bluuebunny/crossref_metadata_2025 huggingface dataset:
A review of local construction practices applied on unreinforced adobe buildings in South America
Authors: Cocco Giulia , Brando Giuseppe , Spacone Enrico
Published: September 2022

The historical earthquake activity that involved Andean countries in the last centuries makes the seismic risk evaluation associated to buildings in these areas an issue of crucial concern. Planning seismic risk mitigation policies requires an extensive knowledge of the territorial built environment, of the adopted construction techniques and of the adopted anti-seismic presidiums, in particular when applied during the reconstruction processes carried out after destructive events of the past. In this perspective, this paper contributes to the analysis of adobe vernacular buildings, which represent a spread typology in Latin America and the Caribbean, stressing the past construction practices, their fragilities, and the mitigation measures applied till today. To this purpose, the city center of Cusco, in Peru, where residential buildings are mostly made of adobe, is considered as a meaningful field of observation, because of the long history of the center, which allows to recognize also old construction techniques and the additions/raisings applied during the buildings life, as well as due to the relevant historical seismicity, which permits to appreciate the reconstruction processes implemented after seismic events occurred in the past.
Biofilms possibly harbor occult SARS-CoV-2 may explain lung cavity, re-positive and long-term positive results
Authors: He Daqian , Fu Chaojiang , Ning Mingjie , Hu Xianglin , Li Shanshan , Chen Ying
Published: September 2022

During the COVID-19 pandemic, there have been an increasing number of COVID-19 patients with cavitary or cystic lung lesions, re-positive or long-term positive nucleic acid tests, but the mechanism is still unclear. Lung cavities may appear at long time interval from initial onset of coronavirus infection, generally during the absorption phase of the disease. The main histopathological characteristic is diffuse alveolar damage and may have more severe symptoms after initial recovery from COVID-19 and an increased mortality rate. There are many possible etiologies of pulmonary cavities in COVID-19 patients and we hypothesize that occult SARS-CoV-2, in the form of biofilm, is harbored in the airway lacuna with other pathogenic microorganisms, which may be the cause of pulmonary cavities and repeated and long-term positive nucleic acid tests.
Quaternary volcanism in the Yura Monogenetic Field near Arequipa city, southern Peru
Authors: Aguilar Rigoberto , Arteaga David , Manrique Nélida , van Wyk de Vries Benjamin , Cueva Kevin , Taipe Edu , Guillou Hervé , Scao Vincent
Published: September 2022

Arequipa (Peru) is an area where volcanic activity has been persistent during the Quaternary. Studies carried out in this area have highlighted the emplacement of ignimbrite deposits, large volcanic clusters and stratovolcanoes. Monogenetic volcanism is also present, although poorly explored and studied. Due to its location over an ignimbrite plain and poor state of preservation, the only identified monogenetic cone in the Arequipa basin was the Nicholson volcano, while other monogenetic centers remained unknown. This lack of information about the recent volcanism can lead to inadequate definition of scenarios in a hazard assessment in the region. The present study has investigated monogenetic volcanism in the northwestern edge of the Arequipa basin based on geological survey, geochronology and geochemical data. Here, we report for the first time five small volcanic centers such as Yura Viejo, Ccapua, Uyupampa, El Chiral and Patacocha, which together with the Nicholson volcano form the Yura Monogenetic Field. Stratigraphic considerations and new 40Ar/39Ar ages allow us to place the eruptive activity in the Middle–Upper Pleistocene (c. 195–54 ka). Phreatomagmatic, Strombolian and effusive eruptions characterize the monogenetic activity of the field. As a result of these eruptions, small scoria cones, maars, and lava flows/coulées were generated. The eruptive products show ubiquitous olivine phenocryst-rich (<10 vol%) set in a fine pilotaxitic groundmass, suggesting rapid ascent of basaltic magmas to the surface controlled by the tectonic setting. The analyzed rocks lie in a narrow range of basaltic-andesite composition (50.9–55.6 wt% SiO2) being the most mafic Pleistocene - Recent volcanic products identified in the Arequipa basin, along with the least differentiated magmas from the nearby Chachani volcanic cluster. This work shows how monogenetic volcanism can occur contemporaneous and closely spaced to larger volcanic clusters and active stratovolcanoes. We hope the information provided here will contribute to improve the risk management by highlighting the scenario of monogenetic eruptions that should be considered in the hazard assessment.
Probabilistic geothermal resource assessment in Maichen Sag, south China
Authors: Wang Mingchuan , Yang Fan , Zhang Ying , Zhang Dianwei , Feng Jianyun , Luo Jun , Zeng Yan
Published: September 2022

