bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Circulating Immune Subsets in Primary Colorectal Cancer
Authors: Lu Can , Schardey Josefine , Wirth Ulrich , von Ehrlich-Treuenstätt Viktor , Neumann Jens , Gießen-Jung Clemens , Werner Jens , Bazhin Alexandr V. , Kühn Florian
Published: December 2022

The development and progression of colorectal cancer (CRC) are known to be affected by the interplay between tumor and immune cells. However, the impact of CRC cells on the systemic immunity has yet to be elucidated. We aimed to comprehensively evaluate the circulating immune subsets and transcriptional profiles of CRC patients. In contrast to healthy controls (HCs), CRC patients had a lower percentage of B and T lymphocytes, T helper (Th) cells, non-classical monocytes, dendritic cells, and a higher proportion of polymorphonuclear myeloid-derived suppressor cells, as well as a reduced expression of CD69 on NK cells. Therefore, CRC patients exhibit a more evident systemic immune suppression than HCs. A diagnostic model integrating seven immune subsets was constructed to distinguish CRC patients from HCs with an AUC of 1.000. Moreover, NR3C2, CAMK4, and TRAT1 were identified as candidate genes regulating the number of Th cells in CRC patients. The altered composition of circulating immune cells in CRC could complement the regional immune status of the tumor microenvironment and contribute to the discovery of immune-related biomarkers for the diagnosis of CRC.
Sex Remains Negative Prognostic Factor in Contemporary Cohort of High-Risk Non-Muscle-Invasive Bladder Cancer
Authors: Bilski Konrad , Kozikowski Mieszko , Skrzypczyk Michał A. , Dobruch Aleksandra , Hendricksen Kees , D’Andrea David , Czech Anna Katarzyna , Dobruch Jakub
Published: December 2022

Sex-specific differences in outcomes of patients diagnosed with high-risk non-muscle-invasive bladder cancer (HR-NMIBC) have been reported with controversial findings. This study aims to investigate sex-specific diversities in the treatment and oncologic outcomes of primary HR-NMIBC in a multicenter setting. A multicenter retrospective analysis of 519 patients (388 men and 131 women) treated with transurethral resection (TUR) for primary HR-NMIBC was performed. Univariable and multivariable Cox regression models were used to investigate the association of clinico-pathologic features and generate hazard ratios (HRs). Second-look TUR (reTUR) was performed in 406 (78%) patients. A total of 218 (42%) of patients were subjected to an induction course of intravesical BCG (Bacillus Calmette–Guérin) plus maintenance therapy. The median follow-up was 44 months. Among the entire cohort, 238 (46%) and 86 patients (17%) had recurred and progressed to muscle-invasive disease (MIBC), respectively. Female sex was associated with increased risk of disease recurrence in the entire cohort: HR = 1.94, 95% CI = 1.48–2.55, p < 0.001 and HR = 1.91, 95% CI = 1.39–2.60, p < 0.001 in univariate and multivariate analysis, respectively. In patients subjected to reTUR and treated additionally with BCG, female sex was associated with increased risk of disease recurrence in univariate analysis (HR 1.81, 95% CI 1.07–3.06, p = 0.03), but not in multivariate analysis (HR 1.99, 95% CI 0.98–4.02, p = 0.06). There was no difference between sexes with regard to disease progression. HR-NMIBC diagnosed in females is associated with higher risk of disease recurrence when compared to males.
Cost-Effectiveness of Risk-Reducing Surgery for Breast and Ovarian Cancer Prevention: A Systematic Review
Authors: Wei Xia , Oxley Samuel , Sideris Michail , Kalra Ashwin , Sun Li , Yang Li , Legood Rosa , Manchanda Ranjit
Published: December 2022

Policymakers require robust cost-effectiveness evidence of risk-reducing-surgery (RRS) for decision making on resource allocation for breast cancer (BC)/ovarian cancer (OC)/endometrial cancer (EC) prevention. We aimed to summarise published data on the cost-effectiveness of risk-reducing mastectomy (RRM)/risk-reducing salpingo-oophorectomy (RRSO)/risk-reducing early salpingectomy and delayed oophorectomy (RRESDO) for BC/OC prevention in intermediate/high-risk populations; hysterectomy and bilateral salpingo-oophorectomy (BSO) in Lynch syndrome women; and opportunistic bilateral salpingectomy (OBS) for OC prevention in baseline-risk populations. Major databases were searched until December 2021 following a prospective protocol (PROSPERO-CRD42022338008). Data were qualitatively synthesised following a PICO framework. Twenty two studies were included, with a reporting quality varying from 53.6% to 82.1% of the items scored in the CHEERS checklist. The incremental cost-effectiveness ratio/incremental cost-utility ratio and cost thresholds were inflated and converted to US$2020, using the original currency consumer price index (CPI) and purchasing power parities (PPP), for comparison. Eight studies concluded that RRM and/or RRSO were cost-effective compared to surveillance/no surgery for BRCA1/2, while RRESDO was cost-effective compared to RRSO in one study. Three studies found that hysterectomy with BSO was cost-effective compared to surveillance in Lynch syndrome women. Two studies showed that RRSO was also cost-effective at ≥4%/≥5% lifetime OC risk for pre-/post-menopausal women, respectively. Seven studies demonstrated the cost-effectiveness of OBS at hysterectomy (n = 4), laparoscopic sterilisation (n = 4) or caesarean section (n = 2). This systematic review confirms that RRS is cost-effective, while the results are context-specific, given the diversity in the target populations, health systems and model assumptions, and sensitive to the disutility, age and uptake rates associated with RRS. Additionally, RRESDO/OBS were sensitive to the uncertainty concerning the effect sizes in terms of the OC-risk reduction and long-term health impact. Our findings are relevant for policymakers/service providers and the design of future research studies.
New Insights into the Phenotype Switching of Melanoma
Authors: Pagliuca Chiara , Di Leo Luca , De Zio Daniela
Published: December 2022

