bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the functional and transcriptomic effects of pro-inflammatory cytokines on human EndoC-βH5 beta cells
Authors: Frørup Caroline , Gerwig Rebekka , Svane Cecilie Amalie Søndergaard , Mendes Lopes de Melo Joana , Henriksen Kristine , Fløyel Tina , Pociot Flemming , Kaur Simranjeet , Størling Joachim
Published: April 2023

Objective

EndoC-βH5 is a newly established human beta-cell model which may be superior to previous model systems. Exposure of beta cells to pro-inflammatory cytokines is widely used when studying immune-mediated beta-cell failure in type 1 diabetes. We therefore performed an in-depth characterization of the effects of cytokines on EndoC-βH5 cells.

Methods

The sensitivity profile of EndoC-βH5 cells to the toxic effects of interleukin-1β (IL-1β), interferon γ (IFNγ) and tumor necrosis factor-α (TNFα) was examined in titration and time-course experiments. Cell death was evaluated by caspase-3/7 activity, cytotoxicity, viability, TUNEL assay and immunoblotting. Activation of signaling pathways and major histocompatibility complex (MHC)-I expression were examined by immunoblotting, immunofluorescence, and real-time quantitative PCR (qPCR). Insulin and chemokine secretion were measured by ELISA and Meso Scale Discovery multiplexing electrochemiluminescence, respectively. Mitochondrial function was evaluated by extracellular flux technology. Global gene expression was characterized by stranded RNA sequencing.

Results

Cytokines increased caspase-3/7 activity and cytotoxicity in EndoC-βH5 cells in a time- and dose-dependent manner. The proapoptotic effect of cytokines was primarily driven by IFNγ signal transduction. Cytokine exposure induced MHC-I expression and chemokine production and secretion. Further, cytokines caused impaired mitochondrial function and diminished glucose-stimulated insulin secretion. Finally, we report significant changes to the EndoC-βH5 transcriptome including upregulation of the human leukocyte antigen (HLA) genes, endoplasmic reticulum stress markers, and non-coding RNAs, in response to cytokines. Among the differentially expressed genes were several type 1 diabetes risk genes.

Conclusion

Our study provides detailed insight into the functional and transcriptomic effects of cytokines on EndoC-βH5 cells. This information should be useful for future studies using this novel beta-cell model.
The role of aldosterone in the pathogenesis of diabetic retinopathy
Authors: Liu Kangcheng , Zou Hua , Fan Huimin , Hu Hanying , Cheng Yanhua , Liu Jingying , Wu Xiaojian , Chen Bolin , You Zhipeng
Published: April 2023

Aldosterone, as a mineralocorticoid of adrenal origin, has effects that are not limited to the urinary tract. As an important regulator in Vasoactive hormone pathways, aldosterone may play an effect in the pathogenesis of diabetic retinopathy (DR) through the regulation of oxidative stress, vascular regulation, and inflammatory mechanisms. This implies that mineralocorticoids, including aldosterone, have great potential and value for the diagnosis and treatment of DR. Because early studies did not focus on the intrinsic association between mineralocorticoids and DR, targeted research is still in its infancy and there are still many obstacles to its application in the clinical setting. Recent studies have improved the understanding of the effects of aldosterone on DR, and we review them with the aim of exploring possible mechanisms for the treatment and prevention of DR.
The prioritization of solutions for reducing the influence of climate change on the environment by using the conception of bipolar complex fuzzy power Dombi aggregation operators
Authors: Mahmood Tahir , Rehman Ubaid Ur , Santos-García Gustavo
Published: April 2023

This article aims to examine the causes and consequences of climate change on the environment and then prioritize the solution for reducing its influence on the environment under the setting of the bipolar complex fuzzy set (BCFS). Climate change is illustrated by the transformation of wind, temperature, and precipitation; regardless of its natural causes, it is generally connected with human movement and ozone-depleting substances. It is an important task to determine the reasons, effects, and, especially, solutions for reducing the effects of climate change. The prioritization of the solution for reducing the influence of climate change is a multi-attribute decision-making (MADM) dilemma, and for solving such a dilemma, we need a proper MADM technique. Thus, in this study, we first interpreted various aggregation operators (AOs) such as bipolar complex fuzzy (BCF) power Dombi averaging (BCFPDA); BCF power Dombi weighted averaging (BCFPDWA); BCF power Dombi ordered weighted averaging (BCFPDOWA); BCF power Dombi geometric (BCFPDG); BCF power Dombi weighted geometric (BCFPDWG); and BCF power Dombi ordered weighted geometric (BCFPDOWG) and then interpreted an MADM approach based on the invented operators. Furthermore, we studied a numerical example regarding the prioritization of solutions for the reduction of the influence of climate change on the environment and achieved the best solution, i.e., DBCFS−4= ocean and sea protection. Finally, the advantages of this approach are compared with those of other approaches.
Short-term effects of increasing compost application rates on soil C and greenhouse gas (N2O and CO2) emissions in a California central coast vineyard
Authors: Wong Connie T. F. , Falcone Mia , Rich Geovan , Stubler Craig , Malama Bwalya , Lazcano Cristina , Decock Charlotte
Published: April 2023

