bluuebunny/crossref_metadata_2025 huggingface dataset:
Ferroptosis, a Potential Therapeutic Target in Alzheimer’s Disease
Authors: Chen Kai , Jiang Xiaobing , Wu Moxin , Cao Xianming , Bao Wendai , Zhu Ling-Qiang
Published: August 2021

Cell death is a common phenomenon in the progression of Alzheimer’s disease (AD). However, the mechanism of triggering the death of neuronal cells remains unclear. Ferroptosis is an iron-dependent lipid peroxidation-driven cell death and emerging evidences have demonstrated the involvement of ferroptosis in the pathological process of AD. Moreover, several hallmarks of AD pathogenesis were consistent with the characteristics of ferroptosis, such as excess iron accumulation, elevated lipid peroxides, and reactive oxygen species (ROS), reduced glutathione (GSH), and glutathione peroxidase 4 (GPX4) levels. Besides, some ferroptosis inhibitors can relieve AD-related pathological symptoms in AD mice and exhibit potential clinical benefits in AD patients. Therefore, ferroptosis is gradually being considered as a distinct cell death mechanism in the pathogenesis of AD. However, direct evidence is still lacking. In this review, we summarize the features of ferroptosis in AD, its underlying mechanisms in AD pathology, and review the application of ferroptosis inhibitors in both AD clinical trials and mice/cell models, to provide valuable information for future treatment and prevention of this devastating disease.
I-V Curves of an Apigenin Dye and Their Analysis by a New Parabolic Function
Authors: Sanusi Kayode , Ajayi Olukayode S. , Borisade Adegoke O. , Elusiyan Regina B. , Yilmaz Yusuf , Ceylan Ümit
Published: August 2021

A new parabolic function for I-V curves’ analysis has been proposed. The new “analytical tool” provides a simple way to describe photophysical processes at an approximately monolayer surface of a dye-sensitized solar cell. It may now be possible to estimate factors such as hole–electron recombination, surface defects, and electron diffusion at the semiconductor layer. The theoretical approach that was previously reported by our group for predicting the photovoltaic performance of potential dye sensitizers has also been validated. The experimental photovoltaic and DFT/TD-DFT data of apigenin and those of the highly rated black dyes were used for the validation.
Electron-to Hole Transport Change Induced by Solvent Vapor Annealing of Naphthalene Diimide Doped with Poly(3-Hexylthiophene)
Authors: Janus Krzysztof , Danielewicz Kinga , Chlebosz Dorota , Goldeman Waldemar , Kiersnowski Adam
Published: August 2021

Herein we report on fabrication and properties of organic field-effect transistors (OFETs) based on the spray-coated films of N,N′-dioctyl naphthalene diimide (NDIC8) doped with 2.4 wt% of poly (3-hexylthiophene) (P3HT). OFETs with the untreated NDIC8:P3HT films revealed electron conductivity [μe* = 5 × 10–4 cm2×(Vs)−1]. After the annealing in chloroform vapor the NDIC8:P3HT films revealed the hole transport only [μh* = 0.9 × 10–4 cm2×(Vs)−1]. Due to the chemical nature and energy levels, the hole transport was not expected for NDIC8-based system. Polarized optical- and scanning electron microscopies indicated that the solvent vapor annealing of the NDIC8:P3HT films caused a transition of their fine-grained morphology to the network of branched, dendritic crystallites. Grazing incidence wide-angle X-ray scattering studies indicated that the above transition was accompanied by a change in the crystal structure of NDIC8. The isotropic crystal structure of NDIC8 in the untreated film was identical to the known crystal structure of the bulk NDIC8. After the solvent annealing the crystal structure of NDIC8 changed to a not-yet-reported polymorph, that, unlike in the untreated film, was partially oriented with respect to the OFET substrate.
Light-Controlled Friction by Carboxylic Azobenzene Molecular Self-Assembly Layers
Authors: Xue Dandan , Ma Liran , Tian Yu , Zeng Qingdao , Tu Bin , Luo Wendi , Wen Shizhu , Luo Jianbin
Published: August 2021

Nowadays, reversible friction regulation has become the focus of scientists in terms of the flexible regulatory structure of photosensitive materials and theories since this facilitates rapid development in this field. Meanwhile, as an external stimulus, light possesses great potential and advantages in spatiotemporal control and remote triggering. In this work, we demonstrated two photo-isomerized organic molecular layers, tetra-carboxylic azobenzene (NN4A) and dicarboxylic azobenzene (NN2A), which were selected to construct template networks on the surface of the highly oriented pyrolytic graphite (HOPG) to study the friction properties, corresponding to the arrangement structure of self-assembled layers under light regulation. First of all, the morphology of the self-assembled layers were characterized by a scanning tunneling microscope (STM), then the nanotribological properties of the template networks were measured by atomic force microscope (AFM). Their friction coefficients are respectively changed by about 0.6 and 2.3 times under light control. The density functional theory (DFT) method was used to calculate the relationship between the force intensity and the friction characteristics of the self-assembled systems under light regulation. Herein, the use of external light stimulus plays a significant role in regulating the friction properties of the interface of the nanometer, hopefully serving as a fundamental basis for further light-controlling research for the future fabrication of advanced on-surface devices.
Reversible Switching of Single-Molecule Magnetic Behaviour by Desorption/Adsorption of Solvent Ligand in a New Dy(III)-Based Metal Organic Framework
Authors: Song Xiao-Jiao , Hu Zhao-Bo , Li Miao-Miao , Feng Xin , Kong Ming , Xue Xiao-Ming , Zhang Yi-Quan , Song You
Published: August 2021

