bluuebunny/crossref_metadata_2025 huggingface dataset:
Parabolic relationship between SMAD3 expression level and the reprogramming efficiency of goat induced mammary epithelial cells
Authors: Wu Yulian , Zhang Dandan , Ye Sheng , Liu Quanhui , Huang Ben
Published: October 2022

Mammary epithelial cells are the only cells of mammary glands with lactation capacity. They are closely related to mammary development and milk yield. Our earlier studies showed that the transformation of goat fibroblasts into induced mammary epithelial cells (iMECs) was closely correlated with SMAD3 overexpression. Therefore, we further explored the role of SMAD3 on iMECs reprogramming in this study. The SMAD3 gene was overexpressed in goat ear fibroblasts using the tetracycline-induced expression method. The outcomes demonstrated that goat ear fibroblasts can be converted into iMECs by overexpressing the SMAD3 gene. In contrast, it was discovered that SMAD3 downregulation by RNA interference significantly decrease the reprogramming efficiency of iMECs. These results show that SMAD3 plays a key regulatory role in the reprogramming of iMECs. Surprisingly, we also found a parabolic relationship between SMAD3 expression level and iMECs reprogramming efficiency, and that the reprogramming efficiency was maximum when the addition of doxycycline concentration was 5 μg/ml. In light of this, our findings may offer new perspectives on the regulatory mechanism governing mammary epithelial cell fate in goats as well as a fresh approach to studying mammary development and differentiation in vitro.
Genome elimination from the germline cells in diploid and triploid male water frogs Pelophylax esculentus
Authors: Chmielewska Magdalena , Kaźmierczak Mikołaj , Rozenblut-Kościsty Beata , Kolenda Krzysztof , Dudzik Anna , Dedukh Dmitrij , Ogielska Maria
Published: October 2022

Hybridogenesis is a hemiclonal reproductive strategy in diploid and triploid hybrids. Our study model is a frog P. esculentus (diploid RL and triploids RLL and RRL), a natural hybrid between P. lessonae (LL) and P. ridibundus (RR). Hybridogenesis relies on elimination of one genome (L or R) from gonocytes (G) in tadpole gonads during prespermatogenesis, but not from spermatogonial stem cells (SSCs) in adults. Here we provide the first comprehensive study of testis morphology combined with chromosome composition in the full spectrum of spermatogenic cells. Using genomic in situ hybridization (GISH) and FISH we determined genomes in metaphase plates and interphase nuclei in Gs and SSCs. We traced genomic composition of SSCs, spermatocytes and spermatozoa in individual adult males that were crossed with females of the parental species and gave progeny. Degenerating gonocytes (24%–39%) and SSCs (18%–20%) led to partial sterility of juvenile and adult gonads. We conclude that elimination and endoreplication not properly completed during prespermatogenesis may be halted when gonocytes become dormant in juveniles. After resumption of mitotic divisions by SSCs in adults, these 20% of cells with successful genome elimination and endoreplication continue spermatogenesis, while in about 80% spermatogenesis is deficient. Majority of abnormal cells are eliminated by cell death, however some of them give rise to aneuploid spermatocytes and spermatozoa which shows that hybridogenesis is a wasteful process.
Mixed oxides from calcined layered double hydroxides for glycerol carbonate production to contribute to the biodiesel economy
Authors: Dalma Argüello , Nancy Bálsamo , Griselda Eimer , Mónica Crivello
Published: October 2022

The glycerol generated as a by-product in the production of biodiesel could be used as a renewable raw material to economically promote the production process. The catalytic conversion of glycerol to a product with higher added value, such as glycerol carbonate, has attracted great interest in the chemical, pharmaceutical, and lithium battery industries, among others, due to its low toxicity, hydration capacity, and biodegradability. Layered-double hydroxide (LDH) materials, the precursors of the catalysts, were synthesized by a direct coprecipitation method to incorporate a third metal ion in addition to magnesium and aluminum ions. This method is the easiest regularly applied technique to design these low cost anionic nanoclay. The atomic percentage of Cu, Zn, or Ni incorporated was 15% of the Mg load in the material. The synthesis atomic ratio, (M2++Mg2+)/Al3+ had a constant value of 3, where M represents the transition metal incorporated. LDHs produced the corresponding mixed metal oxides by thermal decomposition. These materials have excellent properties for reactions catalyzed by the basic sites, high surface area, homogeneous cation dispersion, and thermal stability. The physicochemical material properties were characterized by XRD, N2 sorption, MP-AES, TPD-CO2, SEM, and XPS. The mixed oxides were evaluated in the catalytic conversion of glycerol to glycerol carbonate. The addition of Cu, Ni, or Zn to the matrix of Mg and Al produced changes in its physicochemical properties and mostly in the catalytic activity. X-ray diffractograms of LDHs showed the typical characteristic structure of layers even with metallic ions of Cu, Ni, or Zn incorporated, because their ionic radii are similar to that of the Mg ion, 0.69, 0.73, and 0.74 Å, respectively. The obtained mixed oxides showed a high catalytic activity towards the conversion of glycerol to glycerol carbonate under mild reaction conditions, a 1:2 ratio of glycerol:ethylene carbonate and solvent free. Relative yields higher than 80% were obtained, attributable to an adequate distribution of basicity and textural parameters. The catalysts were used in successive reaction cycles without significant loss of activity.
Artificial intelligence-assisted remote detection of ST-elevation myocardial infarction using a mini-12-lead electrocardiogram device in prehospital ambulance care
Authors: Chen Ke-Wei , Wang Yu-Chen , Liu Meng-Hsuan , Tsai Being-Yuah , Wu Mei-Yao , Hsieh Po-Hsin , Wei Jung-Ting , Shih Edward S. C. , Shiao Yi-Tzone , Hwang Ming-Jing , Wu Ya-Lun , Hsu Kai-Cheng , Chang Kuan-Cheng
Published: October 2022

