bluuebunny/crossref_metadata_2025 huggingface dataset:
Estrogen Biosynthesis and Signal Transduction in Ovarian Disease
Authors: Xu Xue-Ling , Huang Zheng-Yuan , Yu Kun , Li Jun , Fu Xiang-Wei , Deng Shou-Long
Published: March 2022

Estrogen mainly binds to estrogen receptors (ERs) to regulate menstrual cycles and reproduction. The expression of ERalpha (ERα), ERbeta (ERβ), and G-protein-coupled estrogen receptor (GPER) mRNA could be detected in ovary, suggesting that they play an important role in estrogen signal transduction in ovary. And many studies have revealed that abnormal expression of estrogen and its receptors is closely related to ovarian disease or malignant tumors. With the continuous development and research of animal models, tissue-specific roles of both ERα and ERβ have been demonstrated in animals, which enable people to have a deeper understanding of the potential role of ER in regulating female reproductive diseases. Nevertheless, our current understanding of ERs expression and function in ovarian disease is, however, incomplete. To elucidate the biological mechanism behind ERs in the ovary, this review will focus on the role of ERα and ERβ in polycystic ovary syndrome (PCOS), ovarian cancer and premature ovarian failure (POF) and discuss the major challenges of existing therapies to provide a reference for the treatment of estrogen target tissue ovarian diseases.
Ulmus davidiana var. japonica Extracts Suppress Lipopolysaccharide-Induced Apoptosis Through Intracellular Calcium Modulation in U937 Macrophages
Authors: Yun Jang-Hyuk , Kim Hyun-Ouk , Jeong Jae-Hun , Min Yerin , Park Kwang-Hyun , Si Chuanling , Choi Sun-Eun
Published: March 2022

This study was aimed to examine the antiapoptotic effect of Ulmus davidiana extracts through regulation of the intracellular cation mobilization in U937 human monocytic cells. To investigate the modulatory effects on lipopolysaccharide-induced apoptosis and the Ca2+ signaling pathway, we measured the levels of intracellular Ca2+ and various protein markers such as Bax, Bcl-2, and PARP. To isolate biopotent molecules, the branches of U. davidiana were processed sequentially using 60% ethanol, supercritical fluid extraction, and ethyl acetate extraction of the remaining samples to obtain single fractions and catechin-glycoside, which is one of the known bioeffector molecules of U. davidiana. Lipopolysaccharide increased intracellular Ca2+ mobilization in U937 cells by inducing transient oscillations and markedly increased Bax and PARP protein expression and decreased Bcl-2 expression. All U. davidiana and catechin-glycoside significantly reduced lipopolysaccharide-induced intracellular Ca2+ mobilization and downregulated apoptosis-related molecules. These results suggest that U. davidiana and catechin-glycoside may be useful for improving immune system function.
Numerical Simulation of Alpine Flash Flood Flow and Sedimentation in Gullies With Large Gradient Variations
Authors: Ding Yufei , Liu Xingnian , Chen Ridong
Published: March 2022

Compared with floods occurring over plains, alpine flash floods are formed over scattered locations with complex terrain and data is often lacking regarding the land topography, flow and sedimentation, causing difficulties when developing mathematical models to predict flash floods. The existing flash flood models mainly focus on the influence of water flow, such as the sharp increase in flow discharge caused by convergence at steep slopes, disregarding the sediment load carried by the water flow. However, under the effect of high-intensity sediment transport, the sedimentation in gullies may lead to surges in water level, causing the phenomenon of “great disasters resulting from minor flooding”. In this study, an efficient and accurate water-sediment coupling model was established with a Godunov-type finite volume method based 2D flow model, and a sediment module and OPENMP parallel computing module were added as well. Firstly, a common gully in mountainous area with large gradient variations was used as a generalized model to explore the impact of sedimentation on the flow field of the gully and compared with the physical model. Then, the alpine flash flood incident in Gengdi Village was simulated with the computer model. The calculation results show that the high-intensity sedimentation significantly increased the magnitude of alpine flash floods. Calculated by this mathematical model, the research results verified that this mathematic model can efficiently, accurately and concisely predict the occurrence of flash floods in gullies with large gradient variations. The model also provides a flow and sediment modeling method that incorporates the effect of high-intensity sediment transport into the traditional flash flood flow model. Thus, this model can be a powerful tool for detecting flash floods.
Sea Turtle Epibiosis: Global Patterns and Knowledge Gaps
Authors: Robinson Nathan J. , Pfaller Joseph B.
Published: March 2022

