bluuebunny/crossref_metadata_2025 huggingface dataset:
Developing Ecological Flow Needs in a Highly Altered Region: Application of California Environmental Flows Framework in Southern California, USA
Authors: Taniguchi-Quan Kristine T. , Irving Katie , Stein Eric D. , Poresky Aaron , Wildman Jr Richard A. , Aprahamian Amanda , Rivers Cindy , Sharp Grant , Yarnell Sarah M. , Feldman Jamie R.
Published: February 2022

Flow alteration is a pervasive issue across highly urbanized watersheds that can impact the physical and biological condition of streams. In highly altered systems, flows may support novel ecosystems that may not have been found under natural conditions and reference-based environmental flow targets may not be relevant. Moreover, stream impairments such as altered channel morphology may make reference-based environmental flow targets less effective in supporting ecosystem functions. Here, we develop an approach for determining ecological flow needs in highly modified systems to support existing ecological uses utilizing the California Environmental Flows Framework (CEFF). CEFF was established to provide guidance on developing environmental flow recommendations across California’s diverse physical landscape and broad array of management contexts. This paper illustrates the application of CEFF in informing ecologically-based flow restoration in a highly altered region of South Orange County, California. The steps of CEFF were implemented including a stakeholder process to establish goals and provide input throughout the project; identifying the natural ranges of functional flow metrics, or distinct components of the natural flow regime that support ecosystem functions; refining ecological flow needs to account for altered channel morphology and the life history needs of riparian and fish species; and assessing flow alteration to inform management strategies. Key considerations and lessons learned are discussed in the context of developing ecological flow needs in highly altered systems including when non-flow related management actions (i.e., channel rehabilitation) are necessary to achieve ecological goals.
Antibiotic Resistance in Black Sea Microbial Communities
Authors: Prekrasna Ievgeniia , Pavlovska Mariia , Dzhulai Artem , Dykyi Evgen , Alygizakis Nikiforos , Slobodnik Jaroslav
Published: February 2022

Background: Antibiotic resistance genes (ARGs) are considered as pollutants and are found in natural and anthropogenically impacted environments. Distribution of ARGs in marine environment poses a threat to human health turning the water body into a pool for the ARGs’ transmission.

Objectives: A large-scale study of antibiotic resistance in microbial communities has been performed in the Black Sea, both in the coastal and offshore regions.

Methods: The quantitative distribution of the genes responsible for the inactivation of the beta-lactam (blaCMY, blaSHV), vancomycin (vanA, vanB), macrolides (ermB) and colistin (mcr-1) was assessed with real-time quantitative PCR. Concentrations of the antibiotics belonging to the classes of beta-lactam/cephalosporin/carbapenem, macrolides and glycopeptides were determined by LC-ESI-QTOF-MS.

Results: The present study revealed the distribution of antibiotic resistance genes targeting the response to all antibiotics included in our analysis at various locations across the Black Sea. According to the ARGs copy number normalized to the 16S rRNA, vanB (2 × 10−1 ± 1 × 10−1) and blaSHV (4 × 10−2 ± 1 × 10−2) were the most numerous genes, followed by blaCMY (1 × 10−2 ± 3 × 10−3) and mcr-1 (3 × 10−2 ± 2 × 10−2). The less abundant gene was ermB (1 × 10−3 ± 5 × 10−4) and vanA (1 × 10−5 ± 5 × 10−4). The mcr-1, blaCMY and blaSHV had moderate positive correlation with markers of ruminant faecal pollution. The concentration of antibiotics in seawater was below the detection limit. The abundance of all ARGs included in the study was significantly higher (p-value<0.05) within the northwest coastal area when compared to the offshore stations. The results clearly indicate an alarming antibiotic resistance problem in the region and call for a regular monitoring of ARGs abundance in the Black Sea and its major freshwater tributaries.
Evidence of Warming From Long-Term Records of Climate and Permafrost in the Hinterland of the Qinghai–Tibet Plateau
Authors: Zhou Fujun , Yao Miaomiao , Fan Xingwen , Yin Guoan , Meng Xianglian , Lin Zhanju
Published: February 2022