Objective

To implement an all-day online artificial intelligence (AI)-assisted detection of ST-elevation myocardial infarction (STEMI) by prehospital 12-lead electrocardiograms (ECGs) to facilitate patient triage for timely reperfusion therapy.

Methods

The proposed AI model combines a convolutional neural network and long short-term memory (CNN-LSTM) to predict STEMI on prehospital 12-lead ECGs obtained from mini-12-lead ECG devices equipped in ambulance vehicles in Central Taiwan. Emergency medical technicians (EMTs) from the 14 AI-implemented fire stations performed the on-site 12-lead ECG examinations using the mini portable device. The 12-lead ECG signals were transmitted to the AI center of China Medical University Hospital to classify the recordings as “STEMI” or “Not STEMI”. In 11 non-AI fire stations, the ECG data were transmitted to a secure network and read by available on-line emergency physicians. The response time was defined as the time interval between the ECG transmission and ECG interpretation feedback.

Results

Between July 17, 2021, and March 26, 2022, the AI model classified 362 prehospital 12-lead ECGs obtained from 275 consecutive patients who had called the 119 dispatch centers of fire stations in Central Taiwan for symptoms of chest pain or shortness of breath. The AI's response time to the EMTs in ambulance vehicles was 37.2 ± 11.3 s, which was shorter than the online physicians' response time from 11 other fire stations with no AI implementation (113.2 ± 369.4 s, P < 0.001) after analyzing another set of 335 prehospital 12-lead ECGs. The evaluation metrics including accuracy, precision, specificity, recall, area under the receiver operating characteristic curve, and F1 score to assess the overall AI performance in the remote detection of STEMI were 0.992, 0.889, 0.994, 0.941, 0.997, and 0.914, respectively. During the study period, the AI model promptly identified 10 STEMI patients who underwent primary percutaneous coronary intervention (PPCI) with a median contact-to-door time of 18.5 (IQR: 16–20.8) minutes.

Conclusion

Implementation of an all-day real-time AI-assisted remote detection of STEMI on prehospital 12-lead ECGs in the field is feasible with a high diagnostic accuracy rate. This approach may help minimize preventable delays in contact-to-treatment times for STEMI patients who require PPCI.
Novel insights into exhaustive exercise-induced myocardial injury: Focusing on mitochondrial quality control
Authors: Shi Mingyue , Dong Zhao , Zhao Kai , He Xiaole , Sun Yang , Ren Jun , Ge Wei
Published: October 2022

Regular moderate-intensity exercise elicits benefit cardiovascular health outcomes. However, exhaustive exercise (EE) triggers arrhythmia, heart failure, and sudden cardiac death. Therefore, a better understanding of unfavorable heart sequelae of EE is important. Various mechanisms have been postulated for EE-induced cardiac injury, among which mitochondrial dysfunction is considered the cardinal machinery for pathogenesis of various diseases. Mitochondrial quality control (MQC) is critical for clearance of long-lived or damaged mitochondria, regulation of energy metabolism and cell apoptosis, maintenance of cardiac homeostasis and alleviation of EE-induced injury. In this review, we will focus on MQC mechanisms and propose mitochondrial pathophysiological targets for the management of EE-induced myocardial injury. A thorough understanding of how MQC system functions in the maintenance of mitochondrial homeostasis will provide a feasible rationale for developing potential therapeutic interventions for EE-induced injury.
Disparities in cardiovascular disease prevalence among middle-aged and older adults: Roles of socioeconomic position, social connection, and behavioral and physiological risk factors
Authors: Zhang Ji , Fang Yian , Yao Yao , Zhao Yang , Yue Dahai , Sung Meekang , Jin Yinzi , Zheng Zhi-Jie
Published: October 2022

Introduction

Cardiovascular disease (CVD) remains the leading cause of premature death globally and a major contributor to decreasing quality of life. In the present study, we investigated the contribution of social, behavioral, and physiological determinants of CVD and their different patterns among middle-aged and older adults.

Methods

We used harmonized data from 6 nationally representative individual-level longitudinal studies across 25 countries. We restricted the age to ≥50 years and defined cases as a self-reported history of CVD. The exposure variables were the demographic status (age and sex), socioeconomic position (education level, employment, and household income level), social connections (marital status and family size), behavioral factors (smoking, alcohol drinking, and frequency of moderate to vigorous physical activity), and physiological risk factors (obesity, presence of hypertension, and presence of diabetes). Mixed logistic regression models were fitted to investigate the associations, and dominance analysis was conducted to examine the relative contributions.