Two metal-organic frameworks (MOFs), [Dy(BDC)(NO3)(DMF)2]n (1, H2BDC = terephthalic acid) and [Dy(BDC)(NO3)]n (1a), were synthesized. The structures of MOFs 1 and 1a are easy to be reversibly transformed into each other by the desorption or adsorption of coordination solvent molecules. Accordingly, their magnetic properties can also be changed reversibly, which realizes our goals of manipulating on/off single-molecule magnet behaviour. MOF 1 behaves as a single-molecule magnet either with or without DC field. Contrarily, no slow magnetic relaxation was observed in 1a both under zero field and applied field.
Protozoan-Viral-Bacterial Co-Infections Alter Galectin Levels and Associated Immunity Mediators in the Female Genital Tract
Authors: Fichorova Raina N. , DeLong Allison K. , Cu-Uvin Susan , King Caroline C. , Jamieson Denise J. , Klein Robert S. , Sobel Jack D. , Vlahov David , Yamamoto Hidemi S. , Mayer Kenneth H.
Published: August 2021

Co-infections with sexually transmittable pathogens are common and more likely in women with disturbed vaginal bacteriome. Among those pathogens, the protozoan parasite Trichomonas vaginalis (TV) is most common after accounting for the highly persistent DNA viruses human papillomavirus (HPV) and genital herpes. The parasitic infection often concurs with the dysbiotic syndrome diagnosed as bacterial vaginosis (BV) and both are associated with risks of superimposed viral infections. Yet, the mechanisms of microbial synergisms in evading host immunity remain elusive. We present clinical and experimental evidence for a new role of galectins, glycan-sensing family of proteins, in mixed infections. We assessed participants of the HIV Epidemiology Research Study (HERS) at each of their incident TV visits (223 case visits) matched to controls who remained TV-negative throughout the study. Matching criteria included age, race, BV (by Nugent score), HIV status, hysterectomy, and contraceptive use. Non-matched variables included BV status at 6 months before the matched visit, and variables examined at baseline, within 6 months of and/or at the matched visit e.g. HSV-2, HPV, and relevant laboratory and socio-demographic parameters. Conditional logistic regression models using generalized estimating equations calculated odds ratios (OR) for incident TV occurrence with each log10 unit higher cervicovaginal concentration of galectins and cytokines. Incident TV was associated with higher levels of galectin-1, galectin-9, IL-1β and chemokines (ORs 1.53 to 2.91, p <0.001). Galectin-9, IL-1β and chemokines were up and galectin-3 down in TV cases with BV or intermediate Nugent versus normal Nugent scores (p <0.001). Galectin-9, IL-1β and chemokines were up in TV-HIV and down in TV-HPV co-infections. In-vitro, TV synergized with its endosymbiont Trichomonasvirus (TVV) and BV bacteria to upregulate galectin-1, galectin-9, and inflammatory cytokines. The BV-bacterium Prevotella bivia alone and together with TV downregulated galectin-3 and synergistically upregulated galectin-1, galectin-9 and IL-1β, mirroring the clinical findings of mixed TV–BV infections. P. bivia also downregulated TVV+TV-induced anti-viral response e.g. IP-10 and RANTES, providing a mechanism for conducing viral persistence in TV-BV co-infections. Collectively, the experimental and clinical data suggest that galectin-mediated immunity may be dysregulated and exploited by viral–protozoan–bacterial synergisms exacerbating inflammatory complications from dysbiosis and sexually transmitted infections.
Hurricane Irma Simulation at South Florida Using the Parallel CEST Model
Authors: Li Yuepeng , Chen Qiang , Kelly Dave M. , Zhang Keqi
Published: August 2021

In this study, a parallel extension of the Coastal and Estuarine Storm Tide (CEST) model is developed and applied to simulate the storm surge tide at South Florida induced by hurricane Irma occurred in 2017. An improvement is also made to the existing advection algorithm in CEST. This is achieved through the introduction of high-order, monotone Semi-Lagrangian advection. Distributed memory parallelization is developed via the Message Passing Interface (MPI) library. The parallel CEST model can therefore be run efficiently on machines ranging from multicore laptops to massively High Performance Computing (HPC) system. The principle advantage of being able to run the CEST model on multiple cores is that relatively low run-time is possible for real world storm surge simulations on grids with high resolution, especially in the locality where the hurricane makes landfall. The computational time is critical for storm surge model forecast to finish simulations in 30 min, and results are available to users before the arrival of the next advisory. In this study, simulation of hurricane Irma induced storm surge was approximately 22 min for 4 day simulation, with the results validated by field measurements. Further efficiency analysis reveals that the parallel CEST model can achieve linear speedup when the number of processors is not very large.
Optimization of Coastal Protections in the Presence of Climate Change
Authors: Miura Yuki , Dinenis Philip C. , Mandli Kyle T. , Deodatis George , Bienstock Daniel
Published: August 2021

