bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospective Association between Multimorbidity and Falls and Its Mediators: Findings from the Irish Longitudinal Study on Ageing
Authors: Jacob Louis , Shin Jae Il , Kostev Karel , Haro Josep Maria , López-Sánchez Guillermo F. , Smith Lee , Koyanagi Ai
Published: August 2022

This study including older adults from Ireland aimed to analyze the prospective association between multimorbidity and falls and to identify the mediators in this relationship. The present study used data from two consecutive waves of the Irish Longitudinal Study on Ageing (TILDA) survey. Multimorbidity was assessed at Wave 1 (2009–2011) and was defined as the presence of at least two chronic conditions. Falls occurring at Wave 2 (2012–2013) were self-reported. Mediating variables considered were polypharmacy, cognitive impairment, sleep problems, pain, low handgrip strength, difficulty in activities of daily living (ADL), obesity, and underweight. Multivariable binary logistic regression and mediation analysis using the Karlson Holm Breen method were conducted. This study included 6900 adults aged ≥50 years (51.6% women; mean [SD] age 63.1 [8.9] years). Compared to no chronic conditions at baseline, there was a positive and significant association between multimorbidity and falls at follow-up, with ORs ranging from 1.32 (95% CI = 1.06–1.64) for 2 conditions to 1.92 (95% CI = 1.54–2.38) for ≥4 conditions. Pain (23.5%), polypharmacy (13.3%), and difficulty in ADL (10.7%) explained the largest proportion of the multimorbidity-fall relationship. Multimorbidity increased risk for incident falls in older adults from Ireland. Interventions should be implemented to reduce fall risk in people with multimorbidity, especially targeting the identified mediators.
The Pathological Culprit of Neuropathic Skin Pain in Long COVID-19 Patients: A Case Series
Authors: Grieco Teresa , Gomes Vito , Rossi Alfredo , Cantisani Carmen , Greco Maria Elisabetta , Rossi Giovanni , Sernicola Alvise , Pellacani Giovanni
Published: August 2022

Cutaneous neurosensory symptoms have become increasingly reported findings in COVID-19; however, these virus-related manifestations are largely overlooked, and their pathology is poorly understood. Moreover, alterations of skin sensibility currently recognize no clear histopathology substrate. The purpose of this study was to provide pathology evidence of neurosensory skin system involvement in COVID-19 patients complaining of subjective neurological symptoms affecting the skin. Out of 142 patients, six long COVID-19 cases complaining of cutaneous subjective neurological symptoms assessed on an NTSS-6 questionnaire underwent histopathological and immunohistochemical analyses of skin areas affected by paroxysmal diffuse burning and itching sensations. Two patients also performed electroneurography examination. The histology investigation showed hypertrophic glomus vascular bodies with hypertrophic S100+ perineural sheath cells and adjacent hypertrophy of the nerve branches associated with increased basophil polysaccharide matrix. Electroneurography revealed disturbances of A-delta and C dermal neuronal fibers. The main limitation of this study consisted of a limited number of skin biopsy samples, requiring further investigation. Histopathology findings are consistent with hypertrophy of nerve endings, suggesting a condition such as “dermal hyperneury”, a recently reported small nerve hypertrophy condition affecting sensory C fibers. Such a neuropathic basis could explain dysesthesia experienced by the patients, as previously described in postherpetic neuralgia.
Impact of SARS-CoV-2 Pandemic on the Management of Patients with Hepatocellular Carcinoma
Authors: Guarino Maria , Cossiga Valentina , Capasso Mario , Mazzarelli Chiara , Pelizzaro Filippo , Sacco Rodolfo , Russo Francesco Paolo , Vitale Alessandro , Trevisani Franco , Cabibbo Giuseppe ,   on behalf of the Associazione Italiana per lo Studio del Fegato (AISF) HCC Special Interest Group
Published: August 2022

Worldwide, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) significantly increases mortality and morbidity. The Coronavirus Disease 2019 (COVID-19) outbreak has had a considerable impact on healthcare systems all around the world, having a significant effect on planned patient activity and established care pathways, in order to meet the difficult task of the global pandemic. Patients with hepatocellular carcinoma (HCC) are considered a particularly susceptible population and conceivably at increased risk for severe COVID-19 because of two combined risk factors: chronic advanced liver disease and HCC itself. In these challenging times, it is mandatory to reshape clinical practice in a prompt way to preserve the highest standards of patient care and safety. However, due to the stay-at-home measures instituted to stop the spread of COVID-19, HCC surveillance has incurred a dramatic drop, and care for HCC patients has been rearranged by refining the algorithm for HCC treatment to the COVID-19 pandemic, permitting these patients to be safely managed by identifying those most at risk of neoplastic disease progression.
Hydrothermal Synthesis and In Vivo Fluorescent Bioimaging Application of Eu3+/Gd3+ Co-Doped Fluoroapatite Nanocrystals
Authors: Gedara Sriyani Menike Korale , Ding Zi-You , Balasooriya Iresha Lakmali , Han Yingchao , Wickramaratne Merita Nirmali
Published: August 2022

