bluuebunny/crossref_metadata_2025 huggingface dataset:
Factors Influencing Success in Advanced Engineering Mathematics Courses: A Case Study
Authors: Athavale Prashant , Mondal Sumona , Rivera Seema
Published: June 2021

Several studies have been conducted to understand the predictors of academic performance of various levels of high school and undergraduate students as quantified by the grade point average. This study focuses specifically on engineering students as they differ from other undergraduate students in their background and expectations. We focus on quantifying essential predictors of the performance of engineering students in an advanced mathematics course. We collected data from 72 participants recruited from engineering students enrolled in the advanced engineering mathematics (AEM) course in a research university. We chose this course to represent a standard engineering mathematics course covering several essential topics. We consider several factors in our analysis, such as cellphone usage and the academic background, e.g., the academic year, number of minors, and majors, performance in prerequisite courses. We perform several regression analyses to understand the effects of cellphone usage, course schedule, and academic background on performance in the AEM course and its prerequisites. In particular, we use the stepwise regression technique using forward selection and backward elimination procedures. We discovered a few interesting findings in this case study. Firstly, for the participants in this study, we find that the daily average “screen time” on their cellphones is not a statistically significant predictor of student performance. This finding contradicts some prior studies on this participant and may indicate adaption and integration of the technology by the new generation of students in recent years. We also found that the lecturing schedule was not an influential factor for their academic performance. These findings are especially relevant during the COVID-19 pandemic, as they suggest that advanced engineering students have adapted to the use of technology and are flexible concerning lecture schedules. Another unexpected finding is that this study brings new evidence that the number of minors taken by the participants is a negative predictor of their grade in the AEM course. This observation may indicate that course-work from non-major classes may adversely impact their performance in mathematical engineering courses.
The Value of Different Single or Combined Indexes of the Captopril Challenge Test in the Diagnosis of Primary Aldosteronism
Authors: Xiang Qiao , Chen Tao , Yu Kai , Li Yuanmei , Li Qianrui , Tian Haoming , Ren Yan
Published: June 2021

Objective

The result interpretation of the captopril challenge test (CCT) for the diagnosis of primary aldosteronism (PA) is not standardized. Superiorities of different indexes in the CCT have not been fully investigated. We aimed to comprehensively evaluate the value and influence factors of different CCT-associated indexes in the diagnosis of PA.

Methods

We enrolled 312, 85, 179 and 97 patients in the groups of PA, essential hypertension (EH), unilateral PA (UPA) and bilateral PA (BPA), respectively. For each single index investigated, we computed diagnostic estimates including the area under the receiver operating characteristic curve (AUC). We performed pre-specified subgroup analyses to explore influence factors. We assessed the diagnostic value of combined indexes in binary logistic regression models.

Results

Post-CCT aldosterone to renin ratio (ARR) (AUC = 0.8771) and plasma aldosterone concentration (PAC) (AUC = 0.8769) showed high value in distinguishing PA from EH, and their combination (AUC = 0.937) was even superior to either alone. The diagnostic efficacy was moderately high for post-CCT aldosterone to angiotensin II ratio (AA2R) (AUC = 0.834) or plasma renin activity (PRA) (AUC = 0.795) but low for the suppression percentage of PAC (AUC = 0.679). Post-CCT PAC had a significantly higher AUC in the UPA than BPA subgroup (AUC = 0.914 vs 0.827, P<0.05).

Conclusion

We can take post-CCT ARR and PAC altogether into account to distinguish PA from EH, while caution should be taken to interpret CCT results with the suppression percentage of PAC. Post-CCT PAC may perform better to identify the unilateral than bilateral form of PA.
Toward Thing-to-Thing Optical Wireless Power Transfer: Metal Halide Perovskite Transceiver as an Enabler
Authors: Nguyen Dinh Hoa , Matsushima Toshinori , Qin Chuanjiang , Adachi Chihaya
Published: June 2021

This paper proposes a novel conceptual system of optical wireless power transfer (OWPT) between objects, which is different from the existing OWPT systems such that a single device—an optical transceiver—is employed. This optical transceiver, which is capable of both absorbing and emitting light, is fabricated from a metal halide perovskite known for its superior features that can help significantly reduce the whole system size and cost. The proposed system contributes to realizing a thing-to-thing OWPT network, in which surfaces of objects/things are covered by perovskite transceivers (fully or partially), enabling them to wirelessly charge or discharge from the others.
Detection and Sourcing of CDOM in Urban Coastal Waters With UV-Visible Imaging Spectroscopy
Authors: Harringmeyer Joshua P. , Kaiser Karl , Thompson David R. , Gierach Michelle M. , Cash Curtis L. , Fichot Cédric G.
Published: June 2021