The Qinghai–Tibet Plateau (QTP) is characterized by its extreme climate and dominated by periglacial processes. Permafrost conditions vary greatly, and the recent changes on the QTP are not well known in the hinterland. Here, we examine the changes in climate and permafrost temperatures in several different regions. Climate data were obtained from three weather stations from 1957 to 2019. Annual mean air temperature (Ta) has gradually increased at .031°C/yr–.039°C/yr. Climate warming has been more rapid in the past two decades, particularly during the cold season (November to February). Precipitation has also been slowly increasing during the instrumental record. However, there is pronounced heterogeneity in the seasonal distribution of precipitation, with very little falling between October and April. Ground temperatures and active-layer thickness (ALT) have been investigated over ∼20 years at five sites representative of the hinterland of the QTP. These sites are located along the Qinghai–Tibet Highway, which crosses the permafrost zone and traverses the mountainous area and basin areas. Annual mean ground temperatures within the active layer (Tal ∼ 1 m depth) indicate recent ground warming at all sites, at rates near .05°C/yr. The ALT at five sites has been increasing steadily by 2–9 cm/yr, with an average of 4.6 cm/yr. The temperature near the permafrost table (Tps) has been increasing at .01°C/yr and .06°C/yr, with an average of .03°C/yr. Permafrost temperatures at 15 m depth (Tg) have been increasing by about .01°C/yr–.02°C/yr. The southern boundary (AD site) of the permafrost has warmed the least among the five locations. In high mountainous areas where permafrost temperatures are low (e.g., KLS site), the annual mean Tg has increased by nearly .02°C/yr. The rate of permafrost warming at a basin site (BLH), with relatively high ground temperatures, was approximately .01°C/yr. The GIPL2.0 model simulation results indicate that the annual mean permafrost temperature at 1 m depth at these sites will increase by .6°C–1.8°C in the next 100 years (to 2100) and that ALT will increase by ∼40–100 cm. We also discuss the impacts of permafrost changes on the environment and infrastructure on the QTP. This study provides useful information to understand observed and anticipated permafrost changes in this region, under different shared socioeconomic pathways, which will allow engineers to develop adaptation measures.
Seeing Is Be-Leaving: Perception Informs Migratory Decisions in Sierra Nevada Bighorn Sheep (Ovis canadensis sierrae)
Authors: Berger Danielle J. , German David W. , John Christian , Hart Ronan , Stephenson Thomas R. , Avgar Tal
Published: February 2022

Seasonal migration is a behavioral response to predictable variation in environmental resources, risks, and conditions. In behaviorally plastic migrants, migration is a conditional strategy that depends, in part, on an individual’s informational state. The cognitive processes that underlie how facultative migrants understand and respond to their environment are not well understood. We compared perception of the present environment to memory and omniscience as competing cognitive mechanisms driving altitudinal migratory decisions in an endangered ungulate, the Sierra Nevada bighorn sheep (Ovis canadensis sierrae) using 1,298 animal years of data, encompassing 460 unique individuals. We built a suite of statistical models to partition variation in fall migratory status explained by cognitive predictors, while controlling for non-cognitive drivers. To approximate attribute memory, we included lagged attributes of the range an individual experienced in the previous year. We quantified perception by limiting an individual’s knowledge of migratory range to the area and attributes visible from its summer range, prior to migrating. Our results show that perception, in addition to the migratory propensity of an individual’s social group, and an individual’s migratory history are the best predictors of migration in our system. Our findings suggest that short-distance altitudinal migration is, in part, a response to an individual’s perception of conditions on alterative winter range. In long-distance partial migrants, exploration of migratory decision-making has been limited, but it is unlikely that migratory decisions would be based on sensory cues from a remote target range. Differing cognitive mechanisms underpinning short and long-distance migratory decisions will result in differing levels of behavioral plasticity in response to global climate change and anthropogenic disturbance, with important implications for management and conservation of migratory species.
The Integrated Use of Dendrochronological Data and Paleoecological Records From Northwest European Peatlands and Lakes for Understanding Long-Term Ecological and Climatic Changes—A Review
Authors: Edvardsson Johannes , Helama Samuli , Rundgren Mats , Nielsen Anne Birgitte
Published: February 2022

Our overall understanding of long-term climate dynamics is largely based on proxy data generated from archives such as ice cores, ocean sediments, tree rings, speleothems, and corals, whereas reconstructions of long-term changes in vegetation and associated climate during the Holocene are largely based on paleoecological records from peat and lake sequences, primarily pollen and plant macrofossil data. However, since no proxy can provide a complete picture of the past, it is important to integrate different types of data, and to use methods that can support the paleoecological and paleoclimatic interpretations. Here we review how tree-ring data and dendrochronological approaches can be integrated with stratigraphic records to provide complementary paleoecological and paleoclimatic information. The review includes multiproxy studies in which dendrochronological data have been either compared or integrated with stratigraphic records, mainly pollen records, with the aim to contribute to a better understanding of long-term ecosystem and climate dynamics. We mainly focus on studies from northwest Europe in which tree-ring data and at least one type of paleoecological proxy record from the same site or area has been either compared or integrated. We find that integration of dendrochronological data and paleoecological records from peat and lake sequences is a powerful but underutilized approach to reconstruct long-term ecological and climatic changes. One likely reason for its limited use is the contrasting character of the two categories of data, including their different time resolution and occurrence, making them difficult to integrate. For example, subfossil wood providing annual dendrochronological data usually only occurs sporadically in peat and lake sediments, and the presence/absence of the trees are normally expected to be recorded in the pollen data with multi-decadal or coarser resolution. Therefore, we also discuss methods to compare and integrate dendrochronological and stratigraphic records, as well as the relevant paleoecological and paleoclimatic information provided by dendrochronology, pollen, and peat stratigraphy, with the aim to facilitate new multi-proxy initiatives that will contribute to a better understanding of long-term ecosystem and climate dynamics and thereby a firmer basis for future nature conservation initiatives.
Association Between a TLR2 Gene Polymorphism (rs3804099) and Proteinuria in Kidney Transplantation Recipients
Authors: Fei Shuang , Gui Zeping , Feng Dengyuan , Wang Zijie , Zheng Ming , Chen Hao , Sun Li , Tao Jun , Han Zhijian , Ju Xiaobing , Gu Min , Tan Ruoyun , Li Xinli
Published: February 2022

Background: The occurrence of proteinuria is one of the evaluation indicators of transplanted kidney damage and becomes an independent risk factor for poor prognosis after kidney transplantation. Our research sought to understand these potential associations and detect the underlying impact of single-nucleotide polymorphisms (SNPs) on proteinuria in kidney transplant recipients.

