bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference
Authors: Zhou Yongsong , Jin Xiaoye , Wu Buling , Zhu Bofeng
Published: February 2022

Ancestry informative markers (AIMs) are useful to infer individual biogeographical ancestry and to estimate admixture proportions of admixed populations or individuals. Although a growing number of AIM panels for forensic ancestry origin analyses were developed, they may not efficiently infer the ancestry origins of most populations in China. In this study, a set of 52 ancestry informative deletion/insertion polymorphisms (AIDIPs) were selected with the aim of effectively differentiate continental and partial Chinese populations. All of the selected markers were successfully incorporated into a single multiplex PCR panel, which could be conveniently and efficiently detected on capillary electrophoresis platforms. Genetic distributions of the same 50 AIDIPs in different continental populations revealed that most loci showed high genetic differentiations between East Asian populations and other continental populations. Population genetic analyses of different continental populations indicated that these 50 AIDIPs could clearly discriminate East Asian, European, and African populations. In addition, the 52 AIDIPs also exhibited relatively high cumulative discrimination power in the Eastern Han population, which could be used as a supplementary tool for forensic investigation. Furthermore, the Eastern Han population showed close genetic relationships with East Asian populations and high ancestral components from East Asian populations. In the future, we need to investigate genetic distributions of these 52 AIDIPs in Chinese Han populations in different regions and other ethnic groups, and further evaluate the power of these loci to differentiate different Chinese populations.
Statistical Approach of the Role of the Conserved CSB-PiggyBac Transposase Fusion Protein (CSB-PGBD3) in Genotype-Phenotype Correlation in Cockayne Syndrome Type B
Authors: Damaj-Fourcade Rayanne , Meyer Nicolas , Obringer Cathy , Le May Nicolas , Calmels Nadège , Laugel Vincent
Published: February 2022

Cockayne syndrome is a rare condition that encompasses a very wide spectrum of clinical severity. Mutations upstream of a transposon called PiggyBac Transposable Element Derived 3 in intron 5 of the CSB/ERCC6 gene could bring about less severe forms than mutations located downstream of that transposon insertion. Our aim was to study genotype-phenotype correlation by determining whether the position of each mutation of the CSB/ERCC6 gene has an impact on the phenotype. A hundred and forty-seven Cockayne patients, who had two pathogenic mutations in the CSB/ERCC6 gene and for whom clinical data was available, were retrospectively selected and included in the study. Data analysis was performed under the Bayesian paradigm. Analysis of the proportion of the different subtypes of Cockayne syndrome according to the position of the mutations was done using an ordinal logistic regression model. Using a vague prior, the risk of developing a more severe subtype when exposed to 2 mutations downstream compared to 2 mutations upstream was 2.0 [0.9–4.5]. Estimations varied through the sensitivity analysis. We could reasonably conclude that a relationship between the number of downstream mutations and the Cockayne syndrome clinical expression exists but it is still difficult to give a precise estimate of this relationship. The real effect could be more complex that the one described in the initial model and other genetic factors might be taken into consideration together with the mutation site to better explain clinical variability.
Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications
Authors: Shang Yanjie , Ren Lipin , Zhang Xiangyan , Li Yi , Zhang Changquan , Guo Yadong
Published: February 2022

The Calliphoridae (blowflies) are significant for forensic science, veterinary management, medical science, and economic issues. However, the phylogenetic relationships within this family are poorly understood and controversial, and the status of the Calliphoridae has been a crucial problem for understanding the evolutionary relationships of the Oestroidea these years. In the present study, seven mitochondrial genomes (mitogenomes), including six calliphorid species and one Polleniidae species, were sequenced and annotated. Then a comparative mitochondrial genomic analysis among the Calliphoridae is presented. Additionally, the phylogenetic relationship of the Calliphoridae within the larger context of the other Oestroidea was reconstructed based on the mitogenomic datasets using maximum likelihood (ML) and Bayesian methods (BI). The results suggest that the gene arrangement, codon usage, and base composition are conserved within the calliphorid species. The phylogenetic analysis based on the mitogenomic dataset recovered the Calliphoridae as monophyletic and inferred the following topology within Oestroidea: (Oestridae (Sarcophagidae (Calliphoridae + (Polleniidae + (Mesembrinellidae + Tachinidae))))). Although the number of exemplar species is limited, further studies are required. Within the Calliphoridae, the Chrysomyinae were recovered as sister taxon to Luciliinae + Calliphorinae. Our analyses indicated that mitogenomic data have the potential for illuminating the phylogenetic relationships in the Oestroidea as well as for the classification of the Calliphoridae.
How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation
Authors: Dessalles Renaud , Pan Yunbei , Xia Mingtao , Maestrini Davide , D’Orsogna Maria R. , Chou Tom
Published: February 2022