It is crucial for financial providers, investment groups, resource developers, and exploration companies to rate new geothermal projects in terms of resources and reserves. In general, the existing volumetric method is constrained by limited information when projects are at the early stage of development. The main objective of this study is to estimate the probabilistic potential thermal energy of the M research area in the Maichen Sag, a geothermal prospect in South China, through stochastic methodologies. The probabilistic assessment methodology provides a way to embody the uncertainty and risk in geothermal projects and to quantify the power potential in a probable range. In this study, proxy numerical models were built by combining the Experimental Design (ED) and Response Surface Methodology (RSM) with the Monte Carlo Simulation technique. An improved workflow for combined ED-RSM that uses two-level Full Factorial and Box–Behnken designs was proposed. For comparative analysis, the typical volumetric technique was also implemented in this study. The ED-RSM results show that the M area has P10, P50, and P90 reserves of 5.7 × 1014 J, 5.3 × 1014 J, and 5 × 1014 J, respectively, and these numbers from the typical volumetric method are 1.5 × 1015 J, 9 × 1014 J, and 5.1 × 1014 J, respectively. In this study, the operability, applicability, and accessibility of ED-RSM in the assessment of geothermal potential and its ability to provide a reliable output are demonstrated.
In vitro propagation of XXY human Klinefelter spermatogonial stem cells: A step towards new fertility opportunities
Authors: Galdon Guillermo , Deebel Nicholas A. , Zarandi Nima Pourhabibi , Teramoto Darren , Lue YanHe , Wang Christina , Swerdloff Ronald , Pettenati Mark J. , Kearns William G. , Howards Stuart , Kogan Stanley , Atala Anthony , Sadri-Ardekani Hooman
Published: September 2022

Klinefelter Syndrome (KS) is characterized by a masculine phenotype, supernumerary sex chromosomes (47, XXY), and impaired fertility due to loss of spermatogonial stem cells (SSCs). Early testicular cryopreservation could be an option for future fertility treatments in these patients, including SSCs transplantation or in vitro spermatogenesis. It is critically essential to adapt current in vitro SSCs propagation systems as a fertility option for KS patients. KS human testicular samples (13,15- and 17-year-old non-mosaic KS boys) were donated by patients enrolled in an experimental testicular tissue banking program. Testicular cells were isolated from cryopreserved tissue and propagated in long-term culture for 110 days. Cell-specific gene expression confirmed the presence of all four main cell types found in testes: Spermatogonia, Sertoli, Leydig, and Peritubular cells. A population of ZBTB16+ undifferentiated spermatogonia was identified throughout the culture using digital PCR. Flow cytometric analysis also detected an HLA-/CD9+/CD49f+ population, indicating maintenance of a stem cell subpopulation among the spermatogonial cells. FISH staining for chromosomes X and Y showed most cells containing an XXY karyotype with a smaller number containing either XY or XX. Both XY and XX populations were able to be enriched by magnetic sorting for CD9 as a spermatogonia marker. Molecular karyotyping demonstrated genomic stability of the cultured cells, over time. Finally, single-cell RNAseq analysis confirmed transcription of ID4, TCN2, and NANOS 3 within a population of putative SSCs population. This is the first study showing successful isolation and long-term in vitro propagation of human KS testicular cells. These findings could inform the development of therapeutic fertility options for KS patients, either through in vitro spermatogenesis or transplantation of SSC, in vivo.
Exercise, type 1 diabetes mellitus and blood glucose: The implications of exercise timing
Authors: Fitzpatrick Ross , Davison Gareth , Wilson Jason J. , McMahon Gerard , McClean Conor
Published: September 2022

The scientific literature shows that exercise has many benefits for individuals with type 1 diabetes. Yet, several barriers to exercise in this population exist, such as post-exercise hypoglycaemia or hyperglycaemia. Several studies suggest that the timing of exercise may be an important factor in preventing exercise-induced hypoglycaemia or hyperglycaemia. However, there is a paucity of evidence solely focused on summarising findings regarding exercise timing and the impact it has on glucose metabolism in type 1 diabetes. This report suggests that resistance or high-intensity interval exercise/training (often known as HIIT) may be best commenced at the time of day when an individual is most likely to experience a hypoglycaemic event (i.e., afternoon/evening) due to the superior blood glucose stability resistance and HIIT exercise provides. Continuous aerobic-based exercise is advised to be performed in the morning due to circadian elevations in blood glucose at this time, thereby providing added protection against a hypoglycaemic episode. Ultimately, the evidence concerning exercise timing and glycaemic control remains at an embryonic stage. Carefully designed investigations of this nexus are required, which could be harnessed to determine the most effective, and possibly safest, time to exercise for those with type 1 diabetes.
Proteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic mouse
Authors: Diaz Lozano Isabel M. , Sork Helena , Stone Virginia M. , Eldh Maria , Cao Xiaofang , Pernemalm Maria , Gabrielsson Susanne , Flodström-Tullberg Malin
Published: September 2022