Competition for space drives many marine propagules to colonize the external surfaces of other marine organisms, a phenomenon known as epibiosis. Epibiosis appears to be a universal phenomenon among sea turtles and an extensive body of scientific literature exists describing sea turtle-epibiont interactions. When viewed in isolation, however, these epibiont “species lists” provide limited insights into the factors driving patterns in taxonomic diversity on a global scale. We conducted an exhaustive literature review to collate information on sea turtle-epibiont interactions into a global database. As studies involving meio- and micro-epibionts, as well as plants, are limited, we exclusively focused on animal, macro-epibionts (>1 mm). We identified 304 studies that included a combined total of 1,717 sea turtle-epibiont interactions involving 374 unique epibiont taxa from 23 Higher Taxon categories (full Phylum or select phyla differentiated by Subphylum/Class/Subclass). We found that loggerhead turtles hosted the highest taxonomic richness (262 epibiont taxa) and diversity, including representative taxa from 21 Higher Taxon categories, followed by hawksbill, green, olive ridley, leatherback, Kemp’s ridley, and flatback turtles. In addition, the taxonomic richness for all turtle species except leatherbacks was projected to increase with additional studies. We found that taxonomic richness not only varies between species but also between well-studied populations of loggerhead turtles. Lastly, we assessed biases in the current literature and identified knowledge gaps for certain species (e.g., Kemp’s ridleys and flatbacks), life stages (e.g., juveniles), habitats (e.g., oceanic habitats), and geographic regions (e.g., central Pacific, east Atlantic, and east Indian oceans). Our hope is that this database will serve as a foundational platform for future studies investigating global patterns of the diversity, ecological function, and evolutionary origins of sea turtle epibiosis.
Comprehensive Transcriptome Analysis of GS3 Near-Isogenic Lines During Panicle Development in Rice (Oryza sativa L.)
Authors: Liang Wenhua , Hu Fengqin , Qi Weicong , Zhao Chunfang , Chen Tao , Wang Cailin , Lv Yuanda , Zhang Yadong
Published: March 2022

Panicle architecture is an important agronomic trait in rice that affects rice yields and quality. The GRAIN SIZE 3 (GS3) locus has been identified as a major quantitative trait locus (QTL) affecting grain length and weight. The current understanding of the function of the GS3 gene, especially concerning the regulatory mechanism of panicle development, is still in its infancy. In this study, we generated GS3 near-isogenic lines (NILs) by successive crossing and backcrossing of TD70 (large grain) with Kasalath (small grain), using Kasalath as the recurrent parent. To identify potential transcription dynamic changes in rice panicle formation and grain shape, we deeply analyzed transcriptional profiles for the NILs (NIL-GS3 and NIL-gs3) at three different panicle developmental stages (S, M, and L). A total of 887, 1,768, and 1,478 differentially expressed genes (DEGs) were identified at stages S, M, and L, respectively. We also found 542 differential expressed long non-coding RNAs (lncRNAs). Co-expression analysis further revealed significant clusters associated with different development periods in NIL-gs3 lines. Gene Ontology and KEGG enrichment analysis revealed G-protein signaling and hormones pathway were successively activated at the M and L stages of NIL-gs3, which indicated activation of the G-protein signaling pathway might trigger the down-streaming hormone signaling transduction. we found that other hormones such ABA, Auxin, CK were significantly enriched in the L stage in the NIL-gs3. We highlighted the synergistic interplay of G-protein and multiple hormones signaling pathways and their essential roles in regulating rice panicle formation and the grain shape. Our study provides an invaluable resource for further molecular mechanistic studies that affect rice grain size and provide new insight for directed selection by marker-assisted backcross breeding.
Localization of Nerve Growth Factor Expression to Structurally Damaged Cartilaginous Tissues in Human Lumbar Facet Joint Osteoarthritis
Authors: Seidel Matthias F. , Netzer Cordula , Chobaz Véronique , Hügle Thomas , Geurts Jeroen
Published: March 2022

Purpose

Nerve Growth Factor (NGF) is a pivotal mediator of chronic pain and plays a role in bone remodelling. Through its high affinity receptor TrkA, NGF induces substance P (SP) as key downstream mediator of pain and local inflammation. Here we analysed NGF, TrkA and SP tissue distribution in facet joint osteoarthritis (FJOA), a major cause of chronic low back pain.

Methods

FJOA specimens (n=19) were harvested from patients undergoing intervertebral fusion surgery. Radiologic grading of FJOA and spinal stenosis, followed by immunohistochemistry for NGF, TrkA and SP on consecutive tissue sections, was performed in ten specimens. Explant cultures (n=9) were used to assess secretion of NGF, IL-6, and SP by FJOA osteochondral tissues under basal and inflammatory conditions.

Results

NGF was predominantly expressed in damaged cartilaginous tissues (80%), occasionally in bone marrow (20%), but not in osteochondral vascular channels. NGF area fraction in cartilage was not associated with the extent of proteoglycan loss or radiologic FJOA severity. Consecutive sections showed that NGF and SP expression was localized at structurally damaged cartilage, in absence of TrkA expression. SP and TrkA were expressed in subchondral bone marrow in both presence and absence of NGF. Low level NGF, but not SP secretion, was detected in four out of eighteen FJOA explants under both basal or inflammatory conditions (n=2 each).