Materials and Methods: There were 200 recipients enrolled in this study, from which blood samples were extracted for SNP mutation–related gene detection. RNA sequencing was performed in kidney tissues after kidney transplantation, and the significantly differentially expressed genes (DEGs) were analyzed between the control group and the proteinuria group. Then, the intersection of genes with SNP mutations and DEGs was conducted to obtain the target genes. Multiple genetic models were used to investigate the relationship between SNPs and proteinuria. In addition, the effect of SNP mutation in the target gene was further validated in human renal podocytes.

Results: According to the sequencing results, 26 significant SNP mutated genes and 532 DEGs were found associated with proteinuria after kidney transplantation. The intersection of SNP mutated genes and DEGs showed that the Toll-like receptor 2 (TLR2) gene was significantly increased in the transplanted renal tissues of patients with proteinuria after kidney transplantation, which was consistent with the results of immunohistochemical staining. Further inheritance model results confirmed that mutations at rs3804099 of the TLR2 gene had significant influence on the occurrence of proteinuria after kidney transplantation. In the in vitro validation, we found that, after the mutation of rs3804099 on the TLR2 gene, the protein expressions of podocalyxin and nephrin in podocytes were significantly decreased, while the protein expressions of desmin and apoptosis markers were significantly increased. The results of flow cytometry also showed that the mutation of rs3804099 on the TLR2 gene significantly increased the apoptotic rate of podocytes.

Conclusion: Our study suggested that the mutation of rs3804099 on the TLR2 gene was significantly related to the generation of proteinuria after kidney transplantation. Our data provide insights into the prediction of proteinuria and may imply potential individualized therapy for patients after kidney transplantation.
Gene Region Association Analysis of Longitudinal Quantitative Traits Based on a Function-On-Function Regression Model
Authors: Li Shijing , Li Shiqin , Su Shaoqiang , Zhang Hui , Shen Jiayu , Wen Yongxian
Published: February 2022

In the process of growth and development in life, gene expressions that control quantitative traits will turn on or off with time. Studies of longitudinal traits are of great significance in revealing the genetic mechanism of biological development. With the development of ultra-high-density sequencing technology, the associated analysis has tremendous challenges to statistical methods. In this paper, a longitudinal functional data association test (LFDAT) method is proposed based on the function-on-function regression model. LFDAT can simultaneously treat phenotypic traits and marker information as continuum variables and analyze the association of longitudinal quantitative traits and gene regions. Simulation studies showed that: 1) LFDAT performs well for both linkage equilibrium simulation and linkage disequilibrium simulation, 2) LFDAT has better performance for gene regions (include common variants, low-frequency variants, rare variants and mixture), and 3) LFDAT can accurately identify gene switching in the growth and development stage. The longitudinal data of the Oryza sativa projected shoot area is analyzed by LFDAT. It showed that there is the advantage of quick calculations. Further, an association analysis was conducted between longitudinal traits and gene regions by integrating the micro effects of multiple related variants and using the information of the entire gene region. LFDAT provides a feasible method for studying the formation and expression of longitudinal traits.
Effects of Dietary Astragalus Polysaccharide Supplementation on the Th17/Treg Balance and the Gut Microbiota of Broiler Chickens Challenged With Necrotic Enteritis
Authors: Song Bochen , Li Peng , Yan Shaojia , Liu Yan , Gao Mingkun , Lv Huiyuan , Lv Zengpeng , Guo Yuming
Published: February 2022

This study aimed to investigate the effects of dietary astragalus polysaccharide (APS) supplementation on the immune function, gut microbiota and metabolism of broiler chickens challenged with necrotic enteritis (NE). Two hundred forty Arbor Acres broiler chicks (one day old) were randomly assigned using a 2 × 2 factorial arrangement into two groups fed different levels of dietary APS (0 or 200 ppm of diet) and two disease challenge groups (control or NE challenged). The results showed that NE infection significantly increased FCR, mortality rate, Th17/Treg (Th17 cells% in blood and ileum, Th17/Treg, IL-17 and IL-17/IL-10 in blood), NO, lysozyme activity and IL-1β in blood, intestinal immune cell proportion and activity (Tc%, Treg% and monocyte phagocytic activity in ileum), intestinal inflammatory cytokines (TLR2, NF-κB, TNF-α and IL- 6) gene expression levels, and the number of Clostridium perfringens in cecum. NE infection significantly reduced body weight gain, thymus index, lymphocyte proliferation activity in blood and ileum, villus height and V/C in jejunum, Th cells% and Mucin2 gene expression in ileum. Dietary APS supplementation significantly increased body weight, feed intake, proportion of immune cells (T cells in blood and Tc, Treg in ileum), lymphocyte proliferation activity, V/C in jejunum, and ZO-1 gene expression in ileum. Dietary APS supplementation significantly reduced FCR and mortality rate, Th17/Treg, Th17%, intestinal pathology scores, intestinal inflammatory cytokine gene expression levels, and the number of Clostridium perfringens in cecum. In addition, broilers challenged with NE significantly increased Staphylococcus and Turicibacter and reduced α diversity of microbiota in ileum. Dietary APS supplementation significantly increased α diversity, Romboutsia, Halomonas, propionic acid, butyric acid, formononetin, taurine, cholic acid and equol and downregulated uric acid, L-arginine and serotonin in ileum. Spearman’s correlation analysis revealed that Romboutsia, Turicibacter, Staphylocpccus, Halomonas, Streptococcus, Escherichia-Shigella, Prevotella, uric acid, L-arginine, jerivne, sodium cholate and cholic acid were related to inflammation and Th17/Treg balance. In conclusion, APS alleviated intestinal inflammation in broilers challenged with NE probably by regulating intestinal immune, Th17/Treg balance, as well as intestinal microbiota and metabolites.
The Ability of Resveratrol to Attenuate Ovalbumin-Mediated Allergic Asthma Is Associated With Changes in Microbiota Involving the Gut-Lung Axis, Enhanced Barrier Function and Decreased Inflammation in the Lungs
Authors: Alharris Esraah , Mohammed Amira , Alghetaa Hasan , Zhou Juhua , Nagarkatti Mitzi , Nagarkatti Prakash
Published: February 2022

