bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of zygote vitrification timing on pregnancy rate in frozen-thawed IVF/ICSI cycles
Authors: Makieva Sofia , Stähli Celine , Xie Min , Gil Ana Velasco , Sachs Maike Katja , Leeners Brigitte
Published: January 2023

Introduction: Cryopreservation of bipronuclear (2PN) stage zygotes is an integral part of IVF laboratory practice in countries with strict embryo culture legislation. Vitrification of zygotes is compatible with several strategies in infertility treatments holding a freeze-all indication and allows for effective workload management in settings with limited resources. Although it yields high survival rates and clinical outcomes, the ideal timing to commence vitrification of zygotes is elusive while it is empirically practiced in the window between 17 and 21 h post-insemination (hpi). We aimed to deduce the association between pregnancy rate and the time interval from insemination (IVF and ICSI) to vitrification to contribute to the standardization ofzygote cryopreservation.

Methods: A retrospective analysis of data on vitrification timings and pregnancy outcomes collected between 2011 and 2019 was performed. All included women received an embryo transfer after warming of vitrified zygotes at the 2PN stage.

Results: A total of 468 embryo transfers were included of which 182 (38.9%) resulted in pregnancy and 286 (61.1%) not. Vitrification was on average performed 18.74 ±0.63 hpi in the pregnant group and 18.62 ± 0.64 hpi in the non-pregnant group (OR 1.36, 95% CI 1.01; 1.83, p = 0.045). A multivariate analysis controlling for uterine pathologies, maternal age, AMH, the number of MII oocytes, previous history of pregnancy success, endometriosis, AFC, nicotine intake and male factor infertility showed no predictive value of vitrification timing on pregnancy rate. Three time intervals between insemination and vitrification were defined: 17:00 to 18:00 hpi (Group A), 18:01 to 19:00 hpi (Group B) and 19:01 to 21:00 hpi (Group C). Pregnancy occurred in 40/130 women (30.80%) in Group A, in 115/281 women (40.90%) in Group B and in 27/57 women (47.40%) in Group C. Univariate but not multivariate analysis showed a significantly higher pregnancy rate after the latest time interval between insemination and 2PN vitrification when compared to the earliest (Group C vs. A, OR 2.03, 95% CI 1.07; 3.84, p = 0.031).

Discussion: These findings encourage further investigation on the impact of vitrification timing on clinical outcomes and hold the potential to standardize cryopreservation of zygotes from IVF/ICSI cycles to eventually improve the quality of long-term ART outcomes.
Leishmania infantum infecting the carnivore Nasua nasua from urban forest fragments in an endemic area of visceral leishmaniasis in Brazilian Midwest
Authors: de Macedo Gabriel Carvalho , Barreto Wanessa Teixeira Gomes , de Oliveira Carina Elisei , Santos Filipe Martins , Porfírio Grasiela Edith de Oliveira , Xavier Samanta Cristina das Chagas , Alves Fernanda Moreira , da Silva Alanderson Rodrigues , de Andrade Gisele Braziliano , Rucco Andreza Castro , de Assis William Oliveira , Jansen Ana Maria , Roque André Luiz Rodrigues , Herrera Heitor Miraglia
Published: January 2023

Introduction

The aim of the present study was to investigate the occurrence of Leishmania infantum in South American coatis inhabiting two forest fragments in Campo Grande, Mato Grosso do Sul, Midwest region of Brazil, an endemic area of human and canine visceral leishmaniasis (VL).

Material and methods

A total of 110 South American coatis were sampled in the conservation unit “Parque Estadual do Prosa” (PEP) and in the residential area “Vila da Base Aérea” (VBA) from March 2018 to April 2019. As a longitudinal study that include up to six recaptures of the same individual, a total of 190 capture events were obtained. Blood, bone marrow and skin samples were obtained for parasitological (axenic culture), serological (Enzyme Linked Immunosorbent Assay – ELISA and Dual-path Platform immunoassay – DPP® CVL) and molecular diagnostic assays (targeting kDNA for Leishmania spp. and L. infantum; and HSP70 followed by sequence analysis).

Results

Seropositivity for L. infantum was found in 33 individuals, six in PEP and 27 in VBA. Furthermore, L. infantum was detected by molecular analysis in 16 individuals, seven from PEP and nine from VBA. We also isolated L. infantum from bone marrow of one individual and detected a single positive skin sample in molecular assay from other individual, both from VBA.

Discussion

An overall infection rate of 36.4% (40/110) was observed, significantly higher in the VBA (49.1%) than in the PEP (21.6%), probably because VBA presents: (i) a large number of resident dogs and chickens that would be attracting sandflies; (ii) a denser population of this wild mammal species; and (iii) physical barriers and a lack of functional connectivity in the surroundings, preventing these animals to disperse out. We conclude that South American coati populations living in urban forest fragments of Campo Grande are affected by the epidemiological scenario of VL, known to involve dogs, vectors and humans. We highlight the importance of investigate the parasitism by L. infantum in this and other potential L. infantum reservoirs that inhabit urbanized regions endemic to VL.
Malaria disrupts the rhesus macaque gut microbiome
Authors: Farinella Danielle N. , Kaur Sukhpreet , Tran ViLinh , Cabrera-Mora Monica , Joyner Chester J. , Lapp Stacey A. , Pakala Suman B. , Nural Mustafa V. , DeBarry Jeremy D. , Kissinger Jessica C. , Jones Dean P. , Moreno Alberto , Galinski Mary R. , Cordy Regina Joice
Published: January 2023

