bluuebunny/crossref_metadata_2025 huggingface dataset:
High folate receptor expression in gliomas can be detected in vivo using folate-based positron emission tomography with high tumor-to-brain uptake ratio divulging potential future targeting possibilities
Authors: Miner Maxwell W. G. , Liljenbäck Heidi , Virta Jenni , Kärnä Salli , Viitanen Riikka , Elo Petri , Gardberg Maria , Teuho Jarmo , Saipa Piritta , Rajander Johan , Mansour Hasan Mansour A , Cleveland Nathan A. , Low Philip S. , Li Xiang-Guo , Roivainen Anne
Published: May 2023

Introduction

Non-invasive imaging techniques such as positron emission tomography (PET) are extremely important for cancer detection and characterization especially for difficult to biopsy or extremely delicate organs such as the brain. The folate analogue 1,4,7-triazacylononane-1,4,7-triacetic acid-conjugated folate radiolabeled with aluminum fluoride-18 ([18F]FOL) has been previously shown to accumulate preferentially in tumor cells with an overexpression of folate receptors (FRs) and here was investigated for its ability to detect orthotopic gliomas in a rat model. In addition, we studied the expression of FRs in human glioblastoma samples to investigate if an analogous relationship may exist.

Methods

Nine BDIX rats were injected with BT4C rat glioma cells into the right hemisphere of the brain. Animals were imaged with gadolinium-enhanced magnetic resonance imaging at on days prior to PET/computed tomography (CT) imaging. Animals were divided into two groups, and were PET/CT imaged with either [18F]FOL or 2-deoxy-2-18F-fluoro-D-glucose ([18F]FDG) on 19 and 32-days post glioma grafting. Two subjects were also PET/CT imaged with [18F]FOL on day 16. Biodistribution was studied and brains were cryosectioned for autoradiography, immunofluorescence, and histological studies. Patient-derived paraffin-embedded glioblastomas were sectioned and stained with similar methods.

Results

PET imaging showed an increase of [18F]FOL tumor-to-brain uptake ratio (TBR) over the study duration from day 16/19 (3.3 ± 0.9) increasing to 5.7 ± 1.0 by day 32. [18F]FDG PET-imaged rats had a consistent TBR of 1.6 ± 0.1 throughout the study. Ex vivo autoradiography results revealed an exceptionally high TBR of 116.1 ± 26.9 for [18F]FOL while the [18F]FDG values were significantly lower giving 2.9 ± 0.6 (P<0.0001). Immunostaining demonstrated an increased presence of FR-α in the BT4C gliomas versus the contralateral brain tissue, while FR-β was present only on glioma periphery. Human sections assayed showed similar FRs expression characteristics.

Conclusion

This study shows upregulation of FR-α inside glioma regions in both human and animal tissue, providing a biochemical basis for the observed increased [18F]FOL uptake in animal PET images. These results suggest that FRs targeting imaging and therapeutic compounds may possess clinically relevant translational abilities for the detection and treatment of gliomas.
Production of monoclonal antibody of heat-labile toxin A subunit to identify enterotoxigenic Escherichia coli by epitope mapping using synthetic peptides
Authors: Park Jun-Young , Cho Seung-Hak
Published: May 2023

Background

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea through two enterotoxins, a heat-labile toxin and a heat-stable toxin. These toxins alter the cellular signaling pathways, ultimately triggering an increase in chloride secretion and watery diarrhea.

Objective

For the development of an ETEC vaccine, we attempted to construct a peptide-specific monoclonal antibody library against heat-labile enterotoxin A subunit (LT-A) by epitope mapping using synthetic peptides.

Methods

Sera produced by five mice immunized with recombinant LT-A protein were examined for specific recognition with synthetic 15-mer and 34-mer peptides of LT-A proteins using enzyme-linked immunosorbent assay. The analysis revealed that the synthetic peptides number 8, 16, 24, 33, 36, 38, and 39 reacted with an anti-LT-A polyclonal antibody. For the possible prediction of LT-A epitopes, each full-length protein sequence was subjected to BCPreds analysis and three-dimensional protein structure analysis. The data showed that three peptides (synthetic peptide numbers: 33, 36, and 38–39) have identical antigenic specificities with LT-A protein, suggesting the usefulness of these linear peptide epitopes.

Results

Based on these peptides, we produced monoclonal antibodies to improve the specificity of LT-A detection. Monoclonal antibodies produced from two peptides (numbers 33 and 36) showed affinity for an LT-A recombinant antigen. Moreover, peptide epitope prediction analysis showed that the sites of the three peptides were identical to those exhibiting actual antigenicity. Also, it was confirmed that the amino acid sequence that actually showed antigenicity was included in the peptide predicted only by ETEC-LT-A-33. Also, the specificity of the antibody for ETEC-LT-A-33 was validated using bacterial cells, and the neutralizing effect of the antibody was determined by assessing cytokine release in infected HCT-8 cells.