In this study, Eu3+/Gd3+ co-doped fluoroapatitååe (Eu/Gd:FAP) nanocrystals were synthesized by the hydrothermal method as a fluorescent bioimaging agent. The phase composition, morphology, fluorescence, and biosafety of the resulting samples were characterized. Moreover, the in vivo fluorescent bioimaging application of Eu/Gd:FAP nanocrystals was evaluated in mice with subcutaneously transplanted tumors. The results showed that the Eu/Gd:FAP nanocrystals were short rod-like particles with a size of 59.27 ± 13.34 nm × 18.69 ± 3.32 nm. With an increasing F substitution content, the Eu/Gd:FAP nanocrystals displayed a decreased size and enhanced fluorescence emission. Eu/Gd:FAP nanocrystals did not show hemolysis and cytotoxicity, indicating good biocompatibility. In vivo fluorescent bioimaging study demonstrated that Eu/Gd:FAP nanocrystals could be used as a bioimaging agent and displayed stable fluorescence emitting in tumors, indicating an accumulation in tumor tissue due to the passive targeting ability. In addition, any adverse effects of Eu/Gd:FAP nanocrystals on major organs were not observed. This study shows that biocompatible rare earth co-doped FAP nanocrystals have the potential to be used as a bioimaging agent in vivo.
When We Study the Ability to Attend, What Exactly Are We Trying to Understand?
Authors: Tsotsos John
Published: August 2022

When we study the human ability to attend, what exactly do we seek to understand? It is not clear what the answer might be to this question. There is still so much to know, while acknowledging the tremendous progress of past decades of research. It is as if each new study adds a tile to the mosaic that, when viewed from a distance, we hope will reveal the big picture of attention. However, there is no map as to how each tile might be placed nor any guide as to what the overall picture might be. It is like digging up bits of mosaic tile at an ancient archeological site with no key as to where to look and then not only having to decide which picture it belongs to but also where exactly in that puzzle it should be placed. I argue that, although the unearthing of puzzle pieces is very important, so is their placement, but this seems much less emphasized. We have mostly unearthed a treasure trove of puzzle pieces but they are all waiting for cleaning and reassembly. It is an activity that is scientifically far riskier, but with great risk comes a greater reward. Here, I will look into two areas of broad agreement, specifically regarding visual attention, and dig deeper into their more nuanced meanings, in the hope of sketching a starting point for the guide to the attention mosaic. The goal is to situate visual attention as a purely computational problem and not as a data explanation task; it may become easier to place the puzzle pieces once you understand why they exist in the first place.
HEROHE Challenge: Predicting HER2 Status in Breast Cancer from Hematoxylin–Eosin Whole-Slide Imaging
Authors: Conde-Sousa Eduardo , Vale João , Feng Ming , Xu Kele , Wang Yin , Della Mea Vincenzo , La Barbera David , Montahaei Ehsan , Baghshah Mahdieh , Turzynski Andreas , Gildenblat Jacob , Klaiman Eldad , Hong Yiyu , Aresta Guilherme , Araújo Teresa , Aguiar Paulo , Eloy Catarina , Polónia Antonio
Published: August 2022

Breast cancer is the most common malignancy in women worldwide, and is responsible for more than half a million deaths each year. The appropriate therapy depends on the evaluation of the expression of various biomarkers, such as the human epidermal growth factor receptor 2 (HER2) transmembrane protein, through specialized techniques, such as immunohistochemistry or in situ hybridization. In this work, we present the HER2 on hematoxylin and eosin (HEROHE) challenge, a parallel event of the 16th European Congress on Digital Pathology, which aimed to predict the HER2 status in breast cancer based only on hematoxylin–eosin-stained tissue samples, thus avoiding specialized techniques. The challenge consisted of a large, annotated, whole-slide images dataset (509), specifically collected for the challenge. Models for predicting HER2 status were presented by 21 teams worldwide. The best-performing models are presented by detailing the network architectures and key parameters. Methods are compared and approaches, core methodologies, and software choices contrasted. Different evaluation metrics are discussed, as well as the performance of the presented models for each of these metrics. Potential differences in ranking that would result from different choices of evaluation metrics highlight the need for careful consideration at the time of their selection, as the results show that some metrics may misrepresent the true potential of a model to solve the problem for which it was developed. The HEROHE dataset remains publicly available to promote advances in the field of computational pathology.
Discrete Element Simulation of the Macro-Meso Mechanical Behaviors of Gas-Hydrate-Bearing Sediments under Dynamic Loading
Authors: Jiang Yujing , Li Meng , Luan Hengjie , Shi Yichen , Zhang Sunhao , Yan Peng , Li Baocheng
Published: August 2022

