bluuebunny/crossref_metadata_2025 huggingface dataset:
New insight into Salpa thompsoni distribution via glider-borne acoustics
Authors: Hann Ashley M. , Bernard Kim S. , Kohut Josh , Oliver Matthew J. , Statscewich Hank
Published: January 2023

Salpa thompsoniis an ephemerally abundant pelagic tunicate in the waters of the Southern Ocean that makes significant contributions to carbon flux and nutrient recycling in the region. WhileS. thompsoni, hereafter referred to as “salps”, was historically described as a polar-temperate species with a latitudinal range of 40 – 60°S, observations of salps in coastal waters of the Western Antarctic Peninsula have become more common in the last 50 years. There is a need to better understand the variability in salp densities and vertical distribution patterns in Antarctic waters to improve predictions of their contribution to the global carbon cycle. We used acoustic data obtained from an echosounder mounted to an autonomous underwater Slocum glider to investigate the anomalously high densities of salps observed in Palmer Deep Canyon, at the Western Antarctic Peninsula, in the austral summer of 2020. Acoustic measurements of salps were made synchronously with temperature and salinity recordings (all made on the glider downcasts), and asynchronously with chlorophyll-ameasurements (made on the glider upcasts and matched to salp measurements by profile) across the depth of the water column near Palmer Deep Canyon for 60 days. Using this approach, we collected high-resolution data on the vertical and temporal distributions of salps, their association with key water masses, their diel vertical migration patterns, and their correlation with chlorophyll-a. While salps were recorded throughout the water column, they were most prevalent in Antarctic Surface Water. A peak in vertical distribution was detected from 0 – 50 m regardless of time of day or point in the summer season. We found salps did not undergo diel vertical migration in the early season, but following the breakdown of the remnant Winter Water layer in late January, marginal diel vertical migration was initiated and sustained through to the end of our study. There was a significant, positive correlation between salp densities and chlorophyll-a. To our knowledge, this is the first high resolution assessment of salp spatial (on the vertical) and temporal distributions in the Southern Ocean as well as the first to use glider-borne acoustics to assess salpsin situ.
Monitoring Black Sea environmental changes from space: New products for altimetry, ocean colour and salinity. Potentialities and requirements for a dedicated in-situ observing system
Authors: Grégoire Marilaure , Alvera-Azcaráte Aida , Buga Luminita , Capet Arthur , Constantin Sorin , D’ortenzio Fabrizio , Doxaran David , Faugeras Yannis , Garcia-Espriu Aina , Golumbeanu Mariana , González-Haro Cristina , González-Gambau Verónica , Kasprzyk Jean-Paul , Ivanov Evgeny , Mason Evan , Mateescu Razvan , Meulders Catherine , Olmedo Estrella , Pons Leonard , Pujol Marie-Isabelle , Sarbu George , Turiel Antonio , Vandenbulcke Luc , Rio Marie-Hélène
Published: January 2023

In this paper, satellite products developed during the Earth Observation for Science and Innovation in the Black Sea (EO4SIBS) ESA project are presented. Ocean colour, sea level anomaly and sea surface salinity datasets are produced for the last decade and validated with regional in-situ observations. New data processing is tested to appropriately tackle the Black Sea’s particular configuration and geophysical characteristics. For altimetry, the full rate (20Hz) altimeter measurements from Cryosat-2 and Sentinel-3A are processed to deliver a 5Hz along-track product. This product is combined with existing 1Hz product to produce gridded datasets for the sea level anomaly, mean dynamic topography, geostrophic currents. This new set of altimetry gridded products offers a better definition of the main Black Sea current, a more accurate reconstruction and characterization of eddies structure, in particular, in coastal areas, and improves the observable wavelength by a factor of 1.6. The EO4SIBS sea surface salinity from SMOS is the first satellite product for salinity in the Black Sea. Specific data treatments are applied to remedy the issue of land-sea and radio frequency interference contamination and to adapt the dielectric constant model to the low salinity and cold waters of the Black Sea. The quality of the SMOS products is assessed and shows a significant improvement from Level-2 to Level -3 and Level-4 products. Level-4 products accuracy is 0.4-0.6 psu, a comparable value to that in the Mediterranean Sea. On average SMOS sea surface salinity is lower than salinity measured by Argo floats, with a larger error in the eastern basin. The adequacy of SMOS SSS to reproduce the spatial characteristics of the Black Sea surface salinity and, in particular, plume patterns is analyzed. For ocean colour, chlorophyll-a, turbidity and suspended particulate materials are proposed using regional calibrated algorithms and satellite data provided by OLCI sensor onboard Sentinel-3 mission. The seasonal cycle of ocean colour products is described and a water classification scheme is proposed. The development of these three types of products has suffered from important in-situ data gaps that hinder a sound calibration of the algorithms and a proper assessment of the datasets quality. We propose recommendations for improving the in-situ observing system that will support the development of satellite products.
Bacterial community in African catfish (Clarias gariepinus) recirculating aquaculture systems under different stocking densities
Authors: Clols-Fuentes Júlia , Nguinkal Julien A. , Unger Patrick , Kreikemeyer Bernd , Palm Harry W.
Published: January 2023