Previous studies have suggested that a relationship exists between severity and transmissibility of malaria and variations in the gut microbiome, yet only limited information exists on the temporal dynamics of the gut microbial community during a malarial infection. Here, using a rhesus macaque model of relapsing malaria, we investigate how malaria affects the gut microbiome. In this study, we performed 16S sequencing on DNA isolated from rectal swabs of rhesus macaques over the course of an experimental malarial infection with Plasmodium cynomolgi and analyzed gut bacterial taxa abundance across primary and relapsing infections. We also performed metabolomics on blood plasma from the animals at the same timepoints and investigated changes in metabolic pathways over time. Members of Proteobacteria (family Helicobacteraceae) increased dramatically in relative abundance in the animal’s gut microbiome during peak infection while Firmicutes (family Lactobacillaceae and Ruminococcaceae), Bacteroidetes (family Prevotellaceae) and Spirochaetes amongst others decreased compared to baseline levels. Alpha diversity metrics indicated decreased microbiome diversity at the peak of parasitemia, followed by restoration of diversity post-treatment. Comparison with healthy subjects suggested that the rectal microbiome during acute malaria is enriched with commensal bacteria typically found in the healthy animal’s mucosa. Significant changes in the tryptophan-kynurenine immunomodulatory pathway were detected at peak infection with P. cynomolgi, a finding that has been described previously in the context of P. vivax infections in humans. During relapses, which have been shown to be associated with less inflammation and clinical severity, we observed minimal disruption to the gut microbiome, despite parasites being present. Altogether, these data suggest that the metabolic shift occurring during acute infection is associated with a concomitant shift in the gut microbiome, which is reversed post-treatment.
Characterization of Cellulomonas sp. HM71 as potential probiotic strain for human health
Authors: Yadav Monika , Kumar Tarun , Maurya Ranjeet , Pandey Rajesh , Chauhan Nar Singh
Published: January 2023

Cellulomonas sp. HM71, a human gut microbe possesses metabolic machinery to catabolize antigenic gluten, hence, holds promises as microbial therapy to treat gluten-derived celiac disease. However, its efficacy, safety, and survivability in the gastrointestinal ecosystem await functional elucidation. The current study is designed to characterize Cellulomonas sp. HM71 for its physiological, genomic, and probiotic properties. The morphological and physiological assessment indicates it as a coccus-shaped gram-positive bacterium growing optimally at 30°C in a neutral environment (pH 7.0). Cellulomonas sp. HM71 showed continuous growth even in stressful environments (salinity up to 3% NaCl and 6% KCl), variable temperature (25°C to 35°C) and pH (5-9), antibiotics, and gastric and intestinal conditions. The Cellulomonas sp. HM71 genome harbors diversified genetic machinery to modulate humongous metabolic potential for the host. This was substantiated by the hemolytic and CaCo-2 cell line assay which confirms its cellular adherence and biosafety. Notably, genome analysis did not identify any pathogenic islands. Probiotic characterization indicates its potential to overcome waterborne infections and digestion-related disorders. Cumulatively, Cellulomonas sp. HM71 can be considered a probiotic strain for improving human health because of the highlighted functions.
Gut microbiota-dependent trimethylamine n-oxide pathway contributes to the bidirectional relationship between intestinal inflammation and periodontitis
Authors: Wang Qiqi , Sun Yue , Zhou Tianyu , Jiang Cong , A Lan , Xu Wenzhou
Published: January 2023

Background

Intestinal inflammation and periodontitis influence the development of each other through the bidirectional relationship. As the intestinal microbiome metabolite, trimethylamine-N-oxide (TMAO) could contribute to chronic inflammation in the gut by influencing the gut microbial composition and intestinal immunity. Increased circulating TMAO levels often accompany clinical findings in patients with experimental periodontitis. However, the role of TMAO in the bidirectional relationship between intestinal inflammation and periodontitis remains unclear. Thus, we explored whether TMAO influences the periodontitis process by affecting intestinal immunity and microbial composition in this article.

Methods

Periodontitis was induced by unilateral ligation of the first molar in mice, and 3,3-dimethyl-1-butanol (DMB) was used as an inhibitor to reduce TMAO circulating. Twenty-five BALB/c mice were randomly assigned to five study sets (n = 5/group): no periodontitis with DMB (Control group), periodontitis (P) group, periodontitis with TMAO (P+TMAO) group, periodontitis with TMAO and DMB (P+TMAO+DMB) group, and periodontitis with DMB (P+DMB) group. The effect of TMAO was determined by assessing changes in intestinal histology, intestinal flora composition, periodontal tissue, and periodontal pro-inflammatory factors at ten days.

Results

The outcomes indicated a marked improvement in the intestinal inflammation severity, and intestinal flora diversity was reduced. Firmicutes number and the ratio of Firmicutes/Bacteroidetes were improved in the P+TMAO group. In addition, the alveolar bone resorption and the degree of periodontal tissue inflammation were more severe in the P+TMAO group than in other groups. Immunohistochemistry showed higher levels of TGF-β and IL-1β expression in the periodontal tissues of P+TMAO.

