bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity and temporal distribution of Fusarium oxysporum f. sp. vasinfectum races and genotypes as influenced by Gossypium cultivar
Authors: Dyer David R. , Newman Molli , Lawrence Kathy S.
Published: October 2022

This study assess the population diversity and temporal variability of caused byFusarium oxysporumf. sp.vasinfectum(FOV) races/genotypes infecting cotton cultivars with either FOV orMeloidogyne incognitaresistance. All plants sampled demonstrated typical symptoms of FOV including wilting, chlorosis and necrosis of the leaves, and discoloration of the vascular tissue in the stem. A diverse population of FOV was characterized. Eight races/genotypes of FOV were collected throughout the three site years. FOV race 1 was the most predominant in all tests (AUDPC=101.1); statistically higher numbers of isolates from LA-108 (AUDPC=59.9), race 8 (AUDPC=47.5), and race 2 (AUDPC=38.6) were also found compared to other races and genotypes collected. FOV race 1, race 2, race 8, and 108 were the most virulent races identified. The genotypes MDS-12, LA-110, and LA-127/140 were found in all tests but at a low incidence, and LA-112 was only found in trace amounts. MDS-12, LA-110, LA-112, and LA-127/140 produced less disease pressure. FOV race 4 which is highly virulent and present in California and Texas was not found in Alabama. A positive correlation was observed between the accumulation of growing degree days and FOV race 1, race 2, race 8, LA-108, and LA-110. Later symptom expression influenced by seasonal heat partially mitigates damage allowing cotton to produce bolls though they may be reduced in number and lint quality. Plant resistance to the FOV as expressed in these cultivars appears to provide better protection thanM. incognitaresistance. PhytoGen 72, which is resistant to FOV races/genotypes had low levels of FOV infection even though it sustained a high level ofM. incognitaroot population density. TheM. incognitaresistant cultivars Deltapine 1558NR B2RF and PhytoGen 480 W3FE supported a lower nematode population density, however, FOV disease incidence was not reduced. FOV races/genotypes did not vary significantly between the nematode resistant and nematode susceptible cultivars.
Identification of a prognostic risk-scoring model and risk signatures based on glycosylation-associated cluster in breast cancer
Authors: Gao Shengnan , Wu Xinjie , Lou Xiaoying , Cui Wei
Published: October 2022

Breast cancer is a heterogeneous disease whose subtypes represent different histological origins, prognoses, and therapeutic sensitivity. But there remains a strong need for more specific biomarkers and broader alternatives for personalized treatment. Our study classified breast cancer samples from The Cancer Genome Atlas (TCGA) into three groups based on glycosylation-associated genes and then identified differentially expressed genes under different glycosylation patterns to construct a prognostic model. The final prognostic model containing 23 key molecules achieved exciting performance both in the TCGA training set and testing set GSE42568 and GSE58812. The risk score also showed a significant difference in predicting overall clinical survival and immune infiltration analysis. This work helped us to understand the heterogeneity of breast cancer from another perspective and indicated that the identification of risk scores based on glycosylation patterns has potential clinical implications and immune-related value for breast cancer.
Exploration of shared features of B cell receptor and T cell receptor repertoires reveals distinct clonotype clusters
Authors: Hong Sang Bin , Shin Yong-Won , Hong Ja Bin , Lee Sang Kun , Han Buhm
Published: October 2022

Although B cells and T cells are integral players of the adaptive immune system and act in co-dependent ways to orchestrate immune responses, existing methods to study the immune repertoire have largely focused on separate analyses of B cell receptor (BCR) and T cell receptor (TCR) repertoires. Based on our hypothesis that the shared history of immune exposures and the shared cellular machinery for recombination result in similarities between BCR and TCR repertoires in an individual, we examine any commonalities and interrelationships between BCR and TCR repertoires. We find that the BCR and TCR repertoires have covarying clonal architecture and diversity, and that the pattern of correlations appears to be altered in immune-mediated diseases. Furthermore, hierarchical clustering of public B and T cell clonotypes in both health and disease based on correlation of clonal proportion revealed distinct clusters of B and T cell clonotypes that exhibit increased sequence similarity, share motifs, and have distinct amino acid characteristics. Our findings point to common principles governing memory formation, recombination, and clonal expansion to antigens in B and T cells within an individual. A significant proportion of public BCR and TCR repertoire can be clustered into nonoverlapping and correlated clusters, suggesting a novel way of grouping B and T cell clonotypes.
Association of smoking status with non-small cell lung cancer patients harboring uncommon epidermal growth factor receptor mutation
Authors: Ko How-Wen , Shie Shian-Sen , Wang Chih-Wei , Chiu Chi-Tsun , Wang Chih-Liang , Yang Tsung-Ying , Chou Shou-Chu , Liu Chien-Ying , Kuo Chih-Hsi Scott , Lin Yu-Ching , Li Li-Fu , Yang Cheng-Ta , Wang Chin-Chou
Published: October 2022

Introduction

Uncommon epidermal growth factor receptor (EGFR) mutations include single and complex mutations. However, the association of the smoking status of patients with uncommon and complex EGFR mutations remains unclear.

Methods

This retrospective study evaluates the spectrum of uncommon EGFR mutations and investigates the influence of smoking status on the frequency of various uncommon EGFR mutations using a multi-institutional medical database.