Compost application is commonly considered by winegrape producers to improve soil health while sequestering carbon (C) and mitigating climate change. However, inputs of available C and nitrogen (N) as nutrients can induce emissions of greenhouse gases (GHG) such as carbon dioxide (CO2) and nitrous oxide (N2O). A 2-year field experiment in a Mediterranean vineyard on the California Central Coast was conducted to investigate the short-term effects of compost application at four different rates on soil C dynamics and greenhouse gas emissions. Two years of greenhouse gas sampling were performed using static chambers at vineyard management events in two functional locations (tractor row and under the vines). Soil samples were collected annually in spring at the same locations at 0–15, 15–30 and 30–60 cm depth, and during greenhouse gas sampling at 0–15 cm. The increasing compost application rate did not increase soil C stock, cumulative greenhouse gas emissions and global warming potential. The increase in active soil C observed to the depth of 60 cm suggests that increasing the compost application rate up to the rate of 13.5 Mg ha-1 year-1 can facilitate the early stages of C stabilization and sequestration. Compost application did not have a significant effect on grape yield or cover crop growth during the study. Our results provided important information on the potential environmental tradeoffs as greenhouse gas emissions from compost applications, which should be taken into account when considering the vineyard C budget.
Impact of COVID-19 and green finance on transportation energy carbon emissions in China: From the perspective of an automobile energy consumption structure
Authors: Liu Lingyun , Cheng Yanxin , Guan Ningning , Liu Yazhen , Zhang Xin , Li Yang , Yang Zining
Published: April 2023

Background: In China, the transportation sector is the main energy consumer and the main source of carbon emissions. Reducing carbon emissions in the transportation sector is an important goal for China, especially during the current period of economic development. Due to the impact of pandemic shocks, the rapid development of green finance is conducive to supporting the transportation sector in achieving a carbon peak. Thus, we examined whether the development of green finance is still effective under the impact of a pandemic and the actual effect of green finance on the reduction of carbon emissions.

Methods: In this study, we searched the internet for consumption structure data of vehicles and green finance indices of 30 Chinese provinces and cities from 2016 to 2021. A regression discontinuity model was constructed to test the effect of pandemic shock and green finance development on the reduction of transportation energy carbon emissions.

Results: The results show that the impact of the COVID-19 pandemic has helped people change their preference toward more energy-efficient vehicles and reduce carbon emissions in the transportation sector. Green finance can effectively contribute to the reduction of transportation energy carbon emissions; however, the overall mitigation effect is limited.

Conclusion: The empirical evidence is not only helpful in assessing the long-term impact of the COVID-19 pandemic but also conducive to the appropriate establishment of policy tools for supporting green finance development, which is further conducive to reducing carbon emissions in the transportation sector.
Soil C:N:P stoichiometry and its influencing factors in forest ecosystems in southern China
Authors: Lu Mengzhen , Zeng Fuping , Lv Siwei , Zhang Hao , Zeng Zhaoxia , Peng Wanxia , Song Tongqing , Wang Kelin , Du Hu
Published: April 2023

Introduction

Soil carbon and nutrient contents and their stoichiometric characteristics play a vital role in indicating plant growth and element balance, which can be used to indicate nutrient limitation. However, it has been less studied about their driving factors within forest soils at the regional scale in southern China.

Methods

In this study, soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) were analyzed in the topsoil (0–10 cm) at 345 sampling plots representing different forest types in Guangxi Province.

Results

The results showed that the mean contents of C, N, and P were 29.80, 2.46, and 0.51 g/kg, respectively, and soil C:N, C:P, and N:P were 13.95, 69.60, and 5.53 respectively. The ratios also showed remarkable correlations with each other. C, N, and P contents and their ratios presented significant differences among different soil and vegetation types. C, N, and P concentrations increased with the increase of elevation and latitude, and decrease with the increase of average annual temperature (MAT). Conversely, C:N showed an opposite trend. C, N, and N:P were also increased with increasing average annual precipitation (MAP). Collectively, soil type, vegetation type, geographical, and climatic factors explained 43.46, 64.02, 68.61, 32.93, 39.64, and 37.87% of the variance in C, N, P, C:N, C:P, and N:P, respectively. For Soil C, both latitude and MAP had strong influences. Soil type was the largest explanation for soil N and P contents. Latitude and longitude were the key factors determining the soil stoichiometric ratios.

Discussion

Overall, soil type, geographical and climatic factors were the most vital explanation variables for soil nutrients and their stoichiometric ratios. These results could help improve our understanding of soil stoichiometry within forest ecosystems in southern China.
Applying amplification refractory mutation system technique to detecting cell-free fetal DNA for single-gene disorders purpose
Authors: Tan Yu , Jian Hui , Zhang Ranran , Wang Jing , Zhou Cong , Xiao Yuanyuan , Liang Weibo , Wang Li
Published: April 2023