Conclusions

Our data suggest that TMAO could influence periodontal immunity and promote periodontal inflammation by affecting the intestinal microenvironment, revealing TMAO may affect the development of periodontitis through the bidirectional relationship of the oral-gut axis.
Colorimetric High-Throughput Screening Assay to Engineer Fungal Peroxygenases for the Degradation of Thermoset Composite Epoxy Resins
Authors: Dolz Mikel , Mateljak Ivan , Méndez-Sánchez Daniel , Sánchez-Moreno Israel , Gomez de Santos Patricia , Viña-Gonzalez Javier , Alcalde Miguel
Published: January 2023

At present, the end-of-life management of thermoset composite epoxy resins is limited to incineration and landfill storage, highlighting the demand for the development of more sustainable measures. Due to their broad spectrum of C-H oxyfunctionalization reactions, fungal unspecific peroxygenases (UPOs) are becoming important biotechnological tools in organic synthesis while their potential use in biodegradation processes should not be underestimated. Here, we present a colorimetric screening assay aimed at engineering UPOs for the degradation of epoxy resins. We based our study on Hexflow® RTM-6, a commercial epoxy resin used extensively in the aeronautics sector. UPO mutants from the short and long families were initially benchmarked by GC/MS to determine their potential N-dealkylation activity on N,N-bis(2-hydroxypropyl)-p-toluidine (NNBT), the main structural scaffold of Hexflow® RTM-6. A reliable high-throughput colorimetric screening method was developed to quantify the lactaldehyde released by UPO attack on the tertiary amine of NNBT. Based on an evolved UPO from Psathyrella aberdarensis that was expressed by yeast, a small subset of mutant libraries with different mutational loadings was constructed and screened for NNBT N-dealkylation, thereby establishing a directed evolution platform as a vehicle to engineer UPO composite degrading variants.
Quantitative prediction of multistage fractures of ultra-deep tight sandstone based on the theory of minimum energy dissipation
Authors: Liu Shuizhen , Feng Jianwei , Osafo Josephine Anima , Li Guisheng , Li Gang
Published: January 2023

Due to strong reservoir heterogeneity and low-resolution limit of geophysical data, it is difficult to predict fractures in ultra-deep reservoirs by conventional methods. In this research, we established a novel geomechanical model for prediction of fracture distribution in brittle reservoirs, especially for ultra-deep tight sandstone reservoirs. Methodologically, we intended to introduce the minimum energy dissipation principle considering time variable, combined with the generalized Hooke’s law containing damage variable, and obtained the energy dissipation rate expression corresponding to the energy dissipation process of brittle rocks. Combined with the three-shear energy yield criterion, the Lagrangian multiplier was introduced to deduce and construct the constitutive model and the failure criterion of rocks under the framework of the theory of minimum energy dissipation. Based on the law of conservation of energy, the stress-energy coupling characterization model of fracture density parameter was derived. Finally, all the improved geomechanical equations were incorporated into a finite element software to quantitatively simulate the distributions of tectonic stress filed and fractures based on paleo-structure restoration of Keshen anticline during the middle and late Himalayan periods. Its predictions agreed well with measured fracture density from reservoir cores and image logs.
Application of geophysical prospecting methods ERT and MASW in the landslide of Daofu County, China
Authors: Zhang Gang , Tu Fangzhou , Tang Yushu , Chen Xingchang , Xie Kuilin , Dai Sen
Published: January 2023

Natural disasters such as debris flow caused by earthquakes seriously threaten the local infrastructure and economy, as well as the lives of people in the area. As the material source of debris flow, it has significance to accurately and effectively study the underground structure of the landslide to prevent debris flow disasters. A landslide has a complex structural system, and its underground characteristics play an important role in its stability. The early identification of fracture surfaces and unstable bodies, and assessment of potential hazards are essential for prevention and protection. The research object of this paper is a landslide that occurred in Yige Village, Xianshui Town, Daofu County, which is on the Xianshui River Earthquake Zone, an area subject to frequent earthquakes. In western Sichuan, the frequent occurrence of landslides has caused considerable economic losses. Developing methods for efficient and accurate risk assessment is a top priority. The Daofu landslide is a typical example of a landslide directly threatening the road below and forming a debris flow channel. The lithology is composed of Jurassic sedimentary rocks, such as marl and clay, covered by limestone. In this study, we combined traditional methods (drilling and field investigation) with two geophysical techniques, multichannel analysis of surface waves (MASW) and electrical resistivity tomography (ERT) to effectively determine the electrical characteristics, velocity characteristics and spatial structure of the landslide. It is found that the buried depth of the sliding surface of the landslide is about 16–20 m. The sliding body above the sliding surface forms a low velocity and low resistivity Quaternary cover. The rock mass below the sliding surface is Triassic Zhuwo Formation sandstone and slate with high velocity and high resistivity. According to comprehensive analysis, the landslide lacks sufficient stability under rainstorm. Our study shows that the use of MASW and ERT can quickly and effectively characterize the subsurface of landslides to assess landslide risk and prevent debris flow hazards.
A method of calculating water and soil loading on top of shallow shield tunnels near water areas
Authors: Zhu Zeqi , Chang Liuming , Cui Lan , Sheng Qian
Published: January 2023