Results

Between 2010 and 2019, 5,608 non-small cell lung cancer (NSCLC) patients were analyzed. EGFR mutations were detected in 3,155 (56.3%) patients. Among the 399 (12.6%) patients with uncommon mutations, 198 had single uncommon and 201 complex mutations, including 87 exon 20 insertions, 79 de novo T790M, 70 complex common, and 52 complex uncommon mutations. For comparison, we also included 402 patients with common EGFR mutations. The percentage of ever-smokers was significantly higher in patients with uncommon EGFR mutations than in patients with common EGFR mutations (25.8% vs. 17.4%, p = 0.005). Furthermore, the percentage of ever-smokers was higher in those with a complex mutation than in those with a single uncommon mutation (30.3% vs. 21.2%, p = 0.040). Among patients carrying uncommon EGFR mutations, ever-smokers had significantly more complex uncommon EGFR mutations than never-smokers (22.3% vs. 9.8%, p = 0.002). Among patients carrying G719X, L861Q, and S768I, ever-smokers tended to have complex EGFR mutations more frequently than never-smokers (64.7% vs. 28.7%, 50.0% vs. 18.7%, 88.9% vs. 81.2%, respectively).

Conclusions

Our study demonstrates not only a comprehensive spectrum of uncommon EGFR mutations, but also a positive relationship between smoking status and uncommon EGFR mutation frequency, especially complex uncommon EGFR mutations. The results suggest that smoking contributes to the development of complex EGFR mutations.
CEACAM 1, 3, 5 and 6 -positive classical monocytes correlate with interstitial lung disease in early systemic sclerosis
Authors: Yokoyama Kana , Mitoma Hiroki , Kawano Shotaro , Yamauchi Yusuke , Wang Qiaolei , Ayano Masahiro , Kimoto Yasutaka , Ono Nobuyuki , Arinobu Yojiro , Akashi Koichi , Horiuchi Takahiko , Niiro Hiroaki
Published: October 2022

Background

Systemic sclerosis (SSc) is a multiple-organ disease characterized by vascular damage, autoimmunity, and tissue fibrosis. Organ injuries such as interstitial lung diseases (ILD), resulting from inflammatory and fibrosis processes, lead to poor prognosis. Although autoantibodies are detected in the serum of patients with SSc, the mechanisms by which immune cells are involved in tissue inflammation and fibrosis is not fully understood. Recent studies have revealed carcinoembryonic antigen related cell adhesion molecule (CEACAM)-positive monocytes are involved in murine bleomycin-induced lung fibrosis. We investigated CEACAM-positive monocytes in patients with SSc to clarify the role of monocytes in the pathogenesis of SSc.

Methods

The proportion of of CEACAM-positive classical monocytes in healthy controls (HCs) and patients with rheumatoid arthritis (RA) and SSc was evaluated using flow cytometry. The correlation between the proportion of CEACAM-positive monocytes and clinical parameters was analyzed in patients with SSc. Gene expression microarrays were performed in CEACAM-positive and negative monocytes in patients with SSc. Infiltration of CEACAM-positive monocytes into scleroderma skin was evaluated by immunohistochemical staining.

Results

The proportion of CEACAM-positive classical monocytes was increased in patients with early SSc within 2 years after diagnosis, which positively correlated with ESR, serum IgG, and serum KL-6 and negatively correlated with %forced vital capacity. The percentage of CEACAM-positive monocytes decreased after immunosuppressive therapy. CEACAM6-positive cells among classical monocytes were significantly increased in patients with SSc compared with HCs and patients with rheumatoid arthritis. SSc serum induced CEACAM6 expression on monocytes from HCs. Functionally, CEACAM-positive monocytes produced higher levels of TNF-α and IL-1β compared to CEACAM-negative cells and showed activation of the NF-κB pathway. Furthermore, CEACAM6-positive monocytes infiltrated the dermis of SSc.

Conclusions

CEACAM-positive monocytes showed inflammatory phenotypes and may be involved in the tissue inflammation and fibrosis in early SSc. CEACAM-positive monocytes may be one of biomarkers to detect patients with progressive ILD, requiring therapeutic intervention.
Preclinical characterization and phase I clinical trial of CT053PTSA targets MET, AXL, and VEGFR2 in patients with advanced solid tumors
Authors: Ma Yu-Xiang , Liu Fu-Rong , Zhang Yang , Chen Qun , Chen Zhi-Qiang , Liu Qian-Wen , Huang Yan , Yang Yun-Peng , Fang Wen-Feng , Xi Ning , Kang Ning , Zhuang Yu-Lei , Zhang Qi , Jiang Ying-Zhi , Zhang Li , Zhao Hong-Yun
Published: October 2022

Background

CT053PTSA is a novel tyrosine kinase inhibitor that targets MET, AXL, VEGFR2, FLT3 and MERTK. Here, we present preclinical data about CT053PTSA, and we conducted the first-in-human (FIH) study to evaluate the use of CT053PTSA in adult patients with pretreated advanced solid tumors.

Methods

The selectivity and antitumor activity of CT053PTSA were assessed in cell lines in vitro through kinase and cellular screening panels and in cell line-derived tumor xenograft (CDX) and patient-derived xenograft (PDX) models in vivo. The FIH, phase I, single-center, single-arm, dose escalation (3 + 3 design) study was conducted, patients received at least one dose of CT053PTSA (15 mg QD, 30 mg QD, 60 mg QD, 100 mg QD, and 150 mg QD). The primary objectives were to assess safety and tolerability, to determine the maximum tolerated dose (MTD), dose-limiting toxicity (DLT), and the recommended dose of CT053PTSA for further study. Secondary objectives included pharmacokinetics, antitumor activity.