Non-invasive prenatal diagnosis for single-gene disorders (NIPD) is still in development and deserves further study. The advent of next-generation sequencing technology significantly improved the detection of multiple mutations for non-invasive prenatal diagnosis for single-gene disorder purposes. However, bespoke amplicon-based NGS assays are costly. In this study, we developed a new strategy for non-invasive prenatal screening for single-gene disorders based on a capillary electrophoresis (CE) platform using an amplification refractory mutation system (ARMS)-PCR technique. Allele-specific primers for several disease-correlated mutations were designed, and subsequently, sensitivity and specificity assays were conducted. Assays on simulated two-person DNA mixtures showed that three primers targeting the mutant allele could detect minor DNA components in 1:500 mixtures. All primers showed positive results at 0.01 ng of the template DNA. Cell-free fetal DNA was extracted from a pregnant woman’s peripheral blood for the detection of paternally inherited mutations. Our results showed that one primer successfully amplified the mutant allele of fetal DNA in maternal plasma, which was confirmed by genotyping the genomic DNA extracted from amniotic fluid. This study suggested that the ARMS-PCR technique, a fast and cost-effective method, might be a promising method used to target de novo or paternally inherited pathogenic mutations in maternal plasma.
Whole transcriptome sequencing reveals HOXD11-AGAP3, a novel fusion transcript in the Indian acute leukemia cohort
Authors: Desai Sagar Sanjiv , Ravindran Febina , Panchal Amey , Ojha Nishit , Jadhav Sachin , Choudhary Bibha
Published: April 2023

Introduction: Acute leukemia is a heterogeneous disease with distinct genotypes and complex karyotypes leading to abnormal proliferation of hematopoietic cells. According to GLOBOCAN reports, Asia accounts for 48.6% of leukemia cases, and India reports ~10.2% of all leukemia cases worldwide. Previous studies have shown that the genetic landscape of AML in India is significantly different from that in the western population by WES.

Methods: We have sequenced and analyzed 9 acute myeloid leukemia (AML) transcriptome samples in the present study. We performed fusion detection in all the samples and categorized the patients based on cytogenetic abnormalities, followed by a differential expression analysis and WGCNA analysis. Finally, Immune profiles were obtained using CIBERSORTx.

Results: We found a novel fusion HOXD11-AGAP3 in 3 patients, BCR-ABL1 in 4, and KMT2A-MLLT3 in one patient. Categorizing the patients based on their cytogenetic abnormalities and performing a differential expression analysis, followed by WGCNA analysis, we observed that in the HOXD11-AGAP3 group, correlated co-expression modules were enriched with genes from pathways like Neutrophil degranulation, Innate Immune system, ECM degradation, and GTP hydrolysis. Additionally, we obtained HOXD11-AGAP3-specific overexpression of chemokines CCL28 and DOCK2. Immune profiling using CIBRSORTx revealed differences in the immune profiles across all the samples. We also observed HOXD11-AGAP3-specific elevated expression of lincRNA HOTAIRM1 and its interacting partner HOXA2.

Discussion: The findings highlight population-specific HOXD11-AGAP3, a novel cytogenetic abnormality in AML. The fusion led to alterations in immune system represented by CCL28 and DOCK2 over-expression. Interestingly, in AML, CCL28 is known prognostic marker. Additionally, non-coding signatures (HOTAIRM1) were observed specific to the HOXD11-AGAP3 fusion transcript which are known to be implicated in AML.
Case report: Anal tuberculosis presenting as an anal fistula
Authors: Chaudhry Muhammad Qasim , Abid Shahab , Kayani Naila
Published: April 2023

This is a case of a young gentleman, who presented with complaints of hematochezia, weight loss and fluctuating fever for the past five months. The patient was a known case of Hirschsprung disease and Ulcerative colitis (IUC) and underwent a rectal Duhamel procedure in the past. On examination there was a fistula with an external opening at the anal verge. The clinical suspicion at this point was enterocutaneous fistula, abscess, and incontinence secondary to Hirschsprung disease. Investigations including MRI and sigmoidoscopy were carried out. A tissue from the anorectal junction was taken for histopathology review. Histopathological analysis suggested granulomatous inflammation with collection of epithelioid histiocytes along with caseating necrosis. This was consistent with the diagnosis of anal tuberculosis. The patient was started on a quadruple regimen of anti-tuberculous drugs (ATT). The patient six months into treatment has shown significant clinical improvement.
CD90 is not constitutively expressed in functional innate lymphoid cells
Authors: Schroeder Jan-Hendrik , Beattie Gordon , Lo Jonathan W. , Zabinski Tomasz , Powell Nick , Neves Joana F. , Jenner Richard G. , Lord Graham M.
Published: April 2023

Huge progress has been made in understanding the biology of innate lymphoid cells (ILC) by adopting several well-known concepts in T cell biology. As such, flow cytometry gating strategies and markers, such as CD90, have been applied to indentify ILC. Here, we report that most non-NK intestinal ILC have a high expression of CD90 as expected, but surprisingly a sub-population of cells exhibit low or even no expression of this marker. CD90-negative and CD90-low CD127+ ILC were present amongst all ILC subsets in the gut. The frequency of CD90-negative and CD90-low CD127+ ILC was dependent on stimulatory cues in vitro and enhanced by dysbiosis in vivo. CD90-negative and CD90-low CD127+ ILC were a potential source of IL-13, IFNγ and IL-17A at steady state and upon dysbiosis- and dextran sulphate sodium-elicited colitis. Hence, this study reveals that, contrary to expectations, CD90 is not constitutively expressed by functional ILC in the gut.
Recommendations for the design of in situ sampling strategies to reconstruct fine-scale ocean currents in the context of SWOT satellite mission
Authors: Barceló-Llull Bàrbara , Pascual Ananda
Published: April 2023

