bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on the Smart Dyeing and Performance of Poplar Veneers Modified by Deep Eutectic Solvents
Authors: Liu Yadong , Song Kuiyan
Published: December 2024

Imitation precious wood materials have become a research focus due to their good quality, high safety level, excellent performance, rich color, varied textures, and high utilization rates. However, their uneven dyeing, poor color stability, and lack of durability limit their further application. This study utilized a neural network model optimized with the Gray Wolf Algorithm (GWA) for color matching, using acidic dyes as raw materials and deep eutectic solvents (DESs) for modification. Functional reagents like nano tungsten trioxide (WO3) and titanium dioxide (TiO2) were introduced alongside polyvinyl alcohol (PVA) as a modifier. A dyeing-enhancement modification process was employed to create a poplar veneer that exhibited uniform and stable color performance with a smooth surface, mimicking that of precious wood. Computerized color matching was used to adjust the dye formulation for staining, ensuring stable colorimetric values on the veneer surface, which closely resembled natural precious wood. The average mean squared error in dye concentration prediction, after processing with the Gray Wolf Algorithm and a basic neural network algorithm, decreased from 0.13 to 0.006, ensuring repeatability and consistency in wood dyeing. Analysis and characterization using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and permeability testing revealed that nano TiO2 and WO3 particles were uniformly distributed within the wood cell lumens and firmly bonded. Mechanical testing on PVA-glued veneers showed that compared to untreated poplar veneers, the tensile strength of the imitation wood increased by approximately 62.5%, and the bending strength reached 809.09 MPa, significantly improving the flexibility and tensile properties of the poplar veneer. This study is the first to adopt a DES-modified dyeing-enhancement modification process to improve the dyeing performance, uniformity, durability, and structural stability of wood, showcasing its great potential in architectural decoration, high-end furniture, and artisanal crafts.
Uncertainty Analysis of Forest Aboveground Carbon Stock Estimation Combining Sentinel-1 and Sentinel-2 Images
Authors: Qiu Bo , Li Sha , Cao Jun , Zhang Jialong , Yang Kun , Luo Kai , Huang Kai , Jiang Xinzhou
Published: December 2024

Accurate estimation of forest aboveground carbon stock (AGC) is essential for understanding carbon accounting and climate change. In previous studies, the extracted factors, such as spectral textures, vegetation indices, and textural features, were used to estimate the AGC. However, few studies examined how different factors affect estimation accuracy in detail. Meanwhile, there are also many uncertainties in the collection and processing of the field data. To quantify the various uncertainties in the process of AGC estimation, we used the random forest (RF) to establish estimation models based on field data and Sentinel-1/2 images in Shangri-La. The models included the band information model (BIM), the vegetation index model (VIM), the texture information model (TIM), the Sentinel-2 factor model (S-2M), and the Sentinel-1/2 factor model (S-1/2M). Then, uncertainties resulting from the plot scale and estimation models were calculated using error equations. Our goal is to analyze the influence of different factors on AGC estimation and to assess the uncertainty of plot scale and estimation models quantitatively. The results showed that (1) the uncertainty of the measurement was 3.02%, while the error of the monocarbon stock model was the main uncertainty at the plot scale, which was 9.09%; (2) the BIM had the lowest accuracy (R2 = 0.551) and the highest total uncertainty (22.29%); by gradually introducing different factors in the process of modeling, the accuracies improved significantly (VIM: R2 = 0.688, TIM: R2 = 0.715, S-2M: R2 = 0.826), and the total uncertainty decreased to some extent (VIM: 14.12%, TIM: 12.56%, S-2M: 10.79%); (3) the S-1/2M with the introduction of Sentinel-1 synthetic aperture radar (SAR) data has the highest accuracy (R2 = 0.872) and the lowest total uncertainty (8.43%). The inaccuracy of spectral features is highest, followed by vegetation indices, while textural features have the lowest inaccuracy. Uncertainty in the remote-sensing-based estimation model remains a significant source of uncertainty compared to the plot scale. Even though the uncertainty at the plot scale is relatively small, this error should not be ignored. The uncertainty in the estimation process could be further reduced by improving the precision of the measurement and the fitting of the monocarbon stock estimation model.
Spatial and Temporal Distribution of Habitat Pattern of Trichiurus japonicus in the Northern South China Sea Under Future Climate Scenarios
Authors: Zhang Junyi , Li Jiajun , Zhang Kui , Xu Youwei , Xu Shannan , Chen Zuozhi
Published: December 2024

The impact of climate change on fish distribution has drawn increasing attention worldwide. Studying the distribution patterns and habitat evolution trends of largehead hairtail (Trichiurus japonicus), an important fishery resource in the northern South China Sea (NSCS), is of great significance for the management and sustainable utilization of fishery resources. This study uses an ensemble species distribution model to analyze the seasonal distribution patterns of T. japonicus in the NSCS and predict the changes in highly suitable habitats of T. japonicus under four future climate scenarios (IPCC Shared Socioeconomic Pathways SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). The results show that the area of suitable habitats in the Beibu Gulf is expected to increase, while that in the offshore of Guangdong will significantly decrease. In different seasons, there are differences in environmental factors affecting the distribution of T. japonicus, among which sea bottom temperature (SBT) and bathymetry (BM) are key factors. Under the SSP1-2.6 scenario, the area of highly suitable habitats for T. japonicus is expected to decrease by 30.54% by the 2100s, while under the SSP5-8.5 scenario, it is expected to decrease by 53.67%. Our research results show that the active range of T. japonicus in the NSCS has different adaptive responses to different climate change scenarios, which has an important impact on the development and management of T. japonicus resources.
Potential Impact of DOM on Fish Biodiversity in the Jinshui River Basin Environment
Authors: Cheng Shoutao , Zhang Jiasheng , Xue Hao , Yang Qi , Liu Jing , Zhang Lingsong , Liu Na , Wang Yeyao , Meng Fansheng
Published: December 2024

