bluuebunny/crossref_metadata_2025 huggingface dataset:
Multidisciplinary lines of evidence reveal East/Northeast Asian origins of agriculturalist/pastoralist residents at a Han dynasty military outpost in ancient Xinjiang
Authors: Allen Edward , Yu Yao , Yang Xiaomin , Xu Yiran , Du Panxin , Xiong Jianxue , Chen Dian , Tian Xiaohong , Wu Yong , Qin Xiaoli , Sheng Pengfei , Wang Chuan-Chao , Wen Shaoqing
Published: August 2022

Han/non-Han interactions were engrained among the border regions of ancient Imperial China. Yet, little is known about either the genetic origins or the lifeways of these border peoples. Our study applies tools from ancient deoxyribonucleic acid (DNA) and stable isotope analysis to the study of a Han dynasty population at the Shichengzi site in modern-day Xinjiang. Isotopic analysis (δ13C and δ15N) of human (n = 8), animal (n = 26), and crop remains (n = 23) from Shichengzi indicated that dietary patterns among site inhabitants could be split among agro-pastoral and agricultural groups based on differences in the collagen 15N ratios. DNA analysis divided the four Shichengzi samples into two groups, with one group primarily harboring the ancient Northeast Asian (ANA) related ancestry, while the other showed a dominant Late Neolithic Yellow River (YR_LN) related ancestry. Both ancient DNA and stable isotope evidence point to the Northeast Asian origins of pastoralists and East Asian origins of Han agriculturalists, who, nonetheless, shared a single burial space at Shichengzi. This study thus provides clear evidence for the multiple origins and identities of populations across the porous border represented by the Han Empire and surrounding regions and proposes a new model for the interpretation of border culture in early Imperial China.
Ensemble modeling for American chestnut distribution: Locating potential restoration sites in Pennsylvania
Authors: Henderson Alec F. , Santoro Jennifer A. , Kremer Peleg
Published: August 2022

The American chestnut (Castanea dentata Borkh.) was an economically, ecologically, and culturally important tree in eastern American hardwood forests. However, the American chestnut is currently functionally absent from these forests due to the introduction of an invasive fungus (Cryphonectria parasitica (Murr.) Barr) and causal agent of chestnut blight in the early 1900s. Field experiments are being carried out to develop a blight-resistant American chestnut tree, but range-wide restoration will require localized understanding of its current distribution and what factors contribute to suitable American chestnut habitat. While previous studies have researched species distribution of the American chestnut, it is important to understand how species distribution modeling (SDM) technique impacts model results. In this paper we create an ensemble model that combines multiple different SDM techniques to predict areas of suitable American chestnut habitat in Pennsylvania. Results indicate that model accuracy varied considerably by SDM technique – with artificial neural networks performing the worst (Area-Under-the-Curve, AUC = 0.705) and gradient boosting models performing the best (AUC = 0.877). Even though SDM technique accuracy varied, most models identified the same environmental variables as the most important: ratio of sand to clay in the soil, canopy cover, topographic convergence index, and topographic position index. This study offers insight into the best SDM techniques to use, as well as a method of combining SDMs for higher prediction confidence.
Distinctive gene expression patterns in pregnancy-associated breast cancer
Authors: Wang Dan , Peng Huiyu , Hu Yuyao , Piao Xue , Gao Dianshuai , Sha Yan
Published: August 2022

Pregnancy-associated breast cancer (PABC) is diagnosed during pregnancy or within 1 year postpartum, but the unique aspects of its etiology and pathogenesis have not been fully elucidated. This study aimed to ascertain the molecular mechanisms of PABC to facilitate diagnosis and therapeutic development. The Limma package was used to characterize the differentially expressed genes in PABC as compared to non-pregnancy-associated breast cancer (NPABC) and normal breast tissue. A total of 871 dysregulated genes were identified in the PABC versus NPABC groups and 917 in the PABC versus normal groups, with notable differences in the expression of MAGE and CXCL family genes. The dysregulated genes between the PABC and normal groups were mainly associated with signal transduction and immune response, while Kyoto Encyclopedia of Genes and Genomes analysis revealed that the dysregulated genes were enriched in immune-related pathways, including the major histocompatibility complex (MHC) class II protein complex, the type I interferon signaling pathway, regulation of α-β T-cell proliferation, and the T-cell apoptotic process. Through protein-protein interaction network construction, CD44 and BRCA1 were identified as prominent hub genes with differential expression in PABC versus NPABC. Furthermore, a cluster with eleven hub genes was identified in PABC versus normal adjacent tissues, of which the expression of EGFR, IGF1, PTGS2, FGF1, CAV1, and PLCB1 were verified to be differentially expressed in an independent cohort of PABC patients. Notably, IGF1, PTGS2, and FGF1 were demonstrated to be significantly related to patient prognosis. Our study reveals a distinctive gene expression pattern in PABC and suggests that IGF1, PTGS2, and FGF1 might serve as biomarkers for diagnosis and prognosis of PABC.
Identified novel heterozygous HTRA1 pathogenic variants in Chinese patients with HTRA1-associated dominant cerebral small vessel disease
Authors: Chen Mei-Jiao , Zhang Yi , Luo Wen-Jiao , Dong Hai-Lin , Wei Qiao , Zhang Juan , Ruan Qi-Qi , Ni Wang , Li Hong-Fu
Published: August 2022

Background: Homozygous and compound heterozygous mutations in HTRA1 cause cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL). Recently, heterozygous pathogenic variants in HTRA1 were described in patients with autosomal dominant cerebral small vessel disease (CSVD). Here, we investigated the genetic variants in a cohort of Chinese patients with CSVD.

