bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of short-term experimental manipulation of captive social environment on uropygial gland microbiome and preen oil volatile composition
Authors: Whittaker Danielle J. , Atyam Amruth , Burroughs Nathan A. , Greenberg Jonathan M. , Hagey Travis J. , Novotny Milos V. , Soini Helena A. , Theis Kevin R. , Van Laar Tricia A. , Slade Joel W. G.
Published: January 2023

Introduction

Avian preen oil, secreted by the uropygial gland, is an important source of volatile compounds that convey information about the sender’s identity and quality, making preen oil useful for the recognition and assessment of potential mates and rivals. Although intrinsic factors such as hormone levels, genetic background, and diet can affect preen oil volatile compound composition, many of these compounds are not the products of the animal’s own metabolic processes, but rather those of odor-producing symbiotic microbes. Social behavior affects the composition of uropygial microbial communities, as physical contact results in microbe sharing. We experimentally manipulated social interactions in captive dark-eyed juncos (Junco hyemalis) to assess the relative influence of social interactions, subspecies, and sex on uropygial gland microbial composition and the resulting preen oil odor profiles.

Methods

We captured 24 birds at Mountain Lake Biological Station in Virginia, USA, including birds from two seasonally sympatric subspecies – one resident, one migratory. We housed them in an outdoor aviary in three phases of social configurations: first in same-sex, same-subspecies flocks, then in male-female pairs, and finally in the original flocks. Using samples taken every four days of the experiment, we characterized their uropygial gland microbiome through 16S rRNA gene sequencing and their preen oil volatile compounds via GC-MS.

Results

We predicted that if social environment was the primary driver of uropygial gland microbiome composition, and if microbiome composition in turn affected preen oil volatile profiles, then birds housed together would become more similar over time. Our results did not support this hypothesis, instead showing that sex and subspecies were stronger predictors of microbiome composition. We observed changes in volatile compounds after the birds had been housed in pairs, which disappeared after they were moved back into flocks, suggesting that hormonal changes related to breeding condition were the most important factor in these patterns.

Discussion

Although early life social environment of nestlings and long-term social relationships have been shown to be important in shaping uropygial gland microbial communities, our study suggests that shorter-term changes in social environment do not have a strong effect on uropygial microbiomes and the resulting preen oil volatile compounds.
Temperature fluctuation alters optimal predator community composition for anticipated biological control
Authors: Laubmeier Amanda N. , Tabassum Nusrat , Tenhumberg Brigitte
Published: January 2023

Alongside pesticides and specialist predators, natural communities of generalist beetle and spider predators play an important role in suppressing agricultural pests. However, the predation pressure of natural communities can be unpredictable. Overall predation pressure is influenced by a dense network of potential intraguild interactions, which are further shaped by species traits and environmental factors. Understanding how these different influences combine to impact pest control is especially important in the context of changing global temperatures. Recent empirical studies have demonstrated that the foraging behavior of arthropod predators is influenced by an interaction between temperature and predator body size. To explore the consequences of these findings for intraguild interactions and pest control, we expand a previously published model describing interactions between arthropod predators and a pest population. The model assumed that interaction strengths are influenced by body size and habitat preference. In our updated model, we incorporate the effect of temperature on predator foraging activity. We parameterize the model to match empirically observed predator community composition in 10 agricultural fields and use simulations to demonstrate how temperature-dependent behaviors change the expected efficiency of the natural predator community. Then, we use an optimization approach to identify the most efficient composition of natural predators for pest control. We then evaluate whether the most efficient predator compositions would change with increasing average daily temperature and its variability, as is expected under future temperature change. We find that optimal communities often include predators with complementary foraging activity and that in 2 fields, the optimal community changes drastically under future temperatures. We also note that at some temperatures, foraging activity reduces the negative effects of intraguild interference on pest consumption. This work allows us to assess the effect of climate change on the efficiency of natural predator communities to control pest populations and provide guidance for farmers to design pest management strategies tailored to different climate scenarios.
Tree rings of Rhododendron arboreum portray signal of monsoon precipitation in the Himalayan region
Authors: Dhyani Rupesh , Bhattacharyya Amalava , Joshi Rajesh , Shekhar Mayank , Chandra Kuniyal Jagdish , Singh Ranhotra Parminder
Published: January 2023

