bluuebunny/crossref_metadata_2025 huggingface dataset:
Krebs von den lungen-6 as a clinical marker for hypersensitivity pneumonitis: A meta-analysis and bioinformatics analysis
Authors: He Jie , Zhang Jiangliu , Ren Xinyi
Published: November 2022

Aim

Hypersensitivity pneumonitis (HP), also referred to as exogenous allergic alveolitis, is one of the most common interstitial lung diseases (ILDs). A potential immune biomarker, Krebs von den lgen-6 (KL-6) characterizes the progression and severity of HP. The meta-analysis in this study was conducted to elucidate the variations in the concentrations of KL-6 in different types of HP.

Methods

A systematic search of various databases such as EMBASE, Pubmed, CNKI, VIP, Web of Science, and WanFang was carried out to find relevant published articles between January 1980 and August 2022 that explored the relationship between KL-6 and allergic pneumonia. Standardized mean difference (SMD) and 95% confidence interval (CI) were used as effect sizes for comparison among different groups. The GSE47460 and GSE150910 datasets were downloaded to extract and validate the differences in KL-6 mRNA expression between HP lung tissue and healthy controls. Furthermore, the single-cell sequencing dataset GSE135893 was downloaded to extract KL-6 mRNA expression in type II alveolar epithelial cells to validate the differences between HP and healthy controls. Two researchers evaluated the quality of the included studies by employing Newcastle-Ottawa Scale. All the qualified studies were subjected to statistical analyses carried out utilizing RevMan 5.2, Stata 11.0, and R software 4.1.3.

Results

Twenty studies aligned perfectly with the inclusion criteria of the meta. The concentrations of KL-6 were substantially higher in the blood of HP patients as compared to the control group. Subgroup analyses were carried out in accordance with the allergen source and the results revealed that patients with different allergens had higher blood KL-6 concentrations than healthy controls. Additionally, different subgroups of subjects were created for meta-analysis as per the fibrosis status, race, measurement method, and sample type. The concentration of KL-6 in blood was much higher in all HP subgroups than in healthy control groups. Moreover, the bioinformatics analysis revealed that KL-6 mRNA expression was higher in HP lung tissue and type II alveolar epithelial cells as compared to healthy controls.

Conclusion

The present meta-analysis and bioinformatics analysis suggested that the concentration levels of KL-6 varied between HP patients and healthy individuals, and the KL-6 concentrations may be higher in the blood samples of HP patients.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, CRD42022355334.
Putative critical quality attribute matrix identifies mesenchymal stromal cells with potent immunomodulatory and angiogenic “fitness” ranges in response to culture process parameters
Authors: Robb Kevin P. , Audet Julie , Gandhi Rajiv , Viswanathan Sowmya
Published: November 2022

Adipose-derived mesenchymal stromal cells (MSC(AT)) display immunomodulatory and angiogenic properties, but an improved understanding of quantitative critical quality attributes (CQAs) that inform basal MSC(AT) fitness ranges for immunomodulatory and/or angiogenic applications is urgently needed for effective clinical translation. We constructed an in vitro matrix of multivariate readouts to identify putative CQAs that were sensitive enough to discriminate between specific critical processing parameters (CPPs) chosen for their ability to enhance MSC immunomodulatory and angiogenic potencies, with consideration for donor heterogeneity. We compared 3D aggregate culture conditions (3D normoxic, 3D-N) and 2D hypoxic (2D-H) culture as non-genetic CPP conditions that augment immunomodulatory and angiogenic fitness of MSC(AT). We measured multivariate panels of curated genes, soluble factors, and morphometric features for MSC(AT) cultured under varying CPP and licensing conditions, and we benchmarked these against two functional and therapeutically relevant anchor assays – in vitro monocyte/macrophage (MΦ) polarization and in vitro angiogenesis. Our results showed that varying CPP conditions was the primary driver of MSC(AT) immunomodulatory fitness; 3D-N conditions induced greater MSC(AT)-mediated MΦ polarization toward inflammation-resolving subtypes. In contrast, donor heterogeneity was the primary driver of MSC(AT) angiogenic fitness. Our analysis further revealed panels of putative CQAs with minimum and maximum values that consisted of twenty MSC(AT) characteristics that informed immunomodulatory fitness ranges, and ten MSC(AT) characteristics that informed angiogenic fitness ranges. Interestingly, many of the putative CQAs consisted of angiogenic genes or soluble factors that were inversely correlated with immunomodulatory functions (THBS1, CCN2, EDN1, PDGFA, VEGFA, EDIL3, ANGPT1, and ANG genes), and positively correlated to angiogenic functions (VEGF protein), respectively. We applied desirability analysis to empirically rank the putative CQAs for MSC(AT) under varying CPP conditions and donors to numerically identify the desirable CPP conditions or donors with maximal MSC(AT) immunomodulatory and/or angiogenic fitness. Taken together, our approach enabled combinatorial analysis of the matrix of multivariate readouts to provide putative quantitative CQAs that were sensitive to variations in select CPPs that enhance MSC immunomodulatory/angiogenic potency, and donor heterogeneity. These putative CQAs may be used to prospectively screen potent MSC(AT) donors or cell culture conditions to optimize for desired basal MSC(AT) immunomodulatory or angiogenic fitness.
Crosstalk of four kinds of cell deaths defines subtypes of cutaneous melanoma for precise immunotherapy and chemotherapy
Authors: Wan Qi , Wei Ran , Wei Xin , Deng Ying-ping
Published: November 2022