Conclusion

NGF is associated with SP expression and structural cartilage damage in osteoarthritic facet joints, but not with radiologic disease severity. NGF tissue distribution in FJOA differs from predominant subchondral bone expression reported for knee OA.
Inflammatory Microenvironment of Skin Wounds
Authors: Wang Zhen , Qi Fang , Luo Han , Xu Guangchao , Wang Dali
Published: March 2022

Wound healing is a dynamic and highly regulated process that can be separated into three overlapping and interdependent phases: inflammation, proliferation, and remodelling. This review focuses on the inflammation stage, as it is the key stage of wound healing and plays a vital role in the local immune response and determines the progression of wound healing. Inflammatory cells, the main effector cells of the inflammatory response, have been widely studied, but little attention has been paid to the immunomodulatory effects of wound healing in non-inflammatory cells and the extracellular matrix. In this review, we attempt to deepen our understanding of the wound-healing microenvironment in the inflammatory stage by focusing on the interactions between cells and the extracellular matrix, as well as their role in regulating the immune response during the inflammatory stage. We hope our findings will provide new ideas for promoting tissue regeneration through immune regulation.
IFN-γ-Primed hUCMSCs Significantly Reduced Inflammation via the Foxp3/ROR-γt/STAT3 Signaling Pathway in an Animal Model of Multiple Sclerosis
Authors: Ling Xiao , Wang Teng , Han Chao , Wang Pin , Liu Xiaoli , Zheng Chengyun , Bi Jianzhong , Zhou Xiaoyan
Published: March 2022

Our previous study showed that interferon gamma (IFN-γ) might enhance the immunosuppressive properties of mesenchymal stem cells (MSCs) by upregulating the expression of indoleamine 2,3-dioxygenease. Therefore, we treated experimental autoimmune encephalomyelitis (EAE) mice, an animal model of multiple sclerosis (MS), with IFN-γ-primed human umbilical cord MSCs (IFN-γ-hUCMSCs). This study aimed to investigate the potential therapeutic effects of IFN-γ-hUCMSCs transplantation and to identify the biological pathways involved in EAE mice. Firstly, the body weights and clinical scores of EAE mice were recorded before and after treatment. Then, the inflammatory cytokine levels in splenic cell supernatants were quantified by enzyme-linked immunosorbent assay. Finally, the mRNA expression levels of signal transducer and activator of transduction 3 (STAT3), retinoic acid-related orphan receptor gamma t (ROR-γt), and forkhead box P3 (Foxp3) were detected by quantitative reverse transcription polymerase chain reaction. We observed that IFN-γ-hUCMSCs transplantation significantly alleviated body weight loss and decreased the clinical scores of mice. Additionally, IFN-γ-hUCMSCs transplantation could regulate the production of inflammatory cytokines, interleukin (IL)-10 and IL-17, thereby showing more potent treatment efficacy than human umbilical cord MSCs (hUCMSCs) transplantation (p < 0.05). Compared with the EAE group, the expressions of STAT3 and ROR-γt in the transplantation groups were significantly decreased, but the expression of Foxp3 was significantly upregulated in the IFN-γ-hUCMSCs transplantation group compared to that in the hUCMSCs transplantation group. We assumed that IFN-γ-hUCMSCs may affect the balance of T helper 17 (Th17) cells/regulatory T cells (Tregs) through the Foxp3/ROR-γt/STAT3 signaling pathway to reduce the inflammatory response, thereby improving the clinical symptoms of EAE mice. Our study demonstrated that transplantation of IFN-γ-hUCMSCs could reduce inflammation in EAE mice via the Foxp3/ROR-γt/STAT3 signaling pathway, highlighting the therapeutic effects of IFN-γ-hUCMSCs in patients with MS.
Soluble Immune-Related Proteins as New Candidate Serum Biomarkers for the Diagnosis and Progression of Lymphangioleiomyomatosis
Authors: Liu Xuefei , Xu Yanping , Wu Xueying , Liu Yanpu , Wu Qiang , Wu Jialiang , Zhang Henghui , Zhou Min , Qu Jieming
Published: March 2022

Background

The goal of this study was to analyze serum from lymphangioleiomyomatosis (LAM) patients and healthy controls to identify novel biomarkers that could shed light on disease diagnosis and pathogenesis.

Methods

From April 2017 to October 2019, qualified serum samples were obtained to explore differences in 59 immune proteins between 67 LAM patients and 49 healthy controls by the Luminex method.

Results

We characterized 22 serum immune proteins that were differentially expressed in LAM patients compared with healthy people. Fifty-nine proteins were then classified into eight categories according to their biological function, and the results showed that LAM patients displayed significantly higher levels of growth factors (p = 0.006) and lower levels of costimulatory molecules (p = 0.008). LAG-3 was not only likely to have better predictive value than VEGF-D but also showed a significant difference between patients without elevated VEGF-D and healthy people. IL-18 was positively correlated with lung function and six-minute walk test (6MWT) distance and negatively correlated with St. George’s Respiratory Questionnaire (SGRQ) score and pulmonary artery systolic pressure (PASP), which suggested that IL-18 was related to disease severity. PD-1 was significantly different between patients with pneumothorax and/or chylothorax and those without complications.