Under the action of dynamic loadings such as earthquakes and volcanic activities, the mechanical properties of gas-hydrate-bearing sediments will deteriorate, leading to a decrease in the stability of hydrate reservoirs and even inducing geological disasters such as submarine landslides. In order to study the effect of dynamic loading on the mechanical properties of hydrate sediments, triaxial compression tests of numerical specimens were carried out by using particle flow code (PFC2D), and the macro-meso mechanical behaviors of specimens were investigated. The results show that the loading frequency has a small effect on the stiffness of the hydrate sediment, while it has a large effect on the peak strength. The peak strength increases and then decreases with the increase in loading frequency. Under the same loading frequency, the peak strength of the hydrate sediment increases with the increase in loading amplitude, and the stiffness of the specimen decreases with the increase in loading amplitude. The maximum shear expansion of the specimen changes with the movement of the phase change point and the rearrangement of the particles. The maximum shear expansion of the specimen changes with the movement of the phase change point and the change of the bearing capacity of the particles after the rearrangement, and the more forward the phase change point is, the stronger the bearing capacity of the specimen in the plastic stage. The shear dilatancy angle and the shear dilatancy amount both increase linearly with the increase in loading amplitude. The influence of loading frequency and amplitude on the contact force chain, displacement, crack expansion, and the number of cementation damage inside the sediment is mainly related to the average axial stress to which the specimen is subjected, and the number of cracks and cementation damage of the sediment specimen increases with the increase in the average axial stress to which the sediment specimen is subjected. As the rate of cementation damage increases, the distribution of shear zones becomes more obvious.
A Real-Time Ship Detector via a Common Camera
Authors: Zhao Penghui , Yu Xiaoyuan , Chen Zongren , Liang Yangyan
Published: August 2022

Advanced radars and satellites, suitable for remote monitoring, inappropriately reach the economical requirements of short-range detection. Compared with far-sightedness skills, common visible-light sensors offer more ample features conducive to distinguishing the classes. Therefore, ship detection based on visible-light cameras should cooperate with remote detection technologies. However, compared with detectors applied in inland transportation, the lack of fast ship detectors, detecting multiple ship classes, is non-negligible. To fill this gap, we propose a real-time ship detector based on fast U-Net and remapping attention (FRSD) via a common camera. The fast U-Net offered compresses features in the channel dimension to decrease the number of training parameters. The remapping attention introduced boosts the performance in various rain–fog weather conditions while maintaining the real-time speed. The ship dataset proposed contains more than 20,000 samples, alleviating the lack of ship datasets containing various classes. Data augmentation of the cross-background is especially proposed to further promote the diversity of the detecting background. In addition, the rain–fog dataset proposed, containing more than 500 rain–fog images, simulates various marine rain–fog scenarios and soaks the testing image to validate the robustness of ship detectors. Experiments demonstrate that FRSD performs relatively robustly and detects 9 classes with an mAP of more than 83%, reaching a state-of-the-art level.
Gulf of Naples Advanced Model (GNAM): A Multiannual Comparison with Coastal HF Radar Data and Hydrological Measurements in a Coastal Tyrrhenian Basin
Authors: Kokoszka Florian , Saviano Simona , Botte Vincenzo , Iudicone Daniele , Zambianchi Enrico , Cianelli Daniela
Published: August 2022

High-resolution modelling systems have increasingly become an essential requirement to investigate ocean dynamics over a wide range of spatial and temporal scales, and to integrate the punctual ocean observations. When applied in coastal areas, they also have the potential to provide a detailed representation of transport and exchange processes at the sub-basin scale. This paper presents a validation exercise between the surface fields generated by the regional ocean modeling system (ROMS), developed for the Tyrrhenian Sea and downscaled for the Gulf of Naples (GNAM Gulf of Naples advanced model), and a 4 year-long (2009–2012) record of high-frequency radar (HFR) data. The comparison between hourly and seasonal model results and HFR surface fields is focused on the Gulf of Naples (GoN), where an observational network of three HFR sites has been operational since 2004, and on a specific subdomain characterized by the presence of the Sarno river, a long-term ecological research station (LTER-MC) and one important canyon area. An evaluation on a transect delimiting inshore–offshore zones in the GoN is also presented. The GNAM model was also compared with in situ hydrological parameters of temperatures and salinities retrieved at the LTER-MC fixed monitoring station. According to the skill metrics, basic circulation features are accurately reproduced by the circulation model, despite some model drawbacks in terms of increment of energy content in the surface current field occurring during specific seasonal events. The results allow us to identify potential model errors and to suggest useful improvements, the outcome also confirms the unique capability of HF radar systems to provide fine-scale measurements for the validation of numerical models and to counterbalance the lack of high-resolution measurements in coastal areas.
Experimental Investigation on the Vertical Structure Characteristics of Internal Solitary Waves
Authors: Peng Pai , Du Hui , Wei Gang , Wang Shaodong , Xuan Pu , Cai Shuqun , Xie Jieshuo
Published: August 2022