Water quality is crucial for the ecological health of rivers. However, assessing environmental stressors in large river basins has been challenging due to limited biodiversity monitoring tools. Combining environmental DNA and water quality monitoring presents new possibilities for evaluating the impact of dissolved organic matter (DOM) on fish diversity. Case studies from the Jinshui River, Futou Lake, and Gan River in the Jinshui River Basin demonstrated that eDNA biomonitoring reached 84.62% OTU asymptote (176 OTUs) and 91.06% species asymptote (49 species). The Gan River had 1.21 and 1.26 times more fish OTUs than Futou Lake and the Jinshui River, with 20 overlapping species among the areas. We identified typical excitation-emission matrix (EEM) components of DOM and three PARAFAC fluorescent components: C1 (microbial humic-like), C2 (terrestrial humic-like), and C3 (tryptophan-like). Sequence diversity was positively correlated with EC, TDS, pH, NH3-N, DO, CODMn, biological index (BIX), and freshness index (β/α). Taxonomic diversity positively correlated with spectral slope ratio (SR) and C3. Functional diversity positively correlated with SR but negatively correlated with humification index (HIX). The combined eDNA and DOM monitoring approach shows promise for future assessments of fish biodiversity in river basin environments.
The Characteristics and Expression Analysis of the Tomato KWL Gene Family Under Biotic Stress
Authors: Su Mei , Ru Xuejuan , Chen Yang , Wang Hongjuan , Luo Jia , Wu Hong
Published: December 2024

Background: Tomatoes are renowned for their popularity and nutritional value across the globe, yet their production and quality face significant challenges from various biotic stresses in their growing environments. Kiwellin (KWL) has been implicated in plant disease resistance. However, our comprehension of this gene family in plants is still remarkably insufficient. Methods: We conducted a comprehensive genomic analysis of the KWL gene family in tomatoes. The tertiary structures of SlKWLs were predicted by AlphaFold2. EMBOSS was used for codon analysis. RNA-seq and RT-qPCR analysis were performed to explore the expression profile of SlKWLs. Results: Our findings identified 12 distinct SlKWL members distributed across four chromosomes within the tomato genome. By examining their gene structure, conserved motifs, functional domains, and phylogenetic relationships, we elucidated the complex evolutionary relationships and potential functions of these genes. Notably, we identified numerous cis-regulatory elements within the promoter regions of the SlKWL genes which are associated with responses to both abiotic and biotic stresses, as well as hormone signaling pathways. This finding strongly implies that SlKWLs are integral to plant growth and adaptation to diverse stress conditions. Furthermore, RNA-seq and RT-qPCR analysis revealed an upregulation of five SlKWLs expressed subsequent to Phytophthora infestans infection. Particularly, SlKWL2 and SlKWL3 exhibited substantially elevated expression levels, underscoring their active involvement in biotic stress responses. Conclusions: Collectively, these findings advance our comprehension of the SlKWL gene family and provide a robust foundation for future investigations into the roles of SlKWL genes in tomato stress responses.
Correction: Vannini, A.; Petraglia, A. Wood Distillate Mitigates Ozone-Induced Visible and Photosynthetic Plant Damage: Evidence from Ozone-Sensitive Tobacco (Nicotiana tabacum L.) BelW3. Horticulturae 2024, 10, 480
Authors: Vannini Andrea , Petraglia Alessandro
Published: December 2024

In the original publication [...]
Preemergent Liverwort Control by Organic Mulching in Containerized Ornamental Production
Authors: Sidhu Manjot Kaur , Chaudhari Sushila , Lopez Roberto G. , Patterson Eric L. , Saha Debalina
Published: December 2024

Liverwort (Marchantia polymorpha) competes for resources within containers, resulting in a reduction in the quality and market value of ornamentals. Therefore, the objective of this study was (1) to assess the impact of different mulch types, depths, and their moisture-holding-capacity on liverwort control and (2) to quantify if phytotoxicities develop on ornamental plants due to the mulches. The percent water retention of four different organic mulches [rice hull (RH), cocoa hull (CH), pine bark (PB), or red hardwood (HW)] was determined in a laboratory experiment. In a greenhouse experiment, the Hosta plantaginea (Plantain Lily) varieties ‘Curly Fries’ and ‘Pandora’s Box’ were mulched with either RH, HW, CH, or PB at a depth of 0.63, 1.27, 2.54, or 5.08 cm. Liverwort thalli coverage on the container surface was visually estimated bi-weekly, and the fresh weight of the thalli was recorded at the end of the experiment. The results indicated that CH mulch retained the highest amount of moisture (86%). The RH and HW mulches, at depths of 1.27 cm or more, provided excellent (>80%) liverwort control in ‘Curly Fries’. All mulches at depths of 1.27 cm or more showed excellent (100%) liverwort control for ‘Pandora’s Box’. Overall, RH and PB mulches at all depths provided excellent liverwort control and no reduction in the growth of ‘Curly Fries’ and ‘Pandora’s Box’.
Drug-Resistant Tuberculosis in Rural Eastern Cape, South Africa: A Study of Patients’ Characteristics in Selected Healthcare Facilities
Authors: Faye Lindiwe , Hosu Mojisola , Apalata Teke
Published: December 2024