Asthma is a chronic respiratory disease highly prevalent worldwide. Recent studies have suggested a role for microbiome-associated gut–lung axis in asthma development. In the current study, we investigated if Resveratrol (RES), a plant-based polyphenol, can attenuate ovalbumin (OVA)-induced murine allergic asthma, and if so, the role of microbiome in the gut–lung axis in this process. We found that RES attenuated allergic asthma with significant improvements in pulmonary functions in OVA-exposed mice when tested using plethysmography for frequency (F), mean volume (MV), specific airway resistance (sRaw), and delay time(dT). RES treatment also suppressed inflammatory cytokines in the lungs. RES modulated lung microbiota and caused an abundance of Akkermansia muciniphila accompanied by a reduction of LPS biosynthesis in OVA-treated mice. Furthermore, RES also altered gut microbiota and induced enrichment of Bacteroides acidifaciens significantly in the colon accompanied by an increase in butyric acid concentration in the colonic contents from OVA-treated mice. Additionally, RES caused significant increases in tight junction proteins and decreased mucin (Muc5ac) in the pulmonary epithelium of OVA-treated mice. Our results demonstrated that RES may attenuate asthma by inducing beneficial microbiota in the gut-lung axis and through the promotion of normal barrier functions of the lung.
Various Subtypes of EGFR Mutations in Patients With NSCLC Define Genetic, Immunologic Diversity and Possess Different Prognostic Biomarkers
Authors: Lei Youming , Wang Kun , Liu Yinqiang , Wang Xuming , Xiang Xudong , Ning Xiangu , Ding Wanbao , Duan Jin , Li Dingbiao , Zhao Wei , Li Yi , Zhang Fujun , Luo Xiaoyu , Shi Yunfei , Wang Ying , Huang Depei , Bai Yuezong , Zhang Hushan
Published: February 2022

Based on data analysis of 9649 Chinese primary NSCLC patients, we calculated the exact proportion of EGFR subtypes in NSCLC and evaluated the TMB level, PD-L1 expression level and tumor immune microenvironment among different EGFR mutation subtypes. Postoperative follow-up data for 98 patients were collected and analyzed. The results showed that several uncommon EGFR mutation subtypes have a higher proportion of TMB-high or strong positive PD-L1 expression than the total EGFR mutation group. In addition, different subtypes have different characteristics related to the immune microenvironment, such as G719 mutations being associated with more CD8+ T cell infiltration into tumors; except for EGFR 19del, CD8+ T cell infiltration into tumors of other EGFR mutation subtypes were similar to that of wildtype EGFR. Moreover, follow-up results revealed that components of the immune microenvironment have prognostic value for NSCLC patients, with different prognostic biomarkers for NSCLC patients with and without EGFR mutations. These results suggest that patients with different EGFR mutations need to be treated differently. The prognosis of NSCLC patients may be assessed through components of tumor immune microenvironment, and ICIs treatment may be considered for those with some uncommon EGFR mutation subtypes.
Baicalein—A Potent Pro-Homeostatic Regulator of Microglia in Retinal Ischemic Injury
Authors: Pan Li , Sze Ying Hon , Yang Menglu , Tang Jing , Zhao Siming , Yi Irvin , To Chi-Ho , Lam Chuen , Chen Dong Feng , Cho Kin-Sang , Do Chi-Wai
Published: February 2022