The mechanism by which pancreatic beta cells are destroyed in type 1 diabetes (T1D) remains to be fully understood. Recent observations indicate that the disease may arise because of different pathobiological mechanisms (endotypes). The discovery of one or several protein biomarkers measurable in readily available liquid biopsies (e.g. blood plasma) during the pre-diabetic period may enable personalized disease interventions. Recent studies have shown that extracellular vesicles (EVs) are a source of tissue proteins in liquid biopsies. Using plasma samples collected from pre-diabetic non-obese diabetic (NOD) mice (an experimental model of T1D) we addressed if combined analysis of whole plasma samples and plasma-derived EV fractions increases the number of unique proteins identified by mass spectrometry (MS) compared to the analysis of whole plasma samples alone. LC-MS/MS analysis of plasma samples depleted of abundant proteins and subjected to peptide fractionation identified more than 2300 proteins, while the analysis of EV-enriched plasma samples identified more than 600 proteins. Of the proteins detected in EV-enriched samples, more than a third were not identified in whole plasma samples and many were classified as either tissue-enriched or of tissue-specific origin. In conclusion, parallel profiling of EV-enriched plasma fractions and whole plasma samples increases the overall proteome depth and facilitates the discovery of tissue-enriched proteins in plasma. If applied to plasma samples collected longitudinally from the NOD mouse or from models with other pathobiological mechanisms, the integrated proteome profiling scheme described herein may be useful for the discovery of new and potentially endotype specific biomarkers in T1D.
Numerical Simulation and Experimental Study on Gas Flow in an Open Lattice Structure for an Advanced Space Nuclear Power System
Authors: Wang Zhipeng , Zhao Jing , Ye Zishen , Shi Lei
Published: September 2022

Helium flow in the rod bundle channel with an open lattice structure is an important phenomenon for the advanced gas-cooled nuclear core design. In this study, thermal analysis with helium flow in various channel designs is conducted based on CFD methods to determine a dimension-optimized rod bundle channel. An experimental study then follows in order to pick up an appropriate gas flow model in further numerical simulation. Finally, helium flow in the bundle channels consisting of 217 rods is simulated using this chosen flow model, which shows to satisfy the requirements of basic thermal analysis of a newly designed gas-cooled reactor with an open lattice structure. Generally, this work will contribute to the design and analysis of the future advanced space nuclear power system.
A comparative study on LinkedIn and Sina Weibo users’ perceptions of the carbon-neutral city
Authors: Zeng Liyun , Li Rita Yi Man , Mao Yunyi , Chen Hong , Zeng Huiling
Published: September 2022

A carbon-neutral city is one of the most critical topics in carbon neutrality. To study the general public and professionals’ focus, we analysed the posts on Weibo and LinkedIn through Pycharm, Navicat Premium, KHCoder, and Tableau. This study included 1908 microposts (14,668 sentences) on Weibo and 533 posts (3733 sentences) on LinkedIn. On Weibo, the most influential users were governments and organisations; for example, Baotou Daily, Beijing Ecological Environment, 922 Green Travel, Baotou Evening News, and Baoding Evening News. On LinkedIn, the most influential person was the co-director of Carbon Neutral Cities Alliance. The most popular topics on LinkedIn included “city,” “carbon,” “climate,” “neutral,” “energy,” “emission,” “sustainability,” “sustainable,” “neutrality” and the keywords of “world”; while “carbon,” “city,” “energy,” “development,” “new,” “green,” “promote,” “neutrality,” “construction” and “industry” are more prevalent in Weibo. Both LinkedIn and Weibo users focus on “energy” and related issues. LinkedIn users mentioned “climate” and “sustainability” most in their posts, but Weibo users concerned about green development in the construction industry.
Enriched spatial analysis of air pollution: Application to the city of Bogotá, Colombia
Authors: Jin Zhexu , Velásquez Angel Mario Andrés , Mura Ivan , Franco Juan Felipe
Published: September 2022

Air pollution is a global health issue, which especially affects people living in highly urbanized areas. Many large cities in the developing world are highly heterogeneous in population density and socioeconomic conditions. Under these circumstances, relying on classical air quality indexes may not be sufficient to provide a detailed view of the impact of air pollution. In the paper, we propose an enriched spatial analysis of air pollution. By performing spatial temporal Kriging on PM2.5 concentration, we obtain a detailed map of its spatial distribution. Then, we integrate the population and socioeconomic features to produce a measure of the inequality between different demographic groups. We consider as a working case the city of Bogotá, where demographic features are heterogeneous across different districts. The results of our analyses identify a highly polluted cluster located in the south-west cluster of the city. Within this cluster, we observe a disproportionate representation of people from several vulnerable groups. Overall, our analysis points out significant inequities with regard to the exposure to poor air quality. The analysis we conduct for the city of Bogotá is perfectly repeatable on any urban area equipped with an air quality monitoring network.
Integration of three machine learning algorithms identifies characteristic RNA binding proteins linked with diagnosis, immunity and pyroptosis of IgA nephropathy
Authors: Zhang Xueqin , Chao Peng , Jiang Hong , Yang Shufen , Muhetaer Gulimire , Zhang Jun , Song Xue , Lu Chen
Published: September 2022

Objective: RNA-binding proteins (RBPs) are essential for most post-transcriptional regulatory events, which exert critical roles in nearly all aspects of cell biology. Here, characteristic RBPs of IgA nephropathy were determined with multiple machine learning algorithms.