It is generally acknowledged that interdependent critical infrastructure in coastal urban areas is constantly threatened by storm-induced flooding. Due to changing climate effects, such as sea level rise (SLR), the occurrence of catastrophic events will be more frequent and may trigger an increased likelihood of severe hazards. Planning a protective measure or mitigation strategy is a complex problem given the constraints that it must fit within a prescribed and limited fiscal budget and be beneficial to the community it protects both socially and economically. This article proposes a methodology for optimizing protective measures and mitigation strategies for interdependent infrastructures subjected to storm-induced flooding and climate change impacts such as SLR. Optimality is defined in this methodology as a maximum reduction in overall expected losses within a prescribed budget (compared to the expected losses in the case of doing nothing for protection/mitigation). Protective measures can include seawalls, barriers, artificial dunes, restoration of wetlands, raising individual buildings, sealing parts of the infrastructure, strategic retreat, insurance, and many more. The optimal protective strategy can be a combination of several protective measures implemented over space and time. The optimization process starts with parameterizing the protective measures. Storm-induced flooding and SLR, and their corresponding consequences, are estimated using a GIS-based subdivision-redistribution methodology (GISSR) developed by the authors for finding a rough solution in the first brute-force iterations of the optimization loop. A storm surge computational model called GeoClaw is subsequently used to simulate ensembles of synthetic storms in order to fine-tune and achieve the optimal solution. Damage loss, including economic impacts, is quantified based on calculated flood estimates. The suitability of the potential optimal solution is examined and assessed with input from stakeholders' interviews. It should be mentioned that the results and conclusions provided in this work depend on the assumptions made about future sea level rise (SLR). The authors acknowledge that there are other, more severe predictions for sea level rise (SLR), than the one used in this paper.
On the Difficulty of Defining “Difficult” in Second-Language Vowel Acquisition
Authors: Munro Murray J.
Published: August 2021

Hierarchies of difficulty in second-language (L2) phonology have long played a role in the postulation and evaluation of learning models. In L2 pronunciation teaching, hierarchies are assumed to be helpful in the development of instructional strategies based on anticipated areas of difficulty. This investigation addressed the practicality of defining a pedagogically useful hierarchy of difficulty for English tense and lax close vowels (/i I u ʊ/) produced by Cantonese speakers. Unlike their English counterparts, Cantonese close tense-lax pairs are allophonic variants with [i u] occurring before alveolars and [I ʊ] before velars. Each tense-lax pair represents a “phonemic split” in which members of a single L1 category are realized contrastively in L2. Despite evidence that English tense-lax distinctions are challenging for Cantonese speakers, no previous empirical work has closely considered the problem from the standpoint of vowel intelligibility across multiple phonetic contexts and in different words sharing the same rhyme. In a picture-based word-elicitation task, 18 Cantonese-speaking participants produced 31 high-frequency CV and CVC words. Vowels were evaluated for intelligibility by phonetically-trained judges. A series of mixed-effects binary logistic models were fitted to the scores, with vowel quality, phonetic context (rhyme) and word as factors, and length of Canadian residence and daily use of English as co-variates. As expected, the general hierarchy of difficulty for vowels that emerged (/i/ > /u/ > /ʊ/ > /I/) was complicated by large differences across phonetic contexts. Results were not readily explicable in terms of transfer; moreover, different words with the same rhyme were not produced with equal intelligibility. The most serious modeling complication was the sizeable inter-speaker variability in difficulties, which could not be accounted for by model co-variates. Although some difficulties were roughly systematic at the group level, it is argued that establishing a pedagogically useful hierarchy on such data would prove intractable. Rather, L2 learners might be better served by assessment and instructional targeting of their individual problem areas than by a focus on errors predicted from hierarchies of difficulty.
A Brief Research Report on the Perception and Satisfaction of Italian University Students With Disabilities and Specific Learning Disabilities at the Emergency Remote Teaching During the COVID-19 Lockdown
Authors: Carpinelli Luna , Bruno Giorgia , Savarese Giulia
Published: August 2021

Introduction: The COVID-19 pandemic has inevitably transformed face-to-face teaching to remote teaching (e-learning or blended) which has had psychological and social impacts on the mental health of university students.

Object: In this study, we surveyed university students with disabilities and specific learning disabilities (SLDs) on their perceptions of and satisfaction with emergency remote teaching (ERT) during the lockdown phase (March–April 2020) and following restrictions due to the COVID-19 pandemic. We compared the responses of students with disabilities and SLDs with those of normotypical students.

Methodology: A questionnaire was completed remotely: five items on the ERT were designed as ad hoc questions and five items were taken from the Short Form 12 Health Survey (SF-12) to evaluate physical and mental self-perceived health. There was a total of 163 students surveyed, 67 students with disabilities and/or SLDs and 96 normotypical students.