Conclusion

The monoclonal antibodies produced in this study are useful toolsfor vaccine production against ETEC and can be used to identify peptide antigencandidates.
The increased cfRNA of TNFSF4 in peripheral blood at late gestation and preterm labor: its implication as a noninvasive biomarker for premature delivery
Authors: Wang Zhe , Ou Qingjian , Gao Lu
Published: May 2023

Introduction

Given the important roles of immune tolerance and inflammation in both preterm and term labor, some inflammation-related genes could be related to the initiation of labor, even preterm labor. Inspection of cell-free RNA (cfRNA) engaged in inflammation in maternal blood may represent the varied gestational age and may have significant implications for the development of noninvasive diagnostics for preterm birth.

Methods

To identify potential biomarkers of preterm birth, we investigated the cfRNA and exosomal miRNA in the peripheral blood of pregnant women at different gestational ages that undergo term labor or preterm labor. 17 inflammatory initiation-related cfRNAs were screened by overlapping with the targets of decreasing miRNAs during gestation and highly expressed cfRNAs at late gestation in maternal blood. To reveal the origins and mechanisms of these screened cfRNAs, the datasets of single-cell RNA sequencing from peripheral blood mononuclear cells of pregnant women, the fetal lung, and the placenta across different gestational ages were analyzed.

Results

During late gestation, TNFSF4 expression increased exclusively in pro-inflammatory macrophages of maternal blood, whereas its receptor, TNFRSF4, increased expression in T cells from the decidua, which suggested the potential cell-cell communication of maternally-originated pro-inflammatory macrophages with the decidual T cells and contributed to the initiation of labor. Additionally, the cfRNA of TNFSF4 was also increased in preterm labor compared to term labor in the validation cohorts. The EIF2AK2 and TLR4 transcripts were increased in pro-inflammatory macrophages from both fetal lung and placenta but not in those from maternal mononuclear cells at late gestation, suggesting these cfRNAs are possibly derived from fetal tissues exclusively. Moreover, EIF2AK2 and TLR4 transcripts were found highly expressed in the pro-inflammatory macrophages from decidua as well, which suggested these specific fetal-origin macrophages may function at the maternal-fetal interface to stimulate uterine contractions, which have been implicated as the trigger of parturition and preterm labor.

Discussion

Taken together, our findings not only revealed the potential of peripheral TNFSF4 as a novel cfRNA biomarker for noninvasive testing of preterm labor but further illustrated how maternal and fetal signals coordinately modulate the inflammatory process at the maternal-fetal interface, causing the initiation of term or preterm labor.
A novel antimicrobial peptide screened by a Bacillus subtilis expression system, derived from Larimichthys crocea Ferritin H, exerting bactericidal and parasiticidal activities
Authors: Chen Meiling , Lin Nengfeng , Liu Xiande , Tang Xin , Wang Zhiyong , Zhang Dongling
Published: May 2023

Antimicrobial peptides (AMPs) may be the most promising substitute for antibiotics due to their effective antimicrobial activities and multiple function mechanisms against pathogenic microorganisms. In this study, a novel AMP containing 51 amino acids, named Lc1687, was screened from the large yellow croaker (Larimichthys crocea) via a B. subtilis system. Bioinformatics and circular dichroism (CD) analyses showed that Lc1687 is a novel anionic amphiphilic α-helical peptide, which was derived from the C-terminal of a Ferritin heavy subunit. The recombinant Lc1687 (named rLc1687) purified from Escherichia coli exhibited strong activities against Gram-positive (Gram+) bacterium Staphylococcus aureus, Gram-negative (Gram-) bacteria Vibrio vulnificus, V. parahaemolyticus, and Scuticociliatida. Scanning electron microscope (SEM) and transmission electron microscopy (TEM) revealed the possible function mechanisms of this peptide, which is to target and disrupt the bacterial cell membranes, including pore-forming, loss of fimbriae, and cytoplasm overflow, whereas gel retardation assay revealed that peptide Lc1687 cannot bind bacterial DNA. The peptide stability analysis showed that rLc1687 acts as a stable antimicrobial agent against Gram+ and Gram- bacteria at temperatures ranging from 25 to 100°C, pH 3-12, and UV radiation time ranging from 15 to 60 min. A hemolytic activity assay confirmed that this peptide may serve as a potential source for clinical medicine development. Taken together, Lc1687 is a novel AMP as it is a firstly confirmed Ferritin fragment with antimicrobial activity. It is also a promising agent for the development of peptide-based antibacterial and anti-parasitic therapy.
Genetically confirmed chronic granulomatous disease in a Kenyan child: case report
Authors: Marangu-Boore Diana , Kambuni Fred , Onyinkwa Mary , Ramprakash Stalin , C.P. Raghuram , Eley Brian , Bhattad Sagar
Published: May 2023

Introduction

We report the first case of genetically confirmed chronic granulomatous disease (CGD) in a Kenyan child.

Clinical findings

A 7-month-old male infant, the only child of non-consanguineous parents, presented with cough, fever, fast breathing, oral thrush, and axillary lymphadenopathy ipsilateral to the Calmette–Guérin bacillus scar. He had been hospitalized 5 weeks prior for severe pneumonia. Plain chest radiography showed bilateral patchy airspace opacification; chest computed tomography revealed multiple large lung nodules and left axillary lymphadenopathy. HIV ELISA was negative; tuberculin skin test was positive; lymph node biopsy macroscopically revealed caseous granulomas seen on histology; isoniazid- and rifampicin-susceptible Mycobacterium tuberculosis complex isolate was detected on the Hain test. First-line anti-tuberculous drugs were added to his empiric treatment comprising piperacillin–tazobactam, amikacin, cotrimoxazole, and fluconazole. He was discharged after 10 days based on clinical resolution.

