bluuebunny/crossref_metadata_2025 huggingface dataset:
Source water microorganism assessment in three cities in China: A comparative study
Authors: Liu Yang , Smith Charlotte D. , Li Hongxing , Wang Duochun
Published: November 2022

Reservoirs, rivers and groundwater are the top three sources of drinking water supplies in China. As microbial contamination of drinking water is still a prominent water quality problem in rural areas, understanding the microbial quality of these sources is important to the public’s health and economic prosperity of communities. In this study, three types of source water samples were collected from three cities in China. Bacterial contamination indicators testing showed that: total coliforms (TCs) and potential E. coli were not detected in groundwater, but both were detected in river and reservoir water. Total bacteria (TB) of rivers and Res-Ⅰ (sampling site Ⅰ of reservoir water) were greater than 100 CFU/ml, while less than 100 CFU/ml from Res-Ⅱ (sampling site Ⅱ of reservoir water) and groundwater. Salmonella spp. were isolated from river water and no pathogenic microorganisms were isolated from the other two types of water sources by selective culture. Microbial communities testing by 16S rRNA gene amplicon sequencing indicated that, there were 14,114 operational taxonomic unit (OTU) of microbial abundance from all 30 samples, and most OTUs were only present in river water (15.17%), reservoir water (10.46%) or groundwater (43.91%), while 1540 OTUs (10.91%) were shared by all three types of water sources. There were significant differences in the microbial communities of the three types of source water (p < 0.05). Based on the Ace, Chao, and Shannon-Weaver, and Simpson indexes, the species diversity of bacteria in groundwater was higher than in river water or reservoir water (p < 0.05), with the reservoir water having the lowest diversity of bacteria. More than seven potential pathogenic bacteria were detected in 30 water samples, for example, E. coli, Staphylococcus aureus, Clostridioides difficile and Bacteroides fragilis were present in all three types of water sources, while other pathogenic bacteria occurred only in some of the water samples. Clostridium perfringens were detected in river water and groundwater. This study adds information on the microbial communities of various drinking water sources in rural China, which is valuable to water treatment and waterborne pathogen studies. In addition, this study supports the idea that 16S rRNA gene amplicon sequencing could be used as a supplementary tool for sources water quality monitoring.
Leaf toughness increases with tree height and is associated with internal leaf structure and photosynthetic traits in a tropical rain forest
Authors: Kenzo Tanaka , Mohamad Mohizah , Ichie Tomoaki
Published: November 2022

Although leaf toughness is an essential plant adaptation to herbivore pressure and environmental stress, the relationships of leaf toughness with leaf anatomy and photosynthetic traits, and its spatial variations within tropical rainforests, remain poorly understood. We measured these traits in 103 tree species belonging to 27 families from the canopy to understory using a canopy crane system in a tropical rainforest in Sarawak, Malaysia. We focused on the leaf anatomical trait of bundle-sheath extensions (BSEs) around the vascular bundle due to their diverse ecophysiological functions. We divided the trees into heterobaric species with BSEs and homobaric species lacking BSEs, to investigate the relationships of leaf toughness with tree height, leaf functional traits such as carbon (C) and nitrogen (N) content, thickness, leaf mass per area (LMA) and the maximum photosynthetic rate (Pmax). Leaf toughness, LMA, thickness and C and N contents increased with height regardless of BSE presence. Heterobaric leaves had greater toughness than homobaric leaves, whereas leaf thickness, LMA and C were similar between the two leaf types throughout the height gradient. We found that standardized toughness per thickness or C was greater in heterobaric species, as BSEs consist mainly of fibrous tissue. Pmax was higher for heterobaric than homobaric leaves in the upper canopy presumably due to the functions of BSEs, including water conductivity, but did not differ with plant type in the lower layers. In other words, heterobaric species efficiently exploit the advantages of tougher leaves and higher Pmax by having BSEs. The increased proportion of heterobaric species, with their tougher leaves and higher Pmax, in the upper canopy is consistent with adaptation to physically stressful conditions in the tropical rainforest canopy, including high herbivore pressure and strong light.
Characterization of pregnancy outcome of women with an offspring with inborn errors of metabolism: A population-based study
Authors: Epstein Weiss Tali , Erez Offer , Hazan Itai , Babiev Amit-Shira , Staretz Chacham Orna
Published: November 2022

Introduction:Inborn errors of metabolism (IEM) are scarce, and their diagnosis is often made after birth. This has led to the perception that most fetuses affected by these disorders do not become clinically apparent during pregnancy.Our aim was to determine the obstetrical characteristics of women with an offspring affected by IEM.

Methods:This population-based retrospective cohort study included all women who delivered at the Soroka University Medical Center (SUMC) from 1988 to 2017 who met the inclusion criteria. Mothers who had an offspring with IEM were included in the study group, and those who had offsprings without IEM comprised the comparison group.