Conclusion

We performed a large-scale serum immune factor analysis of LAM. Our study provides evidence that LAG-3 may be a novel candidate serum biomarker for the diagnosis of LAM. Future independent validation in prospective studies is warranted.
Anti-IgLON5 Disease – The Current State of Knowledge and Further Perspectives
Authors: Madetko Natalia , Marzec Weronika , Kowalska Agata , Przewodowska Dominika , Alster Piotr , Koziorowski Dariusz
Published: March 2022

Anti-IgLON5 disease is a relatively new neurological entity with the first cases reported in 2014. So far, less than 70 articles on this topic have been published. Due to its unspecific symptomatology, diverse progression, novelty and ambiguous character, it remains a difficulty for both clinical practitioners and scientists. The aim of this review is to summarize the current knowledge concerning anti-IgLON5 disease; mechanisms underlying its cause, symptomatology, clinical progression, differential diagnosis and treatment, which could be helpful in clinical practice and future research.
Ecological Functions of Polychaetes Along Estuarine Gradients
Authors: Martins Amanda Domingues , Barros Francisco
Published: March 2022

Function in ecology can be understood as the role that each component plays in the surrounding environment. It can be studied through the functional traits of organisms and depends on variations of abundance in time and space. Nevertheless, traits should be clearly associated with functions. The functions performed by estuarine macrofauna along estuarine gradients and its variation in time are scarcely studied. We expected that the functional structure (i.e., the set of functions in a site) would not change significantly over estuarine gradients, even with changes in taxonomic composition, since different taxa may have similar traits, allowing the performance of the same functions. We used polychaete assemblages along three tropical estuaries sampled four different times, to test for differences in functional intensity between estuarine salinity zones (Venice system). From a literature search we selected the most frequent ecological functions performed by estuarine benthic assemblages and we explicitly established which polychaete functional traits, or combinations of traits, were directly related to these functions. Nutrient cycling, bioturbation and fragmentation of organic matter were the most frequent functions. We discovered that the last two were present throughout the entire salinity gradient (i.e., along different salinity zones) but with different intensities. The intensity of functions may also show significant variability in time. Nutrient cycling and fragmentation of organic matter showed strong variation among estuarine zones. Using traits explicitly associated with ecological functions is necessary to investigate function and function intensity. Future studies should investigate how precisely traits may alter specific environmental characteristics and ecosystem properties.
Ocean Acidification Affects Volatile Infochemicals Production and Perception in Fauna and Flora Associated With Posidonia oceanica (L.) Delile
Authors: Mutalipassi Mirko , Mazzella Valerio , Schott Matthias , Fink Patrick , Glaviano Francesca , Porzio Lucia , Lorenti Maurizio , Buia Maria Cristina , von Elert Eric , Zupo Valerio
Published: March 2022

Communication among marine organisms are generally based on production, transmission, and interpretation of chemical cues. Volatile organic compounds (VOCs) can act as infochemicals, and ocean acidification can alter their production in the source organisms as well as the interpretation of the information they drive to target organisms. Two diatoms (Cocconeis scutellum var. parva and Diploneis sp.) and a macroalga (Ulva prolifera), all common epiphytes of Posidonia oceanica leaves, were isolated and cultured at two pH conditions (8.2 and 7.7). Their biomass was collected, and the VOCs produced upon wounding were extracted and analyzed using gas chromatography. Chemotactic reactions of invertebrates triggered by VOCs were tested using a static choice experimental arena and a flow-through flume system. Odor choice experiments were performed on several invertebrates associated with P. oceanica meadows to investigate the modification of behavioral responses due to the growth of algae in acidified environments. Complex patterns of behavioral responses were recorded after exposure to algal VOCs. This study demonstrated that a) ocean acidification alters the bouquet of VOCs released by diatoms and macroalgae and b) these compounds act as infochemicals and trigger peculiar behavioral responses in benthic invertebrates. In addition, behavioral responses are species-specific, dose-dependent, and are modified by environmental constraints. In fact, the static diffusion in choice arenas produced different responses as compared to flow-through flume systems. In conclusion, we demonstrate that in future marine environments higher CO2 concentrations (leading to a pH 7.7 by the end of this century) will modify the production of VOCs by micro- and macroalgae as well as the recognition of these infochemicals by marine invertebrates.
Responses of Pearl Oysters to Marine Heatwaves as Indicated by HSP70
Authors: Xu Yang , Liang Jian , He Guixiang , Liu Xiaolong , Yang Ke , Masanja Fortunatus , Deng Yuewen , Zhao Liqiang
Published: March 2022