Diagnoses, interventions, and outcome

An inborn error of immunity (IEI) was considered given the recurrent fevers and atypical lung nodules. Genetic analysis revealed a hemizygous pathogenic variant on CYBB in keeping with X-linked CGD. The child’s fevers recurred 2 weeks post-discharge but completely resolved on prophylactic itraconazole and cotrimoxazole. He underwent a successful haplo-identical hematopoietic stem cell transplantation at an experienced center in India with his father as the donor and is currently doing well on post-transplant follow-up.

Conclusion

Genetic testing is relatively accessible and cost-effective for the diagnosis of IEI in low-and-middle-income countries. Expert multi-disciplinary collaboration is key for successful outcomes.
Gasdermin D-mediated pyroptosis: mechanisms, diseases, and inhibitors
Authors: Dai Zhen , Liu Wan-Cong , Chen Xiao-Yi , Wang Xiao , Li Jun-Long , Zhang Xiang
Published: May 2023

Gasdermin D (GSDMD)-mediated pyroptosis and downstream inflammation are important self-protection mechanisms against stimuli and infections. Hosts can defend against intracellular bacterial infections by inducing cell pyroptosis, which triggers the clearance of pathogens. However, pyroptosis is a double-edged sword. Numerous studies have revealed the relationship between abnormal GSDMD activation and various inflammatory diseases, including sepsis, coronavirus disease 2019 (COVID-19), neurodegenerative diseases, nonalcoholic steatohepatitis (NASH), inflammatory bowel disease (IBD), and malignant tumors. GSDMD, a key pyroptosis-executing protein, is linked to inflammatory signal transduction, activation of various inflammasomes, and the release of downstream inflammatory cytokines. Thus, inhibiting GSDMD activation is considered an effective strategy for treating related inflammatory diseases. The study of the mechanism of GSDMD activation, the formation of GSDMD membrane pores, and the regulatory strategy of GSDMD-mediated pyroptosis is currently a hot topic. Moreover, studies of the structure of caspase-GSDMD complexes and more in-depth molecular mechanisms provide multiple strategies for the development of GSDMD inhibitors. This review will mainly discuss the structures of GSDMD and GSDMD pores, activation pathways, GSDMD-mediated diseases, and the development of GSDMD inhibitors.
Systemic priming and intranasal booster with a BcfA-adjuvanted acellular pertussis vaccine generates CD4+ IL-17+ nasal tissue resident T cells and reduces B. pertussis nasal colonization
Authors: Yount Kacy S. , Hall Jesse M. , Caution Kyle , Shamseldin Mohamed M. , Guo Myra , Marion Keirsten , Fullen Audra R. , Huang Yimin , Maynard Jennifer A. , Quataert Sally A. , Deora Rajendar , Dubey Purnima
Published: May 2023

Introduction

Resurgence of pertussis, caused by Bordetella pertussis, necessitates novel vaccines and vaccination strategies to combat this disease. Alum-adjuvanted acellular pertussis vaccines (aPV) delivered intramuscularly reduce bacterial numbers in the lungs of immunized animals and humans, but do not reduce nasal colonization. Thus, aPV-immunized individuals are sources of community transmission. We showed previously that modification of a commercial aPV (Boostrix) by addition of the Th1/17 polarizing adjuvant Bordetella Colonization Factor A (BcfA) attenuated Th2 responses elicited by alum and accelerated clearance of B. pertussis from mouse lungs. Here we tested whether a heterologous immunization strategy with systemic priming and mucosal booster (prime-pull) would reduce nasal colonization.

Methods

Adult male and female mice were immunized intramuscularly (i.m.) with aPV or aPV/BcfA and boosted either i.m. or intranasally (i.n.) with the same formulation. Tissue-resident memory (TRM) responses in the respiratory tract were quantified by flow cytometry, and mucosal and systemic antibodies were quantified by ELISA. Immunized and naïve mice were challenged i.n. with Bordetella pertussis and bacterial load in the nose and lungs enumerated at days 1-14 post-challenge.

Results

We show that prime-pull immunization with Boostrix plus BcfA (aPV/BcfA) generated IFNγ+ and IL-17+ CD4+ lung resident memory T cells (TRM), and CD4+IL-17+ TRM in the nose. In contrast, aPV alone delivered by the same route generated IL-5+ CD4+ resident memory T cells in the lungs and nose. Importantly, nasal colonization was only reduced in mice immunized with aPV/BcfA by the prime-pull regimen.