Methods: A total of 95 Chinese index patients with typical characteristics of CSVD were collected. Whole exome sequencing was performed in the probands, followed by Sanger sequencing. Pathogenicity prediction software was applied to evaluate the pathogenicity of the identified variants.

Results: We detected five heterozygous HTRA1 pathogenic variants in five index patients. These pathogenic variants included four known variants (c.543delT, c.854C>T, c.889G>A, and c.824C>T) and one novel variant (c.472 + 1G>A). Among them, c.854C>T, c.824C>T, and c.472 + 1G>A have never been reported in China and c.889G>A was once reported in homozygous but never in heterozygous. Three of them were distributed in exon 4, one in exon 2, and another splicing variant in intron 1. Four out of five probands presented typical features of CARASIL but less severe. The common clinical features included lacunar infarction, cognitive decline, alopecia, and spondylosis. All of them showed leukoencephalopathy, and the main involved cerebral area include periventricular and frontal area, centrum semiovale, thalamus, and corpus callosum. Anterior temporal lobes and external capsule involvement were also observed. Three probands had intracranial microbleeds.

Conclusion: Our study expanded the mutation spectrum of HTRA1, especially in Chinese populations, and provided further evidence for “hot regions” in exon 1–4, especially in exon 4, in heterozygous HTRA1 pathogenic variants. Our work further supported that patients with heterozygous HTRA1 pathogenic variants presented with similar but less-severe features than CARASIL but in an autosomal dominantly inherited pattern.
LncRNAs divide and rule: The master regulators of phase separation
Authors: Somasundaram Kumaravel , Gupta Bhavana , Jain Nishkarsh , Jana Samarjit
Published: August 2022

Most of the human genome, except for a small region that transcribes protein-coding RNAs, was considered junk. With the advent of RNA sequencing technology, we know that much of the genome codes for RNAs with no protein-coding potential. Long non-coding RNAs (lncRNAs) that form a significant proportion are dynamically expressed and play diverse roles in physiological and pathological processes. Precise spatiotemporal control of their expression is essential to carry out various biochemical reactions inside the cell. Intracellular organelles with membrane-bound compartments are known for creating an independent internal environment for carrying out specific functions. The formation of membrane-free ribonucleoprotein condensates resulting in intracellular compartments is documented in recent times to execute specialized tasks such as DNA replication and repair, chromatin remodeling, transcription, and mRNA splicing. These liquid compartments, called membrane-less organelles (MLOs), are formed by liquid–liquid phase separation (LLPS), selectively partitioning a specific set of macromolecules from others. While RNA binding proteins (RBPs) with low complexity regions (LCRs) appear to play an essential role in this process, the role of RNAs is not well-understood. It appears that short nonspecific RNAs keep the RBPs in a soluble state, while longer RNAs with unique secondary structures promote LLPS formation by specifically binding to RBPs. This review will update the current understanding of phase separation, physio-chemical nature and composition of condensates, regulation of phase separation, the role of lncRNA in the phase separation process, and the relevance to cancer development and progression.
Mathematical model and genomics construction of developmental biology patterns using digital image technology
Authors: Ni Shiwei , Chen Fei , Chen Guolong , Yang Yufeng
Published: August 2022

Biological pattern formation ensures that tissues and organs develop in the correct place and orientation within the body. A great deal has been learned about cell and tissue staining techniques, and today’s microscopes can capture digital images. A light microscope is an essential tool in biology and medicine. Analyzing the generated images will involve the creation of unique analytical techniques. Digital images of the material before and after deformation can be compared to assess how much strain and displacement the material responds. Furthermore, this article proposes Development Biology Patterns using Digital Image Technology (DBP-DIT) to cell image data in 2D, 3D, and time sequences. Engineered materials with high stiffness may now be characterized via digital image correlation. The proposed method of analyzing the mechanical characteristics of skin under various situations, such as one direction of stress and temperatures in the hundreds of degrees Celsius, is achievable using digital image correlation. A DBP-DIT approach to biological tissue modeling is based on digital image correlation (DIC) measurements to forecast the displacement field under unknown loading scenarios without presupposing a particular constitutive model form or owning knowledge of the material microstructure. A data-driven approach to modeling biological materials can be more successful than classical constitutive modeling if adequate data coverage and advice from partial physics constraints are available. The proposed procedures include a wide range of biological objectives, experimental designs, and laboratory preferences. The experimental results show that the proposed DBP-DIT achieves a high accuracy ratio of 99,3%, a sensitivity ratio of 98.7%, a specificity ratio of 98.6%, a probability index of 97.8%, a balanced classification ratio of 97.5%, and a low error rate of 38.6%.
The emerging roles and mechanism of m6a in breast cancer progression
Authors: Zhou Mengying , Dong Menglu , Yang Xue , Gong Jun , Liao Xinghua , Zhang Qi , Liu Zeming
Published: August 2022

Breast cancer (BC) has continued to be the leading cause of cancer deaths in women, accompanied by highly molecular heterogeneity. N6-methyladenosine (m6A), a methylation that happens on adenosine N6, is the most abundant internal mRNA modification type in eukaryotic cells. Functionally, m6A methylation is a reversible modification process and is regulated by 3 enzymes with different functions, namely “writer”, “reader”, and “eraser”. Abnormal m6A modifications trigger the expression, activation, or inhibition of key signaling molecules in critical signaling pathways and the regulatory factors acting on them in BC. These m6A-related enzymes can not only be used as markers for accurate diagnosis, prediction of prognosis, and risk model construction, but also as effective targets for BC treatment. Here, we have emphasized the roles of different types of m6A-related enzymes reported in BC proliferation, invasion, and metastasis, as well as immune regulation. The comprehensive and in-depth exploration of the molecular mechanisms related to m6A will benefit in finding effective potential targets and effective stratified management of BC.
Fibroblasts in intestinal homeostasis, damage, and repair
Authors: Chalkidi Niki , Paraskeva Christina , Koliaraki Vasiliki
Published: August 2022

