. Larger interaction strength increased the delamination time but barely affected the formation time.
Balancing the scales: achieving the optimal beta-lactam to beta-lactamase inhibitor ratio with continuous infusion piperacillin/tazobactam against extended spectrum beta-lactamase producing
Enterobacterales
Authors: Cojutti Pier Giorgio , Pai Manjunath P. , Tonetti Tommaso , Siniscalchi Antonio , Viale Pierluigi , Pea Federico 
Published: February 2024

ABSTRACT

Piperacillin/tazobactam (TZP) is administered intravenously in a fixed ratio (8:1) with the potential for inadequate tazobactam exposure to ensure piperacillin activity against
Enterobacterales
. Adult patients receiving continuous infusion (CI) of TZP and therapeutic drug monitoring (TDM) of both agents were evaluated. Demographic variables and other pertinent laboratory data were collected retrospectively. A population pharmacokinetic approach was used to select the best kidney function model predictive of TZP clearance (CL). The probability of target attainment (PTA), cumulative fraction of response (CFR) and the ratio between piperacillin and tazobactam were computed to identify optimal dosage regimens by continuous infusion across kidney function. This study included 257 critically ill patients (79.3% male) with intra-abdominal, bloodstream, and hospital-acquired pneumonia infections in 89.5% as the primary indication. The median (min-max range) age, body weight, and estimated glomerular filtration rate (eGFR) were 66 (23–93) years, 75 (39–310) kg, and 79.2 (6.4–234) mL/min, respectively. Doses of up to 22.5 g/day were used to optimize TZP based on TDM. The 2021 chronic kidney disease epidemiology equation in mL/min best modeled TZP CL. The ratio of piperacillin:tazobactam increased from 6:1 to 10:1 between an eGFR of <20 mL/min and >120 mL/min. At conventional doses, the PTA is below 90% when eGFR is ≥100 mL/min. Daily doses of 18 g/day and 22.5 g/day by CI are expected to achieve a >80% CFR when eGFR is 100–120 mL/min and >120–160 mL/min, respectively. Inadequate piperacillin and tazobactam exposure is likely in patients with eGFR ≥ 100 mL/min. Dose regimen adjustments informed by TDM should be evaluated in this specific population.
Ex vivo
drug susceptibility and resistance mediating genetic polymorphisms of
Plasmodium falciparum
in Bobo-Dioulasso, Burkina Faso
Authors: Somé A. Fabrice , Conrad Melissa D. , Kabré Zachari , Fofana Aminata , Yerbanga R. Serge , Bazié Thomas , Neya Catherine , Somé Myreille , Kagambega Tegawinde Josue , Legac Jenny , Garg Shreeya , Bailey Jeffrey A. , Ouédraogo Jean-Bosco , Rosenthal Philip J. , Cooper Roland A. 
Published: February 2024

ABSTRACT

Malaria remains a leading cause of morbidity and mortality in Burkina Faso, which utilizes artemether–lumefantrine as the principal therapy to treat uncomplicated malaria and seasonal malaria chemoprevention with monthly sulfadoxine–pyrimethamine plus amodiaquine in children during the transmission season. Monitoring the activities of available antimalarial drugs is a high priority. We assessed the
ex vivo
susceptibility of
Plasmodium falciparum
to 11 drugs in isolates from patients presenting with uncomplicated malaria in Bobo-Dioulasso in 2021 and 2022. IC
50
values were derived using a standard 72 h growth inhibition assay. Parasite DNA was sequenced to characterize known drug resistance-mediating polymorphisms. Isolates were generally susceptible, with IC
50
values in the low-nM range, to chloroquine (median IC
50
10 nM, IQR 7.9–24), monodesethylamodiaquine (22, 14–46) piperaquine (6.1, 3.6–9.2), pyronaridine (3.0, 1.3–5.5), quinine (50, 30–75), mefloquine (7.1, 3.7–10), lumefantrine (7.1, 4.5–12), dihydroartemisinin (3.7, 2.2–5.5), and atovaquone (0.2, 0.1–0.3) and mostly resistant to cycloguanil (850, 543–1,290) and pyrimethamine (33,200, 18,400–54,200), although a small number of outliers were seen. Considering genetic markers of resistance to aminoquinolines, most samples had wild-type PfCRT K76T (87%) and PfMDR1 N86Y (95%) sequences. For markers of resistance to antifolates, established PfDHFR and PfDHPS mutations were highly prevalent, the PfDHPS A613S mutation was seen in 19% of samples, and key markers of high-level resistance (PfDHFR I164L; PfDHPS K540E) were absent or rare (A581G). Mutations in the PfK13 propeller domain known to mediate artemisinin partial resistance were not detected. Overall, our results suggest excellent susceptibilities to drugs now used to treat malaria and moderate, but stable, resistance to antifolates used to prevent malaria.
Lineage-specific evolution of
Aquibium
, a close relative of
Mesorhizobium
, during habitat adaptation
Authors: Kim Minkyung , Kim Wonjae , Park Yerim , Jung Jaejoon , Park Woojun 
Published: February 2024