Results:A total of 388,813 pregnancies were included in the study, and 184 of them were complicated by a fetus with IEM. The number of Bedouin women was higher in the IEM-affected infant group than in the comparison group (90.8%vs. 53.3%,p< 0.001); women who had a fetus with IEM had a higher rate of polyhydramnios (7.1%vs. 3.2%,p= 0.005), HELLP syndrome (3.3%vs. 1.1%,p= 0.014), and preterm birth (20.7%vs. 10.1%,p< 0.001); neonates with IEM had lower mean birth weight (p< 0.001), lower Apgar scores at 1′ and 5′ minutes (p< 0.001), and a higher rate of fetal growth restriction (FGR) (p< 0.001), postpartum death <28 days (p< 0.001), and neonatal death (p< 0.001) than those in the comparison group. Pregnancies with IEM fetuses were independently associated with preterm birth (OR 2.00; CI 1.4–3), polyhydramnios (OR 2.08; CI 1.17–3.71), and FGR (OR 2.24; CI 1.2–4.19). Each family of metabolic diseases is independently associated with specific pregnancy complications (i.e., mitochondrial diseases are associated with HELLP syndrome (OR 5.6; CI 1.8–17), and lysosomal storage disease are associated with nonimmune hydrops fetalis (OR 26.4; CI 3.39–206).

Conclusion:This study reports for the first time, an independent association of IEM with specific complications of pregnancy. This observation has clinical implications, as the identification of specific pregnancy complications in a population at risk for IEM can assist in the prenatal diagnosis of an affected fetus.
Identification of COVID-19 severity biomarkers based on feature selection on single-cell RNA-Seq data of CD8+ T cells
Authors: Lu Jian , Meng Mei , Zhou XianChao , Ding Shijian , Feng KaiYan , Zeng Zhenbing , Huang Tao , Cai Yu-Dong
Published: November 2022

The global outbreak of the COVID-19 epidemic has become a major public health problem. COVID-19 virus infection triggers a complex immune response. CD8+ T cells, in particular, play an essential role in controlling the severity of the disease. However, the mechanism of the regulatory role of CD8+ T cells on COVID-19 remains poorly investigated. In this study, single-cell gene expression profiles from three CD8+ T cell subtypes (effector, memory, and naive T cells) were downloaded. Each cell subtype included three disease states, namely, acute COVID-19, convalescent COVID-19, and unexposed individuals. The profiles on each cell subtype were individually analyzed in the same way. Irrelevant features in the profiles were first excluded by the Boruta method. The remaining features for each CD8+ T cells subtype were further analyzed by Max-Relevance and Min-Redundancy, Monte Carlo feature selection, and light gradient boosting machine methods to obtain three feature lists. These lists were then brought into the incremental feature selection method to determine the optimal features for each cell subtype. Their corresponding genes may be latent biomarkers to determine COVID-19 severity. Genes, such as ZFP36, DUSP1, TCR, and IL7R, can be confirmed to play an immune regulatory role in COVID-19 infection and recovery. The results of functional enrichment analysis revealed that these important genes may be associated with immune functions, such as response to cAMP, response to virus, T cell receptor complex, T cell activation, and T cell differentiation. This study further set up different gene expression pattens, represented by classification rules, on three states of COVID-19 and constructed several efficient classifiers to distinguish COVID-19 severity. The findings of this study provided new insights into the biological processes of CD8+ T cells in regulating the immune response.
Retinoids in cancer chemoprevention and therapy: Meta-analysis of randomized controlled trials
Authors: Chen Shuting , Hu Qinchao , Tao Xiaoan , Xia Juan , Wu Tong , Cheng Bin , Wang Juan
Published: November 2022

Retinoids, natural and synthetic derivatives of vitamin A, have many regulatory functions in human body, including regulating cellular proliferation, differentiation, apoptosis. Moreover, retinoids have been used successfully for the treatment of certain malignancies, especially acute promyelocytic leukemia (APL) in adults and neuroblastoma in children. However, retinoids have not yet been translated into effective systemic treatments for most solid cancers. Some recent studies have shown that retinoids promote tumorigenesis. Therefore, we performed this meta-analysis to systematically evaluate the efficacy of retinoids in the chemoprevention and treatment of cancers. We performed literature search of several electronic databases, including PubMed, Embase and Cochrane Library from 2000 January to 2021 November. Various outcomes were applied to investigate the potential of retinoids for prevention and treatment of cancers. The primary outcomes in this study were disease recurrence and clinical response. The secondary outcomes included overall survival (OS), cancer development, disease progression and event-free survival. We identified 39 randomized controlled trials with 15,627 patients in this study. Our results showed that lower recurrence rate and better clinical response were obtained in retinoids treated patients with cancer or premalignancy as compared with control. The differences were statistically significant (RR = 0.85, 95% CI = 0.74–0.96, p = 0.01; RR = 1.24, 95% CI = 1.03–1.49, p = 0.02, respectively). Retinoids treatment was not associated with improvement in overall survival, cancer development, disease progression or event-free survival. Subgroup analysis conducted based on cancer type showed that patients benefited from retinoids treatment in APL, renal cell carcinoma, hepatocellular carcinoma, lung cancer, Kaposi sarcoma, and complete hydatidiform mole. No significant therapeutic effect was noted in head and neck cancer, acute myeloid leukemia (AML), melanoma, breast cancer, bladder cancer, cervical intraepithelial neoplasia (CIN) or cervical carcinoma. Subgroup analysis based on tumor classification demonstrated that retinoids group obtained a lower recurrence rate and better clinical response than control group in solid cancers. In conclusion, clinical application of retinoids was associated with reduction in disease recurrence and improvement in clinical response, illustrating that retinoids play a key role in cancer prevention and therapy. Further research is needed to broaden the utility of retinoids in other types of cancers.