Results and Conclusion: Students with disabilities and SLDs were more satisfied with remote teaching than the normotypical students. In fact, only 22% of the students with disabilities or SLDs indicated that they were dissatisfied with the teaching method used due to difficulties encountered, including those related to a weak technological infrastructure. We found that among all the students, important social and emotional aspects emerged as a consequence of the absence of interactions and relationships with both faculty and peer groups.
Synthetic Fuels in a Transport Transition: Fuels to Prevent a Transport Underclass
Authors: Styring Peter , Duckworth Emily L. , Platt Edward G.
Published: August 2021

The Paris Agreement set policy scenarios to address mitigating against the climate emergency, by reducing greenhouse gas emissions to limit the temperature increase to 1.5°C. There has been a drive toward electrifying transport, with battery electric vehicles (BEVs) at the forefront. Reliance on single-technology policy development can lead to consequential impacts, often not considered, or dismissed. Energy cannot be created or destroyed but can be transformed. While BEVs may represent zero tailpipe emissions, the battery energy must be sourced elsewhere. An ideal policy scenario will come from “renewable” sources; however, current global energy mixes require the electricity to come from carbon-burning point source emitters. Therefore, the emissions are deferred to low socioeconomic regions. The move to ban new internal combustion engine (ICE) vehicle sales has been accelerated. High BEV costs will preclude low-income groups from making purchases. Such groups typically rely on used cars for mobility. Without considered consequential policy analysis, transport underclasses may result, where private transport is only accessible by the wealthy. Synthetic fuels derived from CO2represent a social bridge in the energy transition, also helping to accelerate toward net zero. The Covid-19 lockdown provided a unique opportunity to experience an environment with reduced transport-related emissions. Global studies allowed the consequential effects of pollution reduction to be studied. These are surprising and offer the opportunity for policies, driven by science, to be developed. Here, we consider the consequential effects of clean air policies, and how these can be used to propose dynamic responses to policy recommendations.
Nonintrusive Monitoring for Electric Vehicles Based on Zero-Shot Learning
Authors: Hu Jingwei , Ren Rufei , Hu Jie , Sun Qiuye
Published: August 2021

Monitoring the charging behavior of electric vehicle clusters will contribute to developing more effective energy management strategies for grid operators. A low implementation cost leads to a wide application prospect in nonintrusive monitoring for EVs. Aiming at the problem that traditional nonintrusive monitoring methods cannot identify unknown devices accurately due to the lack of classes, a nonintrusive monitoring method based on zero-shot learning (ZSL) is proposed in this article, one which can monitor the unknown types of EVs connected to charging piles. First, the charging characteristics of known EVs and unknown EVs are extracted by dictionary learning. Then EVs are classified by ZSL based on sparse coding. Furthermore, EVs are decomposed based on the proposed multimode factorial hidden Markov model (FHMM). Finally, the EV dataset of Pecan Street is used to verify the effectiveness and accuracy of the proposed method.
Frontiers of (Pareto) Optimal and Sustainable Water Management for Hydropower and Ecology
Authors: Perona Paolo , Niayifar Amin , Schwemmle Robin , Razurel Pierre , Flury Reto , Winz Elias , Barry D. A.
Published: August 2021

River regulation alters the natural flow regime of streams with consequent impacts on terrestrial and aquatic habitats of the riparian zone. The severity of such impacts can be modulated by changing the redistribution rules at water intakes and reservoirs. Contrary to minimal-flow policies, non-proportional and proportional redistribution policies result in variable environmental flow releases, namely Dynamic Environmental Flows (DEFs), which improve the global (i.e., ecological and economic) efficiency of water use practice, e.g., for energy production. DEF assessment is based on different indicators. However, the choice and aggregation method of different hydrological and fish habitat indicators affects the assessment of the global power plant performance, i.e., the Frontier of efficient solutions (sensu Pareto). This study investigates DEF assessment, and shows the extent to which the choice and method of aggregation of different indicators impacts the Frontier of Pareto-efficient solutions. The findings are supported by six case studies of hydropower practice that differ in terms of river morphology, energy production amount and technique. The relative importance of several types of indicators is examined as is their influence on optimal and sustainable water allocation solutions that lie on the Pareto Frontier. The analysis shows that DEFs arising from either proportional or non-proportional redistribution rules can positively impact strategies of sustainable management of freshwater resources.
Modeling Sprawling Locomotion of the Stem Amniote Orobates: An Examination of Hindlimb Muscle Strains and Validation Using Extant Caiman
Authors: Zwafing Michelle , Lautenschlager Stephan , Demuth Oliver E. , Nyakatura John A.
Published: August 2021