Long-term water seepage in shield tunnels has a serious impact on water and soil loading on the outer surfaces of a shield segment near water areas. A theoretical analysis was used to obtain a formula to express the average vertical seepage gradient at the top of the tunnel. A formula for calculating the coefficient of lateral earth pressure for the principal stress arch effect was utilized. A model that takes into consideration the effects of long-term water seepage on the shield tunnel’s water and soil load was designed. Based on this calculation model, the variation law of the water and soil loading on top of shield tunnel near water area with the internal friction angle in the soil body, the density of the soil, the tunnel depth-to-diameter ratio, the water head of the external section, and the amount of water seepage per unit length is studied. Based on the geological conditions and field survey results of water and soil loading of two typical segments of the Maliuzhou Waterway section of the Hengqin Tunnel, a comparative analysis of the theoretical results and field survey measurements was performed for different calculated conditions. The research shows that the proposed model is able to perform a reasonably effective evaluation of the water and soil pressure at the top of the shield tunnel for the marine and land segments of the shield tunnel; and, when compared with Dimitrios Kolymbas’ effective stress method and Terzaghi’s Principle, the method shown in this paper has fewer errors. The results of the associated research are sufficient to reasonably design and propose a theoretical basis for underwater shield tunnels.
Improving human mesenchymal stem cell-derived hepatic cell energy metabolism by manipulating glucose homeostasis and glucocorticoid signaling
Authors: Rodrigues Joana Saraiva , Faria-Pereira Andreia , Camões Sérgio Póvoas , Serras Ana Sofia , Morais Vanessa Alexandra , Ruas Jorge Lira , Miranda Joana Paiva
Published: January 2023

Introduction

The development of reliable hepatic in vitro models may provide insights into disease mechanisms, linking hepatocyte dysmetabolism and related pathologies. However, several of the existing models depend on using high concentrations of hepatocyte differentiation-promoting compounds, namely glucose, insulin, and dexamethasone, which is among the reasons that have hampered their use for modeling metabolism-related diseases. This work focused on modulating glucose homeostasis and glucocorticoid concentration to improve the suitability of a mesenchymal stem-cell (MSC)-derived hepatocyte-like cell (HLC) human model for studying hepatic insulin action and disease modeling.

Methods

We have investigated the role of insulin, glucose and dexamethasone on mitochondrial function, insulin signaling and carbohydrate metabolism, namely AKT phosphorylation, glycogen storage ability, glycolysis and gluconeogenesis, as well as fatty acid oxidation and bile acid metabolism gene expression in HLCs. In addition, we evaluated cell morphological features, albumin and urea production, the presence of hepatic-specific markers, biotransformation ability and mitochondrial function.

Results

Using glucose, insulin and dexamethasone levels close to physiological concentrations improved insulin responsiveness in HLCs, as demonstrated by AKT phosphorylation, upregulation of glycolysis and downregulation of Irs2 and gluconeogenesis and fatty acid oxidation pathways. Ammonia detoxification, EROD and UGT activities and sensitivity to paracetamol cytotoxicity were also enhanced under more physiologically relevant conditions.

Conclusion

HLCs kept under reduced concentrations of glucose, insulin and dexamethasone presented an improved hepatic phenotype and insulin sensitivity demonstrating superior potential as an in vitro platform for modeling energy metabolism-related disorders, namely for the investigation of the insulin signaling pathway.
Validation of dynamic risk stratification and impact of BRAF in risk assessment of thyroid cancer, a nation-wide multicenter study
Authors: Pérez-Fernández Laura , Sastre Julia , Zafón Carles , Oleaga Amelia , Castelblanco Esmeralda , Capel Ismael , Galofré Juan C. , Guadalix-Iglesias Sonsoles , De la Vieja Antonio , Riesco-Eizaguirre Garcilaso
Published: January 2023

Introduction

The dynamic risk stratification (DRS) is a relatively new system in thyroid cancer that considers the response to primary treatment to improve the initial risk of recurrence. We wanted to validate DRS system in a nationwide multicenter study and explore if the incorporation of BRAFV600E into DRS helps to better categorize and predict outcomes.

Materials and methods

Retrospective study of 685 patients from seven centers between 1991 and 2016, with a mean age of 48 years and a median follow-up time of 45 months (range 23-77). The overall BRAFV600E prevalence was 53.4%. We classified patients into four categories based on DRS (‘excellent’, ‘indeterminate’, ‘biochemical incomplete’, and ‘structural incomplete’ response). Cox regression was used to calculate adjusted hazard ratios (AHR) and proportions of variance explained (PVEs).

