bluuebunny/crossref_metadata_2025 huggingface dataset:
SOURCE: Sea Observations Utility for Reprocessing, Calibration and Evaluation
Authors: Oliveri Paolo , Simoncelli Simona , Di Pietro Pierluigi , Fratianni Claudia , Mattia Gelsomina , Delrosso Damiano , Guarnieri Antonio
Published: January 2022

SOURCE utility for reprocessing, calibration, and evaluation is a software designed for web applications that permits to calibrate and validate ocean models within a selected spatial domain using in-situ observations. Nowadays, in-situ observations can be freely accessed online through several marine data portals together with the metadata information about the data provenance and its quality. Metadata information and compliance with modern data standards allow the user to select and filter the data according to the level of quality required for the intended use and application. However, the available data sets might still contain anomalous data, bad data flagged as good, due to several reasons, i.e., the general quality assurance procedures adopted by the data infrastructure, the selected data type, the timeliness of delivery, etc. In order to provide accurate model skill scores, the SOURCE utility performs a secondary quality check, or re-processing, of observations through gross check tests and a recursive statistical quality control. This first and basic SOURCE implementation uses Near Real Time moored temperature and salinity observations distributed by the Copernicus Marine Environment and Monitoring Service (CMEMS) and two model products from Istituto Nazionale di Geofisica e Vulcanologia (INGV), the first an analysis and the second a reanalysis, distributed during CMEMS phase I for the Mediterranean Sea. The SOURCE tool is freely available to the scientific community through the ZENODO open access repository, consistent with the open science principles and for that it has been designed to be relocatable, to manage multiple model outputs, and different data types. Moreover, its observation reprocessing module provides the possibility to characterize temperature and salinity variability at each mooring site and continuously monitor the ocean state. Highest quality mooring time series at 90 sites and the corresponding model values have been obtained and used to compute model skill scores. The SOURCE output also includes mooring climatologies, trends, Probability Density Functions and averages at different time scales. Model skill scores and site statistics can be used to visually inspect both model and sensor performance in Near Real Time at the single site or at the basin scale. The SOURCE utility uptake allows the interested user to adapt it to its specific purpose or domain, including for example additional parameters and statistics for early warning applications.
Composition of Seagrass Root Associated Bacterial Communities Are Linked to Nutrients and Heavy Metal Concentrations in an Anthropogenically Influenced Estuary
Authors: Martin Belinda C. , Middleton Jen A. , Skrzypek Grzegorz , Kendrick Gary A. , Cosgrove Jeff , Fraser Matthew W.
Published: January 2022

Seagrasses are globally recognized as bioindicators of marine eutrophication and contamination. Seagrasses also harbor a distinct root microbial community that largely reflects the conditions of the surrounding environment as well as the condition of the seagrass. Hence monitoring changes in the root microbial community could act as an additional biological indicator that reflects both the seagrass health condition, as well as potential deterioration in coastal waters. We used 16S rRNA gene sequencing combined with analysis of seagrass nutrients (C, N, δ15N, δ13C) and tissue metal concentrations to investigate potential links between seagrass (Halophila ovalis) root bacteria and seagrass nutrient and metal concentrations within an anthropogenically influenced estuary. We found seagrass tissue nitrogen (%) and δ15N values were 2–5 times higher than global averages for this species. Seagrass root associated bacteria formed distinct communities that clustered by site and were correlated to both seagrass nutrient and metal concentration, with some putative sulfide oxidizing bacteria (Sulfurimonas and Sulfurovum) correlated with greater nutrient concentrations, and putative iron cycling bacteria (Lewinella and Woeseia) correlated with greater Fe and As concentrations. Our findings shed further light on the relationship between seagrass and their microbes, as well as provide additional assessment of the use of both seagrass and their microbes as indicators of estuarine and seagrass condition.
The Ever-Changing and Challenging Role of Ocean Observation: From Local Initiatives to an Oceanwide Collaborative Effort
Authors: Silveira Tanya Mendes , Carapuço Mafalda Marques , Miranda Jorge Miguel
Published: January 2022

Ocean observation has seen a rapid evolution and has become crucial in providing the much needed data and information toward a well-supported and accurate description of ocean processes which influence the environmental, economic, and societal systems. There has been a significant progress in technologies which have enabled the expansion of the sampling and observing systems both on temporal and spatial scales. Furthermore, online, free access, data portals have grown in number and quality, provided by data aggregators, which have promoted the creation of standardized methods for marine data acquisition and management. Ocean observation is now global, but it depends on the single institutions and laboratories’ capability to guarantee the operation of instruments and longevity in data acquisition. International collaborative initiatives are crucial to support the ever-growing databases and feed the services and products that are fundamental to Blue Growth. Collaboration must be developed at local and regional levels and the monitoring system must ensure data consistency, integrity, and redundancy. The “Atlantic Observatory – Data and Monitoring Infrastructure” project, is an example of a Portuguese effort to bring together on-going initiatives working in the Atlantic area and provide access to high quality marine environmental data covering the Atlantic Ocean basin.
Fast Changes in the Bioenergetic Balance of Krill in Response to Environmental Stress
Authors: Lagos Paulo F. , Curtsdotter Alva , Agüera Antonio , Sabadel Amandine J. M. , Burrit David J. , Lamare Miles D.
Published: January 2022