The mammalian intestine is a self-renewing tissue that ensures nutrient absorption while acting as a barrier against environmental insults. This is achieved by mature intestinal epithelial cells, the renewing capacity of intestinal stem cells at the base of the crypts, the development of immune tolerance, and the regulatory functions of stromal cells. Upon intestinal injury or inflammation, this tightly regulated mucosal homeostasis is disrupted and is followed by a series of events that lead to tissue repair and the restoration of organ function. It is now well established that fibroblasts play significant roles both in the maintenance of epithelial and immune homeostasis in the intestine and the response to tissue damage mainly through the secretion of a variety of soluble mediators and ligands and the remodeling of the extracellular matrix. In addition, recent advances in single-cell transcriptomics have revealed an unexpected heterogeneity of fibroblasts that comprise distinct cell subsets in normal and inflammatory conditions, indicative of diverse functions. However, there is still little consensus on the number, terminology, and functional properties of these subsets. Moreover, it is still unclear how individual fibroblast subsets can regulate intestinal repair processes and what is their impact on the pathogenesis of inflammatory bowel disease. In this mini-review, we aim to provide a concise overview of recent advances in the field, that we believe will help clarify current concepts on fibroblast heterogeneity and functions and advance our understanding of the contribution of fibroblasts in intestinal damage and repair.
Investigating mammary glands of lactating goats for the presence of tertiary lymphoid organs
Authors: Tsugami Yusaku , Nakayama Sayaka , Suzuki Naoki , Nii Takahiro , Isobe Naoki
Published: August 2022

Ectopic tertiary lymphoid organs (TLOs) have been identified in many organs, such as the lungs, nasal cavities, and kidneys of both mice and humans. Although lymphocyte aggregates have been observed in the mammary glands of ruminants, the details remain unclear. In this study, we investigated the mammary glands of lactating goats for the presence of TLOs. The localization of CD20 (B cells), CD3 (T cells), MECA79 (high endothelial venules), CD40 (follicular dendritic cells), BCL6 (germinal center), and IgA was examined by immunohistochemistry. The concentrations of IgG, IgA, lactoferrin, β-defensin-1, cathelicidin-2, cathelicidin-7, S100A7, and S100A8 in milk were measured by ELISA. The localization and amount of tight junction (TJ) proteins (claudin-3 and claudin-4) were examined using immunofluorescence and western blotting. We found that 19 out of 30 udders contained lymphocyte aggregates, which showed positive reactions against CD20, CD3, CD40, and MECA79. In addition, large-sized aggregations showed separate localization of B cells and T cells and a positive reaction against BCL6, although BCL6 was sparsely localized in the aggregations. These results indicate that mammary glands of lactating goats contain TLOs. The IgG and IgA concentrations in the milk of TLO-positive goats and the number of IgA-positive cells were higher than those in negative goats. Furthermore, claudin-4 was localized in the TJ region and the amount was higher in TLO-positive mammary glands than that in the negative group, indicating the presence of leakages at TJs. In conclusion, a majority of lactating goat udders have TLOs, which contribute to local immunity by producing immunoglobulins.
Hallmark-guided subtypes of hepatocellular carcinoma for the identification of immune-related gene classifiers in the prediction of prognosis, treatment efficacy, and drug candidates
Authors: Guo Chengbin , Tang Yuqin , Yang Zhao , Li Gen , Zhang Yongqiang
Published: August 2022

Hepatocellular carcinoma (HCC), accounting for ~90% of all primary liver cancer, is a prevalent malignancy worldwide. The intratumor heterogeneity of its causative etiology, histology, molecular landscape, and immune phenotype makes it difficult to precisely recognize individuals with high mortality risk or tumor-intrinsic treatment resistance, especially immunotherapy. Herein, we comprehensively evaluated the activities of cancer hallmark gene sets and their correlations with the prognosis of HCC patients using gene set variation analysis (GSVA) and identified two HCC subtypes with distinct prognostic outcomes. Based on these subtypes, seven immune-related genes (TMPRSS6, SPP1, S100A9, EPO, BIRC5, PLXNA1, and CDK4) were used to construct a novel prognostic gene signature [hallmark-guided subtypes-based immunologic signature (HGSIS)] via multiple statistical approaches. The HGSIS-integrated nomogram suggested an enhanced predictive performance. Interestingly, oncogenic hallmark pathways were significantly enriched in the high-risk group and positively associated with the risk score. Distinct mutational landscapes and immune profiles were observed between different risk groups. Moreover, immunophenoscore (IPS) and tumor immune dysfunction and exclusion (TIDE) analysis showed different sensitivities of HGSIS risk groups for immune therapy efficacy, and the pRRophetic algorithm indicated distinguishable responses for targeted/chemotherapies in different groups. KIF2C was picked out as the key target concerning HGSIS, and the top 10 small molecules were predicted to bind to the active site of KIF2C via molecular docking, which might be further used for candidate drug discovery of HCC. Taken together, our study offers novel insights for clinically significant subtype recognition, and the proposed signature may be a helpful guide for clinicians to improve the treatment regimens.
The role of the complement system in Multiple Sclerosis: A review
Authors: Saez-Calveras Nil , Stuve Olaf
Published: August 2022

