bluuebunny/crossref_metadata_2025 huggingface dataset:
Barriers to Accessing Addiction Treatment for Women at Risk of Homelessness
Authors: Rizzo Davinia , Mu Temika , Cotroneo Sophia , Arunogiri Shalini
Published: February 2022

Women remain under-represented in addiction treatment, comprising less than a third of clients in treatment services. Shame, stigma, and fear of legal and social repercussions (e.g., child protection involvement) are major barriers impacting on treatment-seeking for women. This is compounded for women at risk of homelessness, with practical and logistical reasons for not engaging in treatment. We conducted a qualitative study with both clinicians and service-providers, and women with lived experience of addiction and at risk of homelessness, to identify barriers to access and help-seeking within this vulnerable population. Adult women with lived experience of homelessness and addiction were invited to participate in an online focus group. Interviews were transcribed and analyzed using framework analysis. Analysis resulted in the identification of barriers to access in three areas. These were system-related, socio-cultural, and emotional barriers. We also present findings from the focus group recorded in real-time, using the novel method of digital illustration. This study highlights key factors impacting on help-seeking and access to treatment for addiction faced by women at risk of homelessness. The findings of this study highlight important areas of consideration for clinicians and service-providers working with women who experience addiction, as well as informing future research directions for this priority population. Findings are discussed in the context of exigent literature.
Common Variable Immunodeficiency-Associated Cancers: The Role of Clinical Phenotypes, Immunological and Genetic Factors
Authors: Bruns Luzia , Panagiota Victoria , von Hardenberg Sandra , Schmidt Gunnar , Adriawan Ignatius Ryan , Sogka Eleni , Hirsch Stefanie , Ahrenstorf Gerrit , Witte Torsten , Schmidt Reinhold Ernst , Atschekzei Faranaz , Sogkas Georgios
Published: February 2022

Objective

The aim of this study was to investigate the prevalence of cancer and associating clinical, immunological, and genetic factors in a German cohort of patients with common variable immunodeficiency (CVID).

Methods

In this retrospective monocenter cohort study, we estimated the standardized incidence ratio (SIR) for different forms of cancer diagnosed in CVID patients. Furthermore, we evaluated the likely association of infectious and non-infectious CVID-related phenotypes with the diagnosis of cancer by calculation of the odds ratio. The genetic background of CVID in patients with cancer was evaluated with sequential targeted next-generation sequencing (tNGS) and whole-exome sequencing (WES). Patients’ family history and WES data were evaluated for genetic predisposition to cancer.

Results

A total of 27/219 patients (12.3%) were diagnosed with at least one type of cancer. Most common types of cancer were gastric cancer (SIR: 16.5), non-melanoma skin cancer (NMSC) (SIR: 12.7), and non-Hodgkin lymphoma (NHL) (SIR: 12.2). Immune dysregulation manifesting as arthritis, atrophic gastritis, or interstitial lung disease (ILD) was associated with the diagnosis of cancer. Furthermore, diagnosis of NMSC associated with the diagnosis of an alternative type of cancer. Studied immunological parameters did not display any significant difference between patients with cancer and those without. tNGS and/or WES yielded a definite or likely genetic diagnosis in 11.1% of CVID patients with cancer. Based on identified variants in cancer-associated genes, the types of diagnosed cancers, and family history data, 14.3% of studied patients may have a likely genetic susceptibility to cancer, falling under a known hereditary cancer syndrome.

Conclusions

Gastric cancer, NMSC, and NHL are the most frequent CVID-associated types of cancer. Manifestations of immune dysregulation, such as arthritis and ILD, were identified as risk factors of malignancy in CVID, whereas studied immunological parameters or the identification of a monogenic form of CVID appears to have a limited role in the evaluation of cancer risk in CVID.
Exploring the Ecological Implications of Microbiota Diversity in Birds: Natural Barriers Against Avian Malaria
Authors: Palinauskas Vaidas , Mateos-Hernandez Lourdes , Wu-Chuang Alejandra , de la Fuente José , Aželytė Justė , Obregon Dasiel , Cabezas-Cruz Alejandro
Published: February 2022