A Dynamic Energy Budget (DEB) model is applied to predict rapid metabolic shifts in an ecologically important krill, Nyctiphanes australis, in response to temperature and ultraviolet radiation (UVR). Specifically, we predict changes in fatty acids, amino acids and respiration rate in response to several light and temperature treatments. Environmental variability can alter the metabolic equilibrium and the mechanisms marine ectotherms used to obtain energy, which is a topical point given the current level of environmental change. Environmental variability also includes multiple stressors, which can have additive, antagonistic or synergistic effects on metabolism. In consequence, disentangling and quantifying the effects of multiple stressors on metabolism and the energy balance of ecthothermal species, such as krill, can be challenging. Here we apply a DEB model to direct measurements of fatty acids, amino acids and respiration rate of krill experimentally exposed simultaneously to several doses of UVR and temperatures. We found that on average light escalates metabolic rates by a factor of two, and temperature has an effect 1.35 times greater than the effect of light over respiration rates at temperatures from 9 to 19°C. The DEB model predicted shifts in metabolic function and indicated that the combined effect of light and elevated temperatures decrease the total of fatty acid concentrations at a higher rate than amino acids when krill are exposed to environmentally relevant temperatures and light treatments. Our results demonstrate that, when krill experience warmer conditions and higher levels of solar radiation, the mobilization of energy-relevant metabolites from the reserves increases by up to 36% and increase the total energetic cost by up to 45%. These findings suggest that ectothermal species with a fast metabolism, such as krill, quickly deplete energy reserves to compensate for changes in the environment. This renders krill susceptible to the effects of climate variability if the current climatic trend for the region continues to show temperature increases, even if solar radiation levels remain unchanged.
Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy
Authors: Kürzel Karlotta , Kaiser Stefanie , Lörz Anne-Nina , Rossel Sven , Paulus Eva , Peters Janna , Schwentner Martin , Martinez Arbizu Pedro , Coleman Charles Oliver , Svavarsson Jörundur , Brix Saskia
Published: January 2022

Correct identification of species is required to assess and understand the biodiversity of an ecosystem. In the deep sea, however, this is only possible to a limited extent, as a large part of the fauna is undescribed and the identification keys for most taxa are inadequate or missing. With the progressive impact of climate change and anthropogenic activities on deep-sea ecosystems, it is imperative to define reliable methods for robust species identification. In this study, different techniques for the identification of deep-sea species are tested, including a combination of morphological, molecular (DNA barcoding, and proteomic fingerprinting), biogeographical and ecological modeling approaches. These are applied to a family of isopods, the Haploniscidae, from deep waters around Iceland. The construction of interactive identification keys based on the DELTA format (DEscription Language for TAxonomy) were a major pillar of this study, the evaluation of which was underpinned by the application of the supplementary methods. Overall, interactive keys have been very reliable in identifying species within the Haploniscidae. Especially in a deep-sea context, these types of keys could become established because they are easy to adapt and flexible enough to accommodate newly described species. Remarkably, in this study, the interactive key enabled identification of a supposedly new species within the Haploniscidae that was later verified using both molecular genetic – and proteomic methods. However, these keys are limited given that they are based on purely morphological characteristics, including where species with strong ontogenetic or sexual dimorphism occur as both genders are not always described. In this case, integrative taxonomy is the method of choice and the combination presented here has been shown to be very promising for correct identification of deep-sea isopods.
Challenges for Marine Ecological Assessments: Completeness of Findable, Accessible, Interoperable, and Reusable Biodiversity Data in European Seas
Authors: Ramírez Francisco , Sbragaglia Valerio , Soacha Karen , Coll Marta , Piera Jaume
Published: January 2022

The ongoing contemporary biodiversity crisis may result in much of ocean’s biodiversity to be lost or deeply modified without even being known. As the climate and anthropogenic-related impacts on marine systems accelerate, biodiversity knowledge integration is urgently required to evaluate and monitor marine ecosystems and to support suitable responses to underpin a sustainable future. The Census of Marine Life (CoML, 2000–2010) was the largest global research program on marine biodiversity. A decade after, and coinciding with the steep increase of digitalization of our society, we review existing findability, accessibility, interoperability, and reusability (FAIR) biodiversity data coming from one of the most reliable online information systems: the Global Biodiversity Information Facility (GBIF). We evaluate the completeness of available datasets with respect to the CoML benchmark, along with progresses in understanding spatial–temporal patterns of marine biodiversity in the European Seas in the last decades. Overall, we observe severe biases in available biodiversity data toward the north-western marine regions (particularly around the United Kingdom and the North Sea), the most recent years (with a peak in the number of reported occurrences in the 2010s) and the most conspicuous, abundant, and likely “appealing” taxa (e.g., crustaceans, echinoderms or fish). These biases may hamper research applications, but also global-scale data needs and integrative assessments required to support cost-effective progresses toward global biodiversity conservation. National to international joint efforts aimed at enhancing data acquisition and mobilization from poorly known regions, periods, and taxa are desirable if we aim to address these potential biases for the effective monitoring of marine ecosystems and the evaluation of ongoing impacts on biogeographic patterns and ecosystem functioning and services.
Nitrogen Isotope Sclerochronology—Insights Into Coastal Environmental Conditions and Pinna nobilis Ecology
Authors: Peharda Melita , Gillikin David P. , Schöne Bernd R. , Verheyden Anouk , Uvanović Hana , Markulin Krešimir , Šarić Tomislav , Janeković Ivica , Župan Ivan
Published: January 2022