The complement system has been involved in the pathogenesis of multiple neuroinflammatory and neurodegenerative conditions. In this review, we evaluated the possible role of complement activation in multiple sclerosis (MS) with a focus in progressive MS, where the disease pathogenesis remains to be fully elucidated and treatment options are limited. The evidence for the involvement of the complement system in the white matter plaques and gray matter lesions of MS stems from immunohistochemical analysis of post-mortem MS brains,in vivoserum and cerebrospinal fluid biomarker studies, and animal models of Experimental Autoimmune Encephalomyelitis (EAE). Complement knock-out studies in these animal models have revealed that this system may have a “double-edge sword” effect in MS. On the one hand, complement proteins may aid in promoting the clearance of myelin degradation products and other debris through myeloid cell-mediated phagocytosis. On the other, its aberrant activation may lead to demyelination at the rim of progressive MS white matter lesions as well as synapse loss in the gray matter. The complement system may also interact with known risk factors of MS, including as Epstein Barr Virus (EBV) infection, and perpetuate the activation of CNS self-reactive B cell populations. With the mounting evidence for the involvement of complement in MS, the development of complement modulating therapies for this condition is appealing. Herein, we also reviewed the pharmacological complement inhibitors that have been tested in MS animal models as well as in clinical trials for other neurologic diseases. The potential use of these agents, such as the C5-binding antibody eculizumab in MS will require a detailed understanding of the role of the different complement effectors in this disease and the development of better CNS delivery strategies for these compounds.
A safe and effective vaccine against bovine leukemia virus
Authors: Suárez Archilla Guillermo , Gutiérrez Gerónimo , Camussone Cecilia , Calvinho Luis , Abdala Alejandro , Alvarez Irene , Petersen Marcos , Franco Lautaro , Destefano Gabriel , Monti Gustavo , Jacques Jean-Rock , Joris Thomas , Willems Luc , Trono Karina
Published: August 2022

Previous attempts to develop a vaccine against bovine leukemia virus (BLV) have not been successful because of inadequate or short-lived stimulation of all immunity components. In this study, we designed an approach based on an attenuated BLV provirus by deleting genes dispensable for infectivity but required for efficient replication. The ability of the vaccine to protect from natural BLV infection was investigated in the context of dairy productive conditions in an endemic region. The attenuated vaccine was tested in a farm in which the prevalence rose from 16.7% in young cattle at the beginning of the study to more than 90% in adult individuals. Sterilizing immunity was obtained in 28 out of 29 vaccinated heifers over a period of 48 months, demonstrating the effectiveness of the vaccine. As indicated by the antiviral antibody titers, the humoral response was slightly reduced compared to wild-type infection. After initial post-vaccination bursts, the proviral loads of the attenuated vaccine remained most frequently undetectable. During the first dairy cycle, proviral DNA was not detected by nested-PCR in milk samples from vaccinated cows. During the second dairy cycle, provirus was sporadically detected in milk of two vaccinated cows. Forty-two calves born from vaccinated cows were negative for proviral DNA but had antiviral antibodies in their peripheral blood. The attenuated strain was not transmitted to sentinels, further supporting the safety of the vaccine. Altogether, these data thus demonstrate that the vaccine against BLV is safe and effective in herd conditions characterized by a very high incidence. This cost-effective approach will thus decrease the prevalence of BLV without modification of production practices. After facing a series of challenges pertaining to effectiveness and biosafety, the vaccine is now available for further large-scale delivery. The different challenges and hurdles that were bypassed may be informative for the development of a vaccine against HTLV-1.
Effect of diet on molecular relationships between Atlantic cod larval muscle growth dynamics, metabolism, and antioxidant defense system
Authors: Vo Tu A. , Galloway Trina F. , Arukwe Augustine , Edvardsen Rolf B. , Hamre Kristin , Karlsen Ørjan , Rønnestad Ivar , Kjørsvik Elin
Published: August 2022

We studied molecular effects (RNAseq and qPCR) of first feeding prey types (copepods or rotifers/Artemia) on skeletal muscle myogenesis and growth dynamics (proliferation, differentiation), metabolism (glycolysis, gluconeogenesis, oxidative phosphorylation), and antioxidant defense system (production/regulation of reactive oxygen species (ROS) in cod (Gadus morhua) larval skeletal muscle. Larval somatic growth rates were significantly higher in copepod fed larvae, although shifts in gene expressions related to muscle growth dynamics between hypertrophy and hyperplasia and generation and regulation of ROS mostly occurred around 5-, 10-, and 15-mm standard length (SL) for both groups. Gene expression for cell membrane proteins (such as nox1 and igf1r) peaked at 7 mm SL in all larvae, corresponding with increased ROS expressions in cod muscle during the exponential stratified hyperplasia phase from 7 mm SL. Expression for muscle differentiation (mef2a) occurred continuously (strongest from 10 mm SL). Expressions for muscle proliferation (pcna) and hydrogen peroxide (H2O2) generation (sod1 and sod2) occurred in the 5 - 15 mm SL range, peaking at 10 mm SL in all larvae. A downregulation of sod1 and sod2 in skeletal muscle from 15 mm SL indicated the first response of the defense antioxidant system. Gene expressions related to glucose metabolism (slc2A11, pfk, fpb2, ldha) was 3 - 10 times higher in copepod-fed larvae than in rotifer/Artemia-fed larvae between 7 – 10 mm (live prey period). Copepods move faster than rotifers, and cod larvae will also gradually increase their active swimming periods, due to less viscous forces. Active swimming during the strongest muscle stratified hyperplasia phase (7 – 10 mm SL) could promote a better delivery and transport across the muscle membrane and intracellular flux through glycolysis and oxidative phosphorylation and would contribute to the observed earlier and more effective glucose metabolism in the larvae fed copepods. We suggest that active swimming is an important factor promoting cod larval muscle growth, especially during the strongest muscle hyperplasia phase between 7 and 10 mm SL. The rapid movements of copepods and better nutritional composition could play important roles in stabilizing ROS levels, promoting high swimming activities and enhancing long-term muscle growth in cod.
Echofilter: A Deep Learning Segmention Model Improves the Automation, Standardization, and Timeliness for Post-Processing Echosounder Data in Tidal Energy Streams
Authors: Lowe Scott C. , McGarry Louise P. , Douglas Jessica , Newport Jason , Oore Sageev , Whidden Christopher , Hasselman Daniel J.
Published: August 2022

