bluuebunny/crossref_metadata_2025 huggingface dataset:
Network-Based Topological Exploration of the Impact of Pollution Sources on Surface Water Bodies
Authors: Sebestyén Viktor , Czvetkó Tímea , Abonyi János
Published: January 2022

We developed a digital water management toolkit to evaluate the importance of the connections between water bodies and the impacts caused by pollution sources. By representing water bodies in a topological network, the relationship between point loads and basic water quality parameters is examined as a labelled network. The labels are defined based on the classification of the water bodies and pollution sources. The analysis of the topology of the network can provide information on how the possible paths of the surface water network influence the water quality. The extracted information can be used to develop a monitoring- and evidence-based decision support system. The methodological development is presented through the analysis of the physical-chemical parameters of all surface water bodies in Hungary, using the emissions of industrial plants and wastewater treatment plants. Changes in water quality are comprehensively assessed based on the water quality data recorded over the past 10 years. The results illustrate that the developed method can identify critical surface water bodies where the impact of local pollution sources is more significant. One hundred six critical water bodies have been identified, where special attention should be given to water quality improvement.
Effects of Cone Penetrometer Testing on Shallow Hydrogeology at a Contaminated Site
Authors: Putt Andrew D. , Kelly Erin R. , Lowe Kenneth A. , Rodriguez Miguel , Hazen Terry C.
Published: January 2022

Penetration testing is a popular and instantaneous technique for subsurface mapping, contaminant tracking, and the determination of soil characteristics. While the small footprint and reproducibility of cone penetrometer testing makes it an ideal method for in-situ subsurface investigations at contaminated sites, the effects to local shallow groundwater wells and measurable influence on monitoring networks common at contaminated sites is unknown. Physical and geochemical parameters associated with cone penetrometer testing were measured from a transect of shallow groundwater monitoring wells adjacent to penetrometer testing. For wells screened above the depth of cone refusal, the physical advancement and retraction of the cone had a significant effect (p < 0.01) on water level for several pushes within 10 meters of a monitoring well, and a measured increase in specific conductivity. No effect on geochemistry or water level was observed in continuous monitoring data from wells screened below the depth of cone refusal, but variability in specific conductivity from these wells during penetration testing was only a fraction of the natural variation measured during precipitation events. Continuous measurements of specific conductivity and water level demonstrated that the effects of penetration testing have limited spatial and temporal distributions with a null effect post-testing.
Different Radial Growth Responses to Climate Change of Three Dominant Conifer Species in Temperate Forest, Northeastern China
Authors: Wang Hui , Ning Yangcui , Liu Chunlan , Xu Peng , Zhang Wentao
Published: January 2022

We conducted dendroclimatological study on three dominant conifer tree species, Pinus koraiensis, Larix olgensis, and Picea jezoensis, in northeastern China for a better understanding of climate change impacts on temperate forest growth, by discussing the radial growth relationships of these tree species and projecting their radial growth trends under the future climate change scenarios. Based on the tree-ring samples collected from the upper altitude of Changbai Mountain, ring width chronologies were built to examine the growth relationships, and regression equations were established to project the future growth of the species under future climate change projected by the five general circulation models (GCMs) and four representative concentration pathway (RCP) scenarios. Although both temperature and precipitation showed varying degrees of relationships with growth of these three tree species, the limiting climate factors were species-specific. The tree-ring growth of P. koraiensis was limited by the summer temperature and precipitation at the end of growth, namely, significant positive correlations with the current July temperature and the previous September precipitation. Growth of L. olgensis was limited by the temperature before growing season, for its chronology was negatively correlated with the current February and previous December temperature (p < 0.05). The climatic conditions before and after growing season seemed to be the limiting factors of P. jezoensis growth, which was negatively correlated with the current February to April temperature and the current September temperature (p < 0.05), and positively correlated with the current August precipitation (p < 0.05). Under the gradual increasing of temperature predicted by the five GCMs and four RCP scenarios, the radial growth of P. Koraiensis will relatively increase, while that of L. olgensis and P. jezoensis will relatively decrease comparing to the base-line period (1981–2010). The specific growth–climate relationships and the future growth trends are species dependent. P. Koraiensis was the more suitable tree species for the forestation to maintain the sustainable forest in Changbai Mountain.
Stingray Habitat Use Is Dynamically Influenced by Temperature and Tides
Authors: Elston Chantel , Cowley Paul D. , von Brandis Rainer G. , Lea James
Published: January 2022