Pinna nobilis is a large bivalve endemic to the Mediterranean Sea that lives in shallow coastal areas. Due to its size and relatively fast shell growth rates, it is an interesting taxon for high-resolution study of nitrogen isotopes of carbonate bound organic matter (δ15NCBOM). In this study we tested if P. nobilis shells can be used as an indicator of the nitrogen isotope baseline of the system, if it can provide high-resolution data on environmental δ15N variability, and if the chemical properties of the shell and biomineralization process change in response to mass mortality events spreading in the Mediterranean. Shells were opportunistically collected during 2019 and 2020 by skin diving, as a part of a project on mortality monitoring, from four shallow coastal localities in the eastern Adriatic. Shell powder for δ15NCBOM analysis was collected by milling sample swaths from the internal (low-resolution) and external (high resolution) shell surface. Significant differences in δ15NCBOM, obtained from the internal shell surface, were observed between sampling localities with different anthropogenic influences, with lowest values (∼3–4‰) recorded for shells obtained from Pag Bay, and highest (∼6–8‰) for shells sampled in Lim and Kaštela Bays. High-resolution samples from the external shell surface of Pinna nobilis showed spatial and temporal variations in δ15NCBOM values, with temporal resolution of 1–3 weeks. High-resolution δ15NCBOM data obtained from the shell Kas1 corresponded to a time interval from spring 2018 to summer 2019 and had a pronounced increase of δ15NCBOM values closest to the shell margin coupled with a decrease in δ13Cshell values, indicating that this animal was experiencing stressful conditions several months prior to its death. According to our findings, δ15NCBOM values from P. nobilis shells can serve as an indicator of the isotopic baseline of the ecosystem potentially as a powerful tool to study bivalve physiology.
Effects of Low-Cost Repair Techniques on Restoration of Mechanical Properties of Fire-Damaged Concrete
Authors: Noman Muhammad , Yaqub Muhammad , Abid Muhammad , Musarat Muhammad Ali , Vatin Nikolai Ivanovich , Usman Muhammad
Published: January 2022

Researchers have conducted numerous investigations on various repair techniques to restore the mechanical properties of fire-damaged concrete. However, most of the techniques are either expensive or require high technical skills. As a continuous work, this study involved an experimental investigation of the effects of various low-cost repair techniques to restore the mechanical properties of fire-damaged concrete. Sixty cylindrical concrete samples were subjected to heat ranging from 400°C to 800°C in a propane gas furnace. The samples were categorized into six groups, including the following: undamaged, fire-damaged, and fire-damaged and repaired using water curing; fire-damaged and repaired using cement-based slurry injection; re-curing fire-damaged and repaired with steel wire mesh along with epoxy resin wrapping; and fire-damaged and repaired using epoxy injection. The samples were tested for non-destructive and destructive tests, including ultrasonic pulse velocity, rebound hammer, and compressive strength. The results showed that the use of cement-based slurry injection along with the water-curing repair technique could regain almost 90% of its ultimate strength and secant stiffness, making it the most effective low-cost repair technique for fire-damaged concrete exposed up to 700°C.
The Correlation Between the Types of Initial Bacterial Infection and Clinical Prognosis in Patients With Septic AKI
Authors: Li Tian , Liu Jing yuan , Liu Jing feng , Duan Meili , Li Ang
Published: January 2022

Background

Acute kidney injury (AKI) is a common complication of sepsis and is an independent risk factor for mortality. It is unclear whether different bacteria play different roles in the occurrence and development of sepsis-associated AKI (S-AKI). We observed the clinical characteristics and outcomes of patients that have types of bacterial infection, and different infections sites before the occurrence of AKI, respectively.

Methods

Data of patients who were diagnosed with sepsis and later developed AKI from 2008 to 2019 were retrieved from the MIMIC-IV 1.0 database. Patients were first divided into the two groups according to the bacterial culture results obtained prior to AKI occurrence: bacterial cultured positive (N = 1,785) and bacterial cultured negative (N = 8,777). Patients with bacteria culture positive were divided into culture bacteria Gram-positive (CGP, N = 1248) and Gram-negative (CGN, N = 537) groups.