ABSTRACT

The novel genus
Aquibium
that lacks nitrogenase was recently reclassified from the
Mesorhizobium
genus. The genomes of
Aquibium
species isolated from water were smaller and had higher GC contents than those of
Mesorhizobium
species. Six
Mesorhizobium
species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24
Mesorhizobium
species. Therefore, they were classified as the non-N
2
-fixing
Mesorhizobium
lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific
fur/mur
indicated that
Mesorhizobium
species may have evolved from
Aquibium
species through an ecological transition. Halotolerant and alkali-resistant
Aquibium
and
Mesorhizobium microcysteis
belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (
mrpABCDEFG
). These genes were not present in the N
2
-fixing
Mesorhizobium
lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in
Aquibium
species, close relatives of
Mesorhizobium
species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.

IMPORTANCE

Phylogenetic analyses revealed that the
Aquibium
lineage (AL) and non-N
2
-fixing
Mesorhizobium
lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N
2
-fixing
Mesorhizobium
lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
Japanese encephalitis virus inhibits superinfection of Zika virus in cells by the NS2B protein
Authors: Yuan Honggen , Rao Jingwei , Zhang Jinhua , Ye Jing , Cao Shengbo , Chen Huanchun , Song Yunfeng 
Published: February 2024

ABSTRACT

Superinfection exclusion (SIE) is a phenomenon in which a preexisting infection prevents a secondary infection. SIE has been described for several flaviviruses, such as West Nile virus vs Nhumirim virus and Dengue virus vs yellow fever virus. Zika virus (ZIKV) is an emerging flavivirus posing threats to human health. The SIE between ZIKV and Japanese encephalitis virus (JEV) is investigated in this study. Our results demonstrate for the first time that JEV inhibits ZIKV infection in both mammalian and mosquito cells, whether co-infects or subsequently infects after ZIKV. The exclusion effect happens at the stage of ZIKV RNA replication. Further studies show that the expression of JEV NS2B protein is sufficient to inhibit the replication of ZIKV, and the outer membrane region of NS2B (46–103 aa) is responsible for this SIE. JEV infection and NS2B expression also inhibit the infection of the vesicular stomatitis virus. In summary, our study characterized a SIE caused by JEV NS2B. This may have potential applications in the prevention and treatment of ZIKV or other RNA viruses.

IMPORTANCE
The reemerged Zika virus (ZIKV) has caused severe symptoms in humans and poses a continuous threat to public health. New vaccines or antiviral agents need to be developed to cope with possible future pandemics. In this study, we found that infection of Japanese encephalitis virus (JEV) or expression of NS2B protein well inhibited the replication of ZIKV. It is worth noting that both the P3 strain and vaccine strain SA14-14-2 of JEV exhibited significant inhibitory effects on ZIKV. Additionally, the JEV NS2B protein also had an inhibitory effect on vesicular stomatitis virus infection, suggesting that it may be a broad-spectrum antiviral factor. These findings provide a new way of thinking about the prevention and treatment of ZIKV.
Oncolytic Newcastle disease virus induced degradation of YAP through E3 ubiquitin ligase PRKN to exacerbate ferroptosis in tumor cells
Authors: Sun Yifan , Tang Lanlan , Kan Xianjin , Tan Lei , Song Cuiping , Qiu Xusheng , Liao Ying , Nair Venugopal , Ding Chan , Liu Xiufan , Sun Yingjie 
Published: February 2024