Ultraviolet (UV)-visible imaging spectroscopy is an emerging and highly anticipated technology, expected to improve the remote sensing of coastal waters and expand its range of applications. Upcoming NASA satellite missions including PACE and GLIMR will feature imaging spectrometers capable of measuring hyperspectral remote-sensing reflectance (Rrs) across the visible range and well into the near-infrared and ultraviolet domains. The availability of UV reflectance is expected to facilitate the remote sensing of chromophoric dissolved organic matter (CDOM) in optically complex waters, thereby improving coastal water-quality monitoring. Although this argument is well supported by the dominance of CDOM absorption in the UV domain, few studies have directly evaluated the potential advantages conferred by UV reflectance for monitoring CDOM-related coastal water quality. Here, we took advantage of a 6-week wastewater diversion event in Santa Monica Bay, California in 2015 and the availability of Portable Remote Imaging SpectroMeter (PRISM) imagery acquired during the diversion to assess if UV-visible imaging spectroscopy could facilitate the detection of CDOM and help differentiate wastewater effluent-derived CDOM from other sources. A comparison of local empirical algorithms with varying amounts of spectral information implemented on PRISM data showed that incorporating UV Rrs as a predictor significantly improved retrieval of CDOM absorption coefficients (ag). Optimal performance was reached when combining Rrs(365), Rrs(400), and Rrs(700) as predictors of ag in a multiple linear regression. The use of the entire UV-visible spectrum (365–700 nm) in a partial-least-squares regression (PLSR) did not improve retrievals, indicating that a few carefully chosen predictors in the UV-visible domain were sufficient to empirically differentiate CDOM from phytoplankton in coastal waters minimally influenced by sediments or bottom reflectance. Finally, the development of a new fluorescence-based indicator of effluent-derived CDOM (effluent fluorescence ratio, EFR) helped demonstrate the feasibility of remotely detecting CDOM from wastewater. A PLSR-based algorithm using Rrs(365–700) provided reasonable EFR retrievals and successfully identified effluent-derived CDOM at the wastewater outfall when implemented on PRISM imagery. Although further work should investigate the influence of effluent-CDOM fluorescence on Rrs more mechanistically, these results confirmed that UV-visible imaging spectrometers can facilitate coastal CDOM-related water quality monitoring and expand its range of applications.
Nitrogen Addition and Arbuscular Mycorrhizal Fungi Beta Diversity: Patterns and Mechanisms
Authors: Lu Yawen , Liu Xiang , Zhou Shurong
Published: June 2021

Global nitrogen eutrophication, which is disrupting the intimate plant–arbuscular mycorrhizal fungi (AMF) symbiosis, can alter the diversity and physiological functions of soil AMF greatly. However, shifts of beta diversity and the intrinsic patterns of AMF community dissimilarities in response to nitrogen addition remain unclear. Based on a 7-year nitrogen addition experiment in a Qinghai–Tibet Plateau alpine meadow, we detected the changes in soil AMF alpha diversity (richness and genus abundance) and the community composition beta diversity by partitioning the two components of Simpson and nestedness dissimilarities along (turnover) and within (variation) nitrogen addition treatments, and fitted with environmental factor dissimilarities. We found that nitrogen addition decreased AMF richness by decreasing the most dominant AMF genus of Glomus but increasing the abundance of the rare genera. The turnover of the AMF community overall beta diversity along the nitrogen addition gradients was induced by the increased nestedness dissimilarity, while the variation within treatments was explained by both increased Simpson and nestedness dissimilarities, which was significantly correlated with soil pH. Our study found both Simpson and nestedness dissimilarities worked on the AMF community dissimilarity after nitrogen addition and the significant variation within the same treatment, which would be important in the future for predicting global AMF or microbial diversity changes in response to nitrogen eutrophication.
Environmental Stress Selects for Innovations That Drive Vibrio Symbiont Diversity
Authors: Soto William , Nishiguchi Michele K.
Published: June 2021

Symbiotic bacteria in the Vibrionaceae are a dynamic group of γ-Proteobacteria that are commonly found throughout the world. Although they primarily are free-living in the environment, they can be commonly found associated with various Eukarya, either as beneficial or pathogenic symbionts. Interestingly, this dual lifestyle (free-living or in symbiosis) enables the bacteria to have enormous ecological breadth, where they can accommodate a variety of stresses in both stages. Here, we discuss some of the most common stressors thatVibriobacteria encounter when in their free-living state or associated with an animal host, and how some of the mechanisms that are used to cope with these stressors can be used as an evolutionary advantage that increases their diversity both in the environment and within their specific hosts.
Ecology and Evolution of Gall-Inducing Arthropods: The Pattern From the Terrestrial Fossil Record
Authors: Labandeira Conrad C.
Published: June 2021