Background

Cell death patterns can give therapeutic and biological clues that facilitate the development of individualized treatments for this lethal form of skin cancer.

Methods

We employed unsupervised clustering to establish robust classifications based on the four kinds of cell death-associated gene expression of 462 melanoma patients in the Cancer Genome Atlas (TCGA) and tested their reproducibility in two independent melanoma cohorts of 558 patients. We then used dimensionality reduction of graph learning to display the different characteristics of cell death patterns and immune microenvironments.

Results

We examined 570 cell death-associated gene expression data of melanoma patients for exploration, independent verification, and comprehensive classification of five reproducible melanoma subtypes (CS1 to CS5) with different genomic and clinical features. Patients in death-inactive subtypes (CS1, CS2, and CS5) had the least immune and stromal cell infiltration, and their prognosis was the poorest. A death-active subtype (CS4), on the other hand, had the highest infiltrated immune and stromal cells and elevated immune-checkpoints. As a result, these patients had the highest response to immunotherapy and the best prognosis. An additional subtype (CS3) had more diversified cell death and immune characteristics with moderate prognoses. Based on graph learning, we successfully divided the CS3 subtype into two subgroups (group A and group B) with distinct survival outcomes and immune features. Finally, we identified eight potential chemical drugs that were specifically targeted for the therapy of melanoma subtypes.

Conclusions

This research defines the intrinsic subtypes of melanoma based on the crosstalk of four kinds of cell deaths, which affords a blueprint for clinical strategies and guiding precise immunotherapy and chemotherapy for melanoma patients.
Reducing sea turtle bycatch with net illumination in an Indonesian small-scale coastal gillnet fishery
Authors: Gautama Dwi Ariyoga , Susanto Hendro , Riyanto Mochammad , Wahju Ronny I. , Osmond Michael , Wang John H.
Published: November 2022

Small-scale fisheries are economically and culturally important throughout the world’s coastal waters. These fisheries, however, often have high bycatch rates of protected marine species. Bycatch in small scale gillnet fisheries is thought to be a major driver behind the declines of several sea turtle populations. Recent studies addressing this issue have identified net illumination as a potentially effective bycatch reduction technology (BRT) to reduce sea turtle interactions with gillnet fisheries. In Southeast Asia, small-scale gillnet fisheries make up a large components of fishing effort often in areas that overlap with important sea turtle habitat. We conducted controlled experiments of net illumination as a potential BRT to reduce sea turtle bycatch in a coastal gillnet fishery based in Paloh, West Kalimantan, Indonesia. Results indicated that net illumination significantly reduced multi-species sea turtle bycatch by 61.4% and specifically green sea turtles (Chelonia mydas) by 59.5%, while the CPUE of total catch and target species remained similar. Moreover, this study suggests that Indonesian fishers can increase their overall market value when using net illumination as the market value per unit effort (MVPUE) of both the total catch and target catch showed significant increases. These results suggest that net illumination could be an effective sea turtle conservation tool for small-scale coastal gillnet fisheries in Indonesia and potentially throughout Southeast Asia. In addition, data from the control treatments of this study also provided the first observer based sea turtle bycatch estimate for a small-scale gillnet fishery in Southeast Asia. Challenges to the broad scale implementation of net illumination to reduce this bycatch of sea turtles include the cost, availability of the technology, socialization of the BRT to fishers, and government interest and support for net illumination as a tool for bycatch reduction.
Decadal intensified and slantwise Subpolar Front in the Japan/East Sea
Authors: Chen Shiyao , Wang Huizan , Chen Wen , Zhang Yun , Zhang Yongchui
Published: November 2022