Systematic Review Registration: PROSPERO, identifier CRD42022296706.
Resolution of otitis media in a humanized mouse model
Authors: Son Ye Lin , Pak Kwang , Muradagha Nada , Heo Kyung Wook , Leichtle Anke , Kurabi Arwa
Published: November 2022

Otitis media (OM) is one of the largest public health problems of children and has devastating impacts in developing countries. The substantial medical and human costs involved have led to research to understand the disease and improve treatment. Animal models of OM have yielded critical information about the immune, inflammatory and genetic mechanisms of OM. However, it is important to link animal studies to human immune and inflammatory responses. In recent years, “humanized” mice have become a valuable tool to study the human immune system in an animal model. Here we describe the first use of humanized mice to study OM. We demonstrate that humanized mice with a sufficient degree of engraftment recapitulate a normal middle ear (ME) inflammatory response to bacterial infection, including the recruitment of human immune cells, and exhibit normal recovery. Moreover, these animals exhibit regulated expression of human-specific immune and inflammatory genes in the ME. In contrast, mice with insufficient engraftment fail to resolve OM. This model has many potential uses in OM research, including using hematopoietic stem cells from patients with differing degrees of OM susceptibility, to understand the role of human immune responses in proneness to this common childhood disease.
ImmUniverse Consortium: Multi-omics integrative approach in personalized medicine for immune-mediated inflammatory diseases
Authors: Vetrano Stefania , Bouma Gerben , Benschop Robert J. , Birngruber Thomas , Costanzo Antonio , D’Haens G. R. A. M. , Frasca Loredana , Hillenbrand Rainer , Iversen Lars , Johansen Claus , Kaser Arthur , Koenen Hans J. P. M. , Noehammer Christa , Peyrin-Biroulet Laurent , Raes Jeroen , Ricotti Leonardo , Rosenstiel Philip , Satagopam Venkata P. , Schreiber Stefan , Vermeire Severine , Wollenberg Andreas , Weidinger Stephan , Ziemek Daniel , Danese Silvio ,   ImmUniverse Consortium
Published: November 2022

Immune mediated inflammatory diseases (IMIDs) are a heterogeneous group of debilitating, multifactorial and unrelated conditions featured by a dysregulated immune response leading to destructive chronic inflammation. The immune dysregulation can affect various organ systems: gut (e.g., inflammatory bowel disease), joints (e.g., rheumatoid arthritis), skin (e.g., psoriasis, atopic dermatitis), resulting in significant morbidity, reduced quality of life, increased risk for comorbidities, and premature death. As there are no reliable disease progression and therapy response biomarkers currently available, it is very hard to predict how the disease will develop and which treatments will be effective in a given patient. In addition, a considerable proportion of patients do not respond sufficiently to the treatment. ImmUniverse is a large collaborative consortium of 27 partners funded by the Innovative Medicine Initiative (IMI), which is sponsored by the European Union (Horizon 2020) and in-kind contributions of participating pharmaceutical companies within the European Federation of Pharmaceutical Industries and Associations (EFPIA). ImmUniverse aims to advance our understanding of the molecular mechanisms underlying two immune-mediated diseases, ulcerative colitis (UC) and atopic dermatitis (AD), by pursuing an integrative multi-omics approach. As a consequence of the heterogeneity among IMIDs patients, a comprehensive, evidence-based identification of novel biomarkers is necessary to enable appropriate patient stratification that would account for the inter-individual differences in disease severity, drug efficacy, side effects or prognosis. This would guide clinicians in the management of patients and represent a major step towards personalized medicine. ImmUniverse will combine the existing and novel advanced technologies, including multi-omics, to characterize both the tissue microenvironment and blood. This comprehensive, systems biology-oriented approach will allow for identification and validation of tissue and circulating biomarker signatures as well as mechanistic principles, which will provide information about disease severity and future disease progression. This truly makes the ImmUniverse Consortium an unparalleled approach.
Role of FK506-sensitive signals in asthmatic lung inflammation
Authors: Tomiaki Chihiro , Miyauchi Kosuke , Ki Sewon , Suzuki Yoshie , Suzuki Narumi , Morimoto Hiroshi , Mukoyama Yohei , Kubo Masato
Published: November 2022

Asthma is airway inflammatory diseases caused by the activation of group 2 innate lymphoid cells (ILC2s) and type 2 helper T (TH2) cells. Cysteine proteases allergen cause tissue damage to airway epithelial cells and activate ILC2-mediated type 2 airway inflammation. FK506 is an immunosuppressive agent against calcium-dependent NFAT activation that is also effective against asthmatic inflammation. However, the effects of FK506 on cysteine protease allergen-mediated airway inflammation remain unclear. In this study, we investigated the suppressive effects of FK506 on airway inflammation. FK506 had a partial inhibitory effect on ILC2-dependent eosinophil inflammation and a robust inhibitory effect on T cell-dependent eosinophil inflammation in a cysteine protease-induced mouse asthma model. The infiltration of T1/ST2+ CD4 T cells in the lungs contributed to the persistence of eosinophil infiltration in the airway; FK506 completely inhibited the infiltration of T1/ST2+ CD4 T cells. In the initial phase, FK506 treatment targeted lung ILC2 activation induced by leukotriene B4 (LTB4)-mediated calcium signaling, but not IL-33 signaling. FK506 also inhibited the IL-13-dependent accumulation of T1/ST2+ CD4 T cells in the lungs of the later responses. These results indicated that FK506 potently suppressed airway inflammation by targeting ILC2 activation and T1/ST2+ CD4 T cell accumulation.
Cold stimuli, hot topic: An updated review on the biological activity of menthol in relation to inflammation
Authors: Cheng Haojin , An Xuemei
Published: November 2022

Background

Rising incidence of inflammation-related diseases is an increasing concern nowadays. However, while menthol is a wildly-used and efficacious complementary medicine, its pharmacological mechanism still remains uncertain. Superimposed upon that, the aim of this review is to summarize the contemporary evidence of menthol’s anti-inflammatory activity.