Marine heatwaves (MHWs) can severely affect bivalves and ecosystems they support. Heat shock proteins (HSPs) are a group of molecular chaperones playing a critical role in the cellular protection and thermo tolerance and thereby constraining physiological responses of marine bivalves to MHWs. Here, we cloned the full-length of HSP70 cDNA from the Pinctada maximal (PmHSP70) and evaluated the expression of PmHSP70 in pearl oysters under acute and repeatedly occurring MHWs conditions. The full-length of PmHSP70 is 2,474 bp, containing an ORF of 1,956 bp encoding 655 amino acids with a predicted molecular weight of 71.23 kDa and 5.26 theoretical isoelectric point. Under the scenario of acute MHWs, the expression of PmHSP70 was significantly highly expressed at 32 and 36°C, and reached the highest at 12 and 72 h, respectively, indicating that pearl oysters rapidly up-regulated the expression of HSP70 in response to MHWs. In the repeatedly occurring MHWs scenario, the thermal response of pearl oysters was alleviated, as best exemplified by significantly lowered expression levels of PmHSP70. Therefore, we speculate that long-term and repeated MHWs can alleviate the thermal stress of pearl oysters. This finding is encouraging and will provide us with meaningful insights into the acclimation of marine bivalves to extreme environments in the future.
Major Expansion of Marine Forests in a Warmer Arctic
Authors: Assis Jorge , Serrão Ester A. , Duarte Carlos M. , Fragkopoulou Eliza , Krause-Jensen Dorte
Published: March 2022

Accelerating warming and associated loss of sea ice are expected to promote the expansion of coastal marine forests (macrophytes) along the massive Arctic coastlines. Yet, this region has received much less attention compared to other global oceans. The available future projections of Arctic macrophytes are still limited to few species and regions, and mostly focused at lower latitude ranges, thus precluding well-informed IPCC impact assessments, conservation and management. Here we aim to quantify potential distributional changes of Arctic intertidal and subtidal brown macroalgae and eelgrass by the year 2100, relative to present. We estimate habitat suitability by means of species distribution modeling, considering changes in seawater temperature, salinity, nutrients and sea ice cover under two greenhouse gas emission scenarios, one consistent with the Paris Agreement (RCP 2.6) and the other representing limited mitigation strategies (RCP 8.5). As data on substrate conditions do not exist, the models were restricted to the depth range supporting Arctic macrophytes (down to 5 m for eelgrass and 30 m for brown macroalgae). Models projected major expansions of Arctic macrophytes between 69,940 and 123,360 km2, depending on the climate scenario, with polar distribution limits shifting northwards by up to 1.5 latitude degrees at 21.81 km per decade. Such expansions in response to changing climate will likely elicit major changes in biodiversity and ecosystem functions in the future Arctic. Expansions are, however, less intense than those already realized over the past century, indicating an overall slowing down despite accelerated warming as habitats become increasingly occupied.
Influence of Surface Heterogeneity on Morphology of Interfacial Nanobubble
Authors: Yang Haichang , Zhang Fanfan , Xing Yaowen , Gui Xiahui , Cao Yijun
Published: March 2022

Gaseous domains formed on solid–liquid interface have attracted scientists’ attentions in recent 2 decades, and the existence of interfacial nanobubble (INB) has been basically confirmed. However, an overall understanding on INB is still lacking. This research studied the influence of surface chemical heterogeneity on the morphology of INB by molecular dynamics simulations technique. The results showed that the gaseous domains could not nucleate on the hydrophilic substrate, while only dense gas layer (DGL) could be observed from the time-averaged density map for homogeneously hydrophobic substrate due to the random moving of INB. If there was a hydrophobic patch on the hydrophilic surface, INB could form on the hydrophobic patch with contact line being pinned at the boundary of the patch. In this case, the contact angle (gas-side) increased with the gas oversaturation degree and decreased with surface hydrophobicity of the patch. For the case that there existed a more hydrophobic patch/site on the hydrophobic surface, the INB could have moved randomly along the hydrophobic surface, but its receding contact line was pinned by the more hydrophobic patch/site. Hence, the INB could only move in the vicinity of this pinning patch/site, so that an INB profile instead of a DGL formed due to the pinning effect, and the apparent contact angle of the INB is significantly lower than the actual one. Throughout this study, the apparent INB we observed from experiments may be different from its instantaneous state and is significantly affected by surface heterogeneity.
The Role of Bias Extension Testing to Guide Forming of Non-Crimp Fabrics
Authors: Jimenez Martin Claudia , Maes Vincent K. , McMahon Turlough , Kratz James
Published: March 2022