Insect and mite galls on land plants have a spotty but periodically rich and abundant fossil record of damage types (DTs), ichnotaxa, and informally described gall morphotypes. The earliest gall is on a liverwort of the Middle Devonian Period at 385 million years ago (Ma). A 70-million-year-long absence of documented gall activity ensues. Gall activity resumes during the Pennsylvanian Period (315 Ma) on vegetative and reproductive axial organs of horsetails, ferns, and probably conifers, followed by extensive diversification of small, early hemipteroid galler lineages on seed-plant foliage during the Permian Period. The end-Permian (P-Tr) evolutionary and ecological crisis extinguished most gall lineages; survivors diversified whose herbivore component communities surpassed pre-P-Tr levels within 10 million years in the mid-to late Triassic (242 Ma). During the late Triassic and Jurassic Period, new groups of galling insects colonized Ginkgoales, Bennettitales, Pinales, Gnetales, and other gymnosperms, but data are sparse. Diversifying mid-Cretaceous (125–90 Ma) angiosperms hosted a major expansion of 24 gall DTs organized as herbivore component communities, each in overlapping Venn-diagram fashion on early lineages of Austrobaileyales, Laurales, Chloranthales, and Eurosidae for the Dakota Fm (103 Ma). Gall diversification continued into the Ora Fm (92 Ma) of Israel with another 25 gall morphotypes, but as ichnospecies on a different spectrum of plant hosts alongside the earliest occurrence of parasitoid attack. The End-Cretaceous (K-Pg) extinction event (66 Ma) almost extinguished host–specialist DTs; surviving gall lineages expanded to a pre-K-Pg level 10 million years later at the Paleocene-Eocene Thermal Maximum (PETM) (56 Ma), at which time a dramatic increase of land surface temperatures and multiplying of atmosphericpCO2levels induced a significant level of increased herbivory, although gall diversity increased only after the PETM excursion and during the Early Eocene Climatic Optimum (EECO). After the EECO, modern (or structurally convergent) gall morphotypes originate in the mid-Paleogene (49–40 Ma), evidenced by the Republic, Messel, and Eckfeld floras on hosts different from their modern analogs. During subsequent global aridification, the early Neogene (20 Ma) Most flora of the Czech Republic records several modern associations with gallers and plant hosts congeneric with their modern analogs. Except for 21 gall DTs in New Zealand flora, the gall record decreases in richness, although an early Pleistocene (3 Ma) study in France documents the same plant surviving as an endemic northern Iran but with decreasing associational, including gall, host specificity.
Genetic Determinants for Bacterial Osteomyelitis: A Focused Systematic Review of Published Literature
Authors: Xie Xiaoping , Li Jiangbi , Gu Feng , Zhang Ke , Su Zilong , Wen Qiangqiang , Sui Zhenjiang , Zhou Pengcheng , Yu Tiecheng
Published: June 2021

Background: Osteomyelitis is an inflammatory process characterized by progressive bone destruction. Moreover, chronic bacterial osteomyelitis is regarded as a difficult-to-treat clinical entity due to its long-standing course and frequent infection recurrence. However, the role of genetic factors in the occurrence and development of bacterial osteomyelitis is poorly understood.

Methods: We performed a systematic review to assess the frequency of individual alleles and genotypes of single-nucleotide polymorphisms (SNPs) among patients with bacterial osteomyelitis and healthy people to identify whether the SNPs are associated with the risk of developing bacterial osteomyelitis. Then, gene ontology and Kyoto Encyclopedia of Gene and Genomes analyses were performed to identify the potential biological effects of these genes on the pathogenesis of bacterial osteomyelitis.

Result: Fourteen eligible studies containing 25 genes were analyzed. In this review, we discovered that the SNPs in IL1B, IL6, IL4, IL10, IL12B, IL1A, IFNG, TNF, PTGS2, CTSG, vitamin D receptor (VDR), MMP1, PLAT, and BAX increased the risk of bacterial osteomyelitis, whereas those in IL1RN and TLR2 could protect against osteomyelitis. The bioinformatic analysis indicated that these osteomyelitis-related genes were mainly enriched in inflammatory reaction pathways, suggesting that inflammation plays a vital role in the development of bacterial osteomyelitis. Furthermore, functional notation for 25 SNPs in 17 significant genes was performed using the RegulomeDB and NCBI databases. Four SNPs (rs1143627, rs16944, rs2430561, and rs2070874) had smaller scores from regulome analysis, implying significant biological function.

Conclusion: We systematically summarized several SNPs linked to bacterial osteomyelitis and discovered that these gene polymorphisms could be a genetic factor for bacterial osteomyelitis. Moreover, further large-scale cohort studies are needed to enhance our comprehensive understanding of the development of osteomyelitis to provide earlier individualized preventions and interventions for patients with osteomyelitis in clinical practice.
Non-invasive Prenatal Testing, What Patients Do Not Learn, May Be Due to Lack of Specialist Genetic Training by Gynecologists and Obstetricians?
Authors: Liehr Thomas
Published: June 2021