An experimental investigation of the vertical structure characteristics of internal solitary waves (ISWs) was systematically carried out in a large gravitationally stratified fluid flume. Four different stratifications were established, and basic elements of ISWs were measured by a conductivity probe array. The vertical distributions of the amplitude, characteristic frequency and waveform of two types of ISWs under different stratifications were obtained, and the experimental results were compared with the theoretical model. The study shows that most vertical structures of the amplitude under different stratifications agree with those of the theoretical model, while there are some deviations for ISWs with large amplitudes. Neither the two-layer model nor the continuously stratified model can effectively describe the variation in the characteristic frequency at different depths with amplitude. For a single small-amplitude ISW, the characteristic frequency first increases and then decreases with increasing depth. The characteristic frequency is largest at the depth of the maximum buoyancy frequency. For an ISW with a relatively large amplitude, there is likely to be a local minimum of the characteristic frequency near the depth where the maximum buoyancy frequency lies. In different stratifications, the sech2 function of KdV theory can describe the waveforms of ISWs at different depths well.
Collision Avoidance Decision Method for Unmanned Surface Vehicle Based on an Improved Velocity Obstacle Algorithm
Authors: Li Yun , Zhang Haiyu
Published: August 2022

To ensure navigation safety, unmanned surface vehicles (USVs) need to have autonomous collision avoidance capability. A large number of studies on ship collision avoidance are available, and most of these papers assume that the target ships keep straight or follows the International Regulations for Preventing Collisions at Sea (COLREGS). However, in the actual navigation process, the target ship may temporarily turn. Based on the above reasons, this paper proposes a multi-ship collision avoidance decision method for USVs based on the improved velocity obstacle algorithm. In the basic dynamic ship domain model, a collision risk model is constructed to improve the accuracy of the risk assessment between the USV and target ships. The velocity obstacle algorithm is combined with the dynamic ship domain, and the collision avoidance timing and method are judged according to the collision risk. The simulation results show that the decision method can handle the situation that the target ship temporarily turns and has an emergency collision avoidance capability. Compared with the traditional VO algorithm, the collision avoidance time of the method is shorter, and the number of course changes is less.
The Port System in Addressing Sustainability Issues—A Systematic Review of Research
Authors: Balić Katarina , Žgaljić Dražen , Ukić Boljat Helena , Slišković Merica
Published: August 2022

The aim of this paper is to analyse the main scientific contributions in the field of sustainable seaports, with a particular focus on passenger seaports and passenger seaports’ commitment to sustainability. The focus of this analysis is on the methods used to improve and develop a sustainable seaport. A search of the Web of Science Core Collection that addresses this topic consists of scientific articles published from 2012 to 2022. The articles are divided into seven groups by research area (technical/technological, legal, organisational, economic, social, environmental, and other) and five groups by applied methodology (literature review, theoretical approach, qualitative approach/methods, quantitative approach/methods, and other). The results show that most of the papers were published in the field of the environmental impacts of a sustainable seaport and a sustainable passenger seaport. In addition, most papers used quantitative approach/methods.
Research on an Extensible Monitoring System of a Seafloor Observatory Network in Laizhou Bay
Authors: Chen Jie , Liu Hailin , Lv Bin , Liu Chao , Zhang Xiaonan , Li Hui , Cao Lin , Wan Junhe
Published: August 2022

An extensible remote monitoring system for a seafloor observatory network in Laizhou Bay was established to realize long-term, continuous and on-line monitoring for a marine ranching environment. This paper deals with data communication, device management and data quality control. A control model is introduced that is structured into four layers, enabling bidirectional information flow. Based on the control model, the standardized communication protocol and device object model-oriented dynamic management method are designed as plug-and-play, for data processing and control of a large number of devices. An improved data quality control method is proposed to reduce the data error rate. The monitoring system was developed based on socket network programming, MySQL database technologies and modular ideas. The seafloor observatory network was successfully deployed in Laizhou Bay marine ranching. The experimental results demonstrate that the monitoring system obtains better performance. The proposed algorithms can also be used in many other similar systems with adaptive requirements.
Material Source of Sediments from West Clarion–Clipperton Zone (Pacific): Evidence from Rare Earth Element Geochemistry and Clay Minerals Compositions
Authors: Qiu Zhongrong , Tao Chunhui , Ma Weilin , Dias Ágata Alveirinho , Hu Siyi , Shao Yuexiao , Yang Kehong , Zhang Weiyan
Published: August 2022