The increased production rate targets of the aerospace industry has driven the development of dry fibre processes and biaxial Non-Crimp Fabrics (NCFs). Understanding the forming behaviour of NCFs at scale is key to achieving high quality parts at high rates. The bias extension test is commonly used to characterise the shear behaviour of dry fabrics, for example as input to drape forming models. In industry, it is still often used as a standalone material selection tool as part of initial material selection processes. It is however well known that the boundary conditions of this test are often not representative of full-scale forming trials. A direct comparison with wrinkles observed during a forming experiment is carried out to show that the bias extension test overpredicts wrinkle height. Overall, the bias extension is considered unsuitable on its own for predicting preform quality in an NCF forming process where excess length is generated due to part geometry. If the bias extension is to be used as an NCF material ranking tool, wrinkle height data should be captured alongside force shear data, as shown in this study.
Assessment of Severe Plastic Deformation Processes in Bulk and Nanostructured Metallic Glass
Authors: Singh Shiv Prakash , Ebrahimi Mahmoud , Attarilar Shokouh , Wang Liqiang , Wang Qudong , Djavanroodi Faramarz
Published: March 2022

The metallic glasses are known as amorphous and metastable materials. These materials have superior mechanical properties over crystalline materials with the same chemistry. Continuous efforts were made to improve the properties of metallic glass. The severe plastic deformation (SPD) method is used to improve the ductility of the glass. SPD causes the deformation at the atomic level in the disordered structure of the glass. Many methods are reported, such as cryogenic cycling, high-pressure torsion, and equal channel angular pressing, which are used for the SPD. In recent works on nanostructured metallic glasses, it has been evidenced that some properties, for example, mechanical, thermal, and magnetic, have improved compared to the bulk metallic glass. This paper has reviewed the recent progress in the SPD of the bulk and nanostructured metallic glasses. Different methods for the SPD have been addressed here. The effect of SPD on the properties of metallic glass is deliberated in this paper. Moreover, the challenging tasks of deformation occurrence in the glass and its characterization were considered, trying to develop a sound understanding of SPD in bulk and nanostructured metallic glasses.
Genomic Investigation Reveals a Community Typhoid Outbreak Caused by Contaminated Drinking Water in China, 2016
Authors: Hu Bin , Hou Peibin , Teng Lin , Miao Song , Zhao Lijiang , Ji Shengxiang , Li Tao , Kehrenberg Corinna , Kang Dianmin , Yue Min
Published: March 2022

Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi (S. Typhi) and remains a significant public health burden in developing countries. In China, typhoid fever is endemic with a limited number of reported outbreaks. Recently, Chinese local Center for Disease Prevention and Control is starting to apply whole genome sequencing for tracking the source of outbreak isolates. In this study, we conducted a retrospective investigation into a community outbreak of typhoid fever in Lanling, China, in 2016. A total of 26 S. Typhi isolates were recovered from the drinking water (n = 1) and patients' blood (n = 24) and stool (n = 1). Phylogenetic analysis indicated the persistence of the outbreak isolates in drinking water for more than 3 months. The genomic comparison demonstrated a high similarity between the isolate from water and isolates from patients in their genomic content, virulence gene profiles, and antimicrobial resistance gene profile, indicating the S. Typhi isolate from drinking water was responsible for the examined outbreak. The result of pulsed-field gel electrophoresis (PFGE) revealed these isolates had identical PFGE pattern, indicating they are clonal variants. Additionally, phylogeographical analysis of global S. Typhi isolates suggested the outbreak isolates are evolutionarily linked to the isolates from the United Kingdom and Vietnam. Taken together, this study highlights the drinking water and international travel as critical control points of mitigating the outbreak, emphasizing the necessity of regular monitoring of this pathogen in China.
Transfusion Complications in Thalassemia: Patient Knowledge and Perspectives
Authors: Patterson Sashoy , Singleton Ashley , Branscomb Jane , Nsonwu Vivien , Spratling Regena
Published: March 2022

Chronic transfusion, used to manage clinically significant forms of thalassemia, carries complication risks including iron overload, alloimmunization, and allergic or hemolytic reactions. Dissemination and implementation of evidence-based guidelines for minimizing these risks are complicated by the small numbers and increasing dispersion of the thalassemia population. This elevates patients' role in understanding and communicating with providers about treatment. The present study sought to assess thalassemia patients' knowledge of transfusion, complications, and guidelines; their experience of clinicians' following guidelines; and their perspectives on ways to store and share personal transfusion data. A convenience sample of 32 patients participated in structured interviews. Most, if not all, understood iron overload, chelation therapy, blood typing, and cross-matching. Awareness of each of five of evidence-based transfusion guidelines that were discussed ranged from 72 to 88%. Patients expressed privacy concerns about each of three data storage options, slightly less for a registry than for a wallet card or smartphone app. The registry also avoided concerns that the other options placed extra burden on patients. Recommendations include increased education on the meaning and significance of packed, washed red blood cells, leuko-reduction, and detailed cross-matching, and implementation of a nationwide registry to make transfusion data available to providers anywhere at the point of care. Registry implementation should be sensitive to patients' privacy and security concerns, but also help them appropriately weigh those against safety benefits. These actions could help reduce transfusion complications in thalassemia by improving patient efficacy and increasing adherence to evidence-based guidelines.
Efficacy of Intense Pulsed Light in the Treatment of Recurrent Chalaziosis
Authors: Zhu Yirui , Huang Xiaodan , Lin Lin , Di Mengshu , Chen Ruida , Dong Jilian , Jin Xiuming
Published: March 2022