The specificity of T cells is that each T cell has only one T cell receptor (TCR). A T cell clone represents a collection of T cells with the same TCR sequence. Thus, the number of different T cell clones in an organism reflects the number of different T cell receptors (TCRs) that arise from recombination of the V(D)J gene segments during T cell development in the thymus. TCR diversity and more specifically, the clone abundance distribution, are important factors in immune functions. Specific recombination patterns occur more frequently than others while subsequent interactions between TCRs and self-antigens are known to trigger proliferation and sustain naive T cell survival. These processes are TCR-dependent, leading to clone-dependent thymic export and naive T cell proliferation rates. We describe the heterogeneous steady-state population of naive T cells (those that have not yet been antigenically triggered) by using a mean-field model of a regulated birth-death-immigration process. After accounting for random sampling, we investigate how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells, or “clone counts”). By using reasonable physiological parameter values and fitting predicted clone counts to experimentally sampled clone abundances, we show that realistic levels of heterogeneity in immigration rates cause very little change to predicted clone-counts, but that modest heterogeneity in proliferation rates can generate the observed clone abundances. Our analysis provides constraints among physiological parameters that are necessary to yield predictions that qualitatively match the data. Assumptions of the model and potentially other important mechanistic factors are discussed.
Single-Cell Transcriptomics Reveals Peripheral Immune Responses in Anti-Synthetase Syndrome-Associated Interstitial Lung Disease
Authors: Zhu Lili , Cao Zhong , Wang Shiyao , Zhang Changshui , Fang Lei , Ren Yanhong , Xie Bingbing , Geng Jing , Xie Sheng , Zhao Ling , Ma Li , Dai Huaping , Wang Chen
Published: February 2022

Objective

Interstitial lung diseases (ILDs) secondary to anti-synthetase syndrome (ASS) greatly influence the prognoses of patients with ASS. Here we aimed to investigate the peripheral immune responses to understand the pathogenesis of this condition.

Methods

We performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from 5 patients with ASS-ILD and 3 healthy donors (HDs). Flow cytometry of PBMCs was performed to replenish the results of scRNA-seq.

Results

We used scRNA-seq to depict a high-resolution visualization of cellular landscape in PBMCs from patients with ASS-ILD. Patients showed upregulated interferon responses among NK cells, monocytes, T cells, and B cells. And the ratio of effector memory CD8 T cells to naïve CD8 T cells was significantly higher in patients than that in HDs. Additionally, Th1, Th2, and Th17 cell differentiation signaling pathways were enriched in T cells. Flow cytometry analyses showed increased proportions of Th17 cells and Th2 cells, and decreased proportion of Th1 cells in patients with ASS-ILD when compared with HDs, evaluated by the expression patterns of chemokine receptors.

Conclusions

The scRNA-seq data analyses reveal that ASS-ILD is characterized by upregulated interferon responses, altered CD8 T cell homeostasis, and involvement of differentiation signaling pathways of CD4 T cells. The flow cytometry analyses show that the proportions of Th17 cells and Th2 cells are increased and the proportion of Th1 cells is decreased in patients with ASS-ILD. These findings may provide foundations of novel therapeutic targets for patients with this condition.
Immune-Mediated Cerebellar Ataxia Associated With Neuronal Surface Antibodies
Authors: Jia Yu , Li Mingyu , Li Dawei , Zhang Mengyao , Wang Huifang , Jiao Lidong , Huang Zhaoyang , Ye Jing , Liu Aihua , Wang Yuping
Published: February 2022

Background

Immune-mediated cerebellar ataxias (IMCAs) are common in paraneoplastic cerebellar degeneration (PCD) but rarely occur in patients with neuronal surface antibodies (NSAbs). Although cerebellar ataxias (CAs) associated with anti-NMDAR and anti-CASPR2 have been reported in a few cases, they have never been studied systematically. This study aimed to analyze the characteristics of anti-NSAbs-associated CAs.

Methods

A retrospective investigation was conducted to identify patients using the keywords IMCAs and NSAbs. We collected the clinical data of 14 patients diagnosed with anti-NSAbs-associated CAs.

Results

The median age was 33 years (16-66), and the male-to-female ratio was 4:3. Nine were positive for NMDAR-Ab, two for LGI1-Ab, two for CASPR2-Ab, and one for AMPA2R-Ab. CAs were initial symptoms in three patients and presented during the first two months of the disease course (10 days on average) among the rest of the patients. After the immunotherapy, two cases were free from symptoms, and eight cases recovered satisfactorily (10/14, 71.4%). Compared with other causes of IMCAs, anti-NSAbs were more frequently associated with additional extra-cerebellar symptoms (85.7%), mostly seizures (78.6%) and mental abnormalities (64.3%). In the CSF analysis, pleocytosis was detected in ten patients (71.4%) and oligoclonal bands (OB) were observed in nine patients (64.3%). Moreover, compared with PCD and anti-GAD65-Ab-associated CAs, anti-NSAbs-associated CAs showed a better response to immunotherapy.

Conclusion

IMCAs are rare and atypical in autoimmune encephalitis with neuronal surface antibodies. Compared with other forms of IMCAs, more symptoms of encephalopathy, a higher rate of pleocytosis and positive OB in CSF, and positive therapeutic effect were the key features of anti-NSAbs-associated CAs.
The Role of HMGB1 in Rheumatic Diseases
Authors: Dong Yuanji , Ming Bingxia , Dong Lingli
Published: February 2022