The geochemistry and mineralogy of sediments provide relevant information for the understanding of the origin and metallogenic mechanism of ferromanganese nodules and crusts. At present, there are still few studies on the sediment origin of the Clarion–Clipperton Zone (CCZ) of the east Pacific, particularly on the systematic origin of sediments with a longer history/length. Here, bulk sediment geochemistry and clay mineral compositions were analyzed on a 5.7 m gravity core (GC04) obtained at the CCZ, an area rich in polymetallic nodules. The results indicate that the average total content of rare earth elements (REE), including yttrium (REY), in sediments is 454.7 ppm and the REEs distribution patterns normalized by the North American Shale Composite of samples are highly consistent, with all showing negative Ce anomalies and more obvious enrichment in heavy REE (HREE) than that of light REE (LREE). Montmorillonite/illite ratio, discriminant functions and smear slide identification indicate multiple origins for the material, and are strongly influenced by contributions from marine biomass, while terrestrial materials, seamount basalts and their alteration products and authigenic source also make certain contributions. The REY characteristics of the sediments in the study area are different from those of marginal oceanic and back-arc basins, and more similar to pelagic deep-sea sediments. Based on LREE/HREE-1/δCe and LREE/HREE-Y/Ho diagrams, we conclude that samples from the study area had pelagic sedimentary properties which suffered from a strong “seawater effect”.
Characterization of Fine-Scale Turbulence Generated in a Laboratory Orbital Shaker and Its Influence on Skeletonema costatum
Authors: Yu Lin , Li Yifan , Yao Zhongzhi , You Long , Jiang Zong-Pei , Fan Wei , Pan Yiwen
Published: August 2022

Turbulence is one of the ubiquitous aspects of aquatic systems and affects many physical and biological processes. Based on direct velocity measurements and a computational fluid dynamics (CFD) simulation, we characterized the distribution of the turbulent kinetic dissipations rates (ε) in an orbital shaker system within a range of rotation frequencies. CFD was able to estimate the ε distribution in containers accurately, which was confirmed by other two methods and was independent of velocity measurement. The results showed that ε was linearly correlated with the rotational frequencies. Despite the existence of gradients of ε and the fact that a mean circular horizontal flow was formed within the tank, the energy levels of the whole tank varied spatially within an order of magnitude and the ε distributions at different rotational frequencies were similar, suggesting that the ε distribution in the whole tank could be seen as quasi-homogeneous. To investigate the influence of turbulence on algae growth, culture experiments of a typical diatom—Skeletonema costatum were carried out under different turbulence conditions. Our results suggested turbulence mixing promoted nutrient uptake and growth of Skeletonema costatum, which could be attributed to the break of the diffusion-limited resource concentration boundary layer surrounding phytoplankton.
Experimental and Numerical Resistance Analysis for a Cruise Ship W/O Fin Stabilizers
Authors: Yao Rulin , Yu Long , Fan Qidong , Wang Xuefeng
Published: August 2022

Applying fin stabilizers is an effective solution for ship rolls on waves in a seaway. They generally consist of one or two pairs of retractable fins that are symmetrically mounted to both sides of the ship, effectively reducing the roll motion at low or moderate speeds. Fin stabilizers are commonly used by cruise ships for the comfort and safety of passengers. However, there is still little experimental and numerical analysis of the fins’ effect on hydrodynamic performance. In this study, the resistance performance of a cruise ship was investigated with/without fin stabilizers at different fin angles and ship velocities by model tests and numerical analysis. The CFD analysis provides a flow-detailed interpretation of the physical phenomenon, especially at an asymmetric maximum fin angle. The significant fin-induced resistance is newly discovered and averages up to 19% in calm water conditions, while the added resistance in waves is evaluated with a smaller increment up to 1.31%. By comparing the numerical and experimental results, this study provides insight into the resistance induced by overhanging fins, which provides an accurate prediction reference for cruise ship performance and benefits the fin stabilizers’ design and selection.
Effects of Tsunami Shelters in Pandeglang, Banten, Indonesia, Based on Agent-Based Modelling: A Case Study of the 2018 Anak Krakatoa Volcanic Tsunami
Authors: Lee Han Soo , Sambuaga Ricard Diago , Flores Constanza
Published: August 2022

On 22 December 2018, the volcanic eruption of Anak Krakatoa in the Sunda Strait, Indonesia, triggered a tsunami causing 437 deaths. The highest death toll and the second highest number of damaged houses were recorded in Panimbang. This study proposes optimum evacuation shelters to reduce the mortality rate. A digital elevation model (DEM) and information dataset are used. The suggested horizontal evacuation shelters (HESs) are places of worship, schools, and government offices. Multimodal agent-based modelling (ABM), to analyse the sensitivity of parameters and the effect of vertical evacuation shelters (VESs) under multiple scenarios, is presented for the volcanic tsunami in December 2018. A tsunami hazard map is created by combining relative weights and parameter scores for topography, slope, and the distance from the shoreline and rivers. In the ABM results, the transportation mode choice depicts a significant decrease in the number of casualties. The mortality rate is sensitive to the milling time caused by delay time τ and agent decision-making time σ. VESs are proposed at the hot spots based on the location of deaths in the sensitivity tests and the high and very-high risk zones in the hazard map. As a result, combinations of VESs and HESs show a decrement in the number of deaths by 1.2–2 times compared to those with HESs only. The proposed VESs in the study area have a significant positive impact on decreasing the mortality rate.
Analysis of Influencing Factors of SST in Tropical West Indian Ocean Based on COBE Satellite Data
Authors: Tang Chaoli , Hao Dewei , Wei Yuanyuan , Zhao Fengmei , Lin Han , Wu Xin
Published: August 2022