Methods: Our study included three gene expression datasets of IgA nephropathy (GSE37460, GSE73953, GSE93798). Differential expression of RBPs between IgA nephropathy and normal samples was analyzed via limma, and hub RBPs were determined through MCODE. Afterwards, three machine learning algorithms (LASSO, SVM-RFE, random forest) were integrated to determine characteristic RBPs, which were verified in the Nephroseq database. Immune cell infiltrations were estimated through CIBERSORT. Utilizing ConsensusClusterPlus, IgA nephropathy were classified based on hub RBPs. The potential upstream miRNAs were predicted.

Results: Among 388 RBPs with differential expression, 43 hub RBPs were determined. After integration of three machine learning algorithms, three characteristic RBPs were finally identified (DDX27, RCL1, and TFB2M). All of them were down-regulated in IgA nephropathy than normal specimens, with the excellent diagnostic efficacy. Additionally, they were significantly linked to immune cell infiltrations, immune checkpoints, and pyroptosis-relevant genes. Based on hub RBPs, IgA nephropathy was stably classified as two subtypes (cluster 1 and 2). Cluster 1 exhibited the relatively high expression of pyroptosis-relevant genes and characteristic RBPs. MiR-501-3p, miR-760, miR-502-3p, miR-1224-5p, and miR-107 were potential upstream miRNAs of hub RBPs.

Conclusion: Collectively, our findings determine three characteristic RBPs in IgA nephropathy and two RBPs-based subtypes, and thus provide a certain basis for further research on the diagnosis and pathogenesis of IgA nephropathy.
HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data
Authors: Wang Xuwen , Xu Ying , Zhang Yinbin , Wang Shenjie , Zhang Xuanping , Yi Xin , Zhang Shuqun , Wang Jiayin
Published: September 2022

Homologous recombination deficiency (HRD) is a critical feature guiding drug and treatment selection, mainly for ovarian and breast cancers. As it cannot be directly observed, HRD status is estimated on a small set of genomic instability features from sequencing data. The existing methods often perform poorly when handling targeted panel sequencing data; however, the targeted panel is the most popular sequencing strategy in clinical practices. Thus, we proposed HRD-MILN to overcome the computational challenges from targeted panel sequencing. HRD-MILN incorporated a multi-instance learning framework to discover as many loss of heterozygosity (LOH) associated with HRD status to cluster as possible. Then the HRD score is obtained based on the association between the LOHs and the cluster in the sample to be estimated, and finally, the HRD status is estimated based on the score.

In comparison experiments on targeted panel sequencing data, the Precision of HRD-MILN could achieve 87%, significantly improved from 63% reported by the existing methods, where the highest margin of improvement reached 14%. It also presented advantages on whole exome sequencing data. Based on our best knowledge, HRD-MILN is the first practical tool for estimating HRD status from targeted panel sequencing data and could benefit clinical applications.
Clinical characteristics and in silico analysis of congenital pseudarthrosis of the tibia combined with neurofibromatosis type 1 caused by a novel NF1 mutation
Authors: Xu Jingfang , Zhang Ying , Zhu Kun , Li Jiabin , Guan Yuelin , He Xinyu , Jin Xuejing , Bai Guannan , Hu Lidan
Published: September 2022

Congenital pseudarthrosis of the tibia (CPT) is a rare congenital bone malformation, which has a strong relationship with Neurofibromatosis type 1 (NF1). NF1 is an autosomal dominant disease leading to multisystem disorders. Here, we presented the genotypic and phenotypic characteristics of one unique case of a five-generation Chinese family. The proband was CPT accompanied with NF1 due to NF1 mutation. The proband developed severe early-onset CPT combined with NF1 after birth. Appearance photos and X-ray images of the left limb of the proband showed significant bone malformation. Slit-lamp examination showed Lisch nodules in both eyes of the proband. Whole-exome sequencing (WES) and Sanger sequencing confirmed the truncation variant of NF1 (c.871G>T, p. E291*). Sequence conservative and evolutionary conservation analysis indicated that the novel mutation (p.E291*) was highly conserved. The truncated mutation led to the loss of functional domains, including CSRD, GRD, TBD, SEC14-PH, CTD, and NLS. It may explain why the mutation led to a severe clinical feature. Our report expands the genotypic spectrum of NF1 mutations and the phenotypic spectrum of CPT combined with NF1.
The cytokine network in acute myeloid leukemia
Authors: Luciano Michela , Krenn Peter W. , Horejs-Hoeck Jutta
Published: September 2022