Understanding the abundance and distribution of fish in tidal energy streams is important for assessing the risks presented by the introduction of tidal energy devices into the habitat. However, tidal current flows suitable for tidal energy development are often highly turbulent and entrain air into the water, complicating the interpretation of echosounder data. The portion of the water column contaminated by returns from entrained air must be excluded from data used for biological analyses. Application of a single algorithm to identify the depth-of-penetration of entrained air is insufficient for a boundary that is discontinuous, depth-dynamic, porous, and varies with tidal flow speed.

Using a case study at a tidal energy demonstration site in the Bay of Fundy, we describe the development and application of deep machine learning models with a U-Net based architecture that produce a pronounced and substantial improvement in the automated detection of the extent to which entrained air has penetrated the water column.

Our model, Echofilter, was found to be highly responsive to the dynamic range of turbulence conditions and sensitive to the fine-scale nuances in the boundary position, producing an entrained-air boundary line with an average error of 0.33 m on mobile downfacing and 0.5–1.0 m on stationary upfacing data, less than half that of existing algorithmic solutions. The model’s overall annotations had a high level of agreement with the human segmentation, with an intersection-over-union score of 99% for mobile downfacing recordings and 92–95% for stationary upfacing recordings. This resulted in a 50% reduction in the time required for manual edits when compared to the time required to manually edit the line placement produced by the currently available algorithms. Because of the improved initial automated placement, the implementation of the models permits an increase in the standardization and repeatability of line placement.
A new species of Phymatolithon Foslie, P. abuqirensis (Hapalidiaceae, Hapalidiales), from Mediterranean Egypt
Authors: Kittle Ronald P. , Richards Joseph L. , Sauvage Thomas , Gabriel Daniela , Schmidt William E. , Fredericq Suzanne
Published: August 2022

Phymatolithon Foslie is one of the most studied and ecologically important genera of crustose coralline algae (CCA) due to their dominant abundance in various marine ecosystems worldwide. The taxonomy of the genus is complex and has been revised and updated many times based on morphological and molecular analyses. We report on a crustose coralline algal species collected in June 2011 via snorkeling in the subtidal zone along the beach Abu Qir on the Mediterranean coast of Egypt, as part of a larger macroalgal diversity survey in the region. The species shows significant sequence divergences (3.5%–14.8% in rbcL; 2.9%–11% in psbA) from other closely related Phymatolithon taxa. Morpho-anatomically, this species possesses the characters considered collectively diagnostic of the genus Phymatolithon, namely, thalli non-geniculate epithelial cells and non-photosynthetic and domed-shaped meristematic cells, usually as short with progressive elongation of their perithallial derivatives. Based on molecular and morphological analyses, we determined that these specimens encompass a new, distinct species that we herein name Phymatolithon abuqirensis. Including this new species, the total number of described Phymatolithon species found in the Mediterranean Sea is now six.
Numerical study of storm surge-induced coastal inundation in Laizhou Bay, China
Authors: Li Zhao , Li Shuiqing , Hu Po , Mo Dongxue , Li Jian , Du Mei , Yan Jie , Hou Yijun , Yin Baoshu
Published: August 2022

Storm surge inundation can induce great disasters in coastal regions, and Laizhou Bay (LZB), located in the Bohai Sea, is a bay that frequently experiences coastal storm flooding. In this study, we perform a numerical study of the effects of wind and waves on the storm surge-induced coastal inundation in the LZB using the coupled model ADCIRC+SWAN. Two historical typhoons (No. 9216 Typhoon Polly (TY9216) and No. 1909 Typhoon Lekima (TY1909)) are considered, wave effects in terms of wind-wave-induced surface stress and radiation stress are included, and two widely used wind data sources (CFS and ERA5) are used. The results indicate that the total inundation area and average inundation depth in the LZB during TY1909 are 10.70%-19.16% larger than during TY9216, and the CFS wind field reproduces a 14.31%-23.05% more intense inundation simulation than does the ERA5 wind field. The wave-induced surface stress plays the primary role in increasing the inundation area and average depth by up to 11.42%-18.50% and 5.82%-8.75%, respectively, and the wave-induced radiation stress also increases the inundation area and average depth by 3.80%-6.60% and 3.70%-4.57%, respectively. The results highlight the importance of considering wave effects in storm surge-induced coastal inundation simulations, and we demonstrate that the wave effects on the inundation area can be quite sensitive to the choice of wind field source.
Skin temperature change in patients with meibomian gland dysfunction following intense pulsed light treatment
Authors: Yun Jeongseop , Min Ji Sang
Published: August 2022

Purpose

We investigated the change in skin temperature of treated areas during intense pulsed light (IPL) treatment in patients who have meibomian gland dysfunction (MGD) to determine whether there is superficial telangiectatic blood vessel ablation.