Abiotic factors often have a large influence on the habitat use of animals in shallow marine environments. Specifically, tides may alter the physical and biological characteristics of an ecosystem while changes in temperature can cause ectothermic species to behaviorally thermoregulate. Understanding the contextual and relative influences of these abiotic factors is important in prioritizing management plans, particularly for vulnerable faunal groups like stingrays. Passive acoustic telemetry was used to track the movements of 60 stingrays at a remote and environmentally heterogeneous atoll in Seychelles. This was to determine if habitat use varied over daily, diel and tidal cycles and to investigate the environmental drivers behind these potential temporal patterns. Individuals were detected in the atoll year-round, but the extent of their movement and use of multiple habitats increased in the warmer NW-monsoon season. Habitat use varied over the diel cycle, but was inconsistent between individuals. Temperature was also found to influence stingray movements, with individuals preferring the deeper and more thermally stable lagoon habitat when extreme (hot or cold) temperature events were observed on the flats. Habitat use also varied over the tidal cycle with stingrays spending a higher proportion of time in the lagoon during the lowest tides, when movement on the flats were constrained due to shallow waters. The interplay of tides and temperature, and how these varied across diel and daily scales, dynamically influenced stingray habitat use consistently between three species in an offshore atoll.
Tuning and Development of an Individual-Based Model of the Herring Spawning Migration
Authors: Kelly Cian , Michelsen Finn Are , Kolding Jeppe , Alver Morten Omholt
Published: January 2022

Norwegian spring spawning herring is a migratory pelagic fish stock that seasonally navigates between distant locations in the Norwegian Sea. The spawning migration takes place between late winter and early spring. In this article, we present an individual-based model that simulated the spawning migration, which was tuned and validated against observation data. Individuals were modelled on a continuous grid coupled to a physical oceanographic model. We explore the development of individual model states in relation to local environmental conditions and predict the distribution and abundance of individuals in the Norwegian Sea for selected years (2015–2020). Individuals moved position mainly according to the prevailing coastal current. A tuning procedure was used to minimize the deviations between model and survey estimates at specific time stamps. Furthermore, 4 separate scenarios were simulated to ascertain the sensitivity of the model to initial conditions. Subsequently, one scenario was evaluated and compared with catch data in 5 day periods within the model time frame. Agreement between model and catch data varies throughout the season and between years. Regardless, emergent properties of the migration are identifiable that match observations, particularly migration trajectories that run perpendicular to deep bathymetry and counter the prevailing current. The model developed is efficient to implement and can be extended to generate multiple realizations of the migration path. This model, in combination with various sources of fisheries-dependent data, can be applied to improve real-time estimates of fish distributions.
Annual Lateral Organic Carbon Exchange Between Salt Marsh and Adjacent Water: A Case Study of East Headland Marshes at the Yangtze Estuary
Authors: Yuan Yiquan , Li Xiuzhen , Xie Zuolun , Xue Liming , Yang Bin , Zhao Wenzhen , Craft Christopher B.
Published: January 2022

Blue carbon (C) ecosystems (mangroves, salt marshes, and seagrass beds) sequester high amounts of C, which can be respired back into the atmosphere, buried for long periods, or exported to adjacent ecosystems by tides. The lateral exchange of C between a salt marsh and adjacent water is a key factor that determines whether a salt marsh is a C source (i.e., outwelling) or sink in an estuary. We measured salinity, particulate organic carbon (POC), and dissolved organic carbon (DOC) seasonally over eight tidal cycles in a tidal creek at the Chongming Dongtan wetland from July 2017 to April 2018 to determine whether the marsh was a source or sink for estuarine C. POC and DOC fluxes were significantly correlated in the four seasons driven by water fluxes, but the concentration of DOC and POC were positively correlated only in autumn and winter. DOC and POC concentrations were the highest in autumn (3.54 mg/L and 4.19 mg/L, respectively) and the lowest in winter and spring (1.87 mg/L and 1.51 mg/L, respectively). The tidal creek system in different seasons showed organic carbon (OC) export, and the organic carbon fluxes during tidal cycles ranged from –12.65 to 4.04 g C/m2. The intensity showed significant seasonal differences, with the highest in summer, the second in autumn, and the lowest in spring. In different seasons, organic carbon fluxes during spring tides were significantly higher than that during neap tides. Due to the tidal asymmetry of the Yangtze River estuary and the relatively young stage, the salt marshes in the study area acted as a strong lateral carbon source.
Antibiotics Alter Pocillopora Coral-Symbiodiniaceae-Bacteria Interactions and Cause Microbial Dysbiosis During Heat Stress
Authors: Connelly Michael T. , McRae Crystal J. , Liu Pi-Jen , Martin Cecily E. , Traylor-Knowles Nikki
Published: January 2022