HMGB1, a highly conserved non-histone nuclear protein, is widely expressed in mammalian cells. HMGB1 in the nucleus binds to the deoxyribonucleic acid (DNA) to regulate the structure of chromosomes and maintain the transcription, replication, DNA repair, and nucleosome assembly. HMGB1 is actively or passively released into the extracellular region during cells activation or necrosis. Extracellular HMGB1 as an alarmin can initiate immune response alone or combined with other substances such as nucleic acid to participate in multiple biological processes. It has been reported that HMGB1 is involved in various inflammatory responses and autoimmunity. This review article summarizes the physiological function of HMGB1, the post-translational modification of HMGB1, its interaction with different receptors, and its recent advances in rheumatic diseases and strategies for targeted therapy.
Mucosal Defense Against Giardia at the Intestinal Epithelial Cell Interface
Authors: Solaymani-Mohammadi Shahram
Published: February 2022

Human giardiasis, caused by the protozoan parasite Giardia duodenalis (syn. Giardia lamblia, Giardia intestinalis, Lamblia intestinalis), is one of the most commonly-identified parasitic diseases worldwide. Chronic G. duodenalis infections cause a malabsorption syndrome that may lead to failure to thrive and/or stunted growth, especially in children in developing countries. Understanding the parasite/epithelial cell crosstalk at the mucosal surfaces of the small intestine during human giardiasis may provide novel insights into the mechanisms underlying the parasite-induced immunopathology and epithelial tissue damage, leading to malnutrition. Efforts to identify new targets for intervening in the development of intestinal immunopathology and the progression to malnutrition are critical. Translating these findings into a clinical setting will require analysis of these pathways in cells and tissues from humans and clinical trials could be devised to determine whether interfering with unwanted mucosal immune responses developed during human giardiasis provide better therapeutic benefits and clinical outcomes for G. duodenalis infections in humans.
Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation
Authors: Korte Benjamin G. , Giese Morgan A. , Ramakrishnan Gayathri , Ma Stella , Bennin David , Rindy Julie , Dewey Colin N. , Huttenlocher Anna
Published: February 2022

Neutrophils in the tumor microenvironment exhibit altered functions. However, the changes in neutrophil behavior during tumor initiation remain unclear. Here we used Translating Ribosomal Affinity Purification (TRAP) and RNA sequencing to identify neutrophil, macrophage and transformed epithelial cell transcriptional changes induced by oncogenic RasG12Vin larval zebrafish. We found that transformed epithelial cells and neutrophils, but not macrophages, had significant changes in gene expression in larval zebrafish. Interestingly, neutrophils had more significantly down-regulated genes, whereas gene expression was primarily upregulated in transformed epithelial cells. The antioxidant, thioredoxin (txn), a small thiol that regulates reduction-oxidation (redox) balance, was upregulated in transformed keratinocytes and neutrophils in response to oncogenic Ras. To determine the role of thioredoxin during tumor initiation, we generated a zebrafish thioredoxin mutant. We observed an increase in wound-induced reactive oxygen species signaling and neutrophil recruitment in thioredoxin-deficient zebrafish. Transformed keratinocytes also showed increased proliferation and reduced apoptosis in thioredoxin-deficient larvae. Using live imaging, we visualized neutrophil behavior near transformed cells and found increased neutrophil recruitment and altered motility dynamics. Finally, in the absence of neutrophils, transformed keratinocytes no longer exhibited increased proliferation in thioredoxin mutants. Taken together, our findings demonstrate that tumor initiation induces changes in neutrophil gene expression and behavior that can impact proliferation of transformed cells in the early tumor microenvironment.
A Hypothesis Regarding Neurosecretory Inhibition of Stress Mediators by Colchicine in Preventing Stress-Induced Familial Mediterranean Fever Attacks
Authors: Korkmaz Cengiz , Cansu Döndü Üsküdar , Cansu Güven Barıs
Published: February 2022

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disease characterized by recurrent episodes of fever and serositis. Colchicine (Col) has a crucial role in the prevention of amyloidosis and FMF attacks. The effect of Col on innate immune cells is based on the inhibition of the microtubule system. The microtubule system is also very important for neurosecretory functions. The inhibitory effect of Col on neurosecretory functions is an overlooked issue. Considering that the neuroimmune cross-talk process plays a role in the development of inflammatory diseases, the effect of Col on the neuronal system becomes important. FMF attacks are related to emotional stress. Therefore, the effect of Col on stress mediators is taken into consideration. In this hypothetical review, we discuss the possible effects of Col on the central nervous systems (CNS) and peripheral nervous systems (PNS) in light of mostly experimental study findings using animal models. Studies to be carried out on this subject will shed light on the pathogenesis of FMF attacks and the other possible mechanisms of action of Col apart from the anti-inflammatory features.
Insights Gained and Future Outlook From scRNAseq Studies in Autoimmune Rheumatic Diseases
Authors: Zheng Zihan , Chang Ling , Li Jingyi , Wu Yuzhang , Chen Guangxing , Zou Liyun
Published: February 2022