Results

In total, 413,203 observations were included in the final analysis, with the CVD prevalence ranging from 10.4% in Mexico to 28.8% in the United States. Physiological risk factors were the main driver of CVD prevalence with the highest dominance proportion, which was higher in developing countries (China, 57.5%; Mexico, 72.8%) than in developed regions (United States, England, 10 European countries, and South Korea). Socioeconomic position and behavioral factors also highly contributed but were less significant in developing countries than in developed regions. The relative contribution of socioeconomic position ranged from 9.4% in Mexico to 23.4% in the United States, and that of behavioral factors ranged from 5.7% in Mexico to 26.1% in England.

Conclusion

The present study demonstrated the different patterns of determinant contributions to CVD prevalence across developing and developed countries. With the challenges produced by different risk factors, the implementation of tailored prevention and control strategies will likely narrow disparities in the CVD prevalence by promoting health management and enhancing the capacity of health systems across different countries.
Systematic total arch replacement with thoraflex hybrid graft in acute type A aortic dissection: A single centre experience
Authors: Chivasso Pierpaolo , Mastrogiovanni Generoso , Bruno Vito Domenico , Miele Mario , Colombino Mario , Triggiani Donato , Cafarelli Francesco , Leone Rocco , Rosapepe Felice , De Martino Matteo , Morena Elvira , Iesu Ivana , Citro Rodolfo , Masiello Paolo , Iesu Severino
Published: October 2022

Introduction

In the last two decades, a more aggressive approach has been encouraged to treat patients with acute type A aortic dissection (ATAAD), extending the repair to the aortic arch and proximal descending thoracic aorta with the frozen elephant trunk (FET) implantation. Here, we report our single-centre experience with the FET technique for the systematic treatment of emergency type A aortic dissection.

Materials and methods

Between December 2017 and January 2022, 69 consecutive patients were admitted with ATAAD; of those, 66 patients (62.9 ± 10.2 years of age, 81.8% men) underwent emergency hybrid aortic arch and FET repair with the multibranched Thoraflex hybrid graft and were enrolled in the study. Primary endpoints were 30 days- and in-hospital mortality. Secondary endpoints were postoperative morbidity and follow-up survival. To better clarify the impact of age on surgical outcomes, we have divided the study population into two groups: group A for patients <70 years of age (47 patients), and group B for patients ≥70 years (19 patients). Time-to-event analysis has been conducted using the Log-rank test and is displayed with Kaplan-Meier curves. A multiple Cox proportional Hazard model was developed to identify predictors of long-term survival with a stepwise backward/forward selection process.

Results

30-days- and in-hospital mortality were 10.6 and 13.6%, respectively. Stroke occurred in three (4.5%) patients. Two (3.0%) patients experienced spinal cord ischemia. We did not find any statistically significant difference between the two groups in terms of main post-operative outcomes. The multivariable Cox proportional hazard model showed left ventricular ejection fraction (HR: 0.83, 95% CI: 0.79–0.92, p < 0.01), peripheral vascular disease (HR: 15.8, 95% CI: 3.9–62.9, p < 0.01), coronary malperfusion (HR: 0.10, 95% CI: 0.01–0.77, p =0.03), lower limbs malperfusion (HR: 5.1, 95% CI: 1.10–23.4, p = 0.04), and cardiopulmonary bypass time (HR: 1.02, 95% CI: 1–1.04, p = 0.01) as independent predictors of long term mortality.

Conclusions

Frozen elephant trunk repair to treat emergency type A aortic dissection appears to be associated with good early and mid-term clinical outcomes even in the elderly.
ArcticBeach v1.0: A physics-based parameterization of pan-Arctic coastline erosion
Authors: Rolph Rebecca , Overduin Pier Paul , Ravens Thomas , Lantuit Hugues , Langer Moritz
Published: October 2022

In the Arctic, air temperatures are increasing and sea ice is declining, resulting in larger waves and a longer open water season, all of which intensify the thaw and erosion of ice-rich coasts. Climate change has been shown to increase the rate of Arctic coastal erosion, causing problems for Arctic cultural heritage, existing industrial, military, and civil infrastructure, as well as changes in nearshore biogeochemistry. Numerical models that reproduce historical and project future Arctic erosion rates are necessary to understand how further climate change will affect these problems, and no such model yet exists to simulate the physics of erosion on a pan-Arctic scale. We have coupled a bathystrophic storm surge model to a simplified physical erosion model of a permafrost coastline. This Arctic erosion model, called ArcticBeach v1.0, is a first step toward a physical parameterization of Arctic shoreline erosion for larger-scale models. It is forced by wind speed and direction, wave period and height, sea surface temperature, all of which are masked during times of sea ice cover near the coastline. Model tuning requires observed historical retreat rates (at least one value), as well as rough nearshore bathymetry. These parameters are already available on a pan-Arctic scale. The model is validated at three study sites at 1) Drew Point (DP), Alaska, 2) Mamontovy Khayata (MK), Siberia, and 3) Veslebogen Cliffs, Svalbard. Simulated cumulative retreat rates for DP and MK respectively (169 and 170 m) over the time periods studied at each site (2007–2016, and 1995–2018) are found to the same order of magnitude as observed cumulative retreat (172 and 120 m). The rocky Veslebogen cliffs have small observed cumulative retreat rates (0.05 m over 2014–2016), and our model was also able to reproduce this same order of magnitude of retreat (0.08 m). Given the large differences in geomorphology between the study sites, this study provides a proof-of-concept that ArcticBeach v1.0 can be applied on very different permafrost coastlines. ArcticBeach v1.0 provides a promising starting point to project retreat of Arctic shorelines, or to evaluate historical retreat in places that have had few observations.
pH induced stress enhances lipid accumulation in microalgae grown under mixotrophic and autotrophic condition
Authors: Alkhamis Yousef Ahmed , Mathew Roshmon Thomas , Nagarajan Ganesan , Rahman Sheikh Mustafizur , Rahman Md. Moshiur
Published: October 2022