Results

We found 21.6% recurrences and 2.3% cancer-related deaths. The proportion of patients that developed recurrence in excellent, indeterminate, biochemical incomplete and structural incomplete response to therapy was 1.8%, 54%, 91.7% and 96.2% respectively. Considering the outcome at the end of the follow up, patients showed no evidence of disease (NED) in 98.2, 52, 33.3 and 25.6% respectively. Patients in the structural incomplete category were the only who died (17.7%). Because they have similar outcomes in terms of NED and survival, we integrated the indeterminate and biochemical incomplete response into one unique category creating the 3-tiered DRS system. The PVEs of the AJCC/TNM staging, ATA risk classification, 4-tiered DRS, and 3-tiered DRS to predict recurrence at five years were 21%, 25%, 57% and 59% respectively. BRAFV600E was significantly associated with biochemical incomplete response (71.1 vs 28.9%) (HR 2.43; 95% CI, 1.21 to 5.23; p=0.016), but not with structural incomplete response or distant metastases. BRAF status slightly changes the AHR values of the DRS categories but is not useful for different risk grouping.

Conclusions

This is the first multicenter study to validate the 4-tiered DRS system. Our results also show that the 3-tiered DRS system, by integrating indeterminate and biochemical incomplete response into one unique category, may simplify response to therapy keeping the system accurate. BRAF status does not provide any additional benefit to DRS.
An adaptive neural fuzzy virtual inertia control method for VSC-HVDC system
Authors: Zhu Lin , Liu Qi , Liu Shan , Wang Zhen , Meng Jianhui , Gu Likang , Zhou Zixin
Published: January 2023

Compared to conventional DC transmission, Voltage source converter based high voltage direct current transmission (VSC-HVDC) has the advantages of independently controllable transmission power, no commutation failure, no reactive power compensation and low harmonic levels. However, VSC-HVDC transmission cannot provide effective frequency support and regulation for the system after grid connection. For this reason, an adaptive neural fuzzy virtual inertia control method is proposed to impose a control strategy on the converter at the receiving end of a VSC-HVDC transmission. The method uses the frequency change rate and the amount of change of frequency as constraints to dynamically adjust the virtual inertia and damping coefficients. It provides larger inertial support when the frequency fluctuation is large and smaller inertial support when the frequency fluctuation is small, thus adapting to different operating conditions. Finally, a hardware-in-the-loop simulation platform is built. The superiority and application prospect of the proposed strategy in frequency stability of the system are verified by comparing the proposed strategy with the traditional virtual control strategy.
Understanding the structure and determinants of economic linkage network: The case of three major city clusters in Yangtze River Economic belt
Authors: Zhang Xiaoyan , Ma Weiyan , Sheng Sanhua
Published: January 2023

The economic linkages between cities within the Yangtze River Economic Belt city cluster are important for precisely implementing the Yangtze River Economic Belt strategy. Accordingly, this study used the revised gravity model, social network method, and spatial Durbin model to analyze the economic linkage strength, spatial-temporal differentiation, and driving factors of the three major city cluster in the Yangtze River Economic Belt from 2006–2020. The results confirm that the Chengdu-Chongqing urban agglomeration has formed a network structure with Chengdu and Chongqing as the two poles; the urban agglomeration in the middle reaches of the Yangtze River has formed a point-axis development pattern of Wuhan, Changsha and Nanchang. The Yangtze River Delta urban agglomeration formed a multi-center radiation and sub-network development pattern. Additionally, the characteristics of network structure significantly affected the flow of factors, the level of economic development was the basis for strengthening communication and cooperation between cities. Meanwhile, the advanced industrial structures played an important role in promoting industrial linkages, and human capital exerts an obvious spatial spillover effect. Therefore, these three major urban agglomerations should implement differentiated development strategies and enhance the synergy of their linkage networks, thus promoting high-quality development.
Anthropogenic nutrient loading affects both individual species and the trophic structure of river fish communities
Authors: Horka Petra , Musilova Zuzana , Holubova Katerina , Jandova Katerina , Kukla Jaroslav , Rutkayova Jitka , Jones John Iwan
Published: January 2023

Although the concept of trophic interactions has been used for a long time, there are still considerable gaps in our understanding of the effect of various environmental factors on trophic interactions within river fish assemblages. Carbon (δ13C) and nitrogen (δ15N) stable isotope ratios of 20 species of fish belonging to both eurytopic and rheophilic ecological groups from a large temperate rivers were used to evaluate overall trophic niche use and trophic position of species, and to find out how environmental variability associated with nutrient loading affects individual and community-wide aspects of trophic structure. The study was carried out at 11 sites along the European rivers Vltava and Elbe, representing a continuous gradient of pollution and habitat degradation. Corrected Standard Ellipse Area (SEAc) was significantly larger for the group of eurytopic ecological species than for rheophilic species. Despite narrower isotopic niche space, rheophilic fish species occupied a higher trophic position, suggesting that these species use resources more enriched in 15N. Of the 11 environmental variables tested, nutrients had a significant effect on trophic niche area of species (SEAc), indicating that eutrophication is of critical importance for fish assemblages. Isotopic niche area of species was found to be positively influenced by total phosphorus, and negatively affected by concentrations of nitrate (N-NO3−) and ammonia (N-NH4+). A negative association between oxygen demand and a measure of trophic diversity - mean distance to centroid (CD)- and a measure of density and clustering of species - mean nearest neighbor distance (MNND)- were found, indicating that the oxygen demand is a key factor influencing community trophic structure. An observed pattern where nutrient loading influenced both individual species and trophic structure of the fish assemblage provides strong support for an anthropogenic influence on riverine food webs.
Exploring perceptions, knowledge, and attitudes regarding pharmacogenetic testing in the medically underserved
Authors: Gawronski Brian E. , Cicali Emily J. , McDonough Caitrin W. , Cottler Linda B. , Duarte Julio D.
Published: January 2023

Introduction: Pharmacogenetic testing may hold promise in addressing health disparities, as medically underserved patients appear to be prescribed medications with pharmacogenetic guidelines at higher rates. While routine clinical implementation of testing in medically underserved populations has not yet been achieved, using patient perspectives to inform implementation should increase the likelihood of success. The aim of this study was to assess the perceptions, knowledge, and attitudes regarding pharmacogenetic testing in medically underserved patients.