Results

CT053 (free-base form of CT053PTSA) inhibited MET, AXL, VEGFR2, FLT3 and MERTK phosphorylation and suppressed tumor cell angiogenesis by blocking VEGF and HGF, respectively, in vitro. Moreover, cell lines with high MET expression exhibited strong sensitivity to CT053, and CT053 blocked the MET and AXL signaling pathways. In an in vivo study, CT053 significantly inhibited tumor growth in CDX and PDX models. Twenty eligible patients were enrolled in the FIH phase I trial. The most common treatment-related adverse events were transaminase elevation (65%), leukopenia (45%) and neutropenia (35%). DLTs occurred in 3 patients, 1/6 in the 100 mg group and 2/4 in the 150 mg group, so the MTD was set to 100 mg. CT053PTSA was rapidly absorbed after the oral administration of a single dose, and the Cmax and AUC increased proportionally as the dose increased. A total of 17 patients in this trial underwent tumor imaging evaluation, and 29.4% had stable disease.

Conclusions

CT053PTSA has potent antitumor and antiangiogenic activity in preclinical models. In this FIH phase I trial, CT053PTSA was well tolerated and had a satisfactory safety profile. Further trials evaluating the clinical activity of CT053PTSA are ongoing.
Molecular profiling of core immune-escape genes highlights LCK as an immune-related prognostic biomarker in melanoma
Authors: Wang Fang , Zheng Anfu , Zhang Duoli , Zou Tao , Xiao Mintao , Chen Jie , Wen Bo , Wen Qinglian , Wu Xu , Li Mingxing , Du Fukuan , Chen Yu , Zhao Yueshui , Shen Jing , Xiang Shixin , Li Jing , Deng Shuai , Zhang Zhuo , Yi Tao , Xiao Zhangang
Published: October 2022

The tumor microenvironment is complicated and continuously evolving. This study was devoted to the identification of potential prognostic biomarkers based on the tumor microenvironment associated with immunotherapy for melanoma. This study integrates a couple of melanoma single cell and transcriptome sequencing datasets and performs a series of silico analyses as nicely as validation of molecular biology techniques. A core set of immune escape related genes was identified through Lawson et al. and the ImmPort portal. The differential proteins were identified through the cBioPortal database. Regression analysis was used to profile independent prognostic factors. Correlation with the level of immune cell infiltration was evaluated by multiple algorithms. The capacity of LCK to predict response was assessed in two independent immunotherapy cohorts. High LCK expression is associated with better prognosis, high levels of TILs and better clinical staging. Pathway analysis showed that high expression of LCK was significantly associated with activation of multiple tumor pathways as well as immune-related pathways. LCK expression tends to be higher in immunotherapy-responsive patients and those with lower IC50s treated with chemotherapeutic agents. RT-qPCR detected that LCK expression was significantly upregulated in melanoma cell lines. Single-cell transcriptome analysis showed that LCK was specifically highly expressed on T cells. CellChat analysis confirmed that LCK in C2 subpopulations and T cell subpopulations exerted immune promotion between cells by binding to CD8 receptors. In conclusion, LCK is a reliable biomarker for melanoma and will contribute to its immunotherapy.
Antibody based conditioning for allogeneic hematopoietic stem cell transplantation
Authors: Saha Asim , Blazar Bruce R.
Published: October 2022

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapeutic option for many patients with hematological malignancies and nonmalignant hematopoietic disorders. To achieve stable engraftment of donor hematopoietic stem cells (HSCs), recipient HSC deletion is needed to create space for incoming donor HSCs and donor HSCs must escape immune rejection by the recipient. Conventional allo-HSCT requires high dose of irradiation and/or chemotherapy to produce sufficient host stem cell and immune system ablation to permit donor HSC engraftment. However, these procedures also result in nonspecific tissue injury that can cause short- and long-term adverse effects as well as incite and amplify graft-versus-host-disease (GVHD). The delivery of targeted radiotherapy to hematopoietic tissues with the use of a radioimmunoconjugate (ROIC) as a part of transplant preparative regimen has shown clinical benefits. ROIC clinical data provide evidence for decreased relapse without increased transplant-related mortality by delivering higher targeted radiation to sites of malignancy than when given in a nontargeted fashion. An alternative approach to allo-HSCT has been developed and tested in preclinical mouse models in which nonmyeloablative preconditioning with low dose of the alkylating agent (busulfan) or lower systemic dose of irradiation combined with co-stimulatory pathway blockade (CTLA4-Ig, anti-CD40L monoclonal antibody) and/or immunosuppressive drugs have been used. Under these conditions, mixed chimerism and transplantation tolerance to fully MHC mismatched donor marrow was observed. Recently, several novel proof-of-concept antibody-mediated preconditioning methods have been developed that can selectively target hematopoietic stem and immune cells with minimal overall toxicity. Antibody-drug-conjugate (ADC) combined with reduced intensity conditioning or high dose ADC as single dose monotherapy have shown promise for allo-HSCT in preclinical models. The purpose of the current review is to discuss the literature exploring antibody-based conditioning that includes native antibody, radiolabeled antibody conjugates, and ADC for allo-HSCT.
A CD8+ T cell-associated immune gene panel for prediction of the prognosis and immunotherapeutic effect of melanoma
Authors: Sun Shanwen , Zhi Zhengke , Su Yang , Sun Jingxian , Li Qianjun
Published: October 2022

Background

Skin cutaneous melanoma (SKCM) is the most frequently encountered tumor of the skin. Immunotherapy has opened a new horizon in melanoma treatment. We aimed to construct a CD8+ T cell-associated immune gene prognostic model (CDIGPM) for SKCM and unravel the immunologic features and the benefits of immunotherapy in CDIGPM-defined SKCM groups.