Autoimmune rheumatic diseases have a major impact on public health as one of the most common morbidities, and many of these disorders involve both local and systemic manifestations with severe consequences for patient health and quality of life. However, treatment options for many of these diseases remain inadequate for a substantial portion of patients, and progress in developing novel therapeutics has been slow. This lack of progress can be largely attributed to an insufficient understanding of the complex mechanisms driving pathogenesis. Recently, the emergence of single-cell RNA sequencing (scRNAseq) has offered a powerful new tool for interrogating rheumatic diseases, with the potential to assess biological heterogeneity and individual cell function in rheumatic diseases. In this review, we discuss the major insights gained from current scRNAseq interrogations of human rheumatic diseases. We highlight novel cell populations and key molecular signatures uncovered, and also raise a number of hypotheses for follow-up study that may be of interest to the field. We also provide an outlook into two emerging single-cell technologies (repertoire sequencing and spatial transcriptomics) that have yet to be utilized in the field of rheumatic diseases, but which offer immense potential in expanding our understanding of immune and stromal cell behavior. We hope that scRNAseq may serve as a wellspring for the generation and interrogation of novel hypotheses regarding autoreactive lymphocytes and tissue infiltration patterns, and help uncover novel avenues for therapeutic development.
A Comparative Study of Machine Learning Techniques for Multi-Class Classification of Arboviral Diseases
Authors: Tabosa de Oliveira Thomás , da Silva Neto Sebastião Rogério , Teixeira Igor Vitor , Aguiar de Oliveira Samuel Benjamin , de Almeida Rodrigues Maria Gabriela , Sampaio Vanderson Souza , Endo Patricia Takako
Published: February 2022

Among the neglected tropical diseases (NTDs), arboviral diseases present a significant number of cases worldwide. Their correct classification is a complex process due to the similarity of symptoms and the lack of tests in Brazil countryside is a big challenge to be overcome. Given this context, this paper proposes a comparative study of machine learning techniques for multi-class classification of arboviral diseases, which considers three classes: DENGUE, CHIKUNGUNYA and OTHERS, and uses clinical and socio-demographic data from patients. Feature selection techniques were also used for selecting the best subset of attributes for each model. Gradient boosting machines presented the best result in the metrics and a good subset of attributes for daily usage by the physicians that resulted in a 76.58% recall on the CHIKUNGUNYA class.
LAMP Detection of Virus-Derived DNA of Zika Virus in Vector Mosquito
Authors: Aonuma Hiroka , Iizuka Itoe , Li Jian-Chiuan , Ote Manabu , Tajima Shigeru , Saijo Masayuki , Chen Chun-Hong , Kanuka Hirotaka
Published: February 2022

Detection of infectious viruses in mosquitoes is one of the prerequisite measures to monitor the prevalence of vector-borne viral diseases. Determining which mosquitoes are currently infected with arboviruses such as Zika, dengue, and chikungunya virus is not yet practical in endemic areas due to multiple causes including the difficulty of dealing with the virus’ unstable RNA. In this study, instead of handling viral RNA, virus-derived DNA (vDNA) was introduced as a target template for nucleic acid amplification. In combination with loop-mediated isothermal amplification (LAMP), we examined a LAMP-based vDNA detection assay (vDNA-LAMP) targeting Zika virus (ZIKV). The vDNA-LAMP reaction amplifying part of the NS3 region of ZIKV successfully detected its vDNA from crude DNA purified from artificially infected cultured cells and Aedes mosquitoes. This rapid, simple, and versatile method may provide a promising field-surveillance method for arbovirus circulation via vector mosquitoes.
The Spiekeroog Coastal Observatory: A Scientific Infrastructure at the Land-Sea Transition Zone (Southern North Sea)
Authors: Zielinski Oliver , Pieck Daniela , Schulz Jan , Thölen Claudia , Wollschläger Jochen , Albinus Michelle , Badewien Thomas H. , Braun Axel , Engelen Bert , Feenders Christoph , Fock Swaantje , Lehners Carola , Lõhmus Kertu , Lübben Andrea , Massmann Gudrun , Meyerjürgens Jens , Nicolai Helmo , Pollmann Thomas , Schwalfenberg Kai , Stone Jana , Waska Hannelore , Winkler Holger
Published: February 2022

Coastal observatories are key to improve the understanding of processes within the coastal area and their interactions with regional and global environmental changes. The land-sea transition zone is an essential area that allows research on unique scientific questions under anthropogenic and natural influences. Amid the Wadden Sea UNESCO world natural heritage site – the largest tidal flat region worldwide – the barrier island Spiekeroog is an excellent location for an observatory studying land-sea interactions. The integrated Spiekeroog Coastal Observatory (SCO) operated by the Institute for Chemistry and Biology of the Marine Environment (ICBM, University of Oldenburg) is dedicated to interdisciplinary marine and terrestrial ecosystem research. Its position within the tidal area and the multitude of research-field addressed establishes the SCO as a unique coastal observatory with the potential to identify patterns in long-term variability and simultaneously understanding short-term changes. The establishment of the Time-Series Station (TSS) Spiekeroog in a tidal channel west of Spiekeroog back in 2002 laid the foundation of the SCO. Since then, the observatory is expanding continuously and is now representing a valuable asset supporting education, industry, government, and environmental conservation efforts in the area. Summing up the infrastructure and technical components, the importance of the SCO is evident, and individual projects greatly benefit from the collaboration with the partners in and the elements of the SCO. Harmonizing the infrastructure and competences of contributing partners will be a next step to further consolidate the SCO. A challenge poses the maintenance of the SCO based on projects, which is focused on the addition of new facilities, not maintaining, refurbishing, or (if necessary) deconstructing existing infrastructure. Therefore, structural support and funding opportunities not linked to projects but aiming to sustain observational capacities are required.
Proteogenomic Study of the Effect of an Improved Mixed Diet of Live Preys on the Aquaculture of Octopus vulgaris Paralarvae
Authors: Varó Inmaculada , Prado-Álvarez María , Ortea Ignacio , Morales Amalia E. , García-Fernández Pablo , Domingues Pedro , Tur Ricardo , Dios Sonia , Gestal Camino
Published: February 2022