Symbioses between eukaryotes and their associated microbial communities are fundamental processes that affect organisms’ ecology and evolution. A unique example of this is reef-building corals that maintain symbiotic associations with dinoflagellate algae (Symbiodiniaceae) and bacteria that affect coral health through various mechanisms. However, little is understood about how coral-associated bacteria communities affect holobiont heat tolerance. In this study, we investigated these interactions in four Pocillopora coral colonies belonging to three cryptic species by subjecting fragments to treatments with antibiotics intended to suppress the normal bacteria community, followed by acute heat stress. Separate treatments with only antibiotics or heat stress were conducted to compare the effects of individual stressors on holobiont transcriptome responses and microbiome shifts. Across all Pocillopora species examined, combined antibiotics and heat stress treatment significantly altered coral-associated bacteria communities and caused major changes in both coral and Cladocopium algal symbiont gene expression. Individually, heat stress impaired Pocillopora protein translation and activated DNA repair processes, while antibiotics treatments caused downregulation of Pocillopora amino acid and inorganic ion transport and metabolism genes and Cladocopium photosynthesis genes. Combined antibiotics-heat stress treatments caused synergistic effects on Pocillopora and Cladocopium gene expression including enhanced expression of oxidative stress response genes, programed cell death pathways and proteolytic enzymes that indicate an exacerbated response to heat stress following bacteria community suppression. Collectively, these results provide further evidence that corals and their Symbiodiniaceae and bacteria communities engage in highly coordinated metabolic interactions that are crucial for coral holobiont health, homeostasis, and heat tolerance.
Reef Sediments Can Act As a Stony Coral Tissue Loss Disease Vector
Authors: Studivan Michael S. , Rossin Ashley M. , Rubin Ewelina , Soderberg Nash , Holstein Daniel M. , Enochs Ian C.
Published: January 2022

Stony coral tissue loss disease (SCTLD) was first observed in 2014 near Virginia Key in Miami-Dade County, Florida. Field sampling, lab experiments, and modeling approaches have suggested that reef sediments may play a role in SCTLD transmission, though a positive link has not been tested experimentally. We conducted an ex situ transmission assay using a statistically-independent disease apparatus to test whether reef sediments can transmit SCTLD in the absence of direct contact between diseased and healthy coral tissue. We evaluated two methods of sediment inoculation: batch inoculation of sediments collected from southeast Florida using whole colonies of diseased Montastraea cavernosa, and individual inoculations of sediments following independent, secondary infections of ∼5 cm2 coral fragments. Healthy fragments of the coral species Orbicella faveolata and M. cavernosa were exposed to these diseased sediment treatments, as well as direct disease contact and healthy sediment controls. SCTLD transmission was observed for both batch and individual diseased sediment inoculation treatments, albeit with lower proportions of infected individuals as compared to disease contact controls. The time to onset of lesions was significantly different between species and among disease treatments, with the most striking infections occurring in the individual diseased sediment treatment in under 24 h. Following infection, tissue samples were confirmed for the presence of SCTLD signs via histological examination, and sediment subsamples were analyzed for microbial community variation between treatments, identifying 16 SCTLD indicator taxa in sediments associated with corals experiencing tissue loss. This study demonstrated that reef sediments can indeed transmit SCTLD through indirect exposure between diseased and healthy corals, and adds credence to the assertion that SCTLD transmission occurs via an infectious agent or agents. This study emphasizes the critical need to understand the roles that sediment microbial communities and coastal development activities may have on the persistence of SCTLD throughout the endemic zone, especially in the context of management and conservation strategies in Florida and the wider Caribbean.
Automated Detection, Classification and Counting of Fish in Fish Passages With Deep Learning
Authors: Kandimalla Vishnu , Richard Matt , Smith Frank , Quirion Jean , Torgo Luis , Whidden Chris
Published: January 2022

The Ocean Aware project, led by Innovasea and funded through Canada's Ocean Supercluster, is developing a fish passage observation platform to monitor fish without the use of traditional tags. This will provide an alternative to standard tracking technology, such as acoustic telemetry fish tracking, which are often not appropriate for tracking at-risk fish species protected by legislation. Rather, the observation platform uses a combination of sensors including acoustic devices, visual and active sonar, and optical cameras. This will enable more in-depth scientific research and better support regulatory monitoring of at-risk fish species in fish passages or marine energy sites. Analysis of this data will require a robust and accurate method to automatically detect fish, count fish, and classify them by species in real-time using both sonar and optical cameras. To meet this need, we developed and tested an automated real-time deep learning framework combining state of the art convolutional neural networks and Kalman filters. First, we showed that an adaptation of the widely used YOLO machine learning model can accurately detect and classify eight species of fish from a public high resolution DIDSON imaging sonar dataset captured from the Ocqueoc River in Michigan, USA. Although there has been extensive research in the literature identifying particular fish such as eel vs. non-eel and seal vs. fish, to our knowledge this is the first successful application of deep learning for classifying multiple fish species with high resolution imaging sonar. Second, we integrated the Norfair object tracking framework to track and count fish using a public video dataset captured by optical cameras from the Wells Dam fish ladder on the Columbia River in Washington State, USA. Our results demonstrate that deep learning models can indeed be used to detect, classify species, and track fish using both high resolution imaging sonar and underwater video from a fish ladder. This work is a first step toward developing a fully implemented system which can accurately detect, classify and generate insights about fish in a wide variety of fish passage environments and conditions with data collected from multiple types of sensors.
Compressive Behavior and Analytical Model of Ultra-Early Strength Concrete-Filled FRP Tube With Zero Curing Time
Authors: Liu Yue , Xie Jia-Zhan , Yan Jing-Liang
Published: January 2022