Purpose

High recurrence rate of chalaziosis and serious side effects of repeated surgical excision may help increase awareness of recurrent and refractory chalaziosis as a serious disorder affecting many aspects of life. This present study was aimed to investigate the efficacy and safety of intense pulse light (IPL) therapy and meibomian gland expression (MGX) in cases of recurrent chalaziosis after excision surgery.

Methods

Forty-two consecutive recurrent chalaziosis cases (35 patients) treated with IPL-MGX were enrolled. All patients initially underwent excision with curettage. One week after lesion excision, IPL-MGX were performed at least 3 times. Another set of age- and sex-matched consecutive cases of recurrent chalaziosis, who received excision with curettage, but went without IPL-MGX treatment, were collected to calculate recurrence rate. Treatment efficacy and safety were measured before IPL-MGX treatment and 1 month after the final treatment.

Results

The majority of patients received 4 sessions of IPL-MGX therapy (20 patients; 57.1%) or 3 sessions of IPL-MGX therapy (10 patients; 28.6%), resulting in a lower recurrence rate of 11.4% compared to that of recurrent chalaziosis without IPL-MGX cases (45.6%, P < 0.001). The NIBUT was significantly prolonged from 3.9 ± 1.8 to 5.1 ± 1.7 s at 4 weeks after the final treatment (P = 0.001). Similarly, mean TMH score improved and was statistically significant when compared with baseline (0.17 ± 0.07 vs. 0.21± 0.09; P = 0.008). Furthermore, meibum quality and expressibility scores significantly improved at 4 weeks following the final treatment (both P < 0.001). Other variables, such as intraocular pressure and visual acuity, remained unaffected following treatment.

Conclusion

The combination of IPL treatment and MGX offers a low risk and effective option in decreasing the recurrence rate of recurrent chalaziosis by improving meibomian gland function. IPL-MGX may be considered for first-line treatment in recurrent or refractory cases post excision.
Ensuring That Fundamentals of Quantitative Microbiology Are Reflected in Microbial Diversity Analyses Based on Next-Generation Sequencing
Authors: Schmidt Philip J. , Cameron Ellen S. , Müller Kirsten M. , Emelko Monica B.
Published: March 2022

Diversity analysis of amplicon sequencing data has mainly been limited to plug-in estimates calculated using normalized data to obtain a single value of an alpha diversity metric or a single point on a beta diversity ordination plot for each sample. As recognized for count data generated using classical microbiological methods, amplicon sequence read counts obtained from a sample are random data linked to source properties (e.g., proportional composition) by a probabilistic process. Thus, diversity analysis has focused on diversity exhibited in (normalized) samples rather than probabilistic inference about source diversity. This study applies fundamentals of statistical analysis for quantitative microbiology (e.g., microscopy, plating, and most probable number methods) to sample collection and processing procedures of amplicon sequencing methods to facilitate inference reflecting the probabilistic nature of such data and evaluation of uncertainty in diversity metrics. Following description of types of random error, mechanisms such as clustering of microorganisms in the source, differential analytical recovery during sample processing, and amplification are found to invalidate a multinomial relative abundance model. The zeros often abounding in amplicon sequencing data and their implications are addressed, and Bayesian analysis is applied to estimate the source Shannon index given unnormalized data (both simulated and experimental). Inference about source diversity is found to require knowledge of the exact number of unique variants in the source, which is practically unknowable due to library size limitations and the inability to differentiate zeros corresponding to variants that are actually absent in the source from zeros corresponding to variants that were merely not detected. Given these problems with estimation of diversity in the source even when the basic multinomial model is valid, diversity analysis at the level of samples with normalized library sizes is discussed.
Interspecies Regulation Between Staphylococcus caprae and Staphylococcus aureus Colonized on Healed Skin After Injury
Authors: Ogura Kohei , Furuya Hiroka , Takahashi Natsuki , Shibata Kana , Endo Maho , Watanabe Shinya , Cui Longzhu , Miyoshi-Akiyama Tohru , Okamoto Shigefumi , Ogai Kazuhiro , Sugama Junko
Published: March 2022