Production of biodiesel together with wastewater treatment and CO2 sequestration is a promising technology. The growing levels of carbon dioxide in the atmosphere increase the amount of dissolved CO2 in natural watercourses, triggering the increase in concentrations of bicarbonate and hydrogen ions while dropping those of carbonate and hydroxyl ions. The active carbon cycling in coastal areas, which can result in periodic and daily fluctuations in pH and CO2 concentrations that may surpass those anticipated for the extensive marine ecosystems, is regarded as one of the consequences of climate change. Studies were conducted to examine the effects of various pH levels on algal growth and lipid production in order to better understand how the growth of algae may be influenced in such conditions. In the present study, the influence of three different pH levels (6, 8, and 10) was studied to evaluate microalgae’s carbohydrate utilisation and lipid accumulation during the operation’s starvation phase (SP). Microalgae, in the study, were cultivated in two modes, namely mixotrophic [growth phase (GP)] and autotrophic [pH-induced (SP)] conditions. Enhancement in biomass formation, and intracellular carbohydrate accumulation were recorded during the GP operation, while noticeable lipid productivities (Total/neutral, 26.93/10.3%) were observed during SP operation at pH 8. Pigment analysis showed variations in both the procedures where higher Chl a concentration was noticed in GP, and higher Chl b was detected during SP. Nile red fluorescent staining strongly supports the existence of intracellular lipid bodies (LB). GC analysis of fatty acid methyl esters (FAME) showed the existence of a substantial amount of saturated fatty acids (SFA) compared with unsaturated fatty acids (USFA). Efficient wastewater treatment with nutrient assimilation was reported during the GP operation, demonstrating the phyco-remediation.
A micro- and macro-scale look at the biochemical methanogenic potential of the organic fraction of municipal solid waste generated in a large city of a developing country
Authors: Ibarra-Esparza Fernanda E. , Verduzco Garibay Marycarmen , Lara-Topete Gary Ossmar , González-López Martín Esteban , Orozco-Nunnelly Danielle A. , Aguilar-Juárez Oscar , Senés-Guerrero Carolina , Gradilla-Hernández Misael Sebastián
Published: October 2022

The management of municipal solid waste (MSW) is a complex and expensive task. This is especially the case in developing countries, where waste generation rates are continuously increasing and where current MSW management strategies are focused on inadequate practices, such as landfilling and incineration, which result in numerous health and environmental problems. The anaerobic digestion (AD) of MSW has been implemented worldwide as a solution to decrease the amount of waste ending up in landfills. This process allows for the recovery of energy from the organic fraction of MSW (OFMSW) in the form of biogas, which is largely composed of methane. Therefore, the goal of the present study was to evaluate the biochemical methane potential (BMP) of the OFMSW generated within different socioeconomic strata of the Metropolitan Area of Guadalajara (MAG), Mexico. From a microscale perspective, the microbial communities within the experimental AD system were analyzed using high-throughput sequencing of the 16S rRNA gene to assess the relationship between these communities and the biogas composition. This microbial identification revealed a typical AD composition consisting of the following six phyla: Actinobacteria, Bacteroidetes, Chloroflexi, Euryarchaeota, Firmicutes, and Proteobacteria. Furthermore, through the identification of Methanobacterium and Methanosaeta, two methanogenesis pathways (hydrogenotrophic and acetoclastic) were pinpointed. From a macroscale perspective, a multi-stage Gompertz kinetic model was used to describe cumulative biogas production. This model considered the complex nature of the OFMSW substrate in order to estimate the potential level of biogas production in the MAG using a weighted average that was based on the size of the population in each socioeconomic stratum evaluated (732.8 mL⋅g−1 VS). This novel contribution to the literature provides an estimation of the potential economic, energetic, and environmental benefits of treating the OFMSW produced in the MAG through AD. Through this approach, an estimated 8.5 MWh·year−1 of electrical power could be produced, translating into 1.13 million USD of yearly revenue and resulting in reduced GHG emissions (10,519 tonne CO2eq⋅year−1).
Weather index insurance for transition to sustainable cotton production under climate change in Xinjiang, China
Authors: Yang Zhongna , He Yanlong , Aamir Muhammad , Javed Iqbal , Li Gucheng , Zhang Qing , Wang Shengde , Zhou Lijiang , Qin Jun
Published: October 2022