Results

Overall, 1,785 patients were included in the present analysis. The patients in CGN group were older (70 vs. 66, p < 0.001), had lower body mass index (BMI) (27.0 vs. 28.4, p < 0.001), higher acute physiology III (APS III) score (63.0 vs. 58, p = 0.001), shorter time from positive microbial culture to diagnosis of AKI (2.94 vs. 3.16 days, p = 0.013) and longer intensive care unit (ICU) stay time (5.94 vs. 4.77 days, p < 0.001) compared with those in the CGP group (n = 1,248). In the culture gram-negative bacteria in patients with positive blood cultures (CGNb) group, the rate of vasopressors using (73.1 vs. 56.4%, P = 0.007), the Sequential Organ Failure Assessment (SOFA) score (10 vs. 9, p = 0.005), and the level of lactate (3.7 vs. 2.5, p = 0.001) were higher than those in the culture gram-positive bacteria in patients with positive blood cultures (CGPb) group. The time from positive microbial culture to the diagnosis of AKI was shorter (2.23 vs. 3 days, p = 0.001) in the CGNb group. However, there was no significant difference in the continuous renal replacement treatment (CRRT) application or short-term mortality rates between CGN and CGP groups.

Conclusion

The Gram types of bacteria cultured prior to S-AKI occurrence was not related to AKI stage, CRRT application, and short-term mortality. Compared with the Gram-positive bacterial infections, Gram-negative bacterial infections take a shorter time to develop into AKI, and had a higher disease severity score.
Computed Tomography Predictors of Mortality or Disease Progression in Systemic Sclerosis–Interstitial Lung Disease: A Systematic Review
Authors: Landini Nicholas , Orlandi Martina , Bruni Cosimo , Carlesi Edoardo , Nardi Cosimo , Calistri Linda , Morana Giovanni , Tomassetti Sara , Colagrande Stefano , Matucci-Cerinic Marco
Published: January 2022

Objective

Although interstitial lung disease (ILD) is a major cause of morbidity and mortality in systemic sclerosis (SSc), its prognostication remains challenging. Given that CT represents the gold standard imaging technique in ILD assessment, a systematic review on chest CT findings as predictors of mortality or ILD progression in SSc-ILD was performed.

Materials and Methods

Three databases (Medline, Embase, and Web of Science) were searched to identify all studies analyzing CT mortality or ILD progression predictors in SSc-ILD, from inception to December 2020. ILD progression was defined by worsening of forced vital capacity and/or CT ILD findings. Manuscripts not written in English, with not available full-text, not focusing on SSc-ILD or with SSc-ILD not extrapolated, otherwise with overlap syndromes, pediatric patients, <10 cases or predictors other than CT features were excluded.

Results

Out of 3,513 citations, 15 full-texts (2,332 patients with SSc-ILD) met the inclusion criteria. ILD extent and extensive ILD, ILD densitometric analysis parameters, fibrotic extent and reticulation extent resulted as independent mortality predictors. Extensive ILD is also an independent predictor of death, need for supplemental oxygen or lung transplantation. Honeycombing extent is an independent risk factor for respiratory mortality. Independent predictors of ILD progression were not identified.

Conclusions

ILD extent and extensive ILD independently predict mortality in SSc-ILD on CT, as well as ILD densitometric analysis, fibrotic extent and reticulation extent. Extensive ILD is also a predictor of death, need for supplemental oxygen, or lung transplantation. Honeycombing extent predicts respiratory mortality. CT predictors of ILD progression need to be further investigated.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/, PROSPERO, identifier: CRD420202005001.
Assessing Viability and Stress Tolerance of Probiotics—A Review
Authors: Wendel Ulrika
Published: January 2022

The interest in probiotics has increased rapidly the latest years together with the global market for probiotic products. Consequently, establishing reliable microbiological methods for assuring the presence of a certain number of viable microorganisms in probiotic products has become increasingly important. To assure adequate numbers of viable cells, authorities are enquiring for information on viability rates within a certain shelf-life in colony forming units (CFU). This information is obtained from plate count enumeration, a method that enables detection of bacterial cells based on their ability to replicate. Although performing plate count enumeration is one manner of assessing viability, cells can still be viable without possessing the ability to replicate. Thus, to properly assess probiotic viability, further analysis of a broader group of characteristics using several types of methods is proposed. In addition to viability, it is crucial to identify how well the cells in a probiotic product can survive in the gastrointestinal tract (GIT) and thus be able to mediate the desired health benefit while passing through the human body. A broad spectrum of different assay designs for assessing probiotic gastric tolerance have been used in research and quality control. However, the absence of any consensus on how to assess these qualities makes it difficult to compare between laboratories and to translate the results into in vivo tolerance. This review presents and discusses the complexity of assuring that a probiotic is suitable for beneficial consumption. It summarizes the information that can be subtracted from the currently available methods for assessment of viability and stress tolerance of a probiotic, hereby altogether defined as “activity.” Strengths and limitations of the different methods are presented together with favorable method combinations. Finally, the importance of choosing a set of analyses that reveals the necessary aspects of probiotic activity for a certain product or application is emphasized.
Cytotoxin-Associated Gene A-Negative Helicobacter pylori Promotes Gastric Mucosal CX3CR1+CD4+ Effector Memory T Cell Recruitment in Mice
Authors: Sun Heqiang , He Taojun , Wu Yanan , Yuan Hanmei , Ning Jie , Zhang Zhenhua , Deng Xinli , Li Bin , Wu Chao
Published: January 2022

Background

Helicobacter pylori can cause many kinds of gastric disorders, ranging from gastritis to gastric cancer. Cytotoxin-associated gene A (CagA)+H. pylori is more likely to cause gastric histopathologic damage than CagA–H. pylori. However, the underlying mechanism needs to be further investigated.