Fiber-reinforced polymer (FRP) has been widely used in civil engineering due to its light weight, high strength, convenient construction, and strong corrosion resistance. One of the important applications of FRP composites is the concrete-filled FRP tube (CFFT), which can greatly improve the compressive strength and ductility of concrete as well as facilitate construction. In this article, the compressive performances of a normal concrete-filled FRP tube (N-CFFT) column with 5-hour curing time and an ultra-early strength concrete-filled FRP tube (UES–CFFT) column with zero curing time were studied by considering the characteristics of rapid early strength improvement of ultra-early strength concrete and the confinement effect of the FRP tube. Monotonic axial compression tests were carried out on 3 empty FRP tubes (FTs) without an internal filler and 6 CFFT (3 N-CFFTs and 3 UES-CFFTs) specimens. All specimens were cylinders of 200 mm in diameter and 600 mm in height, confined by glass fiber–reinforced polymer (GFRP). Test results indicated that the compressive bearing capacity of the specimens increased significantly by adopting the ultra-early strength concrete as the core concrete of the CFFT, although the curing time was zero. It was also shown that the compressive behavior of the UES–CFFT specimens with zero curing time increased significantly than that of the N-CFFT specimens with 5-hour curing time because the former was able to achieve rapid strength enhancement in a very short time than the latter. The ultimate compressive strength of UES–CFFT specimens with zero curing time reached 78.3 MPa, which was 66.2 and 97.2% higher than that of N-CFFT with 5-hour curing time and FT specimens, respectively. In addition, a simple confinement model to predict the strength of UES–CFFT with zero curing time in ultimate condition was introduced. Compared with the existing models, the proposed model could predict the ultimate strength of UES–CFFT specimens with zero curing time with better accuracy.
Varying Dose of Atropine in Slowing Myopia Progression in Children Over Different Follow-Up Periods by Meta-Analysis
Authors: Gan Jiahe , Li Shi-Ming , Wu Shanshan , Cao Kai , Ma Dandan , He Xi , Hua Ziyu , Kang Meng-Tian , Wei Shifei , Bai Weiling , Wang Ningli
Published: January 2022

Purpose:To evaluate the efficacy and safety of atropine for slowing myopia progression and to investigate whether the treatment effect remains constant with continuing treatment.

Method:Studies were retrieved from MEDLINE, EMBASE, and the Cochrane Library from their inception to May 2021, and the language was limited to English. Randomized controlled trials (RCTs) and cohort studies involving atropine in at least one intervention and placebo/non-atropine treatment in another as the control were included and subgroup analysis based on low dose (0.01%), moderate dose (0.01%–<0.5%), and high dose (0.5–1.0%) were conducted. The Cochrane Collaboration and Newcastle-Ottawa Scale were used to evaluate the quality of RCTs and cohort studies, respectively.

Results:Twelve RCTs and fifteen cohort studies involving 5,069 children aged 5 to 15 years were included. The weighted mean differences in myopia progression between the atropine and control groups were 0.73 diopters (D), 0.67 D, and 0.35 D per year for high-dose, moderate-dose, and low-dose atropine, respectively (χ2= 13.76;P= 0.001,I2= 85.5%). After removing studies that provided extreme findings, atropine demonstrated a significant dose-dependent effect on both refractive change and axial elongation, with higher dosages of atropine resulting in less myopia progression (r= 0.85;P= 0.004) and less axial elongation (r= −0.94;P= 0.005). Low-dose atropine showed less myopia progression (−0.23 D;P= 0.005) and less axial elongation (0.09 mm,P< 0.001) in the second year than in the first year, whereas in high-dose atropine more axial elongation (−0.15 mm,P= 0.003) was observed. The higher dose of atropine was associated with a higher incidence of adverse effects, such as photophobia with an odds ratio (OR) of 163.57, compared with an OR of 6.04 for low-dose atropine and 8.63 for moderate-dose atropine (P= 0.03).

Conclusion:Both the efficacy and adverse effects of atropine are dose-dependent in slowing myopia progression in children. The efficacy of high-dose atropine was reduced after the first year of treatment, whereas low-dose atropine had better efficacy in a longer follow-up period.
Efficacy and Safety of Ocriplasmin Use for Vitreomacular Adhesion and Its Predictive Factors: A Systematic Review and Meta-Analysis
Authors: Chen Xi , Li Min , You Ran , Wang Wei , Wang Yanling
Published: January 2022