Natural antibodies (Abs), produced in response to bacterial gut microbiota, drive resistance to infection in vertebrates. In natural systems, gut microbiota diversity is expected to shape the spectrum of natural Abs and resistance to parasites. This hypothesis has not been empirically tested. In this ‘Hypothesis and Theory’ paper, we propose that enteric microbiota diversity shapes the immune response to the carbohydrate α-Gal and resistance to avian malaria. We further propose that anti-α-Gal Abs are transmitted from mother to eggs for early malaria protection in chicks. Microbiota modulation by anti-α-Gal Abs is also proposed as a mechanism favoring the early colonization of bacterial taxa with α1,3-galactosyltransferase (α1,3GT) activity in the bird gut. Our preliminary data shows that bacterial α1,3GT genes are widely distributed in the gut microbiome of wild and domestic birds. We also showed that experimental infection with the avian malaria parasiteP. relictuminduces anti-α-Gal Abs in bird sera. The bird-malaria-microbiota system allows combining field studies with infection and transmission experiments in laboratory animals to test the association between microbiota composition, anti-α-Gal Abs, and malaria infection in natural populations of wild birds. Understanding how the gut microbiome influences resistance to malaria can bring insights on how these mechanisms influence the prevalence of malaria parasites in juvenile birds and shape the host population dynamics.
ACE and ACE2 Gene Variants Are Associated With Severe Outcomes of COVID-19 in Men
Authors: Martínez-Gómez Laura E. , Herrera-López Brígida , Martinez-Armenta Carlos , Ortega-Peña Silvestre , Camacho-Rea María del Carmen , Suarez-Ahedo Carlos , Vázquez-Cárdenas Paola , Vargas-Alarcón Gilberto , Rojas-Velasco Gustavo , Fragoso José Manuel , Vidal-Vázquez Patricia , Ramírez-Hinojosa Juan P. , Rodríguez-Sánchez Yunuen , Barrón-Díaz David , Moreno Mariana L. , Martínez-Ruiz Felipe de J. , Zayago-Angeles Dulce M. , Mata-Miranda Mónica Maribel , Vázquez-Zapién Gustavo Jesús , Martínez-Cuazitl Adriana , Barajas-Galicia Edith , Bustamante-Silva Ludwing , Zazueta-Arroyo Diana , Rodríguez-Pérez José Manuel , Hernández-González Olivia , Coronado-Zarco Roberto , Lucas-Tenorio Vania , Franco-Cendejas Rafael , López-Jácome Luis Esau , Vázquez-Juárez Rocío Carmen , Magaña Jonathan J. , Cruz-Ramos Marlid , Granados Julio , Hernández-Doño Susana , Delgado-Saldivar Diego , Ramos-Tavera Luis , Coronado-Zarco Irma , Guajardo-Salinas Gustavo , Muñoz-Valle José Francisco , Pineda Carlos , Martínez-Nava Gabriela Angélica , López-Reyes Alberto
Published: February 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, affecting more than 219 countries and causing the death of more than 5 million people worldwide. The genetic background represents a factor that predisposes the way the host responds to SARS-CoV-2 infection. In this sense, genetic variants of ACE and ACE2 could explain the observed interindividual variability to COVID-19 outcomes. In order to improve the understanding of how genetic variants of ACE and ACE2 are involved in the severity of COVID-19, we included a total of 481 individuals who showed clinical manifestations of COVID-19 and were diagnosed by reverse transcription PCR (RT-PCR). Genomic DNA was extracted from peripheral blood and saliva samples. ACE insertion/deletion polymorphism was evaluated by the high-resolution melting method; ACE single-nucleotide polymorphism (SNP) (rs4344) and ACE2 SNPs (rs2285666 and rs2074192) were genotyped using TaqMan probes. We assessed the association of ACE and ACE2 polymorphisms with disease severity using logistic regression analysis adjusted by age, sex, hypertension, type 2 diabetes, and obesity. The severity of the illness in our study population was divided as 31% mild, 26% severe, and 43% critical illness; additionally, 18% of individuals died, of whom 54% were male. Our results showed in the codominant model a contribution of ACE2 gene rs2285666 T/T genotype to critical outcome [odds ratio (OR) = 1.83; 95%CI = 1.01–3.29; p = 0.04] and to require oxygen supplementation (OR = 1.76; 95%CI = 1.01–3.04; p = 0.04), in addition to a strong association of the T allele of this variant to develop critical illness in male individuals (OR = 1.81; 95%CI = 1.10–2.98; p = 0.02). We suggest that the T allele of rs2285666 represents a risk factor for severe and critical outcomes of COVID-19, especially for men, regardless of age, hypertension, obesity, and type 2 diabetes.
Development of a Dendritic Cell/Tumor Cell Fusion Cell Membrane Nano-Vaccine for the Treatment of Ovarian Cancer
Authors: Zhang Lei , Zhao Wei , Huang Jinke , Li Fangxuan , Sheng Jindong , Song Hualin , Chen Ying
Published: February 2022

Ovarian cancer (OC) is a malignant tumor that seriously affects women’s health. In recent years, immunotherapy has shown great potential in tumor treatment. As a major contributor of immunotherapy, dendritic cells (DCs) - based tumor vaccine has been demonstrated to have a positive effect in inducing immune responses in animal experiments. However, the effect of tumor vaccines in clinical trials is not ideal. Therefore, it is urgent to improve the existing tumor vaccines for tumor treatment. Here, we developed a fusion cell membrane (FCM) nano-vaccine FCM-NPs, which is prepared by fusing DCs and OC cells and coating the FCM on the poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with the immune adjuvant CpG-oligodeoxynucleotide (CpG-ODN). The fusion process promoted the maturation of DCs, thus up-regulating the expression of costimulatory molecule CD80/CD86 and accelerating lymph node homing of DCs. Furthermore, FCM-NPs has both the immunogenicity of tumor cells and the antigen presenting ability of DCs, it can stimulate naive T lymphocytes to produce a large number of tumor-specific cytotoxic CD8+ T lymphocytes. FCM-NPs exhibited strong immuno-activating effect both in vitro and in vivo. By establishing subcutaneous transplanted tumor model, patient-derived xenograft tumor model and abdominal metastatic tumor model, FCM-NPs was proved to have the effect of delaying the growth and inhibiting the metastasis of OC. FCM-NPs is expected to become a new tumor vaccine for the treatment of ovarian cancer.
SARS-CoV-2 Infection Triggers Phosphorylation: Potential Target for Anti-COVID-19 Therapeutics
Authors: Chatterjee Bhaswati , Thakur Suman S.
Published: February 2022