Methods

Using the pharmacopeias and electronic databases, including Web of Science, PubMed, and CNKI, this study analyzed the relevant research articles and review articles from 2002 to 2022 and concluded those results and conjectures to finish this article.

Results

The decrease in pro-inflammatory cytokines and related inflammatory markers, as well as associated pathway activation, was found to play the greatest role in the protective effects of menthol against inflammatory damage or association with protection against chronic inflammation.

Conclusion

This review mainly concludes the progress in menthol’s anti-inflammatory activity. Further studies are needed to establish relationships between the mechanisms of action and to clarify the clinical relevance of any anti-inflammatory effects.
A longitudinal study of C1q and anti-C1q autoantibodies in homologous and heterologous pregnancies for predicting pre-eclampsia
Authors: Agostinis Chiara , Zito Gabriella , Toffoli Miriam , Peterlunger Isabel , Simoni Livia , Balduit Andrea , Curtolo Erica , Mangogna Alessandro , Belmonte Beatrice , Vacca Davide , Romano Federico , Stampalija Tamara , Salviato Tiziana , Defendi Federica , Di Simone Nicoletta , Kishore Uday , Ricci Giuseppe , Bulla Roberta
Published: November 2022

C1q, the recognition molecule of the classical pathway of the complement system, plays a central role in pregnancy. Lack of C1q is characterized by poor trophoblast invasion and pregnancy failure. C1q can be the target of an antibody response: anti‐C1q autoantibodies (anti-C1q) are present in several infectious and autoimmune diseases. The presence of these autoantibodies has been detected also in 2-8% of the general population. Recent evidence indicates that women who undergo assisted reproductive technology (ART) have an increased risk of developing pre-eclampsia (PE), particularly oocyte donation (OD) pregnancies. The aim of this study was to characterize the levels of C1q and anti-C1q in PE gestations, in healthy spontaneous, homologous and heterologous ART pregnancies. Serum of the following four groups of women, who were followed throughout two or three trimesters, were collected: PE, patients diagnosed with PE; OD, oocyte donation recipients; HOM, homologous ART women; Sp, spontaneous physiological pregnancy. Our results indicate that PE patients have lower levels of anti-C1q. In ART pregnant women, the trend of C1q and anti-C1q levels were similar to PE patients, even though these women did not develop PE-like symptoms during pregnancy. This finding suggests an immunological dysfunction at the foetal-maternal interface in ART pregnancies, a hypothesis confirmed by the observation of C1q deposition in placentae derived from OD, comparable to PE. Since significantly lower levels of anti-C1q were detected in PE compared to healthy control sera, we hypothesize the possible binding on placental syncytiotrophoblast microvesicles (STBM), which are increased in the circulation of PE mothers. Furthermore, the characterization of the binding-epitope of anti-C1q revealed that “physiological” autoantibodies were mainly directed against C1q globular domain. We concluded that anti-C1q could have a physiological role in pregnancy: during the healthy spontaneous pregnancy the raised levels of these autoantibodies can be important for the clearance of STBM. In PE and in pathological pregnancies (but also in OD pregnancies), the increase in syncytiotrophoblast apoptosis and consequent increase of the circulating STMB levels lead to a consumption of C1q and anti-C1q.
Circulating Levels of Anti-C1q and Anti-Factor H Autoantibodies and Their Targets in Normal Pregnancy and Preeclampsia
Authors: Dijkstra Douwe Jan , Lokki A. Inkeri , Gierman Lobke Marijn , Borggreven Nicole Veronique , van der Keur Carin , Eikmans Michael , Gelderman Kyra Andrea , Laivuori Hannele ,   The FINNPEC Core Investigator Group, Iversen Ann-Charlotte , van der Hoorn Marie-Louise P. , Trouw Leendert Adrianus
Published: November 2022

Preeclampsia (PE) generally manifests in the second half of pregnancy with hypertension and proteinuria. The understanding of the origin and mechanism behind PE is incomplete, although there is clearly an immune component to this disorder. The placenta constitutes a complicated immune interface between fetal and maternal cells, where regulation and tolerance are key. Stress factors from placental dysfunction in PE are released to the maternal circulation evoking the maternal response. Several complement factors play a role within this intricate landscape, including C1q in vascular remodeling and Factor H (FH) as the key regulator of alternative pathway complement activation. We hypothesize that decreased levels of C1q or FH, or disturbance of their function by autoantibodies, may be associated with PE. Autoantibodies against C1q and FH and the concentrations of C1q and FH were measured by ELISA in maternal sera from women with preeclamptic and normal pregnancies. Samples originated from cohorts collected in the Netherlands (n=63 PE; n=174 control pregnancies, n=51 nonpregnant), Finland (n=181 PE; n=63 control pregnancies) and Norway (n=59 PE; n=27 control pregnancies). Serum C1q and FH concentrations were higher in control pregnancy than in nonpregnant women. No significant differences were observed for serum C1q between preeclamptic and control pregnancy in any of the three cohorts. Serum levels of FH were lower in preeclamptic pregnancies compared to control pregnancies in two of the cohorts, this effect was driven by the early onset PE cases. Neither anti-C1q autoantibodies nor anti-FH autoantibodies levels differed between women with PE and normal pregnancies. In conclusion, levels of anti-C1q and anti-FH autoantibodies are not increased in PE. C1q and FH are increased in pregnancy, but importantly, a decrease in FH concentration is associated with PE.
Circular RNAs as emerging regulators in COVID-19 pathogenesis and progression
Authors: Gao Xiaojun , Fang Dan , Liang Yu , Deng Xin , Chen Ni , Zeng Min , Luo Mao
Published: November 2022