Conclusions

These results suggest that TH17 polarized TRM generated by aPV/BcfA may reduce nasal colonization thereby preventing pertussis transmission and subsequent resurgence.
Current insights into the hepatic microenvironment and advances in immunotherapy for hepatocellular carcinoma
Authors: Zhao Ming , Huang Hui , He Feng , Fu Xiangsheng
Published: May 2023

Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and shows high global incidence and mortality rates. The liver is an immune-tolerated organ with a specific immune microenvironment that causes traditional therapeutic approaches to HCC, such as chemotherapy, radiotherapy, and molecular targeted therapy, to have limited efficacy. The dramatic advances in immuno-oncology in the past few decades have modified the paradigm of cancer therapy, ushering in the era of immunotherapy. Currently, despite the rapid integration of cancer immunotherapy into clinical practice, some patients still show no response to treatment. Therefore, a rational approach is to target the tumor microenvironment when developing the next generation of immunotherapy. This review aims to provide insights into the hepatic immune microenvironment in HCC and summarize the mechanisms of action and clinical usage of immunotherapeutic options for HCC, including immune checkpoint blockade, adoptive therapy, cytokine therapy, vaccine therapy, and oncolytic virus-based therapy.
The role of tumor-infiltrating lymphocytes in triple-negative breast cancer and the research progress of adoptive cell therapy
Authors: Li Ruonan , Cao Lili
Published: May 2023

The treatment outcome of breast cancer is closely related to estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. Triple-negative breast cancer (TNBC) lacking ER, PR, and HER2 expression has limited treatment options and a poor prognosis. Tumor-infiltrating lymphocytes (TILs) play a role in promoting or resisting tumors by affecting the tumor microenvironment and are known as key regulators in breast cancer progression. However, treatments for TNBC (e.g., surgery, chemotherapy and radiotherapy) have non-satisfaction’s curative effect so far. This article reviews the role of different types of TILs in TNBC and the research progress of adoptive cell therapy, aiming to provide new therapeutic approaches for TNBC.
Brentuximab vedotin use in pediatric anaplastic large cell lymphoma
Authors: Agrusa Jennifer E. , Egress Emily R. , Lowe Eric J.
Published: May 2023

Anaplastic large cell lymphoma (ALCL) is the most common type of mature T-cell non-Hodgkin lymphoma in children/adolescents. ALCL is characterized by expression of CD30 in the neoplastic lymphoid cells with frequent expression of anaplastic lymphoma kinase (ALK), especially within the pediatric population. Despite multiple efforts to optimize the use of conventional chemotherapy, outcomes in children, adolescents, and adults with ALCL remain suboptimal. Thus, there is a need to improve survival for those with high-risk disease and decrease therapy exposures and toxicities for those with low-risk disease. Targeted therapies, such as the anti-CD30 antibody-drug conjugate, brentuximab vedotin, are new important therapeutic options. Phase I and II studies in adults with relapsed/refractory CD30+ lymphomas, including ALCL, demonstrated the safety and efficacy of brentuximab vedotin, leading to FDA approval for relapsed/refractory ALCL in adults and successful incorporation into frontline therapies. Clinical trials in the pediatric population demonstrated similar results in those with relapsed/refractory ALCL. Incorporation of brentuximab vedotin into upfront therapy for children and adolescents with ALCL showed that this novel combination therapy has clinical advantages in comparison to conventional agents alone. Brentuximab vedotin is well-tolerated in both the pediatric and adult populations, even when used in combination with conventional agents. Brentuximab vedotin is an ideal agent to treat ALCL with excellent targeted activity and limited toxicity. Future studies are needed to identify how brentuximab vedotin should be utilized when combined with immunotherapy or other targeted agents (e.g., ALK inhibitors) in both the upfront and relapsed/refractory setting.
Spatial and seasonal variations of near-inertial kinetic energy in the upper Ross Sea and the controlling factors
Authors: Zhang Yimin , Yang Wei , Zhao Wei , Zhang Yongli , Shen Jiawei , Wei Hao
Published: May 2023

The spatial distribution and seasonal variation of near-inertial kinetic energy (NIKE) in the upper Ross Sea (RS) are examined using the 1/4° NEMO3.6-LIM3 sea ice physical–biological coupled model. The annual-mean surface and mixed layer-integrated NIKE have large values at the shelf break around Iselin Bank and the northeast area outside the continental shelf. The spatial distribution of the surface and mixed layer-integrated NIKE in the austral summer RS is mainly controlled by the near-inertial wind stress magnitude (NIWSM), which acts as the energy source. The northeast high NIKE agrees with the large NIWSM there. Semidiurnal tides only contribute to the NIKE peak around the Iselin Bank and shelf break. The change of mixed layer depth (MLD) can induce spatial discrepancies between surface and mixed layer-integrated NIKE. The shallower MLD in the western RS limits the near-inertial energy in a thin layer, which has induced the large surface NIKE there. The NIKE in the upper RS has a pronounced seasonal variation with the largest surface and mixed layer-integrated NIKE both observed during austral summer. The seasonal variation of NIWSM and sea ice concentration play an important role in inducing the seasonal variation of NIKE. While the NIWSM acts as the main energy source of NIKE, the presence of sea ice can prevent the wind from directly acting on the surface ocean, inducing the low NIKE during austral winter.
Remote sensing and machine learning method to support sea surface pCO2 estimation in the Yellow Sea
Authors: Li Wei , Liu Chunli , Zhai Weidong , Liu Huizeng , Ma Wenjuan
Published: May 2023