The SARS-CoV-2 infection triggers host kinases and is responsible for heavy phosphorylation in the host and also in the virus. Notably, phosphorylations in virus were achieved using the host enzyme for its better survival and further mutations. We have attempted to study and understand the changes that happened in phosphorylation during and post SARS-CoV-2 infection. There were about 70 phosphorylation sites detected in SARS-CoV-2 viral proteins including N, M, S, 3a, and 9b. Furthermore, more than 15,000 host phosphorylation sites were observed in SARS-CoV-2-infected cells. SARS-CoV-2 affects several kinases including CMGC, CK2, CDK, PKC, PIKFYVE, and EIF2AK2. Furthermore, SARS-CoV-2 regulates various signaling pathways including MAPK, GFR signaling, TGF-β, autophagy, and AKT. These elevated kinases and signaling pathways can be potential therapeutic targets for anti-COVID-19 drug discovery. Specific inhibitors of these kinases and interconnected signaling proteins have great potential to cure COVID-19 patients and slow down the ongoing COVID-19 pandemic.
Trained Immunity: An Overview and the Impact on COVID-19
Authors: Brueggeman Justin M. , Zhao Juan , Schank Madison , Yao Zhi Q. , Moorman Jonathan P.
Published: February 2022

Effectively treating infectious diseases often requires a multi-step approach to target different components involved in disease pathogenesis. Similarly, the COVID-19 pandemic has become a global health crisis that requires a comprehensive understanding of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) infection to develop effective therapeutics. One potential strategy to instill greater immune protection against COVID-19 is boosting the innate immune system. This boosting, termed trained immunity, employs immune system modulators to train innate immune cells to produce an enhanced, non-specific immune response upon reactivation following exposure to pathogens, a process that has been studied in the context of in vitro and in vivo clinical studies prior to the COVID-19 pandemic. Evaluation of the underlying pathways that are essential to inducing protective trained immunity will provide insight into identifying potential therapeutic targets that may alleviate the COVID-19 crisis. Here we review multiple immune training agents, including Bacillus Calmette-Guérin (BCG), β-glucan, and lipopolysaccharide (LPS), and the two most popular cell types involved in trained immunity, monocytes and natural killer (NK) cells, and compare the signaling pathways involved in innate immunity. Additionally, we discuss COVID-19 trained immunity clinical trials, emphasizing the potential of trained immunity to fight SARS-CoV-2 infection. Understanding the mechanisms by which training agents activate innate immune cells to reprogram immune responses may prove beneficial in developing preventive and therapeutic targets against COVID-19.
Vitamin B6 Metabolism Determines T Cell Anti-Tumor Responses
Authors: Bargiela David , Cunha Pedro P. , Veliça Pedro , Foskolou Iosifina P. , Barbieri Laura , Rundqvist Helene , Johnson Randall S.
Published: February 2022

Targeting T cell metabolism is an established method of immunomodulation. Following activation, T cells engage distinct metabolic programs leading to the uptake and processing of nutrients that determine cell proliferation and differentiation. Redirection of T cell fate by modulation of these metabolic programs has been shown to boost or suppress immune responses in vitro and in vivo. Using publicly available T cell transcriptomic and proteomic datasets we identified vitamin B6-dependent transaminases as key metabolic enzymes driving T cell activation and differentiation. Inhibition of vitamin B6 metabolism using the pyridoxal 5’-phosphate (PLP) inhibitor, aminoxyacetic acid (AOA), suppresses CD8+ T cell proliferation and effector differentiation in a dose-dependent manner. We show that pyridoxal phosphate phosphatase (PDXP), a negative regulator of intracellular vitamin B6 levels, is under the control of the hypoxia-inducible transcription factor (HIF1), a central driver of T cell metabolism. Furthermore, by adoptive transfer of CD8 T cells into a C57BL/6 mouse melanoma model, we demonstrate the requirement for vitamin B6-dependent enzyme activity in mediating effective anti-tumor responses. Our findings show that vitamin B6 metabolism is required for CD8+ T cell proliferation and effector differentiation in vitro and in vivo. Targeting vitamin B6 metabolism may therefore serve as an immunodulatory strategy to improve anti-tumor immunotherapy.
Targeting Microglia to Treat Degenerative Eye Diseases
Authors: Wang Sean K. , Cepko Constance L.
Published: February 2022

Microglia have been implicated in many degenerative eye disorders, including retinitis pigmentosa, age-related macular degeneration, glaucoma, diabetic retinopathy, uveitis, and retinal detachment. While the exact roles of microglia in these conditions are still being discovered, evidence from animal models suggests that they can modulate the course of disease. In this review, we highlight current strategies to target microglia in the eye and their potential as treatments for both rare and common ocular disorders. These approaches include depleting microglia with chemicals or radiation, reprogramming microglia using homeostatic signals or other small molecules, and inhibiting the downstream effects of microglia such as by blocking cytokine activity or phagocytosis. Finally, we describe areas of future research needed to fully exploit the therapeutic value of microglia in eye diseases.
Antigen-Presenting Cell-Like Neutrophils Foster T Cell Response in Hyperlipidemic Patients and Atherosclerotic Mice
Authors: Zhao Tingrui , Jiang Qingsong , Li Wenming , Wang Yin , Zou Yao , Chai Xinyu , Yuan Zhiyi , Ma Limei , Yu Ruihong , Deng Tao , Yu Chao , Wang Tingting
Published: February 2022