The Subpolar Front in the Japan/East Sea (JES) could far-reaching influence the atmospheric processes over the downstream regions. However its variability on decadal timescale remains less understood. In this study, the decadal trends in the intensity and position of the SPF in the JES during the time period 1985−2020 are analyzed by using four categories of satellite observed high-resolution sea surface temperature products. The results show that there is a significant intensification trend of the SPF at a rate of 0.37°C/100km/decade. The SPF is further divided into three regions based on the meridional sea surface temperature gradient (MSSTG): the eastern (135−138°E), central (130−135°E) and western (128−130°E) regions, respectively. These three regions showed different meridional movements with the eastern SPF moving poleward by 0.08°/decade, the central SPF moving equatorward by −0.11°/decade and the western SPF showing no significant displacements. The reverse meridional movements between the central and eastern SPF increased its skewness. The frontogenesis rate equation is employed to identify the mechanisms of these decadal trends. Results show that the geostrophic advection term, especially its zonal component, had a crucial role in the decadal trends of the intensity and position of the central and eastern SPF. The decadal trend of the central SPF was mainly attributed to the zonal geostrophic advection of the MSSTG associated with the enhancement of the Subpolar Front Current (SFC) in the upstream region, whereas the decadal trend in the eastern SPF was mainly driven by the zonal geostrophic shear advection controlled by the shear of the SFC in the downstream region. Before 2002, the eastern SPF moved poleward at a rate of 0.27°/decade, whereas there was no obvious trend after 2002. Further decomposition showed that this shift was caused by meridional Ekman advection of the MSSTG.
UMOTMA: Underwater multiple object tracking with memory aggregation
Authors: Hao Zhicheng , Qiu Jun , Zhang Haimiao , Ren Guangbo , Liu Chang
Published: November 2022

Underwater multi-object tracking (UMOT) is an important technology in marine animal ethology. It is affected by complex factors such as scattering, background interference, and occlusion, which makes it a challenging computer vision task. As a result, the stable continuation of trajectories among different targets has been the key to the tracking performance of UMOT tasks. To solve such challenges, we propose an underwater multi-object tracking algorithm based on memory aggregation (UMOTMA) to effectively associate multiple frames with targets. First, we propose a long short-term memory (LSTM)-based memory aggregation module (LSMAM) to enhance memory utilization between multiple frames. Next, LSMAM embeds LSTM into the transformer structure to save and aggregate features between multiple frames. Then, an underwater image enhancement module ME is introduced to process the original underwater images, which improves the quality and visibility of the underwater images so that the model can extract better features from the images. Finally, LSMAM and ME are integrated with a backbone network to implement the entire algorithm framework, which can fully utilize the historical information of the tracked targets. Experiments on the UMOT datasets and the underwater fish school datasets show that UMOTMA generally outperforms existing models and can maintain the stability of the target trajectory while ensuring high-quality detection. The code is available via Github.
Anti-glutathione S-transferase theta 1 antibodies correlate with graft loss in non-sensitized pediatric kidney recipients
Authors: Comoli Patrizia , Cioni Michela , Ray Bryan , Tagliamacco Augusto , Innocente Annalisa , Caridi Gianluca , Bruschi Maurizio , Hariharan Jayasree , Fontana Iris , Trivelli Antonella , Magnasco Alberto , Nocco Angela , Klersy Catherine , Muscianisi Stella , Ghiggeri Gian Marco , Cardillo Massimo , Verrina Enrico , Nocera Arcangelo , Ginevri Fabrizio
Published: November 2022

Introduction

Immunity to Human leukocyte antigen (HLA) cannot explain all cases of ABMR, nor the differences observed in the outcome of kidney recipients with circulating DSAs endowed with similar biologic characteristics. Thus, increasing attention has recently been focused on the role of immunity to non-HLA antigenic targets.