Methods: We developed a survey instrument to assess respondent views on pharmacogenetic testing. The survey instrument was developed through a process of literature review, expert input, iterative pilot testing, and final refinement. The survey instrument was fielded to US adults with an estimated household income of $42,000 per year or less.

Results: During the survey instrument development, 59 pilot testers provided 133 comments which lead to 38 revisions to the survey instrument. The nationwide survey resulted in 1,060 respondents, of which half (49.8%) reported having no health insurance or being on Medicaid. Most patients (78.9%) had not previously heard of pharmacogenetic testing. After being provided an explanation of pharmacogenetic testing, 60.5% were very or moderately interested in receiving testing if there were no cost and 75.8% of respondents agreed or strongly agreed that pharmacogenetic testing should be available to help with medication selection regardless of cost. Respondents shared that their greatest concern with pharmacogenetic testing was that the test would cost them money, which was expressed by over half (52.7%). This was followed by concerns that the results could reveal a risk for a disease, could affect health insurance, and would not improve care.

Discussion: Our results indicate a strong interest in pharmacogenetic testing and identify key perceptions, attitudes, concerns, and potential barriers that can be addressed as pharmacogenetic testing is clinically implemented in medically underserved patient populations.
Chronic granulomatous disease associated with Duchenne muscular dystrophy caused by Xp21.1 contiguous gene deletion syndrome: Case report and literature review
Authors: Bi Shaohua , Dai Liying , Jiang Liangliang , Wang Lili , Teng Mia , Liu Guanghui , Teng Ru-Jeng
Published: January 2023

Chronic granulomatous disease (CGD) and Duchenne muscular dystrophy (DMD) are X-linked recessive disorders whose genes are 4.47 Mb apart within Xp21.1. A combination of both diseases is rare with only five cases reported in the literature where it is known as Xp21.1 “contiguous gene deletion syndrome”. We describe a male neonate who presented with sepsis at 19 days of age. The diagnosis of CGD with DMD was established through copy number variation sequencing (CNV-seq) with an extensive 7.5 Mb deletion of Xp21.2-Xp11.4 of the proband. One of his elder sisters and his mother are carriers. The deletion includes six known genes: glycerol kinase (GK), dystrophin (DMD), cilia- and flagella-associated protein 47 (CFAP47), gp91 (CYBB), Kell antigen (XK), and retinitis pigmentosa GTPase regulator (RPGR). Laboratory assays revealed an increased creatine kinase (CK) level, decreased gp91 expression, and a positive nitroblue tetrazolium test. Due to the extensive gene deletion and the poor prognosis, the family determined to pursue conservative management without further laboratory workup. The patient passed away from a fulminant infection at the age of three-month at a local medical facility. To the best of our knowledge, this case of Xp21.1 contiguous gene deletion syndrome represents the most extensive deletion of genes in this region ever reported. A literature review of similar cases is presented.
Cuproptosis-related LncRNAs signature as biomarker of prognosis and immune infiltration in pancreatic cancer
Authors: Chen Hui , Yu Yang , Zhou Lei , Chen Junliang , Li Zeyu , Tan Xiaodong
Published: January 2023

Background: Pancreatic cancer (PC) is a malignant gastrointestinal tumor with a terrible prognosis. Cuproptosis is a recently discovered form of cell death. This study is intended to explore the relationship between cuproptosis-related lncRNAs (CRLncs) signature with the prognosis and the tumor microenvironment (TME) of PC.

Methods: Transcript sequencing data of PC samples with clinical information were obtained from the Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and LASSO regression analysis were employed to construct the prognostic signature based on CRLncs associated with PC survival. A nomogram was created according to this signature, and the signaling pathway enrichment was analyzed. Subsequently, we explored the link between this prognostic signature with the mutational landscape and TME. Eventually, drug sensitivity was predicted based on this signature.

Results: Forty-six of 159 CRLncs were most significantly relevant to the prognosis of PC, and a 6-lncRNA prognostic signature was established. The expression level of signature lncRNAs were detected in PC cell lines. The AUC value of the ROC curve for this risk score predicting 5-year survival in PC was .944, which was an independent prognostic factor for PC. The risk score was tightly related to the mutational pattern of PC, especially the driver genes of PC. Single-sample gene set enrichment analysis (ssGSEA) demonstrated a significant correlation between signature with the TME of PC. Ultimately, compounds were measured for therapy in high-risk and low-risk PC patients, respectively.