Platforms for “non-invasive prenatal testing” (NIPT), or also referred to as “non-invasive prenatal screening” (NIPS) have been available for over 10 years, and are the most recent tools available to obtain information about genetic condition(s) of an unborn child. The highly praised advantage of NIPT-screening is that results can provide early hints on the detection of fetal trisomies and gonosomal numerical aberrations as early as the 10th week of gestation onward, without any need for invasive procedures, such as amniocenteses or alternatives. Understandably, the public along with gynecologists and obstetricians eagerly await these early test results. Their general hope for normal (=negative) test results is also justified, as in >95% of the tested cases such an outcome is to be expected. However, pregnant women can be disappointed and confused, particularly regarding the genetic information and proposed care when the results are positive, and these emotions are also common with false-positive and false-negative NIPT results. Finally, such concerns in understanding the advantages and limitations of this routinely ordered screening tool end up at Clinical Geneticists and Genetic counselors. In this review, general background on NIPT, differences of NIPT platforms, advantages and limitations of NIPT, as well as consequences of insufficient counseling before and after NIPT are summarized. To provide comprehensive care in all pregnancies situations, professionals need a careful attitude toward offering NIPT along with specially training and qualifications in counseling for these procedures. Often it is gynecologists and obstetricians who discuss the use of NIPT with patients; however, although these physicians have a highly qualified background and knowledge in their respective specialty area(s), they may lack specific training on the interpretation of NIPT-screening results. These potential knowledge gaps must be closed quickly and comprehensively by the corresponding scientific societies to ensure optimal patient care.
PER1 Is a Prognostic Biomarker and Correlated With Immune Infiltrates in Ovarian Cancer
Authors: Chen Mali , Zhang Lili , Liu Xiaolong , Ma Zhen , Lv Ling
Published: June 2021

Background: Period circadian protein homolog 1 (PER1) is an important component of the biorhythm molecular oscillation system and plays an important part in the development and progression of mammalian cancer. However, the correlations of PER1 with prognosis and tumor-infiltrating lymphocytes in ovarian cancer (OV) remain unclear.

Methods: The Oncomine and TIMER databases were used to examine the expression of PER1 in OV. Kaplan–Meier Plotter and PrognoScan were used to evaluate the relationship between PER1 and prognosis. Kaplan–Meier Plotter was used to analyze the relationships between PER1 and clinicopathological features of OV patients. The relationship between PER1 expression and immune infiltration in OV was investigated using the TIMER database and CIBERSORT algorithm. The STRING database was used to analyze PER1-related protein functional groups, the GeneMANIA online tool was used to analyze gene groups with similar functions to those of PER1, and Network Analyst was used to identify transcription factors that regulate PER1. The correlation between PER1 and immunoinvasion of OV was analyzed using TIMER. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect PER1 expression.

Results: PER1 was differentially expressed in different cancer tissues, and its expression in various OV subtypes was lower than that in normal ovarian tissue. OV patients with low PER1 expression had a reduced overall survival rate. Decreased PER1 expression in stage 1 and stage 1+2 OV patients was related to poor prognosis, while increased PER1 expression in stage 3+4 patients and TP53 mutation were related to poor overall survival and progression-free survival. We identified eight genes whose expression was strongly correlated with that of PER1, as well as four transcription factors that regulate PER1. In OV, PER1 expression levels were positively correlated with infiltration levels of cells including neutrophils, regulatory T cells, and M2 macrophages, and closely related to a variety of immune markers. Reduced expression of PER1 was significantly associated with poor overall survival.

Conclusion: These findings suggest that PER1 could be used as a prognostic biomarker to determine prognosis and immune infiltration in OV patients.
Evaluating Birth Outcomes From a Community-Based Pregnancy Support Program for Refugee Women in Georgia
Authors: Mosley Elizabeth A. , Pratt Michelle , Besera Ghenet , Clarke Lasha S. , Miller Heidi , Noland Tracy , Whaley Bridget , Cochran Jennifer , Mack Amber , Higgins Melinda
Published: June 2021

Refugee women face numerous and unique barriers to sexual and reproductive healthcare and can experience worse pregnancy-related outcomes compared with U.S.-born and other immigrant women. Community-based, culturally tailored programs like Embrace Refugee Birth Support may improve refugee access to healthcare and health outcomes, but empirical study is needed to evaluate programmatic benefits. This community-engaged research study is led by the Georgia Doula Access Working Group, including a partnership between academic researchers, Emory Decatur Hospital nurses, and Embrace. We analyzed hospital clinical records (N = 9,136) from 2016 to 2018 to assess pregnancy-related outcomes of Embrace participants (n = 113) and a comparison group of women from the same community and racial/ethnic backgrounds (n = 9,023). We controlled for race, language, maternal age, parity, insurance status, preeclampsia, and diabetes. Embrace participation was significantly associated with 48% lower odds of labor induction (OR = 0.52, p = 0.025) and 65% higher odds of exclusive breastfeeding intentions (OR = 1.65, p = 0.028). Embrace showed positive but non-significant trends for reduced cesarean delivery (OR = 0.83, p = 0.411), higher full-term gestational age (OR = 1.49, p = 0.329), and reduced low birthweight (OR = 0.77, p = 0.55). We conclude that community-based, culturally tailored pregnancy support programs like Embrace can meet the complex needs of refugee women. Additionally, community-engaged, cross-sector research approaches could ensure the inclusion of both community and clinical perspectives in research design, implementation, and dissemination.
9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Authors: Yan Kexin , Lu Yuxiu , Yan Zhangyong , Wang Yutao
Published: June 2021

Purpose

To identify CD8+T cell-related factors and the co-expression network in melanoma and illustrate the interactions among CD8+T cell-related genes in the melanoma tumor microenvironment.