With global climate changing, the carbon dioxide (CO2) absorption rates increased in marginal seas. Due to the limited availability of in-situ spatial and temporal distribution data, the current status of the sea surface carbon dioxide partial pressure (pCO2) in the Yellow Sea is unclear. Therefore, a pCO2 model based on a random forest algorithm has been developed, which was trained and tested using 14 cruise data sets from 2011 to 2019, and remote sensing satellite sea surface temperature, chlorophyll concentration, diffuse attenuation of downwelling irradiance, and in-situ salinity were used as the input variables. The seasonal and interannual variations of modeled pCO2 were discussed from January 2003 and December 2021 in the Yellow Sea. The results showed that the model developed for this study performed well, with a root mean square difference (RMSD) of 43 μatm and a coefficient of determination (R2) of 0.67. Moreover, modeled pCO2 increased at a rate of 0.36 μatm year-1 (R2 = 0.27, p < 0.05) in the YS, which is much slower than the rate of atmospheric pCO2 (pCO2air) rise. The reason behind it needs further investigation. Compared with pCO2 from other datasets, the pCO2 derived from the RF model exhibited greater consistency with the in-situ pCO2 (RMSD = 55 μatm). In general, the RF model has significant improvement over the previous models and the global data sets.
Study on the size effect of elastic modulus of rock considering the joint spacing
Authors: Zhao Tao , Hu Gaojian
Published: May 2023

The relationship between the rock’s elastic modulus and deformation characteristics, affected by joint spacing and ductility, was not determined. This study investigates the size effect of the elastic modulus of rock with parallel joints using numerical simulation and regression analysis. The results showed an exponential relationship between elastic modulus and spacing of parallel joints and a negative exponential relationship between elastic modulus and rock size. The characteristic size of elastic modulus has a power function relationship with the parallel joints spacing, and the characteristic elastic modulus of rock has a power function relationship with the parallel joints spacing. The general and specific forms of these relationships are provided. Establishing these relationships allows for predicting and calculating the elastic modulus of the mine rock mass and serves as a reference for the deformation analysis of the rock.
Adverse pregnancy outcomes associated with antiretroviral therapy initiated before pregnancy and during pregnancy: a retrospective study in Hubei province, China
Authors: Tan Yuting , Wu Songjie , Yan Yajun , Zou Shi , Feng Ling , Guo Wei , Wu Mengmeng , Luo Mingqi , Liang Ke
Published: May 2023

Background

Antiretroviral therapy (ART) initiation before pregnancy was reported to have an increased risk of adverse pregnancy outcomes (APOs) than ART initiation during pregnancy. However, the risks of APOs associated with different ART regimens initiated before or during pregnancy remain unknown.

Methods

Pregnant women living with HIV (PWLHIV) from Hubei Province, China, were retrospectively enrolled between January 1, 2004, and December 31, 2021. The trends of ART initiation time and application of different ART regimens were evaluated over time, separately. Using no ART exposure before and during pregnancy as control, the risks of APOs associated with protease inhibitor (PI) based regimens and non-nucleoside reverse transcriptase inhibitors (NNRTIs) based regimens initiated before pregnancy were analyzed; and the risks of APOs associated with PI-based regimens, NNRTIs based regimens and zidovudine (AZT) monotherapy initiated during pregnancy were analyzed. APOs, including low birthweight (LBW), stillbirth, preterm birth (PTB) and early miscarriage, were reviewed.

Results

Among 781 PWLHIV including 1,010 pregnancies, 522 pregnancies (51.7%) were exposed to ART before or during pregnancy. Of them, the proportion of ART initiation before pregnancy per year increased from around 20% in the early period to more than 60% after 2019. Efavirenz (EFV)-nucleoside reverse transcriptase inhibitors (NRTIs) (32.2%), LPV/r-NRTIs (31.2%), and nevirapine (NVP)-NRTIs (27.4%) were the most commonly used regimens, and the proportion of LPV/r-NRTIs used per year has increased to around 50.0% in recent years. LPV/r-NRTIs was associated with higher risks of LBW whether initiated before pregnancy [adjusted OR (aOR) = 2.59, 95%CI 1.04–6.45, p = 0.041] or during pregnancy (aOR = 2.19, 95%CI 1.03–4.67, p = 0.041), compared with no exposure to ART before and during pregnancy. However, no matter initiated before or during pregnancy, LPV/r-NRTIs had no significantly increased risks of stillbirth, PTB and early miscarriage, and EFV /NVP-NRTIs and AZT monotherapy had no significantly increased risks of LBW, stillbirth, PTB and early miscarriage when compared with no exposure to ART before and during pregnancy.

Conclusion

Our data suggests that LPV/r-NRTIs has been widely used among PWLHIV in recent years. However, the potential risk of LBW should be continuously monitored among PWLHIV whether LPV/r-NRTIs is initiated before or during pregnancy.
Deep learning-based classification system of bacterial keratitis and fungal keratitis using anterior segment images
Authors: Won Yeo Kyoung , Lee Hyebin , Kim Youngjun , Han Gyule , Chung Tae-Young , Ro Yong Man , Lim Dong Hui
Published: May 2023

Introduction

Infectious keratitis is a vision threatening disease. Bacterial and fungal keratitis are often confused in the early stages, so right diagnosis and optimized treatment for causative organisms is crucial. Antibacterial and antifungal medications are completely different, and the prognosis for fungal keratitis is even much worse. Since the identification of microorganisms takes a long time, empirical treatment must be started according to the appearance of the lesion before an accurate diagnosis. Thus, we developed an automated deep learning (DL) based diagnostic system of bacterial and fungal keratitis based on the anterior segment photographs using two proposed modules, Lesion Guiding Module (LGM) and Mask Adjusting Module (MAM).