Materials and methods

Mice were intragastrically administered equal amounts of CagA+ or CagA–H. pylori. Four weeks later, 24 chemokines in stomachs were measured using a mouse chemokine array, and the phenotypes of the recruited gastric CD4+ T cells were analyzed. The migration pathway was evaluated. Finally, the correlation between each pair among the recruited CD4+ T cell sub-population, H. pylori colonization level, and histopathologic damage score were determined by Pearson correlation analysis.

Results

The concentration of chemokines, CCL3 and CX3CL1, were significantly elevated in CagA–H. pylori-infected gastric mucosa than in CagA+H. pylori-infected gastric mucosa. Among them, CX3CL1 secreted by gastric epithelial cells, which was elicited more effectively by CagA–H. pylori than by the CagA+ strain, dramatically promoted mucosal CD4+ T cell migration. The expression of CX3CR1, the only known receptor of CX3CL1, was upregulated on the surface of gastric CD4+ T cells in CagA–H. pylori-infected stomach. In addition, most of the CX3CR1-positive gastric CD4+ T cells were CD44+CD69–CCR7– effector memory T cells (Tem). Pearson correlation analysis showed that the recruited CX3CR1+CD4+ Tem cell population was negatively correlated with H. pylori colonization level and histopathologic damage score.

Conclusion

CagA–H. pylori promotes gastric mucosal CX3CR1+CD4+ Tem recruitment in mice.
Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper
Authors: Hsieh Dai-Keng , Chuang Shu-Cheng , Chen Chun-Yi , Chao Ya-Ting , Lu Mei-Yeh Jade , Lee Miin-Huey , Shih Ming-Che
Published: January 2022

Colletotrichum scovillei causes anthracnose of chili pepper in many countries. Three strains of this pathogen, Coll-524, Coll-153, and Coll-365, show varied virulence on chili pepper. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, comparative genomic analysis and gene transformation to show gene function were applied in this study. Compared to Coll-524, Coll-153, and Coll-365 had numerous gene losses including 32 candidate effector genes that are mainly exist in acutatum species complex. A cluster of 14 genes in a 34-kb genomic fragment was lost in Coll-365. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. CsPLAA encoding a phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of CsPLAA with one transcription factor CsBZTF and one C6 zinc finger domain-containing protein CsCZCP was found to enhance the pathogenicity of Coll-365. Introduction of CsGIP, which encodes a hypothetical protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the highest virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365.
Over-Expression and Prognostic Significance of FATP5, as a New Biomarker, in Colorectal Carcinoma
Authors: Geng Qi-Shun , Yang Mei-Jia , Li Li-Feng , Shen Zhi-Bo , Wang Long-Hao , Zheng Yuan-Yuan , Xue Wen-Hua , Zhao Jie
Published: January 2022

Background: Fatty acid transporters (FATPs) family play an important role in the uptake and metabolism regulation of long-chain fatty acids, which influence the occurrence and developing of multiple tumors. Fatty acid transporter 5(FATP5), a member of FATPs family, participates in fatty acid transport and lipid metabolism and is related to tumor development, whose mechanism in colorectal cancer (CRC) remains unclear.

Methods: In this study, we comprehensively utilized a range of relevant bioinformatic tools along with multiple databases to analyze the expression of FATPs family and investigate the biological function and prognostic value of FATP5 in CRC. Besides, cell proliferation and cell cycle distribution analysis, western blotting and immunohistochemistry (IHC) further validated the conclusion of bioinformatics analysis.

Results: FATP5 is the only member of FATPs family which was overexpressed in CRC. In the survival analysis based on the GSE39582 databases, the low expression of FATP5 predicts poor prognosis in CRC. Similar results were also observed in GSE17536, GSE28814 and TCGA colon cohorts. The potential function of DNA methylation regulated the abnormal expression of FATP5 in CRC. In addition, enrichment analysis indicated that FATP5 also participates in the regulation of cell cycle. Furthermore, Gene Set Enrichment Analysis (GSEA) showed a strong negative correlation between FATP5 and cell growth, implying that it may participate in regulating cancer cell proliferation by the regulation of cell cycle G2/M transition. At last, we identified that FATP5 was overexpressed in colorectal carcinoma tissues through immunohistochemistry staining, and played an important role in cell cycle by cell proliferation and cell cycle distribution analysis.