Method

Single-cell SKCM transcriptomes were utilized in conjunction with immune genes for the screening of CD8+ T cell-associated immune genes (CDIGs) for succeeding assessment. Thereafter, through protein-protein interaction (PPI) networks analysis, univariate COX analysis, and multivariate Cox analysis, six genes (MX1, RSAD2, IRF2, GBP2, IFITM1, and OAS2) were identified to construct a CDIGPM. We detected cell proliferation of SKCM cells transfected with IRF2 siRNA. Then, we analyzed the immunologic features and the benefits of immunotherapy in CDIGPM-defined groups.

Results

The overall survival (OS) was much better in low-CDIGPM group versus high CDIGPM group in TCGA dataset and GSE65904 dataset. On the whole, the results unfolded that a low CDIGPM showed relevance to immune response-correlated pathways, high expressions of CTLA4 and PD-L1, a high infiltration rate of CD8+ T cells, and more benefits from immunotherapy.

Conclusion

CDIGPM is an good model to predict the prognosis, the potential immune escape from immunotherapy for SKCM, and define immunologic and molecular features.
SDF-1 expression and tumor-infiltrating lymphocytes identify clinical subtypes of triple-negative breast cancer with different responses to neoadjuvant chemotherapy and survival
Authors: Wang Ruo-Xi , Ji Peng , Gong Yue , Shao Zhi-Ming , Chen Sheng
Published: October 2022

Background

In this study, we investigated the prediction and prognostic value of SDF-1 for triple-negative breast cancer (TNBC) patients who underwent neoadjuvant chemotherapy (NAC) following standard radical surgery.

Methods

A total of 303 TNBC patients were included in this study. The NAC regimen was weekly paclitaxel plus carboplatin (PC) for all patients. SDF-1 and CXCR4 expression were measured at baseline and surgery via enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry (IHC), respectively. Correlations between variables and treatment response were studied, and Cox proportional hazards regression analysis was implemented for prognostic evaluation.

Results

Of the 303 patients, 103 (34.0%) experienced pathological complete response (pCR) after completion of NAC. Serum SDF-1 expression before NAC was significantly correlated with the abundance of TILs. A higher pCR rate was more likely to be observed in patients with lower serum SDF-1 levels before NAC (P=0.001, OR=0.997, 95% CI: 0.996-0.999) and higher levels of TILs (P=0.005). In the multivariate survival model for nonpCR patients, serum SDF-1 expression at surgery served as an independent prognostic value for survival (high level, HR=1.980, 95% CI: 1.170-3.350, low level was used as a reference; P=0.011). Additionally, the predictive and prognostic value of serum SDF-1 expression was significant in patients with high abundance of TILs but not in patients with low abundance of TILs.

Conclusions

This study contributes to the clarification of the value of serum SDF-1 to predict pCR and survival for TNBC patients who underwent NAC. This new serum marker, together with TILs, might help identify clinical subtypes of TNBC with different treatment responses and survival and play an important role in tailoring and modifying the NAC strategy for advanced TNBCs in the future.
Tidy up - The unfolded protein response in sepsis
Authors: Vivas Wolfgang , Weis Sebastian
Published: October 2022

Pathogens, their toxic byproducts, and the subsequent immune reaction exert different forms of stress and damage to the tissue of the infected host. This stress can trigger specific transcriptional and post-transcriptional programs that have evolved to limit the pathogenesis of infectious diseases by conferring tissue damage control. If these programs fail, infectious diseases can take a severe course including organ dysfunction and damage, a phenomenon that is known as sepsis and which is associated with high mortality. One of the key adaptive mechanisms to counter infection-associated stress is the unfolded protein response (UPR), aiming to reduce endoplasmic reticulum stress and restore protein homeostasis. This is mediated via a set of diverse and complementary mechanisms, i.e. the reduction of protein translation, increase of protein folding capacity, and increase of polyubiquitination of misfolded proteins and subsequent proteasomal degradation. However, UPR is not exclusively beneficial since its enhanced or prolonged activation might lead to detrimental effects such as cell death. Thus, fine-tuning and time-restricted regulation of the UPR should diminish disease severity of infectious disease and improve the outcome of sepsis while not bearing long-term consequences. In this review, we describe the current knowledge of the UPR, its role in infectious diseases, regulation mechanisms, and further clinical implications in sepsis.
Monocyte programming by cancer therapy
Authors: Patysheva Marina , Frolova Anastasia , Larionova Irina , Afanas'ev Sergey , Tarasova Anna , Cherdyntseva Nadezhda , Kzhyshkowska Julia
Published: October 2022