Retinal ischemia is a common cause of many retinal diseases, leading to irreversible vision impairment and blindness. Excessive neuroinflammation, including microglial activation and T-cell responses, has been identified as a critical factor associated with neurodegeneration in retinal ischemia. Baicalein is a natural flavonoid reported to have broad anti-inflammatory and neuroprotective bioactivities. Herein, the effects of baicalein on microglia activation in vitro and in vivo were investigated. We found that baicalein exhibited robust anti-inflammatory effect on cultured human and mouse microglia, as demonstrated by decreased induction of pro-inflammatory cytokines and the phosphorylation of phosphoinositide 3-kinase (PI3K) and nuclear factor kappa B (NFκB). Proteomic analysis further unraveled baicalein’s effect on modulating IL-17 signaling pathways and its upstream regulator IL-1β. Intravitreal administration of baicalein in the mouse model of retinal ischemia/reperfusion (I/R) injury attenuated microglial activation and retinal T-cell infiltration, particularly the T helper 17 cells. Additionally, baicalein was shown to exert neuroprotective effects by significantly reducing the retinal ganglion cell (RGC) loss after I/R injury, leading to an improved retinal function and spatial vision. These results suggest that baicalein, a natural flavonoid, acts as a negative regulator of activated microglia and immune responses both in vitro and in vivo, effectively alleviating neurodegeneration in retinal I/R injury. This finding indicates that baicalein could be a potential therapeutic agent against currently incurable degenerative retinal diseases.
Diverse Macrophages Constituted the Glioma Microenvironment and Influenced by PTEN Status
Authors: Zhou Fengqi , Shi Qinyu , Fan Xiao , Yu Ruilei , Wu Zhiqiang , Wang Binbin , Tian Wei , Yu Tianfu , Pan Minhong , You Yongping , Wang Yingyi
Published: February 2022

The glioma immune microenvironment (GIM), consisting of glioma cells, stromal cells, and immune cells, accelerates the initiation, development, immune evasion, chemoresistance, and radioresistance of glioblastoma (GBM), whereas the immunosuppressive mechanisms of GBM have not been thoroughly elucidated to date. The glioma data downloaded from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases were used to evaluate the composition of tumor-infiltrating immune cells (TICs) by the CIBERSORT algorithm. RNA-seq datasets from the TCGA and CGGA were used to analyze the relationship between immune scores with patients’ characteristics and TICs, which showed higher ratios of tumor-inhibiting/tumor-promoting signatures (M2/M1 macrophages) along with higher immune scores. The distribution of TICs among different glioma patients and the correlation with hazard ratio (HR) analysis suggested that M2 macrophages were abundant in malignant gliomas and indicated an unfavorable prognosis. We further analyzed TCGA cases with available mutation and copy-number alteration information, which showed that the status of PTEN could influence the immune microenvironment of glioma patients. Tissue microarrays of 39 GBM patients were carried out to confirm the clinical significance of PTEN and macrophage markers. We found that the high expression of PTEN was associated with a more extended survival period of glioma patients, positively correlated with M2 macrophages and negatively with M1 macrophages. Transwell and flow cytometry analyses demonstrated that PTEN status could prevent M1 to M2 polarization and M2 macrophage recruitment of gliomas in vitro. The newly discovered immunoregulatory activity of PTEN opens innovative avenues for investigations relevant to counteracting cancer development and progression.
Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Andaman Sea of Thailand
Authors: Chavanich Suchana , Kusdianto Heru , Kullapanich Chitrasak , Jandang Suppakarn , Wongsawaeng Doonyapong , Ouazzani Jamal , Viyakarn Voranop , Somboonna Naraporn
Published: February 2022

As seawater temperature rises, repeated thermal bleaching events have negatively affected the reefs of the Andaman Sea for over decades. Studies on the coral-associated microbial diversity of prokaryotes and microbial eukaryotes (microbiome) in healthy and bleached corals are important to better understand the coral holobionts that involved augmented resistance to stresses, and this information remains limited in the Andaman Sea of Thailand. The present study thereby described the microbiomes of healthy (unbleached) and bleached colonies of four prevalent corals, Acropora humilis, Platygyra sp., Pocillopora damicornis, and Porites lutea, along with the surrounding seawater and sediments, that were collected during a 2016 thermal bleaching event, using 16S and 18S rRNA genes next-generation sequencing (NGS). Both prokaryotic and eukaryotic microbes showed isolated community profiles among sample types (corals, sediment, and seawater) [analysis of similarities (ANOSIM): p = 0.038 for prokaryotes, p < 0.001 for microbial eukaryotes] and among coral genera (ANOSIM: p < 0.001 for prokaryotes and microbial eukaryotes). In bleached state corals, we found differences in microbial compositions from the healthy state corals. Prevalent differences shared among bleached coral genera (shared in at least three coral genera) included a loss of reported coral-beneficial microbes, such as Pseudomonadales, Alteromonadales, and Symbiodinium; meanwhile an increase of putative coral-pathogenic Malassezia and Aspergillus. This difference could affect carbon and nitrogen availability for coral growth, reflective of a healthy or bleached state. Our findings in part supported previously microbial dysbiosis knowledge of thermal bleaching coral microbiomes around South East Asia marine geography, and together ongoing efforts are to support the understanding and management of microbial diversity to reduce the negative impacts to corals in massive thermal bleaching events.
Invasive Dreissena Mussel Coastal Transport From an Already Invaded Estuary to a Nearby Archipelago Detected in DNA and Zooplankton Surveys
Authors: Larson Courtney E. , Barge Jonathan T. , Hatzenbuhler Chelsea L. , Hoffman Joel C. , Peterson Greg S. , Pilgrim Erik M. , Wiechman Barry , Rees Christopher B. , Trebitz Anett S.
Published: February 2022