Acute myeloid leukemia (AML) is a highly heterogeneous malignancy of the blood and bone marrow, characterized by clonal expansion of myeloid stem and progenitor cells and rapid disease progression. Chemotherapy has been the first-line treatment for AML for more than 30 years. Application of recent high-throughput next-generation sequencing technologies has revealed significant molecular heterogeneity to AML, which in turn has motivated efforts to develop new, targeted therapies. However, due to the high complexity of this disease, including multiple driver mutations and the coexistence of multiple competing tumorigenic clones, the successful incorporation of these new agents into clinical practice remains challenging. These continuing difficulties call for the identification of innovative therapeutic approaches that are effective for a larger cohort of AML patients. Recent studies suggest that chronic immune stimulation and aberrant cytokine signaling act as triggers for AML initiation and progression, facets of the disease which might be exploited as promising targets in AML treatment. However, despite the greater appreciation of cytokine profiles in AML, the exact functions of cytokines in AML pathogenesis are not fully understood. Therefore, unravelling the molecular basis of the complex cytokine networks in AML is a prerequisite to develop new therapeutic alternatives based on targeting cytokines and their receptors.
Epstein-Barr virus perpetuates B cell germinal center dynamics and generation of autoimmune-associated phenotypes in vitro
Authors: SoRelle Elliott D. , Reinoso-Vizcaino Nicolás M. , Horn Gillian Q. , Luftig Micah A.
Published: September 2022

Human B cells encompass functionally diverse lineages and phenotypic states that contribute to protective as well as pathogenic responses. Epstein-Barr virus (EBV) provides a unique lens for studying heterogeneous B cell responses, given its adaptation to manipulate intrinsic cell programming. EBV promotes the activation, proliferation, and eventual outgrowth of host B cells as immortalized lymphoblastoid cell lines (LCLs)in vitro, which provide a foundational model of viral latency and lymphomagenesis. Although cellular responses and outcomes of infection can vary significantly within populations, investigations that capture genome-wide perspectives of this variation at single-cell resolution are in nascent stages. We have recently used single-cell approaches to identify EBV-mediated B cell heterogeneity inde novoinfection and within LCLs, underscoring the dynamic and complex qualities of latent infection rather than a singular, static infection state. Here, we expand upon these findings with functional characterizations of EBV-induced dynamic phenotypes that mimic B cell immune responses. We found that distinct subpopulations isolated from LCLs could completely reconstitute the full phenotypic spectrum of their parental lines. In conjunction with conserved patterns of cell state diversity identified within scRNA-seq data, these data support a model in which EBV continuously drives recurrent B cell entry, progression through, and egress from the Germinal Center (GC) reaction. This “perpetual GC” also generates tangent cell fate trajectories including terminal plasmablast differentiation, which constitutes a replicative cul-de-sac for EBV from which lytic reactivation provides escape. Furthermore, we found that both established EBV latency andde novoinfection support the development of cells with features of atypical memory B cells, which have been broadly associated with autoimmune disorders. Treatment of LCLs with TLR7 agonist or IL-21 was sufficient to generate an increased frequency of IgD-/CD27-/CD23-/CD38+/CD138+plasmablasts. Separately,de novoEBV infection led to the development of CXCR3+/CD11c+/FCRL4+B cells within days, providing evidence for possible T cell-independent origins of a recently described EBV-associated neuroinvasive CXCR3+B cell subset in patients with multiple sclerosis. Collectively, this work reveals unexpected virus-driven complexity across infected cell populations and highlights potential roles of EBV in mediating or priming foundational aspects of virus-associated immune cell dysfunction in disease.
Correlation of antigen-specific immune response with disease severity among COVID-19 patients in Bangladesh
Authors: Bhuiyan Taufiqur Rahman , Al Banna Hasan , Kaisar M. Hasanul , Karmakar Polash Chandra , Hakim Al , Akter Afroza , Ahmed Tasnuva , Tauheed Imam , Islam Shaumik , Hasnat Mohammad Abul , Sumon Mostafa Aziz , Rashed Asif , Ghosh Shuvro , Clemens John D. , Banu Sayera , Shirin Tahmina , Weiskopf Daniela , Sette Alessandro , Chowdhury Fahima , Qadri Firdausi
Published: September 2022

Coronavirus disease 2019 (COVID-19) is a protean disease causing different degrees of clinical severity including fatality. In addition to humoral immunity, antigen-specific T cells may play a critical role in defining the protective immune response against SARS-CoV-2, the virus that causes this disease. As a part of a longitudinal cohort study in Bangladesh to investigate B and T cell-specific immune responses, we sought to evaluate the activation-induced marker (AIM) and the status of different immune cell subsets during a COVID-19 infection. We analyzed a total of 115 participants, which included participants with asymptomatic, mild, moderate, and severe clinical symptoms. We observed decreased mucosal-associated invariant T (MAIT) cell frequency on the initial days of the COVID-19 infection in symptomatic patients compared to asymptomatic patients. However, natural killer (NK) cells were found to be elevated in symptomatic patients just after the onset of the disease compared to both asymptomatic patients and healthy individuals. Moreover, we found a significant increase of AIM+ (both OX40+CD137+ and OX40+CD40L+) CD4+ T cells in moderate and severe COVID-19 patients in response to SARS-CoV-2 peptides (especially spike peptides) compared to pre-pandemic controls who are unexposed to SARS-CoV-2. Notably, we did not observe any significant difference in the CD8+ AIMs (CD137+CD69+), which indicates the exhaustion of CD8+ T cells during a COVID-19 infection. These findings suggest that patients who recovered from moderate and severe COVID-19 were able to mount a strong CD4+ T-cell response against shared viral determinants that ultimately induced T cells to mount further immune responses to SARS-CoV-2.
Sex hormones, intestinal inflammation, and the gut microbiome: Major influencers of the sexual dimorphisms in obesity
Authors: Brettle Holly , Tran Vivian , Drummond Grant R. , Franks Ashley E. , Petrovski Steve , Vinh Antony , Jelinic Maria
Published: September 2022