Methods

The medical records of 90 patients (90 eyes) with MGD who underwent IPL treatment were reviewed. The patients had undergone IPL treatment four times every 4 weeks. Ocular Surface Disease Index (OSDI) scores, dry eye (DE), and MGD parameters were obtained before the first and after the fourth IPL treatments. The skin temperatures of the upper and lower lids were measured before every IPL treatment.

Results

The skin temperatures of the lower lids were 31.89 ± 0.72°C at the first IPL (IPL#1), 30.89 ± 0.63°C at the second IPL (IPL#2), 30.14 ± 0.95°C at the third IPL (IPL#3), and 29.74 ± 0.87°C at the fourth IPL (IPL#4) treatments. The skin temperatures of upper lids were 32.01 ± 0.69°C at IPL#1, 31.13 ± 0.75°C at IPL#2, 30.34 ± 1.07°C at IPL#3, and 29.91 ± 0.76°C at IPL#4. The skin temperature of the upper and lower lids significantly decreased with every IPL treatment. Schirmer 1 test (ST) result was 12.97 ± 10.22 mm before IPL#1 and 14.45 ± 9.99 mm after IPL#4. Tear break-up time (TBUT) was 3.15 ± 1.38 s before IPL#1 and 5.53 ± 2.34 s after IPL#4. Corneal staining scores (CFS) was 1.61 ± 3.09 before IPL#1 and 0.50 ± 0.78 after IPL#4. Lipid layer thickness (LLT) was 71.88 ± 26.34 nm before IPL#1 and 68.38 ± 24.16 nm after IPL#4. Lid margin abnormality score (LAS) was 1.96 ± 0.62 before IPL#1 and 0.86 ± 0.67 after IPL#4. Meibum expressibility (ME) was 1.67 ± 0.87 before IPL#1 and 1.03 ± 1.67 after IPL#4. Meibum quality (MQ) was 18.18 ± 6.34 before IPL#1 and 10.16 ± 5.48 after IPL#4. OSDI was 35.38 ± 19.97 before IPL#1 and 15.48 ± 34.32 after IPL#4. OSDI scores, DE, and MGD parameters significantly improved after the fourth IPL treatment but not ST and LLT.

Conclusion

Our study showed that the occurrence of superficial telangiectatic vessels were indirectly reduced by the decrease in skin temperature accompanying IPL treatments in patients with MGD.
Applications of rare earth elements in cancer: Evidence mapping and scientometric analysis
Authors: Wang Jinyu , Li Sheng
Published: August 2022

Cancer is one of the most important public health issues worldwide. Radiation therapy (XRT), chemotherapy, and targeted therapy are some of the main types of cancer therapy. Metals are used extensively in cancer diagnosis and therapy, and rare earth elements occupy an important niche in these areas. In recent years, an increasing number of studies have focused on the application of lanthanides in cancer diagnosis and therapy. However, no research has analyzed the current status and future trends of lanthanides in treating cancer. We downloaded data from publications from the Web of Science Core Collection. We used VOSviewer 1.16.16 software and Excel 2016 to analyze literature information, including publication years, journals, countries, institutes, authors, keywords, and co-cited references. A total of 7,849 publications were identified. The first study on the association of rare earth elements with cancer was published in 1945. However, before 1979, the number of publications per year was no more than 10. After 1980, the number of yearly publications increased. The United States was the most productive country (2,726, 34.73%), and the institution with the most frequent contributions was the Chinese Academy of Sciences (211, 2.69%). We observed close collaboration between countries and between institutes. The 7,839 publications were published in 1,579 journals, and Radiology was both the most productive journal (183, 2.33%) and cited journal (5,863 citations). A total of 33,987 authors investigated rare earth elements and cancer. Only 0.45% of the authors published more than 10 publications, and 79.07% of the authors published only one publication. Of the top 10 high-yield authors, seven were from developed countries and three were from China. However, among the top 10 co-cited authors, there was only one high-yield author. The main research topics in the application of lanthanide complex-doped nanomaterials in the diagnosis and treatment of cancer include magnetic resonance imaging contrast agents, photodynamic therapy, anticancer drug delivery, the efficacy and safety of yttrium-90 radioimmunotherapy and chemoembolization for the treatment of HCC, gadolinium magnetic resonance imaging (MRI) contrast agent for cancer diagnosis, and cerium oxide nanoparticles. In recent years, especially since 2016, the research frontiers are emerging in cerium oxide nanoparticles and photodynamic therapy. Studies related to the application of rare earth elements and cancer have significantly increased over the past 20 years. The United States contributed the most articles in the field, followed by China and Germany, and cooperation among countries was frequent. The Chinese Academy of Sciencess, Northwestern University, and Stanford University were the three most productive institutions, and cooperation among institutions was frequent. Many high-quality journals have published relevant research, but there are few highly productive journals.
Use of Andrographis paniculata (Burm.f.) Wall. ex Nees and risk of pneumonia in hospitalised patients with mild coronavirus disease 2019: A retrospective cohort study
Authors: Tanwettiyanont Jeeranan , Piriyachananusorn Napacha , Sangsoi Lilit , Boonsong Benjawan , Sunpapoa Chamlong , Tanamatayarat Patcharawan , Na-Ek Nat , Kanchanasurakit Sukrit
Published: August 2022

Background

Andrographis paniculata (Burm.f.) Wall. ex Nees (AP) has been widely used in Thailand to treat mild COVID-19 infections since early 2020; however, supporting evidence is scarce and ambiguous. Thus, this study aimed to examine whether the use of AP is associated with a decreased risk of pneumonia in hospitalised mild COVID-19 patients.