Fish farming in Recirculating Aquaculture Systems (RAS) is a sustainable and efficient practice to produce fish. Knowledge of microbial communities, particularly harmful pathogens on fish, is required to better understand microbiological processes occurring at different RAS compartments and to optimize the overall RAS management. In this study, we assessed the influence of differentClarias gariepinusstocking densities in RAS on the water microbiome composition. Molecular targeting the V3-V4 16S rRNA hypervariable region was used to infer Amplicon Sequence Variants (ASV), identify microbes, and assess their abundance and diversity. We identified bacterial pathogens in the rearing environment associated with common fish farming practices. Our findings show that microbiomes differ across all systems (high, medium and low stocking densities) and within sampling points (water inflow, outflow and sedimentation tank). The medium-density system had the most fish biomass, resulting in high ASVs cumulative abundance. In water samples from high- and low-density systems, we discovered a wide range of phyla, withMycobacteriumsp. being the most common potentially pathogenic group. We discuss the effects of fish biomass and water physicochemical properties on the microbiome.
Dynamics of O2 and pCO2 in a Southeast Asia seagrass meadow: Metabolic rates and carbon sink capacity
Authors: Chou Wen-Chen , Fan Lan-Feng , Hung Chin-Chang , Shih Yung-Yen , Huang Wei-Jen , Lui Hon-Kit , Chen Tzong-Yueh
Published: January 2023

Dissolved oxygen (DO) and partial pressure of CO2 (pCO2) were measured at half-hourly intervals from June 29 to September 9, 2019, in a seagrass meadow in the Southeast Asia archipelagos region. The open water mass balance of the O2 approach was used to calculate metabolic rates (i.e., gross primary production (GPP), community respiration (CR), and net community production (NCP). The calculations show that GPP and CR rates in the seagrass meadow of Dongsha Island were approximately 2.5 times higher than the global means (GPP, 507 ± 173 vs. 225 ± 11 mmol O2 m-2 d-1; CR, 497 ± 171 vs. 188 ± 10 mmol O2 m-2 d-1), while NCP was similar to the global mean (8 ± 61 vs. 27 ± 6 mmol O2 m-2 d-1), suggesting that seagrass meadows with high GPP may not necessarily hold high potential for carbon sequestration. The current data set also reveal that NCP tended to increase with GPP only at lower GPP levels, while NCP did not increase with GPP anymore at higher GPP levels. Moreover, the autotrophic/heterotrophic status did not correspond well to the sink/source behavior of CO2, suggesting that organic carbon metabolism could not be the only dominant factor in determining the sink/source status in a typical seagrass meadow underlain by carbonate sediments, which was further supported by the observed decrease in the trend of pCO2 with a relatively stable NCP level over the study period. These results demonstrate that the metabolism and the relationship between NCP and pCO2 in the seagrass meadows of Dongsha Island may deviate greatly from the global mean condition. To obtain a better assessment of the global potential of seagrass meadows as a nature-based solution for carbon sequestration, more regional-specific studies are still needed in the key regions, such as Indonesia and the Pacific archipelagos, that support extensive seagrass meadows but have not been charted.
The occurrence of humpback whales across the Hawaiian archipelago revealed by fixed and mobile acoustic monitoring
Authors: Lammers Marc O. , Goodwin Beth , Kügler Anke , Zang Eden J. , Harvey Matt , Margolina Tetyana , Martinez Jonathan A. , Merkens Karlina , Hatch Leila T.
Published: January 2023