Monocytes in peripheral blood circulation are the precursor of essential cells that control tumor progression, that include tumor-associated macrophages (TAMs), dendritic cells (DCs) and myeloid-derive suppressor cells (MDSC). Monocytes-derived cells orchestrate immune reactions in tumor microenvironment that control disease outcome and efficiency of cancer therapy. Four major types of anti-cancer therapy, surgery, radiotherapy, chemotherapy, and most recent immunotherapy, affect tumor-associated macrophage (TAM) polarization and functions. TAMs can also decrease the efficiency of therapy in a tumor-specific way. Monocytes is a major source of TAMs, and are recruited to tumor mass from the blood circulation. However, the mechanisms of monocyte programming in circulation by different therapeutic onsets are only emerging. In our review, we present the state-of-the art about the effects of anti-cancer therapy on monocyte progenitors and their dedifferentiation, on the content of monocyte subpopulations and their transcriptional programs in the circulation, on their recruitment into tumor mass and their potential to give origin for TAMs in tumor-specific microenvironment. We have also summarized very limited available knowledge about genetics that can affect monocyte interaction with cancer therapy, and highlighted the perspectives for the therapeutic targeting of circulating monocytes in cancer patients. We summarized the knowledge about the mediators that affect monocytes fate in all four types of therapies, and we highlighted the perspectives for targeting monocytes to develop combined and minimally invasive anti-cancer therapeutic approaches.
Metagenomic analysis among water masses and sediments from the Southern Gulf of Mexico
Authors: Guerrero Abraham , Licea Alexei F. , Lizárraga-Partida M. L.
Published: October 2022

Selected water masses and sediment samples from the Southern Gulf of Mexico, were studied by bacterial sequencing the 16S rRNA to establish their community structure and discuss the results in relation to those reported by other authors using deep water masses or sediment samples. Forty-five water and 21 sediment samples were collected at selected sampling localities. Proteobacteria was the most abundant phylum of the bacterial community in both environments as well as the class Gammaproteobacteria and the order Alteromonadales. Concerning the family taxonomic category, Alteromonadaceae was the most abundant in the water masses, showing an increase in the deepest water masses. Woeseiaceae and Kiloniellaceae were the most abundant families in the sediments. The statistical pairwise comparison among the water masses showed significant differences between the maximum fluorescence (maxF), the minimum oxygen (minO), the Antarctic Intermediate Water (AAIW), and the North Atlantic Deep Water (NADW) water masses. Also, significant differences were observed between the maxF, minO, AAIW, NADW water masses, and the sediment environment. It was concluded that the maxF water mass showed significant differences in the deepest water masses and that the sediment environment presented a different structure of families from the water environment.
Physiological and transcriptomic responses to starvation in the corallivorous crown-of-thorn starfish
Authors: Yang Litong , Zhang Ying , Chen Huizhen , Gao Qian , Luo Peng , Hu Jianxing , Zheng Fanyu , Yuan Yunyu , Fu Liang , Chen Chang
Published: October 2022

The outbreak of coral-eating Acanthaster spp., commonly known as the Crown-of-Thorn Starfish (CoTS), contributes to a significant proportion of coral loss in the tropical Indo-Pacific region. After the dramatic loss of coral due to their predation, CoTS is expected to face food shortages before coral recovers, which is usually accompanied by the sudden disappearance of its population. To reveal the response of CoTS to starvation stress, we conducted a four-month starvation experiment to investigate the physiological and molecular changes in the stomach tissue by combining the metabolites and enzyme activity measurements with transcriptome analysis. The results showed that the concentrations of primary metabolites and associated enzyme activities, as well as the amount of total antioxidant were not significantly altered between fed and starved CoTS in any case. However, starvation suppressed the expression of the genes involved in glycolysis and citrate cycle, development and movement, but enhanced that of the genes associated with sleep promotion, immunity, lysosome and glucose supply. This suggests that long-term starvation may induce CoTS to enter into a dormancy-like status characterized by reduced unnecessary physical activities for survival, accelerated recycling of nutrients, and enhanced immunity.
The distribution of mycosporine-like amino acids in phytoplankton across a Southern Ocean transect
Authors: Weiss Elliot L. , Cape Mattias Rolf , Pan B. Jack , Vernet Maria , James Chase C. , Smyth Tim J. , Ha Sun-Yong , Iriarte José L. , Mitchell B. Greg
Published: October 2022

Interactions between phytoplankton and ultraviolet radiation (UVR: 280 – 400 nm) are undergoing changes dictated by variability in ocean temperature, the depth of mixed layers, nutrient availability, and the thickness of the ozone layer. There are a variety of mechanisms for phytoplankton to cope with UVR stress, one of the most prevalent being the presence of mycosporine-like amino acids (MAAs). Despite the importance of these molecules to phytoplankton fitness under UVR stress, knowledge of the diversity and distribution of these molecules in the world’s oceans is relatively limited. Here, the composition and distribution of MAAs in phytoplankton were examined in a transect across the Southern Ocean, crossing multiple fronts, from eastern New Zealand to the West Antarctic Peninsula in March and April of 2018. The highest concentration of MAAs (> 0.2 μg/L) was found between 50 and 60°S, as well as along a longitudinal gradient between 137.47 and 144.78°W. A strong correlation was found between a model of the preceding month’s UVR dosage experienced in the mixed layer and the ratio of MAAs to chlorophyll-a across the transect, indicating a relationship between the integrated history of light exposure and phytoplankton physiology. Haptophytes accounted for the majority of biomass north of the polar front (PF) and were strongly correlated with a diversity of MAAs. South of the PF a transition to a community dominated by diatoms was observed, with community composition changes strongly correlated to porphyra-334 concentrations. The data presented here provide a baseline for MAA abundance and association with specific phytoplankton taxa across the Southern Ocean amid a changing climate.
Assessing the ability of deep learning techniques to perform real-time identification of shark species in live streaming video from drones
Authors: Purcell Cormac R. , Walsh Andrew J. , Colefax Andrew P. , Butcher Paul
Published: October 2022