Methods

We analyzed humoral auto- and alloimmune responses to the non-HLA antigen glutathione S-transferase theta 1 (GSTT1), along with development of de novo (dn)HLA-DSAs, in a cohort of 146 pediatric non-sensitized recipients of first kidney allograft, to analyze its role in ABMR and graft loss. A multiplex bead assay was employed to assess GSTT1 antibodies (Abs).

Results

We observed development of GSTT1 Abs in 71 recipients after transplantation, 16 with MFI > 8031 (4th quartile: Q4 group). In univariate analyses, we found an association between Q4-GSTT1Abs and ABMR and graft loss, suggesting a potential role in inducing graft damage, as GSTT1 Abs were identified within ABMR biopsies of patients with graft function deterioration in the absence of concomitant intragraft HLA-DSAs. HLA-DSAs and GSTT1 Abs were independent predictors of graft loss in our cohort. As GSTT1 Ab development preceded or coincided with the appearance of dnHLA-DSAs, we tested and found that a model with the two combined parameters proved more fit to classify patients at risk of graft loss.

Discussion

Our observations on the harmful effects of GSTT1Abs, alone or in combination with HLA-DSAs, add to the evidence pointing to a negative role of allo- and auto-non-HLA Abs on kidney graft outcome.
Three-dimensional ultrasound assessment of risk factors for cystocele and Green classification in primipara
Authors: Yin Weiwei , Ma Qianqing , Xie Wen , Zhu Yuting , Wang Junli
Published: November 2022

Background and aims

The present study aimed to analyze the effects of factors on cystocele and the Green classification.

Materials and methods

We conducted a cross-sectional study on 357 primiparous women examined at our hospital from January 2019 to May 2021. The following data were recorded: maternal characteristics, neonatal characteristics, and factors of childbirth. It was added to the multivariate logistic regression model to determine the independent predictors of the cystocele and the Green classification.

Results

A total of 242 women had cystocele, including 71 women with Green type I cystocele, 134 women with Green type II cystocele, and 37 women with Green type III cystocele. In multivariate logistic regression analysis, body mass index (BMI) at delivery was associated with cystocele, while BMI at delivery and the second stage of labor (SSL) > 1 h were independently with the distance from the symphysis pubis to the bladder neck (SPBN) abnormal (P < 0.05). BMI at examination was associated with the large retrovesical angle (RVA) (P < 0.05). BMI at delivery and the fetal right occiput anterior position (ROA) were independently associated with the distance from the symphysis pubis to the posterior wall of the bladder (SPBP) abnormal (P < 0.05), while epidural anesthesia (EDA) was the protective factor (P < 0.05).

Conclusion

Primipara women should strive to avoid exposure to modifiable risk factors such as controlling weight during pregnancy, reducing weight after delivery, and shortening SSL to reduce the occurrence of cystocele.
Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle
Authors: Cohn Alexa R. , Orsi Renato H. , Carroll Laura M. , Liao Jingqiu , Wiedmann Martin , Cheng Rachel A.
Published: November 2022

Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro’s infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.
Identification and characterization of Bacillus thuringiensis and other Bacillus cereus group isolates from spinach by whole genome sequencing
Authors: Zhao Xingchen , Zervas Athanasios , Hendriks Marc , Rajkovic Andreja , van Overbeek Leo , Hendriksen Niels Bohse , Uyttendaele Mieke
Published: November 2022