The new Surface Water and Ocean Topography (SWOT) satellite mission aims to provide sea surface height (SSH) measurements in two dimensions along a wide-swath altimeter track with an expected effective resolution down to 15–30 km. In this context our goal is to optimize the design of in situ experiments aimed to reconstruct fine-scale ocean currents (~20 km), such as those that will be conducted to validate the first available tranche of SWOT data. A set of Observing System Simulation Experiments are developed to evaluate different sampling strategies and their impact on the reconstruction of fine-scale sea level and surface ocean velocities. The analysis focuses (i) within a swath of SWOT on the western Mediterranean Sea and (ii) within a SWOT crossover on the subpolar northwest Atlantic. From this evaluation we provide recommendations for the design of in situ experiments that share the same objective. In both regions of study distinct strategies provide reconstructions similar to the ocean truth, especially those consisting of rosette Conductivity Temperature Depth (CTD) casts down to 1000 m and separated by a range of distances between 5 and 15 km. A good compromise considering the advantages of each configuration is the reference design, consisting of CTD casts down to 1000 m and 10 km apart. Faster alternative strategies in the Mediterranean comprise: (i) CTD casts down to 500 m and separated by 10 km and (ii) an underway CTD with a horizontal spacing between profiles of 6 km and a vertical extension of 500 m. In the Atlantic, the geostrophic velocities reconstructed from strategies that only sample the upper 500 m depth have a maximum magnitude ~50% smaller than the ocean truth. A configuration not appropriate for our objective in both regions is the strategy consisting of an underway CTD sampling one profile every 2.5 km and down to 200 m. This suggests that the thermocline and halocline need to be sampled to reconstruct the geostrophic flow at the upper layer. Concerning seasonality, the reference configuration is a design that provides reconstructions similar to the ocean truth in both regions for the period evaluated in summer and also in winter in the Mediterranean.
Current shear and turbulence during a near-inertial wave
Authors: Röhrs Johannes , Halsne Trygve , Sutherland Graig , Dagestad Knut-Frode , Hole Lars Robert , Broström Göran , Christensen Kai H.
Published: April 2023

Surface currents and turbulent mixing were observed during a near-inertial wave (NIW) using an accousting doppler current profiler (ADCP) and satellite-tracked drifters. Drifter trajectories sampled at three depth levels show characteristics of an Ekman solution superposed with the NIW. Velocity and dissipation estimates from the ADCP reveal strong shear with a distinct constant flux layer in between the roughness length and a critical depth at 4m. Below, a shear free slab layer performing an inertial oscillation is observed. Dissipation, as estimated from the vertical beam of the ADCP, peaks in the wave-enhanced friction layer when the current opposes the wind and wave direction. Below the constant flux layer, maximum turbulence is observed when the NIW is in a phase that is in opposite direction to the time-averaged current. During this phase, currents at various depths rapidly realign in the entire boundary layer.
Biocompacting livestock accelerate drowning of tidal salt marshes with sea level rise
Authors: Elschot Kelly , Baptist Martin J. , van Puijenbroek Marinka E. B.
Published: April 2023

A global concern for coastal ecosystems is the predicted rise in sea-level for which salt marshes must keep pace by increasing in surface elevation sufficiently. Variables that control this elevation change need to be identified to predict the adaptability of marshes to future sea-level rise. Many European marshes are grazed by livestock and these heavy grazers can biocompact the soil, a process often underestimated in studies assessing the long-term survival of marshes. We measured elevation changes for thirteen years in the field in grazed and non-grazed marshes. With a statistical model the most important factors controlling rates of surface elevation change were identified and provided the input for a mathematical model to study future elevation change of grazed and non-grazed salt marshes up to 2100 under three Sea Level Rise and sediment supply scenarios. We found that trampling by grazing cattle significantly reduced the annual rates of elevation gain from 11.9 mm yr-1 in the non-grazed marsh to 3.6 mm yr-1 in the grazed marsh. Next to biocompaction by livestock, precipitation deficit and extreme drought resulted in extra compaction. Our model results showed that cattle presence had a negative impact on the future adaptability of salt marshes to grow vertically for rising sea levels. Biocompaction reduced the total elevation change by 42% if the current linear SLR does not accelerate. For an accelerating and high SLR to 109 cm +NAP in 2100, biocompaction reduced elevation changes by 12% and the grazed marsh can no longer outcompete the rise in sea level from around 2050 onwards, compared to the non-grazed marsh. The grazed marsh will slowly drown but this will not lead to a significant change in vegetation composition yet. For an extreme SLR to 195 cm +NAP in 2100 the elevation changes in both the grazed and non-grazed marshes cannot keep pace with the rise in sea level and the marsh vegetation is expected to show regression to plants typical for a low marsh. A reduction in sediment supply will aggravate the effects of SLR and may result in highly increasing inundation frequencies and subsequent disappearance of the marsh vegetation.
The transcriptome of Litopenaeus vannamei in zoea larvae and adults infected by Vibrio parahaemolyticus
Authors: Chen Nanxiong , Jin Jiaojiao , Chen Yibin , Hu Yicheng , Shen Yuchun , Li Sedong
Published: April 2023

Introduction

The rapid development of the Litopenaeus vannamei industry largely depends on the acquisition of high-quality larvae. Shrimp larval development is a unique metamorphic process that results in mortality due to disease vulnerability. Currently, studies on innate immunity in shrimp are mainly focused on the adult stage, but little has been done on innate immunity in larvae.