Over the last five years remotely piloted drones have become the tool of choice to spot potentially dangerous sharks in New South Wales, Australia. They have proven to be a more effective, accessible and cheaper solution compared to crewed aircraft. However, the ability to reliably detect and identify marine fauna is closely tied to pilot skill, experience and level of fatigue. Modern computer vision technology offers the possibility of improving detection reliability and even automating the surveillance process in the future. In this work we investigate the ability of commodity deep learning algorithms to detect marine objects in video footage from drones, with a focus on distinguishing between shark species. This study was enabled by the large archive of video footage gathered during the NSW Department of Primary Industries Drone Trials since 2016. We used this data to train two neural networks, based on the ResNet-50 and MobileNet V1 architectures, to detect and identify ten classes of marine object in 1080p resolution video footage. Both networks are capable of reliably detecting dangerous sharks: 80% accuracy for RetinaNet-50 and 78% for MobileNet V1 when tested on a challenging external dataset, which compares well to human observers. The object detection models correctly detect and localise most objects, produce few false-positive detections and can successfully distinguish between species of marine fauna in good conditions. We find that shallower network architectures, like MobileNet V1, tend to perform slightly worse on smaller objects, so care is needed when selecting a network to match deployment needs. We show that inherent biases in the training set have the largest effect on reliability. Some of these biases can be mitigated by pre-processing the data prior to training, however, this requires a large store of high resolution images that supports augmentation. A key finding is that models need to be carefully tuned for new locations and water conditions. Finally, we built an Android mobile application to run inference on real-time streaming video and demonstrated a working prototype during fields trials run in partnership with Surf Life Saving NSW.
Estimation of the surface potential of clay mineral taking Na+/K+-specific ion effects into account
Authors: Gao Xiaodan , Zhu Zhihong , Zhang Jin , Wang Jingkuan , Xu Yingde
Published: October 2022

Surface potential is a key electrochemical property of colloids in the study of particle interactions. However, the specific ion effects are not involved in the existing measuring methods. In this study, approaches for the estimation of the surface potential of montmorillonite with or without consideration of the specific ion effects were explored through the montmorillonite particle aggregation in the presence of Li+, Na+, and K+ ions. The montmorillonite aggregation process exhibited remarkable specific ion effects, and the critical coagulation concentration (CCC) values show the following: Li+ (271.8 mm) > Na+ (130.8 mm) > K+ (85.04 mm). Based on the mathematic relationship between electrostatic repulsion and the van der Waals attractive interaction at the CCC, the fluctuation coefficient ß was obtained. The value of β could quantify the strength of the specific ion effects of different cations. Then, the fluctuation coefficient β was introduced into the classical method for calculating the surface potential, considering the specific ion effects. The quantificational sequence of the ionic specificity of K+ and Na+ was as follows: βK = 1.433 > βNa = 1.187. Simultaneously, the surface potential considering specific ion effects can be obtained by introducing this coefficient. Our findings provide ideas for getting reliable surface potentials of charged particles in different electrolyte environments.
Comparison of different types of therapy for overactive bladder: A systematic review and network meta-analysis
Authors: Liu Peng , Li Yan , Shi Benkang , Zhang Qiujie , Guo Hu
Published: October 2022

To compare the efficacy and safety of different interventions [including antimuscarinics, mirabegron, OnabotulinumtoxinA, sacral neuromodulation (SNM) and peripheral tibial nerve stimulation (PTNS)] for treating idiopathic overactive bladder (OAB). PubMed, Embase, Cochrane Library, and other sources were searched for randomized controlled trials (RCTs) comparing interventions for overactive bladder from 1 January 2000 to 19 April 2021. A systematic review and network meta-analysis were performed by two authors independently. Fifty-five RCTs involving 32,507 patients were included in this analysis. Overall, antimuscarinics, mirabegron, OnabotulinumtoxinA, sacral neuromodulation, and peripheral tibial nerve stimulation were more efficacious than placebo, and sacral neuromodulation showed the best effect for reducing micturition frequency, urgency episodes and urgency urinary incontinence episodes. OnabotulinumtoxinA was the best intervention for achieving reductions of 100 and ≥50% in the number of urinary incontinence episodes/day, and peripheral tibial nerve stimulation was the best intervention for reducing urinary incontinence episodes. Antimuscarinics, mirabegron and peripheral tibial nerve stimulation had a similar efficacy for reducing micturition frequency, urinary incontinence episodes and urgency urinary incontinence episodes. The results revealed that all interventions examined herein were efficacious for managing adult overactive bladder syndrome compared with placebo. Furthermore, sacral neuromodulation and OnabotulinumtoxinA were the most efficient treatments for overactive bladder.

Systematic review registration

[https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=251966], identifier [CRD42021251966].
Vascular supply of the metacarpophalangeal joint
Authors: Baksa Gabor , Czeibert Kalman , Sharp Veronika , Handschuh Stephan , Gyebnar Janos , Barany Laszlo , Benis Szabolcs , Nyiri Gabor , Mandl Peter , Petnehazy Ors , Balint Peter Vince
Published: October 2022

Objective

To describe in detail the arterial vasculature of metacarpophalangeal joints 2–5 on cadaver specimens and to compare it to ultrasound imaging of healthy subjects.