Method

We obtained melanoma and paracancerous tissue mRNA matrices from TCGA-SKCM and GSE65904. The CIBERSORT algorithm was used to assess CD8+T cell proportions, and the “estimate” package was used to assess melanoma tumor microenvironment purity. Weighted gene co-expression network analysis was used to identify the most related co-expression modules in TCGA-SKCM and GSE65904. Subsequently, a co-expression network was built based on the joint results in the two cohorts. Subsequently, we identified the core genes of the two most relevant modules of CD8+T lymphocytes according to the module correlation, and constructed the signature using ssGSEA. Later, we compared the signature with the existing classical pathways and gene sets, and confirmed the important prognostic significance of the signature in this paper.

Results

Nine co-expressed genes were identified as CD8+T cell-related genes enriched in the cellular response to interferon−gamma process and antigen processing and presentation of peptide antigen. In the low expression level group, inflammation and immune responses were weaker. Single-cell sequencing and immunohistochemistry indicated that these nine genes were highly expressed in CD8+T cells group.

Conclusion

We identified nine-gene signature, and the signature is considered as the biomarker for T lymphocyte response and clinical response to immune checkpoint inhibitors for melanoma
Case Report: Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disorder Masquerading as Multiple Sclerosis: An Under-Recognized Entity?
Authors: Zheng Yang , Cai Meng-Ting , Li Er-Chuang , Fang Wei , Shen Chun-Hong , Zhang Yin-Xi
Published: June 2021

Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease (MOGAD) covers a wide spectrum of manifestations and is defined by the presence of MOG seropositivity. However, in a proportion of patients, there may be an overlap in some of the clinical and radiological manifestations between MOGAD and multiple sclerosis (MS). Being wary of this entity is critical to ensure appropriate therapy. Herein, we present a case with recurrent episodes of short-segment myelitis typical for multiple sclerosis, but later diagnosed as MOGAD by MOG antibody seropositivity. This case, along with previous reports, highlights an increasingly recognized subgroup in MOGAD with initial clinical phenotypes suggestive of MS, but later showing a disease course and therapeutic response compatible with MOGAD. Given the potential overlap of some clinical phenotypes in patients with MS and those with MOGAD, we recommend MOG antibody testing in all patients with recurrent short-segment myelitis, conus medullaris involvement, and those who demonstrated steroid dependence.
The Role of Ageing and Parenchymal Senescence on Macrophage Function and Fibrosis
Authors: Campbell Ross A. , Docherty Marie-Helena , Ferenbach David A. , Mylonas Katie J.
Published: June 2021

In this review, we examine senescent cells and the overlap between the direct biological impact of senescence and the indirect impact senescence has via its effects on other cell types, particularly the macrophage. The canonical roles of macrophages in cell clearance and in other physiological functions are discussed with reference to their functions in diseases of the kidney and other organs. We also explore the translational potential of different approaches based around the macrophage in future interventions to target senescent cells, with the goal of preventing or reversing pathologies driven or contributed to in part by senescent cell load in vivo.
Targeted Transcriptomics of Frog Virus 3 in Infected Frog Tissues Reveal Non-Coding Regulatory Elements and microRNAs in the Ranaviral Genome and Their Potential Interaction with Host Immune Response
Authors: Tian Yun , Khwatenge Collins N. , Li Jiuyi , De Jesus Andino Francisco , Robert Jacques , Sang Yongming
Published: June 2021

Background

Frog Virus 3 (FV3) is a large dsDNA virus belonging to Ranaviruses of family Iridoviridae. Ranaviruses infect cold-blood vertebrates including amphibians, fish and reptiles, and contribute to catastrophic amphibian declines. FV3 has a genome at ~105 kb that contains nearly 100 coding genes and 50 intergenic regions as annotated in its reference genome. Previous studies have mainly focused on coding genes and rarely addressed potential non-coding regulatory role of intergenic regions.

Results

Using a whole transcriptomic analysis of total RNA samples containing both the viral and cellular transcripts from FV3-infected frog tissues, we detected virus-specific reads mapping in non-coding intergenic regions, in addition to reads from coding genes. Further analyses identified multiple cis-regulatory elements (CREs) in intergenic regions neighboring highly transcribed coding genes. These CREs include not only a virus TATA-Box present in FV3 core promoters as in eukaryotic genes, but also viral mimics of CREs interacting with several transcription factors including CEBPs, CREBs, IRFs, NF-κB, and STATs, which are critical for regulation of cellular immunity and cytokine responses. Our study suggests that intergenic regions immediately upstream of highly expressed FV3 genes have evolved to bind IRFs, NF-κB, and STATs more efficiently. Moreover, we found an enrichment of putative microRNA (miRNA) sequences in more than five intergenic regions of the FV3 genome. Our sequence analysis indicates that a fraction of these viral miRNAs is targeting the 3’-UTR regions of Xenopus genes involved in interferon (IFN)-dependent responses, including particularly those encoding IFN receptor subunits and IFN-regulatory factors (IRFs).