Symptomatic vitreomacular adhesion (sVMA) impedes visual acuity and quality. Ocriplasmin is a recombinant protease, which may be injected into the vitreous cavity to treat this condition, yet controversy remains with respect to its effectiveness and safety, particularly its patient selection standard. In this systematic review, the PubMed, Embase, and the Cochrane Library were searched to identify studies published prior to August 2020 on the impact of ocriplasmin treatment on VMA release, macular hole (MH) closure, and/or related adverse events (AEs). Data were pooled using a random-effects model. Risk ratios (RRs) with 95% CIs were calculated. Of 1,186 articles reviewed, 5 randomized controlled trials and 50 cohort studies were ultimately included, representing 4,159 patients. Ocriplasmin significantly increased the rate of VMA release (RR, 3.61; 95% CI, 1.99–6.53; 28 days after treatment) and MH closure (RR, 3.84; 95% CI, 1.62–9.08; 28 days after treatment) and was associated with visual function improvement. No increased risk for overall AEs was seen in ocriplasmin treatment. The proportion of VMA release and MH closure in patients was 0.50 and 0.36, respectively. VMA release was more likely in patients with absence of epiretinal membrane (ERM). Patients with smaller MH diameter were more likely to achieve MH closure. Evidence from included studies suggests that ocriplasmin is a suitable and safe approach for treating sVMA. ERM and MH status are important factors when considering ocriplasmin treatment.
MAFLD/NAFLD Biopsy-Free Scoring Systems for Hepatic Steatosis, NASH, and Fibrosis Diagnosis
Authors: Segura-Azuara Nancy de los Ángeles , Varela-Chinchilla Carlos Daniel , Trinidad-Calderón Plinio A.
Published: January 2022

Metabolic dysfunction-associated fatty liver disease (MAFLD), formerly known as nonalcoholic fatty liver disease, is the most prevalent liver disorder worldwide. Historically, its diagnosis required biopsy, even though the procedure has a variable degree of error. Therefore, new non-invasive strategies are needed. Consequently, this article presents a thorough review of biopsy-free scoring systems proposed for the diagnosis of MAFLD. Similarly, it compares the severity of the disease, ranging from hepatic steatosis (HS) and nonalcoholic steatohepatitis (NASH) to fibrosis, by contrasting the corresponding serum markers, clinical associations, and performance metrics of these biopsy-free scoring systems. In this regard, defining MAFLD in conjunction with non-invasive tests can accurately identify patients with fatty liver at risk of fibrosis and its complications. Nonetheless, several biopsy-free scoring systems have been assessed only in certain cohorts; thus, further validation studies in different populations are required, with adjustment for variables, such as body mass index (BMI), clinical settings, concomitant diseases, and ethnic backgrounds. Hence, comprehensive studies on the effects of age, morbid obesity, and prevalence of MAFLD and advanced fibrosis in the target population are required. Nevertheless, the current clinical practice is urged to incorporate biopsy-free scoring systems that demonstrate adequate performance metrics for the accurate detection of patients with MAFLD and underlying conditions or those with contraindications of biopsy.
The Patterns of Morphological Change During Intracerebral Hemorrhage Expansion: A Multicenter Retrospective Cohort Study
Authors: Jianbo Chang , Ting Xiao , Yihao Chen , Xiaoning Wang , Hong Shang , Qinghua Zhang , Zeju Ye , Xingong Wang , Fengxuan Tian , Jianjun Chai , Wenbin Ma , Junji Wei , Ming Feng , Yao Jianhua , Renzhi Wang
Published: January 2022

Objectives: Hemorrhage expansion (HE) is a common and serious condition in patients with intracerebral hemorrhage (ICH). In contrast to the volume changes, little is known about the morphological changes that occur during HE. We developed a novel method to explore the patterns of morphological change and investigate the clinical significance of this change in ICH patients.

Methods: The morphological changes in the hematomas of ICH patients with available paired non-contrast CT data were described in quantitative terms, including the diameters of each hematoma in three dimensions, the longitudinal axis type, the surface regularity (SR) index, the length and direction changes of the diameters, and the distance and direction of movement of the center of the hematoma. The patterns were explored by descriptive analysis and difference analysis in subgroups. We also established a prognostic nomogram model for poor outcomes in ICH patients using both morphological changes and clinical parameters.

Results: A total of 1,094 eligible patients from four medical centers met the inclusion criteria. In 266 (24.3%) cases, the hematomas enlarged; the median absolute increase in volume was 14.0 [interquartile range (IQR), 17.9] mL. The initial hematomas tended to have a more irregular shape, reflected by a larger surface regularity index, than the developed hematomas. In subtentorial and deep supratentorial hematomas, the center moved in the direction of gravity. The distance of center movement and the length changes of the diameters were small, with median values of less than 4 mm. The most common longitudinal axis type was anterior–posterior (64.7%), and the axis type did not change between initial and repeat imaging in most patients (95.2%). A prognostic nomogram model including lateral expansion, a parameter of morphological change, showed good performance in predicting poor clinical outcomes in ICH patients.