Materials and methods

We collected data between March 2020 and August 2021 from COVID-19 patients admitted to one hospital in Thailand. Patients whose infection was confirmed by real-time polymerase chain reaction, had normal chest radiography and did not receive favipiravir at admission were included and categorised as either AP (deriving from a dried and ground aerial part of the plant), given as capsules with a total daily dose of 180 mg andrographolide for 5 days or standard of care. They were followed for pneumonia confirmed by chest radiography. Multiple logistic regression was used for the analysis controlling for age, sex, diabetes, hypertension, statin use, and antihypertensive drug use.

Results

A total of 605 out of 1,054 patients (mostly unvaccinated) were included in the analysis. Of these, 59 patients (9.8%) developed pneumonia during the median follow-up of 7 days. The incidence rates of pneumonia were 13.93 (95% CI 10.09, 19.23) and 12.47 (95% CI 8.21, 18.94) per 1,000 person-days in the AP and standard of care groups, respectively. Compared to the standard of care group, the odds ratios of having pneumonia in the AP group were 1.24 (95% CI 0.71, 2.16; unadjusted model) and 1.42 (95% CI 0.79, 2.55; fully adjusted model). All sensitivity analyses were consistent with the main results.

Conclusion

The use of AP was not significantly associated with a decreased risk of pneumonia in mild COVID-19 patients. While waiting for insights from ongoing trials, AP’s use in COVID-19 should be done with caution.
High percentages of peripheral blood T-cell activation in childhood Hodgkin's lymphoma are associated with inferior outcome
Authors: Cai Fengqing , Gao Hui , Yu Zhongsheng , Zhu Kun , Gu Weizhong , Guo Xiaoping , Xu Xiaojun , Shen Hongqiang , Shu Qiang
Published: August 2022

The aims of this study were to investigate the activation of T lymphocytes in peripheral blood from children with Hodgkin's lymphoma (HL) and explore their roles for prognosis in HL. A cohort of 52 newly diagnosed children with HL during the past 10 years was enrolled for analysis in this study. Peripheral blood samples of the patients were acquired before treatment in our hospital, and T-cell subsets were detected by a four-color flow cytometer. CD4+ T cells and CD4+/CD8+ T-cell ratio decreased significantly in patients with HL vs. healthy controls. CD8+ T cells, CD3+CD4+HLA-DR+ T cells, and CD3+CD8+HLA-DR+ T cells increased markedly in patients with HL vs. healthy controls. Receiver-operating characteristic (ROC) curve analysis showed that CD3+CD4+HLA-DR+ T cells and CD3+CD8+HLA-DR+ T cells each distinguished the high-risk group from the low- and intermediate-risk group. The area under the ROC curve for predicting high-risk patients was 0.795 for CD3+CD4+HLA-DR+ T cell and 0.784 for CD3+CD8+HLA-DR+ T cell. A comparison of peripheral blood T-cell subsets that responded differently to therapy showed significantly higher percentages of CD3+CD4+HLA-DR+ T cells and CD3+CD8+HLA-DR+ T cells in patients who achieved complete remission compared to those who did not achieve complete remission. In addition, high percentages of both CD3+CD4+HLA-DR+ T cells and CD3+CD8+HLA-DR+ T cells were associated with inferior event-free survival. Peripheral immune status may be related to disease severity in HL. CD3+CD4+HLA-DR+ T cells and CD3+CD8+HLA-DR+ T cells may be a novel indicator for risk stratification of HL and may be an independent risk factor for inferior outcome in childhood HL.
Soluble angiotensin-converting enzyme 2 association with lipid metabolism
Authors: Nagatomo Izumi , Nakanishi Kaori , Yamamoto Ryohei , Ide Seiko , Ishibashi Chisaki , Moriyama Toshiki , Yamauchi-Takihara Keiko
Published: August 2022

Increased expression of angiotensin-converting enzyme 2 (ACE2) is one of the likely explanations for disease severity in patients with coronavirus disease 2019 (COVID-19). In this study, we aimed to test whether soluble ACE2 (sACE2) levels are correlated to known risk factors of severe COVID-19 including biochemical parameters, body mass index and smoking habits. We cross-sectionally evaluated serum sACE2 levels in obese or tobacco-smoking populations and compared them to those in non-obese and non-smoking healthy participants. Additionally, fibroblast growth factor-21 (FGF21) was investigated as a candidate regulator of sACE2. A total of 220 male participants aged 30–59 years undergoing an annual health checkup were enrolled in this study: 59 obese, 80 smokers, and 81 healthy. Serum sACE2 levels were significantly higher in obese participants but not in tobacco-smoking participants when compared to healthy participants. sACE2 levels were significantly correlated with total cholesterol and triglycerides but not with body mass index. Furthermore, no regulatory relationship was found between FGF21 and sACE2. Lipid metabolism disorders accompanied by upregulation of serum sACE2 may be underlying mechanisms of COVID-19 aggravation and might be a novel breakthrough treatment target.
Bacilloscopy and polymerase chain reaction of slit-skin smears and anti-phenolic glycolipid-I serology for Hansen’s disease diagnosis
Authors: Lima Filipe Rocha , de Paula Natália Aparecida , Simões Mateus Mendonça Ramos , Manso Gabriel Martins da Costa , Albertino Gustavo Sartori , Felisbino Giovani Cesar , Antunes Vanderson Mayron Granemann , Perecin Fernanda André Martins Cruz , Westin Andrezza Telles , Lugão Helena Barbosa , Frade Marco Andrey Cipriani
Published: August 2022