The Himalayas has a significant impact not just on the Indian subcontinent’s monsoon patterns but also on the global climate. Monsoon failure causing drought has become more common in recent years. As a result, it poses a major threat to ecosystem sustainability. We reported for the first time, a climatic-sensitive tree ring chronology of a broadleaf tree, Rhododendron arboreum, spanning 1732–2017 CE from the Himalayan region. We discovered that the climate during the monsoon season limits the growth of this tree in this region. The correlation analysis between tree ring chronology and climate revealed a significant positive relationship with precipitation (r = 0.63, p < 0.001) and a negative relationship with temperature (r = −0.48, p < 0.01) during the months of June–August (JJA). This strong relationship allowed us to reconstruct monsoon precipitation spanning 1780 to 2017 CE which explained 40% of the variance of the observed climate data for the calibration period. The reconstructed data are validated by the existence of a significant association with the gridded JJA precipitation data of the Climate Research Unit (CRU) of this region. The monsoon rainfall record captured extremely wet years during 1793, 1950, 2011, 2013, and 2017 and extremely dry years during 1812, 1833, 1996, 2002, 2004, and 2005. The extremely dry and wet years well coincided with major catastrophic historical and instrumental droughts and floods in the region. Furthermore, the reconstructed data are also validated by the significant positive correlation (r = 0.36, p < 0.001, n = 163) with the all Indian summer monsoon rainfall series. Such data will be useful to predict the incidence of future droughts, which can help to assess the vulnerability of the forest ecosystem to extreme events.
Evaluation of the regional climate model for the forest area of Yunnan in China
Authors: Deng Xiaofan , Zhang Zhe , Zhao Fan , Zhu Zheng , Wang Qiuhua
Published: January 2023

Climate change is becoming increasingly severe. Today, several studies have found that climate change substantially influences the increasing number of forest fires. Regional climate models (RCMs) are currently a vital tool for climate forecasting in researching how to combat forest fires. As China’s forest fire area, Yunnan province has frequent forest fires that generate significant losses, so it is a crucial area for forest fire prevention in China. Therefore, this study uses meteorological observational data from 25 stations in Yunnan over the period 2004–2018 to compares and evaluates the Regional Climate Forecast Model (RegCM) and Weather Research and Forecasting model (WRF) in multiple dimensions. The optimal RCM is then determined for the forest area of Yunnan. The results show that the deviations of RegCM predictions from the spatial mean of the real temperature are less than 3°C, whereas the deviations of WRF are all greater than 3°C. In addition, the RegCM correlation coefficient exceeds 0.8, whereas the WRF correlation coefficient exceeds 0.75. In terms of precipitation, the deviation of RegCM predictions for the whole territory is less than 2 mm, whereas the overall deviation of WRF predictions is great. The correlation coefficient for RegCM and WRF are both less than 0.5, but the RegCM correlation coefficient exceeds that of the WRF. We thus conclude that RegCM is more suitable for predicting the climate of the forest area of Yunnan. This study also provides references for related climate forecasting and research into forest fire dynamics in general.
Assessing carbon stocks and accumulation potential of mature forests and larger trees in U.S. federal lands
Authors: Birdsey Richard A. , DellaSala Dominick A. , Walker Wayne S. , Gorelik Seth R. , Rose Garett , Ramírez Carolyn E.
Published: January 2023

Mature and old-growth forests (collectively “mature”) and larger trees are important carbon sinks that are declining worldwide. Information on the carbon value of mature forests and larger trees in the United States has policy relevance for complying with President Joe Biden’s Executive Order 14072 directing federal agencies to define and conduct an inventory of them for conservation purposes. Specific metrics related to maturity can help land managers define and maintain present and future carbon stocks at the tree and forest stand level, while making an important contribution to the nation’s goal of net-zero greenhouse gas emissions by 2050. We present a systematic method to define and assess the status of mature forests and larger trees on federal lands in the United States that if protected from logging could maintain substantial carbon stocks and accumulation potential, along with myriad climate and ecological co-benefits. We based the onset of forest maturity on the age at which a forest stand achieves peak net primary productivity. We based our definition of larger trees on the median tree diameter associated with the tree age that defines the beginning of stand maturity to provide a practical way for managers to identify larger trees that could be protected in different forest ecosystems. The average age of peak net primary productivity ranged from 35 to 75 years, with some specific forest types extending this range. Typical diameter thresholds that separate smaller from larger trees ranged from 4 to 18 inches (10–46 cm) among individual forest types, with larger diameter thresholds found in the Western forests. In assessing these maturity metrics, we found that the unprotected carbon stock in larger trees in mature stands ranged from 36 to 68% of the total carbon in all trees in a representative selection of 11 National Forests. The unprotected annual carbon accumulation in live above-ground biomass of larger trees in mature stands ranged from 12 to 60% of the total accumulation in all trees. The potential impact of avoiding emissions from harvesting large trees in mature forests is thus significant and would require a policy shift to include protection of carbon stocks and future carbon accumulation as an additional land management objective on federal forest lands.
Epigenetic regulations as drivers of insecticide resistance and resilience to climate change in arthropod pests
Authors: Mogilicherla Kanakachari , Roy Amit
Published: January 2023

Arthropod pests are remarkably capable of rapidly adapting to novel forms of environmental stress, including insecticides and climate change. The dynamic interplay between epigenetics and genetics explains the largely unexplored reality underlying rapid climatic adaptation and the development of insecticide resistance in insects. Epigenetic regulation modulates gene expression by methylating DNA and acetylating histones that play an essential role in governing insecticide resistance and adaptation to climate change. This review summarises and discusses the significance of recent advances in epigenetic regulation that facilitate phenotypic plasticity in insects and their symbiotic microbes to cope with selection pressure implied by extensive insecticide applications and climate change. We also discuss how epigenetic changes are passed on to multiple generations through sexual recombination, which remains enigmatic. Finally, we explain how these epigenetic signatures can be utilized to manage insecticide resistance and pest resilience to climate change in Anthropocene.
Identification of two rare NPRL3 variants in two Chinese families with familial focal epilepsy with variable foci 3: NGS analysis with literature review
Authors: Hu Junji , Gao Xueping , Chen Longchang , Kan Yuling , Du Zhaoli , Xin Shuangqing , Ji Wenkai , Yu Qiang , Cao Lili
Published: January 2023