Melanoma is considered one of the deadliest skin cancers, partly because of acquired resistance to standard therapies. The most recognized driver of resistance relies on acquired melanoma cell plasticity, or the ability to dynamically switch among differentiation phenotypes. This confers the tumor noticeable advantages. During the last year, two new features have been included in the hallmarks of cancer, namely “Unlocking phenotypic plasticity” and “Non-mutational epigenetic reprogramming”. Such are inextricably intertwined as, most of the time, plasticity is not discernable at the genetic level, as it rather consists of epigenetic reprogramming heavily influenced by external factors. By analyzing current literature, this review provides reasoning about the origin of plasticity and clarifies whether such features already exist among tumors or are acquired by selection. Moreover, markers of plasticity, molecular effectors, and related tumor advantages in melanoma will be explored. Ultimately, as this new branch of tumor biology opened a wide landscape of therapeutic possibilities, in the final paragraph of this review, we will focus on newly characterized drugs targeting melanoma plasticity.
MRI Radiomics for Predicting Survival in Patients with Locally Advanced Hypopharyngeal Cancer Treated with Concurrent Chemoradiotherapy
Authors: Siow Tiing Yee , Yeh Chih-Hua , Lin Gigin , Lin Chien-Yu , Wang Hung-Ming , Liao Chun-Ta , Toh Cheng-Hong , Chan Sheng-Chieh , Lin Ching-Po , Ng Shu-Hang
Published: December 2022

A reliable prognostic stratification of patients with locally advanced hypopharyngeal cancer who had been treated with concurrent chemoradiotherapy (CCRT) is crucial for informing tailored management strategies. The purpose of this retrospective study was to develop robust and objective magnetic resonance imaging (MRI) radiomics-based models for predicting overall survival (OS) and progression-free survival (PFS) in this patient population. The study participants included 198 patients (median age: 52.25 years (interquartile range = 46.88–59.53 years); 95.96% men) who were randomly divided into a training cohort (n = 132) and a testing cohort (n = 66). Radiomic parameters were extracted from post-contrast T1-weighted MR images. Radiomic features for model construction were selected from the training cohort using least absolute shrinkage and selection operator–Cox regression models. Prognostic performances were assessed by calculating the integrated area under the receiver operating characteristic curve (iAUC). The ability of radiomic models to predict OS (iAUC = 0.580, 95% confidence interval (CI): 0.558–0.591) and PFS (iAUC = 0.625, 95% CI = 0.600–0.633) was validated in the testing cohort. The combination of radiomic signatures with traditional clinical parameters outperformed clinical variables alone in the prediction of survival outcomes (observed iAUC increments = 0.279 [95% CI = 0.225–0.334] and 0.293 [95% CI = 0.232–0.351] for OS and PFS, respectively). In summary, MRI radiomics has value for predicting survival outcomes in patients with hypopharyngeal cancer treated with CCRT, especially when combined with clinical prognostic variables.
Modeling of Red Blood Cells in Capillary Flow Using Fluid–Structure Interaction and Gas Diffusion
Authors: An Ling , Ji Fenglong , Yin Yueming , Liu Yi , Zhou Chichun
Published: December 2022

Red blood cell (RBC) distribution, RBC shape, and flow rate have all been shown to have an effect on the pulmonary diffusing capacity. Through this study, a gas diffusion model and the immersed finite element method were used to simulate the gas diffusion into deformable RBCs running in capillaries. It has been discovered that when RBCs are deformed, the CO flux across the membrane becomes nonuniform, resulting in a reduced capacity for diffusion. Additionally, when compared to RBCs that were dispersed evenly, our simulation showed that clustered RBCs had a significantly lower diffusion capability.
Development of a Nanoparticle-Based Approach for the Blood–Brain Barrier Passage in a Murine Model of Amyotrophic Lateral Sclerosis
Authors: Violatto Martina Bruna , Pasetto Laura , Casarin Elisabetta , Tondello Camilla , Schiavon Elisa , Talamini Laura , Marchini Gloria , Cagnotto Alfredo , Morelli Annalisa , Lanno Alessia , Passoni Alice , Bigini Paolo , Morpurgo Margherita , Bonetto Valentina
Published: December 2022