Conclusion: This study suggested that FATP5 was overexpression in colorectal carcinoma and predicted favorable prognosis, indicating it as a novel appealing prognostic marker for CRC.
Elucidating the Structural Features of ABCA1 in its Heterogeneous Membrane Environment
Authors: Sunidhi S. , Sacher Sukriti , Atul  , Garg Parth , Ray Arjun
Published: January 2022

ATP Binding Cassette Transporter A1 (ABCA1) plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis. One theory of lipid efflux by the transporter (alternating access) proposes that ABCA1 harbours two different conformations that provide alternating access for lipid binding and release. This is followed by sequestration via a direct interaction between ABCA1 and its partner, ApoA1. The other theory (lateral access) proposes that ABCA1 obtains lipids laterally from the membrane to form a temporary extracellular “reservoir”. This reservoir contains an isolated lipid monolayer due to the net accumulation of lipids in the exofacial leaflet. Recently, a full-length Cryo-EM structure of this 2,261-residue transmembrane protein showed its discreetly folded domains and have detected the presence of a tunnel enclosed within the extracellular domains (ECDs) but not in the TMDs, giving it an outward-facing conformation. This structure was hypothesized to substantiate the lateral access theory. Utilizing long time-scale multiple replica atomistic molecular dynamics simulations (MDS), we simulated the structure in a large heterogeneous lipid environment and found that the protein undergoes several large conformational changes in its extremities. We observed that the cavity enclosed within ATP unbound form of ABCA1 is narrow at the distal ends of TMD as well as the ECD region substantiating the “lateral access” theory. We have also characterized ABCA1 and the lipid dynamics along with the protein-lipid interactions in the heterogeneous environment, providing novel insights into understanding ABCA1 conformation at an atomistic level.
Characterization of Aspergillus nidulans Biofilm Formation and Structure and Their Inhibition by Pea Defensin Psd2
Authors: Corrêa-Almeida Caroline , Borba-Santos Luana P. , Rollin-Pinheiro Rodrigo , Barreto-Bergter Eliana , Rozental Sonia , Kurtenbach Eleonora
Published: January 2022

Approximately four million people contract fungal infections every year in Brazil, primarily caused by Aspergillus spp. The ability of these fungi to form biofilms in tissues and medical devices complicates treatment and contributes to high rates of morbidity and mortality in immunocompromised patients. Psd2 is a pea defensin of 5.4 kDa that possesses good antifungal activity against planktonic cells of representative pathogenic fungi. Its function depends on interactions with membrane and cell wall lipid components such as glucosylceramide and ergosterol. In the present study, we characterized Aspergillus nidulans biofilm formation and determined the effect of Psd2 on A. nidulans biofilms. After 4 hours, A. nidulans conidia adhered to polystyrene surfaces and formed a robust extracellular matrix-producing biofilm at 24 h, increasing thickness until 48 h Psd2 inhibited A. nidulans biofilm formation in a dose-dependent manner. Most notably, at 10 μM Psd2 inhibited 50% of biofilm viability and biomass and 40% of extracellular matrix production. Psd2 significantly decreased the colonized surface area by the biofilm and changed its level of organization, causing a shortening of length and diameter of hyphae and inhibition of conidiophore formation. This activity against A. nidulans biofilm suggests a potential use of Psd2 as a prototype to design new antifungal agents to prevent biofilm formation by A. nidulans and related species.
The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules
Authors: Röder Konstantin , Wales David J.
Published: January 2022

The energy landscape perspective is outlined with particular reference to biomolecules that perform multiple functions. We associate these multifunctional molecules with multifunnel energy landscapes, illustrated by some selected examples, where understanding the organisation of the landscape has provided new insight into function. Conformational selection and induced fit may provide alternative routes to realisation of multifunctionality, exploiting the possibility of environmental control and distinct binding modes.
PIWI-Interacting RNAs (piRNAs): Promising Applications as Emerging Biomarkers for Digestive System Cancer
Authors: Cai Aiting , Hu Yuhao , Zhou Zhou , Qi Qianyi , Wu Yixuan , Dong Peixin , Chen Lin , Wang Feng
Published: January 2022

PIWI-interacting RNAs (piRNAs) are a novel type of small non-coding RNAs (sncRNAs), which are 26–31 nucleotides in length and bind to PIWI proteins. Although piRNAs were originally discovered in germline cells and are thought to be essential regulators for germline preservation, they can also influence gene expression in somatic cells. An increasing amount of data has shown that the dysregulation of piRNAs can both promote and repress the emergence and progression of human cancers through DNA methylation, transcriptional silencing, mRNA turnover, and translational control. Digestive cancers are currently a major cause of cancer deaths worldwide. piRNAs control the expression of essential genes and pathways associated with digestive cancer progression and have been reported as possible biomarkers for the diagnosis and treatment of digestive cancer. Here, we highlight recent advances in understanding the involvement of piRNAs, as well as potential diagnostic and therapeutic applications of piRNAs in various digestive cancers.
The Link Between Masculinity and Spatial Skills Is Moderated by the Estrogenic and Progestational Activity of Oral Contraceptives
Authors: Beltz Adriene M. , Loviska Amy M. , Kelly Dominic P. , Nielson Matthew G.
Published: January 2022