Coastal waters of Lake Superior are generally inhospitable to the establishment of invasive Dreissena spp. mussels (both Dreissena polymorpha and Dreissena bugensis). Dreissena have inhabited the Saint Louis River estuary (SLRE; largest commercial port in the Laurentian Great Lakes) for over three decades, but only in the last few years have small colonies been found in the Apostle Islands National Lakeshore (APIS, an archipelago situated 85 km to the east of SLRE) A 2017 survey determined a low abundance Dreissena spatial distribution in APIS, with the largest colonies on the north and west islands which suggested potential veliger transport from the SLRE via longshore currents. Our objective in this study was to determine if Dreissena veligers are transported by currents at low densities along the south shore of Lake Superior from the SLRE to APIS. To do so, we used both eDNA (water and passive substrate samples) and zooplankton collection methods at eight sites evenly spaced between the SLRE and APIS with three sampling times over five weeks. Dreissena veligers were consistently detected along the south shore, although at low abundances (veligers per m3 range = 0–690, median = 8), and for every 1 km increase in distance from the SLRE, both veliger counts and water eDNA copy numbers decreased on average by 5 and 7%, respectively. D. polymorpha (suited to estuary habitats) was detected two times more than D. bugensis (better suited to deep-lake habitats). There was not a trend in the veliger size distribution along the south shore, and temperature and calcium concentrations fluctuated around the threshold for Dreissena veliger and adult development, averaging 11.0°C and 14.8 ppm, respectively. Three zooplankton taxa representative of the estuary community–Daphnia retrocurva, Diaphanosoma birgei, and Mesocyclops copepodites–decreased as the distance from the SLRE increased mirroring Dreissena veliger abundance patterns. Findings represent multiple sources of evidence of a propagule “conveyor belt” for Dreissena along the south shore of Lake Superior. We conclude that veligers are functioning as a propagule, using coastal currents to spread from the point of invasion, thereby traversing coastal habitat previously reported as inhospitable to distant habitats suitable for colonization.
Advanced Design and Fabrication of Islamic Tile Ceramic Wall Tiles With Indonesian Batik Patterns Using Artistic CAD/CAM and 3D Printing Technology
Authors: Anggoro P. W. , Yuniarto T. , Bawono B. , Setyohadi D. B. , Felasari S. , Widyanarka O. D. W. , Tauviqirrahman M. , Jamari J. , Bayuseno A. P.
Published: February 2022

The ceramic tile wall is a decorative element used inside restaurants, museums, hotels, aristocratic residences, and places of worship. It plays a critical role in the development of a structure with strong personality and unique qualities by providing relief patterns specific to history or era. The demand for distinctive ornamental wall ceramics that can be mass produced with precision and accuracy has been a challenge for numerous ceramic enterprises in Indonesia, which have historically relied on the skills of artistic professionals in a handmaking process. The purpose of this research was therefore to develop and apply a ceramic tile design process that integrates computer design and fabrication methods with traditional ceramic production techniques. Using the ArtCAM 2015R2 software, photos of batik and Islamic themes were effectively converted into a 2.5D computer-aided design model. Additive manufacturing technology was then used in conjunction with Objet30 Pro 3D printer to precisely produce master molds with Islamic nuances such as puzzle and floral patterns, then conventional ceramic fabrication technology was employed to produce ceramic tiles using these molds. By combining computer-aided design and rapid prototyping technologies, a variety of exact and detailed Islamic decorative ceramic wall tiles were produced with dimensional accuracies within 2.00 mm. Furthermore, the proposed approach demonstrated a 90% reduction in design-to-production time from to 10–12 months to roughly 1–1.5 months.
Association Between Ischemic Stroke and COVID-19 in China: A Population-Based Retrospective Study
Authors: Wang Minghuan , Zhang Han , He Yuqin , Qin Chuan , Liu Xingyuan , Liu Mingqian , Tang Yuhong , Li Xiaohua , Yang Guang , Tang Yingxin , Liang Gang , Xu Shabei , Wang Wei
Published: February 2022

Background and Purpose

To investigate the effect of prior ischemic stroke on the outcomes of patients hospitalized with coronavirus disease 2019 (COVID-19), and to describe the incidence, clinical features, and risk factors of acute ischemic stroke (AIS) following COVID-19.

Methods

In this population-based retrospective study, we included all the hospitalized positive patients with COVID-19 at Wuhan City from December 29, 2019 to April 15, 2020. Clinical data were extracted from administrative datasets coordinated by the Wuhan Health Commission. The propensity score matching and multivariate logistic regression analyses were used to adjust the confounding factors.

Results

There are 36,358 patients in the final cohort, in which 1,160 (3.2%) had a prior stroke. After adjusting for available baseline characteristics, patients with prior stroke had a higher proportion of severe and critical illness and mortality. We found for the first time that the premorbid modified Rankin Scale (MRS) grouping (odds ratio [OR] = 1.796 [95% CI 1.334–2.435], p < 0.001) and older age (OR = 1.905 [95% CI 1.211–3.046], p = 0.006) imparted increased risk of death. AIS following COVID-19 occurred in 124 (0.34%) cases, and patients with prior stroke had a much higher incidence of AIS (3.4%). Logistic regression analyses confirmed an association between the severity of COVID-19 with the incidence of AIS. COVID-19 patients with AIS had a significantly higher mortality compared with COVID-19 patients without stroke and AIS patients without COVID-19.