Coronavirus disease 2019 (COVID-19), an infectious acute respiratory disease caused by a newly emerging RNA virus, is a still-growing pandemic that has caused more than 6 million deaths globally and has seriously threatened the lives and health of people across the world. Currently, several drugs have been used in the clinical treatment of COVID-19, such as small molecules, neutralizing antibodies, and monoclonal antibodies. In addition, several vaccines have been used to prevent the spread of the pandemic, such as adenovirus vector vaccines, inactivated vaccines, recombinant subunit vaccines, and nucleic acid vaccines. However, the efficacy of vaccines and the onset of adverse reactions vary among individuals. Accumulating evidence has demonstrated that circular RNAs (circRNAs) are crucial regulators of viral infections and antiviral immune responses and are heavily involved in COVID-19 pathologies. During novel coronavirus infection, circRNAs not only directly affect the transcription process and interfere with viral replication but also indirectly regulate biological processes, including virus-host receptor binding and the immune response. Consequently, understanding the expression and function of circRNAs during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will provide novel insights into the development of circRNA-based methods. In this review, we summarize recent progress on the roles and underlying mechanisms of circRNAs that regulate the inflammatory response, viral replication, immune evasion, and cytokines induced by SARS-CoV-2 infection, and thus highlighting the diagnostic and therapeutic challenges in the treatment of COVID-19 and future research directions.
A recombinant Artemisia vulgaris pollen adjuvanted Art v 1 protein-based vaccine treats allergic rhinitis and bronchial asthma using pre- and co-seasonal ultrashort immunotherapy regimens in sensitized mice
Authors: Babayeva Meruert , Tabynov Kairat , Nurpeisov Tair , Fomin Gleb , Renukaradhya Gourapura J. , Petrovsky Nikolai , Tabynov Kaissar
Published: November 2022

Allergic rhinitis is an important risk factor for bronchial asthma. Allergen-specific immunotherapy (ASIT) is the gold standard for treatment of allergic rhinitis, conjunctivitis, and asthma. A disadvantage of current ASIT methods is the length of therapy which requires numerous allergen administrations. The success of ASIT is determined by its schedule, which, depending on the vaccine and type of allergy, can be pre-seasonal (before the allergy season begins), combined pre/co-seasonal (during the allergy season) etc. The aim of the present study was to evaluate a vaccine based on recombinant Artemisia vulgaris pollen major Art v 1 protein formulated with ISA-51 adjuvant for therapy of allergic rhinitis and bronchial asthma in Artemisia-sensitized mice in an ultrashort (4 subcutaneous injections at weekly intervals) pre- and co-seasonal ASIT regimen.

To simulate co-seasonal ASIT in mice, mice were regularly challenged with intranasal and nebulized Artemisia vulgaris pollen extract at the same time as receiving subcutaneous ASIT. For comparison, we used a previous Art v 1 protein vaccine formulated with SWE adjuvant, which in this study was modified by adding CpG oligonucleotide (Th1-biasing synthetic toll-like receptor 9 agonist), and a commercial vaccine containing a modified Artemisia vulgaris extract with aluminum hydroxide adjuvant. The therapeutic potential of Art v 1 based vaccine formulations with different ASIT regimens was evaluated in high and low (10 times lower) dose regimens.

The ISA-51-adjuvanted vaccine formulations were the only ones among those studied in the ultrashort pre- and co-seasonal ASIT regimens to provide significant reduction in both signs of allergic rhinitis and bronchial asthma in sensitized mice (vs. positive control). In the ISA-51 adjuvanted group, immune response polarization toward Th1/Treg was observed in pre-seasonal ASIT, as reflected in a significant decrease in the serum level of total and Art v 1-specific IgE and increased ratios of allergen-specific IgG2a/IgG1 and IFN-γ/IL-4. The high dose SWE-CpG-adjuvanted vaccine had similar efficacy to the ISA-51 adjuvanted groups whereas the commercial vaccine showed significantly less effectiveness.