Neutrophils constitute abundant cellular components in atherosclerotic plaques. Most of the current studies are focused on the roles of granular proteins released by neutrophils in atherosclerosis. Here, we revealed a unique subset of neutrophils which exhibit the characteristics of antigen-presenting cell (APC) (which were called APC-like neutrophils afterwards) in atherosclerosis. The roles of APC-like neutrophils and relevant mechanisms were investigated in hyperlipidemic patients and atherosclerotic mice. Higher percentages of neutrophils and APC-like neutrophils were found in peripheral blood of hyperlipidemic patients than that of healthy donors. Meanwhile, we also identified higher infiltration of neutrophils and APC-like neutrophils in atherosclerotic mice. Ox-LDL induced Phorbol-12-myristate-13-acetate (PMA)-activated neutrophils to acquire the APC-like phenotype. Importantly, upon over-expression of APC-like markers, neutrophils acquired APC functions to promote the proliferation and interferon-γ production of CD3+ T cells via HLA-DR/CD80/CD86. In accordance with what found in vitro, positive correlation between neutrophils and CD3+ T cells was observed in hyperlipidemic patients. In conclusion, our work identifies a proinflammatory neutrophil subset in both hyperlipidemic patients and atherosclerotic mice. This unique phenotype of neutrophils could activate the adaptive immune response to promote atherosclerosis progression. Thus, this neutrophil subset may be a new target for immunotherapy of atherosclerosis.
The Extremes of Disturbance Reduce Functional Redundancy: Functional Trait Assessment of the Shallow Antarctic Benthos
Authors: Robinson Ben J. O. , Barnes David K. A. , Grange Laura J. , Morley Simon A.
Published: February 2022

Climate-driven changes in disturbance are a major threat to ecosystem Functional diversity. The selective mechanisms underlying ecosystem response to disturbance are far from universal and remain the subject of scientific debate. Ice scouring of the shallow Antarctic benthos is one of the largest disturbance gradients in the natural environment and thus provides an opportunity to investigate how disturbance gradients influence functional structure of a biological assemblage. The Western Antarctic Peninsula, in particular, is a hotspot of climate-driven environmental change. Addressing how this system might respond to species loss is critical. Previous surveys across the shallowest 100 m of the seabed, detected unimodal changes in diversity and a shift in assemblage composition in response to disturbance gradients. This study investigated how functional traits and associated functional diversity change across the depth gradient. Our results revealed that selective mechanisms, such as disturbance filtering and inter-species competition, reduce functional redundancy at the extremes of the disturbance gradient. Our study highlights areas of potential vulnerability to future environmental change due to low functional redundancy. Threatening the important negative (mitigating) feedbacks on climate change, through blue carbon, currently provided by Antarctic continental shelf benthic assemblages.
Responses of a Natural Phytoplankton Community From the Drake Passage to Two Predicted Climate Change Scenarios
Authors: Pausch Franziska , Koch Florian , Hassler Christel , Bracher Astrid , Bischof Kai , Trimborn Scarlett
Published: February 2022

Contrasting models predict two different climate change scenarios for the Southern Ocean (SO), forecasting either less or stronger vertical mixing of the water column. To investigate the responses of SO phytoplankton to these future conditions, we sampled a natural diatom dominated (63%) community from today’s relatively moderately mixed Drake Passage waters with both low availabilities of iron (Fe) and light. The phytoplankton community was then incubated at these ambient open ocean conditions (low Fe and low light, moderate mixing treatment), representing a control treatment. In addition, the phytoplankton was grown under two future mixing scenarios based on current climate model predictions. Mixing was simulated by changes in light and Fe availabilities. The two future scenarios consisted of a low mixing scenario (low Fe and higher light) and a strong mixing scenario (high Fe and low light). In addition, communities of each mixing scenario were exposed to ambient and low pH, the latter simulating ocean acidification (OA). The effects of the scenarios on particulate organic carbon (POC) production, trace metal to carbon ratios, photophysiology and the relative numerical contribution of diatoms and nanoflagellates were assessed. During the first growth phase, at ambient pH both future mixing scenarios promoted the numerical abundance of diatoms (∼75%) relative to nanoflagellates. This positive effect, however, vanished in response to OA in the communities of both future mixing scenarios (∼65%), with different effects for their productivity. At the end of the experiment, diatoms remained numerically the most abundant phytoplankton group across all treatments (∼80%). In addition, POC production was increased in the two future mixing scenarios under OA. Overall, this study suggests a continued numerical dominance of diatoms as well as higher carbon fixation in response to both future mixing scenarios under OA, irrespective of different changes in light and Fe availability.
Making Use of Relicts: Brisingid Seastars Aggregate on Hydrothermally Inactive Sulfide Chimneys Near Black Smokers
Authors: Woods Daniel , Cheadle Michael J. , John Barbara E. , German Christopher R. , Van Dover Cindy L.
Published: February 2022

When hydrothermal activity ceases at black-smoker chimneys on mid-ocean ridges, populations of associated invertebrates hosting chemoautotrophic endosymbionts decline and then disappear, but the chimneys can persist on the seabed as relicts. Suspension-feeding brisingid seastars colonize hydrothermally inactive (relict) chimneys on the East Pacific Rise (EPR), though their distribution relative to available hard substrata and proximity to hydrothermal activity is poorly documented. In this study, brisingid abundance on sulfide and basalt substrata was assessed along an ∼3,700 m ROV Jason II transect at the summit of Pito Seamount (SE Pacific; ∼2,275 m). Brisingids were non-randomly distributed, with highest densities (up to ∼300 m–2) on relict sulfides chimneys near active black smokers. Brisingids were relatively uncommon on basalt substrata, and absent on black smokers. We infer that both relict sulfide structures and proximity to black smokers play key roles in the maintenance of dense brisingid populations on Pito Seamount and in similar environments on the EPR. Our observations suggest that experimental introduction of “artificial” relict chimneys providing microtopographic relief could test whether such an approach might mitigate potential impacts of mineral extraction on populations of suspension-feeding invertebrates.
The Structure of the Seasonal Benthic Diatom Community and Its Relationship With Environmental Factors in the Yellow River Delta
Authors: Liu Xing , Han Jichang , Li Yuhang , Zhu Baohua , Li Yun , Pan Kehou
Published: February 2022