The development of nanoparticles (NPs) to enable the passage of drugs across blood–brain barrier (BBB) represents one of the main challenges in neuropharmacology. In recent years, NPs that are able to transport drugs and interact with brain endothelial cells have been tested. Here, we investigated whether the functionalization of avidin-nucleic-acid-nanoassembly (ANANAS) with apolipoprotein E (ApoE) would allow BBB passage in the SOD1G93A mouse model of amyotrophic lateral sclerosis. Our results demonstrated that ANANAS was able to transiently cross BBB to reach the central nervous system (CNS), and ApoE did not enhance this property. Next, we investigated if ANANAS could improve CNS drug delivery. To this aim, the steroid dexamethasone was covalently linked to ANANAS through an acid-reversible hydrazone bond. Our data showed that the steroid levels in CNS tissues of SOD1G93A mice treated with nanoformulation were below the detection limit. This result demonstrates that the passage of BBB is not sufficient to guarantee the release of the cargo in CNS and that a different strategy for drug tethering should be devised. The present study furthermore highlights that NPs can be useful in improving the passage through biological barriers but may limit the interaction of the therapeutic compound with the specific target.
Intensive Care Unit Acquired Weakness Is Associated with Rapid Changes to Skeletal Muscle Proteostasis
Authors: Ozdemir Mustafa , Bomkamp Matthew P. , Hyatt Hayden W. , Smuder Ashley J. , Powers Scott K.
Published: December 2022

Intensive care unit (ICU)-acquired weakness is a frequent consequence of critical illness that impacts both the limb and respiratory muscles. The cause of ICU-acquired weakness is multifactorial, but both prolonged limb muscle inactivity and mechanical ventilation are risk factors for muscle wasting, which predisposes ICU patients to both short-term complications and long-term disabilities resulting from muscle weakness. Unfortunately, the current research does not provide a detailed understanding of the cellular etiology of ICU-acquired weakness, and no standard treatment exists. Therefore, improving knowledge of the mechanisms promoting muscle atrophy in critically ill patients is essential to developing therapeutic strategies to protect against ICU-induced skeletal muscle wasting. To advance our understanding of the mechanism(s) responsible for ICU-acquired weakness, we tested the hypothesis that ICU-induced muscle inactivity promotes a rapid decrease in anabolic signaling/protein synthesis and accelerates proteolysis in both limb and respiratory muscles. To investigate ICU-induced changes in skeletal muscle proteostasis, adult Sprague Dawley rats were anesthetized and mechanically ventilated for 12 h to simulate ICU care. Measurements of anabolic signaling, protein synthesis, and proteolytic activity in the limb muscles (plantaris and soleus) and respiratory muscles (parasternal and intercostal) revealed ICU-induced reductions in both anabolic signaling (i.e., AKT/mTOR pathway) and muscle protein synthesis. Moreover, simulated ICU care resulted in increased biomarkers of accelerated proteolysis in both limb and respiratory muscles. These novel findings reveal that disturbances in limb and respiratory muscle proteostasis occur rapidly during ICU-induced muscle inactivity, irrespective of the muscle function or muscle fiber type.
Toward Establishing an Ideal Adjuvant for Non-Inflammatory Immune Enhancement
Authors: Seya Tsukasa , Tatematsu Megumi , Matsumoto Misako
Published: December 2022

The vertebrate immune system functions to eliminate invading foreign nucleic acids and foreign proteins from infectious diseases and malignant tumors. Because pathogens and cancer cells have unique amino acid sequences and motifs (e.g., microbe-associated molecular patterns, MAMPs) that are recognized as “non-self” to the host, immune enhancement is one strategy to eliminate invading cells. MAMPs contain nucleic acids specific or characteristic of the microbe and are potential candidates for immunostimulants or adjuvants. Adjuvants are included in many vaccines and are a way to boost immunity by deliberately administering them along with antigens. Although adjuvants are an important component of vaccines, it is difficult to evaluate their efficacy ex vivo and in vivo on their own (without antigens). In addition, inflammation induced by currently candidate adjuvants may cause adverse events, which is a hurdle to their approval as drugs. In addition, the lack of guidelines for evaluating the safety and efficacy of adjuvants in drug discovery research also makes regulatory approval difficult. Viral double-stranded (ds) RNA mimics have been reported as potent adjuvants, but the safety barrier remains unresolved. Here we present ARNAX, a noninflammatory nucleic acid adjuvant that selectively targets Toll-like receptor 3 (TLR3) in antigen-presenting dendritic cells (APCs) to safely induce antigen cross-presentation and subsequently induce an acquired immune response independent of inflammation. This review discusses the challenges faced in the clinical development of novel adjuvants.
Expression of Steroid Receptor RNA Activator 1 (SRA1) in the Adipose Tissue Is Associated with TLRs and IRFs in Diabesity
Authors: Kochumon Shihab , Arefanian Hossein , Sindhu Sardar , Thomas Reeby , Jacob Texy , Al-Sayyar Amnah , Shenouda Steve , Al-Rashed Fatema , Koistinen Heikki A. , Al-Mulla Fahd , Tuomilehto Jaakko , Ahmad Rasheed
Published: December 2022