The occurrence of humpback whales (Megaptera novaeangliae) across the 2600 km of Hawaiian archipelago, which include the remote atolls, banks, and seamounts of Papahānaumokuākea Marine National Monument (PMNM), remains poorly understood. Previous surveys for humpback whales beyond the main Hawaiian Islands have been scarce due to limited access and the challenging winter conditions typically found in PMNM when whales are present. To overcome these limitations, a combination of moored acoustic recorders and a Wave Glider autonomous surface vehicle were used to acoustically monitor eight locations and survey approximately 1500 km of the Hawaiian archipelago for the occurrence of humpback whale song during the 2019-2020 breeding season. Relative song prevalence was established using a machine learning tool and by quantifying the level of song chorusing. A generalized additive model framework was applied to understand the associations between habitat variables and humpback whale song occurrence, and sound propagation modeling was performed to examine whether acoustic propagation influenced observed patterns. Whale song was recorded at all monitored and surveyed locations across the archipelago, albeit in varying amounts. Among the locations monitored with moored recorders, the highest and most sustained seasonal chorusing levels were measured off Maui followed by French Frigate Shoals (Kānemilohai), Hawaii Island, Middle Bank, Oahu, Kauai, Gardner Pinnacles (Pūhāhonu) and Pearl and Hermes Reef (Holoikauaua), respectively. The Wave Glider mission to PMNM revealed that song prevalence was highest at Middle Bank and gradually decreased further to the northwest, reaching a minimum at Gardner Pinnacles (Pūhāhonu). However, song occurrence increased again at Raita Bank, remaining high between Raita Bank and the Northampton Seamounts. The results reveal that nearly the entire Hawaiian archipelago is exploited by humpback whales during the winter and early spring months. Moreover, song occurrence patterns suggest that there may be more structure in the distribution of whales in PMNM than previously known and raises questions about whether multiple subpopulations occur across the archipelago.
Genome rearrangements, male pregnancy and immunological tolerance – the curious case of the syngnathid immune system
Authors: Parker Jamie , Dubin Arseny , Roth Olivia
Published: January 2023

The syngnathid fish group (seahorses, pipefishes and seadragons) is a fascinating lineage associated with an array of evolutionary peculiarities that include diverse morphologies and their unique male pregnancy. These oddities also extend to their immune systems, with a growing body of research highlighting a range of intriguing immunological characteristics and genomic rearrangements, which pose questions regarding their evolutionary history and immune strategies. The functional loss of the major histocompatibility complex class II pathway (MHC II) in the Syngnathus genus and related pathway components in the seahorse (Hippocampus) were two discoveries that initially piqued interest. This sparked discussions concerning immune capabilities, possible facilitative roles in advanced male pregnancy evolution through means of evoking immunological tolerance, as well as a general re-evaluation of how we interpret vertebrate immunological plasticity. Experimental approaches have attempted to clarify further the impact of immune repertoire loss on the efficacy of the syngnathid immune response, specificities regarding the pathways in play during pregnancy as well as the concept of immunological inheritance. The first characterization of the immune cell repertoire of Syngnathus typhle using scRNA-seq represents the latest step to understanding the immune dynamics of these enigmatic fish. This report serves as a review for the immunological insights into the fascinating syngnathid fish group; encompassing their evolutionary history, immune cell populations, links to male pregnancy, and sex specificity, in addition to highlighting future research opportunities in need of investigation.
Identifying drivers of change during the recent two decades in the Visayan Sea using a trophic modeling approach
Authors: Bacalso Regina Therese M. , Romagnoni Giovanni , Wolff Matthias
Published: January 2023

The Visayan Sea is one of the major traditional fishing grounds in the Philippines and is likewise considered as a top contributor to the country’s overall fisheries production. However, fisheries surveys conducted over the past couple of decades have documented changes in the abundance and composition of catches and stocks toward an increasing dominance of invertebrates and low trophic levels fish families. Assessments of the commercially-important pelagic and demersal stocks were used to estimate population parameters that already exceed the sustainable reference limits. These traditional assessments point exclusively to fishing as the likely cause of the observed status and trends, but they fail to incorporate the potential influence of trophic interactions and variable environmental conditions despite a nationally-legislated mandate to apply an ecosystem approach to assessing and managing the country’s fisheries. Thus, an ecosystem model (Ecopath with Ecosim) of the Visayan Sea was constructed to investigate the role and extent of the fishery, trophic interactions, and changing environmental conditions as drivers of stock abundance and ecosystem dynamics. The results suggest that fishing and its corresponding trophic effects are the major drivers of invertebrate and fish biomass and catches in the Visayan Sea over the past two decades, while the environmental trends provide explanations for patterns that cannot be explained by fishing alone. Incorporating sea surface temperature variations and primary productivity anomalies produced the best-fitting models for most of the observed biomass and catch trends. The catches of the small pelagics (i.e., sardines and mackerels) were likewise found to be particularly affected by rainfall, while the biomass and catch of the small demersal fishes also show a sensitivity to chlorophyll-a concentrations. The primary productivity anomalies further showed a significant correlation with the Pacific Decadal Oscillation (PDO), which suggests that bottom-up trophic controls in the system may be affected by long-term regional climatic changes. These findings validate the applicability and necessity of the ecosystem modeling approach in assessing exploited marine ecosystems to complement the analyses from typically single-species population assessments, especially in the face of increasing environmental variability and projected climate change scenarios.
Clinical observation and study of local hyperthermia for treating plantar warts: A pilot study with 38 patients
Authors: Chen XiaoLi , Xu Yan , Hu Li , Chen AiJun
Published: January 2023