Obesity is defined as the excessive accumulation of body fat and is associated with an increased risk of developing major health problems such as cardiovascular disease, diabetes and stroke. There are clear sexual dimorphisms in the epidemiology, pathophysiology and sequelae of obesity and its accompanying metabolic disorders, with females often better protected compared to males. This protection has predominantly been attributed to the female sex hormone estrogen and differences in fat distribution. More recently, the sexual dimorphisms of obesity have also been attributed to the differences in the composition and function of the gut microbiota, and the intestinal immune system. This review will comprehensively summarize the pre-clinical and clinical evidence for these sexual dimorphisms and discuss the interplay between sex hormones, intestinal inflammation and the gut microbiome in obesity. Major gaps and limitations of this rapidly growing area of research will also be highlighted in this review.
The impact of coastal upwelling on coral reef ecosystem under anthropogenic influence: Coral reef community and its response to environmental factors
Authors: Zhu Wentao , Ren Yuxiao , Liu Xiangbo , Huang Duanjie , Xia Jingquan , Zhu Ming , Yin Hongyang , Chen Rouwen , Li Xiubao
Published: September 2022

Mass coral bleaching is a severe threat to coral reefs in the era of global warming, and upwelling areas may serve as thermal refugia for coral reefs by mitigating the effects of heating anomalies. This study seeks to examine the impact of the Qiongdong upwelling (QDU) on the coastal coral reefs of the Hainan Island. The environmental variables (i.e., physiochemical parameters, coastal land use) differed significantly in upwelling and non-upwelling areas. In particular, the presence of colder and more saline water was the important indicator of coastal upwelling. In the QDU, turf algae and macroalgae dominated the algae communities, but habitat-specific environment and coastal development contributed to lower calcified algae, coral larvae replenishment and live corals cover. Lower abundance of coral reefs fishes could be attributed to the disappearance of live corals, increase of algae coverage, low habitat complexity and strong wave exposure at upwelling stations. Upwelling-related environmental parameters, wave exposure, land use and potential local stressors were revealed as major driving factors related to significant spatial changes in stony coral and fish communities. Overall, the present findings suggest that the Qiongdong upwelling has the potential to provide thermal refuge for coral reefs, but is severely affected by local anthropogenic activities.
Uncertainties in ocean biogeochemical simulations: Application of ensemble data assimilation to a one-dimensional model
Authors: Mamnun Nabir , Völker Christoph , Vrekoussis Mihalis , Nerger Lars
Published: September 2022

Marine biogeochemical (BGC) models are highly uncertain in their parameterization. The value of the BGC parameters are poorly known and lead to large uncertainties in the model outputs. This study focuses on the uncertainty quantification of model fields and parameters within a one-dimensional (1-D) ocean BGC model applying ensemble data assimilation. We applied an ensemble Kalman filter provided by the Parallel Data Assimilation Framework (PDAF) into a 1-D vertical configuration of the BGC model Regulated Ecosystem Model 2 (REcoM2) at two BGC time-series stations: the Bermuda Atlantic Time-series Study (BATS) and the Dynamique des Flux Atmosphériques en Méditerranée (DYFAMED). We assimilated 5-day satellite chlorophyll-a (chl-a) concentration and monthly in situ net primary production (NPP) data for 3 years to jointly estimate 10 preselected key BGC parameters and the model state. The estimated set of parameters resulted in improvements in the model prediction up to 66% for the surface chl-a and 56% for NPP. Results show that assimilating satellite chl-a concentration data alone degraded the prediction of NPP. Simultaneous assimilation of the satellite chl-a data and in situ NPP data improved both surface chl-a and NPP simulations. We found that correlations between parameters preclude estimating parameters independently. Co-dependencies between parameters also indicate that there is not a unique set of optimal parameters. Incorporation of proper uncertainty estimation in BGC predictions, therefore, requires ensemble simulations with varying parameter values.
A poor perspective of self weight significantly increases adverse outcomes in non-alcoholic fatty liver disease (NAFLD)
Authors: Fu Clarissa Elysia , Ng Cheng Han , Chew Nicholas W. S. , Heng Zane En Qi , Chin Yip Han , Quek Jingxuan , Lim Wen Hui , Xiao Jieling , Chan Kai En , Tan Darren Jun Hao , Tan Caitlyn , Zhang Sitong , Koh Teng Kiat , Nah Benjamin , Dan Yock Young , Syn Nicholas , Siddiqui Mohammad Shadab , Sanyal Arun J. , Noureddin Mazen , Muthiah Mark
Published: September 2022

Background

Non-alcoholic fatty liver disease (NAFLD) is prevalent amongst overweight and obese individuals, and weight loss remains the main mode of treatment for NAFLD patients. Weight perception plays a key role in the efficacy of such treatment. The current study aims to investigate the prevalence, associating factors and implications of poor weight perception amongst such individuals.