Steroid receptor RNA activator gene (SRA1) emerges as a player in pathophysiological responses of adipose tissue (AT) in metabolic disorders such as obesity and type 2 diabetes (T2D). We previously showed association of the AT SRA1 expression with inflammatory cytokines/chemokines involved in metabolic derangement. However, the relationship between altered adipose expression of SRA1 and the innate immune Toll-like receptors (TLRs) as players in nutrient sensing and metabolic inflammation as well as their downstream signaling partners, including interferon regulatory factors (IRFs), remains elusive. Herein, we investigated the association of AT SRA1 expression with TLRs, IRFs, and other TLR-downstream signaling mediators in a cohort of 108 individuals, classified based on their body mass index (BMI) as persons with normal-weight (N = 12), overweight (N = 32), and obesity (N = 64), including 55 with and 53 without T2D. The gene expression of SRA1, TLRs-2,3,4,7,8,9,10 and their downstream signaling mediators including IRFs-3,4,5, myeloid differentiation factor 88 (MyD88), interleukin-1 receptor-associated kinase 1 (IRAK1), and nuclear factor-κB (NF-κB) were determined using qRT-PCR and SRA1 protein expression was determined by immunohistochemistry. AT SRA1 transcripts’ expression was significantly correlated with TLRs-3,4,7, MyD88, NF-κB, and IRF5 expression in individuals with T2D, while it associated with TLR9 and TRAF6 expression in all individuals, with/without T2D. SRA1 expression associated with TLR2, IRAK1, and IRF3 expression only in individuals with obesity, regardless of diabetes status. Furthermore, TLR3/TLR7/IRAK1 and TLR3/TLR9 were identified as independent predictors of AT SRA1 expression in individuals with obesity and T2D, respectively. Overall, our data demonstrate a direct association between the AT SRA1 expression and the TLRs together with their downstream signaling partners and IRFs in individuals with obesity and/or T2D.
Reactive Oxygen and Nitrogen Species (RONS) and Cytokines—Myokines Involved in Glucose Uptake and Insulin Resistance in Skeletal Muscle
Authors: Llanos Paola , Palomero Jesus
Published: December 2022

Insulin resistance onset in skeletal muscle is characterized by the impairment of insulin signaling, which reduces the internalization of glucose, known as glucose uptake, into the cell. Therefore, there is a deficit of intracellular glucose, which is the main source for energy production in the cell. This may compromise cellular viability and functions, leading to pathological dysfunction. Skeletal muscle fibers continuously generate reactive oxygen and nitrogen species (RONS). An excess of RONS produces oxidative distress, which may evoke cellular damage and dysfunction. However, a moderate level of RONS, which is called oxidative eustress, is critical to maintain, modulate and regulate cellular functions through reversible interactions between RONS and the components of cellular signaling pathways that control those functions, such as the facilitation of glucose uptake. The skeletal muscle releases peptides called myokines that may have endocrine and paracrine effects. Some myokines bind to specific receptors in skeletal muscle fibers and might interact with cellular signaling pathways, such as PI3K/Akt and AMPK, and facilitate glucose uptake. In addition, there are cytokines, which are peptides produced by non-skeletal muscle cells, that bind to receptors at the plasma membrane of skeletal muscle cells and interact with the cellular signaling pathways, facilitating glucose uptake. RONS, myokines and cytokines might be acting on the same signaling pathways that facilitate glucose uptake in skeletal muscle. However, the experimental studies are limited and scarce. The aim of this review is to highlight the current knowledge regarding the role of RONS, myokines and cytokines as potential signals that facilitate glucose uptake in skeletal muscle. In addition, we encourage researchers in the field to lead and undertake investigations to uncover the fundamentals of glucose uptake evoked by RONS, myokines, and cytokines.
Multiomics Analysis of a DNAH5-Mutated PCD Organoid Model Revealed the Key Role of the TGF-β/BMP and Notch Pathways in Epithelial Differentiation and the Immune Response in DNAH5-Mutated Patients
Authors: Yang Wenhao , Chen Lina , Guo Juncen , Shi Fang , Yang Qingxin , Xie Liang , Lu Danli , Li Yingna , Luo Jiaxin , Wang Li , Qiu Li , Chen Ting , Li Yan , Zhang Rui , Chen Lu , Xu Wenming , Liu Hanmin
Published: December 2022

Dynein axonemal heavy chain 5 (DNAH5) is the most mutated gene in primary ciliary dyskinesia (PCD), leading to abnormal cilia ultrastructure and function. Few studies have revealed the genetic characteristics and pathogenetic mechanisms of PCD caused by DNAH5 mutation. Here, we established a child PCD airway organoid directly from the bronchoscopic biopsy of a patient with the DNAH5 mutation. The motile cilia in the organoid were observed and could be stably maintained for an extended time. We further found abnormal ciliary function and a decreased immune response caused by the DNAH5 mutation through single-cell RNA sequencing (scRNA-Seq) and proteomic analyses. Additionally, the directed induction of the ciliated cells, regulated by TGF-β/BMP and the Notch pathway, also increased the expression of inflammatory cytokines. Taken together, these results demonstrated that the combination of multiomics analysis and organoid modelling could reveal the close connection between the immune response and the DNAH5 gene.
Development of a Road Pavement Structure Diagnostic Procedure Based on the Virtual Inertial Point Method
Authors: Tóth Csaba , Primusz Péter
Published: December 2022