Methods

In this study, utilizing a high-throughput Illumina sequencing approach, we compare the transcriptome of L. vannamei Zoea larvae and adults infected by Vibrio parahaemolyticus.

Results

A total of 487,887,650 high quality reads were obtained, assembled, and aggregated into 23,802 genes, among which 3315 were identified as differentially expressed genes. Then GO term enrichment analysis, KEGG pathway enrichment analysis and functional gene analysis were performed. We found that pathways that are involved in the innate immune response, such as mTOR signaling pathway, MAPK signaling pathway, and Notch signaling pathway, were more enriched in the Zoea stage compared to the adult stage, suggesting that innate immunity against Vibrio vulnificus may exist during the Zoea larvae stage.

Discussion

were more enriched in the Zoea stage compared to the adult stage, suggesting that innate immunity against Vibrio vulnificus may exist during the Zoea larvae stage. These findings will provide useful information for the study of innate immunity in shrimp larvae.
Differentiation using minimally-invasive bioimpedance measurements of healthy and pathological lung tissue through bronchoscopy
Authors: Company-Se Georgina , Nescolarde Lexa , Pajares Virginia , Torrego Alfons , Riu Pere J. , Rosell Javier , Bragós Ramon
Published: April 2023

Purpose

To use minimally-invasive transcatheter electrical impedance spectroscopy measurements for tissue differentiation among healthy lung tissue and pathologic lung tissue from patients with different respiratory diseases (neoplasm, fibrosis, pneumonia and emphysema) to complement the diagnosis at real time during bronchoscopic procedures.

Methods

Multi-frequency bioimpedance measurements were performed in 102 patients. The two most discriminative frequencies for impedance modulus (|Z|), phase angle (PA), resistance (R) and reactance (Xc) were selected based on the maximum mean pair-wise Euclidean distances between paired groups. One-way ANOVA for parametric variables and Kruskal–Wallis for non-parametric data tests have been performed with post-hoc tests. Discriminant analysis has also been performed to find a linear combination of features to separate among tissue groups.

Results

We found statistically significant differences for all the parameters between: neoplasm and pneumonia (p < 0.05); neoplasm and healthy lung tissue (p < 0.001); neoplasm and emphysema (p < 0.001); fibrosis and healthy lung tissue (p ≤ 0.001) and pneumonia and healthy lung tissue (p < 0.01). For fibrosis and emphysema (p < 0.05) only in |Z|, R and Xc; and between pneumonia and emphysema (p < 0.05) only in |Z| and R. No statistically significant differences (p > 0.05) are found between neoplasm and fibrosis; fibrosis and pneumonia; and between healthy lung tissue and emphysema.

Conclusion

The application of minimally-invasive electrical impedance spectroscopy measurements in lung tissue have proven to be useful for tissue differentiation between those pathologies that leads increased tissue and inflammatory cells and those ones that contain more air and destruction of alveolar septa, which could help clinicians to improve diagnosis.
Optimizing mycobacteria molecular diagnostics: No decontamination! Human DNA depletion? Greener storage at 4 °C!
Authors: Prajwal Prajwal , Neary Turlough , Rohrbach Katja , Bittel Pascal , Göller Pauline C. , Buch Thorsten , Dümcke Sebastian , Keller Peter M.
Published: April 2023

Introduction

Tuberculosis (TB) is an infectious disease caused by the group of bacterial pathogens Mycobacterium tuberculosis complex (MTBC) and is one of the leading causes of death worldwide. Timely diagnosis and treatment of drug-resistant TB is a key pillar of WHO’s strategy to combat global TB. The time required to carry out drug susceptibility testing (DST) for MTBC via the classic culture method is in the range of weeks and such delays have a detrimental effect on treatment outcomes. Given that molecular testing is in the range of hours to 1 or 2 days its value in treating drug resistant TB cannot be overstated. When developing such tests, one wants to optimize each step so that tests are successful even when confronted with samples that have a low MTBC load or contain large amounts of host DNA. This could improve the performance of the popular rapid molecular tests, especially for samples with mycobacterial loads close to the limits of detection. Where optimizations could have a more significant impact is for tests based on targeted next generation sequencing (tNGS) which typically require higher quantities of DNA. This would be significant as tNGS can provide more comprehensive drug resistance profiles than the relatively limited resistance information provided by rapid tests. In this work we endeavor to optimize pre-treatment and extraction steps for molecular testing.

Methods

We begin by choosing the best DNA extraction device by comparing the amount of DNA extracted by five commonly used devices from identical samples. Following this, the effect that decontamination and human DNA depletion have on extraction efficiency is explored.

Results

The best results were achieved (i.e., the lowest Ct values) when neither decontamination nor human DNA depletion were used. As expected, in all tested scenarios the addition of decontamination to our workflow substantially reduced the yield of DNA extracted. This illustrates that the standard TB laboratory practice of applying decontamination, although being vital for culture-based testing, can negatively impact the performance of molecular testing. As a complement to the above experiments, we also considered the best Mycobacterium tuberculosis DNA storage method to optimize molecular testing carried out in the near- to medium-term. Comparing Ct values following three-month storage at 4 °C and at −20 °C and showed little difference between the two.