Background: The GAP Activity Towards Rags 1 (GATOR1) complex, which includes DEPDC5, NPRL2, and NPRL3, plays a key role in epilepsy. It has been reported that focal epilepsy is associated with mutations in the NPRL3 gene in some cases. We report two rare mutations in the NPRL3 gene in two unrelated Chinese families with focal epilepsy in this study.

Methods: The proband and her brother in family E1 first experienced seizures at 1.5 and 6 years of age, respectively. Despite resection of epileptogenic foci, she still suffered recurrent seizures. The first seizure of a 20-year-old male proband in family E2 occurred when he was 2 years old. To identify pathogenic variants in these families, whole-exome sequencing (WES) was performed on genomic DNA from peripheral blood.

Results: In family E1, the trio-WES analysis of the proband and her brother without apparent structural brain abnormalities identified a heterozygous variant in the NPRL3 gene (c.954C>A, p.Y318*, NM_001077350.3). In family E2, the proband carried a heterozygous NPRL3 mutation (c.1545-1G>C, NM_001077350.3). Surprisingly, the mothers of the two probands each carried the variants, but neither had an attack. Bioinformatics analysis predicted that the mutation (c.954C>A) was in the highly conserved amino acid residues of NPRL3, which affected the α-helix of NPRL3 protein, leading to a truncated protein. The splice variant (c.1545-1G>C) resulted in the loss of the last exon of the NPRL3 gene.

Conclusion: The results of this study provide a foundation for diagnosing NPRL3-related epilepsy by enriching their genotypes and phenotypes and help us identify the genetic etiologies of epilepsy in these two families.
The role of landscape evolution in the genetic diversification of a stream fish Sarcocheilichthys parvus from Southern China
Authors: Li Mingyue , Yang Xishu , Ni Xiaomin , Fu Cuizhang
Published: January 2023

Sarcocheilichthys parvus (Cypriniformes: Gobionidae) is a stream fish which is endemic to sub-tropical coastal drainages in southern China, thus offering a valuable model for understanding how genetic divergence arises in stream-adapting freshwater fishes in this region. Using the mitochondrial Cyt b gene, integrative analyses of phylogeny, population demography, and ancestral area and paleo-drainage reconstructions are carried out to explicitly explore the role of landscape evolution in genetic diversification of S. parvus. The time-calibrated phylogeny of S. parvus indicates the splitting of two major lineages (A and B) at ∼3.66 Ma. Lineage A inhabits the Poyang Lake sub-drainage of the middle Yangtze River, Han River and Pearl River, and can be split into two sub-lineages (A-I and A-II), where sub-lineage A-II can be further sub-divided into three infra-sub-lineages (A-IIa, A-IIb and A-IIc). Except for the infra-sub-lineage A-IIc, which is restricted to the Han River and Pearl River, the other sub-lineages and infra-sub-lineages live exclusively in the Poyang Lake sub-drainage. Lineage B lives in the lower Yangtze River, Qiantang River, Jiaojiang River and Ou River, displaying close genetic relationships among the drainages. Rapid population expansion has occurred since the Late Pleistocene. Our findings indicate that the splitting of lineages A and B could be attributed to geographic isolation due to the Zhe–Min Uplift, acting as a biogeographic barrier before the late Early Pleistocene. Furthermore, the strong genetic divergence within Lineage A could be explained by the isolation role of the Nanling Mountains and Poyang Lake acting as an ecological barrier; while the lack of phylogenetic structure within Lineage B may have been the result of paleo-drainage connections or episodic freshwater connections during the eustatic low stand of sea level in the late Middle–Late Pleistocene.
Transcriptome and pan-cancer system analysis identify PM2.5-induced stanniocalcin 2 as a potential prognostic and immunological biomarker for cancers
Authors: Zhu Dong , Liu Jiliu , Wang Junyi , Zhang Lei , Jiang Manling , Liu Yao , Xiong Ying , He Xiang , Li Guoping
Published: January 2023