The findings support further preclinical safety studies of the Art v 1-based vaccine formulated with ISA-51 adjuvant.
Comparison of macroalgae meadows in warm Atlantic versus cold Arctic regimes in the high-Arctic Svalbard
Authors: Wiktor Józef M. , Tatarek Agnieszka , Kruss Aleksandra , Singh Rakesh Kumar , Wiktor Józef M. , Søreide Janne E.
Published: November 2022

A warmer Arctic with less sea ice will likely improve macroalgae growth conditions, but observational data to support this hypothesis are scarce. In this study, we combined hydroacoustic and video inspections to compare the depth of growth, density and thickness of macroalgae (>10 cm) meadows in two contrasting climate regimes in Svalbard 1) the warm, ice free, Atlantic influenced West Spitsbergen and 2) the cold, Arctic and seasonal ice covered East Spitsbergen. Both places had similar insolation and comparable turbidity levels. Macroalgae communities at both places were similar and were formed mainly by common north Atlantic kelp species:Saccharina latissima, Alaria esculenta, Laminaria digitataandL. hyperborea. However, the density of the bottom coverage and thalli condition were strikingly different between the two sites. Algae at the warmer site were intact and fully developed and occupied most of the available hard substrate. At the colder site, only patchy macroalgae canopies were found and most thallies were physically damaged and trimmed at a uniform height due to physical ice scouring. These differences in macroalgal density and thalli condition were only found at depths down to 5 m. Deeper, no distinct differences were observed between the warm and cold sites. Sea urchins were only observed at the warm site, but in few numbers with no visible negative top-down control on macroalgae growth.
Remediation of water contaminated with polycyclic aromatic hydrocarbons using liquid phase plasma: Influence of electrical discharge condition
Authors: Kim Ui-Jun , Saito Nagahiro , Lee Seung-Hyo
Published: November 2022

Although the number of vessels with exhaust gas cleaning systems (EGCSs or scrubbers) has sharply increased to comply with strengthened regulations for marine environment, secondary pollutions are caused by discharged polycyclic aromatic hydrocarbons (PAHs) from scrubber effluent. Here, liquid-phase plasma (LPP) is employed to remediate water contaminated with PAHs. The increased frequency and pulse width enhanced the degradation efficiency, and 93.3, 90.7, 86.0, and 85.4% for naphthalene (Nap), acenaphthene (Ace), fluorene (Flu), and phenanthrene (Phe), respectively, are degraded at a frequency of 30 kHz and pulse width of 3 μs in 10 min. Considering physical condition of the plasma, long pulse width accelerated electrons, leading to increased generation of active species from intensified collision between electrons and surrounding molecules. Conversely, high frequency decelerated electrons due to the excessive changes in the polarity. However, the increased number of plasma discharges results in the generation of numerous active species. Generations of •OH and O radicals are confirmed by optical emission spectrometry and electron paramagnetic resonance. In addition, changes in functional groups which are corresponding to hydroxyl and oxygen groups are identified by Fourier transform infrared spectroscopy. Total PAHs in real scrubber are reduced from 1.1 to 0.4 μgL-1 with degradation efficiency of 63.6% after 10 min of LPP treatment. This study suggests LPP can be a promising method to protect diverse aqueous environments and provides optimal electrical discharge condition for degradation of organic pollutants.
Concentration and distribution of phytoplankton nitrogen and carbon in the Northwest Atlantic and Indian Ocean: A simple model with applications in satellite remote sensing
Authors: Maniaci Giuseppe , Brewin Robert J. W. , Sathyendranath Shubha
Published: November 2022

Despite the critical role phytoplankton play in marine biogeochemical cycles, direct methods for determining the content of two key elements in natural phytoplankton samples, nitrogen (N) and carbon (C), remain difficult, and such observations are sparse. Here, we extend an existing approach to derive phytoplankton N and C indirectly from a large dataset of in-situ particulate N and C, and Turner fluorometric chlorophyll-a (Chl-a), gathered in the off-shore waters of the Northwest Atlantic and the Arabian Sea. This method uses quantile regression (QR) to partition particulate C and N into autotrophic and non-autotrophic fractions. Both the phytoplankton C and N estimates were combined to compute the C:N ratio. The algal contributions to total N and C increased with increasing Chl-a, whilst the C:N ratio decreased with increasing Chl-a. However, the C:N ratio remained close to the Redfield ratio over the entire Chl-a range. Five different phytoplankton taxa within the samples were identified using data from high-performance liquid chromatography pigment analysis. All algal groups had a C:N ratio higher than Redfield, but for diatoms, the ratio was closer to the Redfield ratio, whereas for Prochlorococcus, other cyanobacteria and green algae, the ratio was significantly higher. The model was applied to remotely-sensed estimates of Chl-a to map the geographical distribution of phytoplankton C, N, and C:N in the two regions from where the data were acquired. Estimates of phytoplankton C and N were found to be consistent with literature values, indirectly validating the approach. The work illustrates how a simple model can be used to derive information on the phytoplankton elemental composition, and be applied to remote sensing data, to map pools of elements like nitrogen, not currently provided by satellite services.
Nuclear transformation of a dinoflagellate symbiont of corals
Authors: Gornik Sebastian G. , Maegele Ira , Hambleton Elizabeth A. , Voss Philipp A. , Waller Ross F. , Guse Annika
Published: November 2022