Falling weight deflectometers (FWD) are utilised worldwide to analyse the condition and the load-bearing capacity of road pavement structures. One of the FWD measurement results, the deflection bowl, may provide surplus information that is suitable for better road pavement structure diagnostics, based on the novel approach presented in this paper. This study presents a computational method that can calculate the layer thicknesses from the deflection data recorded by the non-destructive FWD device. The motivation for this research is that FWD and GPR equipment are often not available at the same time. However, the back-calculation of the pavement layer moduli from the deflections requires knowledge of the exact thicknesses. The developed method is based on the inertia point principle and provides not only the total pavement thickness but also the total asphalt thickness at each FWD drop point. From 25,200 linear elastic layered pavement models, 350 virtual inertia points could be identified. To describe the relationship between the structural model characteristics of the pavement (thickness and subgrade modulus) and the virtual inertia points, we chose the Gaussian process regression, a widely used method in machine learning. In addition to the thicknesses, the point of inertia can also be used to calculate the bearing modulus of the subgrade with high accuracy. Based on the data from the experimental road section, the radius value of the inertia point rc is not sensitive to the stiffness of the layers that compose the pavement structure, depending only on the total pavement thickness and the bearing capacity of the subgrade. The calculation was compared with the AASHTO (1993) procedure, and very similar values for the subgrade-bearing capacity were obtained. Moreover, in the near future, the method can be further developed to provide an estimation of layer thicknesses, together with a deflection measurement, especially adapted to continuous deflection measurement devices (Curviameter and Rolling Wheel Deflectometer).
Genetic Diversity and Maternal Lineage of Indo-Pacific Bottlenose Dolphin (Tursiops aduncus) in the Andaman Sea of Thailand
Authors: Prasitwiset Wareerat , Wongfu Chutima , Poommouang Anocha , Buddhachat Kittisak , Brown Janine L. , Chomdej Siriwadee , Kampuansai Jatupol , Kaewmong Patcharaporn , Kittiwattanawong Kongkiat , Nganvongpanit Korakot , Piboon Promporn
Published: December 2022

Indo-Pacific bottlenose dolphins (Tursiops aduncus) are a coastal species found in Thai waters off the coasts of the Andaman Sea and the Gulf of Thailand. This species was recently re-listed as near-threatened by the IUCN Red List, though the population status in Thai seas is not known. Here, we investigated genetic diversity, population structure, maternal lineage, and demographics by analyzing skin tissue samples (n = 30) of T. aduncus stranded along the Andaman coastline of Thailand between 1990 and 2019. This study was based on 11 microsatellite loci and 265 bp mtDNA control regions compared to data available through the National Center for Biotechnology Information (NCBI). From microsatellites, the observed heterozygosity (Ho) ranged from 0.46 to 0.85. The mean fixation index (F) value for all loci was 0.10 ± 0.04, which suggests some degree of inbreeding. Two genetic clusters (the most likely K at K = 2) were observed in T. aduncus through the population structure analysis using multiple criteria. For the mtDNA control region, a total of 17 haplotypes were found for dolphins in Thai seas (14 haplotypes from our samples; three haplotypes from the NCBI database) with high levels of haplotype diversity (h) at 0.926 ± 0.027 and nucleotide diversity (π) at 0.045 ± 0.002. A decline in the effective population size from 0.05 million years ago also was observed in Thai T. aduncus through Bayesian Skyline Plots analysis. A unique set of haplotypes was identified in our samples, which may have originated from the Australian and Indian Oceans rather than the Western Pacific Ocean. These results improve our understanding of the maternal lineage of the Indo-Pacific bottlenose dolphin, which can be used for monitoring population status and establishing better conservation plans for this species in the Thai Andaman Sea.
Morphological Variation of Strychnos spinosa Lam. Morphotypes: A Case Study at Bonamanzi Game Reserve, KwaZulu-Natal, South Africa
Authors: Mbhele Zoliswa , Zharare Godfrey E. , Zimudzi Clemence , Ntuli Nontuthuko R.
Published: December 2022

Strychnos spinosa Lam. of the Loganiaceae family is associated with versatility, poverty eradication, and rural economic development. However, the morphological diversity of S. spinosa is not well documented. This limits efforts toward its improvement and commercial exploitation. This study aimed to characterize the variability, vegetative and reproductive traits, and heritability of S. spinosa morphotypes at Bonamanzi Game Reserve. The majority of the morphotypes had green, rough, round immature fruits with dark green, elongated, open fully developed leaves. Fruits varied between roundish and pyriform shape as well as green and purple colour. Positive correlation was mainly seen between fruit and seed traits. Principal component analysis indicated fruit and seed traits as major discriminating factors for morphotypes, followed by leaf size and seed thickness. A dendrogram primarily grouped morphotypes according to fruit texture. Genotypic variance and genotypic coefficient of variation were higher than environmental variance and environmental coefficient variation in reproductive traits of S. spinosa. A rough pericarp texture and purple tinge on the immature leaves of some morphotypes was recorded for the first time. Differences in morphological features across S. spinosa morphotypes indicate a high level of diversity that could be utilized by breeders to generate new cultivars. This first report on variability and heritability among S. spinosa morphotypes forms the basis of available germplasm essential for future breeding programs.
Spatial and Temporal Patterns of Genetic Diversity and Structure in Danish Populations of the Alcon Blue Butterfly Phengaris alcon (Denis & Schiffermüller)
Authors: Boe Andreas M. B. , Simonsen Thomas J. , Colding-Jørgensen Camilla T. , Folman Philip H. , Jensen Thomas T. , Spencer Kian J. , Thomsen Philip F. , Nash David R.
Published: December 2022

Phengaris alcon is an endangered, ant-associated butterfly found, amongst other places, in Denmark, where it has undergone a severe decline during the last century. However, the population genetic consequences of this decline remain unknown. To explore past and current patterns in population structure in relation to the decline, we analyzed DNA microsatellite data from 184 recent and 272 historical P. alcon specimens from 44 spatiotemporal locations in Denmark. We thus generated the most temporally and spatially comprehensive population genetic dataset for P. alcon in Denmark so far. Our results for the Bayesian population assignment of recent samples revealed three major current genetic clusters: western Jutland, northern Jutland, and the island of Læsø. Estimates of genetic diversity showed signs of inbreeding in several extant populations. When including data from museum specimens, only a single locatSion showed a decline in heterozygosity between 1967 and 2021. We suggest that the two distinct clusters in western and northern Jutland indicate two temporally separated Holocene colonizations of Denmark, the latter of which may have been aided by changes in agricultural practice in the late Neolithic period. The unique genetic signature of the Læsø populations may be a result of the admixture of northern Jutland and western Swedish populations.
Obligation to Enhance OBIS Data for Sea- and Shorebirds of the Americas
Authors: Hartman Savannah , Hallock Pamela , Muller-Karger Frank
Published: December 2022