Conversations about gender and spatial skills frequently dissolve into a hackneyed debate over nature and nurture. This is particularly true for conversations concerning three-dimensional (3D) mental rotations skill, which shows the largest gender difference of all aspects of cognition, with men—on average—outperforming women. To advance this empirical area of inquiry, biopsychosocial influences on spatial skills should be considered, and a unique opportunity do to that is provided by combined oral contraceptives (OCs). OCs with relatively low estradiol doses and with highly androgenic progestins have been positively related to spatial skills. Gender self-concepts, including masculine and feminine self-perceptions, have also been positively related to spatial skills. It is wholly unknown, however, whether the exogenous sex hormones contained in OCs moderate the link between self-perceived masculinity and 3D mental rotations. This study filled that knowledge gap by utilizing a sample of 141 naturally cycling (NC) women and 229 OC users who completed a computerized survey and cognitive tests. A series of moderation analyses examined whether the link between masculinity and 3D mental rotations depended on pill use or on the estrogenic, progestational, or androgenic activity in OCs, which were operationalized using a novel coding scheme. Results showed that the positive masculinity-3D mental rotations link was only present for NC women, presumably because it was altered by the exogenous hormones in OCs. Indeed, the link was accentuated in users of OCs with relatively low estrogenic and high progestational activity. Future research on menstrual cycle and pill phase is needed, but these findings importantly delineate ways in which biological and psychosocial factors combine to explain variation in spatial skills among women. They also suggest that focus should be placed on the under-investigated progestational activity of OCs, which is facilitated by the novel quantification of OC action used in this study. Thus, this research increases understanding of the neurocognitive and behavioral correlates of ovarian hormones and has implications for the betterment of women’s health.
Inhibition of Exosome Release Alleviates Cognitive Impairment After Repetitive Mild Traumatic Brain Injury
Authors: Hu Tianpeng , Han Zhaoli , Xiong Xiangyang , Li Meimei , Guo Mengtian , Yin Zhenyu , Wang Dong , Cheng Lu , Li Dai , Zhang Shishuang , Wang Lu , Zhao Jing , Liu Qiang , Chen Fanglian , Lei Ping
Published: January 2022

Background

Repetitive mild traumatic brain injury (rmTBI) is closely associated with chronic traumatic encephalopathy (CTE). Neuroinflammation and neuropathological protein accumulation are key links to CTE progression. Exosomes play important roles in neuroinflammation and neuropathological protein accumulation and spread. Here, we explored the role of brain-derived exosomes (BDEs) in mice with rmTBI and how the inhibition of BDE release contributes to neuroprotection.

Methods

GW4869 was used to inhibit exosome release, and behavioural tests, PET/CT and western blotting were conducted to explore the impact of this inhibition from different perspectives. We further evaluated cytokine expression by Luminex and microglial activation by immunofluorescence in mice with rmTBI after exosome release inhibition.

Results

Inhibition of BDE release reversed cognitive impairment in mice with rmTBI, enhanced glucose uptake and decreased neuropathological protein expression. Inhibition of BDE release also changed cytokine production trends and enhanced microglial proliferation.

Conclusion

In this study, we found that BDEs are key factor in cognitive impairment in mice with rmTBI and that microglia are the main target of BDEs. Thus, inhibition of exosome release may be a new strategy for improving CTE prognoses.
New Anti-CGRP Medications in the Treatment of Vestibular Migraine
Authors: Hoskin Justin L. , Fife Terry D.
Published: January 2022

Background

Vestibular migraine (VM) is a condition associated with migraine headache, vertigo, dizziness, and balance disturbances. Treatment options are limited. It is unknown if new calcitonin gene-related peptide (CGRP) migraine medications have efficacy in treating VM.

Methods

We retrospectively reviewed all patients with VM who were prescribed one of the new CGRP medications between January 2016 and July 2020. In total, 28 patients met the inclusion criteria. We specifically evaluated the “older” CGRP medications including erenumab, galcanezumab, fremanezumab, and ubrogepant. Medical records for subsequent visits were assessed to monitor improvement described by patients.

Results

Of the 28 patients identified, three were lost to follow up. For the remaining 25 patients, we divided the patients based on a scale of “significant improvement,” “moderate improvement,” “mild improvement,” or “no improvement.” In total 21 of 25 patients demonstrated some level of improvement in their VM symptoms with 15 having moderate to significant improvement.

Conclusion

Results demonstrated a trend toward improvement, suggesting that the CGRP medications appear to be a decent treatment option for VM. A prospective study evaluating CGRP medications in patients with VM would provide further information about this treatment option.
Epilepsy With Auditory Features: From Etiology to Treatment
Authors: Furia Alessandro , Licchetta Laura , Muccioli Lorenzo , Ferri Lorenzo , Mostacci Barbara , Mazzoni Stefania , Menghi Veronica , Minardi Raffaella , Tinuper Paolo , Bisulli Francesca
Published: January 2022