Assessing climate-induced reductions in cotton yields is critical to developing weather insurance for sustainable agricultural development. Climatic factors such as frost, hail, and drought severely constrain the sustainable development of cotton production in Xinjiang. In this study, based on cotton production and meteorological data from 1988 to 2019 in Aksu, Xinjiang, the H-P filtering method, correlation test, and regression analysis were used to develop a weather index model of cotton yield reduction rate and key meteorological factors. The results showed that the trend yield separated by the H-P filtering method was more stable. The correlation analysis between cotton fertility and meteorological factors concluded that there was a strong positive correlation between precipitation and cotton yield, i.e., the more rainfall, the more unfavorable environment for cotton growth and development. The results of the empirical analysis to determine the net premium rate under different disaster registrations based on the logistic probability distribution model showed that the highest probability of meteorological disasters in the Aksu region was 22.36%, the premium rate was 1.79%, and the net premium was 34.01 RMB per mu. It is found that climate change is closely related to the environment, and human production activities are compatible with the carrying capacity of the environment, otherwise, climate change leads to frequent meteorological disasters, which is not conducive to the sustainable development of agricultural production. It is expected that these research results can provide a relevant basis for the implementation of cotton policy weather insurance in Aksu and other regions and promote the sustainable development of cotton production.
Toxicity of rare earth elements: An overview on human health impact
Authors: Brouziotis Antonios Apostolos , Giarra Antonella , Libralato Giovanni , Pagano Giovanni , Guida Marco , Trifuoggi Marco
Published: October 2022

Rare earth elements (REEs) are metals including the 15 lanthanides together with Yttrium and Scandium. China is the leading country in their exploitation and production (∼90%). REEs are necessary for the production of several technological devices. This extended use of REEs has raised concerns about human health safety. In this review, we investigated the hazard of REEs to human health and the main gaps into the knowledge like as the need to develop further focused research activity. We categorized the research papers collected into eight main sections: environmental exposure, association of REEs with health problems, exposure to REEs due to lifestyle, REE exposure through the food chain, Gd contrast agents causing health problems, occupational REE exposure, and cytotoxicity studies of REEs. This review provided information about the exposome of REEs (the exposure of REEs to the human body), the existing research data, and the gaps that require attention and must be further investigated. More than one third of the literature about REE toxicity to human health concerns their cytotoxicity to human cell lines, while hair, blood serum and blood are the most studied matrices. The main results evidenced that REEs can enter human body via several routes, are associated with numerous diseases, can cause ROS production, DNA damage and cell death, and are more toxic to cancer cells than normal cells.
Computational fluid dynamics simulation of rough bed open channels using openFOAM
Authors: Cho Yun-Hang , Dao My Ha , Nichols Andrew
Published: October 2022

With increased flood risk due to climate change, population expansion and urbanisation; robust waterway design and management are critical. One common type of waterway used to gather and transport ground water is the open channel. Most simulations do not account for the physical roughness of the bed, instead using a roughness coefficient. This means that only the turbulent energy content can be modelled whilst physical turbulent eddies and vortices cannot. Furthermore, many past studies assume the free surface is a rigid lid. This could affect the way that turbulent structures near the free surface behave. Computational Fluid Dynamics simulation of an open channel with a rough bed and rigid lid are conducted using OpenFOAM. Results show good correlation with experimental tests. It can be visually observed that turbulent structures generated from the rough bed do interact with the free surface and thus a rigid lid is perhaps not a great approximation. This is supported by an apparent decrease in the Reynolds shear stress from the free surface and 30% of the flow depth immediately beneath.
Drug-protein interaction prediction via variational autoencoders and attention mechanisms
Authors: Zhang Yue , Hu Yuqing , Li Huihui , Liu Xiaoyong
Published: October 2022

During the process of drug discovery, exploring drug-protein interactions (DPIs) is a key step. With the rapid development of biological data, computer-aided methods are much faster than biological experiments. Deep learning methods have become popular and are mainly used to extract the characteristics of drugs and proteins for further DPIs prediction. Since the prediction of DPIs through machine learning cannot fully extract effective features, in our work, we propose a deep learning framework that uses variational autoencoders and attention mechanisms; it utilizes convolutional neural networks (CNNs) to obtain local features and attention mechanisms to obtain important information about drugs and proteins, which is very important for predicting DPIs. Compared with some machine learning methods on the C.elegans and human datasets, our approach provides a better effect. On the BindingDB dataset, its accuracy (ACC) and area under the curve (AUC) reach 0.862 and 0.913, respectively. To verify the robustness of the model, multiclass classification tasks are performed on Davis and KIBA datasets, and the ACC values reach 0.850 and 0.841, respectively, thus further demonstrating the effectiveness of the model.
A mixed-methods protocol to develop and validate a stewardship maturity matrix for human genomic data in the cloud
Authors: Rahimzadeh Vasiliki , Peng Ge , Cho Mildred
Published: October 2022