Epidemiological studies have shown that air pollution and particulate matter (PM) are closely related to the occurrence of cancer. However, the potential prognostic and immunological biomarkers for air pollution related cancers are lacking. In this study, we proved PM2.5 exposure was correlated with lung cancer through transcriptome analysis. Importantly, we identified STC2 as a key gene regulated by PM2.5, whose expression in epithelial cells was significantly increased after PM2.5 treatment and validated by using RT-qPCR and immunofluorescence. Kaplan-Meier OS curves suggested that high STC2 expression positively correlated with a poor prognosis in lung cancer. Furthermore, we discovered that STC2 was associated with multiple cancers and pathways in cancer. Next, Pan-Cancer Expression Landscape of STC2 showed that STC2 exhibited inconsistent expression across 26 types of human cancer, lower in KIRP in cancer versus adjacent normal tissues, and significantly higher in another cancers. Cox regression results suggested that STC2 expression was positively or negatively associated with prognosis in different cancers. Moreover, STC2 expression was associated with clinical phenotypes including age, gender, stage and grade. Mutation features of STC2 were also analyzed, in which the highest alteration frequency of STC2 was presented in KIRC with amplification. Meanwhile, the effects of copy number variation (CNV) on STC2 expression were investigated across various tumor types, suggesting that STC2 expression was significantly correlated with CNV in tumors. Additionally, STC2 was closely related to tumor heterogeneity, tumor stemness and tumor immune microenvironment like immune cell infiltration. In the meantime, we analyzed methylation modifications and immunological correlation of STC2. The results demonstrated that STC2 expression positively correlated with most RNA methylation genes and immunomodulators across tumors. Taken together, the findings revealed that PM2.5-induced STC2 might be a potential prognostic and immunological biomarker for cancers related to air pollution.
A prognostic model based on clusters of molecules related to epithelial–mesenchymal transition for idiopathic pulmonary fibrosis
Authors: Zhao Jiarui , Wang Can , Fan Rui , Liu Xiangyang , Zhang Wei
Published: January 2023

Background: Most patients with idiopathic pulmonary fibrosis (IPF) have poor prognosis; Effective predictive models for these patients are currently lacking. Epithelial–mesenchymal transition (EMT) often occurs during idiopathic pulmonary fibrosis development, and is closely related to multiple pathways and biological processes. It is thus necessary for clinicians to find prognostic biomarkers with high accuracy and specificity from the perspective of Epithelial–mesenchymal transition.

Methods: Data were obtained from the Gene Expression Omnibus database. Using consensus clustering, patients were grouped based on Epithelial–mesenchymal transition-related genes. Next, functional enrichment analysis was performed on the results of consensus clustering using gene set variation analysis. The gene modules associated with Epithelial–mesenchymal transition were obtained through weighted gene co-expression network analysis. Prognosis-related genes were screened via least absolute shrinkage and selection operator (LASSO) regression analysis. The model was then evaluated and validated using survival analysis and time-dependent receiver operating characteristic (ROC) analysis.

Results: A total of 239 Epithelial–mesenchymal transition-related genes were obtained from patients with idiopathic pulmonary fibrosis. Six genes with strong prognostic associations (C-X-C chemokine receptor type 7 [CXCR7], heparan sulfate-glucosamine 3-sulfotransferase 1 [HS3ST1], matrix metallopeptidase 25 [MMP25], murine retrovirus integration site 1 [MRVI1], transmembrane four L6 family member 1 [TM4SF1], and tyrosylprotein sulfotransferase 1 [TPST1]) were identified via least absolute shrinkage and selection operator and Cox regression analyses. A prognostic model was then constructed based on the selected genes. Survival analysis showed that patients with high-risk scores had worse prognosis based on the training set [hazard ratio (HR) = 7.31, p < .001] and validation set (HR = 2.85, p = .017). The time-dependent receiver operating characteristic analysis showed that the area under the curve (AUC) values in the training set were .872, .905, and .868 for 1-, 2-, and 3-year overall survival rates, respectively. Moreover, the area under the curve values in the validation set were .814, .814, and .808 for 1-, 2-, and 3-year overall survival rates, respectively.

Conclusion: The independent prognostic model constructed from six Epithelial–mesenchymal transition-related genes provides bioinformatics guidance to identify additional prognostic markers for idiopathic pulmonary fibrosis in the future.
Case report: LAMC3-associated cortical malformations: Case report of a novel stop-gain variant and literature review
Authors: Falcicchio Giovanni , Riva Antonella , La Neve Angela , Iacomino Michele , Lastella Patrizia , Suppressa Patrizia , Sciruicchio Vittorio , Trojano Maria , Striano Pasquale
Published: January 2023

Background: Malformations of cortical development (MCDs) can lead to peculiar neuroradiological patterns and clinical presentations (i.e., seizures, cerebral palsy, and intellectual disability) according to the specific genetic pathway of the brain development involved; and yet a certain degree of phenotypic heterogeneity exists even when the same gene is affected. Here we report a man with an malformations of cortical development extending beyond occipital lobes associated with a novel stop-gain variant in LAMC3.

Case presentation: The patient is a 28-year-old man suffering from drug-resistant epilepsy and moderate intellectual disability. He underwent a brain magnetic resonance imaging showing polymicrogyria involving occipital and temporal lobes bilaterally. After performing exome sequencing, a novel stop-gain variant in LAMC3 (c.3871C>T; p. Arg1291*) was identified. According to the cortical alteration of the temporal regions, temporal seizures were detected; instead, the patient did not report occipital seizures. Different pharmacological and non-pharmacological interventions (i.e., vagus nerve stimulation) were unsuccessful, even though a partial seizure reduction was obtained after cenobamate administration.