Conclusions

Using the FV3 model, this study provides a first genome-wide analysis of non-coding regulatory mechanisms adopted by ranaviruses to epigenetically regulate both viral and host gene expressions, which have co-evolved to interact especially with the host IFN response.
First Insight of Meso- and Bentho-Pelagic Fish Dynamics Around Remote Seamounts in the South Atlantic Ocean
Authors: Campanella Fabio , Collins Martin A. , Young Emma F. , Laptikhovsky Vladimir , Whomersley Paul , van der Kooij Jeroen
Published: June 2021

Seamounts have long been recognised as hotspots for pelagic productivity and diversity in the world’s open ocean habitats. Recent studies have suggested that productivity may vary greatly between different seamounts, depending on complex interactions between the bathymetric features and local oceanography. These processes may enhance local primary production which support elevated biomass at higher trophic levels. In addition to enhancing local biomass, seamounts may also act as aggregative features, attracting pelagic species from the surrounding waters. Such characteristics make seamounts attractive targets for fisheries. However, as these unique habitats are localised and relatively small, they are vulnerable to overexploitation, which may have detrimental impact on the wider region. Mapping and quantitative assessments of the fish biomass at different seamounts are crucial prerequisites to identifying vulnerable seamounts and will aid toward understanding the dynamics of these important ecosystems and their vulnerability to fishing pressures. We used fisheries acoustics during two expeditions in 2018 and 2019, to investigate the distribution and abundance of fish and micronekton on and around five little studied seamounts of Tristan da Cunha, a remote archipelago in the South Atlantic Ocean. The results confirmed increased productivity at the seamounts, compared to the surrounding open ocean with higher acoustic backscatter values, a proxy for biomass, particularly at the shallower (~200 m depth) seamounts. Fish largely dominated the backscatter on most of the seamounts especially over the plateau areas where large densities of prey fish, primarily the mesopelagic Maurolicus inventionis, were detected. Very large aggregations, thought to consist of bentho-pelagic fish, were also observed over the slope of McNish Seamount that resulted in very high biomass estimates. Aggregations of this size and magnitude, have, to our knowledge, never been mapped or quantified on seamounts, using acoustic methods. Specific physical processes, such as enhanced retention and vertical mixing that were identified by an oceanographic model, may be some of the drivers of the enhanced fish biomass detected at McNish. The characteristics of the seamounts observed in this work suggest that these habitats are highly suitable for the presence of large predatory fish that can utilise these areas as their primary habitat or as important foraging grounds.
ConvLSTM-Based Wave Forecasts in the South and East China Seas
Authors: Zhou Shuyi , Xie Wenhong , Lu Yuxiang , Wang Yuanlin , Zhou Yulong , Hui Nian , Dong Changming
Published: June 2021

Numerical wave models have been developed for the wave forecast in last two decades; however, it faces challenges in terms of the requirement of large computing resources and improvement of accuracy. Based on a convolutional long short-term memory (ConvLSTM) algorithm, this paper establishes a two-dimensional (2D) significant wave height (SWH) prediction model for the South and East China Seas trained by WaveWatch III (WW3) reanalysis data. We conduct 24-h predictions under normal and extreme conditions, respectively. Under the normal wave condition, for 6-, 12-, and 24-h forecasting, their correlation coefficients are 0.98, 0.93, and 0.83, and the mean absolute percentage errors are 15, 29, and 61%. Under the extreme condition (typhoon), for 6 and 12 h, their correlation coefficients are 0.98 and 0.94, and the mean absolute percentage errors are 19 and 40%, which is better than the model trained by all the data. It is concluded that the ConvLSTM can be applied to the 2D wave forecast with high accuracy and efficiency.
Effect of Structural Relaxation on the Indentation Size Effect and Deformation Behavior of Cu–Zr–Based Nanoglasses
Authors: Sharma A , Nandam Sree Harsha , Hahn Horst , Prasad K. Eswar
Published: June 2021

In this work, the deformation behavior of as-prepared (AP) and structurally relaxed (SR) Cu–Zr–based nanoglasses (NGs) are investigated using nano- and micro-indentation. The NGs are subjected to structural relaxation by annealing them close to the glass transition temperature without altering their amorphous nature. The indentation load, p, vs. displacement, h, curves of SR samples are characterized by discrete displacement bursts, while the AP samples do not show any of them, suggesting that annealing has caused a local change in the amorphous structure. In both the samples, hardness (at nano- and micro-indentation) decreases with increasing p, demonstrating the indentation size effect. The micro-indentation imprints of SR NGs show evidence of shear bands at the periphery, indicating a heterogeneous plastic flow, while AP NG does not display any shear bands. Interestingly, the shear band density decreases with p, highlighting the fact that plastic strain is accommodated entirely by the shear bands in the subsurface deformation zone. The results are explained by the differences in the amorphous structure of the two NGs.
Immune Response, Viral Shedding Time, and Clinical Characterization in COVID-19 Patients With Gastrointestinal Symptoms
Authors: Yang Huan , Xi Xiangyu , Wang Weimin , Gu Bing
Published: June 2021

Background and Aims: Gastrointestinal (GI) symptoms are frequently observed in coronavirus disease (COVID-19) symptoms. Previous studies have mainly focused on epidemiology and characteristics in patients with GI symptoms, little is known about the roles of the immune response in susceptibility to and severity of infection. Here, we analyzed COVID-19 cases to determine immune response and clinical characteristics in COVID-19 patients with GI symptoms.