This article describes a mixed-methods protocol to develop and test the implementation of a stewardship maturity matrix (SMM) for repositories which govern access to human genomic data in the cloud. It is anticipated that the cloud will host most human genomic and related health datasets generated as part of publicly funded research in the coming years. However, repository managers lack practical tools for identifying what stewardship outcomes matter most to key stakeholders as well as how to track progress on their stewardship goals over time. In this article we describe a protocol that combines Delphi survey methods with SMM modeling first introduced in the earth and planetary sciences to develop a stewardship impact assessment tool for repositories that manage access to human genomic data. We discuss the strengths and limitations of this mixed-methods design and offer points to consider for wrangling both quantitative and qualitative data to enhance rigor and representativeness. We conclude with how the empirical methods bridged in this protocol have potential to improve evaluation of data stewardship systems and better align them with diverse stakeholder values in genomic data science.
Evaluating dimensionality reduction for genomic prediction
Authors: Manthena Vamsi , Jarquín Diego , Varshney Rajeev K. , Roorkiwal Manish , Dixit Girish Prasad , Bharadwaj Chellapilla , Howard Reka
Published: October 2022

The development of genomic selection (GS) methods has allowed plant breeding programs to select favorable lines using genomic data before performing field trials. Improvements in genotyping technology have yielded high-dimensional genomic marker data which can be difficult to incorporate into statistical models. In this paper, we investigated the utility of applying dimensionality reduction (DR) methods as a pre-processing step for GS methods. We compared five DR methods and studied the trend in the prediction accuracies of each method as a function of the number of features retained. The effect of DR methods was studied using three models that involved the main effects of line, environment, marker, and the genotype by environment interactions. The methods were applied on a real data set containing 315 lines phenotyped in nine environments with 26,817 markers each. Regardless of the DR method and prediction model used, only a fraction of features was sufficient to achieve maximum correlation. Our results underline the usefulness of DR methods as a key pre-processing step in GS models to improve computational efficiency in the face of ever-increasing size of genomic data.
Effects of exogenous taurine supplementation on the growth, antioxidant capacity, intestine immunity, and resistance against Streptococcus agalactiae in juvenile golden pompano (Trachinotus ovatus) fed with a low-fishmeal diet
Authors: Liu Jia-Xing , Guo Hua-Yang , Zhu Ke-Cheng , Liu Bao-Suo , Zhang Nan , Zhang Dian-Chang
Published: October 2022

Taurine has various biological functions in fish, playing an essential role in growth, resistance to oxidative stress, and intestine immunity. Here, we evaluated the effects of exogenous taurine added to low-fishmeal diets on the growth, anti-oxidative stress, intestine immunity, and Streptococcus agalactiae resistance in juvenile golden pompano (Trachinotus ovatus). Our study showed that exogenous taurine supplementation of 1.2% (T3 group) greatly enhanced the weight gain rate and specific growth rate (SGR) of juvenile golden pompano, significantly upregulating growth-related factor expression in the brain and liver, as well as the levels of growth-related parameters in the serum. Polynomial regression analysis using SGR estimated the optimal dietary taurine level for golden pompano at 1.18%. Moderate exogenous taurine also increased the muscular thickness and villus length within the intestine, maintained intestinal physical barrier stability, activated the Nrf2/Keap-1/HO-1 signaling pathway, increased intestinal antioxidant enzyme gene expression and antioxidant enzyme activity in the serum, and upregulated immunoglobulin and complement levels in parallel with declining reactive oxygen species (ROS) levels in the serum. Antioxidant factor expression was also upregulated in the intestine. Furthermore, supplementation suppressed NF-κB signaling and intestinal pro-inflammatory cytokine gene expression, increased anti-inflammatory cytokine gene expression, and improved intestine immunity. Finally, taurine supplementation improved the survival rate of golden pompano challenged with S. agalactiae. Overall, our findings provide additional information and support for the rational use of taurine in healthy aquatic animal farming.
Epithelial cell alarmin cytokines: Frontline mediators of the asthma inflammatory response
Authors: Duchesne Marc , Okoye Isobel , Lacy Paige
Published: October 2022

The exposure of the airway epithelium to external stimuli such as allergens, microbes, and air pollution triggers the release of the alarmin cytokines IL-25, IL-33 and thymic stromal lymphopoietin (TSLP). IL-25, IL-33 and TSLP interact with their ligands, IL-17RA, IL1RL1 and TSLPR respectively, expressed by hematopoietic and non-hematopoietic cells including dendritic cells, ILC2 cells, endothelial cells, and fibroblasts. Alarmins play key roles in driving type 2-high, and to a lesser extent type 2-low responses, in asthma. In addition, studies in which each of these three alarmins were targeted in allergen-challenged mice showed decreased chronicity of type-2 driven disease. Consequently, ascertaining the mechanism of activity of these upstream mediators has implications for understanding the outcome of targeted therapies designed to counteract their activity and alleviate downstream type 2-high and low effector responses. Furthermore, identifying the factors which shift the balance between the elicitation of type 2-high, eosinophilic asthma and type-2 low, neutrophilic-positive/negative asthma by alarmins is essential. In support of these efforts, observations from the NAVIGATOR trial imply that targeting TSLP in patients with tezepelumab results in reduced asthma exacerbations, improved lung function and control of the disease. In this review, we will discuss the mechanisms surrounding the secretion of IL-25, IL-33, and TSLP from the airway epithelium and how this influences the allergic airway cascade. We also review in detail how alarmin-receptor/co-receptor interactions modulate downstream allergic inflammation. Current strategies which target alarmins, their efficacy and inflammatory phenotype will be discussed.
Metabolic requirements of Th17 cells and of B cells: Regulation and defects in health and in inflammatory diseases
Authors: Bystrom Jonas , Taher Taher E. , Henson Sian M. , Gould David J. , Mageed Rizgar A.
Published: October 2022