Conclusion: Our case report confirms that variants of a gene known to be related to specific clinical and neuroradiological pictures can unexpectedly lead to new phenotypes involving different areas of the brain.
Bispecific killer cell engager with high affinity and specificity toward CD16a on NK cells for cancer immunotherapy
Authors: Nikkhoi Shahryar Khoshtinat , Li Geng , Eleya Suha , Yang Ge , Vandavasi Venu Gopal , Hatefi Arash
Published: January 2023

Introduction

The Fc region of monoclonal antibodies (mAbs) interacts with the CD16a receptor on natural killer (NK) cells with “low affinity” and “low selectivity”. This low affinity/selectivity interaction results in not only suboptimal anticancer activity but also induction of adverse effects. CD16a on NK cells binds to the antibody-coated cells, leading to antibody-dependent cell-mediated cytotoxicity (ADCC). Recent clinical data have shown that the increased binding affinity between mAb Fc region and CD16a receptor is responsible for significantly improved therapeutic outcomes. Therefore, the objective of this study was to develop a bispecific killer cell engager (BiKE) with high affinity and specificity/selectivity toward CD16a receptor for NK cell-based cancer immunotherapy.

Methods

To engineer BiKE, a llama was immunized, then high binding anti-CD16a and anti-HER2 VHH clones were isolated using phage display. ELISA, flow cytometry, and biolayer interferometry (BLI) data showed that the isolated anti-CD16a VHH has high affinity (sub-nanomolar) toward CD16a antigen without cross-reactivity with CD16b-NA1 on neutrophils or CD32b on B cells. Similarly, the data showed that the isolated anti-HER2 VHH has high affinity/specificity toward HER2 antigen. Using a semi-flexible linker, anti-HER2 VHH was recombinantly fused with anti-CD16a VHH to create BiKE:HER2/CD16a. Then, the ability of BiKE:HER2/CD16a to activate NK cells to release cytokines and kill HER2+ cancer cells was measured. As effector cells, both high-affinity haNK92 (CD16+, V176) and low-affinity laNK92 (CD16+, F176) cells were used.

Results and discussion

The data showed that the engineered BiKE:HER2/CD16a activates haNK92 and laNK92 cells to release cytokines much greater than best-in-class mAbs in the clinic. The cytotoxicity data also showed that the developed BiKE induces higher ADCC to both ovarian and breast cancer cells in comparison to Trazimera™ (trastuzumab). According to the BLI data, BiKE:HER2/CD16 recognizes a different epitope on CD16a antigen than IgG-based mAbs; thus, it provides the opportunity for not only monotherapy but also combination therapy with other antibody drugs such as checkpoint inhibitors and antibody-drug conjugates. Taken together, the data demonstrate the creation of a novel BiKE with high affinity and specificity toward CD16a on NK cells with the potential to elicit a superior therapeutic response in patients with HER2+ cancer than existing anti-HER2 mAbs.
Phenotypic and functional alteration of CD45+ immune cells in the decidua of preeclampsia patients analyzed by mass cytometry (CyTOF)
Authors: Fu Min , Zhang Xiaowei , Liu Chunfeng , Lyu Jinli , Liu Xinyang , Zhong Shilin , Liang Yiheng , Liu Ping , Huang Liting , Xiao Zhansong , Wang Xinxin , Liang Xiaoling , Wang Hao , Fan Shangrong
Published: January 2023

Preeclampsia (PE) is a severe placenta-related pregnancy disease that has been associated with maternal systemic inflammation and immune system disorders. However, the distribution and functional changes in immune cells of the maternal–placental interface have not been well characterized. Herein, cytometry by time-of-flight mass spectrometry (CyTOF) was used to investigate the immune atlas at the decidua, which was obtained from four PE patients and four healthy controls. Six superclusters were identified, namely, T cells, B cells, natural killer (NK) cells, monocytes, granulocytes, and others. B cells were significantly decreased in the PE group, among which the reduction in CD27+CD38+ regulatory B cell (Breg)-like cells may stimulate immune activation in PE. The significantly increased migration of B cells could be linked to the significantly overexpressed chemokine C-X-C receptor 5 (CXCR5) in the PE group, which may result in the production of excessive autoantibodies and the pathogenesis of PE. A subset of T cells, CD11c+CD8+ T cells, was significantly decreased in PE and might lead to sustained immune activation in PE patients. NK cells were ultimately separated into four subsets. The significant reduction in a novel subset of NK cells (CD56-CD49a-CD38+) in PE might have led to the failure to suppress inflammation at the maternal–fetal interface during PE progression. Moreover, the expression levels of functional markers were significantly altered in the PE group, which also inferred that shifts in the decidual immune state contributed to the development of PE and might serve as potential treatment targets. This is a worthy attempt to elaborate the differences in the phenotype and function of CD45+ immune cells in the decidua between PE and healthy pregnancies by CyTOF, which contributes to understand the pathogenesis of PE, and the altered cell subsets and markers may inspire the immune modulatory therapy for PE.
Pathways to integrate Indigenous and local knowledge in ocean governance processes: Lessons from the Algoa Bay Project, South Africa
Authors: Rivers Nina , Strand Mia , Fernandes Meredith , Metuge Denning , Lemahieu Anne , Nonyane Chilo Loyolah , Benkenstein Alex , Snow Bernadette
Published: January 2023