Dinoflagellates are a diverse and ecologically important group of single-celled eukaryotes. Many are photosynthetic autotrophs while others are predatory, parasitic, or symbiotic. One major group — the Symbiodiniaceae — is well known for its role as coral symbionts that provide the coral host with vital nutrients. While genetic transformation protocols have been published for some non-symbiotic dinoflagellate species, robust methods for genetic manipulation of coral symbionts are lacking, hindering a detailed molecular understanding of this critical symbiotic interaction. Here, we describe the successful transformation of coral symbiont Breviolum minutum (strain SSB01). Using Golden Gate modular plasmid assembly and electroporation, we drove transient NLS-GFP expression from an endogenous dinoflagellate virus nuclear protein (DVNP) promoter and successfully targeted GFP to the dinoflagellate nucleus. We further determined that puromycin can efficiently select transformed cells using the puromycin N-acetyltransferase (pac) resistance gene. Transformed cells could be maintained under antibiotic selection for at least 12 months without losing resistance, albeit with slowly attenuating fluorescence signal. We thus tested the expression of hybrid GFP-2A-PAC polypeptides under the control of a single promoter sequence to overcome loss of fluorescence, but lack of efficient 2A cleavage seemingly hindered antibiotic selection interfering GFP function. Despite this, our transformation approach now allows unanswered questions of dinoflagellate biology to be addressed, as well as fundamental aspects of dinoflagellate-coral symbiosis.
Design of a rollover index-based sliding mode controller for roll stability of three wheeled vehicles using rear differential braking
Authors: Ketemaw Daniel , Seid Solomon
Published: November 2022

Urban vehicles (like tricycle and bicycle vehicle) are made to handle issues with traffic, air pollution, energy use, and parking restrictions in big cities. However, they are more susceptible to rollovers and stability problems because they are smaller and narrower than normal cars. Now a day, Vehicle manufacturers place a lot of emphasis on the dynamic stability of their products. As a result, develop dynamic model to predict and detect the risk of rollover and designing a controller to reduce it in a delta type configuration of tricycle vehicle is the major concern of this paper. On the basis of a two degree of freedom (2-DOF) bicycle model, develop rollover dynamics, and design state observer for sideslip angle, sliding mode and fuzzy logic controller are the major concern of this paper. The suggested rollover index (RI) accuracy has been evaluated by simulation using a high-fidelity CarSim. The performance analysis to determine the effectiveness of thus proposed controller is conducted using MATLAB/Simulink integrated with the Carsim software. Simulation results with three scenarios are shown with and without the control system. The outcome of the simulation demonstrated that fuzzy sliding mode controller (FSMC) and a fuzzy logic controller can reduces the chance of a vehicle rolling over accident.
Development of a core outcome set in the clinical trials of traditional Chinese medicine for diabetic foot: A study protocol
Authors: Dai Xin Yue , Zi Ming Jie , Liu Chun Xiang , Wang Yi Ming , Gao Rui
Published: November 2022

Background

Diabetic Foot (DF) is one of the most common complications of diabetes, and it is characterized by high morbidity, disability, lethality and low cure rate. Traditional Chinese medicine treatment has certain characteristics and advantages in diabetic foot. Due to selective reporting bias and heterogeneity of research results, on the one hand, relevant clinical studies are of low quality and poor practicability, and on the other hand, similar studies cannot be included in meta-analysis to form high-quality evidence-based evidence and evaluate the value of studies. Therefore, the development of a core set of outcomes (COS-TCM-DF) for traditional Chinese medicine for the treatment of diabetic foot is an important way to address these issues.

Methods

The COS-TCM-DF project will refer to the developed COS methodology and the steps are divided into four stages: (1) a scoping review and analysis of enrolled research protocols to collect and analyze all existing outcomes that have been used in trials on the prevention or treatment of diabetic foot with Chinese Medicine; (2) qualitative interviews with Diabetic foot patient and attendants to Collect additional outcomes related to them; (3) Gather opinionest and obtain initial consensus from key stakeholders, including patients, clinicians, researchers, and pharmaceutical company staff, through a Delphi survey; (4) a consensus meeting was held to develop the final COS-TCM-DF.

Discussion

Currently, there is no COS on measuring or monitoring diabetic foot with TCM in trials or clinical practice. The COS-TCM-DF will be developed to advance the synthesis of evidence regarding the prevention and treatment of diabetic foot in TCM and to promote the standardized and consistent application of results in future studies in this field.

Trial registration

Registered with the Core Outcome Measures in Effectiveness Trials (COMET) database, December 2019 https://www.comet-initiative.org/Studies/Details/1553.
Association analysis of rice resistance genes and blast fungal avirulence genes for effective breeding resistance cultivars
Authors: Tian Dagang , Deng Yun , Yang Xiaoshuang , Li Gang , Li Qixiang , Zhou Haiying , Chen Ziqiang , Guo Xinrui , Su Yan , Luo Yuming , Yang Liming
Published: November 2022