The immune system protects from infections and cancer through complex cellular networks. For this purpose, immune cells require well-developed mechanisms of energy generation. However, the immune system itself can also cause diseases when defective regulation results in the emergence of autoreactive lymphocytes. Recent studies provide insights into how differential patterns of immune cell responses are associated with selective metabolic pathways. This review will examine the changing metabolic requirements of Th17 cells and of B cells at different stages of their development and activation. Both cells provide protection but can also mediate diseases through the production of autoantibodies and the production of proinflammatory mediators. In health, B cells produce antibodies and cytokines and present antigens to T cells to mount specific immunity. Th17 cells, on the other hand, provide protection against extra cellular pathogens at mucosal surfaces but can also drive chronic inflammation. The latter cells can also promote the differentiation of B cells to plasma cells to produce more autoantibodies. Metabolism-regulated checkpoints at different stages of their development ensure the that self-reactive B cells clones and needless production of interleukin (IL-)17 are limited. The metabolic regulation of the two cell types has some similarities, e.g. the utility of hypoxia induced factor (HIF)1α during low oxygen tension, to prevent autoimmunity and regulate inflammation. There are also clear differences, as Th17 cells only are vulnerable to the lack of certain amino acids. B cells, unlike Th17 cells, are also dependent of mechanistic target of rapamycin 2 (mTORC2) to function. Significant knowledge has recently been gained, particularly on Th17 cells, on how metabolism regulates these cells through influencing their epigenome. Metabolic dysregulation of Th17 cells and B cells can lead to chronic inflammation. Disease associated alterations in the genome can, in addition, cause dysregulation to metabolism and, thereby, result in epigenetic alterations in these cells. Recent studies highlight how pathology can result from the cooperation between the two cell types but only few have so far addressed the key metabolic alterations in such settings. Knowledge of the impact of metabolic dysfunction on chronic inflammation and pathology can reveal novel therapeutic targets to treat such diseases.
Deep-water species assemblages on the trawlable bottoms of the Central Mediterranean: Changes or not over time?
Authors: Maiorano Porzia , Ricci Pasquale , Chimienti Giovanni , Calculli Crescenza , Mastrototaro Francesco , D’Onghia Gianfranco
Published: October 2022

Deep-sea communities are impacted by several anthropogenic activities, such as fisheries, which still remain one of the most damaging on the marine environments in terms of biodiversity loss and habitat degradation. The north-western Ionian Sea (Central Mediterranean) experienced long-standing trawl fishing activity with the exploitation of deep-sea demersal resources. The integrate analysis with data of both benthic, demersal and benthopelagic species collected during a time series of experimental trawl survey, yearly carried out in the Ionian basin down to 800 m in depth, allowed to asses the current status of the Ionian deep-sea faunal assemblages and their potential changes overtime. Multivariate analysis and univariate indices, modelled using Generalized Additive Model (GAM) framework, confirm a depth zonation pattern of deep-sea faunal assemblages in the study area, with the presence of two distinct epibathyal and mesobathyal groups. GAM also highlighted a temporal effect on the biodiversity indices, with significant negative trends of diversity and evenness indices as well as a significant increasing of dominance one, over the study period 2012-2020. The benthic community is characterised by more generalist species and a simplified structure, with a severe depletion in habitat-former taxa whereas the demersal and benthopelagic fauna of the Ionian Sea show a general stability in the overall structure if compared with previous studies lasting over two decades. The presence of complex and heterogenous habitats unsuitable for trawl, like cold-water coral communities and canyon systems, provide Essential Fish Habitats (EFHs) for commercial species, acting as potential renewal areas for exploited resources in the neighbouring fishing grounds. These findings encourage an ecosystem-based management including spatial considerations for the objectives of biodiversity conservation combined with those of management of fishery resources.
Characteristics and influencing factors of metal distribution in different wetlands of the Liaohe Delta, Northeastern China
Authors: Yu Yang , Zhang Jiapeng , Qin Jifa , Yang Jisong , Wang Zhikang , Song Ningning , Yu Junbao
Published: October 2022