Warts are benign lesions caused by infection of the keratinocytes by the human papillomavirus (HPV). There is still no consensus on the standard treatment for plantar warts, and the various treatments (both destructive and non-destructive) have variable efficacy with a long list of shortcomings, such as higher recurrence, pain, and scarring. Local hyperthermia was considered a safe, effective, and promising therapy in the treatment of plantar warts. After getting approval from the hospital’s ethics committee, the present study was designed to assess the clinical efficacy of local hyperthermia in the treatment of plantar warts. A total of 38 patients were enrolled in the study, and all patients received a standard regimen in a 5-week schedule, with local 45°C treatment for 30 mins on days 1, 2, 3, 14, 15, 22, 29, and 36. Of the 38 patients, complete resolution of the warts was observed in 13 (34.2%), 8 (21.1%) achieved partial remission, and 17 (44.7%) revealed poor response to the treatment. Patients were followed up for at least 3 months, and there was no recurrence of lesions in the 13 clinically cured patients at the last follow-up. The findings in the current study demonstrate that local hyperthermia is a safe, effective, and promising therapy for the treatment of plantar warts.
EphH, a unique epoxide hydrolase encoded by Rv3338 is involved in the survival of Mycobacterium tuberculosis under in vitro stress and vacuolar pH-induced changes
Authors: Garg Tanu , Das Swetarka , Singh Shriya , Imran Mohmmad , Mukhopadhyay Atri , Gupta Umesh D. , Chopra Sidharth , Dasgupta Arunava
Published: January 2023

Introduction

Mycobacterium tuberculosis (Mtb), one of the deadliest human pathogen, has evolved with different strategies of survival inside the host, leading to a chronic state of infection. Phagosomally residing Mtb encounters a variety of stresses, including increasing acidic pH. To better understand the host-pathogen interaction, it is imperative to identify the role of various genes involved in the survivability of Mtb during acidic pH environment.

Methods

Bio-informatic and enzymatic analysis were used to identify Mtb gene, Rv3338, as epoxide hydrolase. Subsequently, CRISPRi knockdown strategy was used to decipher its role for Mtb survival during acidic stress, nutrient starvation and inside macrophages. Confocal microscopy was used to analyse its role in subverting phagosomal acidification within macrophage.

Results

The present work describes the characterization of Rv3338 which was previously known to be associated with the aprABC locus induced while encountering acidic stress within the macrophage. Bio-informatic analysis demonstrated its similarity to epoxide hydrolase, which was confirmed by enzymatic assays, thus, renamed EphH. Subsequently, we have deciphered its indispensable role for Mtb in protection from acidic stress by using the CRISPRi knockdown strategy. Our data demonstrated the pH dependent role of EphH for the survival of Mtb during nutrient starvation and in conferring resistance against elevated endogenous ROS levels during stress environment.

Conclusion

To the best of our knowledge, this is the first report of an EH of Mtb as a crucial protein for bacterial fitness inside the host, a phenomenon central to its pathogenesis.
Genomic conservation and putative downstream functionality of the phosphatidylinositol signalling pathway in the cnidarian-dinoflagellate symbiosis
Authors: Ashley Immy A. , Kitchen Sheila A. , Gorman Lucy M. , Grossman Arthur R. , Oakley Clinton A. , Suggett David J. , Weis Virginia M. , Rosset Sabrina L. , Davy Simon K.
Published: January 2023

The mutualistic cnidarian–dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon revealed a broad range of functions, including compelling links to processes putatively involved in symbiosis regulation. This analysis establishes a baseline for current understanding of the PI pathway across anthozoans and Symbiodiniaceae, and thus a framework to target future research.
In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens
Authors: Algarni Suad , Han Jing , Gudeta Dereje D. , Khajanchi Bijay K. , Ricke Steven C. , Kwon Young Min , Rhoads Douglas D. , Foley Steven L.
Published: January 2023

Introduction

The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk.

Methods

To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences.

Results and Discussion

In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.
Induced defense strategies of plants against Ralstonia solanacearum
Authors: Shi Haoqi , Liu Yong , Ding Anming , Wang Weifeng , Sun Yuhe
Published: January 2023

Plants respond to Ralstonia solanacearum infestation through two layers of immune system (PTI and ETI). This process involves the production of plant-induced resistance. Strategies for inducing resistance in plants include the formation of tyloses, gels, and callose and changes in the content of cell wall components such as cellulose, hemicellulose, pectin, lignin, and suberin in response to pathogen infestation. When R. solanacearum secrete cell wall degrading enzymes, plants also sense the status of cell wall fragments through the cell wall integrity (CWI) system, which activates deep-seated defense responses. In addition, plants also fight against R. solanacearum infestation by regulating the distribution of metabolic networks to increase the production of resistant metabolites and reduce the production of metabolites that are easily exploited by R. solanacearum. We review the strategies used by plants to induce resistance in response to R. solanacearum infestation. In particular, we highlight the importance of plant-induced physical and chemical defenses as well as cell wall defenses in the fight against R. solanacearum.
Rapid identification and drug resistance screening of respiratory pathogens based on single-cell Raman spectroscopy
Authors: Liu Ziyu , Xue Ying , Yang Chun , Li Bei , Zhang Ying
Published: January 2023