Methods

We used 684 anterior segment photographs from 107 patients confirmed as bacterial or fungal keratitis by corneal scraping culture. Both broad- and slit-beam images were included in the analysis. We set baseline classifier as ResNet-50. The LGM was designed to learn the location information of lesions annotated by ophthalmologists and the slit-beam MAM was applied to extract the correct feature points from two different images (broad- and slit-beam) during the training phase. Our algorithm was then externally validated using 98 images from Google image search and ophthalmology textbooks.

Results

A total of 594 images from 88 patients were used for training, and 90 images from 19 patients were used for test. Compared to the diagnostic accuracy of baseline network ResNet-50, the proposed method with LGM and MAM showed significantly higher accuracy (81.1 vs. 87.8%). We further observed that the model achieved significant improvement on diagnostic performance using open-source dataset (64.2 vs. 71.4%). LGM and MAM module showed positive effect on an ablation study.

Discussion

This study demonstrated that the potential of a novel DL based diagnostic algorithm for bacterial and fungal keratitis using two types of anterior segment photographs. The proposed network containing LGM and slit-beam MAM is robust in improving the diagnostic accuracy and overcoming the limitations of small training data and multi type of images.
Explainable ensemble machine learning model for prediction of 28-day mortality risk in patients with sepsis-associated acute kidney injury
Authors: Yang Jijun , Peng Hongbing , Luo Youhong , Zhu Tao , Xie Li
Published: May 2023

Background

Sepsis-associated acute kidney injury (S-AKI) is a major contributor to mortality in intensive care units (ICU). Early prediction of mortality risk is crucial to enhance prognosis and optimize clinical decisions. This study aims to develop a 28-day mortality risk prediction model for S-AKI utilizing an explainable ensemble machine learning (ML) algorithm.

Methods

This study utilized data from the Medical Information Mart for Intensive Care IV (MIMIC-IV 2.0) database to gather information on patients with S-AKI. Univariate regression, correlation analysis and Boruta were combined for feature selection. To construct the four ML models, hyperparameters were tuned via random search and five-fold cross-validation. To evaluate the performance of all models, ROC, K-S, and LIFT curves were used. The discrimination of ML models and traditional scoring systems was compared using area under the receiver operating characteristic curve (AUC). Additionally, the SHapley Additive exPlanation (SHAP) was utilized to interpret the ML model and identify essential variables. To investigate the relationship between the top nine continuous variables and the risk of 28-day mortality. COX regression-restricted cubic splines were utilized while controlling for age and comorbidities.

Results

The study analyzed data from 9,158 patients with S-AKI, dividing them into a 28-day mortality group of 1,940 and a survival group of 7,578. The results showed that XGBoost was the best performing model of the four ML models with AUC of 0.873. All models outperformed APS-III 0.713 and SAPS-II 0.681. The K-S and LIFT curves indicated XGBoost as the most effective predictor for 28-day mortality risk. The model’s performance was evaluated using ROCpr curves, calibration curves, accuracy, precision, and F1 scores. SHAP force plots were utilized to interpret and visualize the personalized predictive power of the 28-day mortality risk model. Additionally, COX regression restricted cubic splines revealed an interesting non-linear relationship between the top nine variables and 28-day mortality.

Conclusion

The use of ensemble ML models has shown to be more effective than the LR model and conventional scoring systems in predicting 28-day mortality risk in S-AKI patients. By visualizing the XGBoost model with the best predictive performance, clinicians are able to identify high-risk patients early on and improve prognosis.
The pregnancy outcomes in patients with epididymal obstructive azoospermia after microsurgical vasoepididymostomy: a systematic review and meta-analysis
Authors: Wang Zilong , Wang Xinkun , Song Changze , Lu Fuding , Zhai Jiawen , Li Naifa , Jiang Baohong , Tan Senbao , Xuan Xujun
Published: May 2023

Purpose

Pregnancy outcomes (overall patency rate, overall pregnancy rate, natural pregnancy rate, and the ratio of patients with pregnancy by assisted reproductive technology) after microsurgical vasoepididymostomy (MVE) in patients with epididymal obstructive azoospermia (EOA) were assessed through meta-analysis.

Method

We searched PubMed, Embase, Web of Science, and the Cochrane Library databases up to 28 September 2022 for published literature related to retrospective or prospective clinical studies of obstructive azoospermia after apparent microsurgical vasoepididymostomy. Our search terms included obstructive azoospermia, epididymis obstruction, epididymal obstruction and vasoepididymostomy, and epididymovasostomy. Two researchers independently performed the literature search and assessed the eligibility of selected studies according to established inclusion criteria. The meta-analysis was performed using RevMan 5.4 software.