Conclusions: The present study provides a morphological perspective on HE using a novel automatic approach. We identified certain patterns of morphological change in HE, and we believe that some morphological change parameters could help physicians predict the prognosis of ICH patients.
TLR4-Dependent DUOX2 Activation Triggered Oxidative Stress and Promoted HMGB1 Release in Dry Eye
Authors: Wang Bowen , Zeng Hao , Zuo Xin , Yang Xue , Wang Xiaoran , He Dalian , Yuan Jin
Published: January 2022

Dry eye disease (DED) is one of the most common ocular surface diseases worldwide. DED has been characterized by excessive accumulation of reactive oxygen species (ROS), following significant corneal epithelial cell death and ocular surface inflammation. However, the key regulatory factor remains unclear. In this study, we tended to explore whether DUOX2 contributed to DED development and the underlying mechanism. Human corneal epithelial (HCE) cells were treated with hyperosmolarity, C57BL/6 mice were injected of subcutaneous scopolamine to imitate DED. Expression of mRNA was investigated by RNA sequencing (RNA-seq) and quantitative real-time PCR (qPCR). Protein changes and distribution of DUOX2, high mobility group box 1 (HMGB1), Toll-like receptor 4 (TLR4), and 4-hydroxynonenal (4-HNE) were evaluated by western blot assays and immunofluorescence. Cell death was assessed by Cell Counting Kit-8 (CCK8), lactate dehydrogenase (LDH) release, and propidium iodide (PI) staining. Cellular ROS levels and mitochondrial membrane potential (MMP) were analyzed by flow cytometry. RNA-seq and western blot assay indicated a significant increase of DUOX2 dependent of TLR4 activation in DED both in vitro and in vivo. Immunofluorescence revealed significant translocation of HMGB1 within corneal epithelial cells under hyperosmolar stress. Interestingly, after ablated DUOX2 expression by siRNA, we found a remarkable decrease of ROS level and recovered MMP in HCE cells. Moreover, knockdown of DUOX2 greatly inhibited HMGB1 release, protected cell viability and abolished inflammatory activation. Taken together, our data here suggest that upregulation of DUOX2 plays a crucial role in ROS production, thereafter, induce HMGB1 release and cell death, which triggers ocular surface inflammation in DED.
U-shaped GAN for Semi-Supervised Learning and Unsupervised Domain Adaptation in High Resolution Chest Radiograph Segmentation
Authors: Wang Hongyu , Gu Hong , Qin Pan , Wang Jia
Published: January 2022

Deep learning has achieved considerable success in medical image segmentation. However, applying deep learning in clinical environments often involves two problems: (1) scarcity of annotated data as data annotation is time-consuming and (2) varying attributes of different datasets due to domain shift. To address these problems, we propose an improved generative adversarial network (GAN) segmentation model, called U-shaped GAN, for limited-annotated chest radiograph datasets. The semi-supervised learning approach and unsupervised domain adaptation (UDA) approach are modeled into a unified framework for effective segmentation. We improve GAN by replacing the traditional discriminator with a U-shaped net, which predicts each pixel a label. The proposed U-shaped net is designed with high resolution radiographs (1,024 × 1,024) for effective segmentation while taking computational burden into account. The pointwise convolution is applied to U-shaped GAN for dimensionality reduction, which decreases the number of feature maps while retaining their salient features. Moreover, we design the U-shaped net with a pretrained ResNet-50 as an encoder to reduce the computational burden of training the encoder from scratch. A semi-supervised learning approach is proposed learning from limited annotated data while exploiting additional unannotated data with a pixel-level loss. U-shaped GAN is extended to UDA by taking the source and target domain data as the annotated data and the unannotated data in the semi-supervised learning approach, respectively. Compared to the previous models dealing with the aforementioned problems separately, U-shaped GAN is compatible with varying data distributions of multiple medical centers, with efficient training and optimizing performance. U-shaped GAN can be generalized to chest radiograph segmentation for clinical deployment. We evaluate U-shaped GAN with two chest radiograph datasets. U-shaped GAN is shown to significantly outperform the state-of-the-art models.
The Prevalence and Clinical Implications of Rectal SARS-CoV-2 Shedding in Danish COVID-19 Patients and the General Population
Authors: Holm-Jacobsen Julie Niemann , Bundgaard-Nielsen Caspar , Rold Louise Søndergaard , Jensen Ann-Maria , Shakar Shakil , Ludwig Marc , Kirk Karina Frahm , Donneborg Mette Line , Vonasek Julia Helena , Pedersen Benjamin , Arenholt Louise Thomsen Schmidt , Hagstrøm Søren , Leutscher Peter , Sørensen Suzette
Published: January 2022

Background: SARS-CoV-2 has resulted in a global pandemic since its outbreak in Wuhan, 2019. Virus transmission primarily occurs through close contact, respiratory droplets, and aerosol particles. However, since SARS-CoV-2 has been detected in fecal and rectal samples from infected individuals, the fecal-oral route has been suggested as another potential route of transmission. This study aimed to investigate the prevalence and clinical implications of rectal SARS-CoV-2 shedding in Danish COVID-19 patients.