The common octopus is the most demanded cephalopod species for human consumption. Despite important advances realized recently, the main bottleneck for commercial production of the common octopus, Octopus vulgaris, is the mass mortality of paralarvae in the first 15–20 days post-hatching (dph), with the main responsible factors still unknown. Thus, the identification of the limiting culture factors is, therefore, crucial for their aquaculture. This study investigates proteomic and transcriptomic responses of octopus paralarvae fed on an improved live preys-mixed diet (M) compared to an Artemia-based (A) reference diet. M diet resulted in the highest paralarvae specific growth rate obtained to date under culture conditions. This is supported by most of the proteins and genes over-expressed in the M group being linked to the cell cycle and replication, production of structural components, and development of the nervous system. Furthermore, the differential nutritional regulation of several genes and proteins seems to indicate that, instead of fatty acids, the preferred fuels for cephalopods would be proteins and carbohydrates. Also, M diet provides a better nutrient balance, which has allowed carrying out this comparative study in paralarvae under optimal conditions at a more advanced stage of growth (20 dph) than in previous studies. Moreover, the paralarvae culture extended up to 40 dph showed for the first time a proper pre-settlement behavior.
A Snapshot on the Distribution of Coastal Phytoplankton Communities in Five HAB-Affected Bays in Eastern Visayas, Philippines
Authors: Ravelo Stephanie Faith , Yap-Dejeto Leni G. , Silaras Mark Leonard S. , Amparado Ma. Luningning L. , Ocampo Jason A. , Abria Eugene G. , Albina Marietta B.
Published: February 2022

In recent years, harmful algal blooms (HABs), commonly known as red tide, have started to occur year-round in the warm tropical marine waters of Eastern Visayas, Philippines. These are a threat to public safety and cause enormous loss in industries relying on marine resources. The first step in solving this problem is to establish the distribution and succession of phytoplankton communities and harmful microalgae that exist in the region. For the first time, simultaneous monthly monitoring of the phytoplankton community was conducted in five HAB-affected bays of Leyte and Samar islands. We observed spatial differences on the environmental profiles between the five bays in the two islands and these differences may, in part, influence the distribution and abundance of the phytoplankton community residing within these areas. Diatom associated groups were prevalent in all sampling sites, however, HAB causative species were abundant in the bays in Samar during the sampling period. Five (5) genera and nine (9) species that may cause HAB were identified in all five bays. These are potential vectors for paralytic shellfish poisoning, amnesic shellfish poisoning, diarrhetic shellfish poisoning, and fish kill due to hypoxia. The correlation analysis confirmed that the majority of potential HAB vectors correlated with temperature, dissolved oxygen, rainfall, nitrate, and phosphate. The abundance of Pyrodinium bahamense observed in October to November in Samar coincided with several red tide alerts announced by the region’s fishery agency. This however, was never observed to dominate the phytoplankton community. Instead, the following diatoms dominated the five bays; Skeletonema, Pseudo-nitzschia, Bacteriastrum, Chaetoceros, Rhizosolenia and Thalassionema. This is a pioneering study that shows a simultaneous snapshot on the community structure and environmental profiles in these five bays in Eastern Visayas in 2020–2021. It discusses the effects of mariculture to its phytoplankton community and vice versa. Relationships between different phytoplankton species were further observed. This contributes to the knowledge of phytoplankton ecology in warm waters which is necessary to understand future phytoplankton ecosystems affected by sea temperature rise due to climate change.
Temporal Trends of Persistent Organic Pollutants in Sarasota Bay Common Bottlenose Dolphins (Tursiops truncatus)
Authors: Kucklick John , Boggs Ashley , Huncik Kevin , Moors Amanda , Davis Elizabeth , Ylitalo Gina , McConnell Mary , Makris Christina , Wells Randall S.
Published: February 2022

Legacy persistent organic pollutants (POPs) were measured in blubber samples collected from 196 common bottlenose dolphins (Tursiops truncatus) from 2000 to 2016 in the Sarasota Bay, Florida, ecosystem. Legacy POPs included polychlorinated biphenyl congeners (ΣPCB; sum of 37 congeners or congener groups), dichloro-diphenyl-trichloroethane (DDT) and transformation products (ΣDDT), chlordane and related compounds (ΣChlor), mirex, polybrominated diphenyl ether congeners (ΣPBDE, sum of five congeners), dieldrin and hexachlorobenzene (HCB). All POP compounds or compound groups declined in dolphin blubber over the study period. POP classes declined at different rates within classifications (sex, adult or calf). For example, dieldrin decline in male dolphins was greatest (−13% per year) while HCB decline was lower (−6.3% per year). For individual POP classes, rates of decline depended on classification. For example, ΣPCB, the POP class present at the highest concentration relative to other POPs, declined at −8.4, −7.8, and −5.6% per year in adult females, adult males and calves, respectively. Overall POP declines were highest in adult males and lowest in calves. Declines in POP concentration with time based on individual dolphins resampled at different time points were consistent with declines calculated based on yearly or biennial cross-sections taken from 2000 through 2016. Overall rates of decline in Sarasota Bay bottlenose dolphins were like declines seen for Great Lakes fish and about twice the rate of decline observed in arctic temporal trend data sets. POP trends appear to have leveled off since 2009 in Sarasota Bay dolphins. For example, ΣPCBs in calves appear to have stabilized at 21 mg/kg lipid. Recent published work on delphinids with blubber concentrations spanning those observed in the present work suggest that levels of legacy POPs currently observed in Sarasota dolphins may suppress population growth. Results from this study confirm the need for continued monitoring of POPs in the Sarasota Bay bottlenose dolphin population to see if concentrations are continuing to fall or have indeed plateaued.
Dynamical Projections of the Mean and Extreme Wave Climate in the Bohai Sea, Yellow Sea and East China Sea
Authors: Li Delei , Feng Jianlong , Zhu Yuchao , Staneva Joanna , Qi Jifeng , Behrens Arno , Lee Donghyun , Min Seung-Ki , Yin Baoshu
Published: February 2022