Benthic diatoms are the main primary producers and are sensitive to environmental changes in the estuarine ecosystem. Therefore, it is critical to evaluate the impact of environmental stress on the benthic diatom community in the estuarine ecosystem. In this study, the sediment samples from the five sampling sites were collected from the Yellow River Delta in the four seasons, and the abundance of benthic diatoms were determined using the high-throughput sequencing of 18S rRNA genes. The results showed that the motile guild taxa, such as Navicula, Nitzschia, and Amphora, was dominated in the benthic diatom the community throughout the sampling period. The structure of the benthic diatom community was significantly different among seasons (ANOSIM P < 0.01), especially between summer and winter. Redundancy analysis showed that water temperature and the concentrations of silicate, nitrate, ammonium, and pH value are the main driving factors shaping the seasonal assembly of the benthic diatom community. The results will improve knowledge about the benthic diatom community in the estuarine ecosystem and provide a theoretical foundation for estuary environmental management.
Microbial Community Structure and Functional Potential of Deep-Sea Sediments on Low Activity Hydrothermal Area in the Central Indian Ridge
Authors: Namirimu Teddy , Kim Yun Jae , Park Mi-Jeong , Lim Dhongil , Lee Jung-Hyun , Kwon Kae Kyoung
Published: February 2022

Little is known about the community structure and metabolic potential of microbial communities in hydrothermal fields in the Central Indian Ridge (CIR). In this study, a metagenomic sequencing approach was conducted to explore the microbial diversity in three sediment samples collected during the 2019 expedition from two recently discovered hydrothermal vent fields; Invent E and Onnuri Vent Field (OVF). Analysis of unassembled metagenomic reads using the Metagenomic analysis server (MG-RAST) revealed that microbial communities of the two sampling sites were very similar, showing the dominance of Bacteria over Archaea. Proteobacteria, Firmicutes, Bacteroidetes, as well as Euryarchaeota were dominant in all samples. Functional annotation based on KEGG categories shows that the microbial populations in these vent fields possess metabolic capabilities for aerobic respiration, carbon fixation through the Calvin–Bassham–Benson (CBB) cycle, the reverse tricarboxylic acid (rTCA) cycle, and reductive acetyl-CoA pathway as well as sulfur and nitrogen metabolisms. Comparative metagenome analysis with different datasets obtained from different ocean ridges showed that microbial communities at low activity or hydrothermally influenced area differ from highly active hydrothermal communities. This study provides insights into the genetic diversity and functional capability of the microbial communities of slow to intermediate spreading hydrothermal systems.
Effects of the Coastal Uplift on the Kuroshio Ecosystem, Eastern Taiwan, the Western Boundary Current of the North Pacific Ocean
Authors: Chen Chung-Chi , Lu Chun-Yi , Jan Sen , Hsieh Chih-hao , Chung Chih-Ching
Published: February 2022

The Kuroshio is the western boundary current of the North Pacific Ocean. In the subtropical region of eastern Taiwan, a coastal uplift of the isotherms has occurred. To explore its impact on this oligotrophic ecosystem, hydrographic data along the transect line at 23.75°N were measured between September 2012 and September 2014. Results show that the intensity of coastal uplift was positively correlated to the flow volume transport of the Kuroshio. Significant dissolved inorganic nutrients were uplifted to the sunlit zone, especially in the onshore. For example, compared to the offshore, nitrate concentration increased 0.49 μM (or ∼178%) in the upper 100 m of the onshore. The increased nutrients thereafter enhanced the growth of phytoplankton; for instance, the Chl a concentration increased 88.3%, compared to offshore, in the upper 100 m of the onshore. Phytoplankton community was mostly composed of picophytoplankton (<2 μm in size), which were dominated, in terms of relative abundance, by Prochlorococcus (83.6%), followed by Synechococcus (13.8%) and picoeukaryotes (2.7%). The relative abundance of Prochlorococcus increased from onshore toward offshore, but the trend was reversed for Synechococcus and picoeukaryotes, which may be affected by the coastal uplift. The results also suggest that the coastal uplift may support more energy transferred to higher tropical levels in this oligotrophic Kuroshio ecosystem.
Fungal Diversity in Sediments From Deep-Sea Extreme Ecosystems: Insights Into Low- and High-Temperature Hydrothermal Vents, and an Oxygen Minimum Zone in the Southern Gulf of California, Mexico
Authors: Velez Patricia , Salcedo Diana L. , Espinosa-Asuar Laura , Gasca-Pineda Jaime , Hernandez-Monroy Abril , Soto Luis A.
Published: February 2022