The distributions of many sea- and shorebird species span large geographic areas, making them ideal candidates as biomonitors of ecosystem perturbations and long-term environmental trends. The basic question examined in this study was: Does a major open-access data archive contain sufficient temporal- and spatial-scale data to support more detailed inquiry into multi-decadal-scale responses in geographic distributions of specific taxa? The global-scale open-access data platform, Ocean Biodiversity Information System (OBIS), was searched to compile data on bird distributions of the Americas, including the Caribbean Sea. More than 680,000 occurrence records of 210 species, collected between 1965 and 2018, were located and evaluated by marine ecoregion. The Puget Trough/Georgia Basin marine ecoregion, along the United States/Canadian border, and the Virginian marine ecoregion on the US east coast, dominated occurrences, each with more than 100,000 records, while the Gulf of Maine/Bay of Fundy had the most years of records (42). Most records from South America (~29,000) came from the Channels and Fjords of Southern Chile, collected across 16 different years. More than 90% of the recorded data were collected since 1983, and more than 95% of the records were from North American marine ecoregions. We urge additional observations to be shared via OBIS to allow comprehensive large-scale and detailed meta-analyses of spatial and temporal trends in marine and shore-bird communities and their biodiversity.
Photophore Morphogenesis and Extraocular Encephalopsin Expression during the Embryogenesis of Smalleye Pygmy Shark (Squaliolus aliae)
Authors: Duchatelet Laurent , Ho Hsuan-Ching , Mallefet Jérôme
Published: December 2022

Bioluminescence is a common phenomenon in marine organisms, especially in deep water where faint blue light remains. Among elasmobranchs, three families display the ability to emit light, the Etmopteridae, the Dalatiidae, and the Somniosidae. Luminous sharks have thousands of minute light organs, called photophores, that are mainly present ventrally and produce light. The main function of shark luminescence is counterillumination to camouflage the shark silhouette by mimicking the residual ambient light and avoiding being spotted by predators underneath. To perform counterillumination efficiently, luminescence needs to be finely adjusted. A new type of control was recently demonstrated via extraocular photoreception at the level of the light organ. An encephalopsin (i.e., opsin 3) was shown to be expressed in the vicinity of the photophore of an Etmopteridae species, Etmopterus spinax. This opsin was also demonstrated to be expressed concomitantly with the photophore development (i.e., when photophores become able to produce light) during E. spinax embryogenesis. To understand the photophore morphogenesis of different shark families, we analyzed the smalleye pygmy shark, Squaliolus aliae, with a photophore formation which represents the first report on the Dalatiidae family. Since Dalatiidae and Etmopteridae are phylogenetically closely related, the photophore morphogenesis was compared with an Etmopteridae representative, Etmopterus spinax. The results also reveal that Squaliolus aliae shares similar encephalopsin expression pattern as in Etmopterus spinax, which further supports evolutionary conservation of photophore morphogenesis as well as its own encephalopsin-based light perception across the two luminous shark families.
Effects of Climate Change and Environmental Factors on Bamboo (Ferrocalamus strictus), a PSESP Unique to China
Authors: He Honglan , Zheng Xiaofeng , Wang Yingqiong , Wang Wenquan , Li Maobiao , Wang Shuguang , Wang Jin , Wang Changming , Zhan Hui
Published: December 2022

Bamboo is a plant that may replace plastics and wood as a new green environmental protection material that can be developed. Ferrocalamus strictus is a very special and rare bamboo which is a plant species with extremely small populations (PSESP) endemic to Yunnan, China, and it is listed as a China key national first-class protected wild plant. To explore the effects of extreme climate and environmental changes on this PSESP, we conducted a case study on the response of F. strictus to climate under two extreme future emission scenarios. We combined 29 environmental variables, including the temperature, precipitation, altitude, slope, aspect, soil pH, soil organic carbon content, and mean UV-B radiation of the highest month, to analyze the important environmental factors limiting the distribution of F. strictus and identified the priority conservation areas (PCAs) of F. strictus. Under the two future extreme climate scenarios, the core potential suitable distribution area of F. strictus would decrease by 26%–34% in 2040, 44%–46% in 2060, and 23%–58% in 2080, respectively. Bio18 (precipitation in the warmest quarter) and Bio3 (isotherm) were the two key factors limiting the geographical distribution of F. strictus (the contribution rates were 40.1% and 18.45%, respectively). The results of this study show that F. strictus is in urgent need of protection and PSESPs require more attention.
Higher Soil Aggregate Stability in Subtropical Coniferous Plantations Than Natural Forests Due to Microbial and Aggregate Factors
Authors: Cai Lin , Yang Yujing , Chong Yujie , Xiong Jiatai , Wu Juyang , Ai Xunru , Guo Qiuju , Yuan Yiping , Li Zhongqiang
Published: December 2022