The stem amnioteOrobates pabstihas been reconstructed to be capable of relatively erect, balanced, and mechanically power-saving terrestrial locomotion. This suggested that the evolution of such advanced locomotor capabilities preceded the origin of crown-group amniotes. We here further investigate plausible body postures and locomotion ofOrobatesby taking soft tissues into account. Freely available animation software BLENDERis used to first reconstruct the lines of action of hindlimb adductors and retractors forOrobatesand then estimate the muscle strain of these muscles. We experimentally varied different body heights in modeled hindlimb stride cycles ofOrobatesto find the posture that maximizes optimal strains over the course of a stride cycle. To validate our method, we usedCaiman crocodilus. We replicated the identical workflow used for the analysis ofOrobatesand compared the locomotor posture predicted forCaimanbased on muscle strain analysis with this species’ actual postural data known from a previously published X-ray motion analysis. Since this validation experiment demonstrated a close match between the modeled posture that maximizes optimal adductor and retractor muscle strain and thein vivoposture employed byCaiman, using the same method forOrobateswas justified. Generally, the use of muscle strain analysis for the reconstruction of posture in quadrupedal vertebrate fossils thus appears a promising approach. Nevertheless, results forOrobatesremained inconclusive as several postures resulted in similar muscle strains and none of the postures could be entirely excluded. These results are not in conflict with the previously inferred moderately erect locomotor posture ofOrobatesand suggest considerable variability of posture during locomotion.
Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma
Authors: Qin An-Cheng , Qian Yi , Ma Yu-Yuan , Jiang Yong , Qian Wei-Feng
Published: August 2021

Anaplastic thyroid carcinoma (ATC) is one of the most aggressive human malignancies with poor prognosis. However, the underlying mechanisms of ATC remain to be elucidated. Recently, increasing studies have focused on competitive endogenous RNA (ceRNA) to discover valuable biomarkers for the diagnosis of ATC. The present study identified 705 differentially expressed mRNAs and 47 differentially expressed lncRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also conducted. Additionally, an lncRNA/miRNA/mRNA network was constructed which included 1103 regulatory relations. The upregulation of RP11-395G23.3 in ATC cells was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). In the loss of function assays, results suggested silencing of RP11-395G23.3 inhibited cell proliferation and induced cell apoptosis. Mechanically, RP11-395G23.3 could increase ROR1 via sponging miR-124-3p as a ceRNA. Moreover, ROR1 expression was decreased with the downregulation of RP11-395G23.3, but was rescued by the co-transfection of the miR-124-3p inhibitor in ATC cells. Our research suggested that the RP11-395G23.3/miR-124-3p/ROR1 axis potentially acted as a potential target for the diagnosis of ATC.
The Prognostic Value and Function of HOXB5 in Acute Myeloid Leukemia
Authors: Chen Miao , Qu Yi , Yue Pengjie , Yan Xiaojing
Published: August 2021

Background

Currently, cytogenetic and genetic markers are the most important for risk stratification and treatment of patients with acute myeloid leukemia (AML). Despite the identification of many prognostic factors, relatively few have made their way into clinical practice. Therefore, the identification of new AML biomarkers is useful in the prognosis and monitoring of AML and contributes to a better understanding of the molecular basis of the disease. Homeobox (HOX) genes are transcription factors that lead to cell differentiation blockade and malignant self-renewal. However, the roles of HOX genes in AML are still not fully understood and need further exploration, which may provide new strategies for the prognosis and monitoring of AML.

Methods

We analyzed the RNA sequencing and clinical data from The Cancer Genome Atlas (TCGA), VIZOME, GSE13159, and GSE9476 cohorts. Analyses were performed with GraphPad 7, the R language, and several online databases. We applied quantitative polymerase chain reaction, Western Blotting, CCK8 cell proliferation assays, and flow cytometry to verify the conclusions of the bioinformatics analysis.

Results

We identified HOXB5 as the only gene among the HOX family that was not only elevated in AML but also a significant prognostic marker in AML patients. HOXB5 was highly expressed in AML patients with NPM1, FLT3, or DNMT3A mutations and was expressed at the highest level in patients with NPM1-FLT3-DNMT3A triple-mutant AML. Gene Ontology analysis and gene set enrichment analysis revealed that HOXB5 showed a negative correlation with the myeloid cell differentiation signature and that the tumor necrosis factor/nuclear factor κB signaling pathway was involved in the molecular mechanism. Moreover, we performed in silico protein–protein interaction analysis and 450K TCGA DNA methylation data analysis and found that HOXB5 interacted with two HOX genes (HOXA7 and HOXB4) that were commonly regulated by DNA methylation levels.

Conclusion

HOXB5 is associated with the malignant development of AML and may be a treatment target and biomarker for AML prognosis prediction.
Splicing Outcomes of 5′ Splice Site GT>GC Variants That Generate Wild-Type Transcripts Differ Significantly Between Full-Length and Minigene Splicing Assays
Authors: Lin Jin-Huan , Wu Hao , Zou Wen-Bin , Masson Emmanuelle , Fichou Yann , Le Gac Gerald , Cooper David N. , Férec Claude , Liao Zhuan , Chen Jian-Min
Published: August 2021