Respiratory infections rank fourth in the global economic burden of disease. Lower respiratory tract infections are the leading cause of death in low-income countries. The rapid identification of pathogens causing lower respiratory tract infections to help guide the use of antibiotics can reduce the mortality of patients with lower respiratory tract infections. Single-cell Raman spectroscopy is a “whole biological fingerprint” technique that can be used to identify microbial samples. It has the advantages of no marking and fast and non-destructive testing. In this study, single-cell Raman spectroscopy was used to collect spectral data of six respiratory tract pathogen isolates. The T-distributed stochastic neighbor embedding (t-SNE) isolation analysis algorithm was used to compare the differences between the six respiratory tract pathogens. The eXtreme Gradient Boosting (XGBoost) algorithm was used to establish a Raman phenotype database model. The classification accuracy of the isolated samples was 93–100%, and the classification accuracy of the clinical samples was more than 80%. Combined with heavy water labeling technology, the drug resistance of respiratory tract pathogens was determined. The study showed that single-cell Raman spectroscopy–D2O (SCRS–D2O) labeling could rapidly identify the drug resistance of respiratory tract pathogens within 2 h.
Nuclear translocation of spike mRNA and protein is a novel feature of SARS-CoV-2
Authors: Sattar Sarah , Kabat Juraj , Jerome Kailey , Feldmann Friederike , Bailey Kristina , Mehedi Masfique
Published: January 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than other coronaviruses. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) “PRRARSV,” which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel feature of SARS-CoV-2.
Evaluation of anakinra in the management of patients with COVID-19 infection: A randomized clinical trial
Authors: Elmekaty Eman Zeyad I. , Maklad Aya , Abouelhassan Rawan , Munir Waqar , Ibrahim Mohamed Izham Mohamed , Nair Arun , Alibrahim Rim , Iqbal Fatima , Al Bishawi Ahmad , Abdelmajid Alaaeldin , Aboukamar Mohamed , Hadi Hamad Abdel , Khattab Mohammed Abu , Al Soub Hussam , Al Maslamani Muna
Published: January 2023

Background

The global COVID-19 pandemic led to substantial clinical and economic outcomes with catastrophic consequences. While the majority of cases has mild to moderate disease, minority of patients progress into severe disease secondary to the stimulation of the immune response. The hyperinflammatory state contributes towards progression into multi-organ failure which necessitates suppressive therapy with variable outcomes. This study aims to explore the safety and efficacy of anakinra in COVID-19 patients with severe disease leading to cytokine release syndromes.

Methods

In this open-label, multi-center, randomized clinical trial, patients with confirmed COVID-19 infection with evidence of respiratory distress and signs of cytokine release syndrome were randomized in 1:1 ratio to receive either standard of care (SOC) or anakinra (100 mg subcutaneously every 12 h for 3 days then 100 mg subcutaneously once daily for 4 days) in addition to SOC. The primary outcome was treatment success at day 14 as defined by the WHO clinical progression score of ≤3. Primary analysis was based upon intention-to-treat population, with value of p of <0.05.

Results

Out 327 patients screened for eligibility, 80 patients were recruited for the study. The mean age was 49.9 years (SD = 11.7), with male predominance at 82.5% (n = 66). The primary outcome was not statistically different (87.5% (n = 35) in anakinra group vs. 92.5% (n = 37) in SOC group, p = 0.712; OR = 1.762 (95%CI: 0.39–7.93). The majority of reported adverse events were mild in severity and not related to the study treatment. Elevated aspartate aminotransferase was the only significant adverse event which was not associated with discontinuation of therapy.

Conclusion

In patients with severe COVID-19 infection, the addition of anakinra to SOC treatment was safe but was not associated with significant improvement according to the WHO clinical progression scale. Further studies are warranted to explore patients’ subgroups characteristics that might benefit from administered therapy.

Clinical Trial Registration

Trial registration at ClinicalTrials.gov, identifier: NCT04643678.
Fiber-based food packaging materials in view of bacterial growth and survival capacities
Authors: Schmid Paul Jakob , Maitz Stephanie , Plank Nadine , Knaipp Elisabeth , Pölzl Sabine , Kittinger Clemens
Published: January 2023