Conclusion: A prognostic signature of CRLncs for PC was established in the current study, which may serve as a promising marker for the outcomes of PC patients and has important forecasting roles for gene mutations, immune cell infiltration, and drug sensitivity in PC.
Design and immunological evaluation of two-component protein nanoparticle vaccines for East Coast fever
Authors: Lacasta Anna , Kim Hyung Chan , Kepl Elizabeth , Gachogo Rachael , Chege Naomi , Ojuok Rose , Muriuki Charity , Mwalimu Stephen , Touboul Gilad , Stiber Ariel , Poole Elizabeth Jane , Ndiwa Nicholas , Fiala Brooke , King Neil P. , Nene Vishvanath
Published: January 2023

Nanoparticle vaccines usually prime stronger immune responses than soluble antigens. Within this class of subunit vaccines, the recent development of computationally designed self-assembling two-component protein nanoparticle scaffolds provides a powerful and versatile platform for displaying multiple copies of one or more antigens. Here we report the generation of three different nanoparticle immunogens displaying 60 copies of p67C, an 80 amino acid polypeptide from a candidate vaccine antigen of Theileria parva, and their immunogenicity in cattle. p67C is a truncation of p67, the major surface protein of the sporozoite stage of T. parva, an apicomplexan parasite that causes an often-fatal bovine disease called East Coast fever (ECF) in sub-Saharan Africa. Compared to I32-19 and I32-28, we found that I53-50 nanoparticle scaffolds displaying p67C had the best biophysical characteristics. p67C-I53-50 also outperformed the other two nanoparticles in stimulating p67C-specific IgG1 and IgG2 antibodies and CD4+ T-cell responses, as well as sporozoite neutralizing capacity. In experimental cattle vaccine trials, p67C-I53-50 induced significant immunity to ECF, suggesting that the I53-50 scaffold is a promising candidate for developing novel nanoparticle vaccines. To our knowledge this is the first application of computationally designed nanoparticles to the development of livestock vaccines.
CTSB promotes sepsis-induced acute kidney injury through activating mitochondrial apoptosis pathway
Authors: Wang Yuting , Xi Wenjie , Zhang Xinyi , Bi Xinwen , Liu Boyang , Zheng Xiaoming , Chi Xinjin
Published: January 2023

Background

Acute kidney injury is a common and severe complication of sepsis. Sepsis -induced acute kidney injury(S-AKI) is an independent risk factor for mortality among sepsis patients. However, the mechanisms of S-AKI are complex and poorly understand. Therefore, exploring the underlying mechanisms of S-AKI may lead to the development of therapeutic targets.

Method

A model of S-AKI was established in male C57BL/6 mice using cecal ligation and puncture (CLP). The data-independent acquisition (DIA)-mass spectrometry-based proteomics was used to explore the protein expression changes and analyze the key proteomics profile in control and CLP group. The methodology was also used to identify the key proteins and pathways. S-AKI in vitro was established by treating the HK-2 cells with lipopolysaccharide (LPS). Subsequently, the effect and mechanism of Cathepsin B (CTSB) in inducing apoptosis in HK-2 cells were observed and verified.

Results

The renal injury scores, serum creatinine, blood urea nitrogen, and kidney injury molecule 1 were higher in septic mice than in non-septic mice. The proteomic analysis identified a total of 449 differentially expressed proteins (DEPs). GO and KEGG analysis showed that DEPs were mostly enriched in lysosomal-related cell structures and pathways. CTSB and MAPK were identified as key proteins in S-AKI. Electron microscopy observed enlarged lysosomes, swelled and ruptured mitochondria, and cytoplasmic vacuolization in CLP group. TUNEL staining and CTSB activity test showed that the apoptosis and CTSB activity were higher in CLP group than in control group. In HK-2 cell injury model, the CTSB activity and mRNA expression were increased in LPS-treated cells. Acridine orange staining showed that LPS caused lysosomal membrane permeabilization (LMP). CA074 as an inhibitor of CTSB could effectively inhibit CTSB activity. CCK8 and Annexin V/PI staining results indicated that CA074 reversed LPS-induced apoptosis of HK-2 cells. The JC-1 and western blot results showed that LPS inhibited mitochondrial membrane potential and activated mitochondrial apoptosis pathway, which could be reversed by CA074.

Conclusions

LMP and CTSB contribute to pathogenesis of S-AKI. LPS treatment induced HK-2 cell injury by activating mitochondrial apoptosis pathway. Inhibition of CTSB might be a new therapeutic strategy to alleviate sepsis-induced acute kidney injury.
Differential expression of nuclear hormone receptors by dendritic cell subsets in human vaginal mucosa and skin
Authors: Joo HyeMee , Gu Chao , Wiest Matthew , Duluc Dorothee , Fernandez Emyly , Nyarige Verah , Yi Johnny , Oh SangKon
Published: January 2023