Bacillus thuringiensis (Bt), used as a biological control agent (BCA), can persist on plants, and from there can be introduced into the final food product. In routine food safety diagnostics, these Bt residues cannot be distinguished from natural populations of Bacillus cereus present in plants and all are enumerated as “presumptive B. cereus.” In this study, information on eventual use of Bt biopesticides, brand, application times and intervals provided by three food processing companies in Belgium, were integrated with quantitative data on presumptive B. cereus measured from fresh to frozen food products. This information together with data on genomic similarity obtained via whole genome sequencing (WGS) and cry gene profiling using a quantitative real-time PCR (qPCR) assay, confirmed that six out of 11 Bt isolates originated from the applied Bt biocontrol products. These identified Bt strains were shown to carry enterotoxin genes (nhe, hbl, cytK-2) and express Hbl enterotoxin in vitro. It was also noted that these Bt biopesticide strains showed no growth at standard refrigeration temperatures and a low or moderate biofilm-forming ability and cytotoxic activity. Our results also showed that the use of Bt as a BCA on spinach plants in the field led to higher residual counts of Bt in spinach (fresh or frozen) in the food supply chain, but the residual counts exceeding at present commonly assumed safety limit of 105 CFU/g was only found in one fresh spinach sample. It is therefore recommended to establish a pre-harvest interval for Bt biopesticide application in the field to lower the likelihood of noncompliance to the generic B. cereus safety limit. Furthermore, WGS was found to be the best way to identify Bt biopesticide isolates at the strain level for foodborne outbreaks and clinical surveillance. The developed qPCR assay for screening on the presence of cry genes in presumptive B. cereus can be applied as a rapid routine test as an amendment to the already existing test on Bt crystal proteins determined via phase-contrast microscopy.
Remodeling of the microbiota improves the environmental adaptability and disease resistance in Tibetan pigs
Authors: Chang Zhenyu , Bo Suxue , Xiao Qingqing , Wang Yu , Wu Xi , He Yuxuan , Iqbal Mujahid , Ye Yourong , Shang Peng
Published: November 2022

Introduction

The establishment of intestinal microbiota and the maintenance of its equilibrium structure plays an important role in Tibetan pigs during different growth stages. Understanding the structure and function of the intestinal microbiota at different growth stages of Tibetan pigs can provide a theoretical basis for guiding nutritional regulation and feeding management in different stages.

Methods

Fecal samples were collected from the Tibetan piglets at different growth stages, and the 16S rRNA was sequenced to analyze the changes of intestinal microbiota.

Results

Alpha and Beta diversity indexes showed that the diversity of the intestinal microbiota did not change during the three growth stages, and the main components of intestinal microbiota were not significantly different. At the phylum level, Firmicutes and Bacteroidetes were dominant and abundant at different growth stages and were not restricted by age. At the genus level, Streptococcus, Lactobacillus, and Bifidobacterium were the most dominant in the TP10d and TP40d groups, Streptococcus was the most dominant in the TP100d group, followed by Treponema_2 and Lactobacillus. Fusobacteria, Gluconobacter, and Synergistetes were found to be specific genera of 10-day-old Tibetan piglets by LEfSe combined with LDA score. The change of diet made Tenericutes and Epsilonbacteraeota, which are closely related to digestive fiber, become specific bacteria at the age of 40 days. With the consumption of oxygen in the intestine, obligate anaerobes, such as Verrucomicrobia, Fibrobacter, and Planctomycetes, were the characteristic genera of 100 days. KEGG function prediction analysis showed that the intestinal microbiota function of Tibetan pigs changed dynamically with the growth and development of Tibetan piglets.

Discussion

In conclusion, the structure and composition of the intestinal microbiota of Tibetan pigs are significantly different at different growth and development stages, which plays an important role in their immune performance.
Algicidal characteristics of novel algicidal compounds, cyclic lipopeptide surfactins from Bacillus tequilensis strain D8, in eliminating Heterosigma akashiwo blooms
Authors: Shao Xueping , Xie Wanxin , Liang Yiling , Luo Guiying , Li Ling , Zheng Wei , Xu Qingyan , Xu Hong
Published: November 2022

Heterosigma akashiwo blooms have caused severe damage to marine ecosystems, the aquaculture industry and human health worldwide. In this study, Bacillus tequilensis D8 isolated from an H. akashiwo bloom area was found to exert high algicidal activity via extracellular metabolite production. This activity remained stable after exposure to different temperatures and light intensities. Scanning electron microscopy observation and fluorescein diacetate staining indicated that the algicidal substances rapidly destroyed algal plasma membranes and decreased esterase activity. Significant decreases in the maximum photochemical quantum yield and relative electron transfer rate were observed, which indicated photosynthetic membrane destruction. Subsequently, the algicidal compounds were separated and purified by high-performance liquid chromatography and identified as three surfactin homologues by interpreting high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy data. Among these, surfactin-C13 and surfactin-C14 exhibited strong algicidal activity against three HAB-causing species, namely, H. akashiwo, Skeletonema costatum, and Prorocentrum donghaiense, with 24 h-LC50 values of 1.2–5.31 μg/ml. Surfactin-C15 showed strong algicidal activity against S. costatum and weak algicidal activity against H. akashiwo but little activity against P. donghaiense. The present study illuminates the algicidal characteristics and mechanisms of action of surfactins on H. akashiwo and their potential applicability in controlling harmful algal blooms.
Diversity, structure, and distribution of bacterioplankton and diazotroph communities in the Bay of Bengal during the winter monsoon
Authors: Wu Chao , Narale Dhiraj Dhondiram , Cui Zhengguo , Wang Xingzhou , Liu Haijiao , Xu Wenzhe , Zhang Guicheng , Sun Jun
Published: November 2022