Understanding interactions of bacteria with fiber-based packaging materials is fundamental for appropriate food packaging. We propose a laboratory model to evaluate microbial growth and survival in liquid media solely consisting of packaging materials with different fiber types. We evaluated food contaminating species (Escherichia coli, Staphylococcus aureus, Bacillus cereus), two packaging material isolates and bacterial endospores for their growth abilities. Growth capacities differed substantially between the samples as well as between bacterial strains. Growth and survival were strongest for the packaging material entirely made of recycled fibers (secondary food packaging) with up to 10.8 log10 CFU/ml for the packaging isolates. Among the food contaminating species, B. cereus and E. coli could grow in the sample of entirely recycled fibers with maxima of 6.1 log10 and 8.6 log10 CFU/mL, respectively. Escherichia coli was the only species that was able to grow in bleached fresh fibers up to 7.0 log10 CFU/mL. Staphylococcus aureus perished in all samples and was undetectable after 1–6 days after inoculation, depending on the sample. The packaging material strains were isolated from recycled fibers and could grow only in samples containing recycled fibers, indicating an adaption to this environment. Spores germinated only in the completely recycled sample. Additionally, microbial digestion of cellulose and xylan might not be a crucial factor for growth. This is the first study describing bacterial growth in food packaging materials itself and proposing functionalization strategies toward active food packaging through pH-lowering.
Comparative transcriptome profiling reveals the importance of GmSWEET15 in soybean susceptibility to Sclerotinia sclerotiorum
Authors: Xiao Kunqin , Qiao Kaibin , Cui Wenjing , Xu Xun , Pan Hongyu , Wang Fengting , Wang Shoudong , Yang Feng , Xuan Yuanhu , Li Anmo , Han Xiao , Song Zhuojian , Liu Jinliang
Published: January 2023

Soybean sclerotinia stem rot (SSR) is a disease caused by Sclerotinia sclerotiorum that causes incalculable losses in soybean yield each year. Considering the lack of effective resistance resources and the elusive resistance mechanisms, we are urged to develop resistance genes and explore their molecular mechanisms. Here, we found that loss of GmSWEET15 enhanced the resistance to S. sclerotiorum, and we explored the molecular mechanisms by which gmsweet15 mutant exhibit enhanced resistance to S. sclerotiorum by comparing transcriptome. At the early stage of inoculation, the wild type (WT) showed moderate defense response, whereas gmsweet15 mutant exhibited more extensive and intense transcription reprogramming. The gmsweet15 mutant enriched more biological processes, including the secretory pathway and tetrapyrrole metabolism, and it showed stronger changes in defense response, protein ubiquitination, MAPK signaling pathway-plant, plant-pathogen interaction, phenylpropanoid biosynthesis, and photosynthesis. The more intense and abundant transcriptional reprogramming of gmsweet15 mutant may explain how it effectively delayed colonization by S. sclerotiorum. In addition, we identified common and specific differentially expressed genes between WT and gmsweet15 mutant after inoculation with S. sclerotiorum, and gene sets and genes related to gmsweet15_24 h were identified through Gene Set Enrichment Analysis. Moreover, we constructed the protein–protein interaction network and gene co-expression networks and identified several groups of regulatory networks of gmsweet15 mutant in response to S. sclerotiorum, which will be helpful for the discovery of candidate functional genes. Taken together, our results elucidate molecular mechanisms of delayed colonization by S. sclerotiorum after loss of GmSWEET15 in soybean, and we propose novel resources for improving resistance to SSR.
Parameterization of a single H-bond in Orange Carotenoid Protein by atomic mutation reveals principles of evolutionary design of complex chemical photosystems
Authors: Moldenhauer Marcus , Tseng Hsueh-Wei , Kraskov Anastasia , Tavraz Neslihan N. , Yaroshevich Igor A. , Hildebrandt Peter , Sluchanko Nikolai N. , Hochberg Georg A. , Essen Lars-Oliver , Budisa Nediljko , Korf Lukas , Maksimov Eugene G. , Friedrich Thomas
Published: January 2023

Introduction: Dissecting the intricate networks of covalent and non-covalent interactions that stabilize complex protein structures is notoriously difficult and requires subtle atomic-level exchanges to precisely affect local chemical functionality. The function of the Orange Carotenoid Protein (OCP), a light-driven photoswitch involved in cyanobacterial photoprotection, depends strongly on two H-bonds between the 4-ketolated xanthophyll cofactor and two highly conserved residues in the C-terminal domain (Trp288 and Tyr201).

Method: By orthogonal translation, we replaced Trp288 in Synechocystis OCP with 3-benzothienyl-L-alanine (BTA), thereby exchanging the imino nitrogen for a sulphur atom.

Results: Although the high-resolution (1.8 Å) crystal structure of the fully photoactive OCP-W288_BTA protein showed perfect isomorphism to the native structure, the spectroscopic and kinetic properties changed distinctly. We accurately parameterized the effects of the absence of a single H-bond on the spectroscopic and thermodynamic properties of OCP photoconversion and reveal general principles underlying the design of photoreceptors by natural evolution.