The Introduction of this paper argues that current coastal and ocean management approaches like marine spatial planning (MSP) often do not adequately acknowledge and integrate Indigenous and Local Knowledge (ILK). This is problematic because how humans value and perceive coastal and marine resources is integrally linked to how they use and manage these resources, especially in adapting to social-ecological change. Coastal and marine resources are situated within complex social-ecological systems that are culturally, economically, historically and politically embedded. Therefore, management approaches have to integrate transdisciplinary and contextual perspectives in order to be relevant, sustainable and adaptive. Following extensive research in Algoa Bay, South Africa this article highlights several pathways to bridge the gap between existing ILK and current coastal and ocean management approaches. The Methods section discusses how the authors worked in tandem with a bottom-up (engaging with Indigenous and local coastal and marine resource users) and top-down (engaging with coastal governance authorities and practitioners) approach. In order to answer the primary research question “How can ILK be integrated into area-based ocean management like MSP”? the authors employed arts-based participatory methods as well as in-depth interviews and workshops with coastal governance authorities and practitioners over several months. This work then culminated in a one-day multi-stakeholder workshop which brought both ILK holders and coastal authorities and practitioners together to collaboratively identify pathways to integrate this knowledge into coastal and ocean management. In the Results and Discussion section the authors present and discuss five co-identified pathways to integrate ILK in coastal and ocean management which include: adopting contextual approaches to coastal and ocean management; increasing transparency and two-way communication between coastal authorities and users; increasing access to relevant and useable information; reviewing and amending relevant MSP legislation towards a stronger connection between MSP and Indigenous knowledge legislation; as well as amending legislation pertaining to access to coastal and marine areas. In the Conclusion it is argued that ILK coastal communities want to be meaningfully included in how their coastline and ocean resources are managed and also seek increased access to coastal areas. By highlighting pathways to include ILK and the knowledge holders themselves, this paper seeks to contribute to improved protection and sustainable management of marine resource use.
Effect of salinity on the biochemical characteristics and antioxidant activity of exopolysaccharide of Porphyridium purpureum FACHB 806
Authors: Li Qianmei , Chen Yi , Liu Xuan , Li Yi , Xu Jin , Li Tao , Xiang Wenzhou , Li Aifen
Published: January 2023

Porphyridium exopolysaccharide (EPS) is a kind of high-value biopolymer with various biological activities secreted by microalgae belonging to Porphyridium genus. Salinity is one of the important environmental factors affecting the growth of microalgae. In order to study the effect of salinity, the yield, biochemical characteristics and antioxidant activity of EPS in Porphyridium purpureum FACHB 806 cultured at four salinity levels (5‰, 20‰, 35‰ and 50‰) were investigated in this study. The results demonstrated that P. purpureum FACHB 806 could grow at all salinity levels. The highest cell density and EPS yield per cell were 6.6 × 107 cells·mL-1 and 29.1 pg·cell-1, which were obtained in the 20‰ and 50‰ salinity, respectively. With the increase of salinity, the percentage of xylose and galactose decreased while the percentage of glucose increased. Among all salinity levels, the 5‰ salinity group achieved the maximum contents of total carbohydrate and uronic acid of EPS, and the 50‰ salinity obtained the highest protein content of EPS. Compared to the 20‰ and 35‰ salinity groups, EPS of the 5‰ and 50‰ salinity showed stronger hydroxyl radical scavenging ability. These results indicated that salinity could influence the yield, biochemical composition and antioxidant activity of EPS, which will provide a new strategy to improve the yield and antioxidant activity of EPS.
Mixing in the upper western equatorial Pacific driven by westerly wind event
Authors: Shen Duhan , Wang Jianing , Liu Zhiyu , Wang Fan
Published: January 2023

Diapycnal mixing in the upper western equatorial Pacific (WEP) plays an important role in the tropical air–sea interactions and in the formation of the global climate system. Yet, the WEP is uniquely rich in water masses originating from the two hemispheres and in multiscale processes of different dynamical nature, thus creating a complex regime of mixing remains to be fully characterized by elaborate observations. Here, on the basis of microstructure measurements in the WEP, we report the observations on a strong deep cycle turbulence extending well into the upper thermocline by westerly wind event, with the turbulent kinetic energy dissipation rate ε~O(10−8–10−7) W kg−1 and diapycnal diffusivity Kρ∼O(10−4) m2 s−1. Below the deep cycle turbulence layer, turbulence and mixing are generally weak with ε~O(10−10–10−9) W kg−1 and Kρ∼O(10−7–10−6) m2 s−1, a prototype of the weak mixing nature of the low-latitude western Pacific. The observed turbulence below the deep cycle turbulence layer can be satisfactorily scaled by either the MacKinnon–Gregg model or the Richardson number–based model with tuned model parameters.
A decade of humpback whale abundance estimates at Bermuda, an oceanic migratory stopover site
Authors: Grove Thomas , King Ruth , Stevenson Andrew , Henry Lea-Anne
Published: January 2023