Discussion

In summary, for molecular diagnostics aimed at mycobacteria this work highlights the importance of choosing the right DNA extraction device, indicates that decontamination causes significant loss of mycobacterial DNA, and shows that samples preserved for further molecular testing can be stored at 4 °C, just as well at −20 °C. Under our experimental settings, human DNA depletion gave no significant improvement in Ct values for the detection of MTBC.
Prediction models for neutralization activity against emerging SARS-CoV-2 variants: A cross-sectional study
Authors: Goto Atsushi , Miyakawa Kei , Nakayama Izumi , Yagome Susumu , Xu Juan , Kaneko Makoto , Ohtake Norihisa , Kato Hideaki , Ryo Akihide
Published: April 2023

Objective

Despite extensive vaccination campaigns to combat the coronavirus disease (COVID-19) pandemic, variants of concern, particularly the Omicron variant (B.1.1.529 or BA.1), may escape the antibodies elicited by vaccination against SARS-CoV-2. Therefore, this study aimed to evaluate 50% neutralizing activity (NT50) against SARS-CoV-2 D614G, Delta, Omicron BA.1, and Omicron BA.2 and to develop prediction models to predict the risk of infection in a general population in Japan.

Methods

We used a random 10% of samples from 1,277 participants in a population-based cross-sectional survey conducted in January and February 2022 in Yokohama City, the most populous municipality in Japan. We measured NT50 against D614G as a reference and three variants (Delta, Omicron BA.1, and BA.2) and immunoglobulin G against SARS-CoV-2 spike protein (SP-IgG).

Results

Among 123 participants aged 20–74, 93% had received two doses of SARS-CoV-2 vaccine. The geometric means (95% confidence intervals) of NT50 were 65.5 (51.8–82.8) for D614G, 34.3 (27.1–43.4) for Delta, 14.9 (12.2–18.0) for Omicron BA.1, and 12.9 (11.3–14.7) for Omicron BA.2. The prediction model with SP-IgG titers for Omicron BA.1 performed better than the model for Omicron BA.2 (bias-corrected R2 with bootstrapping: 0.721 vs. 0.588). The models also performed better for BA.1 than for BA.2 (R2 = 0.850 vs. 0.150) in a validation study with 20 independent samples.

Conclusion

In a general Japanese population with 93% of the population vaccinated with two doses of SARS-CoV-2 vaccine, neutralizing activity against Omicron BA.1 and BA.2 were substantially lower than those against D614G or the Delta variant. The prediction models for Omicron BA.1 and BA.2 showed moderate predictive ability and the model for BA.1 performed well in validation data.
ERV14 receptor impacts mycelial growth via its interactions with cell wall synthase and transporters in Aspergillus niger
Authors: Zheng Junwei , Yao Linlin , Zeng Xu , Wang Bin , Pan Li
Published: April 2023

Efficient protein secretion is closely correlated with vesicle sorting and packaging, especially with cargo receptor-mediated selective transport for ER exit. Even though Aspergillus niger is considered an industrially natural host for protein production due to its exceptional secretion capacity, the trafficking mechanism in the early secretory pathway remains a black box for us to explore. Here, we identified and characterized all putative ER cargo receptors of the three families in A. niger. We successfully constructed overexpression and deletion strains of each receptor and compared the colony morphology and protein secretion status of each strain. Among them, the deletion of Erv14 severely inhibited mycelial growth and secretion of extracellular proteins such as glucoamylase. To gain a comprehensive understanding of the proteins associated with Erv14, we developed a high-throughput method by combining yeast two-hybrid (Y2H) with next-generation sequencing (NGS) technology. We found Erv14 specifically interacted with transporters. Following further validation of the quantitative membrane proteome, we determined that Erv14 was associated with the transport of proteins involved in processes such as cell wall synthesis, lipid metabolism, and organic substrate metabolism.
Development of plastic-degrading microbial consortia by induced selection in microcosms
Authors: Salinas Jesús , Carpena Víctor , Martínez-Gallardo María R. , Segado Martín , Estrella-González María J. , Toribio Ana J. , Jurado Macarena M. , López-González Juan A. , Suárez-Estrella Francisca , López María J.
Published: April 2023

The increase in the production of highly recalcitrant plastic materials, and their accumulation in ecosystems, generates the need to investigate new sustainable strategies to reduce this type of pollution. Based on recent works, the use of microbial consortia could contribute to improving plastic biodegradation performance. This work deals with the selection and characterization of plastic-degrading microbial consortia using a sequential and induced enrichment technique from artificially contaminated microcosms. The microcosm consisted of a soil sample in which LLDPE (linear low-density polyethylene) was buried. Consortia were obtained from the initial sample by sequential enrichment in a culture medium with LLDPE-type plastic material (in film or powder format) as the sole carbon source. Enrichment cultures were incubated for 105 days with monthly transfer to fresh medium. The abundance and diversity of total bacteria and fungi were monitored. Like LLDPE, lignin is a very complex polymer, so its biodegradation is closely linked to that of some recalcitrant plastics. For this reason, counting of ligninolytic microorganisms from the different enrichments was also performed. Additionally, the consortium members were isolated, molecularly identified and enzymatically characterized. The results revealed a loss of microbial diversity at each culture transfer at the end of the induced selection process. The consortium selected from selective enrichment in cultures with LLDPE in powder form was more effective compared to the consortium selected in cultures with LLDPE in film form, resulting in a reduction of microplastic weight between 2.5 and 5.5%. Some members of the consortia showed a wide range of enzymatic activities related to the degradation of recalcitrant plastic polymers, with Pseudomonas aeruginosa REBP5 or Pseudomonas alloputida REBP7 strains standing out. The strains identified as Castellaniella denitrificans REBF6 and Debaryomyces hansenii RELF8 were also considered relevant members of the consortia although they showed more discrete enzymatic profiles. Other consortium members could collaborate in the prior degradation of additives accompanying the LLDPE polymer, facilitating the subsequent access of other real degraders of the plastic structure. Although preliminary, the microbial consortia selected in this work contribute to the current knowledge of the degradation of recalcitrant plastics of anthropogenic origin accumulated in natural environments.
Genome resequencing and transcriptome analysis reveal the molecular mechanism of albinism in Cordyceps militaris
Authors: Zhao Ying , Liu YuDong , Chen Xun , Xiao Jun
Published: April 2023