Nuclear hormone receptors (NHRs) expressed by dendritic cells (DCs), the major immune inducers and regulators, could play important roles in host immunity. Assessment of NHRs expressed by DCs in the vaginal mucosa (VM), in comparison with those expressed by DCs in other tissues, will thus help us understand the immunology of human vagina. This study identified 16 NHR transcripts that are differentially expressed among 8 different antigen-presenting cell (APC) subsets isolated from human VM, skin, and blood. The expression profiles of NHRs were largely tissue specific. VM APCs expressed increased levels of LXRA, RXRA, ESRRA, ESRRAP2, and PPARG, whereas skin and blood APCs expressed increased levels of NURR1, NOR1 and RARA. Of interest, female sex hormone receptors, ESR1 and PGR, were found to be mainly expressed by non-APC cell types in the VM; ESR1 by HLA-DR+CD34+ and PGR by HLA-DR- cells. ERα and PR were expressed by vimentin+ cells in the VM, but not in human skin. ERα, but not PR, was also expressed in CD10+ cells in the lamina propria of VM. In conclusion, NHR expression by APC subsets is tissue- and cell type-specific. Future studies on the roles of individual NHRs expressed by different cell types, including DC subsets, in the human VM are warranted.
Secondary myeloid neoplasms after CD19 CAR T therapy in patients with refractory/relapsed B-cell lymphoma: Case series and review of literature
Authors: Zhao Aiqi , Zhao Mingzhe , Qian Wenbin , Liang Aibin , Li Ping , Liu Hui
Published: January 2023

Background

Several chimeric antigen receptor T cells (CAR T) targeting CD19 have induced profound and prolonged remission for refractory/relapsed (R/R) B-cell lymphoma. The risk of secondary malignancies, especially myeloid neoplasms, is of particular concern in the CAR T community, which still remains unclear.

Methods

Four patients with R/R B-cell lymphoma after CD19 CAR T therapy diagnosed with secondary myeloid neoplasms (SMN) from 2 hospitals in eastern China were presented, including 3 with myelodysplastic syndrome (MDS) and 1 with acute myeloid leukemia (AML). Using single-cell RNA sequencing (scRNA-seq), we compared the cellular components of bone marrow (BM) samples obtained from one of these MDS patients and a health donor. We also provided a review of recently published literature concerning SMN risk of CAR T therapy.

Results

Relevant demographic, clinical, laboratory, therapeutic and outcome data were collected and presented by chart review. In our case series, the male-female ratio was 3.0 and the median age at MDS onset was 61.25 years old (range, 50-78). Median number of previous systemic therapies was 4.5 (range, 4-5), including autologous hematopoietic stem cell transplantation (auto-HSCT) in one patient. BM assessments prior to CAR T therapy confirmed normal hematopoiesis without myeloid neoplasms. Moreover, for 3 patients with SMN in our series, cytogenetic analysis predicted a relatively adverse outcome. In our experience and in the literature, treatment choices for the patients with SMN included allogeneic hematopoietic stem cell transplantation (allo-HSCT), hypomethylating agent (HMA), period filgrastim, transfusions and other supportive care. Finally, treatment responses of lymphoma, together with SMN, directly correlated with the overall survival of this community. Of note, it appeared that pathogenesis of MDS wasn’t associated with the CAR T toxicities, since all 4 patients experienced a pretty mild CRS of grade 1-2. Additionally, scRNA-seq analysis described the transcriptional alteration of CD34+ cells, identified 13 T/NK clusters, and also indicated increased cytotoxic T cells in MDS BM.

Conclusion

Our study illustrated the onset and progression of SMN after CD19 CAR T therapy in patients with R/R B-cell lymphoma, which provides useful information of this uncommon later event.
Protein post-translational modification in SARS-CoV-2 and host interaction
Authors: Cheng Nana , Liu Mingzhu , Li Wanting , Sun BingYue , Liu Dandan , Wang Guoqing , Shi Jingwei , Li Lisha
Published: January 2023

SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.
Diagnostic and prognostic value of STAP1 and AHNAK methylation in peripheral blood immune cells for HBV-related hepatopathy
Authors: Sun Libo , Lu Junfeng , Li Kang , Zhang Haitao , Zhao Xiaofei , Li Guangming , Li Ning
Published: January 2023

Introduction

Although we had identified that the methylation of AHNAK was a good diagnostic marker for hepatopathy, here we speculate that there was also another marker, STAP1, whose methylation also involved in the detection of hepatopathy.

Methods

We investigated the methylation levels of the AHNAK and STAP1 in peripheral blood mononuclear cells of chronic hepatitis B (CHB) patients, compensatory liver cirrhosis (CLC) patients, decompensated liver cirrhosis (DCLC) patients, hepatocellular carcinoma (HCC) patients and healthy controls by methylation-specific PCR. We also evaluated the differences and changes of methylation and expression of AHNAK and STAP1 at different stages of liver disease using the TCGA and GEO public datasets.

Results

Methylation level of STAP1 in PBMC was positively correlated with the course of liver cancer. The combination of AHNAK and STAP1 methylation was able to predict differrent HBV related hepatopathy. The GEO datasets also supported that the methylation of AHNAK and STAP1 was associated with different types of hepatopathy. The TCGA data showed that the levels of methylation and expression of STAP1 were down-regulated in HCC. We also found the STAP1 methylation level in PBMC and T cells was associated with age, gender, alcohol drinking and anti-HBe. Hyper-methylation of STAP1 was correlated with the poor prognosis of patients but its expression had no association.

Conclusion

We concluded that combination of AHNAK and STAP1 methylation in peripheral blood immune cells can be used as a diagnostic marker for HBV related hepatopathy and STAP1 methylation may be a potential prognostic marker for HBV related HCC. Our clinical study registration number was ChiCTR2000039860.