This study investigated the characteristics and outcomes of drug-resistant tuberculosis patients in selected rural healthcare facilities in the Eastern Cape, South Africa. A retrospective review of clinical records from 456 patients, covering the period from January 2018 to December 2020, revealed a statistically significant relationship between DR-TB types and age groups (Chi-square statistic: 30.74, p-value: 0.015). Younger adults (19–35 years) and middle-aged adults (36–50 years) are more frequently affected by RR-TB and MDR-TB, which are the most prevalent forms of DR-TB. Less common types, including Pre-XDR, XDR, and INH TB, were observed in smaller numbers. The study suggests that DR-TB imposes a heavy burden on the working age population. Gender analysis shows that while the frequency of DR-TB differs between males and females, the percentage distribution of DR-TB types is relatively equal. Both genders are predominantly affected by RR-TB and MDR-TB, which together account for nearly 90% of cases. Pre-XDR, XDR, and INH-resistant TB are much less common, comprising only a small percentage of cases in both males and females. High-risk behaviors such as smoking and drinking are linked to a wider diversity of DR-TB types, while occupations like mining and prison work show higher rates of RR-TB and MDR-TB. In HIV-positive individuals, DR-TB is more common, but the distribution of DR-TB types between HIV-positive and negative groups shows no statistically significant difference. However, HIV-positive individuals have a 20% lower survival rate (65%) compared to HIV-negative patients (85%). Financial stability and comorbidities also significantly influence outcomes, with patients having stable income and fewer high-risk comorbidities experiencing better survival and treatment outcomes. The findings underscore the importance of addressing socioeconomic disparities and strengthening healthcare infrastructure to improve DR-TB treatment outcomes in rural Eastern Cape.
Becoming Housed During Palliative Care Enrollment: Identifying Drivers, Deterrents, and Directions for Future Care
Authors: Johnson Ian M. , Doran Rachel , Sullivan Nora , Enich Michael , Light Michael A.
Published: December 2024

Homelessness is associated with accelerated disease progression, and housing placements are less likely when experiencing serious illness. Little research to date has focused on how to successfully secure housing placement during serious illness and end of life. This study aimed to address this gap by examining factors influencing housing placement among seriously ill palliative care patients experiencing homelessness. By conducting reflexive thematic analysis of medical record data of palliative care patients who became housed during enrollment (n = 16), three themes were identified: (1) trends in placement timing showing most accessed housing within seven months of palliative care involvement due to the relationship between homelessness, disease progression, and goals of care; (2) social support networks that were involved in attaining housing to varying degrees; and (3) changes in internal motivation, such as identity affirmation, relational tasks, and accepting limitation, driven by illness and dying processes. Findings underscore the need for integrated medical and social support, expanded housing options for the seriously ill, and adaptable psychosocial–spiritual care within the housing care continuum.
An Ecological Study Relating the SARS-CoV-2 Epidemiology with Health-Related, Socio-Demographic, and Geographical Characteristics in South Tyrol (Italy)
Authors: Lorenzon Antonio , Palandri Lucia , Uguzzoni Francesco , Cristofor Catalina Doina , Lozza Filippo , Rizzi Cristiana , Poluzzi Riccardo , Bertoli Pierpaolo , Zerzer Florian , Righi Elena
Published: December 2024

The literature associating the spread of SARS-CoV-2 with the healthcare-related, geographical, and demographic characteristics of the territory is inconclusive and contrasting. We studied these relationships during winter 2021/2022 in South Tyrol, a multicultural Italian alpine province, performing an ecological study based on the 20 districts of the area. Data about incidence, hospitalization, and death between November 2021 and February 2022 were collected and associated to territorial variables via bivariate analyses and multivariate regressions. Both exposure variables and outcomes varied widely among districts. Incidence was found to be mainly predicted by vaccination coverage (negative correlation). Mortality and ICU admission rates partially followed this distribution, while the case fatality rate was inversely correlated to average salary, and hospital admission rates increased where hospitals capacity was higher, and from the southern to the northern border of the province. These findings, besides confirming the efficacy of vaccination in preventing both new and severe SARS-CoV-2 cases, highlight that several geographical and socio-demographic variables can be related to disease epidemiology. Remote areas with wage gaps and lower access to care suffered most from the pandemic. Our findings, therefore, underly the existence of health inequity issues that need to be targeted by implementing specifically tailored public health interventions.
Clinical Readiness for Practice of Nursing Students: A Concept Analysis
Authors: Konlan Kennedy Diema , Damiran Dulamsuren , Lee Tae Wha
Published: December 2024