ABSTRACT

Ferroptosis, a form of programmed cell death characterized by iron-dependent lipid peroxidation, has recently gained considerable attention in the field of cancer therapy. There is significant crosstalk between ferroptosis and several classical signaling pathways, such as the Hippo pathway, which suppresses abnormal growth and is frequently aberrant in tumor tissues. Yes-associated protein 1 (YAP), the core effector molecule of the Hippo pathway, is abnormally expressed and activated in a variety of malignant tumor tissues. We previously proved that the oncolytic Newcastle disease virus (NDV) activated ferroptosis to kill tumor cells. NDV has been used in tumor therapy; however, its oncolytic mechanism is not completely understood. In this study, we demonstrated that NDV exacerbated ferroptosis in tumor cells by inducing ubiquitin-mediated degradation of YAP at Lys90 through E3 ubiquitin ligase parkin (PRKN). Blocking YAP degradation suppressed NDV-induced ferroptosis by suppressing the expression of Zrt/Irt-like protein 14 (ZIP14), a metal ion transporter that regulates iron uptake. These findings demonstrate that NDV exacerbated ferroptosis in tumor cells by inducing YAP degradation. Our study provides new insights into the mechanism of NDV-induced ferroptosis and highlights the critical role that oncolytic viruses play in the treatment of drug-resistant cancers.

IMPORTANCE
The oncolytic Newcastle disease virus (NDV) is being developed for use in cancer treatment; however, its oncolytic mechanism is still not completely understood. The Hippo pathway, which is a tumor suppressor pathway, is frequently dysregulated in tumor tissues due to aberrant yes-associated protein 1 (YAP) activation. In this study, we have demonstrated that NDV degrades YAP to induce ferroptosis and promote virus replication in tumor cells. Notably, NDV was found to induce ubiquitin-mediated degradation of YAP at Lys90 through E3 ubiquitin ligase parkin (PRKN). Our study reveals a new mechanism by which NDV induces ferroptosis and provides new insights into NDV as an oncolytic agent for cancer treatment.
HIV-1 RNA genome packaging: it’s G-rated
Authors: Duchon Alice , Hu Wei-Shau 
Published: February 2024

ABSTRACT

A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its progeny. The genome packaging step is a highly regulated and extremely efficient process as a vast majority of virus particles contain two copies of full-length unspliced HIV-1 RNA that form a dimer. Thus, during virus assembly HIV-1 can identify and selectively encapsidate HIV-1 unspliced RNA from an abundant pool of cellular RNAs and various spliced HIV-1 RNAs. Several “

G

” features facilitate the packaging of a dimeric RNA genome. The viral polyprotein

G

ag orchestrates virus assembly and mediates RNA genome packaging. During this process, Gag preferentially binds unpaired

g

uanosines within the highly structured 5′ untranslated region (UTR) of HIV-1 RNA. In addition, the HIV-1 unspliced RNA provides a scaffold that promotes Gag:Gag interactions and virus assembly, thereby ensuring its packaging. Intriguingly, recent studies have shown that the use of different

g

uanosines at the junction of U3 and R as transcription start sites results in HIV-1 unspliced RNA species with 99.9% identical sequences but dramatically distinct 5′ UTR conformations. Consequently, one species of unspliced RNA is preferentially packaged over other nearly identical RNAs. These studies reveal how conformations affect the functions of HIV-1 RNA elements and the complex regulation of HIV-1 replication. In this review, we summarize
cis
- and
trans
-acting elements critical for HIV-1 RNA packaging, locations of Gag:RNA interactions that mediate genome encapsidation, and the effects of transcription start sites on the structure and packaging of HIV-1 RNA.