Methods

An analysis was done on data collected from NHANES between 1999 and 2018. Comparison was made between NAFLD individuals with and without poor weight perception in terms of prevalence, associated characteristics, and clinical outcomes. Multivariate analysis was used to compare effect size of adverse events associated with NAFLD individuals with poor weight perception.

Results

Of the 12,170 NAFLD patients, 19.2% (CI: 18.5 to 19.9%) had poor weight perception. Poor weight perception was significantly associated with lower education levels, reduced levels of exercise and unhealthier lipid profiles. There was an increased risk in all-cause mortality (HR: 1.18, CI: 1.00 to 1.38, p = 0.047), cardiovascular disease mortality (SHR: 1.33, CI: 1.03 to 1.71, p = 0.026), major adverse cardiovascular events (OR: 1.21 CI: 1.10 to 1.32, p < 0.001), and advanced fibrosis (OR: 1.30, CI: 1.03 to 1.64, p = 0.025) for individuals with poor weight perception.

Conclusion

This study highlights the positive association between appropriate weight perception and better outcomes in individuals with NAFLD. Poor weight perception increased the risk of adverse events and decreased inclination toward seeking weight loss treatment. Greater emphasis should be placed on dealing with weight perception in individuals with NAFLD for better treatment outcomes.
Microbial roles in cave biogeochemical cycling
Authors: Zhu Hai-Zhen , Jiang Cheng-Ying , Liu Shuang-Jiang
Published: September 2022

Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.
Insights into the global freshwater virome
Authors: Elbehery Ali H. A. , Deng Li
Published: September 2022

Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the orderCaudovirales, particularly the families ofSiphoviridae,Myoviridae,andPodoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
Transcriptional abnormalities in induced pluripotent stem cell-derived oligodendrocytes of individuals with primary progressive multiple sclerosis
Authors: Plastini Melanie J. , Desu Haritha L. , Ascona Maureen C. , Lang Anna L. , Saporta Mario A. , Brambilla Roberta
Published: September 2022

Multiple sclerosis (MS) is the most common neurological disorder in young adults and is classically defined as a chronic inflammatory demyelinating disease of the central nervous system (CNS). Although MS affects millions of people worldwide, its underlying cause remains unknown making discovery of effective treatments challenging. Whether intrinsic or extrinsic factors contribute to MS initiation and progression is still unclear. This is especially true for primary progressive MS (PPMS), the rarest form of the disease, in which progressive and irreversible loss of neurological function is often observed in the absence of an overt immune-inflammatory response. To test the hypothesis that intrinsic dysfunction in oligodendrocytes (OLs), the primary targets of damage in MS, may contribute to PPMS etiopathology, we differentiated human induced pluripotent stem cell (hiPSC) lines derived from PPMS and healthy individuals into mature OLs to compare their transcriptional profile. PPMS derived OLs displayed hundreds of differentially expressed genes compared to control OLs, many associated with cell adhesion, apoptosis and inflammation, including the inflammasome component Nlrp2, which was highly upregulated. NLRP2 immunoreactivity in OLs was confirmed in post-mortem PPMS brain tissues, with higher expression than in control tissues. Altogether, our findings suggest that mature OLs in PPMS affected individuals carry intrinsic abnormalities that could contribute, at least in part, to the pathophysiology of this form of the disease.
Post-operative neutrophil-to-lymphocyte ratio and outcome after thrombectomy in acute ischemic stroke
Authors: Li Shen-Jie , Cao Shan-Shan , Huang Pei-Sheng , Nie Xin , Fu Yang , Liu Jian-Ren
Published: September 2022

Background

Neutrophil to lymphocyte ratio (NLR) is a novel inflammatory marker to predict adverse cardiovascular events. However, there is a lack of data on hemorrhagic transformation (HT) and neurological outcome after mechanical thrombectomy in acute ischemic stroke (AIS). We investigated whether NLR before and after thrombectomy for patients with AIS was associated with HT and neurological outcomes.

Methods

We performed a retrospective analysis of consecutive patients with anterior circulation AIS who underwent thrombectomy. HT was evaluated by CT within 24 h after thrombectomy. Clinical data had been collected retrospectively; laboratory data were extracted from our electronic hospital information system. NLR was obtained at admission (NLR1) and immediately after thrombectomy (NLR2). The main outcomes were post-interventional intracranial hemorrhage and unfavorable functional status (modified Rankin scale scores of 3–6) 3 months post-stroke.

Results

A total of 258 patients with AIS, according to the NIHSS (median 14), were included. NLR2 was higher in patients who developed HT after thrombectomy and unfavorable neurological outcomes 3 months post-stroke (p < 0.001) than in those without HT or favorable outcomes, even after correction for co-factors [Odds Ratio (OR) 1.35 for HT, 95% confidence interval (CI)1.16–1.57, p < 0.001, and 1.85 for unfavorable outcome, 95%CI 1.57–2.17, p < 0.001]. The optimal cutoff value for the NLR2 as an indicator for auxiliary diagnosis of HT and the unfavorable outcome was 8.4 and 8.8, respectively.