Introduction: The concept of clinical readiness for practice among nursing students is yet to be analyzed, and there is a lack of empirical evidence on its usage among academics and clinicians. Methods: This concept analysis is anchored on a systematic literature review that adhered to the PRISMA guidelines and incorporated the eight iterative steps of Walker and Avant’s concept analysis method. This concept analysis method involved: (1) choosing a concept; (2) determining the objectives of the analysis; (3) identifying usages of the concept; (4) determining the defining attributes; (5) identifying a model case; (6) identifying other cases, including borderline, contrary, and related cases; (7) identifying antecedents and consequences; and (8) defining empirical references. The integrative thematic data synthesis method was adopted. Results: The concept of nursing students’ clinical readiness for practice is said to have four interrelated attributes. These attributes included (1) professional skills, (2) communication skills, (3) self-management skills, and (4) self-confidence. The two antecedents for nursing students’ clinical readiness to practice are (1) personal factors, including demographic characteristics, prior healthcare experience, income, and emotional intelligence; and (2) educational factors, including the clinical learning environment, clinical internship program, learning resource, and learning strategy. The consequence of clinical readiness for the practice of nursing students includes obtaining practice skills that can lead to more personal and job-related satisfactory outcomes. Conclusions: clinical readiness for practice in nursing encompasses the acquisition and integration of professional knowledge, skills, effective communication abilities, and self-management capabilities and the application of these competencies with confidence toward the provision of high-quality care to patients. Clinical Relevance: Understanding the components of clinical readiness is crucial for nursing educators, preceptors, and healthcare institutions to ensure that nursing students are adequately prepared for the challenges they will face in clinical practice. By recognizing the importance of professional knowledge, skills, communication, and self-management in clinical readiness, educators and training institutions can tailor their curricula, programs, and support systems to better prepare nursing students for the demands of real-world healthcare settings. This focus on clinical readiness ultimately delivers safe, effective, and compassionate patient care.
Light-Modulated Circadian Synaptic Plasticity in the Somatosensory Cortex: Link to Locomotor Activity
Authors: Jasińska Małgorzata , Jasek-Gajda Ewa , Ziaja Marek , Litwin Jan A. , Lis Grzegorz J. , Pyza Elżbieta
Published: December 2024

The circadian clock controls various physiological processes, including synaptic function and neuronal activity, affecting the functioning of the entire organism. Light is an important external factor regulating the day–night cycle. This study examined the effects of the circadian clock and light on synaptic plasticity, and explored how locomotor activity contributes to these processes. We analyzed synaptic protein expression and excitatory synapse density in the somatosensory cortex of mice from four groups exposed to different lighting conditions (LD 12:12, DD, LD 16:8, and LL). Locomotor activity was assessed through individual wheel-running monitoring. To explore daily and circadian changes in synaptic proteins, we performed double-immunofluorescence labeling and laser scanning confocal microscopy imaging, targeting three pairs of presynaptic and postsynaptic proteins (Synaptophysin 1/PSD95, Piccolo/Homer 1, Neurexins/PICK1). Excitatory synapse density was evaluated by co-labeling presynaptic and postsynaptic markers. Our results demonstrated that all the analyzed synaptic proteins exhibited circadian regulation modulated by light. Under constant light conditions, only Piccolo and Homer 1 showed rhythmicity. Locomotor activity was also associated with the circadian clock’s effects on synaptic proteins, showing a stronger connection to changes in postsynaptic protein levels. Excitatory synapse density peaked during the day/subjective day and exhibited an inverse relationship with locomotor activity. Continued light exposure disrupted cyclic changes in synapse density but kept it consistently elevated. These findings underscore the crucial roles of light and locomotor activity in regulating synaptic plasticity.
Age-Related sncRNAs in Human Hippocampal Tissue Samples: Focusing on Deregulated miRNAs
Authors: Alberro Ainhoa , Bravo-Miana Rocío Del Carmen , Iñiguez Saioa GS , Iribarren-López Andrea , Arroyo-Izaga Marta , Matheu Ander , Muñoz-Culla Maider , Otaegui David
Published: December 2024

Small non-coding RNAs (sncRNAs), particularly microRNAs (miRNAs), play an important role in transcriptome regulation by binding to mRNAs and post-transcriptionally inhibiting protein production. This regulation occurs in both physiological and pathological conditions, where the expression of many miRNAs is altered. Previous reports by our group and others have demonstrated that miRNA expression is also altered during aging. However, most studies have analyzed human peripheral blood samples or brain samples from animal models, leaving a gap in knowledge regarding miRNA expression in the human brain. In this work, we analyzed the expression of sncRNAs from coronal sections of human hippocampal samples, a tissue with a high vulnerability to deleterious conditions such as aging. Samples from young (n = 5, 27–49 years old), old (n = 8, 58–88 years old), and centenarian (n = 3, 97, 99, and 100 years old) individuals were included. Our results reveal that sncRNAs, particularly miRNAs, are differentially expressed (DE) in the human hippocampus with aging. Besides, miRNA-mediated regulatory networks revealed significant interactions with mRNAs deregulated in the same hippocampal samples. Surprisingly, 80% of DE mRNA in the centenarian vs. old comparison are regulated by hsa-miR-192-5p and hsa-miR-3135b. Additionally, validated hsa-miR-6826-5p, hsa-let-7b-3p, hsa-miR-7846, and hsa-miR-451a emerged as promising miRNAs that are deregulated with aging and should be further investigated.
Understanding the Preclinical Efficacy of Antibody–Drug Conjugates
Authors: Díaz-Tejeiro Cristina , López de Sá Alfonso , Poyatos-Racionero Elisa , Ballestín Pablo , Bartolomé Jorge , Calvo Emiliano , Moreno Víctor , Moris Francisco , Pérez-Segura Pedro , Gyorffy Balazs , Pandiella Atanasio , Ocaña Alberto
Published: December 2024