Conclusions

Coronavirus disease 2019 patients with prior stroke, especially those with the higher premorbid MRS or aged, have worse clinical outcomes. Furthermore, COVID-19 increases the incidence of AIS, and the incidence is positively associated with the severity of COVID-19.
Novel Therapies in Takayasu Arteritis
Authors: Regola Francesca , Uzzo Martina , Toniati Paola , Trezzi Barbara , Sinico Renato Alberto , Franceschini Franco
Published: February 2022

Takayasu Arteritis (TAK) is a large-vessel vasculitis that preferentially involves the aorta and its primary branches. Cardiac involvement is frequent in TAK and is a major determinant of the patient's outcome. Glucocorticoids (GC) are the mainstay of therapy for TAK, with high doses of GC effective to induce remission. However, relapses are common and lead to repeated and prolonged GC treatments with high risk of related adverse events. Potential GC toxicity is a major concern, especially because patients with TAK are young and need to be treated for several years, often for the whole life. Conventional immunosuppressive drugs are used in patients with severe manifestations but present some limitations. New therapeutic approaches are needed for patients with refractory disease or contraindications to conventional therapies. Fortunately, major progress has been made in understanding TAK pathogenesis, leading to the development of targeted biotherapies. In particular, IL-6 and TNF-α pathways seems to be the most promising therapeutic targets, with emerging data on Tocilizumab and TNF inhibitors. On the other hand, new insights on JAK-Inhibitors, Rituximab, Ustekinumab and Abatacept have been explored in recent studies. This review summarizes the emerging therapies used in TAK, focusing on the most recent studies on biologics and analyzing their efficacy and safety.
Has the OSCE Met Its Final Demise? Rebalancing Clinical Assessment Approaches in the Peri-Pandemic World
Authors: Malau-Aduli Bunmi S. , Jones Karina , Saad Shannon , Richmond Cassandra
Published: February 2022

The Objective Structured Clinical Examination (OSCE) has been traditionally viewed as a highly valued tool for assessing clinical competence in health professions education. However, as the OSCE typically consists of a large-scale, face-to-face assessment activity, it has been variably criticized over recent years due to the extensive resourcing and relative expense required for delivery. Importantly, due to COVID-pandemic conditions and necessary health guidelines in 2020 and 2021, logistical issues inherent with OSCE delivery were exacerbated for many institutions across the globe. As a result, alternative clinical assessment strategies were employed to gather assessment datapoints to guide decision-making regarding student progression. Now, as communities learn to “live with COVID”, health professions educators have the opportunity to consider what weight should be placed on the OSCE as a tool for clinical assessment in the peri-pandemic world. In order to elucidate this timely clinical assessment issue, this qualitative study utilized focus group discussions to explore the perceptions of 23 clinical assessment stakeholders (examiners, students, simulated patients and administrators) in relation to the future role of the traditional OSCE. Thematic analysis of the FG transcripts revealed four major themes in relation to participants' views on the future of the OSCE vis-a-vis other clinical assessments in this peri-pandemic climate. The identified themes are (a) enduring value of the OSCE; (b) OSCE tensions; (c) educational impact; and (d) the importance of programs of assessment. It is clear that the OSCE continues to play a role in clinical assessments due to its perceived fairness, standardization and ability to yield robust results. However, recent experiences have resulted in a diminishing and refining of its role alongside workplace-based assessments in the new, peri-pandemic programs of assessment. Future programs of assessment should consider the strategic positioning of the OSCE within the context of utilizing a range of tools when determining students' clinical competence.
Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China
Authors: Zhao Teng , Dang Yun-qi , Wang Ao-nan , Gao He-ting , Zhang Heng-duan , Xing Dan , Li Bo-qi , Li Yong-jiu , Liu Zhu , Li Chun-xiao
Published: February 2022

Objective

Wild animal pathogen surveillance will help to understand the next possible pandemic in advance. Rodents, which have close contact with humans, are generally regarded as a key factor for zoonotic disease control. Given the variation in rodent virus composition in diverse ecologies, we conducted a study on the viral infection of rodents of diverse species in different typical environments of Heilongjiang and Yunnan Provinces, located in northeastern and southwestern China, respectively.

Methods

Viral metagenomics sequencing and bioinformatic analysis were performed to determine the different distributions of rodent-borne viruses in typical environments of Heilongjiang and Yunnan Provinces, China. After viral culture and PCR confirmation, genomic and phylogenetic quantitative analysis was performed on the detected hantaviruses (HVs) and Beilong viruses (BeiVs).

Results

Nineteen rodents from three species and 35 rodents from five species of rodents were collected from Heilongjiang and Yunnan Provinces, respectively. Although the number and number of species of rodents trapped in the northeast were fewer than those in the southwest, viruses annotated from rodents in Heilongjiang were more diverse than those in Yunnan. Rodents carried 22 virus families in Heilongjiang and 13 families in Yunnan. Sequences assembled from Rattus norvegicus were annotated to the M, L, and S segments of HV, and all were clustered within the Seoul-type hantavirus (SEOV). There were 2 (R81Q, S698T) and 4 (K153R, M168I, I279S, and R1790K) amino acid site substitutions in M and L compared with the versions in the most homologous strains. Two BeiV isolates from Rattus norvegicus were closely related to BeiV from brown rats in Hong Kong, with high bootstrap values of >90% in the N segment and > 95% in the L segment. They were further clustered with Tailam virus, forming a distinct group in Paramyxoviridae.