Methods: Based on the presence of GI symptoms, 79 patients in Xuzhou were divided into GI and non-GI groups. A retrospective study investigating the clinical characteristics, selected laboratory abnormalities, immune response, treatment, and clinical outcome was performed to compare patients with or without GI symptoms.

Results: Approximately 25% of patients reported at least one GI symptom. Our results showed significantly higher rates of fatigue, increased LDH, increased CK, higher percentage increase neutrophil-to-lymphocyte ratio (NLR), lymphopenia, and bilateral pneumonia in patients with GI symptoms. No significant changes in serum amylase (SAA), immunoglobulin (Ig) G, IgM, C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6), viral shedding time, liver injury, and kidney injury between the two groups were observed. The clinical type on admission of patients with GI symptoms reported significantly higher rates of critical disease type (20 vs. 3.3%; p = 0.033). However, the survival rate did not differ between the two groups.

Conclusions: Increase in total lymphocytes and NLR as well as the elevation of CRP, SAA, PCT, IL-6, CK, and LDH were closely associated with COVID-19 with GI symptoms, implying reliable indicators COVID-19 patients with GI symptoms were more likely to develop into a severe disease.
Persisting Antibody Response to SARS-CoV-2 in a Local Austrian Population
Authors: Ladage Dennis , Rösgen Delia , Schreiner Clemens , Ladage Dorothee , Adler Christoph , Harzer Oliver , Braun Ralf J.
Published: June 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic recently. The prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into the potential for some level of population immunity. In June 2020, we succeeded in testing almost half of the population of an Austrian town with a higher incidence of COVID-19 infection. We performed a follow-up study to reassess the prevalence of SARS-CoV-2-specific IgA and IgG antibodies with 68 participants of the previous study. We found that the prevalence of IgG or IgA antibodies remained remarkably stable, with 84% of our cohort prevailing SARS-CoV-2-specific antibodies (only a slight decrease from 93% 4 months before). In most patients with confirmed COVID-19 seroconversion potentially provides immunity to reinfection. Our results suggest a stable antibody response observed for at least 6 months post-infection with implications for developing strategies for testing and protecting the population.
Comprehensive Analysis of Clinical Trials Registration for Lupus Nephritis Therapy on ClinicalTrials.gov
Authors: Gao Yanfang , Wang Yuhan , Li Rongshan , Zhou Xiaoshuang
Published: June 2021

Objective: Clinical trials are the most effective method for evaluating therapeutic strategies. The purpose of this study was to comprehensively assess the characteristics of trials on lupus nephritis (LN) and provide a reference for LN treatment and research.

Methods: Registered therapeutic trials on drug interventions for LN were obtained from ClinicalTrials.gov up to December 3, 2020. The general characteristics, methodological characteristics, detailed characteristics, investigated drugs, eligibility criteria, and outcome measures of these trials were analyzed.

Results: A total of 126 eligible trials were evaluated, and these trials mainly investigated the initial treatment of adult proliferative LN. Half of the trials enrolled <50 participants, and 70.7% of the trials lasted for 6–24 months. In total, 95.2% of trials adopted an interventional study design. Of intervention trials, 56.6% were in phase 2 or phase 3, 76.7% were randomized, 77.5% employed a parallel assignment, and 41.7% were masked. The eligibility criteria and outcome measures of the included trials varied and involved a variety of indicators. Chemical agents and biologics are the most widely studied immunotherapies, of which mycophenolate mofetil, tacrolimus, and rituximab are the most studied. In addition, some trials studied cell transplantation treatment.

Conclusions: The majority of clinical trials for LN therapy registered on ClinicalTrials.gov investigated the initial treatment of adult proliferative LN, and most of these trials were randomized, parallel assigned, and insufficiently masked interventional trials with small scale, short duration, various eligibility criteria, and outcome measures. We hope that more large-scale, long-term multicenter, and high-quality RCT trials with standardized inclusion criteria/exclusion criteria and treatment effect evaluation systems will be conducted and that more energy and funding will be put into exploring biological products and stem cell therapies. In addition, trials for membranous LN, childhood-onset LN, and maintenance phase LN are needed to establish optimal treatment strategies.
Serum Hepcidin-25 and Risk of Mortality in Patients on Peritoneal Dialysis
Authors: Zhong Zhong , Luo Dan , Luo Ning , Li Bin , Fu Dongying , Fan Li , Li Zhijian , Chen Wei , Mao Haiping
Published: June 2021

Background: Increased serum hepcidin-25 level is associated with excess mortality in hemodialysis patients. However, there is a dearth of published information about its predictive effect for survival in patients on peritoneal dialysis (PD). The purpose of this study is to evaluate the association of serum hepcidin-25 with the risk of mortality in PD patients.

Methods: Serum hepcidin-25 level was measured using an enzyme-linked immunosorbent assay in a prospective cohort study of PD patients with stored serum samples at baseline. Multivariate linear regression model was used to determine clinical characteristics associated with serum hepcidin-25 concentration. We evaluated the relationship between serum hepcidin-25 and all-cause mortality using a Cox proportional hazards model and the relationship between hepcidin-25 and cardiovascular (CV) and infection-related deaths using competing-risks regression models.