Conclusion

NLR immediately after thrombectomy is a readily available biomarker of HT and neurological outcomes in patients with AIS.
Highly efficient neuromorphic learning system of spiking neural network with multi-compartment leaky integrate-and-fire neurons
Authors: Gao Tian , Deng Bin , Wang Jiang , Yi Guosheng
Published: September 2022

A spiking neural network (SNN) is considered a high-performance learning system that matches the digital circuits and presents higher efficiency due to the architecture and computation of spiking neurons. While implementing a SNN on a field-programmable gate array (FPGA), the gradient back-propagation through layers consumes a surprising number of resources. In this paper, we aim to realize an efficient architecture of SNN on the FPGA to reduce resource and power consumption. The multi-compartment leaky integrate-and-fire (MLIF) model is used to convert spike trains to the plateau potential in dendrites. We accumulate the potential in the apical dendrite during the training period. The average of this accumulative result is the dendritic plateau potential and is used to guide the updates of synaptic weights. Based on this architecture, the SNN is implemented on FPGA efficiently. In the implementation of a neuromorphic learning system, the shift multiplier (shift MUL) module and piecewise linear (PWL) algorithm are used to replace multipliers and complex nonlinear functions to match the digital circuits. The neuromorphic learning system is constructed with resources on FPGA without dataflow between on-chip and off-chip memories. Our neuromorphic learning system performs with higher resource utilization and power efficiency than previous on-chip learning systems.
Incorporation of spatial- and connectivity-based cortical brain region information in regularized regression: Application to Human Connectome Project data
Authors: Steiner Aleksandra , Abbas Kausar , Brzyski Damian , Pączek Kewin , Randolph Timothy W. , Goñi Joaquín , Harezlak Jaroslaw
Published: September 2022

Studying the association of the brain's structure and function with neurocognitive outcomes requires a comprehensive analysis that combines different sources of information from a number of brain-imaging modalities. Recently developed regularization methods provide a novel approach using information about brain structure to improve the estimation of coefficients in the linear regression models. Our proposed method, which is a special case of the Tikhonov regularization, incorporates structural connectivity derived with Diffusion Weighted Imaging and cortical distance information in the penalty term. Corresponding to previously developed methods that inform the estimation of the regression coefficients, we incorporate additional information via a Laplacian matrix based on the proximity measure on the cortical surface. Our contribution consists of constructing a principled formulation of the penalty term and testing the performance of the proposed approach via extensive simulation studies and a brain-imaging application. The penalty term is constructed as a weighted combination of structural connectivity and proximity between cortical areas. Simulation studies mimic the real brain-imaging settings. We apply our approach to the study of data collected in the Human Connectome Project, where the cortical properties of the left hemisphere are found to be associated with vocabulary comprehension.
Brain state transition analysis using ultra-fast fMRI differentiates MCI from cognitively normal controls
Authors: Palmer William C. , Park Sung Min , Levendovszky Swati Rane
Published: September 2022

Purpose

Conventional resting-state fMRI studies indicate that many cortical and subcortical regions have altered function in Alzheimer’s disease (AD) but the nature of this alteration has remained unclear. Ultrafast fMRIs with sub-second acquisition times have the potential to improve signal contrast and enable advanced analyses to understand temporal interactions between brain regions as opposed to spatial interactions. In this work, we leverage such fast fMRI acquisitions from Alzheimer’s disease Neuroimaging Initiative to understand temporal differences in the interactions between resting-state networks in 55 older adults with mild cognitive impairment (MCI) and 50 cognitively normal healthy controls.

Methods

We used a sliding window approach followed by k-means clustering. At each window, we computed connectivity i.e., correlations within and across the regions of the default mode, salience, dorsal attention, and frontoparietal network. Visual and somatosensory networks were excluded due to their lack of association with AD. Using the Davies–Bouldin index, we identified clusters of windows with distinct connectivity patterns, also referred to as brain states. The fMRI time courses were converted into time courses depicting brain state transition. From these state time course, we calculated the dwell time for each state i.e., how long a participant spent in each state. We determined how likely a participant transitioned between brain states. Both metrics were compared between MCI participants and controls using a false discovery rate correction of multiple comparisons at a threshold of. 0.05.

Results

We identified 8 distinct brain states representing connectivity within and between the resting state networks. We identified three transitions that were different between controls and MCI, all involving transitions in connectivity between frontoparietal, dorsal attention, and default mode networks (p<0.04).

Conclusion

We show that ultra-fast fMRI paired with dynamic functional connectivity analysis allows us to capture temporal transitions between brain states. Most changes were associated with transitions between the frontoparietal and dorsal attention networks connectivity and their interaction with the default mode network. Although future work needs to validate these findings, the brain networks identified in our work are known to interact with each other and play an important role in cognitive function and memory impairment in AD.