Conclusion

The rodents from Heilongjiang and Yunnan located in northeast and southwest China, respectively, had different viral spectra, and only one-third (10/32) of virus families were detected in both areas. The predominant viruses were HV and BeiV in the Hantaviridae and Paramyxoviridae families, respectively. Rodent-borne viruses in the same species were similar in different geographic disparate areas owing to their similar close contact with human habitats and human activities. Additional attention should be given to the monitoring of neglected rodent-borne viruses, especially opportunistic viruses with currently low loads.
Optimization, Characteristics, and Functions of Alkaline Phosphatase From Escherichia coli
Authors: Dong Yachao , Xia Yandong , Yin Jie , Zhou Diao , Sang Yidan , Yan Sufeng , Liu Qingshu , Li Yaqi , Wang Leli , Zhao Ying , Chen Cang , Huang Qiuyun , Wang Ying , Abbasi Muhammad Nazeer , Yang Huansheng , Wang Chuni , Li Jianzhong , Tu Qiang , Yin Jia
Published: February 2022

Weaning of piglets could increase the risk of infecting with Gram-negative pathogens, which can further bring about a wide array of virulence factors including the endotoxin lipopolysaccharide (LPS). It is in common practice that the use of antibiotics has been restricted in animal husbandry. Alkaline phosphatase (AKP) plays an important role in the detoxification and anti-inflammatory effects of LPS. This study investigated the protective effects of AKP on intestinal epithelial cells during inflammation. Site-directed mutagenesis was performed to modulate the AKP activity. The enzyme activity tests showed that the activity of the DelSigD153G-D330N mutants in B. subtilis was nearly 1,600 times higher than that of the wild-type AKP. In this study, an in vitro LPS-induced inflammation model using IPEC-J2 cells was established. The mRNA expression of interleukin-(IL-) 6, IL-8, and tumor necrosis factor-α (TNF-α) were extremely significantly downregulated, and that of ASC amino acid transporter 2 (ASCT-2), zonula occludens protein-1 (ZO-1), and occludin-3 (CLDN-3) were significantly upregulated by the DelSigD153G-D330N mutant compared with LPS treatment. This concludes the anti-inflammatory role of AKP on epithelial membrane, and we are hopeful that this research could achieve a sustainable development for the pig industry.
Overexpression of a “Candidatus Liberibacter Asiaticus” Effector Gene CaLasSDE115 Contributes to Early Colonization in Citrus sinensis
Authors: Du Meixia , Wang Shuai , Dong Liting , Qu Rongrong , Zheng Lin , He Yongrui , Chen Shanchun , Zou Xiuping
Published: February 2022

Huanglongbing (HLB), caused by “Candidatus liberibacter asiaticus” (CaLas), is one of the most devastating diseases in citrus but its pathogenesis remains poorly understood. Here, we reported the role of the CaLasSDE115 (CLIBASIA_05115) effector, encoded by CaLas, during pathogen-host interactions. Bioinformatics analyses showed that CaLasSDE115 was 100% conserved in all reported CaLas strains but had sequence differences compared with orthologs from other “Candidatus liberibacter.” Prediction of protein structures suggested that the crystal structure of CaLasSDE115 was very close to that of the invasion-related protein B (IalB), a virulence factor from Bartonella henselae. Alkaline phosphatase (PhoA) assay in E. coli further confirmed that CaLasSDE115 was a Sec-dependent secretory protein while subcellular localization analyses in tobacco showed that the mature protein of SDE115 (mSDE115), without its putative Sec-dependent signal peptide, was distributed in the cytoplasm and the nucleus. Expression levels of CaLasSDE115 in CaLas-infected Asian citrus psyllid (ACP) were much higher (∼45-fold) than those in CaLas-infected Wanjincheng oranges, with the expression in symptomatic leaves being significantly higher than that in asymptomatic ones. Additionally, the overexpression of mSDE115 favored CaLas proliferation during the early stages (2 months) of infection while promoting the development of symptoms. Hormone content and gene expression analysis of transgenic plants also suggested that overexpressing mSDE115 modulated the transcriptional regulation of genes involved in systemic acquired resistance (SAR) response. Overall, our data indicated that CaLasSDE115 effector contributed to the early colonization of citrus by the pathogen and worsened the occurrence of Huanglongbing symptoms, thereby providing a theoretical basis for further exploring the pathogenic mechanisms of Huanglongbing disease in citrus.
Biosurfactant: A Next-Generation Tool for Sustainable Remediation of Organic Pollutants
Authors: Sharma Neha , Lavania Meeta , Lal Banwari
Published: February 2022

Petroleum hydrocarbons are energy resources that majorly contribute pollutants to the environment. These pollutants may cause serious health issues, and hence, for the regulation of these contaminants, the development of sustainable alternative technologies has been considered, without causing further harm to the environment. One such alternative is biosurfactants (having low toxicity and being biodegradable) produced by numerous microbial species that have a tendency to remediate organic pollutants. Biosurfactants are amphiphilic compounds that are categorized into two types based on their molecular mass. Biosurfactants can be generated extracellularly or as a part of the cell membrane of microorganisms (bacteria, fungi, and algae). This review provides a detailed view of the types of biosurfactants, their properties, and the mechanism involved in the degradation of oil spills.