Few studies have focused on the projected future changes in wave climate in the Chinese marginal seas. For the first time, we investigate the projected changes of the mean and extreme wave climate over the Bohai Sea, Yellow Sea, and East China Sea (BYE) during two future periods (2021–2050 and 2071–2100) under the RCP2.6 and RCP8.5 scenarios from the WAM wave model simulations with a resolution of 0.1°. This is currently the highest-resolution wave projection dataset available for the study domain. The wind forcings for WAM are from high-resolution (0.22°) regional climate model (RCM) CCLM-MPIESM simulations. The multivariate bias-adjustment method based on the N-dimensional probability density function transform is used to correct the raw simulated significant wave height (SWH), mean wave period (MWP), and mean wave direction (MWD). The annual and seasonal mean SWH are generally projected to decrease (-0.15 to -0.01 m) for 2021–2050 and 2071–2100 under the RCP2.6 and RCP8.5 scenarios, with statistical significance at a 0.1 level for most BYE in spring and for most of the Bohai Sea and Yellow Sea in annual and winter/autumn mean. There is a significant decrease in the spring MWP for two future periods under both the RCP2.6 and RCP8.5 scenarios. In contrast, the annual and summer/winter 99th percentile SWH are generally projected to increase for large parts of the study domain. Results imply that the projected changes in the mean and 99th percentile extreme waves are very likely related to projected changes in local mean and extreme surface wind speeds, respectively.
Sustainable Composites Using Landfill Bound Materials
Authors: Mort Rebecca , Cecon Victor S. , Mort Paul , McInturff Kelsey , Jiang Shan , Vorst Keith , Curtzwiler Greg
Published: February 2022

The demand for new methods of diverting materials from waste streams has grown as sustainability and landfill reduction goals continue to be set. Municipal solid waste combustion and waste-to-energy (WTE) facilities reduce landfill waste accumulation but ash material by-products are commonly sent to landfills. In this work, we evaluate the potential for fly ash to be used as an inert filler in post-consumer recycled polyethylene to maximize landfill diversion of high-volume materials. Using fly ash from solid waste combustion as a filler increases landfill diversion, reduces associated costs, and offsets the cost of the recycling for post-consumer plastics by blending with a low cost filler. Characterization of the fly ash revealed high variability in ash particle composition and size, which was expected due to the municipal solid waste source. A series of composites were compounded incorporating fly ash into recycled linear low-density polyethylene utilizing various compatibilizers. The composites were characterized for molecular interactions, thermal properties, mechanical properties and changes in melt processing via infrared spectroscopy, differential scanning calorimetry, electromechanical testing, and oscillatory melt rheology, respectively. Mechanical testing of the fly ash composites indicated that the fly ash did not significantly change the Young’s modulus or yield stress and the addition of various compatibilizer additives increased impact strength. The impact strength of the neat polymer decreased drastically from ∼55 kJ/m2 to ∼20 kJ/m2 at 5 wt. % fly ash. However, the addition of PGME compatibilizer at 0.75 wt. % increased the composite’s impact strength to roughly the same value as the neat polymer. Thus, the addition of a compatibilizer could be used to alter the fly ash filler composite’s resistance to flexural shock. These results indicate that fly ash can be added to recycled linear low-density polyethylene up to 10% while maintaining physical properties.
Prevalence, Risk Factors and Intervention for Depression and Anxiety in Pulmonary Hypertension: A Systematic Review and Meta-analysis
Authors: Mai Aaron Shengting , Lim Oliver Zi Hern , Ho Yeung Jek , Kong Gwyneth , Lim Grace En Hui , Ng Cheng Han , Ho Cyrus , Ho Roger , Lim Yinghao , Kuntjoro Ivandito , Tay Edgar , Yip James , Chew Nicholas W. S. , Low Ting-Ting
Published: February 2022

Background

Current guidelines recommend psychological support for patients with pulmonary hypertension suffering from psychological adversity. However, little is known about the prevalence and risk factors of depression and anxiety in patients with pulmonary hypertension (PH).

Methods

Medline and Embase were searched from inception to 6 May 2021. Meta-analysis of proportions using the generalized linear mixed model was conducted to analyze the pooled prevalence rates of depression and anxiety in PH patients. Risk factors for depression and anxiety in PH patients were evaluated using meta regression.