The Bay of Bengal (BoB) is conventionally believed to be a low productive, oligotrophic marine ecosystem, where the diazotroph communities presumed to play a vital role in adding “new” nitrogen through the nitrogen fixation process. However, the diazotroph communities in the oceanic region of the BoB are still poorly understood though it represents most of the seawater volume. The present study investigated a detailed account of the bacterioplankton community structure and distribution in the oceanic BoB during the winter monsoon using high throughput sequencing targeting the 16S rRNA and nifH genes. Our study observed diverse groups of bacterioplankton communities in the BoB including both cyanobacterial and non-cyanobacterial phylotypes. Cyanobacteria (Prochlorococcus spp. and Synechococcus spp.) and Proteobacteria (mainly α-, γ-, and δ-Proteobacteria) were the most abundant groups within the bacterial communities, possessing differential vertical distribution patterns. Cyanobacteria were more abundant in the surface waters, whereas Proteobacteria dominated the deeper layers (75 m). However, within the diazotroph communities, Proteobacteria (mainly γ-Proteobacteria) were the most dominant groups than Cyanobacteria. Function prediction based on PICRUSt revealed that nitrogen fixation might more active to add fixed nitrogen in the surface waters, while nitrogen removal pathways (denitrification and anammox) might stronger in deeper layers. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and silicate were major environmental factors driving the distribution of bacterial communities. Additionally, phosphate was also an important factor in regulating the diazotroph communities in the surface water. Overall, this study provided detailed information on bacterial communities and their vital role in the nitrogen cycles in oligotrophic ecosystems.
Metagenomic insights into the functions of microbial communities in sulfur-rich sediment of a shallow-water hydrothermal vent off Kueishan Island
Authors: Wang Li , Shen Ziyi , Cheng Xinyi , Hwang Jiang-Shiou , Guo Yizhe , Sun Mingye , Cao Junwei , Liu Rulong , Fang Jiasong
Published: November 2022

Hydrothermal vent (HTV) systems are important habitats for understanding the biological processes of extremophiles on Earth and their relative contributions to material and energy cycles in the ocean. Current understanding on hydrothermal systems have been primarily focused on deep-sea HTVs, and little is known about the functions and metabolisms of microorganisms in shallow-water HTVs (SW-HTVs), which are distinguished from deep-sea HTVs by a depth limit of 200 m. In this study, we analyzed metagenomes of sulfur-rich sediment samples collected from a SW-HTV of Kueishan Island, located in a marginal sea of the western Pacific Ocean. Comparing with a previously published report of pelagic samples from the nearby sampling site, microbial communities in the SW-HTV sediments enriching with genes of both aerobic and anaerobic respiration inferred variable environments in the tested sediments. Abundant genes of energy metabolism encoding sulfur oxidation, H2 oxidation, and carbon fixation were detected from the sediment samples. Sixty-eight metagenome-assembled-genomes (MAGs) were reconstructed to further understand the metabolism and potential interactions between different microbial taxa in the SW-HTVs sediment. MAGs with the highest abundant were chemolithotrophic sulfur-oxidization bacteria, including Sulfurovum represented Campylobacteria involved sox multienzyme, sulfide oxidation genes and rTCA cycle, and Gammaproteobacteria involved dsr gene and CBB cycle. In addition, Desulfobacterota with the potential to participate in sulfur-disproportionating processes also had higher abundance than the sample’s overall mean value. The interaction of these bacterial groups allows the microbial communities to efficiently metabolize a large variety of sulfur compounds. In addition, the potential to use simple organic carbon, such as acetate, was found in chemolithotrophic Campylobacterial MAGs. Collectively, our results revealed the complexity of environmental conditions of the vent sediment and highlight the interactive relationships of the dominant microbial populations in driving sulfur cycles in the SW-HTV sediments off Kueishan Island.
Targets and mechanisms of Alpinia oxyphylla Miquel fruits in treating neurodegenerative dementia
Authors: Zeng Peng , Liu Yuan-Cheng , Wang Xiao-Ming , Ye Chao-Yuan , Sun Yi-Wen , Su Hong-Fei , Qiu Shuo-Wen , Li Ya-Nan , Wang Yao , Wang Yan-Chun , Ma Jun , Li Man , Tian Qing
Published: November 2022