Light is an important regulator of most fungal life activities and transmits signals through certain photoreceptor proteins such as phytochromes and cryptochromes. However, the light response mechanism varies across different fungi. The WCC complex composed of white collar-1 (WC-1) and white collar-2 (WC-2) is considered to be the key factor regulating fungal albinism. The photoreceptor protein Vivid (VVD) is the negative regulator of the WCC complex. In this study, we discovered an albino mutant (Alb) generated by 60Co-γ-ray irradiation from Cordyceps militaris (C. militaris). This mutant showed albinism of the mycelia and fruiting bodies under light, and the fruiting bodies developed normally. However, this phenotype in Alb differed from that in the CmWC-1 mutant. This suggests that CmWC1 may not be mutated in Alb. A mutated polyketide synthase (CmPKS) was found through genome resequencing analysis. CmPKS was significantly induced by a light signal, and its mutation reduced melanin accumulation in C. militaris. In addition, we found that a zinc-finger domain-containing protein (CmWC-3) was induced by a light signal and interacted with CmWC-1 and CmVVD. Moreover, CmWC-2 also interacted with CmWC-1 to form the WCC complex and was inhibited by CmVVD. In addition, CmWC-3 directly bound with the CmPKS promoter, but CmWC1 did not. These results suggest that albinism and fruiting body development are two independent processes; the WCC complex of CmWC-1 with CmWC-3 regulates CmPKS expression to regulate color change, whereas CmWC-1 with CmWC-2 affects fruiting body development via the carotenoid pathway. These findings will help us to better understand the albinism mechanism of C. militaris.
Optimizing peritoneal dialysis catheter placement
Authors: Khan Sana F. , Rosner Mitchell H.
Published: April 2023

Long-term success of peritoneal dialysis as a kidney replacement therapy requires a well-functioning peritoneal dialysis catheter. With ongoing reductions in infectious complications, there is an increased emphasis on the impact of catheter-related and mechanical complications. There is currently a marked variation in the utilization of various types of catheters (double cuff vs single cuff, coiled tip vs straight tip), methods of catheter insertion (advanced laparoscopic, open surgical dissection, image guided percutaneous, blind percutaneous), timing of catheter insertion, location of catheter placement (pre-sternal v. abdominal) and peri-operative practices. Specialized approaches to catheter placement in clinical practice include use of extended catheters and embedded catheters. Marked variations in patient lifestyle preferences and comorbidities, specifically in high acuity patient populations (polycystic kidney disease, obesity, cirrhosis) necessitate individualized approaches to catheter placement and care. Current consensus guidelines recommend local procedural expertise, consideration of patient characteristics and appropriate resources to support catheter placement and long-term functioning. This review focuses on an overview of approaches to catheter placement with emphasis on a patient-centered approach.
Functional neurological symptoms are a frequent and relevant comorbidity in patients with multiple sclerosis
Authors: Piliavska Katya , Dantlgraber Michael , Dettmers Christian , Jöbges Michael , Liepert Joachim , Schmidt Roger
Published: April 2023

Introduction

Functional neurological symptoms (FNS) in multiple sclerosis (MS) have shown to be underinvestigated even though neurological diseases such as MS represent a risk factor for developing FNS. Comorbidity of FNS and MS can produce high personal and social costs since FNS patients have high healthcare utilization costs and a quality of life at least as impaired as in patients with disorders with underlying structural pathology. This study aims to assess comorbid FNS in patients with MS (pwMS) and investigate whether FNS in pwMS are associated with poorer health-related quality of life and work ability.

Methods

Newly admitted patients (234) with MS were studied during their stay at Kliniken Schmieder, a neurological rehabilitation clinic in Konstanz, Germany. The degree to which the overall clinical picture was explained by MS pathology was rated by neurologists and allied health practitioners on a five-point Likert scale. Additionally, neurologists rated each symptom reported by the patients. Health-related quality of life was assessed using a self-report questionnaire and work ability was assessed using the mean number of hours worked per day and information regarding disability pension as reported by patients.

Results

In 55.1% of cases, the clinical picture was completely explained by structural pathology due to MS. 17.1% of pwMS presented an overall clinical picture half or less of which could be explained by underlying structural pathology. PwMS with a higher comorbid FNS burden had a lower health-related quality of life and reported fewer working hours per day than pwMS with symptoms explained by structural pathology. Furthermore, pwMS with a full disability pension had a higher comorbid FNS burden than pwMS with no or partial disability pension.