Discussion: Such “molecular surgery” is superior over trial-and-error methods in hypothesis-driven research of complex chemical systems.
Cognitive status predicts preoperative instruction compliance
Authors: Mano Yasuko , Mistry Porus , Tran Khoa , Wright Benjamin , Malekyan Cristin , Gurvich Tatyana , Kaloostian Carolyn , Motamed Arash , Decker Justyne
Published: January 2023

The most common postoperative complication for older adults is perioperative neurocognitive disorder (PNCD). Its greatest risk factor is preoperative cognitive impairment. Cognitive impairment also predicts higher likelihood of postoperative complications. While the cause of disparity in outcomes is likely multifactorial, the ability to correctly follow perioperative instructions may be one modifiable component. The purpose of this study was to determine whether cognitive impairment led to reduced preoperative instruction compliance and if so, identify barriers and enact a tailored care-plan to close the gap. Our preoperative clinic implemented routine Mini-Cog screening to identify older (age ≥ 65) surgical patients at increased risk. All patients received the same instructions and, on day of surgery, were surveyed to determine correct execution of nil per os guidelines, chlorhexidine wipe use and medication management. Data was stratified by cognitive status to evaluate whether impairment predicted instruction execution. Feedback from patients and families were compiled. Of those who screened negative for impairment, 68% correctly followed instructions, while 84.2% of those impaired struggled with ≥1 instruction(s); impaired patients were more likely to incorrectly follow instructions (OR = 10.5, p-value = 0.001). Areas for change were identified and team-based solutions were enacted with additional support for those with impairment. We found a clear difference in correct execution with respect to cognitive status. By improving instructions as an institution and adding additional support for those with impairment, the compliance gap was significantly reduced. Targeting perioperative instructions and tailoring care in this population may be one modifiable component in the outcome disparity they face.
Patients with Alzheimer’s disease dementia show partially preserved parietal ‘hubs’ modeled from resting-state alpha electroencephalographic rhythms
Authors: Lopez Susanna , Del Percio Claudio , Lizio Roberta , Noce Giuseppe , Padovani Alessandro , Nobili Flavio , Arnaldi Dario , Famà Francesco , Moretti Davide V. , Cagnin Annachiara , Koch Giacomo , Benussi Alberto , Onofrj Marco , Borroni Barbara , Soricelli Andrea , Ferri Raffaele , Buttinelli Carla , Giubilei Franco , Güntekin Bahar , Yener Görsev , Stocchi Fabrizio , Vacca Laura , Bonanni Laura , Babiloni Claudio
Published: January 2023

Introduction

Graph theory models a network by its nodes (the fundamental unit by which graphs are formed) and connections. ‘Degree’ hubs reflect node centrality (the connection rate), while ‘connector’ hubs are those linked to several clusters of nodes (mainly long-range connections).

Methods

Here, we compared hubs modeled from measures of interdependencies of between-electrode resting-state eyes-closed electroencephalography (rsEEG) rhythms in normal elderly (Nold) and Alzheimer’s disease dementia (ADD) participants. At least 5 min of rsEEG was recorded and analyzed. As ADD is considered a ‘network disease’ and is typically associated with abnormal rsEEG delta (<4 Hz) and alpha rhythms (8–12 Hz) over associative posterior areas, we tested the hypothesis of abnormal posterior hubs from measures of interdependencies of rsEEG rhythms from delta to gamma bands (2–40 Hz) using eLORETA bivariate and multivariate-directional techniques in ADD participants versus Nold participants. Three different definitions of ‘connector’ hub were used.

Results

Convergent results showed that in both the Nold and ADD groups there were significant parietal ‘degree’ and ‘connector’ hubs derived from alpha rhythms. These hubs had a prominent outward ‘directionality’ in the two groups, but that ‘directionality’ was lower in ADD participants than in Nold participants.

Discussion

In conclusion, independent methodologies and hub definitions suggest that ADD patients may be characterized by low outward ‘directionality’ of partially preserved parietal ‘degree’ and ‘connector’ hubs derived from rsEEG alpha rhythms.
Neural signatures of visuo-motor integration during human-robot interactions
Authors: Marchesotti Silvia , Bernasconi Fosco , Rognini Giulio , De Lucia Marzia , Bleuler Hannes , Blanke Olaf
Published: January 2023

Visuo-motor integration shapes our daily experience and underpins the sense of feeling in control over our actions. The last decade has seen a surge in robotically and virtually mediated interactions, whereby bodily actions ultimately result in an artificial movement. But despite the growing number of applications, the neurophysiological correlates of visuo-motor processing during human-machine interactions under dynamic conditions remain scarce. Here we address this issue by employing a bimanual robotic interface able to track voluntary hands movement, rendered in real-time into the motion of two virtual hands. We experimentally manipulated the visual feedback in the virtual reality with spatial and temporal conflicts and investigated their impact on (1) visuo-motor integration and (2) the subjective experience of being the author of one's action (i.e., sense of agency). Using somatosensory evoked responses measured with electroencephalography, we investigated neural differences occurring when the integration between motor commands and visual feedback is disrupted. Our results show that the right posterior parietal cortex encodes for differences between congruent and spatially-incongruent interactions. The experimental manipulations also induced a decrease in the sense of agency over the robotically-mediated actions. These findings offer solid neurophysiological grounds that can be used in the future to monitor integration mechanisms during movements and ultimately enhance subjective experience during human-machine interactions.
Study protocol to support the development of an all-night binaural beat frequency audio program to entrain sleep
Authors: Gantt Melisa A.
Published: January 2023