Combining data derived from a meta-analysis of human disease-associated 5′ splice site GT>GC (i.e., +2T>C) variants and a cell culture-based full-length gene splicing assay (FLGSA) of forward engineered +2T>C substitutions, we recently estimated that ∼15–18% of +2T>C variants can generate up to 84% wild-type transcripts relative to their wild-type counterparts. Herein, we analyzed the splicing outcomes of 20 +2T>C variants that generate some wild-type transcripts in two minigene assays. We found a high discordance rate in terms of the generation of wild-type transcripts, not only between FLGSA and the minigene assays but also between the different minigene assays. In the pET01 context, all 20 wild-type minigene constructs generated the expected wild-type transcripts; of the 20 corresponding variant minigene constructs, 14 (70%) generated wild-type transcripts. In the pSPL3 context, only 18 of the 20 wild-type minigene constructs generated the expected wild-type transcripts whereas 8 of the 18 (44%) corresponding variant minigene constructs generated wild-type transcripts. Thus, in the context of a particular type of variant, we raise awareness of the limitations of minigene splicing assays and emphasize the importance of sequence context in regulating splicing. Whether or not our findings apply to other types of splice-altering variant remains to be investigated.
Quantitative Soundscape Analysis to Understand Multidimensional Features
Authors: Wilford Dylan Charles , Miksis-Olds Jennifer L. , Martin S. Bruce , Howard Daniel R. , Lowell Kim , Lyons Anthony P. , Smith Michael James
Published: August 2021

A methodology for the analysis of soundscapes was developed in an attempt to facilitate efficient and accurate soundscape comparisons across time and space. The methodology consists of a collection of traditional soundscape metrics, statistical measures, and acoustic indices that were selected to quantify several salient properties of marine soundscapes: amplitude, impulsiveness, periodicity, and uniformity. The metrics were calculated over approximately 30 h of semi-continuous passive acoustic data gathered in seven unique acoustic environments. The resultant metric values were compared toa prioridescriptions and cross-examined statistically to determine which combination most effectively captured the characteristics of the representative soundscapes. The best measures of amplitude, impulsiveness, periodicity, and uniformity were determined to be SPLrms and SPLpk for amplitude, kurtosis for impulsiveness, an autocorrelation based metric for periodicity, and the Dissimilarity index for uniformity. The metrics were combined to form the proposed “Soundscape Code,” which allows for rapid multidimensional and direct comparisons of salient soundscape properties across time and space. This initial characterization will aid in directing further analyses and guiding subsequent assessments to understand soundscape dynamics.
Ever Changing Times: Sustainability Transformations of Galician Small-Scale Fisheries
Authors: Villasante Sebastián , Tubío Ana , Gianelli Ignacio , Pita Pablo , García-Allut Antonio
Published: August 2021

The Galician small-scale fisheries sector has been experiencing important changes. The presence of a wide range of ecological, economic, social and institutional drivers have forced the statu quo toward new transitions with the potential to generate desirable transformative changes. Sustainability transformations mean that changes fundamentally alter the entire system’s ecological and/or social properties and functions. However, there is a limited understanding of how a transformative change may look in small-scale fisheries, when and by whom it can be triggered, supported, and implemented. To cover this research gap, the objectives of this paper are twofold: to document the current state of the art of Galician small-scale fisheries, and to evaluate the innovations and changes that occurred between 1990 and 2020, to explore whether such changes have scaled-up as seeds of desirable transformative changes and, if not, what obstacles and/or barriers have been identified in the scientific literature. We selected two cases, the Galician shellfisheries and the Marine Protected Area of Fishing Interest Os Miñarzos, to understand when and how profound changes in small-scale fisheries took place. We hypothesize that obstacles for building resilience to consolidate transformative changes once triggered are the still moderate effectiveness of the fisheries management systems, the low progress of incorporation of scientific and traditional knowledge into decision-making processes and policy arenas, the lack of studies about socio-economic contribution to coastal communities and commercialization models, and the presence of persistent ecological and economic drivers hindering desirable transformative changes.
An Advanced Finite Element Modeling for the Failure of Notched Ceramic Matrix Composite With TFP Patch Reinforcement
Authors: Zhao Gang , Tang Jianbo , Wang Jun , Chen Yunsheng , Feng Yajie , Chen Yousi , Xin Shiqing , Jian Xigao , Li Shuxin , Zhang Shouhai , Xu Jian
Published: August 2021

An advanced modeling strategy for notched ceramic matrix composite coupons with patch reinforcement was proposed to investigate the failure mechanisms. This model considered the tailored fiber–placed (TFP) yarn details obtained from the design phase and the embedded element concept which was used to successfully overcome the meshing difficulties. Inter-ply “glue” layers were simulated using the surface-based contact cohesive element method, so the delamination due to interfacial material discontinuity and damage can be well reproduced and analyzed. For composite ply, the energy-based composite progressive damage model that is independent of the mesh size was applied. Virtual test campaign was performed with a variety of geometrical and material parameters, and the damage and failure mechanisms based on the stress analysis can be revealed to support the design optimization of patch reinforcement.
Sensitivities of Porous Beds and Plates to Ignition by Firebrands
Authors: Bean Derek , Blunck David L.
Published: August 2021