The time-frequency domain analysis of the sea surface temperature (SST) in the tropical western Indian Ocean was conducted using wavelet analysis, cross wavelet transform (XWT), the Mann–Kendall (MK) test, and other methods based on COBE-SST data for the last 50 years (1974–2020). From the perspective of time-frequency combination, examining the data of precipitation, sea surface heat flux, total cloud cover, and long-wave radiation, helped contribute to exploring the periodic changes of SST. Moreover, the Western Hemisphere Warm Pool (WHWP) was selected to analyze the role of SST from 1974 to 2020. Present results have demonstrated that the SST in the western Indian Ocean was in a stage of rising, particularly in 1998. According to the fast Fourier transform of the filtered SST time series, the tropical western Indian Ocean SST has a short period of 3–6 years, a medium period of about 10 years, and a long period of 40 years. The SST in the tropical western Indian Ocean has a resonance period of 2–6 years with precipitation, a resonance period of 2–6 years with sea surface heat flux, a resonance period of 4–5 years with total cloud cover, and a resonance period of 2–5 years with long-wave radiation. Importantly, SST was negatively associated with precipitation, total cloud cover, and long-wave radiation, and positively for sea surface heat flux before 1997. Seasonal migration activities are significantly correlated with the WHWP and the tropical western Indian Ocean SST. The spatial lattice point correlation coefficient is generally from 0.6 to 0.9, and the inter-annual serial correlation value is more than 0.89. Furthermore, the two exist with a resonance period of 2–5 years.
Diversity of Root-Associated Fungi of the Terrestrial Orchids Gavilea lutea and Chloraea collicensis in a Temperate Forest Soil of South-Central Chile
Authors: Herrera Héctor , Sanhueza Tedy , da Silva Valadares Rafael Borges , Matus Francisco , Pereira Guillermo , Atala Cristian , Mora María de la Luz , Arriagada Cesar
Published: August 2022

The diversity of orchid mycorrhizal fungi (OMF) and other beneficial root-associated fungi in temperate forests has scarcely been examined. This study aimed to analyze the diversity of mycorrhizal and rhizosphere-associated fungal communities in the terrestrial orchids Gavilea lutea and Chloraea collicensis growing in high-orchid-population-density areas in the piedmont of the Andes Cordillera with native forest (Nothofagus-Araucaria) and Coastal Cordillera with an exotic plantation (Pinus-Eucalyptus) in south-central Chile. We focused on rhizosphere-inhabiting and peloton-associated OMF in a native forest (Andes Cordillera) and a mixed forest (Coastal Cordillera). The native terrestrial orchids G. lutea and C. collicensis were localized, mycorrhizal root segments were taken to isolate peloton-associated OMF, and rhizosphere soil was taken to perform the metabarcoding approach. The results revealed that Basidiomycota and Ascomycota were the main rhizosphere-inhabiting fungal phyla, showing significant differences in the composition of fungal communities in both sites. Sebacina was the most-abundant OMF genera in the rhizosphere of G. lutea growing in the native forest soil. In contrast, Thanatephorus was the most abundant mycorrhizal taxa growing in the rhizosphere of orchids from the Coastal Cordillera. Besides, other OMF genera such as Inocybe, Tomentella, and Mycena were detected. The diversity of OMF in pelotons differed, being mainly related to Ceratobasidium sp. and Tulasnella sp. These results provide evidence of differences in OMF from pelotons and the rhizosphere soil in G. lutea growing in the Andes Cordillera and a selection of microbial communities in the rhizosphere of C. collicensis in the Coastal Cordillera. This raises questions about the efficiency of propagation strategies based only on mycorrhizal fungi obtained by culture-dependent methods, especially in orchids that depend on non-culturable taxa for seed germination and plantlet development.
Citrate Regulates the Saccharomyces cerevisiae Mitochondrial GDP/GTP Carrier (Ggc1p) by Triggering Unidirectional Transport of GTP
Authors: Seccia Roberta , De Santis Silvia , Di Noia Maria A. , Palmieri Ferdinando , Miniero Daniela V. , Marmo Raffaele , Paradies Eleonora , Santoro Antonella , Pierri Ciro L. , Palmieri Luigi , Marobbio Carlo M. T. , Vozza Angelo
Published: August 2022