Methods

Eighteen hands of donated human cadavers were arterially injected and investigated with either corrosion casting or cryosectioning. Each layer of cryosectioned specimens was photographed in high-resolution. Images were then segmented for arterial vessels of the metacarpophalangeal (MCP) joints 2–5. The arterial pattern of the joints was reconstructed from the segmented images and from the corrosion cast specimens. Both hands of ten adult healthy volunteers were scanned focusing on the vasculature of the same joints with high-end ultrasound imaging, including color Doppler. Measurements were made on both cryosectioned arteries and Doppler images.

Results

The arterial supply of MCP joints 2–5 divides into a metacarpal and a phalangeal territory, respectively. The metacarpal half receives arteries from the palmar metacarpal arteries or proper palmar digital arteries, while the phalangeal half is supplied by both proper and common palmar digital arteries. Comparing anatomical and ultrasonographic results, we determined the exact anatomic location of normal vessels using Doppler images acquired of healthy joints. All, except three branches, were found with less than 50% frequency using ultrasound. Doppler signals were identified significantly more frequently in MCP joints 2–3 than on 4–5 (p < 0.0001). Similarly, Doppler signals differed in the number of detectable small, intraarticular vessels (p < 0.009), but not that of the large extraarticular ones (p < 0.1373). When comparing measurements acquired by ultrasound and on cadaver vessels, measurements using the former technique were found to be larger in all joints (p < 0.0001).

Conclusion

Using morphological and ultrasonographic techniques, our study provides a high-resolution anatomical maps and an essential reference data set on the entire arterial vasculature of healthy human MCP 2–5 joints. We found that Doppler signal could be detected in less than 50% of the vessels of healthy volunteers except three locations. Intraarticular branches were detected with ultrasound imaging significantly more frequently on healthy MCP 2–3 joints, which should be taken into account when inflammatory and normal Doppler signals are evaluated. Our study also provides reference data for future, higher-resolution imaging techniques.
The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease
Authors: Meszaros Attila , Ahmed Junaid , Russo Giorgio , Tompa Peter , Lazar Tamas
Published: October 2022

Androgen receptor (AR) is a key member of nuclear hormone receptors with the longest intrinsically disordered N-terminal domain (NTD) in its protein family. There are four mono-amino acid repeats (polyQ1, polyQ2, polyG, and polyP) located within its NTD, of which two are polymorphic (polyQ1 and polyG). The length of both polymorphic repeats shows clinically important correlations with disease, especially with cancer and neurodegenerative diseases, as shorter and longer alleles exhibit significant differences in expression, activity and solubility. Importantly, AR has also been shown to undergo condensation in the nucleus by liquid-liquid phase separation, a process highly sensitive to protein solubility and concentration. Nonetheless, in prostate cancer cells, AR variants also partition into transcriptional condensates, which have been shown to alter the expression of target gene products. In this review, we summarize current knowledge on the link between AR repeat polymorphisms and cancer types, including mechanistic explanations and models comprising the relationship between condensate formation, polyQ1 length and transcriptional activity. Moreover, we outline the evolutionary paths of these recently evolved amino acid repeats across mammalian species, and discuss new research directions with potential breakthroughs and controversies in the literature.
Chronic kidney disease risk prediction scores assessment and development in Mexican adult population
Authors: Colli Victor A. , González-Rocha Alejandra , Canales David , Hernández-Alcáraz Cesar , Pedroza Andrea , Pérez-Chan Manuel , Barquera Simón , Denova-Gutierrez Edgar
Published: October 2022

Background

Chronic kidney disease (CKD) is a major public health problem, with considerable growth in prevalence and mortality in recent years. Screening of CKD at primary care is crucial for the implementation of prevention strategies. The aims of this study are to assess CKD risk prediction scores and to develop a risk prediction score for the Mexican adult population.

Methods

Data from the Mexican National Health and Nutrition Survey 2016 was utilized and 3463 participants ≥ 20 years old were included. Reduced renal function with Glomerular filtration rate and/or the presence of albuminuria was defined as CKD. Multiple logistic regression models were performed for the creation of a training and validation model. Additionally, several models were validated in our Mexican population.

Results

The developed training model included sex, age, body mass index, fast plasma glucose, systolic blood pressure, and triglycerides, as did the validation model. The area under the curve (AUC) was 0.78 (95% CI: 0.72, 0.79) for training model, and 0.76 (95% CI: 0.71, 0.80) in validation model for Mexican adult population. Age, female gender, presence of diabetes and hypertension, elevated systolic and diastolic blood pressure, serum and urinary creatinine, and higher HbA1c were significantly associated with the prevalent chronic kidney disease. Previous CKD risk predictive models were evaluated with a representative sample of the Mexican adult population, their AUC was between 0.61 and 0.78.