Forest restoration and soil structure stabilization are the focus of forestry and ecology. However, the combined mechanisms of soil microorganisms and organic and inorganic aggregate binding agents on soil aggregation is unclear. In order to explore the effects of subtropical forest restoration types on soil aggregates and the underlying mechanisms, we collected soil samples from subtropical natural forests and coniferous and broad-leaved plantations that are commonly used for forest restoration. The mean weight diameter (MWD) of the soil aggregate was used to indicate the aggregates’ stability. The soil microbial diversity and structure, the organic and inorganic aggregate binding agents including the mycorrhizal density, the glomalin-related soil protein and the Fe and Al oxides were investigated. Results showed that the Shannon and Simpson indices of soil microbial communities in the coniferous plantations were both significantly higher than those in the natural forests. At the annual level, compared with the natural forests, the plantations decreased the proportion of 0.25–1 mm aggregates while the MWD significantly increased. The forest type also significantly affected the mycorrhizal density, the easily extractable glomalin-related soil proteins (EEG) and the Fe oxide. A variance decomposition analysis showed that soil microbial communities, organic and inorganic binding agents, and their interactions together contributed to the aggregates’ composition and stability by 75.07%. The MWD was positively correlated with the microbial diversity, mycorrhizal density and Fe oxide. We therefore suggest that the combined effects of the soil microbial communities and the organic (mycorrhizal density) and inorganic binding agents (Fe oxide) can be the main mechanisms of soil aggregation in the study area, resulting in a higher soil aggregate stability in the subtropical coniferous plantation than in the natural forest.
Different Modelling Approaches to Determine Suitable Areas for Conserving Egg-Cone Pine (Pinus oocarpa Schiede) Plus Trees in the Central Part of Mexico
Authors: Romero-Sanchez Martin Enrique , Velasco-Garcia Mario Valerio , Perez-Miranda Ramiro , Velasco-Bautista Efrain , Gonzalez-Hernandez Antonio
Published: December 2022

Various spatial modelling methods and tools have been used in ecology and biogeography. The application of these options serves a dual function: first, they offer information about the potential distribution of species to understand the richness and diversity of unassessed areas. Second, spatial modelling methods employ these predictions to select relevant sites to determine natural conservation areas. In this study, we compared three methods for modelling the spatial distribution of Egg-cone Pine (Pinus oocarpa Schiede), an important non-timber pine in Mexico. The final goal is to estimate suitable areas for the conservation and reproduction of superior individuals (plus trees) of P. oocarpa as a conservation strategy outside the known distribution since this species possesses a high ecological and economic value. The model used were a generalised linear model (GLM) as a parametric regression method, random forest (RF) as a machine-learning method, and the MaxEnt model, a standard procedure, implemented using the Kuenm R package. The results suggest that the models used performed well since the AUROC was between 0.95 and 0.98 in all cases. MaxEnt and random forest approaches provided more conservative predictions for the distribution of suitable areas of plus trees of P. oocarpa than the generalised linear model, but the random forest algorithm achieved the best performance. The results of the study allowed the determination of ex situ conservation areas for P. oocarpa plus trees outside of their known distribution.
Genetic Parameters and Genotype–Environment Interactions in Paulownia Clonal Tests in Temperate and Subtropical Regions of China
Authors: Zhao Yang , Feng Yanzhi , Yang Chaowei , Qiao Jie , Zhou Haijiang , Li Fangdong , Wang Baoping
Published: December 2022

Clonal forestry has developed rapidly in recent years and already plays a significant role in commercial tree plantations worldwide. Clonal breeding requires accurate assessments of genetic parameters, together with measurements of clonal productivity, stability, and adaptably. However, relevant studies for clones of Paulownia spp. genotypes are rare. We therefore conducted clonal tests on twenty Paulownia clones established at three sites in the temperate and subtropical regions of China. Trees were planted in a randomized block design, with four replications in each site, twenty plots in each block, and six to eight individuals of the same clone in each plot. We measured the trunk diameter at breast height (DBH), total trunk height (Ht), and individual stand volume of 7-year-old trees to estimate genetic parameters and analyze genotype–environment interactions. A combined analysis of variance indicated that clonal, site, and clone–site interactions significantly affected the three growth traits. Clonal heritability and individual heritability were 0.35–0.84 and 0.07–0.30, respectively. The phenotypic and genetic correlation coefficients among the growth traits were 0.46–0.93 and 0.85–0.99, respectively. There were extremely significant positive linear relationships between the best linear unbiased predictors for DBH and the original DBH values (R2 > 0.98). Clones 10, 2, 18, and 13 were selected for deployment based on a selection intensity of 1.4, GGE biplots, and the relative performance of harmonic means on genotypic values analysis. For these clones, the genetic gains in DBH, Ht, and volume were 18.05%, 21.46%, and 46.03%, respectively. These results provide useful information for the selection of Paulownia clones at the target sites and will provide a sound basis for improving Paulownia clonal breeding programs in the future.
Analyzing TLS Scan Distribution and Point Density for the Estimation of Forest Stand Structural Parameters
Authors: Torralba Jesús , Carbonell-Rivera Juan Pedro , Ruiz Luis Ángel , Crespo-Peremarch Pablo
Published: December 2022