The yeast mitochondrial transport of GTP and GDP is mediated by Ggc1p, a member of the mitochondrial carrier family. The physiological role of Ggc1p in S. cerevisiae is probably to transport GTP into mitochondria in exchange for GDP generated in the matrix. ggc1Δ cells exhibit lower levels of GTP and increased levels of GDP in mitochondria, are unable to grow on nonfermentable substrates and lose mtDNA. Because in yeast, succinyl-CoA ligase produces ATP instead of GTP, and the mitochondrial nucleoside diphosphate kinase is localized in the intermembrane space, Ggc1p is the only supplier of mitochondrial GTP required for the maturation of proteins containing Fe-S clusters, such as aconitase [4Fe-4S] and ferredoxin [2Fe-2S]. In this work, it was demonstrated that citrate is a regulator of purified and reconstituted Ggc1p by trans-activating unidirectional transport of GTP across the proteoliposomal membrane. It was also shown that the binding site of Ggc1p for citrate is different from the binding site for the substrate GTP. It is proposed that the citrate-induced GTP uniport (CIGU) mediated by Ggc1p is involved in the homeostasis of the guanine nucleotide pool in the mitochondrial matrix.
Special Issue: Alternaria alternata: Should We Still Consider This Fungus as a Minor Brother in the Etiology of Respiratory Allergy?
Authors: Quesada Jorge Martínez
Published: August 2022

Allergic diseases represent a major global health problem [...]
Periprosthetic Joint Infections Caused by Candida Species—A Single-Center Experience and Systematic Review of the Literature
Authors: Grzelecki Dariusz , Grajek Aleksandra , Dudek Piotr , Olewnik Łukasz , Zielinska Nicol , Fulin Petr , Czubak-Wrzosek Maria , Tyrakowski Marcin , Marczak Dariusz , Kowalczewski Jacek
Published: August 2022

Background: The aim of this study was to analyze the treatment results of fungal periprosthetic joint infections (PJI) caused by Candida species from a single orthopedic center and to compare them with reports from other institutions. Methods: Eight patients operated on from January 2014 to December 2021 met the inclusion criteria and were analyzed in terms of clinical outcomes. A systematic review of the literature identified 153 patients with Candida PJIs extracted from 12 studies according to the PRISMA (Preferred Reporting Item for Systematic Reviews and Meta-Analyses) guidelines. Results: The success rate of the treatment in the case series was 50%. The most frequent pathogens were Candida albicans (three cases; 37.5%) and Candida parapsilosis (three cases; 37.5%). In one patient (12.5%), bacterial co-infection was noted, and in five patients (62.5%) significant risk factors of PJI were confirmed. The overall success rate on the basis of data collected for systematic review was 65.5%. A sub-analysis of 127 patients revealed statistically significant differences (p = 0.02) with a higher success rate for the knees (77.6%) than for the hips (58%). In 10 studies the analysis of risk factors was performed and among 106 patients in 77 (72.6%) comorbidities predispose to fungal PJI were confirmed. Bacterial co-infection was noted in 84 patients (54.9%). In 93 patients (60.7%) Candida albicans was the culprit pathogen, and in 39 patients (25.5%) Candida parapsilosis was the culprit pathogen. Based on these two most frequent Candida species causing PJI, the success rate of the treatment was statistically different (p = 0.03), and was 60.3% and 83.3%, respectively. The two-stage strategy was more favorable for patients with Candida parapsilosis infections (94.4% success rate) than the one-stage protocol (50% success rate; p = 0.02); as well as in comparison to the two-stage treatment of Candida albicans (65% success rate; p = 0.04). Conclusions: The analysis of the literature showed no differences in the overall success rate between one- and two-stage surgical strategies for all Candida species, but differed significantly comparing the two most frequent strains and concerning PJI localization. The frequent presence of bacterial co-infections makes it necessary to consider the additional administration of antibiotics in the case of fungal PJI.
Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont
Authors: Babb-Biernacki Spenser J. , Esselstyn Jacob A. , Doyle Vinson P.
Published: August 2022

Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.
Multi-Gene Phylogenetic Approach for Identification and Diversity Analysis of Bipolaris maydis and Curvularia lunata Isolates Causing Foliar Blight of Zea mays
Authors: Manzar Nazia , Kashyap Abhijeet Shankar , Maurya Avantika , Rajawat Mahendra Vikram Singh , Sharma Pawan Kumar , Srivastava Alok Kumar , Roy Manish , Saxena Anil Kumar , Singh Harsh Vardhan
Published: August 2022

Bipolaris species are known to be important plant pathogens that commonly cause leaf spot, root rot, and seedling blight in a wide range of hosts worldwide. In 2017, complex symptomatic cases of maydis leaf blight (caused by Bipolaris maydis) and maize leaf spot (caused by Curvularia lunata) have become increasingly significant in the main maize-growing regions of India. A total of 186 samples of maydis leaf blight and 129 maize leaf spot samples were collected, in 2017, from 20 sampling sites in the main maize-growing regions of India to explore the diversity and identity of this pathogenic causal agent. A total of 77 Bipolaris maydis isolates and 74 Curvularia lunata isolates were screened based on morphological and molecular characterization and phylogenetic analysis based on ribosomal markers—nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) region, 28S nuclear ribosomal large subunit rRNA gene (LSU), D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA), and protein-coding gene-glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Due to a dearth of molecular data from ex-type cultures, the use of few gene regions for species resolution, and overlapping morphological features, species recognition in Bipolaris has proven difficult. The present study used the multi-gene phylogenetic approach for proper identification and diversity of geographically distributed B. maydis and C. lunata isolates in Indian settings and provides useful insight into and explanation of its quantitative findings.
Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32
Authors: Hilário Sandra , Gonçalves Micael F. M. , Fidalgo Cátia , Tacão Marta , Alves Artur
Published: August 2022