Epilepsy with auditory features (EAF) is a focal epilepsy belonging to the focal epileptic syndromes with onset at variable age according to the new ILAE Classification. It is characterized by seizures with auditory aura or receptive aphasia suggesting a lateral temporal lobe involvement of the epileptic discharge. Etiological factors underlying EAF are largely unknown. In the familial cases with an autosomal dominant pattern of inheritance several genes have been involved, among which the first discovered, LGI1, was thought to be predominant. However, increasing evidence now points to a multifactorial etiology, as familial and sporadic EAF share a virtually identical electro-clinical characterization and only a few have a documented genetic etiology. Patients with EAF usually have an unremarkable neurological examination and a good response to antiseizure medications. However, it must be underscored that total remission might be lower than expected and that treatment withdrawal might lead to relapses. Thus, a proper understanding of this condition is in order for better patient treatment and counseling. Further studies are still required to further characterize the many facets of EAF.
Modeling Large Vessel Occlusion Stroke for the Evaluation of Endovascular Therapy According to Thrombus Composition
Authors: Freiherr von Seckendorff Aurélien , Delvoye François , Levant Paul , Solo Nomenjanahary Mialitiana , Ollivier Véronique , Bourrienne Marie-Charlotte , Di Meglio Lucas , Piotin Michel , Escalard Simon , Maier Benjamin , Hebert Solène , Smajda Stanislas , Redjem Hocine , Mazighi Mikael , Blanc Raphael , Ho-Tin-Noé Benoit , Désilles Jean-Philippe
Published: January 2022

More than 40% of endovascular therapy (EVT) fail to achieve complete reperfusion of the territory of the occluded artery in patients with acute ischemic stroke (AIS). Understanding factors influencing EVT could help overcome its limitations. Our objective was to study the impact of thrombus cell composition on EVT procedures, using a simulation system for modeling thrombus-induced large vessel occlusion (LVO) in flow conditions. In an open comparative trial, we analyzed the behavior of size-standardized platelet-rich and red blood cells (RBC)-rich thrombi during simulated stent retriever-mediated EVT procedures. Sixteen simulated EVT procedures were performed (8 RBC- vs. 8 platelet-rich thrombi). Platelet-rich thrombi were associated with a higher number of stent retriever passes (p = 0.03) and a longer procedure duration (p = 0.02) compared to RBC-rich thrombi. Conversely, RBC-rich thrombi released more embolic fragments than platelet-rich thrombi (p = 0.004). Both RBC-rich and platelet-rich thrombi underwent drastic compaction after being injected into the in vitro circulation model, and histologic analyses showed that these EVT-retrieved thrombi displayed features comparable to those previously observed in thrombi from patients with AIS patients having LVO, including a marked structural dichotomy between RBC- and platelet-rich areas. Our results show that the injection of in vitro-produced thrombi in artificial cerebrovascular arterial networks is suitable for testing recanalization efficacy and the risk of embolization of EVT devices and strategies in association with thrombus cell composition.
Guillain–Barré Syndrome and Variants Following COVID-19 Vaccination: Report of 13 Cases
Authors: Kim Jee-Eun , Min Young Gi , Shin Je-Young , Kwon Young Nam , Bae Jong Seok , Sung Jung-Joon , Hong Yoon-Ho
Published: January 2022

Background

Amidst growing concern about an increased risk of Guillain–Barré syndrome (GBS) following COVID-19 vaccination, clinical and electrodiagnostic features have not been fully characterized.

Methods

We retrospectively reviewed medical records of the patients diagnosed with GBS and its variants following COVID-19 vaccination at four referral hospitals during the period of the mass vaccination program in South Korea (February to October 2021).

Results

We identified 13 patients with GBS and variants post COVID-19 vaccination: AstraZeneca vaccine (Vaxzevria) in 8, and Pfizer-BioNTech vaccine (Comirnaty) in 5. The mean time interval from vaccination to symptom onset was 15.6 days (range 4–30 days). Electrodiagnostic classification was demyelinating in 7, axonal in 4 and normal in 2 cases. Clinical manifestations were diverse with varying severity: classical GBS in 8 cases, paraparetic variant in 3, Miller-Fisher syndrome in 1 and acute cervicobrachial weakness in 1. Four patients developed respiratory failure, and 2 of them showed treatment-related fluctuations.

Conclusion

Our observations suggest that COVID-19 vaccines may be associated with GBS of distinctive clinical features characterized by severe quadriplegia, disproportionately frequent bilateral facial palsy or atypical incomplete variants. Continuous surveillance and further studies using robust study designs are warranted to fully assess the significance of the association.
The Role of Wideband Tympanometry in the Diagnosis of Meniere's Disease
Authors: Meng Xiangming , Zhu Kangxu , Yue Jing , Han Chengzhou
Published: January 2022

Meniere's disease (MD) is a clinical syndrome characterized by spontaneous recurrent vertigo, usually accompanied by hearing loss, tinnitus, and aural fullness. The cause of MD remains unclear and is generally considered to be associated with endolymphatic hydrops. Studies showed that patients with MD could have eustachian tube dysfunction (ETD). ETD can disrupt the pressure balance between the middle and inner ear and impair the inner ear's function. In recent years, several studies have attempted to identify MD by using wideband tympanometry (WBT). However, there are limited studies in this area. There is no consensus on how to use WBT to diagnose Meniere's disease. Therefore, we endeavored to conduct a narrative review in this aspect based on the latest research findings. Reduction in resonance frequency and absorbance are characteristic of MD and can identify Meniere's disease. The use of an increase in the integrated area of absorbance as an indicator for identifying MD is controversial. WBT seems to be ineffective as a diagnostic tool during the acute episodes of Meniere's disease. Patients with MD may benefit from WBT. WBT has excellent potential for future use in Meniere's disease. However, further large sample sizes, multicenter studies are needed.