Metal distribution in different wetlands under the complex influence of natural and anthropogenic activities in the Liaohe Delta was analyzed to better protect and manage delta areas. Ninety-six soil samples were collected from six wetland types, and the levels, depth distributions, risk, and influencing factors of metals (i.e., As, Cd, Cr, Ni, Cu, Pb, Zn, Mn, Al, and Fe) were analyzed. The results showed that the concentrations of As, Cd, Cr, Ni, Zn, and Al in more than 70% of the soil samples were higher than the background value of Liaoning Province. The concentration of As decreased with distance from the estuary, while that of Cr was higher downstream of Liaohe. The spatial distributions of Cd, Ni, Cu, Pb, and Zn were similar. The concentrations of most metals in the topsoil were higher than those in the subsoil. According to the Nemerow pollution index, higher pollution was observed in the area far away from the Liaohe River and Bohai Sea for the topsoil layer, while for the subsoil layers, higher pollution was observed in the area near the Liaohe estuary. The correlation analysis showed that the wetland type was clearly correlated with Cd, Cu, Al, and S. The concentrations of Cd, Pb, Zn, C, N, P, and S and the electrical conductivity obviously decreased with soil depth, while the concentration of Mn was positively correlated with soil depth. Mn was negatively correlated with total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP), whereas Cd, Pb, and Zn showed positive correlation with TOC, TN, and total sulfur (TS). The general linear model indicated that wetland type had a significant effect on As, Cd, Ni, Cu, Pb, Zn, Al, and Fe (p< 0.01), while depth had a significant effect on Cd, Cr, and Pb (p< 0.01). The findings of this work will contribute to pollution control and ecosystem health conservation of the Liaohe Delta.
Qin-Qiao-Xiao-Du formula alleviate influenza virus infectious pneumonia through regulation gut microbiota and metabolomics
Authors: Lian Bo , He Shasha , Jiang Hui , Guo Yuhong , Cui Xuran , Jiang Tao , Su Rui , Chen Yuehong , Zhao Chunxia , Zhang Mina , Hu Yahui , Ye Haoran , Ning Jiaqi , Xu Xiaolong , Liu Qingquan
Published: October 2022

Qin-Qiao-Xiao-Du (QQXD), a traditional Chinese medicine (TCM) formula, has been used in the clinical treatment of influenza virus pneumonia. However, the effects and mechanisms of QQXD on influenza virus pneumonia remain unknown. Therefore, this study explores the mechanisms of QQXD in the treatment of influenza virus pneumonia from the point of view of intestinal flora and metabolism. The results showed that QQXD was able to reduce mortality, weight loss, lung viral load, lung index, and lung injury in influenza virus mice. A cytokine array found that the QQXD attenuated the expression of serum IL-1α, IL-4, IL-12(P70), and TNF-α. Subsequently, 16s rRNA gene sequencing showed that QQXD could increase the relative abundances of Gemmiger, Anaerofustis, Adlercreutzia, and Streptococcus and decrease those of Dehalobacteriu, Burkholderia, Prevotella, Butyrimimonas, Delftia, and others. Meanwhile, targeted metabolic profiling analysis showed that QQXD could regulate nitrogen metabolism, phenylalanine metabolism, valine, leucine, and isoleucine biosynthesis. Correlation analysis demonstrated that the regulatory effect of QQXD on the cyanoamino acid metabolism pathway was associated with changes in the abundance of Parabacteroides, Pediococcus, and Clostridium in influenza mice. In conclusion, our study revealed that QQXD can inhibit influenza virus replication, suppress cytokine storms, and protect mice from influenza virus infection pneumonia. The mechanisms are likely to be related to improved gut microbiota dysbiosis, increased intestinal carbohydrate metabolism, and up-regulated cyanoamino acid metabolism pathways.
Predictive factors associated with the persistence of chest pain in post-laparoscopic myotomy and fundoplication in patients with achalasia
Authors: Olvera-Prado Héctor , Peralta-Figueroa José , Narváez-Chávez Sofía , Rendón-Macías Mario E. , Perez-Ortiz Andric , Furuzawa-Carballeda Janette , Méndez-Flores Silvia , Núñez-Pompa María del Carmen , Trigos-Díaz Alonso , Areán-Sanz Rodrigo , López-Verdugo Fidel , Coss-Adame Enrique , Valdovinos Miguel A. , Torres-Villalobos Gonzalo
Published: October 2022

Background

Episodic angina-like retrosternal pain is a prevalent symptom for achalasia patients pre- and post-treatment. The cause of postoperative chest pain remains poorly understood. Moreover, there are no reports on their predictive value for chest pain in the long-term post-treatment. The effect of laparoscopic Heller myotomy (LHM) and fundoplication techniques (Dor vs. Toupet) is unclear.

Methods

We analyzed a cohort of 129 achalasia cases treated with LHM and randomly assigned fundoplication technique. All the patients were diagnosed with achalasia by high-resolution manometry (HRM). Patients were followed up at 1-, 6-, 12-, and 24-month post-treatment. We implemented unadjusted and adjusted logistic regression analyses to evaluate the predictive significance of pre- and post-operative clinical factors.

Results

Preoperative chest pain with every meal was associated with an increased risk of occasional postoperative chest pain [unadjusted model: odds ratio (OR) = 12, 95% CI: 2.2–63.9, P = 0.006; adjusted model: OR = 26, 95% CI: 2.6–259.1, P = 0.005]. In type II achalasia, hypercontraction was also associated with an increased risk of chest pain (unadjusted model: OR = 2.6 e9 in all the patients). No significant differences were associated with age, type of achalasia, dysphagia, esophageal shape, and integrated relaxation pressure (IRP) with an increased risk of occasional postoperative chest pain. Also, there was no significant difference between fundoplication techniques or surgical approaches (e.g., length of myotomy).

Conclusion

Preoperative chest pain with every meal was associated with a higher risk of occasionally postoperative chest pain.