Deep-sea sediments are vast microbial habitats that cover almost two-thirds of the planet’s surface. Particularly, sediments in hydrothermal vents and oxygen minimum zones (OMZ) represent emblematic, and poorly understood extreme niches that pose strong selective pressures to life, representing untapped reservoirs of a unique microbial diversity. Nonetheless, the mycobiota in these systems remains relatively unknown. Here, we explored fungal diversity and community structure in deep-sea sediments collected from low- and high-temperature vent systems (Pescadero Basin, Pescadero Transform Fault, and Alarcón Rise) and an OMZ (Alfonso Basin) in the southern Gulf of California, by using high-throughput Illumina sequencing of the ITS1 region. We identified 102 fungal amplicon sequence variants (ASVs), principally affiliated to the Ascomycota and Basidiomycota. Our results also evidenced a high proportion of widely distributed, uncultured phylotypes (e.g., unknown clades closely related to the Basidiomycota such asFungisp. 18 and 19 formerly reported from deep-sea), evidencing the copious occurrence of novel fungal lineages with limited distribution to deep-sea sediments. Overall, the largest number of ASVs was recovered from high-temperature vent systems, corroborating these as diversity hotspots. In addition, clustering patterns across samples and the FUNGuild analysis revealed characteristic assemblages in each ecosystem, which could be linked to site-specific processes. This study provides baseline data paving the way for a better understanding of deep-sea fungal diversity, evidencing its potential importance in ecosystem functioning.
Spatial Distribution, Temporal Changes, and Knowledge Gaps in Basking Shark (Cetorhinus maximus) Sightings in the California Current Ecosystem
Authors: McInturf Alexandra G. , Muhling Barbara , Bizzarro Joseph J. , Fangue Nann A. , Ebert David A. , Caillaud Damien , Dewar Heidi
Published: February 2022

Among the largest fish species, the basking shark (Cetorhinus maximus) is found circumglobally in temperate and tropical waters. Though historical documents have recorded their presence in the California Current Ecosystem (CCE), basking sharks are now only rarely observed in this part of their range. We compiled recent and historical data from systematic surveys (1962–1997) and other sources (1973–2018) to (i) examine temporal patterns of basking shark sightings in the CCE, and (ii) determine the spatial, temporal, and environmental drivers that have affected basking shark presence and distribution here for the last 50 years. We first calculated variation in basking shark sightings and school size over time. We then generated species distribution models using the systematic survey data and evaluated the performance of these models against the more recent non-systematic sightings data. The sightings records indicated that the number of shark sightings was variable across years, but the number and probability of sightings declined in the mid-1980s. The systematic survey data showed up to nearly 4,000 sharks sighted per year until the 1990s, after which there were no sightings reported. In parallel, there was more than a 50% decline in school size from the 1960s to the 1980s (57.2 to 24.0 individuals per group). During the subsequent decades in the non-systematic data (>1990), less than 60 sharks were sighted per year. There were no schools larger than 10 reported, and the mean school size in the last decade (2010s) was 3.53 individuals per group. Low sea surface temperature and high chlorophyllaconcentration increased sightings probability, and prevailing climatic oscillations (El Nino-Southern Oscillation index, North Pacific Gyre Oscillation, Pacific Decadal Oscillation) were also correlated with basking shark presence. Lastly, we observed a significant shift in the seasonality of sightings, from the fall and spring during the systematic survey period to the summer months after the 2000s. We conclude by offering suggestions for future research and conservation efforts; specifically, coordinating the documentation of fisheries mortalities and sightings throughout the Pacific basin would facilitate more robust population estimates and identify sources of mortality. Additionally, monitoring shark fin markets and developing region-specific genetic markers would help ensure that convention on international trade in endangered species (CITES) regulations are being followed.
Microwave Synthesize Karaya Gum-Cu, Ni Nanoparticles Based Bionanocomposite as an Adsorbent for Malachite Green Dye: Kinetics and Thermodynamics
Authors: Saruchi  , Kumar Vaneet , Ghfar Ayman A. , Pandey Sadanand
Published: February 2022

A novel approach was used to synthesize karaya gum-Cu, Ni nanoparticles based bionanocomposite by microwave irradiation method. Synthesized bionanocomposite was characterized by different techniques like Fourier transform infrared spectroscopy (FTIR), Field Emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), High Resolution Transmission Electron Microscopy (HR-TEM), and Energy Dispersive X-Ray Analysis (EDX). The optimized condition for Karaya Gum-Cu-Ni–Bionanocomposite synthesis was the amount of solvent 4 ml, pH 10, time 20 s, power 100 W, monomer, and cross-linker concentration 14.11 mol L-1 and 0.1135 mol L-1, respectively. The maximum % swelling was found to be 1,176%. Different reaction parameters were optimized to get the maximum adsorption of malachite green dye. The maximum dye adsorption was found to be 94.1%. Different models for kinetics and isotherms were applied to analyze the adsorption data. Malachite green sorption onto bionanocomposite is best defined by pseudo second order kinetics, signifying that the dye uptake by the nanocomposite was organized by chemisorption method involving sharing of electrons in-between the cationic part of the dye as well as the anionic part of the bionanocomposite. Correlation coefficient (R2) was close to unity (0.99569). The R2 values of nanocomposite best fit in the Freundlich adsorption isotherm. The study confirmed the synthesized bionanocomposite was an efficient adsorbent for the adsorption of the harmful malachite green dye.
Numerical Simulation of Stainless Steel Powder Feeding in a Coaxial Nozzle for High Powder Efficiency in Laser Direct Energy Deposition
Authors: Kumar Hemanth , M Manjaiah
Published: February 2022