Antibody–drug conjugates (ADCs) represent a therapeutic modality that guides chemotherapies to tumoral cells by using antibodies against tumor-associated antigens (TAAs). The antibody and the chemotherapy or payload are attached by a chemical structure called the linker. The strategy for the development of this type of drug was based on several rational pillars, including the use of a very potent payload and the use of specific antibodies acting only on antigens expressed on tumoral cells. In this article, by using data from all approved ADCs that have received regulatory approval, we analyze the potential contribution of each ADC component to preclinical activity. We suggest that payload potency and the drug-to-antibody ratio (DAR) have a less relevant role in relation to efficacy than previously considered. Additionally, we have observed that some ADCs have been developed against antigens also present in non-transformed tissues, which could suggest that TAA specificity is not a mandatory requirement. Finally, we have identified that ADCs with payloads harboring more favorable physicochemical characteristics showed better potential activity. In this article, we also review other aspects that should be taken into consideration for ADC design, including linker structure, stability, conjugation type, pharmacokinetics, receptor internalization, and recycling. Based on currently available data, our study summaries different concepts that should be considered in the design of novel ADCs in the future.
A Comprehensive Functional Investigation of the Human Translocator Protein 18 kDa (TSPO) in a Novel Human Neuronal Cell Knockout Model
Authors: Bader Stefanie , Jahner Tatjana , Dörfelt Anett , Melchner Doris , Cardon Iseline , Siegmund Heiko I. , Brochhausen Christoph , Rupprecht Rainer , Milenkovic Vladimir M. , Wetzel Christian H.
Published: December 2024

The translocator protein 18 kDa (TSPO) is a multifunctional outer mitochondrial membrane protein associated with various aspects of mitochondrial physiology and multiple roles in health and disease. Here, we aimed to analyse the role of TSPO in the regulation of mitochondrial and cellular functions in a human neuronal cell model. We used the CRISPR/Cas9 technology and generated TSPO knockout (KO) and control (CTRL) variants of human-induced pluripotent stem cells (hiPSCs). In a multimodal phenotyping approach, we investigated cellular and mitochondrial functions in neural progenitor cells (NPCs), astrocytes, and neurons differentiated from hiPSC CTRL and TSPO KO cell lines. Our analysis revealed reduced mitochondrial respiration and glycolysis, altered Ca2+ levels in the cytosol and mitochondrial matrix, a depolarised MMP, and increased levels of reactive oxygen species, as well as a reduced cell size. Notably, TSPO deficiency was accompanied by reduced expression of the voltage-dependent anion channel (VDAC). We also observed a reduced TSPO and VDAC expression in cells derived from patients suffering from major depressive disorder (MDD). Considering the modulatory function of TSPO and the similar functional phenotype of cells derived from patients with depression, we discuss a role of TSPO in the etiology or pathology of MDD. In summary, our findings indicate a general impairment of mitochondrial function in TSPO knockout (KO) cells. This deepens our insight into the intricate role of TSPO in a range of physiological and pathological processes.
Replacing 2 Gy Per Fraction Equivalent Dose with Fractionation-Specific Biological Equivalent Dose for Normal Tissues
Authors: Luo Wei , St Clair William
Published: December 2024

The 2 Gy per fraction equivalent dose (EQD2) is an important quantity used in determining equivalent prescription doses for different fractionation regimens and evaluating different fractionation regimens, but it does not match its definition when it is used for normal tissues. We propose to use the fractionation-specific biological equivalent dose to determine normal tissue dose constraints for different fractionation regimens. The concept of the biological equivalent dose is defined based on the linear-quadratic equation. The EQD2 is derived based on the biological effective dose (BED), mimicking the prescription dose of a standard fractionation regimen with a fractional dose of 2 Gy and a fixed number of fractions. The FEQD(n) is also defined based on the BED as a function of the number of fractions, n, which is determined by the dose prescription. The FEQD(n) mimics any fractionation regimens with any fractional doses and numbers of fractionations. A given dose constraint can have different BED values and EQD2 values for different fractionation regimens. The number of fractions for a given 2 Gy per fraction regimen derived from the EQD2 for the target dose is different from that for the normal tissues. The value of the EQD2 derived for the target represents the total dose for the target for the 2 Gy fractional dose regimen, but the EQD2 value derived for the normal tissues does not represent the total dose for the normal tissue for the same fractionation regimen. The fractionation-specific biological equivalent dose (FEQD(n)) for both target and normal tissues has the same number of fractions for any fractionation regimen, and represents the total dose for either the target or the normal tissue. Based on the clinical outcomes, the FEQD(n) curves for the brainstem, spinal cord, rectum, and lung were derived and can be directly used as dose constraints for various fractionation regimens in clinical practice. The EQD2 does not match its definition and is not realistic when describing the biological equivalent dose for normal tissues. It is also not practical when used in determining tolerance doses or dose constraints. Instead, the FEQD(n) can be used to determine or convert the normal tissue dose constraints for any fractionation regimens in a realistic and practical manner. Using the FEQD(n), the dose constraints as a function of the number of fractions for the brainstem, spinal cord, rectum, and lung, which correspond to the given toxicity rates, were derived and can be directly used in clinical practice.
Methoxyquinolone–Benzothiazole Hybrids as New Aggregation-Induced Emission Luminogens and Efficient Fluorescent Chemosensors for Cyanide Ions
Authors: Mutis-Ayala Mario , Trilleras Jorge , D’Vries Richard , Macías Mario A. , Insuasty Alberto , Abonia Rodrigo , Quiroga Jairo , Illicachi Luis A. , Márquez Edgar , Insuasty Daniel
Published: December 2024