Discussion

These results show that FNS should be addressed diagnostically and therapeutically since such symptoms are an important comorbidity in MS that is related to poorer health-related quality of life and lower work ability.
Unilateral biportal endoscopic foraminotomy and diskectomy combined with piezosurgery for treating cervical spondylotic radiculopathy with neuropathic radicular pain
Authors: Zhang Peng , Jin Yanghui , Zhu Bo , Zheng Mingfeng , Ying Xiaozhang , Zheng Qi
Published: April 2023

Objective

Unilateral biportal endoscopy (UBE) represents a relatively recent development in minimally invasive spine surgery. This study aimed to evaluate the efficacy and safety of UBE foraminotomy and diskectomy combined with piezosurgery for treating cervical spondylotic radiculopathy (CSR) with neuropathic radicular pain.

Methods

We retrospectively analyzed the outcomes in 12 patients with CSR who underwent UBE foraminotomy and diskectomy combined with piezosurgery. The intraoperative blood loss, operative time, visual analog scale (VAS) scores for the neck and arm, neck disability index (NDI) scores, and complications were recorded.

Results

Postoperative VAS scores of the neck and arm and NDI scores were significantly improved. Additionally, a postoperative CT scan revealed adequate enlargement of the cervical canal and nerve root. No specific complications occurred during surgery and the immediate postoperative period.

Conclusions

This primary study indicated that the UBE foraminotomy and diskectomy with piezosurgery is a promising technique for treating cervical spondylotic radiculopathy with neuropathic radicular pain.
Case report: Transvenous coil embolization of a high-grade Galenic dural arteriovenous fistula
Authors: Cornea Christiana M. , Quig Nathan , Yap Edward , Solander Sten Y.
Published: April 2023

Introduction

Galenic dural arteriovenous fistulas (dAVFs) are a rare form of dAVF and rarely described in the literature. Their distinct location requires different surgical approaches than dAVFs occurring at the nearby sites of the straight sinus and torcular Herophili, and their high risk of hemorrhage makes these dAVFs very challenging to approach surgically. In this report, we present a unique case of Galenic dAVF.

Case description

The patient is a 54-year-old female who presented with a 2-year history of progressive headaches, cognitive decline, and papilledema. A cerebral angiogram demonstrated a complex dAVF to the vein of Galen (VoG). She underwent transarterial embolization with Onyx-18 which resulted in minimal reduction in arterial venous shunting. She subsequently underwent a successful transvenous coil embolization resulting in complete occlusion of dAVF. The patient’s postoperative course was complicated by interventricular hemorrhage; however, she had a remarkable clinical recovery with resolution of headaches and improvement in cognitive function. A follow-up angiogram completed 6  months post-embolization demonstrated very mild residual shunting.

Conclusion

In the unique case presented here, we demonstrate the efficacy of transvenous embolization via an occluded straight sinus as an alternative therapeutic option to eliminate cortical venous reflux.
Bibliometric analysis of stroke and quality of life
Authors: Chen Mengtong , Zhang Yuting , Dong Lijuan , Guo Xiaomei
Published: April 2023

Objective

To perform a bibliometric analysis of stroke and quality of life studies between 2000 and 2022 using VOSviewer and CiteSpace.

Methods

The literature data source for this study was the Web of Science Core Collection. CiteSpace and VOSviewer were used to analyze publications in relation to authors, countries, institutions, journals, references, and keywords.

Results

A total of 704 publications were obtained for the bibliometric analysis. The number of publications has gradually increased over 23 years, with an annual increase of 728.6%. Kim S is the most prolific author in the field (10 publications), and the United States and Chinese University of Hong Kong have the most publications. Stroke is the most prolific journal with the most citations per paper (91.58) and the highest impact factor (IF 2021, 10.17). The most high-frequency keywords are “stroke,” “quality of life,” “rehabilitation,” and “depression.”

Conclusion

A bibliometric analysis of stroke and quality of life over the last 23  years provides future research directions.
Linking dietary intake, circadian biomarkers, and clock genes on obesity: A study protocol
Authors: Lages Marlene , Barros Renata , Carmo-Silva Sara , Guarino Maria P.
Published: April 2023

Background

The prevalence of obesity continues to rise, and although this is a complex disease, the screening is made simply with the value of the Body Mass Index. This index only considers weight and height, being limited in portraying the multiple existing obesity phenotypes. The characterization of the chronotype and circadian system as an innovative phenotype of a patient’s form of obesity is gaining increasing importance for the development of novel and pinpointed nutritional interventions.

Objective

The present study is a prospective observational controlled study conducted in Portugal, aiming to characterize the chronotype and determine its relation to the phenotype and dietary patterns of patients with obesity and healthy participants.

Methods

Adults with obesity (study group) and healthy adults (control group), aged between 18 and 75, will be enrolled in this study. Data will be collected to characterize the chronotype, dietary intake, and sleep quality through validated questionnaires. Body composition will also be assessed, and blood samples will be collected to quantify circadian and metabolic biomarkers.

Discussion

This study is expected to contribute to a better understanding of the impact of obesity and dietary intake on circadian biomarkers and, therefore, increase scientific evidence to help future therapeutic interventions based on chronobiology, with a particular focus on nutritional interventions.