Direct energy deposition (DED) is an efficient manufacturing process for the fabrication of complex parts and repair of worn-out turbine blades. In DED, all the injected powder is not going to melt and solidify due to spattering, reflection, ejection, effect of inert gas, and turbulence around the melt pool. In this study, through numerical simulation, the effect of powder size and inert gas flow under coaxial nozzle was analyzed. The number of particle participation in the melt pool by the effect of inert gas and the size of powder particles were analyzed. The powder particle sizes considered for the study were 50–60, 60–70, 70–80, 80–90, 90–100, and 45–90 µm. Argon and helium gases were used as carrier gas and shielding gas, respectively. According to gas–solid multiphase simulation, the convergence distance of the powder flow and powder participation focal point was analyzed through numerical simulation. The simulated results showed that using argon gas as a carrier gas produced high powder efficiency compared to helium gas. The focal point is forming at 11.86 mm, approximately 12 mm from the nozzle exit, which occurred for 60–70-µm particle size. The powder particle participation efficiency obtained was 64.1% using argon gas as carrier gas.
Effects of Health Qigong Exercise on Lower Limb Motor Function in Parkinson's Disease
Authors: Li Xiying , Lv Chuanfen , Liu Xiaolei , Qin Xia
Published: February 2022

Purpose

This study explored the effects of Health Qigong exercise on lower limb motor function in patients with Parkinson's disease (PD).

Patients and Methods

A total of 40 patients with PD were recruited and randomly allocated into the experimental group and the control group. The experimental group completed an intervention of Health Qigong exercise over 12 weeks, while the control group did not perform any regular physical activity. Data relating to gait, lower-limb joint range of motion, Timed Up and Go, as well as scores for motor function scale from the Unified Parkinson's Comprehensive Rating Scale III (UPCRS III) before and after the intervention were collected for Repeated Measure ANOVA.

Results

Compared to the control group, Health Qigong exercise improved the constant- and high-speed stride length and gait velocity of patients, but not constant- and high-speed stride frequency. Left and right hip flexion and extension range were improved as well as left and right knee flexion range. Finally, Timed Up and Go time became significantly slower and UPCRS III score significantly decreased.

Conclusion

Health Qigong exercise can improve walking ability and lower limb joint range of motion in patients with PD, lessen motor difficulties, and improve the quality of life. This non-pharmacological exercise intervention may be a useful adjustment treatment for PD.
A Combined CRISP3 and SPINK1 Prognostic Grade in EPS-Urine and Establishment of Models to Predict Prognosis of Patients With Prostate Cancer
Authors: Chen Lizhu , Zhang Enchong , Guan Johnny , Chen Zhengjie , Ye Jianfeng , Liu Wangmin , He Jieqian , Yin Bo , Song Yongsheng , Zhang Mo
Published: February 2022

Background

Prostate cancer (PCa) is characterized by significant heterogeneity. Thus, novel prognostic indicators are required to improve prognosis and treatment.

Methods

Cysteine rich secretory protein 3 (CRISP3) and serine peptidase inhibitor Kazal type 1 (SPINK1) levels in expressed prostatic secretion (EPS)-urine collected during digital rectal examination of 496 patients histologically diagnosed with PCa were detected via enzyme-linked immunosorbent assay. A combined CRISP3 and SPINK1 prognostic grade (CSPG) was defined using cut-off values from receiver operating characteristic curves. Log-rank Kaplan-Meier survival curves investigated differences in prognosis between groups. Univariate and multivariate Cox analyses investigated the CSPG relationship with biochemical recurrence (BCR), cancer-specific survival (CSS), and overall survival (OS). Three prognostic models were developed and validated.

Conclusions

CRISP3 and SPINK1 levels increased with Gleason score progression, pathological T stage, and metastasis status. CSPG in EPS-urine, which was an effective independent prognostic variable, accurately predicted the prognosis of patients with PCa. Three clinical prognostic models using the CSPG for BCR, CSS, and OS were developed and validated.
Microbial Debromination of Polybrominated Diphenyl Ethers by Dehalococcoides-Containing Enrichment Culture
Authors: Zhao Siyan , Fan Siyan , He Yide , Zhang Yongjun
Published: February 2022

Polybrominated diphenyl ethers (PBDEs), commonly used as flame retardants in a wide variety of consumer products, are emerging persistent pollutants and ubiquitously distributed in the environment. The lack of proper bacterial populations to detoxify these recalcitrant pollutants, in particular of higher brominated congeners, has confounded the attempts to bioremediate PBDE-contaminated sites. In this study, we report a Dehalococcoides-containing enrichment culture, PB, which completely debrominates 0.44 μM tetra-brominated diphenyl ether (BDE) 47 to diphenyl ether within 25 days (0.07 μM Br–/day) and extensively debrominates 62.4 ± 4.5% of 0.34 μM hepta-BDE 183 (0.006 μM Br–/day) with a predominant generation of penta- through tri-BDEs as well as small amounts of diphenyl ether within 120 days. Later, a marked acceleration rate (0.021 μM Br–/day) and more extensive debromination (87.7 ± 2.1%) of 0.38 μM hepta-BDE 183 was observed in the presence of 0.44 μM tetra-BDE 47, which is achieved via the faster growth rate of responsible bacterial populations on lower BDE-47 and debromination by expressed BDE-47 reductive dehalogenases. Therefore, the PB enrichment culture can serve as a potential candidate for in situ PBDE bioremediation since both BDE-47 and BDE-183 are dominant and representative BDE congeners and often coexist in contaminated sites.
How Ciliated Protists Survive by Cysts: Some Key Points During Encystment and Excystment
Authors: Li Yuqing , Wang Yurui , Zhang Shijing , Maurer-Alcalá Xyrus X. , Yan Ying
Published: February 2022