This work describes the synthesis and characterization of new quinolone–benzothiazole hybrids, the study of their aggregation-induced emission (AIE) properties, and the use of these systems as efficient fluorescent probes for cyanide ions. These conjugated derivatives are linked through a double bond favoring electronic communication, and together with their planar geometry, can strongly aggregate under solvophobic environments, leading to aggregation and exhibiting significant AIE behavior. The double bond between electroactive units is prone to nucleophilic addition reactions by cyanide ions, selectively, conducive to turning off the fluorescence properties, making this hybrid system an efficient probe for cyanide ions. These studies were theoretically explained using DFT and TD-DFT calculations.
Genome-Wide Identification of FCS-Like Zinc Finger (FLZ) Family Genes in Three Brassica Plant Species and Functional Characterization of BolFLZs in Chinese Kale Under Abiotic Stresses
Authors: Zhao Yuwan , Chen Shunquan , Qin Mao , Shui Kejuan , Li Riqing , Yang Baoli , Liu Jin , Chen Zhufeng
Published: December 2024

FCS-like zinc finger (FLZ) proteins are plant-specific regulatory proteins, which contain a highly conserved FLZ domain, and they play critical roles in plant growth and stress responses. Although the FLZ family has been systematically characterized in certain plants, it remains underexplored in Brassica species, which are vital sources of vegetables, edible oils, and condiments for human consumption and are highly sensitive to various abiotic stresses. Following the whole-genome triplication events (WGT) in Brassica, elucidating how the FLZ genes have expanded, differentiated, and responded to abiotic stresses is valuable for uncovering the genetic basis and functionality of these genes. In this study, we identified a total of 113 FLZ genes from three diploid Brassica species and classified them into four groups on the basis of their amino acid sequences. Additionally, we identified 109 collinear gene pairs across these Brassica species, which are dispersed among different chromosomes, suggesting that whole-genome duplication (WGD) has significantly contributed to the expansion of the FLZ family. Subcellular localization revealed that six representative BolFLZ proteins are located in the nucleus and cytoplasm. Yeast two-hybrid assays revealed that 13 selected BolFLZs interact with BolSnRK1α1 and BolSnRK1α2, confirming the conservation of the SnRK1α-FLZ module in Brassica species. Expression profile analysis revealed differential expression patterns of BolFLZ across various tissues. Notably, the expression levels of seven BolFLZ genes out of the fifteen genes analyzed changed significantly following treatment with various abiotic stressors, indicating that the BolFLZ genes play distinct physiological roles and respond uniquely to abiotic stresses in Brassica species. Together, our results provide a comprehensive overview of the FLZ gene family in Brassica species and insights into their potential applications for enhancing stress tolerance and growth in Chinese kale.
Influence of ZnSO4 and Methyl Jasmonate on the Metabolites and Bioactivity Present in Lemon-Fruit Membrane Vesicles
Authors: Gomez-Molina Maria , Carvajal Micaela , Garcia-Ibañez Paula
Published: December 2024

Membrane vesicles isolated from vegetable tissues have shown promise in encapsulation technologies used in industries like food and cosmetics, offering innovative approaches to product development. However, their associated linked metabolites have not been studied. Lemon vesicle research not only adds value to the lemon crop (Citrus × limon L.), one of the most widely cultivated fruit trees in the world, is a source of bioactive compounds such as phenolics and organic acids. In this study, the influence of elicitation with ZnSO4 and methyl jasmonate, which modulate the bioactive metabolites, on fruit membrane vesicle bond metabolites was studied. The study showed that foliar application of ZnSO4 increased phenolic compounds as caffeic, sinapic, and chlorogenic acids and the flavonoid hesperidin by about 20% in lemons. Furthermore, a clear interaction between vesicles and citrate and ascorbate that were increased by methyl jasmonate were associated with their higher bioactivity. This was related to the double intrinsic in vitro antioxidant activities of these vesicles.
Preferred Orientation of Hydroxyapatite Ceramics Along the c-Axis Promotes Osteoblast Differentiation
Authors: Suzuki Kitaru , Tamazawa Masaki , Onuma Erika , Honda Michiyo , Aizawa Mamoru
Published: December 2024

Hydroxyapatite (HAp) is similar to the main inorganic components of bone and tooth enamel. Furthermore, it possesses biocompatibility, making it suitable for clinical use in artificial bones. This study aimed to verify whether the preferred orientation of HAp influences osteogenesis. Using the templated grain growth method, we successfully fabricated HAp ceramics with a preferred orientation to m (a)-planes (aHAp) and examined the effects of this orientation on bone differentiation. Osteosarcoma-derived osteoblasts (MG-63) were cultured on aHAp and HAp ceramics made from commercially available powder (iHAp). Electron backscatter diffraction analysis revealed the crystal orientation distribution of HAp ceramics and the numerous exposed a-planes of aHAp. The MG-63 cultured on aHAp exhibited significantly higher alkaline phosphatase activity, a marker of early bone differentiation, compared to iHAp. Furthermore, the two-dimensional electrophoresis results indicated that the expressed proteins differed between aHAp and iHAp. These results indicate that controlling HAp’s crystal structure may promote the osteogenic potential of osteoblasts. In this study, we propose that the a-plane of HAp promotes bone differentiation during the early stages, presenting a promising approach for novel biomaterials, such as high-performance artificial bones.
Structure and Biosynthetic Gene Cluster of Sulfated Capsular Polysaccharide from the Marine Bacterium Vibrio sp. KMM 8419
Authors: Kokoulin Maxim S. , Savicheva Yulia V. , Otstavnykh Nadezhda Y. , Kurilenko Valeria V. , Meleshko Dmitry A. , Isaeva Marina P.
Published: December 2024