Conclusion

The designed CKD risk predictive model satisfactorily predicts using simple and common variables in primary medical care. This model could have multiple benefits; such as, the identification of the population at risk, and prevention of CKD.
Impact of age on the diagnostic performance of unstimulated salivary flow rates and salivary gland ultrasound for primary Sjögren's syndrome
Authors: Lee Kyung-Ann , Kim Se-Hee , Kim Hae-Rim , Kim Hyun-Sook
Published: October 2022

Background

Age-related changes and different patterns of salivary gland abnormalities according to age may affect the diagnostic performance of unstimulated salivary flow rate (USFR) and salivary gland ultrasound (SGUS) for primary Sjögren's syndrome (pSS). We aimed to evaluate the threshold and diagnostic performance of USFR and whether incorporating SGUS or replacing USFR with SGUS affects the performance of the ACR/EULAR criteria for pSS according to age.

Materials and methods

This medical chart review study included patients with suspected pSS who completed evaluations for pSS. Patients were classified based on age at pSS evaluation: elderly (≥65 years), middle-aged (40–64), and young (< 40). The USFR's optimal thresholds were evaluated using the ROC curve. The diagnostic performances of the USFR and modified ACR/EULAR criteria were compared.

Results

In total, 239 pSS patients and 92 patients with idiopathic sicca syndrome were included. The cut-off of USFR ≤ 0.1 mL/min was irrelevant to age, demonstrating the best sensitivity (44.3–53.0%) and specificity (74.1–90.9%). SGUS had a significantly better AUC than USFR in the young (p < 0.01) and middle-aged groups (p < 0.01). The middle-aged group demonstrated better diagnostic performance of the ACR/EULAR criteria incorporating SGUS (AUC 0.957) (p < 0.01) and criteria replacing USFR with SGUS (AUC 0.957) (p < 0.001) compared to the original criteria (AUC 0.916). In the young and elderly groups, adding SGUS to the ACR/EULAR criteria or replacing USFR with SGUS did not significantly increase the AUC.

Conclusions

The thresholds of USFR ≤ 0.1 mL/min was optimal, irrespective of age. Using SGUS can improve diagnostic accuracy of ACR/EULAR criteria by supplementing the USFR, especially in middle-aged patients.
Novel exploration of Raman microscopy and non-linear optical imaging in adenomyosis
Authors: Shen Zhuowei , He Yingying , Shen Zhuoyi , Wang Xuefei , Wang Yang , Hua Zhengyu , Jiang Nan , Song Zejiang , Li Rui , Xiao Zhen
Published: October 2022

Background

Adenomyosis is a common gynecological disease in women. A relevant literature search found that approximately 82% of patients with adenomyosis chose to undergo hysterectomy. However, women of childbearing age are more likely to undergo surgery to preserve the uterus. Because it is difficult to determine the extent of adenomyosis, it is almost impossible to resect adenomyotic tissue and retain the uterus at the same time.

Materials and methods

Following ethics approval and patient consent, tissue samples were resected and prepared to create frozen slices for analysis. One slice was subjected to H&E staining while the remaining slices were photographed with Coherent Anti-Stokes Raman Scattering (CARS), Second-Harmonic Generation (SHG) microscopy, and Raman spectroscopy. Comparative observations and analyses at the same positions were carried out to explore the diagnostic ability of CARS, SHG, and Raman spectroscopy for adenomyosis.

Results

In adenomyotic tissue, we found two characteristic peaks at 1,155 and 1,519 cm–1 in the Raman spectrum, which were significantly different from normal tissue. The substances shown in the CARS spectrum were represented by peaks of 1,519 cm–1. SHG microscopy showed a distribution of collagen at the focus of the adenomyosis.

Conclusion

This study represents a novel analysis of Raman microscopy, CARS, and SHG in the analysis of adenomyotic lesions. We found the diffraction spectrum useful in determining the focal boundary and the diagnosis of adenomyosis in the tested samples.
Prediction of radiographic progression pattern in patients with ankylosing spondylitis using group-based trajectory modeling and decision trees
Authors: Kang Juyeon , Lee Tae-Han , Park Seo Young , Lee Seunghun , Koo Bon San , Kim Tae-Hwan
Published: October 2022

Objective

This study aimed to identify trajectories of radiographic progression of the spine over time and use them, along with associated clinical factors, to develop a prediction model for patients with ankylosing spondylitis (AS).

Methods

Data from the medical records of patients diagnosed with AS in a single center were extracted between 2001 and 2018. Modified Stoke Ankylosing Spondylitis Spinal Scores (mSASSS) were estimated from cervical and lumbar radiographs. Group-based trajectory modeling classified patients into trajectory subgroups using longitudinal mSASSS data. In multivariate analysis, significant clinical factors associated with trajectories were selected and used to develop a decision tree for prediction of radiographic progression. The most appropriate group for each patient was then predicted using decision tree analysis.

Results

We identified three trajectory classes: class 1 had a uniformly increasing slope of mSASSS, class 2 showed sustained low mSASSS, and class 3 showed little change in the slope of mSASSS but highest mSASSS from time of diagnosis to after progression. In multivariate analysis for predictive factors, female sex, younger age at diagnosis, lack of eye involvement, presence of peripheral joint involvement, and low baseline erythrocyte sedimentation rate (log) were significantly associated with class 2. Class 3 was significantly associated with male sex, older age at diagnosis, presence of ocular involvement, and lack of peripheral joint involvement when compared with class 1. Six clinical factors from multivariate analysis were used for the decision tree for classifying patients into three trajectories of radiographic progression.

Conclusion

We identified three patterns of radiographic progression over time and developed a decision tree based on clinical factors to classify patients according to their trajectories of radiographic progression. Clinically, this model holds promise for predicting prognosis in patients with AS.