Results: In total, 513 PD patients were included in this study. The median serum hepcidin-25 level was 40.9 (17.9–85.9) ng/mL. Body mass index and serum ferritin were positively correlated with serum hepcidin-25 levels. During a median follow-up period of 64.1 months, 122 (24%) patients died, including 61 (50%) CV deaths and 32 (26%) infection-related deaths. In multivariable analysis, patients with the highest tertile of serum hepcidin-25 had a greater risk of all-cause [adjusted hazard ratio (aHR) 1.85, 95% confidence interval (95%CI), 1.14 to 3.00, P = 0.013] and infection-related mortality (adjusted subdistribution hazard ratio [aSHR], 2.61; 95%CI, 1.01 to 6.76, P = 0.049) when compared with those in the second tertile. However, no significant relationship was observed between serum hepcidin-25 and CV mortality.

Conclusions: Higher baseline serum hepcidin-25 level was associated with increased risk for all-cause and infection-related mortality in PD patients.
The Bactericidal Tandem Drug, AB569: How to Eradicate Antibiotic-Resistant Biofilm Pseudomonas aeruginosa in Multiple Disease Settings Including Cystic Fibrosis, Burns/Wounds and Urinary Tract Infections
Authors: Hassett Daniel J. , Kovall Rhett A. , Schurr Michael J. , Kotagiri Nalinikanth , Kumari Harshita , Satish Latha
Published: June 2021

The life-threatening pandemic concerning multi-drug resistant (MDR) bacteria is an evolving problem involving increased hospitalizations, billions of dollars in medical costs and a remarkably high number of deaths. Bacterial pathogens have demonstrated the capacity for spontaneous or acquired antibiotic resistance and there is virtually no pool of organisms that have not evolved such potentially clinically catastrophic properties. Although many diseases are linked to such organisms, three include cystic fibrosis (CF), burn/blast wounds and urinary tract infections (UTIs), respectively. Thus, there is a critical need to develop novel, effective antimicrobials for the prevention and treatment of such problematic infections. One of the most formidable, naturally MDR bacterial pathogens is Pseudomonas aeruginosa (PA) that is particularly susceptible to nitric oxide (NO), a component of our innate immune response. This susceptibility sets the translational stage for the use of NO-based therapeutics during the aforementioned human infections. First, we discuss how such NO therapeutics may be able to target problematic infections in each of the aforementioned infectious scenarios. Second, we describe a recent discovery based on years of foundational information, a novel drug known as AB569. AB569 is capable of forming a “time release” of NO from S-nitrosothiols (RSNO). AB569, a bactericidal tandem consisting of acidified NaNO2 (A-NO2–) and Na2-EDTA, is capable of killing all pathogens that are associated with the aforementioned disorders. Third, we described each disease state in brief, the known or predicted effects of AB569 on the viability of PA, its potential toxicity and highly remote possibility for resistance to develop. Finally, we conclude that AB569 can be a viable alternative or addition to conventional antibiotic regimens to treat such highly problematic MDR bacterial infections for civilian and military populations, as well as the economical burden that such organisms pose.
Characterization and Genomic Analysis of BUCT549, a Novel Bacteriophage Infecting Vibrio alginolyticus With Flagella as Receptor
Authors: Li Jing , Tian Fengjuan , Hu Yunjia , Lin Wei , Liu Yujie , Zhao Feiyang , Ren Huiying , Pan Qiang , Shi Taoxing , Tong Yigang
Published: June 2021

Vibrio alginolyticus is one of the most important of pathogens that can infect humans and a variety of aquatic animals, and it can cause food poisoning and septicemia in humans. Widely used antibiotics are gradually losing their usefulness, and phages are gaining more attention as new antibacterial strategies. To have more potential strategies for controlling pathogenic bacteria, we isolated a novel V. alginolyticus phage BUCT549 from seafood market sewage. It was classified as a new member of the family Siphoviridae by transmission electron microscopy and a phylogenetic tree. We propose creating a new genus for BUCT549 based on the intergenomic similarities (maximum is 56%) obtained from VIRIDIC calculations. Phage BUCT549 could be used for phage therapy due to its stability in a wide pH (3.0–11.0) range and high-temperature (up to 60°C) environment. It had a latent period of 30–40 min and a burst size of 141 PFU/infected bacterium. In the phylogenetic tree based on a terminase large subunit, BUCT549 was closely related to eight Vibrio phages with different species of host. Meanwhile, our experiments proved that BUCT549 has the ability to infect a strain of Vibrio parahaemolyticus. A coevolution experiment determined that three strains of tolerant V. alginolyticus evaded phage infestation by mutating the MSHA-related membrane protein expression genes, which caused the loss of flagellum. This research on novel phage identification and the mechanism of infestation will help phages to become an integral part of the strategy for biological control agents.
Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition
Authors: Tláskal Vojtěch , Baldrian Petr
Published: June 2021

Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.