Staphylococcus spp. colonize commensally on the human skin. Some commensal coagulase-negative staphylococci and Staphylococcus aureus are also involved in nosocomial infections. Bacteria were collected from skin healed from pressure injury (PI). After the collection time points, some patients suffered from recurrent PI (RPI). This study analyzed the characteristics of Staphylococcus spp. on healed skin before recurrence between healed skin that suffered from RPI within 6 weeks (RPI group) and healed skin that did not suffer within the duration (non-RPI group) by Staphylococcus spp.-specific sequencing. Of the seven patients in the RPI group, two were dominated by S. aureus and four by Staphylococcus caprae, coagulase-negative human commensal staphylococci in the RPI group. Using mouse models, both S. caprae and S. aureus, but not Staphylococcus epidermidis, colonized on skin healed from injury at significantly higher rates than normal skin. Although subcutaneous injection of S. caprae did not induce lesion formation, the bacterium exhibited high hemolytic activity on human red blood cells. Lesion formation by subcutaneous injection of S. aureus was significantly suppressed in the presence of S. caprae. The hemolytic activity of rabbit blood cells of S. aureus was suppressed by S. caprae, whereas the hemolytic activity of S. caprae was dramatically suppressed by S. aureus. Data indicated that each of the two Staphylococcus spp. suppresses the pathogenicity of the other and that the imbalance between the two is associated with RPI.
Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling
Authors: Frey Beat , Varliero Gilda , Qi Weihong , Stierli Beat , Walthert Lorenz , Brunner Ivano
Published: March 2022

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.
Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion
Authors: Wang Jimin , Konigsberg William H.
Published: March 2022

Almost all DNA polymerases (pols) exhibit bell-shaped activity curves as a function of both pH and Mg2+ concentration. The pol activity is reduced when the pH deviates from the optimal value. When the pH is too low the concentration of a deprotonated general base (namely, the attacking 3′-hydroxyl of the 3′ terminal residue of the primer strand) is reduced exponentially. When the pH is too high the concentration of a protonated general acid (i.e., the leaving pyrophosphate group) is reduced. Similarly, the pol activity also decreases when the concentration of the divalent metal ions deviates from its optimal value: when it is too low, the binding of the two catalytic divalent metal ions required for the full activity is incomplete, and when it is too high a third divalent metal ion binds to pyrophosphate, keeping it in the replication complex longer and serving as a substrate for pyrophosphorylysis within the complex. Currently, there is a controversy about the role of the third metal ion which we will address in this review.
Carbon Dioxide and the Carbamate Post-Translational Modification
Authors: Blake Lynsay I. , Cann Martin J.
Published: March 2022

Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.
Apolipoprotein E Isoform-Dependent Effects on Human Amyloid Precursor Protein/Aβ-Induced Behavioral Alterations and Cognitive Impairments and Insoluble Cortical Aβ42 Levels
Authors: Holden Sarah , Kundu Payel , Torres Eileen R. S. , Sudhakar Reetesh , Krenik Destine , Grygoryev Dmytro , Turker Mitchel S. , Raber Jacob
Published: March 2022

Mice expressing human amyloid precursor protein (APP) containing the dominant Swedish and Iberian mutations (AppNL–F) or also Arctic mutation (AppNL–G–F) show neuropathology and hippocampus-dependent cognitive impairments pertinent to Alzheimer’s disease (AD) in mouse models at 18 and 6 months of age, respectively. Apolipoprotein E, involved in cholesterol metabolism, plays an important role in maintaining the brain. There are three human apolipoprotein E isoforms: E2, E3, and E4. Compared to E3, E4 increases while E2 protects against AD risk. At 6 months of age, prior to the onset of plaque pathology, E3, but not E4, protected against hAPP/Aβ-induced impairments in spatial memory retention in the Morris water maze. However, these earlier studies were limited as hapoE was not expressed outside the brain and E3 or E4 was not expressed under control of an apoE promotor, E2 was often not included, hAPP was transgenically overexpressed and both mouse and hAPP were present. Therefore, to determine whether apoE has isoform-dependent effects on hAPP/Aβ-induced behavioral alterations and cognitive impairments in adult female and male mice at 6 and 18 months of age, we crossed AppNL–G–F and AppNL–F mice with E2, E3, and E4 mice. To distinguish whether genotype differences seen at either time point were due to main effects of hAPP, hapoE, or hAPP × hapoE genetic interactions, we also behavioral and cognitively tested E2, E3, and E4 female and male mice at 6 and 18 months of age. We also compared behavioral and cognitive performance of 18-month-old AppNL–G–F and AppNL–F female and male mice on a murine apoE background along with that of age—and sex-matched C57BL/6J wild-type mice. For many behavioral measures at both time points there were APP × APOE interactions, supporting that apoE has isoform-dependent effects on hAPP/Aβ-induced behavioral and cognitive performance. NL-G-F/E3, but not NL-G-F/E2, mice had lower cortical insoluble Aβ42 levels than NL-G-F/E4 mice. NL-F/E3 and NL-F/E2 mice had lower cortical insoluble Aβ42 levels than NL-F/E4 mice. These results demonstrate that there are apoE isoform-dependent effects on hAPP/Aβ-induced behavioral alterations and cognitive impairments and cortical insoluble Aβ42 levels in mouse models containing only human APP and apoE.