Results

A total of 24 studies involving 2,161 PH patients were included. The pooled prevalence of depression in PH was 28.0% (95% CI: 20.5–36.8) and pooled prevalence of anxiety was 37.1% (95% CI: 28.7–46.4). There was a significantly higher prevalence of anxiety (p = 0.0013) amongst PH patients in Asia (61.1%) compared to Europe (40.3%) and North America (22.9%). In terms of risk factors, congenital heart disease-related pulmonary arterial hypertension (PAH-CHD) were significantly associated with both depression (OR: 1.68, 95% CI: 1.27–2.23, p = 0.024) and anxiety (OR: 1.63, 95% CI: 1.45–1.83, p = 0.002). On the other hand, chronic thromboembolic pulmonary hypertension (CTEPH, OR: 1.18, 95% CI: 1.10–1.26, p = 0.004) was significantly associated with depression, whereas worse pulmonary vascular resistance (β: 0.30, 95% CI: 0.09–0.52, p = 0.005) and cardiac index (β: −0.96, 95% CI: −1.58 to −0.35, p = 0.002) were significantly correlated with anxiety.

Conclusion

The prevalence of anxiety and depression in PH patients is alarmingly high, with an increased prevalence of anxiety in Asia compared to Europe or North America. Psychological support is warranted for patients with PH, particularly those with underlying congenital heart disease, CTEPH, and severe disease.

Systematic Review Registration

CRD42021251733.
Short-Term Efficacy in Polypoidal Choroidal Vasculopathy Patients Treated With Intravitreal Aflibercept or Conbercept
Authors: Xue Yin , Qinhua Cai
Published: February 2022

Purpose

To compare the short-term efficacy in patients with polypoidal choroidal vasculopathy (PCV) treated using either aflibercept or conbercept.

Methods

This prospective study included 41 patients with treatment-naive PCV (42 eyes). All the patients were treated with either aflibercept or conbercept using an initial series of 3 monthly loading injections. Changes in the best-corrected logMAR visual acuity (BCVA) and anatomic outcomes were evaluated at 3 months.

Results

BCVA was improved with reduction in central choroidal thickness (CCT), central foveal thickness (CFT), and subretinal fluid (SRF) after 3 monthly loading injections in both aflibercept (IVA) and conbercept (IVC) groups. There was no significant difference in either visual or anatomic outcomes between the two groups after 3 months of treatment. However, compared with the IVC group, significantly higher BCVA improvement was observed in the patients in the IVA group with baseline BCVA better than 1. A visual outcome improved ≥3 lines in 13 patients in the IVA group (59%), and 9 patients in the IVC group (45%). A relatively high proportion of polyp regression was observed in the IVA group (63%) compared with the IVC group (55%) via OCTA.

Conclusions

Visual and anatomic outcomes were significantly improved in both IVA and IVC groups, but the results suggest a potentially superior short-term response in the IVA group.
A Bibliometric Analysis of Atrophic Gastritis From 2011 to 2021
Authors: Zhang Tai , Zhang Beihua , Tian Wende , Ma Xiangxue , Wang Fengyun , Wang Ping , Wei Yuchen , Liu Lin , Tang Xudong
Published: February 2022

Background

Atrophic gastritis (AG), which is characterized by a decreased number or disappearance of the glandular structures and secretory dysfunction, is linked to chronically inflamed stomach. It has been estimated that the annual incidence of gastric cancer (GC) is 0.1% for patients with AG. Early eradication of Helicobacter pylori (H. pylori) can reduce the risk of GC development. Additionally, the follow-up and management of AG are necessary to prevent GC. Exploring novel methods of the automatized analysis of data for apprehending knowledge in any medical field is encouraged, especially when a body of literature suggests the necessity of doing so. Accordingly, herein, we aim to systematically review the current foci and status of AG research using bibliometric analysis.

Methods

Articles and reviews related to AG published from 2011 to 2021 in the Web of Science Core Collection were retrieved. Microsoft Office Excel 2019 and GraphPad Prism were used to show the annual number of publications and scientific productivity of authors through time. CiteSpace and VOSviewer were used to generate network maps about the collaborations among countries, institutions, and authors as well as reveal hotspots of AG research. The relationships among the author's keywords, cited references, and the top authors were summarized by a Sankey plot (three-fields plot).

Results

A total of 1,432 publications were included in the present study. China remained the most productive country, with the highest number of publications (377, 26.32%). Vanderbilt University contributed the most publications of any single institution (56, 3.91%). James R Goldenring was the most active and influential scholar, with the highest number of publications and greatest centrality. The most prolific journal in this field was World Journal of Gastroenterology (62, 4.32%). Gastroenterology (997, 69.62%) was the most co-cited journal. Exploring the origin of gastric metaplasia, especially spasmolytic polypeptide-expressing metaplasia (SPEM) was a major topic in AG research.