Forming cysts is a common and important bionomic strategy for microorganisms to persist in harsh environments. In ciliated protists, many species have been reported to form cysts when facing unfavorable conditions. Despite traditional studies on the morphological features of cysts and the chemical composition of cyst wall, recent research has focused more on the molecular mechanisms of encystment. The present work reviews studies on developmental features and molecular information of resting cysts in ciliates, and pays more attention to the following questions: what are the inducing factors of encystment and excystment? How does the cell change morphologically during these dynamic processes? And what molecular mechanisms underlie those changes? We also present and summarize the characteristics of cysts from diverse ciliate lineages in a phylogenetic framework, aiming to provide new perspectives for studies on adaptive evolution of unicellular eukaryotes.
Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments
Authors: Koh Xiu Pei , Shen Zhiyong , Woo Chun Fai , Yu Yanping , Lun Hau In , Cheung Sze Wan , Kwan Joseph Kai Cho , Lau Stanley Chun Kwan
Published: February 2022

Escherichia colinot only inhabit the large intestines of human and warm-blooded animals but could also persist in the external environment. However, current knowledge was largely based on host-associated strains. Moreover, crypticEscherichiaclades that were often misidentified asE. coliby conventional diagnostic methods were discovered. Failure to distinguish them fromE. coli sensu strictocould lead to inaccurate conclusions about the population genetics ofE. coli. Based on seven housekeeping genes, we determine the genetic and ecological diversity ofE. coliand cryptic clades as they occupy aquatic habitats with different characteristics and human impact levels in subtropical Hong Kong. Contrary to previous reports, clade II was the most abundant cryptic lineage co-isolated withE. coli, being especially abundant in relatively pristine subtropical aquatic environments. The phylogenetically distinct cryptic clades andE. colishowed limited recombination and significant genetic divergence. Analyses indicated that these clade II strains were ecologically differentiated from typicalE. coli; some may even represent novel environmentalEscherichiaclades that were closely related to the original clade II strains of fecal origins.E. coliof diverse origins exhibited clonality amidst divergent genotypes STs, echoing other studies in that recombination in housekeeping genes was insufficient to disrupt phylogenetic signals of the largely clonalE. coli. Notably, environmentalE. coliwere less diverse than fecal isolates despite contributing many new alleles and STs. Finally, we demonstrated that human activities influenced the distribution ofE. coliand clade II in a small aquatic continuum. Moving from relatively pristine sites toward areas with higher human disturbance, the abundance of clade II isolates and newE. coligenotypes reduces, whileE. colibearing class I integrons and belonging to CCs of public health concern accumulates. Altogether, this work revealed the new genetic diversity ofE. coliand cryptic clades embedded in selected subtropical aquatic habitats, especially relatively pristine sites, which will aid a more thorough understanding of the extent of their genetic and functional variations in relation to diverse habitats with varied conditions.
Plant Growth Stage Drives the Temporal and Spatial Dynamics of the Bacterial Microbiome in the Rhizosphere of Vigna subterranea
Authors: Ajilogba Caroline Fadeke , Olanrewaju Oluwaseyi Samuel , Babalola Olubukola Oluranti
Published: February 2022

Bambara groundnut (BGN) is an underutilized legume commonly found in sub-Saharan Africa. It thrives in marginal soils and is resistant to drought stress. Several studies have been carried out on the nutritional properties of BGN, but very little is known about the effects of plant growth changes and development on rhizosphere bacterial dynamics and function. This study reports on the bacterial dynamics and function in the bulk and rhizosphere soils of BGN at different growth stages (vegetative, flowering, pod-filling, and maturation stages). Aside from the maturation stage that shows distinct community structure from the other growth stages, results obtained showed no significant differences in bacterial community structure among the other growth stages. At a closer level, Actinobacteria, Proteobacteria, and Acidobacteria were dominant in rhizosphere soils at all growth stages. The bulk soil had the least average phyla abundance, while the maturity stage was characterized by the highest average phyla abundance. Rubrobacter, Acidobacterium, and Skermanella were the most predominant genus. It was observed from the analysis of operational taxonomic units that there was significant change in the bacterial structure of the rhizosphere with a higher abundance of potential plant growth-promoting rhizobacteria, at the different growth stages, which include the genera Bacillus and Acidobacterium. Biomarker analysis revealed 7 and 4 highly significant bacterial biomarkers by linear discriminant analysis effect size and random forest analysis at the maturation stage, respectively. The results obtained in this study demonstrated that the bacterial communities of BGN rhizosphere microbiome dynamics and function are influenced by the plant’s growth stages.
The Dynamic Change of Immune Responses Between Acute and Recurrence Stages of Rodent Malaria Infection
Authors: Chen Suilin , Gao Yuanli , Fan Yongling , Guo Shuai , Zhou Jian , Liu Taiping , Xu Wenyue
Published: February 2022

Malaria infections are persistent as frequent recrudescence of the disease may occur following the acute infection stage, but the different immune responses that control the acute and recrudescence stages are still largely unknown. Using single-cell RNA sequencing (scRNA-seq), we showed that the number of Th1 and plasma cells in the spleen was significantly reduced during the recurrence stage compared to the acute stage of Plasmodium chabaudi chabaudi AS (P. chabaudi) infection. Additionally, the ability of both CD4+ T cell responses and B cells to control P. chabaudi recurrence was significantly reduced compared to their roles in the control of acute infection. In contrast, the number of innate immune cells, including red pulp macrophages (RPMs), gamma delta (γδ) T cells, and Dendritic cells (DCs) were significantly increased during the recurrence stage and showed to be critical for P. chabaudi infection recurrence control. Thus, our data strongly suggest the complementary role of innate immune responses in controlling malaria recrudescence when adaptive immune responses are suppressed. These findings shed new light on the development of immune interventions against malaria.