Utilization of rice blast-resistance (R) genes is the most economical and environmentally friendly method to control blast disease. However, rice varieties with R genes influence the outcome of genetic architectures of Magnaporthe oryzae (M. oryzae), and mutations in avirulence (AVR) genes of M. oryzae may cause dysfunction of the corresponding R genes in rice varieties. Although monitoring and characterizing rice R genes and pathogen AVR genes in field populations may facilitate the implementation of effective R genes, little is known about the changes of R genes over time and their ultimate impact on pathogen AVR genes. In this study, 117 main cultivated rice varieties over the past five decades and 35 M. oryzae isolates collected from those diseased plants were analyzed by PCR using gene-specific markers of the nine R genes and six primer pairs targeting the coding sequence or promoter of AVR genes, respectively. The R genes Pigm, Pi9, Pi2, Piz-t, Pi-ta, Pik, Pi1, Pikp, and Pikm were identified in 5, 0, 1, 4, 18, 0, 2, 1, and 0 cultivars, respectively. Significantly, none of these R genes had significant changes that correlated to their application periods of time. Among the four identified AVR genes, AVR-Pik had the highest amplification frequency (97.14%) followed by AVR-Pita (51.43%) and AVR-Pi9 (48.57%); AVR-Piz-t had the lowest frequency (28.57%). All these AVR genes except AVR-Pi9 had 1–2 variants. Inoculation mono-genic lines contained functional genes of Pi2/9 and Pik loci with 14 representative isolates from those 35 ones revealed that the presence of certain AVR-Piz-t, AVR-Pita variants, and AVR-Pik-E + AVR-Pik-D in M. oryzae populations, and these variants negated the ability of the corresponding R genes to confer resistance. Importantly, Pi2, Pi9, and Pigm conferred broad-spectrum resistance to these local isolates. These findings reveal that the complex genetic basis of M. oryzae and some effective blast R genes should be considered in future rice blast-resistance breeding programs.
Expedited retrieval of high-quality Usutu virus genomes via Nanopore sequencing with and without target enrichment
Authors: Holicki Cora M. , Bergmann Felicitas , Stoek Franziska , Schulz Ansgar , Groschup Martin H. , Ziegler Ute , Sadeghi Balal
Published: November 2022

Usutu virus (USUV) is a mosquito-borne zoonotic virus and one of the causes of flavivirus encephalitis in birds and occasionally in humans. USUV rapidly disperses in a susceptible host and vector environment, as is the case in South and Central Europe. However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. The study was based on four samples from succumbed birds commonly collected throughout Germany. The samples were isolated from various sample matrices, organs as well as blood cruor, and included three different USUV lineages. We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. It can be implemented for an array of lab- or field-based objectives, including among others: phylodynamic studies and the analysis of viral quasispecies.
Morphology and molecular phylogeny reveal five new species of Hydnellum (Bankeraceae, Thelephorales) from China
Authors: Song Chang-Ge , Sun Yi-Fei , Wu Dong-Mei , Gao Neng , Liu Shun , Xu Tai-Min , Cui Bao-Kai
Published: November 2022

The genus Hydnellum is a kind of ectomycorrhizal fungi that can play a role in the material cycle by connecting the plant roots to the soil, and some species of Hydnellum are medicinal fungi with vital research value. The species diversity of Hydnellum is unclear in China. In this study, five new species of Hydnellum are described from China based on morphological characters and phylogenetic analyses inferred from two datasets of ITS + LSU and ITS + LSU + SSU + RPB2 sequences. H. chocolatum is characterized by its chocolate basidiomata with the fibrillose, spongy to tomentose pileal surface, and subglobose to globose basidiospores measuring (4.5–)5–6 × 4–5(–5.8) μm. H. concentricum is characterized by its zonate pileal surface, thin context, short stipe, presence of both simple septa and clamp connections in generative hyphae of spines, and subglobose to ellipsoidal basidiospores measuring (3.5–)4–5(–5.2) × (3.2–)3.5–5 μm. H. crassipileatum is characterized by its thick pileus with the reddish brown to grayish brown pileal surface, and subglobose to ellipsoidal basidiospores measuring 4–6(–6.5) × 4–5.5 μm. H. melanocarpum is characterized by its vinaceous brown to black pileus with spongy pileal surface, presence of both simple septa and clamp connections in generative hyphae of spines, and subglobose basidiospores measuring 4.5–5.5(–6) × (3.5–)3.8–5.1 μm. H. radiatum is characterized by its radially aligned stripes on pileal surface, grayish brown context, short stipe, and subglobose to ellipsoidal basidiospores measuring (3.5–)4–5 × 3–4.5(–5) μm. Full descriptions, illustrations, and phylogenetic trees to show the placement of the new species are provided.
Developmental stage variation in the gut microbiome of South China tigers
Authors: Zhang Xianfu , Liao Yanxin , Qin Tao , Ma Jinghua , Liu Jianxun , Zou Jianqiang , Huang Haijun , Zhong Xiaojun , Yang Menghua
Published: November 2022

South China tigers (Panthera tigris amoyensis, SC) are the most threatened tiger subspecies in the world. All the living SCs are captive in zoos or reserves and depend on artificial feeding. The composition of the gut microbiome plays an important role in sustaining the health of the host. A comprehensive understanding of the composition and development of the microbial community of SC is helpful to improve the feeding of captive SC. In this study, we collected 47 fecal samples, 37 of which were from SC of three developmental stages, 5 from adult Amur tigers (Am), and 5 from adult Bengal tigers (Bg), which were all housed in the same zoo. We investigated the diversity, richness, and composition of the bacterial microbiomes and we found that the gut microbiome of SC is strongly affected by host aging. The composition of the gut microbiome of juvenile SC experienced dramatic changes from 5 months old to 1 year old, and it showed much less difference when compared to the samples of 1 year old and the subadult. No significant differences were observed between the samples of subadult and the adult groups. The predominant phylum of 5-month-old SC is Fusobacteriota (33.99%) when the juvenile tigers were older than 5 months, and Firmicutes, but not Fusobacteriota, became the predominant phylum of bacteria in their gut. The gut microbiome of SC, Am, and Bg is possibly affected by their genetic variation; however, the core microbiome of these three subspecies is the same. Our data suggest that the gut microbiome of SC undergoes a developmental progression: a developmental phase (cub), a transitional phase (subadult), and a stable phase (adult). These results expand our understanding of the role of age in the development of the gut microbiome of SC.