Vibrio sp. KMM 8419 (=CB1-14) is a Gram-negative bacterium isolated from a food-net mucus sample of marine polychaete Chaetopterus cautus collected in the Sea of Japan. Here, we report the structure and biosynthetic gene cluster of the capsular polysaccharide (CPS) from strain KMM 8419. The CPS was isolated and studied by one- and two-dimensional 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. The molecular weight of the CPS was about 254 kDa. The CPS consisted of disaccharide repeating units of D-glucose and sulfated and acetylated L-rhamnose established as →2)-α-L-Rhap3S4Ac-(1→6)-α-D-Glcp-(1→. To identify the genes responsible for CPS biosynthesis, whole-genome sequencing of KMM 8419 was carried out. Based on the genome annotations together with the Interproscan, UniProt and AntiSMASH results, a CPS-related gene cluster of 80 genes was found on chromosome 1. This cluster contained sets of genes encoding for the nucleotide sugar biosynthesis (UDP-Glc and dTDP-Rha), assembly (glycosyltransferases (GT)), transport (ABC transporter) and sulfation (PAPS biosynthesis and sulfotransferases) of the sulfated CPS. A hypothetical model for the assembly and transportation of the sulfated CPS was also proposed. In addition, this locus included genes for O-antigen biosynthesis. Further studies of biological activity, the structure–activity relationship in the new sulfated polysaccharide and its biosynthesis are necessary for the development of potent anticancer agents or drug delivery systems.
Integrated Analysis of Single-Cell and Bulk RNA Sequencing Reveals HSD3B7 as a Prognostic Biomarker and Potential Therapeutic Target in ccRCC
Authors: Liu Guicen , Liu Qichen , Zhao Jiawei , Luo Ruyue , Wan Yuan , Luo Zhongli
Published: December 2024

Clear cell renal cell carcinoma (ccRCC) is the most common kidney malignancy, with a poor prognosis for advanced-stage patients. Identifying key biomarkers involved in tumor progression is crucial for improving treatment outcomes. In this study, we employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) to identify biomarkers associated with ccRCC progression and prognosis. Single-cell transcriptomic data were obtained from publicly available datasets, and genes related to tumor progression were screened using Monocle2. Bulk RNA-seq data for ccRCC were retrieved from The Cancer Genome Atlas (TCGA) and integrated with scRNA-seq data to explore tumor heterogeneity. We identified 3 beta-hydroxy steroid dehydrogenase type 7 (HSD3B7) as a candidate biomarker for ccRCC, associated with poor overall survival, disease-specific survival, and progression-free interval. Elevated HSD3B7 expression correlated with aggressive clinical features such as advanced TNM stages, histologic grades, and metastasis. Functional studies demonstrated that HSD3B7 promotes cell proliferation, migration, and invasion in vitro, while its silencing significantly inhibits tumor growth in vivo. Our findings reveal that HSD3B7 is a novel biomarker for ccRCC, providing insights into its role in tumor progression and potential as a target for therapy. This study highlights the value of integrating scRNA-seq and bulk RNA-seq data to uncover key regulators of tumor biology and lays the foundation for developing personalized therapeutic strategies for ccRCC patients.
DeepEnhancerPPO: An Interpretable Deep Learning Approach for Enhancer Classification
Authors: Mu Xuechen , Huang Zhenyu , Chen Qiufen , Shi Bocheng , Xu Long , Xu Ying , Zhang Kai
Published: December 2024

Enhancers are short genomic segments located in non-coding regions of the genome that play a critical role in regulating the expression of target genes. Despite their importance in transcriptional regulation, effective methods for classifying enhancer categories and regulatory strengths remain limited. To address this challenge, we propose a novel end-to-end deep learning architecture named DeepEnhancerPPO. The model integrates ResNet and Transformer modules to extract local, hierarchical, and long-range contextual features. Following feature fusion, we employ Proximal Policy Optimization (PPO), a reinforcement learning technique, to reduce the dimensionality of the fused features, retaining the most relevant features for downstream classification tasks. We evaluate the performance of DeepEnhancerPPO from multiple perspectives, including ablation analysis, independent tests, assessment of PPO’s contribution to performance enhancement, and interpretability of the classification results. Each module positively contributes to the overall performance, with ResNet and PPO being the most significant contributors. Overall, DeepEnhancerPPO demonstrates superior performance on independent datasets compared to other models, outperforming the second-best model by 6.7% in accuracy for enhancer category classification. The model consistently ranks among the top five classifiers out of 25 for enhancer strength classification without requiring re-optimization of the hyperparameters and ranks as the second-best when the hyperparameters are refined. This indicates that the DeepEnhancerPPO framework is highly robust for enhancer classification. Additionally, the incorporation of PPO enhances the interpretability of the classification results.
Platelet-Derived Growth Factor Subunit A Strengthens the Neurovascular Unit and Inhibits Retinal Vascular Regression Under Hyperoxic Conditions
Authors: Yokota Kaito , Yamada Haruhiko , Mori Hidetsugu , Hattori Yuki , Omi Masatoshi , Yamamoto Yuichi , Toyama Keiko , Imai Hisanori
Published: December 2024