Result

A total of 504 patients with EOA were included in 10 studies (including 2 prospective clinical studies and 8 retrospective clinical studies). The mean patency rate after MVE was 72% (95% CI 68–76%). The overall pregnancy rate was 34% (95% CI 30–38%). The natural pregnancy rate is 21% (95% CI 17–24%). The ratio of patients with pregnancy by assisted reproductive technology (ART) was 34.9%. For the factors affecting pregnancy outcomes after MVE, the overall pregnancy rates in patients receiving bilateral MVE were significantly higher than those receiving unilateral MVE (75.4 vs. 24.6%). The mean best sperm count and sperm motility in patients with overall pregnancy were significantly higher than those with failing pregnancies. For the subgroup meta-analysis of microsurgical vasoepididymostomy, there were no statistically significant differences in the overall patency rate (68 vs. 70%), the overall pregnancy rate (33 vs. 37%), the natural pregnancy rate (20 vs. 23%), the ratio of ART (30 vs. 28%) in end-to-side or end-to-end anastomosis, and longitudinal or triangular intussusception MVE.

Conclusion

Vasectomy patency rates are higher, but natural pregnancy rates are lower in EOA male infertility patients after MVE. Altering the MVE procedures alone does not significantly improve pregnancy outcomes, but ART after MVE could improve the chance of pregnancy regardless of sperm parameters. We recommended that human sperms from EOA male infertility patients should be cryopreserved during intraoperative MVE for application in the subsequent ICSI treatment procedure.
Manipulation of glycogen and sucrose synthesis increases photosynthetic productivity in cyanobacteria
Authors: Cantrell Michael , Cano Melissa , Sebesta Jacob , Paddock Troy , Xiong Wei , Chou Katherine J. , Yu Jianping
Published: May 2023

Photosynthetic productivity is limited by low energy conversion efficiency in naturally evolved photosynthetic organisms, via multiple mechanisms that are not fully understood. Here we show evidence that extends recent findings that cyanobacteria use “futile” cycles in the synthesis and degradation of carbon compounds to dissipate ATP. Reduction of the glycogen cycle or the sucrose cycle in the model cyanobacterium Synechocystis 6803 led to redirection of cellular energy toward faster growth under simulated outdoor light conditions in photobioreactors that was accompanied by higher energy charge [concentration ratio of ATP/(ATP + ADP)]. Such manipulation of energy metabolism may have potential in engineering microalgal chassis cells to increase productivity of biomass or target metabolites.
Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex
Authors: Himmelstrand Kajsa , Brandström Durling Mikael , Karlsson Magnus , Stenlid Jan , Olson Åke
Published: May 2023

Introduction

Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.

Methods

In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.

Results and Discussion

Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
Characterization and transcriptomic analysis of a native fungal pathogen against the rice pest Nilaparvata lugens
Authors: Wang Zheng-Liang , Wang Yan-Dan , Cheng Yi-Qing , Ye Zi-Hong , Liu Guang-Fu , Yu Xiao-Ping
Published: May 2023

The brown planthopper (BPH), Nilaparvata lugens, is one of the most destructive pests of rice. Given the threats posed by insecticide resistance to its control, eco-friendly strategies based on microbial pathogens emerged as a promising biocontrol alternative. In the present study, we isolated a native fungal pathogen against BPH from infected BPH cadavers and preliminarily identified as a strain of Aspergillus fumigatus based on morphological and molecular methods. Laboratory bioassay revealed that this fungal strain was highly virulent to BPH both at nymphal and adult stages, with the median lethal times (LT50) of 7.5 and 5.8 days under high conidial concentration of 1 × 109 conidia mL–1. A genome-wide view of gene expressions in BPH against fungal attack was analyzed by transcriptomic sequencing and consequently a large number of differentially expressed genes that mainly involved in host immune defense and cell detoxification were found. RNAi-mediated knockdown of an upregulated gene encoding a serine protease (NlSPN) could cause a significant decrease in BPH survival. Combination of dsRNA injection and fungal infection showed an additive effect on BPH mortality, which provided clues to develop new pest management strategies against BPH.
Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula
Authors: Dutta Avishek , Connors Elizabeth , Trinh Rebecca , Erazo Natalia , Dasarathy Srishti , Ducklow Hugh W. , Steinberg Deborah K. , Schofield Oscar M. , Bowman Jeff S.
Published: May 2023

The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.
Effects of different cultivation media on root bacterial community characteristics of greenhouse tomatoes
Authors: Zhang Xinjian , Li Qiang , Zhou Fangyuan , Fan Susu , Zhao Xiaoyan , Zhang Chi , Yan Kun , Wu Xiaoqing
Published: May 2023