The increasing occurrence of severe wildfires, coupled with the expansion of the wildland urban interface has increased the number of structures in danger of being destroyed by wildfires. Ignition by firebrands is a significant avenue for fire spread and structure loss; thus, understanding processes and parameters that control the ignition of fuel beds by firebrands is important for reducing these losses. In this study the effect of fuel bed characteristics (i.e., particle size and porous or solid fuel bed) on ignition behavior was considered. Modelling and analysis was conducted to better understand parameters that are dominant in controlling ignition. The fuel beds, made from Douglas-fir shavings, Douglas-fir plates, or cardboard plates, were heated with a cartridge heater (i.e., surrogate firebrand) to observe ignition. Smaller particles were observed to ignite more readily in porous beds than larger particles when heat transfer from the heater is primarily through conduction. This occurs in large part due to differences in contact area between the fuel bed and the heater coupled with thermal properties of the fuel bed. As particle sizes increased, ignition was more likely to occur at extended times (>100 s) due to the increased importance of radiation heat transfer. Douglas-fir plates were primarily observed to ignite at times where conduction was the dominant mode of heat transfer (<10 s). Heat flux delivered to the fuel bed was observed to be a more accurate predictor of ignition likelihood and ignition time than heater temperatures. The characteristic ratio of transport and chemical timescales can be used, in conjunction with the measured heat flux and thermal diffusivity of the fuel beds, as a first approximation to predict ignition for the porous fuel beds. This suggests that future work focusing on these parameters may produce a general characterization of fuel bed ignition probability across fuel beds materials and morphologies.
An Epidemiological Meta-Analysis on the Worldwide Prevalence, Resistance, and Outcomes of Spontaneous Bacterial Peritonitis in Cirrhosis
Authors: Tay Phoebe Wen Lin , Xiao Jieling , Tan Darren Jun Hao , Ng Cheng , Lye Yan Nerng , Lim Wen Hui , Teo Vanessa Xin Yi , Heng Ryan Rui Yang , Yeow Marcus Wei Xuan , Lum Lionel Hon Wai , Tan Eunice Xiang Xuan , Kew Guan Sen , Lee Guan Huei , Muthiah Mark D.
Published: August 2021

Background and Aims: Spontaneous bacterial peritonitis (SBP) is a common and potentially fatal complication of liver cirrhosis. This study aims to analyze the prevalence of SBP among liver cirrhotic patients according to geographical location and income level, and risk factors and outcomes of SBP.

Methods: A systematic search for articles describing prevalence, risk factors and outcomes of SBP was conducted. A single-arm meta-analysis was performed using generalized linear mix model (GLMM) with Clopper-Pearson intervals.

Results: Ninety-Nine articles, comprising a total of 5,861,142 individuals with cirrhosis were included. Pooled prevalence of SBP was found to be 17.12% globally (CI: 13.63–21.30%), highest in Africa (68.20%; CI: 12.17–97.08%), and lowest in North America (10.81%; CI: 5.32–20.73%). Prevalence of community-acquired SBP was 6.05% (CI: 4.32–8.40%), and 11.11% (CI: 5.84–20.11%,) for healthcare-associated SBP. Antibiotic-resistant microorganisms were found in 11.77% (CI: 7.63–17.73%) of SBP patients. Of which, methicillin-resistant Staphylococcus aureus was most common (6.23%; CI: 3.83–9.97%), followed by extended-spectrum beta-lactamase producing organisms (6.19%; CI: 3.32–11.26%), and lastly vancomycin-resistant enterococci (1.91%; CI: 0.41–8.46%). Subgroup analysis comparing prevalence, antibiotic resistance, and outcomes between income groups was conducted to explore a link between socioeconomic status and SBP, which revealed decreased risk of SBP and negative outcomes in high-income countries.

Conclusion: SBP remains a frequent complication of liver cirrhosis worldwide. The drawn link between income level and SBP in liver cirrhosis may enable further insight on actions necessary to tackle the disease on a global scale.
A New High-Throughput-Screening-Assay for Photoantimicrobials Based on EUCAST Revealed Unknown Photoantimicrobials in Cortinariaceae
Authors: Fiala Johannes , Schöbel Harald , Vrabl Pamela , Dietrich Dorothea , Hammerle Fabian , Artmann Desirée Josefine , Stärz Ronald , Peintner Ursula , Siewert Bianka
Published: August 2021