We constructed annual abundance of a migratory baleen whale at an oceanic stopover site to elucidate temporal changes in Bermuda, an area with increasing anthropogenic activity. The annual abundance of North Atlantic humpback whales visiting Bermuda between 2011 and 2020 was estimated using photo-identification capture-recapture data for 1,204 whales, collected between December 2009 and May 2020. Owing to a sparse data set, we combined a Cormack-Jolly-Seber (CJS) model, fit through maximum likelihood estimation, with a Horvitz-Thompson estimator to calculate abundance and used stratified bootstrap resampling to derive 95% confidence intervals (CI). We accounted for temporal heterogeneity in detection and sighting ratesviaa catch-effort model and, guided by goodness-of-fit testing, considered models that accounted for transience. A model incorporating modified sighting effort and time-varying transience was selected using (corrected) Akaike’s Information Criterion (AICc). The survival probability of non-transient animals was 0.97 (95% CI 0.91-0.98), which is comparable with other studies. The rate of transience increased gradually from 2011 to 2018, before a large drop in 2019. Abundance varied from 786 individuals (95% CI 593-964) in 2016 to 1,434 (95% CI 924-1,908) in 2020, with a non-significant linear increase across the period and interannual fluctuations. These abundance estimates confirm the importance of Bermuda for migrating North Atlantic humpback whales and should encourage a review of cetacean conservation measures in Bermudian waters, including area-based management tools. Moreover, in line with the time series presented here, regional abundance estimates should be updated across the North Atlantic to facilitate population monitoring over the entire migratory range.
Frequency-diverse MIMO metasurface antenna for computational imaging with aperture rotation technique
Authors: Wang Tong , Han Jiaqi , Ma Xiangjin , Liu Haixia , Li Long
Published: January 2023

Metasurface antennas have been proposed for computational imaging (CI) systems, which can reconstruct images without using mechanical scanning or large antenna arrays. In a CI system based on metasurface antennas, a variety of different radiation fields, which can be applied to sample the objects, are generated by exciting different frequency points in broadband. According to the compressed sensing theory, the imaging performance of the system is mainly limited by frequency-diversity radiation modes. In general, it is difficult to achieve rich radiation modes; therefore, a special design of metasurface aperture is required. In this paper, we propose a frequency-diversity MIMO metasurface antenna that consists of 2 × 2 sub-apertures with randomly distributed surface impedance. By employing the aperture rotation technique (ART) which rotates the MIMO metasurface antenna around the panel axis, the pseudo-randomness of the radiation fields is utilized. The diversity of the radiation field is improved on the premise of ensuring the relatively low complexity of the system. The ART significantly improves the measurement richness at the cost of increasing the measurement time. The performance of the proposed method is evaluated through simulations and experiments, suggesting that the proposed 2 × 2 MIMO metasurface antenna and the ART are effective to reconstruct high-quality images.
Predicting melanoma survival and metastasis with interpretable histopathological features and machine learning models
Authors: Couetil Justin , Liu Ziyu , Huang Kun , Zhang Jie , Alomari Ahmed K.
Published: January 2023

Introduction

Melanoma is the fifth most common cancer in US, and the incidence is increasing 1.4% annually. The overall survival rate for early-stage disease is 99.4%. However, melanoma can recur years later (in the same region of the body or as distant metastasis), and results in a dramatically lower survival rate. Currently there is no reliable method to predict tumor recurrence and metastasis on early primary tumor histological images.

Methods

To identify rapid, accurate, and cost-effective predictors of metastasis and survival, in this work, we applied various interpretable machine learning approaches to analyze melanoma histopathological H&E images. The result is a set of image features that can help clinicians identify high-risk-of-metastasis patients for increased clinical follow-up and precision treatment. We use simple models (i.e., logarithmic classification and KNN) and “human-interpretable” measures of cell morphology and tissue architecture (e.g., cell size, staining intensity, and cell density) to predict the melanoma survival on public and local Stage I–III cohorts as well as the metastasis risk on a local cohort.

Results

We use penalized survival regression to limit features available to downstream classifiers and investigate the utility of convolutional neural networks in isolating tumor regions to focus morphology extraction on only the tumor region. This approach allows us to predict survival and metastasis with a maximum F1 score of 0.72 and 0.73, respectively, and to visualize several high-risk cell morphologies.

Discussion

This lays the foundation for future work, which will focus on using our interpretable pipeline to predict metastasis in Stage I & II melanoma.
Normal tension glaucoma: A dynamic optical coherence tomography angiography study
Authors: Van Eijgen Jan , Heintz Alexander , van der Pluijm Claire , Delporte Margaux , De Witte Dries , Molenberghs Geert , Barbosa-Breda João , Stalmans Ingeborg
Published: January 2023

Purpose

Vascular dysregulation seems to play a role in the pathogenesis of glaucoma, in particular normal tension glaucoma (NTG). The development of optical coherence tomography angiography (OCTA) enabled the measurement of the retinal microvasculature non-invasively and with high repeatability. Nonetheless, only a few studies transformed OCTA into a dynamic examination employing a sympathomimetic stimulus. The goal of this study was to use this dynamic OCTA exam (1) to differentiate healthy individuals from glaucoma patients and (2) to distinguish glaucoma subcategories, NTG and high-tension primary open angle glaucoma (POAG).