Methods: Hospitalized and non-hospitalized adults and children who were recently tested with a pharyngeal COVID-19 test, were included in the study. A rectal swab was collected from all participants. Hospitalized adults and COVID-19 positive children were followed with both pharyngeal and rectal swabs until two consecutive negative results were obtained. RT-qPCR targeting the envelope gene was used to detect SARS-CoV-2 in the samples. Demographic, medical, and biochemical information was obtained through questionnaires and medical records.

Results: Twenty-eight of 52 (53.8%) COVID-19 positive adults and children were positive for SARS-CoV-2 in rectal swabs. Seven of the rectal positive participants were followed for more than 6 days. Two of these (28.6%) continued to test positive in their rectal swabs for up to 29 days after the pharyngeal swabs had turned negative. Hospitalized rectal positive and rectal negative adults were comparable regarding demographic, medical, and biochemical information. Furthermore, no difference was observed in the severity of the disease among the two groups.

Conclusions: We provided evidence of rectal SARS-CoV-2 shedding in Danish COVID-19 patients. The clinical importance of rectal SARS-CoV-2 shedding appears to be minimal.
Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds
Authors: Higgins Edward , Parr Thomas B. , Vaughn Caryn C.
Published: January 2022

Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.
First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016
Authors: Hadad Ronza , Golparian Daniel , Velicko Inga , Ohlsson Anna-Karin , Lindroth Ylva , Ericson Eva-Lena , Fredlund Hans , Engstrand Lars , Unemo Magnus
Published: January 2022

The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.
microRNA-Based Network and Pathway Analysis for Neuropathic Pain in Rodent Models
Authors: Zheng Yi-Li , Su Xuan , Chen Yu-Meng , Guo Jia-Bao , Song Ge , Yang Zheng , Chen Pei-Jie , Wang Xue-Qiang
Published: January 2022

Neuropathic pain (NP) is poorly managed, and in-depth mechanisms of gene transcriptome alterations in NP pathogenesis are not yet fully understood. To determine microRNA-related molecular mechanisms of NP and their transcriptional regulation in NP, PubMed, Embase, Web of Science and CINAHL Complete (EBSCO) were searched from inception to April 2021. Commonly dysregulated miRNAs in NP were assessed. The putative targets of these miRNAs were determined using TargetScan, Funrich, Cytoscape and String database. A total of 133 literatures containing miRNA profiles studies and experimentally verify studies were included. Venn analysis, target gene prediction analysis and functional enrichment analysis indicated several miRNAs (miR-200b-3p, miR-96, miR-182, miR-183, miR-30b, miR-155 and miR-145) and their target genes involved in known relevant pathways for NP. Targets on transient receptor potential channels, voltage-gated sodium channels and voltage-gated calcium channels may be harnessed for pain relief. A further delineation of signal processing and modulation in neuronal ensembles is key to achieving therapeutic success in future studies.
Response Systems, Antagonistic Responses, and the Behavioral Repertoire
Authors: Ortu Daniele , Bugg Ryan M.
Published: January 2022

While response systems are often mentioned in the behavioral and physiological literature, an explicit discussion of what response systems are is lacking. Here we argue that response systems can be understood as an interaction between anatomically constrained behavioral topographies occasioned by currently present stimuli and a history of reinforcement. “New” response systems can develop during the lifetime as the organism gains instrumental control of new fine-grained topographies. Within this framework, antagonistic responses compete within each response system based on environmental stimulation, and competition is resolved at the striatum-thalamo-cortical loops level. While response systems can be by definition independent from one another, separate systems are often recruited at the same time to engage in complex responses, which themselves may be selected by reinforcement as functional units.
Isolation and Characterization of Primary Retinal Microglia From the Human Post-mortem Eyes for Future Studies of Ocular Diseases
Authors: Wang Luoziyi , Qian Yiwen , Che Xin , Jiang Jing , Suo Jinshan , Wang Zhiliang
Published: January 2022

Microglia, the primary resident immunocytes in the retina, continuously function as immune system supervisors in sustaining intraocular homeostasis. Microglia relate to many diseases, such as diabetic retinopathy, glaucoma, and optic nerve injury. To further investigate their morphology and functions in vitro, a reliable culture procedure of primary human retinal microglia is necessary. However, the culture condition of microglia from the adult retina is unclear. Researchers created several protocols, but most of them were carried out on rodents and newborns. This study describes a protocol to isolate and characterize human primary retinal microglia from human post-mortem eyes. The whole procedure started with removing the retinal vessels, mechanical separation and enzymatic dissociation, filtration, and centrifugation. Then, we cultured the cell suspensions on a T-75 flask for 18 days and then shook retinal microglia from other retinal cells. We found numerous retinal microglia grow and attach to Müller cells 10 days after seeding and increase rapidly on days 14–18. Iba1 and P2RY12 were used to qualify microglia through immunofluorescence. Moreover, CD11b and P2RY12 were positive in flow cytometry, which helps to discriminate microglia from other cells and macrophages. We also observed a robust response of retinal microglia in lipopolysaccharide (LPS) treatment with proinflammatory cytokines. In conclusion, this study provides an effective way to isolate and culture retinal microglia from adult human eyes, which may be critical for future functional investigations.
Effect of Deep Brain Stimulation on Cerebellar Tremor Compared to Non-Cerebellar Tremor Using a Wearable Device in a Patient With Multiple Sclerosis: Case Report
Authors: Xie Tao , Padmanaban Mahesh , Javed Adil , Satzer David , Towle Theresa E. , Warnke Peter , Towle Vernon L.
Published: January 2022