The genus Diaporthe includes pathogenic species distributed worldwide and affecting a wide variety of hosts. Diaporthe amygdali and Diaporthe eres have been found to cause cankers, dieback, or twig blights on economically important crops such as soybean, almond, grapevine, and blueberry. Despite their importance as plant pathogens, the strategies of species of Diaporthe to infect host plants are poorly explored. To provide a genomic basis of pathogenicity, the genomes of D. amygdali CAA958 and D. eres CBS 160.32 were sequenced and analyzed. Cellular transporters involved in the transport of toxins, ions, sugars, effectors, and genes implicated in pathogenicity were detected in both genomes. Hydrolases and oxidoreductases were the most prevalent carbohydrate-active enzymes (CAZymes). However, analyses of the secreted proteins revealed that the secretome of D. eres CBS 160.32 is represented by 5.4% of CAZymes, whereas the secreted CAZymes repertoire of D. amygdali CAA958 represents 29.1% of all secretomes. Biosynthetic gene clusters (BGCs) encoding compounds related to phytotoxins and mycotoxins were detected in D. eres and D. amygdali genomes. The core gene clusters of the phytotoxin Fusicoccin A in D. amygdali are reported here through a genome-scale assembly. Comparative analyses of the genomes from 11 Diaporthe species revealed an average of 874 CAZymes, 101 secondary metabolite BGCs, 1640 secreted proteins per species, and genome sizes ranging from 51.5 to 63.6 Mbp. This study offers insights into the overall features and characteristics of Diaporthe genomes. Our findings enrich the knowledge about D. eres and D. amygdali, which will facilitate further research into the pathogenicity mechanisms of these species.
A Fun-Guide to Innate Immune Responses to Fungal Infections
Authors: Burgess Thomas B. , Condliffe Alison M. , Elks Philip M.
Published: August 2022

Immunocompromised individuals are at high risk of developing severe fungal infections with high mortality rates, while fungal pathogens pose little risk to most healthy people. Poor therapeutic outcomes and growing antifungal resistance pose further challenges for treatments. Identifying specific immunomodulatory mechanisms exploited by fungal pathogens is critical for our understanding of fungal diseases and development of new therapies. A gap currently exists between the large body of literature concerning the innate immune response to fungal infections and the potential manipulation of host immune responses to aid clearance of infection. This review considers the innate immune mechanisms the host deploys to prevent fungal infection and how these mechanisms fail in immunocompromised hosts. Three clinically relevant fungal pathogens (Candida albicans, Cryptococcus spp. and Aspergillus spp.) will be explored. This review will also examine potential mechanisms of targeting the host therapeutically to improve outcomes of fungal infection.
Endophytic Diaporthe Associated with Morinda officinalis in China
Authors: Luo Mei , Guo Wei , Zhao Minping , Manawasinghe Ishara S. , Guarnaccia Vladimiro , Liu Jiawei , Hyde Kevin D. , Dong Zhangyong , You Chunping
Published: August 2022

Diaporthe species are endophytes, pathogens, and saprobes with a wide host range worldwide. However, little is known about endophytic Diaporthe species associated with Morinda officinalis. In the present study, 48 endophytic Diaporthe isolates were obtained from cultivated M. officinalis in Deqing, Guangdong Province, China. The nuclear ribosomal internal transcribed spacer (ITS), partial sequences of translation elongation factor 1-α (tef1-α), partial calmodulin (cal), histone H3 (his), and Beta-tubulin (β-tubulin) gene regions were sequenced and employed to construct phylogenetic trees. Based on morphology and combined multigene phylogeny, 12 Diaporthe species were identified, including five new species of Diaporthe longiconidialis, D. megabiguttulata, D. morindendophytica, D. morindae, and D. zhaoqingensis. This is the first report of Diaporthe chongqingensis, D. guangxiensis, D. heliconiae, D. siamensis, D. unshiuensis, and D. xishuangbanica on M. officinalis. This study provides the first intensive study of endophytic Diaporthe species on M. officinalis in China. These results will improve the current knowledge of Diaporthe species associated with this traditional medicinal plant. Furthermore, results from this study will help to understand the potential pathogens and biocontrol agents from M. officinalis and to develop a disease management platform.
Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species
Authors: de Carvalho Jamile Ambrósio , Monteiro Ruan Campos , Hagen Ferry , Camargo Zoilo Pires de , Rodrigues Anderson Messias
Published: August 2022

Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.