Methods

Retinal vessel density (VD) in NTG patients (n = 16), POAG patients (n = 12), and healthy controls (n = 14) was compared before and during a hand grip test with a hydraulic dynamometer.

Results

At baseline, mean peripapillary VD was lower in POAG and NTG (42.6 and 48.5%) compared to healthy controls (58.1%; p < 0.001) and higher in NTG compared to POAG (p = 0.024) when corrected for mean arterial pressure (MAP). Peripapillary and macular (superficial and deep) VD differences were found for gender, age, and baseline MAP. No change in VD occurred (pre-/post-stimulus) in any of the groups.

Conclusion

Retinal VD loss in glaucoma patients was confirmed and the necessity to correct for gender, age and especially MAP was established. Although replication in a larger population is necessary, OCTA might not be the most suitable method to dynamically evaluate the retinal microvasculature.
CARE-NS, a research strategy for neurosyphilis
Authors: Du Fang-Zhi , Zhang Xu , Zhang Rui-Li , Wang Qian-Qiu
Published: January 2023

Neurosyphilis is a major clinical manifestation of syphilis. In recent years, an increase in neurosyphilis cases has been reported in many countries. The overall incidence of neurosyphilis remains unknown, and there is a lack of understanding of the disease pathogenesis, which hampers clinical management, development of prevention strategies, and control. This article proposes the CARE-NS research strategy to enhance the clinical management of neurosyphilis, which consists of six key features: comprehensive management including multidisciplinary treatment (C), alleviating neurological impairment and sequelae (A), risk factors and clinical epidemiology (R), etiology and pathogenesis (E), new diagnostic indicators and strategies (N), and social impact and cost-effectiveness analysis (S).
A scoping review on the use and usefulness of online symptom checkers and triage systems: How to proceed?
Authors: Pairon Anthony , Philips Hilde , Verhoeven Veronique
Published: January 2023

Background

Patients are increasingly turning to the Internet for health information. Numerous online symptom checkers and digital triage tools are currently available to the general public in an effort to meet this need, simultaneously acting as a demand management strategy to aid the overburdened health care system. The implementation of these services requires an evidence-based approach, warranting a review of the available literature on this rapidly evolving topic.

Objective

This scoping review aims to provide an overview of the current state of the art and identify research gaps through an analysis of the strengths and weaknesses of the presently available literature.

Methods

A systematic search strategy was formed and applied to six databases: Cochrane library, NICE, DARE, NIHR, Pubmed, and Web of Science. Data extraction was performed by two researchers according to a pre-established data charting methodology allowing for a thematic analysis of the results.

Results

A total of 10,250 articles were identified, and 28 publications were found eligible for inclusion. Users of these tools are often younger, female, more highly educated and technologically literate, potentially impacting digital divide and health equity. Triage algorithms remain risk-averse, which causes challenges for their accuracy. Recent evolutions in algorithms have varying degrees of success. Results on impact are highly variable, with potential effects on demand, accessibility of care, health literacy and syndromic surveillance. Both patients and healthcare providers are generally positive about the technology and seem amenable to the advice given, but there are still improvements to be made toward a more patient-centered approach. The significant heterogeneity across studies and triage systems remains the primary challenge for the field, limiting transferability of findings.

Conclusion

Current evidence included in this review is characterized by significant variability in study design and outcomes, highlighting the significant challenges for future research.

An evolution toward more homogeneous methodologies, studies tailored to the intended setting, regulation and standardization of evaluations, and a patient-centered approach could benefit the field.
Reproducibility and rigor in rheumatology research
Authors: Alnaimat Fatima , Sweis Nadia J. , Sweis Jaleel Jerry G. , Ascoli Christian , Korsten Peter , Rubinstein Israel , Sweiss Nadera J.
Published: January 2023

The pillars of scientific progress in rheumatology are experimentation and observation, followed by the publication of reliable and credible results. These data must then be independently verified, validated, and replicated. Peer and journal-specific technical and statistical reviews are paramount to improving rigor and reproducibility. In addition, research integrity, ethics, and responsible conduct training can help to reduce research misconduct and improve scientific evidence. As the number of published articles in rheumatology grows, the field has become critical for determining reproducibility. Prospective, longitudinal, randomized controlled clinical trials are the gold standard for evaluating clinical intervention efficacy and safety in this space. However, their applicability to larger, more representative patient populations with rheumatological disorders worldwide could be limited due to time, technical, and cost constraints involved with large-scale clinical trials. Accordingly, analysis of real-world, patient-centered clinical data retrieved from established healthcare inventories, such as electronic health records, medical billing reports, and disease registries, are increasingly used to report patient outcomes. Unfortunately, it is unknown whether this clinical research paradigm in rheumatology could be deployed in medically underserved regions.