Tremor of the upper extremity is a significant cause of disability in some patients with multiple sclerosis (MS). The MS tremor is complex because it contains an ataxic intentional tremor component due to the involvement of the cerebellum and cerebellar outflow pathways by MS plaques, which makes the MS tremor, in general, less responsive to medications or deep brain stimulation (DBS) than those associated with essential tremor or Parkinson's disease. The cerebellar component has been thought to be the main reason for making DBS less effective, although it is not clear whether it is due to the lack of suppression of the ataxic tremor by DBS or else. The goal of this study was to clarify the effect of DBS on cerebellar tremor compared to non-cerebellar tremor in a patient with MS. By wearing an accelerometer on the index finger of each hand, we were able to quantitatively characterize kinetic tremor by frequency and amplitude, with cerebellar ataxia component on one hand and that without cerebellar component on the other hand, at the beginning and end of the hand movement approaching a target at DBS Off and On status. We found that cerebellar tremor surprisingly had as good a response to DBS as the tremor without a cerebellar component, but the function control on cerebellar tremor was not as good due to its distal oscillation, which made the amplitude of tremor increasingly greater as it approached the target. This explains why cerebellar tremor or MS tremor with cerebellar component has a poor functional transformation even with a good percentage of tremor control. This case study provides a better understanding of the effect of DBS on cerebellar tremor and MS tremor by using a wearable device, which could help future studies improve patient selection and outcome prediction for DBS treatment of this disabling tremor.
Multi-Scale Graph Representation Learning for Autism Identification With Functional MRI
Authors: Chu Ying , Wang Guangyu , Cao Liang , Qiao Lishan , Liu Mingxia
Published: January 2022

Resting-state functional MRI (rs-fMRI) has been widely used for the early diagnosis of autism spectrum disorder (ASD). With rs-fMRI, the functional connectivity networks (FCNs) are usually constructed for representing each subject, with each element representing the pairwise relationship between brain region-of-interests (ROIs). Previous studies often first extract handcrafted network features (such as node degree and clustering coefficient) from FCNs and then construct a prediction model for ASD diagnosis, which largely requires expert knowledge. Graph convolutional networks (GCNs) have recently been employed to jointly perform FCNs feature extraction and ASD identification in a data-driven manner. However, existing studies tend to focus on the single-scale topology of FCNs by using one single atlas for ROI partition, thus ignoring potential complementary topology information of FCNs at different spatial scales. In this paper, we develop a multi-scale graph representation learning (MGRL) framework for rs-fMRI based ASD diagnosis. The MGRL consists of three major components: (1) multi-scale FCNs construction using multiple brain atlases for ROI partition, (2) FCNs representation learning via multi-scale GCNs, and (3) multi-scale feature fusion and classification for ASD diagnosis. The proposed MGRL is evaluated on 184 subjects from the public Autism Brain Imaging Data Exchange (ABIDE) database with rs-fMRI scans. Experimental results suggest the efficacy of our MGRL in FCN feature extraction and ASD identification, compared with several state-of-the-art methods.
Silica Nanoparticles Promote α-Synuclein Aggregation and Parkinson’s Disease Pathology
Authors: Yuan Xin , Yang Yingxu , Xia Danhao , Meng Lanxia , He Mingyang , Liu Chaoyang , Zhang Zhentao
Published: January 2022

Silica nanoparticles (SiO2 NPs) are increasingly investigated for their potential in drug delivery systems. However, the neurotoxicity of SiO2 NPs remains to be fully clarified. Previously SiO2 NPs have been reported to be detected in the central nervous system, especially in the dopaminergic neurons which are deeply involved in Parkinson’s disease (PD). In this article, we characterized the effects of SiO2 NPs on inducing PD-like pathology both in vitro and in vivo. Results showed that SiO2 NPs promote more severe hyperphosphorylation and aggregation of α-synuclein, mitochondria impairment, oxidative stress, autophagy dysfunction, and neuronal apoptosis in the α-Syn A53T transgenic mice intranasally administrated with SiO2 NPs compared with the control group. Our findings provide new evidence supporting that SiO2 NPs exposure might have a strong capability of promoting the initiation and development of PD.