The dried and ripe fruits of Alpinia oxyphylla and ripe fruits of Alpinia oxyphylla Miquel (AO) have the effects of tonifying kidney-essence and nourishing intelligence and thus have been widely used in treating dementia. Alzheimer’s disease (AD) is a typical form of neurodegenerative dementia with kidney-essence deficiency in Traditional Chinese Medicine (TCM). So far, there is a lack of systematic studies on the biological basis of tonifying kidney-essence and nourishing intelligence and the corresponding phytochemicals. In this study, we investigated the targets of AO in tonifying kidney-essence and nourishing intelligence based on the key pathophysiological processes of neurodegenerative dementia. According to ultra-high-performance liquid chromatography with triple quadrupole mass spectrometry data and Lipinski’s rule of five, 49 bioactive phytochemicals from AO were identified, and 26 of them were found to target 168 key molecules in the treatment of neurodegenerative dementia. Nine phytochemicals of AO were shown to target acetylcholinesterase (ACHE), and 19 phytochemicals were shown to target butyrylcholinesterase (BCHE). A database of neurodegenerative dementia with kidney-essence deficiency involving 731 genes was constructed. Furthermore, yakuchinone B, 5-hydroxy-1,7-bis (4-hydroxy-3-methoxyphenyl) heptan-3-one (5-HYD), oxyhylladiketone, oxyphyllacinol, butyl-β-D-fructopyranoside, dibutyl phthalate, chrysin, yakuchinone A, rhamnetin, and rhamnocitrin were identified as the key phytochemicals from AO that regulate the pathogenesis of neurodegenerative dementia in a multitargeted manner. The approach of studying the pharmacological mechanism underlying the effects of medicinal plants and the biological basis of TCM syndrome may be helpful in studying the translation of TCM.
Topology of diffusion changes in corpus callosum in Alzheimer's disease: An exploratory case-control study
Authors: Kumar Sumeet , De Luca Alberto , Leemans Alexander , Saffari Seyed Ehsan , Hartono Septian , Zailan Fatin Zahra , Ng Kok Pin , Kandiah Nagaendran
Published: November 2022

Aim

This study aims to assess the integrity of white matter in various segments of the corpus callosum in Alzheimer's disease (AD) by using metrics derived from diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI) and white matter tract integrity model (WMTI) and compare these findings to healthy controls (HC).

Methods

The study was approved by the institutional ethics board. 12 AD patients and 12 HC formed the study population. All AD patients were recruited from a tertiary neurology memory clinic. A standardized battery of neuropsychological assessments was administered to the study participants by a trained rater. MRI scans were performed with a Philips Ingenia 3.0T scanner equipped with a 32-channel head coil. The protocol included a T1-weighted sequence, FLAIR and a dMRI acquisition. The dMRI scan included a total of 71 volumes, 8 at b = 0 s/mm2, 15 at b = 1,000 s/mm2 and 48 at b = 2,000 s/mm2. Diffusion data fit was performed using DKI REKINDLE and WMTI models.