Background

Given that the stages of sleep have specific brainwave patterns, it may be feasible to manipulate brainwaves to induce stages of sleep to improve better sleep quality. Binaural beat frequencies (BBFs) are an auditory-neurologic technique that uses auditory tones via headphones to manipulate brainwave activity in turn affecting the listener's state of consciousness. However, BBFs are often sold in only one frequency which may not allow the listener to transition through the phases of sleep. This study is Phase 2 of a four-phase feasibility study to assess if systematically sequencing a variety of BBFs can improve sleep efficiency.

Methods

This protocol uses a two cohort unblinded and double-blinded, randomized, pre- and post-intervention methods and crossover matched group design. In Cohort 1, a sample of 106 participants with poor sleep quality will be randomized into two groups. All participants will start with 1 week of no intervention. Group 1 will use theta/delta BBF for 2 weeks followed by 1 week of no intervention followed by music for 2 weeks. Group 2 will do the reverse. In Cohort 2, 62 participants will be blinded and randomized into two groups. Group 3 will use music for 2 weeks followed by a 1-week break followed by music embedded with theta/delta BBF for 2 weeks. Group 4 will do the reverse. Using Cohort 1 music only as a control, data will be collected using sleep actigraphy, sleep quality questionnaires, and sleep diaries with a crossover and match group analysis between cohorts to compare the effect of no intervention vs. music vs. BBF only vs. music with BBF on sleep quality.

Discussion

Phase 1 concluded that theta BBF was able to decrease stress to help induce sleep. Phase 2 will assess if theta and delta BBFs, with breaks to allow for REM, will be able to sustain sleep to improve sleep efficiency. The data from Phase 1 and 2 will provide information to help construct an all-night audio program with the appropriate BBF and timing to trigger the correct sleep stage for better sleep efficiency. If this concept is feasible, it could be beneficial for many sleep disorders.
Efficacy and safety of whole-body vibration therapy for post-stroke spasticity: A systematic review and meta-analysis
Authors: Zhang Qi , Zheng Shuqi , Li Shuiyan , Zeng Yuting , Chen Ling , Li Gege , Li Shilin , He Longlong , Chen Shuping , Zheng Xiaoyan , Zou Jihua , Zeng Qing
Published: January 2023

Background

One of the main objectives of stroke rehabilitation is to alleviate post-stroke spasticity. Over the recent years, many studies have explored the potential benefits of whole-body vibration (WBV) treatment for post-stroke spasticity, but it is still controversial.

Objective

The current study aims to assess the efficacy and safety of WBV for post-stroke spasticity and determine the appropriate application situation.

Methods

From their establishment until August 2022, the following databases were searched: PubMed, Web of Science, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Medline, China National Knowledge Infrastructure (CNKI), and Wanfang. Only randomized controlled trials (RCTs) that were published in either English or Chinese were taken into consideration. We independently filtered the research, gathered the data from the studies, and evaluated the research quality (Cochrane RoB tool) and the overall evidence quality (GRADE). Rev Man 5.4 software was utilized to conduct statistical analysis.

Results

In this analysis, 11 RCTs with 475 patients that reported on the effectiveness of WBV therapy for post-stroke spasticity were taken into account. Compared to the control groups, the results revealed that WBV combined with conventional rehabilitation at a vibration frequency lower than 20 Hz (SMD = −0.58, 95% CI: −0.98 to −0.19,P= 0.004) was more effective in relieving upper (SMD = −0.53, 95% CI: −1.04 to 0.03,P= 0.03) and lower limb spasticity (SMD = −0.21, 95% CI: −0.40 to −0.01,P= 0.04); similarly, it was superior for patients aged under 60 years (SMD = −0.41, 95% CI: −0.66 to −0.17,P= 0.0008) with acute and subacute stroke (SMD = −0.39, 95% CI: −0.68 to −0.09,P= 0.01). The valid vibration for reducing spasticity was found to last for 10 min (SMD = −0.41, 95% CI: −0.75 to −0.07,P= 0.02). None of the included studies revealed any serious adverse impact.

Conclusion

Moderate-quality evidence demonstrated when WBV was used as an adjuvant, vibration <20 Hz for 10 min was effective and secure in treating upper and lower limb spasticity in patients with acute and subacute stroke under the age of 60 years.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022293951.