Antimicrobial resistance is one of the biggest health and subsequent economic threat humanity faces. Next to massive global awareness campaigns, governments and NGOs alike stress the need for new innovative strategies to treat microbial infections. One of such innovative strategies is the photodynamic antimicrobial chemotherapy (PACT) in which the synergistic effects of photons and drugs are exploited. While many promising reports are available, PACT – and especially the drug-design part behind – is still in its infancy. Common best-practice rules, such as the EUCAST or CLSI protocols for classic antibiotics as well as high-throughput screenings, are missing, and this, in turn, hampers the identification of hit structures. Hit-like structures might come from synthetic approaches or from natural sources. They are identified via activity-guided synthesis or isolation strategies. As source for new antimicrobials, fungi are highly ranked. They share the same ecological niche with many other microbes and consequently established chemical strategies to combat with the others. Recently, in members of the Cortinariaceae, especially of the subgenus Dermocybe, photoactive metabolites were detected. To study their putative photoantimicrobial effect, a photoantimicrobial high-throughput screening (HTS) based on The European Committee on Antimicrobial Susceptibility Testing (EUCAST) was established. After validation, the established HTS was used to evaluate a sample set containing six colorful representatives from the genus Cortinarius (i.e., Cortinarius callisteus, C. rufo-olivaceus, C. traganus, C. trivialis, C. venetus, and C. xanthophyllus). The assay is built on a uniform, light-emitting diode (LED)-based light irradiation across a 96-well microtiter plate, which was achieved by a pioneering arrangement of the LEDs. The validation of the assay was accomplished with well-known photoactive drugs, so-called photosensitizers, utilizing six distinct emission wavelengths (λexc = 428, 478, 523, 598, or 640 nm) and three microbial strains (Candida albicans, Staphylococcus aureus, and Escherichia coli). Evaluating the extracts of six Cortinarius species revealed two highly promising species, i.e., C. rufo-olivaceus and C. xanthophyllus. Extracts from the latter were photoactive against the Gram-positive S. aureus (c = 7.5 μg/ml, H = 30 J/cm2, λ = 478 nm) and the fungus C. albicans (c = 75 μg/ml, H = 30 J/cm2, λ = 478 nm).
Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens
Authors: Morales-Cedeño Luzmaria R. , de los Santos-Villalobos Sergio , Santoyo Gustavo
Published: August 2021

In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.
New Contributions to the Diversity of Hypotrichous Ciliates: Description of a New Genus and Two New Species (Protozoa, Ciliophora)
Authors: Ma Jiyang , Zhang Tengyue , Song Weibo , Shao Chen
Published: August 2021

Ciliated protists (ciliates) are extremely diverse and play important ecological roles in almost all kinds of habitats. In this study, two new hypotrichs, Wilbertophrya sinica n. g. and n. sp. and Bakuella xianensis n. sp., from China are investigated. Wilbertophrya n. g. can be separated from related genera mainly by the combination of lacking a buccal cirrus, pretransverse cirri, and caudal cirri, while possessing frontoterminal cirri. Analyses based on morphological and molecular data confirm the validity of the species, W. sinica n. sp., which is characterized as follows: body 50–115 μm × 15–35 μm in vivo; midventral complex comprises four or five cirral pairs only and terminates above mid-body; three frontal, two frontoterminal cirri, and two to four transverse cirri; about 15 macronuclear nodules; colorless cortical granules sparsely distributed. Another new species, B. xianensis n. sp., was isolated from a freshwater wetland and is defined as follows: body 115–150 μm × 40–65 μm in vivo; about 70 macronuclear nodules; dark-brownish cortical granules in groups; midventral complex comprises 8–12 cirral pairs forming a row that terminates posteriorly in mid-body region and two or three short midventral rows that are continuous with the row of midventral pairs; three frontal, four to six frontoterminal, and three to five fine transverse cirri; three bipolar dorsal kineties. Phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequence data suggest that the new genus Wilbertophrya n. g. belongs to an isolated clade, which might represent an undescribed taxon at the family level, whereas B. xianensis n. sp. groups with several congeners and members of other related genera are within the core urostylids.
Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images
Authors: Dasgupta Bhaskar , Miyashita Osamu , Uchihashi Takayuki , Tama Florence
Published: August 2021

ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or aggregated proteins during heat or other cellular shocks. The function of this protein relies on the interconversion between different conformations in its native condition. A recent high-speed-atomic-force-microscopy (HS-AFM) experiment on ClpB from Thermus thermophilus shows four predominant conformational classes, namely, open, closed, spiral, and half-spiral. Analyses of AFM images provide only partial structural information regarding the molecular surface, and thus computational modeling of three-dimensional (3D) structures of these conformations should help interpret dynamical events related to ClpB functions. In this study, we reconstruct 3D models of ClpB from HS-AFM images in different conformational classes. We have applied our recently developed computational method based on a low-resolution representation of 3D structure using a Gaussian mixture model, combined with a Monte-Carlo sampling algorithm to optimize the agreement with target AFM images. After conformational sampling, we obtained models that reflect conformational variety embedded within the AFM images. From these reconstructed 3D models, we described, in terms of relative domain arrangement, the different types of ClpB oligomeric conformations observed by HS-AFM experiments. In particular, we highlighted the slippage of the monomeric components around the seam. This study demonstrates that such details of information, necessary for annotating the different conformational states involved in the ClpB function, can be obtained by combining HS-AFM images, even with limited resolution, and computational modeling.
Advances of Endothelial Progenitor Cells in the Development of Depression
Authors: Yang Nana , Sun Shiyu , Duan Guangqing , Lv Kaixuan , Liang Chen , Zhang Linlin , Yu Jielun , Tang Yaohui , Lu Guohua
Published: August 2021

Depression is a major psychological disease of human beings. With the severity of depression, it elevates the risk of cardiovascular disease (CVD), especially acute coronary syndrome (ACS), resulting in serious harm to human health. The number of endothelial progenitor cells (EPCs) is closely related to the development of depression. It has been reported that the number of peripheral blood EPCs in patients with depression was reduced. However, effects on the function of EPCs in depression are still unclear. This paper aims to analyze and summarize the research of EPCs in depression, and we envision that EPCs might act as a new target for evaluating the severity of depression and its complications.