The bacilloscopy of the slit-skin smear (SSS) is the exclusive laboratory test associated with dermato-neurological evaluation for Hansen’s disease (HD) diagnosis; however, it is negative in the majority of PB or primary neural forms. Thus, a PCR technique involving different sequences and target genes has been performed with an aim to increase the sensitivity and specificity of M. leprae identification, especially in patients with low bacillary loads. Additionally, serological assays based on antibody response reflect infection levels and indicate that this could be a simpler, less invasive technique for estimating M. leprae exposure. Serological tests and PCR have been shown to be more sensitive and accurate than the SSS. Our study aimed to measure accuracy and performance among the SSS and PCR of dermal scrapings stored on filter paper and APGL-I serology for diagnosis in HD. A cross-sectional study analyzing the medical records (n = 345) of an HD outpatient-dermatology clinic from 2014 to 2021 was conducted. Accuracy performance parameters, correlation, and concordance were used to assess the value among the SSS, PCR, and APGL-I exams in HD. The SSS presented 24.5% sensitivity, 100% specificity, 37.4% accuracy, and the lowest negative predictive value (21.5%). The PCR assay had 41, 100, and 51% sensitivity, specificity, and accuracy, respectively. PCR and APGL-I serology increased the detection of HD cases by 16 and 20.6%, respectively. PCR was positive in 51.3% of patients when the SSS was negative. The SSS obtained moderate concordance with PCR [k-value: 0.43 (CI: 0.33–0.55)] and APGL-I [k-value: 0.41 (CI: 0.31–0.53)]. A moderate positive correlation was found between the APGL-I index and the bacillary index (r = 0.53; P < 0.0001). Thus, the use of the SSS is a low sensitivity and accuracy method due to its low performance in HD detection. The use of PCR and serological tests allows for a more sensitive and accurate diagnosis of patients.
Application of MinION sequencing as a tool for the rapid detection and characterization of Listeria monocytogenes in smoked salmon
Authors: Azinheiro Sarah , Roumani Foteini , Costa-Ribeiro Ana , Prado Marta , Garrido-Maestu Alejandro
Published: August 2022

Microbial pathogens may be present in different types of foods, and hence the development of novel methods to assure consumers' safeness is of great interest. Molecular methods are known to provide sensitive and rapid results; however, they are typically targeted approaches. In recent years, the advent of non-targeted approaches based on next-generation sequencing (NGS) has emerged as a rational way to proceed. This technology allows for the detection of several pathogens simultaneously. Furthermore, with the same set of data, it is possible to characterize the microorganisms in terms of serotype, virulence, and/ or resistance genes, among other molecular features. In the current study, a novel method for the detection of Listeria monocytogenes based on the “quasimetagenomics” approach was developed. Different enrichment media and immunomagnetic separation (IMS) strategies were compared to determine the best approach in terms of L. monocytogenes sequences generated from smoked salmon samples. Finally, the data generated were analyzed with a user-friendly workflow that simultaneously provided the species identification, serotype, and antimicrobial resistance genes. The new method was thoroughly evaluated against a culture-based approach, using smoked salmon inoculated with L. monocytogenes as the matrix of choice. The sequencing method reached a very low limit of detection (LOD50, 1.2 CFU/ 25 g) along with high diagnostic sensitivity and specificity (100%), and a perfect correlation with the culture-based method (Cohen's k = 1.00). Overall, the proposed method overcomes all the major limitations reported for the implementation of NGS as a routine food testing technology and paves the way for future developments taking its advantage into consideration.
Uptake and transport of antibiotic kasugamycin in castor bean (Ricinus communis L.) seedlings
Authors: Zhang Hongzhen , Zhang Chenghua , Xiang Xiaolong , Zhang Qilun , Zhao Wei , Wei Guoyu , Hu Anlong
Published: August 2022

Kasugamycin (KSM), an aminoglycoside antibiotic, has been widely used for the management of plant diseases, especially for the control of rice blast in Asia. However, its uptake mechanism and transport in plants are still obscure. The castor bean (Ricinus communis L.) seeding, a model plant for phloem transport, was used to study the mechanism of uptake and transport of KSM. Results showed that cotyledon-applied KSM could transport into the phloem and distributed in root and shoot of plant. The temperature, concentration, and pH had significant effects on the uptake of KSM, indicating that the uptake of KSM was mediated by an active carrier system. Compared with the control, competitive inhibitors of sugar transporters D-glucose, D-chiro-inositol, and phloridzin inhibited 71.03%, 67.95%, and 61.73% uptake of KSM, respectively. Energy inhibitor dinitrophenol (DNP) and carbonyl cyanide chlorophenylhydrazone (CCCP) also affected the uptake of KSM, and the inhibition rates were 34.23% and 48.06%. All the results showed that the uptake of KSM was mediated by a sugar transporter, and it could transport from shoot to root in plants via the phloem. The study preliminary elucidated the plant–microbe interactions in the context of the transport of microbial secondary metabolites in plants. It has certain significance for scientific application of antibiotics and biological control of plant diseases and provides theoretical basis for the development of bidirectional transport pesticides.