Conclusions

This bibliometric study provides a comprehensive analysis of the scientific progress of AG over the past decade. Metaplasia is a hot topic and could be a promising area of research in the coming years.
Virome and Blood Meal-Associated Host Responses in Ixodes persulcatus Naturally Fed on Patients
Authors: Li Liang-Jing , Ning Nian-Zhi , Zheng Yuan-Chun , Chu Yan-Li , Cui Xiao-Ming , Zhang Ming-Zhu , Guo Wen-Bin , Wei Ran , Liu Hong-Bo , Sun Yi , Ye Jin-Ling , Jiang Bao-Gui , Yuan Ting-Ting , Li Jie , Bian Cai , Bell-Sakyi Lesley , Wang Hui , Jiang Jia-Fu , Song Ju-Liang , Cao Wu-Chun , Tsan-Yuk Lam Tommy , Ni Xue-Bing , Jia Na
Published: February 2022

The long-lasting co-evolution of ticks with pathogens results in mutual adaptation. Blood-feeding is one of the critical physiological behaviors that have been associated with the tick microbiome; however, most knowledge was gained through the study of laboratory-reared ticks. Here we detached Ixodes persulcatus ticks at different stages of blood-feeding from human patients and performed high-throughput transcriptomic analysis on them to identify their virome and genes differentially expressed between flat and fully fed ticks. We also traced bloodmeal sources of those ticks and identified bats and three other potential mammalian hosts, highlighting the public health significance. We found Jingmen tick virus and 13 putative new viruses belonging to 11 viral families, three of which even exhibited high genetic divergence from viruses previously reported in the same tick species from the same geographic region. Furthermore, differential expression analysis suggested a downregulation of antioxidant genes in the fully fed I. persulcatus ticks, which might be related to bloodmeal-related redox homeostasis. Our work highlights the significance of active surveillance of tick viromes and suggests a role of reactive oxygen species (ROS) in modulating changes in the microbiome during blood-feeding.
Sugarcane–Peanut Intercropping System Enhances Bacteria Abundance, Diversity, and Sugarcane Parameters in Rhizospheric and Bulk Soils
Authors: Pang Ziqin , Fallah Nyumah , Weng Peiying , Zhou Yongmei , Tang Xiumei , Tayyab Muhammad , Liu Yueming , Liu Qiang , Xiao Yijie , Hu Chaohua , Kan Yongjun , Lin Wenxiong , Yuan Zhaonian
Published: February 2022

Sugarcane–legume intercropping systems can effectively control pests and diseases as well as improve the fertility and health of farmland soil. However, little is known about the response of bacterial abundance, diversity, and community composition in the rhizosphere and non-rhizosphere soils under the sugarcane–peanut farming system. A field experiment was conducted with two treatments: sugarcane monoculture and sugarcane–peanut intercropping to examine the response of sugarcane parameters and edaphic factors. We also deciphered bacterial abundance, diversity, and community composition in the root endosphere, rhizosphere, and bulk soil by leveraging Illumina sequencing to conduct the molecular characterization of the 16S rRNA gene and nitrogenase (nifH) gene. We observed that sugarcane–peanut intercropping exhibited the advantages of tremendously increasing cane stalk height, stalk weight, and millable stalk number/20 m, and edaphic factors, namely, pH (1.13 and 1.93), and available phosphorus exhibited a fourfold and sixfold increase (4.66 and 6.56), particularly in the rhizosphere and bulk soils, respectively. Our result also showed that the sugarcane–peanut intercropping system significantly increased the bacterial richness of the 16S rRNA gene sequencing data by 13.80 and 9.28% in the bulk soil and rhizosphere soil relative to those in the monocropping sugarcane system, respectively. At the same time, sugarcane intercropping with peanuts significantly increased the Shannon diversity of nitrogen-fixing bacteria in the sugarcane rhizosphere soil. Moreover, most edaphic factors exhibited a positive regularity effect on bacterial community composition under the intercropping system. A linear discriminant analysis with effect size analysis of the 16S rRNA sequencing data revealed that bacteria in the root endosphere of the intercropped cane proliferated profoundly, primarily occupied by Devosia, Rhizobiales, Myxococcales, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Bradyrhizobium, and Sphingomonas. In conclusion, our findings demonstrated that sugarcane–peanut intercropping can enhance edaphic factors, sugarcane parameters, and bacterial abundance and diversity without causing adverse impacts on crop production and soil.
Genome and Comparative Transcriptome Dissection Provide Insights Into Molecular Mechanisms of Sclerotium Formation in Culinary-Medicinal Mushroom Pleurotus tuber-regium
Authors: Sun Xueyan , Wu Junyue , Zhang Shuhui , Luo Lu , Mo Cuiyuan , Sheng Li , Ma Aimin
Published: February 2022

Pleurotus tuber-regium is an edible and medicinal sclerotium-producing mushroom. The sclerotia of this mushroom also serve as food and folk medicine. Based on the description of its monokaryon genome, sequenced with Illumina and PacBio sequencing technologies, comparative transcriptomic analysis using RNA sequencing (RNA-seq) was employed to study its mechanism of sclerotium formation. The de novo assembled genome is 35.82 Mb in size with a N50 scaffold size of 4.29 Mb and encodes 12,173 putative proteins. Expression analysis demonstrated that 1,146 and 1,249 genes were upregulated and downregulated with the formation of sclerotia, respectively. The differentially expressed genes were associated with substrate decomposition, the oxidation-reduction process, cell wall synthesis, and other biological processes in P. tuber-regium. These genomic and transcriptomic resources provide useful information for the mechanism underlying sclerotium formation in P. tuber-regium.