Tomato, as a typical greenhouse crop, is commonly first planted as seedlings in a variety of substrates before being transplanted into soil. However, there is rare research on the characteristics of the bacterial community in tomato roots under this planting mode. In this study, tomatoes were planted in pots containing three different cultivation media, including soil and two types of substrates in a greenhouse, followed by a transplanting treatment. After collecting tomato root samples, high-throughput sequencing and bioinformatic analysis were used to compare the differences in bacterial diversity and functions between tomato roots before and after transplanting in different cultivation media. In total, 702776 sequences were obtained, and the OTUs were belonging to 109 genera, 58 families, 41 orders, 14 classes, and 12 phyla. Among the three cultivation media, the β-diversity was significant, and there was a slight difference in bacterial species diversity along with a large difference in their abundance at the genus level. Soil and both substrates had 79 bacterial genera in common, these genera accounted for 68.70%, 76.70%, and 71.17% of the total genera found in the soil, substrate 1, and substrate 2, respectively. After being transplanted from the two substrates to the soil, the bacterial community structure and abundance exhibited similarities with those found in the soil. Furthermore, based on microbial function prediction, the microbial communities in the two-substrate environment demonstrated a greater potential for promoting growth, while the microbial communities in the soil exhibited a greater tendency to exert their antibacterial potential. Our findings offer theoretical support for the creation of artificially reconstructed microbial communities in greenhouse cultivation.
Etiology of recurrent cystitis in postmenopausal women based on vaginal microbiota and the role of Lactobacillus vaginal suppository
Authors: Sekito Takanori , Wada Koichiro , Ishii Ayano , Iwata Takehiro , Matsubara Takehiro , Tomida Shuta , Watanabe Masami , Araki Motoo , Sadahira Takuya
Published: May 2023

Background

The vaginal microbiota can be altered by uropathogenic bacteria associated with recurrent cystitis (RC), and the vaginal administration of Lactobacillus have suggested certain effects to prevent RC. The relationship between vaginal microbiota and the development of RC has not been elucidated. We aimed to clarify the etiology of RC from vaginal microbiota and importance of vaginal Lactobacillus.

Methods

Vaginal samples obtained from 39 postmenopausal women were classified into four groups: healthy controls; uncomplicated cystitis; RC; and prevention (prevented RC by Lactobacillus crispatus-containing vaginal suppositories). Principal coordinate analysis and beta-diversity analysis was used to assess 16S rRNA gene sequencing data from the vaginal microbiome.

Results

Cluster analysis divided the vaginal bacterial communities among 129 vaginal samples into three clusters (A, B, and C). Fourteen of 14 (100%) samples from the RC group and 51 of 53 (96%) samples from the prevention group were in clusters B and C, while 29 of 38 (76%) samples from the healthy group and 14 of 24 (58%) samples from the uncomplicated cystitis group were in cluster A. The principal coordinate analysis showed that plots in the uncomplicated cystitis group were similar to the healthy group, indicating a large separation between the RC group and the uncomplicated cystitis group. On beta-diversity analysis, there were significant differences between the healthy group and the uncomplicated cystitis group (p = 0.045), and between the RC group and the uncomplicated cystitis group or the healthy group (p = 0.001, p = 0.001, respectively). There were no significant differences between the RC group and the prevention group (p = 0.446). The top six taxa were as follows: Prevotella, Lactobacillus, Streptococcus, Enterobacteriaceae, Anaerococcus, and Bifidobacterium. Among patients with RC, Lactobacillus was undetectable before administration of suppositories, while the median relative abundance of Lactobacillus was 19% during administration of suppositories (p = 0.0211), reducing the average cystitis episodes per year (6.3 vs. 2.4, p = 0.0015).

Conclusion

The vaginal microbiota of postmenopausal women with RC is differed from healthy controls and uncomplicated cystitis in terms of lack of Lactobacillus and relatively dominant of Enterobacteriaceae. Vaginal administration of Lactobacillus-containing suppositories can prevent RC by stabilizing vaginal dysbiosis and causing a loss of pathogenic bacteria virulence.
Effects of coal-derived compound fertilizers on soil bacterial community structure in coal mining subsidence areas
Authors: Meng Huisheng , Wang Shuaibing , Zhang Jie , Wang Xiangying , Qiu Chen , Hong Jianping
Published: May 2023

The land damaged by coal mining can be recovered to healthy condition through various reclamation methods. Fertilization is one of the effective methods to improve soil fertility and microbial activity. However, the effects of coal-derived compound fertilizers (SH) on bacterial communities in coal mining subsidence areas still remain unclear. Here, we studied the effects on the nutrient characteristics and bacterial communities in fertilizer-reclaimed soil (CK, without fertilizer; CF, common compound fertilizers; SH, coal-derived compound fertilizers) in coal mining subsidence areas and we applied SH with four different nitrogen application rates (90, 135, 180, and 225 kg/hm2). The results showed that the application of SH significantly increased the contents of available nitrogen (AN), available phosphorus (AP), available potassium (AK), total phosphorus (TP) and soil organic matter (SOM) compared with CK, as well as the bacterial richness (Chao1) and diversity (Shannon) in reclaimed soil that increased first and then decreased with the increase of nitrogen application. Under the same nitrogen application rate (135 kg/hm2), the nutrient content, Chao1 and Shannon of SH2 treatments were higher than those of CF treatment. Meanwhile, SH increased the relative abundance of Proteobacteria, Actinobacteria and Gemmatimonadetes. LEfSe analysis indicated that the taxa of Acidobacteria and Actinobacteria were significantly improved under SH treatments. Canonical correspondence analysis (CCA) and Variance partitioning analysis (VPA) showed that SOM was the most important factor affecting the change of bacterial community structure in reclaimed soil. In conclusion, application of SH can not only increase nutrient content and bacterial diversity of reclaimed soil, but also improve bacterial community structure by increasing bacterial abundance.