In recent decades, the feasibility of using terrestrial laser scanning (TLS) in forest inventories was investigated as a replacement for time-consuming traditional field measurements. However, the optimal acquisition of point clouds requires the definition of the minimum point density, as well as the sensor positions within the plot. This paper analyzes the effect of (i) the number and distribution of scans, and (ii) the point density on the estimation of seven forest parameters: above-ground biomass, basal area, canopy base height, dominant height, stocking density, quadratic mean diameter, and stand density index. For this purpose, 31 combinations of TLS scan positions, from a single scan in the center of the plot to nine scans, were analyzed in 28 circular plots in a Mediterranean forest. Afterwards, multiple linear regression models using height metrics extracted from the TLS point clouds were generated for each combination. In order to study the influence of terrain slope on the estimation of forest parameters, the analysis was performed by using all the plots and by creating two categories of plots according to their terrain slope (slight or steep). Results indicate that the use of multiple scans improves the estimation of forest parameters compared to using a single one, although using more than three to five scans does not necessarily improves the accuracy. Moreover, it is also shown that lower accuracies are obtained in plots with steep slope. In addition, it was observed that each forest parameter has a strategic distribution depending on the field of view of the TLS. Regarding the point density analysis, the use of 1% to 0.1% (≈136 points·m−2) of the initial point cloud density (≈37,240.86 points·m−2) generates an R2adj difference of less than 0.01. These findings are useful for planning more efficient forest inventories, reducing acquisition and processing time as well as costs.
Application of BLUP-GGE in Growth Variation Analysis in Southern-Type Populus deltoides Seedlings in Different Climatic Regions
Authors: Li Zhenghong , Liu Ning , Zhang Weixi , Dong Yufeng , Ding Mi , Huang Qinjun , Ding Changjun , Su Xiaohua
Published: December 2022

In the present study, using the BLUP-GGE approach, southern-type (ST) Populus deltoides genotypes were analyzed and evaluated, and variations in growth traits, seedling height (H), and ground diameter (GD) were studied in various climatic regions, which could facilitate the increase of the breeding range of ST. The test materials were 119 one-year-old ST genotypes, and the test sites were Ningyang (NY) and Hainan (HN). A linear mixed-effects model was constructed, and the BLUP values of H and GD were obtained using the linear unbiased prediction (BLUP) method. GGE-Biplots were generated. The H variation was greater than the GD variation. The effects of environment, block, and genotype–environment interaction (G×E) were highly significant. The goodness of fit of the GGE-Biplots obtained by extracting the BLUP values was >95%. According to the GGE-biplot results, the performance of each genotype varied considerably. The genotype No. 13 had the highest average GD and the highest average H. In NY, the genotypes No. 93 and 115 had the highest H and GD, and in HN, the genotype No. 9 had the highest H and GD. ST had a better second-year survival rate in NY than in HN. The hybridization of tropical Populus deltoides can be performed using the No. 13 and 117 genotypes, which grow rapidly and have high yields.
Expression Pattern Analysis of Larch WRKY in Response to Abiotic Stress
Authors: Wang Chen , Zhao Qingrong , Zhang Lei , Zhang Hanguo
Published: December 2022

Larix olgensis is one of the most common tree species in Northeast China; it has the advantages of fast growth and good wood properties. In order to accelerate larch molecular breeding and to provide good candidate genes for larch improvement, based on the existing transcriptome data of Larix olgensis, four WRKY family genes with complete CD regions were obtained by BLAST comparison on the NCBI website. The results of bioinformatics analysis and gene expression after abiotic stress showed that there were some differences in the expression of WRKY1, WRKY2, WRKY3 and WRKY4 in roots, stems and leaves under each treatment. Under the treatment of a 40% PEG6000 solution (polyethylene glycol), the expression of WRKY2 was significantly up-regulated in each time period and WRKY1, WRKY3 and WRKY4 were down-regulated in varying degrees compared with the control group, indicating that they were involved in the response to drought stress. Under the treatment of the 0.2mol/L NaCl solution, the expression of WRKY2 was up-regulated in roots, stems and leaves. The expression amount and the expression trend of the other three genes were different in roots, stems and leaves under different treatment durations, indicating that they were also involved in a salt-stress response. Under the treatment of the 0.1 mol/L NaHCO3 solution, the expression of WRKY4 was significantly down-regulated in all time periods, while WRKY2 was significantly up-regulated. The other two genes were regulated to a certain extent, indicating that they also had a physiological response under alkaline conditions. These results lay a foundation for the study of gene function of these four WRKY transcription factors.
Cutting Force and Surface Roughness during Straight-Tooth Milling of Walnut Wood
Authors: Jiang Shangsong , Buck Dietrich , Tang Qi , Guan Jun , Wu Zhanwen , Guo Xiaolei , Zhu Zhaolong , Wang Xiaodong
Published: December 2022

Walnut (Juglans regia L.) is widely used in wood furnishings, and machinability is a key factor for improving product quality and enterprise benefits. This work focused on the influence of the rake angle, depth of cut, and cutting speed on the cutting force and machined surface roughness during the straight-tooth milling of walnut. On the basis of the experimental findings, a mathematical model was created using a response surface methodology to determine the relationship between the cutting force and the cutting conditions, as well as the relationship between the surface roughness and the cutting conditions. Variance analysis was used to study the significant contributions of the interactions of various factors and two-level interactions to the cutting force and surface roughness. The optimized combination of milling conditions, resulting in lowest cutting force and surface roughness, was determined to be a rake angle of 5°, a depth of cut of 0.6 mm, and a cutting speed of 45 m/s.