Retinopathy of prematurity (ROP) is primarily caused by the exposure of preterm infants with underdeveloped blood vessels to high oxygen concentrations. This damages the astrocytes that promote normal vascular development, leading to avascularity, pathological neovascularization, and retinal detachment, and even blindness as the disease progresses. In this study, the aim was to investigate the differences in the characteristics of astrocytes and blood vessels between wild-type (WT) and genetically modified mice overexpressing platelet-derived growth factor subunit A (PDGF-A) in the retina immediately after high oxygen exposure, a protocol in the oxygen-induced retinopathy (OIR) model of ROP. Our results showed that PDGF-A mice exhibited an increased population of astrocytes and higher vascular density than WT mice and that PDGF-A strengthened the resistance to hyperoxic conditions. In the OIR model, PDGF-A mice had reduced avascular zone areas following hyperoxia exposure. Furthermore, immunostaining for NG2 and CD31 showed that pericytes tended to regress earlier than endothelial cells, particularly at the vessel edges in both WT and transgenic mice, indicating relatively higher susceptibility to hyperoxia-induced damage. These findings suggest that PDGF-A plays a crucial role in stabilizing retinal vessels and may serve as a novel therapeutic target for ROP, highlighting the potential significance of PDGF-A in the pathological mechanisms of retinal diseases.
Genome-Wide Identification of the GbUBC Gene Family in Sea-Island Cotton (Gossypium barbadense) and the Active Regulation of Drought Resistance in Cotton by GbUBC23
Authors: Wang Yi , Zong Zheng , Chen Junchen , Sun Xue , Wang Jiahui , Yu Yuehua , Ni Zhiyong
Published: December 2024

Cotton is an economically critical crop worldwide, and drought stress strongly affects its growth and development. Ubiquitination modifies protein activity and is crucial in numerous biological processes. Ubiquitin-conjugating enzymes serve as intermediaries in the protein ubiquitination process and play important roles in plant responses to abiotic stress. However, the impact of ubiquitination on the response of cotton to abiotic stress is not fully understood. Bioinformatic methods were employed in this study to analyze the physiochemical characteristics, gene structure, collinearity, expression patterns, and evolutionary relationships of GbUBC gene family members in sea-island cotton. In sea-island cotton, a minimum of 125 GbUBC genes are irregularly distributed across the 26 chromosomes, with multiple instances of gene duplication observed among the members. Phylogenetic analysis categorized the GbUBC gene family into 15 ubiquitin-conjugating enzyme (E2) subgroups, one ubiquitin E2 enzyme variant (UEV) subgroup, and one COP10 subgroup. GbUBC gene expression pattern analyses revealed that most GbUBC genes responded differently to cold, heat, NaCl, and polyethylene glycol (PEG) treatments, with certain GbUBC genes exhibiting high expression levels in specific fiber development period and organs. Furthermore, molecular biology methods were employed to elucidate the biological functions of GbUBC23. The GbUBC23 gene was highly expressed in the cotyledons of sea-island cotton and was activated by PEG treatment. GbUBC23 is localized to the nucleus and cytomembrane. The silencing of the GbUBC23 gene under drought conditions led to decreased drought tolerance and survival rates in sea-island cotton. Compared with those in the control plants, the activity of proline and superoxide dismutase and the expression levels of the drought-induced genes GbNCED3, GbRD22, GbRD26 were significantly lower, but the levels of malondialdehyde and hydrogen peroxide were significantly higher. Our findings revealed 125 members of the GbUBC gene family in sea-island cotton, with the GbUBC23 gene critically contributing to the abiotic stress response. These findings indicate that the GbUBC gene family may play a crucial role in the drought stress response in sea-island cotton.
Serotonin Signaling in Mouse Preimplantation Development: Insights from Transcriptomic and Structural-Functional Analyses
Authors: Frolova Veronika S. , Nikishina Yulia O. , Shmukler Yuri B. , Nikishin Denis A.
Published: December 2024

Serotonin (5-HT), a versatile signaling molecule, plays a variety of roles in both neurotransmission and tissue regulation. The influence of serotonin on early development was first studied in marine invertebrate embryos and has since been documented in a variety of vertebrate species, including mammals. The present study investigates the expression and functional activity of serotonin components in mouse embryos, focusing on key receptors and transporters. Transcriptomic analyses revealed that mRNA transcripts related to serotonin show marked expression during the oogenesis and preimplantation stages. The results of the immunohistochemical studies show the presence of serotonin, the vesicular monoamine transporter VMAT2, and several membrane receptors (5-HT1B, 5-HT1D, 5-HT2B, 5-HT7) in the early stages of development. A functional analysis performed with the VMAT inhibitor reserpine revealed the crucial role of vesicular transport in the maintenance of serotonin signaling. The findings presented here support the hypothesis that serotonin plays a significant role in oocyte maturation and embryonic development, as well as in interblastomere interactions.