Results and discussion

We detected changes suggesting demyelination and axonal degeneration throughout the corpus callosum of patients with AD, most prominent in the mid-anterior and mid-posterior segments of CC. Axial kurtosis was the most significantly altered metric, being reduced in AD patients in almost all segments of corpus callosum. Reduced axial kurtosis in the CC segments correlated with poor cognition scores in AD patients in the visuospatial, language and attention domains.
Associations between risk of Alzheimer's disease and obstructive sleep apnea, intermittent hypoxia, and arousal responses: A pilot study
Authors: Tsai Cheng-Yu , Wu Sheng-Ming , Kuan Yi-Chun , Lin Yin-Tzu , Hsu Chia-Rung , Hsu Wen-Hua , Liu Yi-Shin , Majumdar Arnab , Stettler Marc , Yang Chien-Ming , Lee Kang-Yun , Wu Dean , Lee Hsin-Chien , Wu Cheng-Jung , Kang Jiunn-Horng , Liu Wen-Te
Published: November 2022

Objectives

Obstructive sleep apnea (OSA) may increase the risk of Alzheimer's disease (AD). However, potential associations among sleep-disordered breathing, hypoxia, and OSA-induced arousal responses should be investigated. This study determined differences in sleep parameters and investigated the relationship between such parameters and the risk of AD.

Methods

Patients with suspected OSA were recruited and underwent in-lab polysomnography (PSG). Subsequently, blood samples were collected from participants. Patients' plasma levels of total tau (T-Tau) and amyloid beta-peptide 42 (Aβ42) were measured using an ultrasensitive immunomagnetic reduction assay. Next, the participants were categorized into low- and high-risk groups on the basis of the computed product (Aβ42 × T-Tau, the cutoff for AD risk). PSG parameters were analyzed and compared.

Results

We included 36 patients in this study, of whom 18 and 18 were assigned to the low- and high-risk groups, respectively. The average apnea–hypopnea index (AHI), apnea, hypopnea index [during rapid eye movement (REM) and non-REM (NREM) sleep], and oxygen desaturation index (≥3%, ODI-3%) values of the high-risk group were significantly higher than those of the low-risk group. Similarly, the mean arousal index and respiratory arousal index (R-ArI) of the high-risk group were significantly higher than those of the low-risk group. Sleep-disordered breathing indices, oxygen desaturation, and arousal responses were significantly associated with an increased risk of AD. Positive associations were observed among the AHI, ODI-3%, R-ArI, and computed product.

Conclusions

Recurrent sleep-disordered breathing, intermittent hypoxia, and arousal responses, including those occurring during the NREM stage, were associated with AD risk. However, a longitudinal study should be conducted to investigate the causal relationships among these factors.
Characteristics of vestibular migraine, probable vestibular migraine, and recurrent vertigo of childhood in caloric and video head impulse tests
Authors: Zhang Qin , Wu Qiong , Chen Jianyong , Wang Xueyan , Zhang Yuzhong , Liu Shuyun , Wang Lu , Shen Jiali , Shen Min , Tang Xinyi , Mei Ling , Chen Xiangping , Jin Yulian , Yang Jun , Zhang Qing
Published: November 2022

Objective

Vertigo is very common in children, but the specific diagnosis and characteristics are not clear. The main objective of this study was to analyze the characteristics of caloric test (CT) and video head impulse test (vHIT) in vestibular migraine of childhood (VMC), probable vestibular migraine of childhood (PVMC), and recurrent vertigo of childhood (RVC), which can provide a reference value for their clinical diagnosis.

Methods

We selected VMC, PVMC and RVC patients under 18 years of age from the outpatient Department of Otolaryngology–Head and Neck Surgery between May 2021 and August 2022. All patients underwent vestibular function examinations, including eye movement recording CT and vHIT. CT results depended on whether both canal paresis and directional preponderance were under normal limits, and vHIT results depended on the gain values of vestibulo-ocular reflex. The results of both tests were analyzed according to the disease type.

Results

Among the 81 pediatric vertigo patients aged 5–17 years, 44 were females and 37 were males. According to the type of vertigo, 29 patients (25.80%) were diagnosed with VMC, 11 (13.58%) with PVMC, and 41 (50.62%) with RVC. The abnormal rates of the CT in VMC, PVMC, and RVC patients were 24.14%, 36.36%, and 17.07%, respectively. There was no significant difference in the abnormal rates among the three groups (P > 0.05). None of the patients showed abnormal vHIT results (all abnormal rates 0.00%). The abnormal CT rates were significantly higher than those of abnormal vHIT rates (P < 0.05).

Conclusions

VMC, PVMC, and RVC are more likely to be diagnosed by symptoms, as neither CT nor vHIT are specific to any conditions. Due to different clinical presentations of vertigo in pediatric patients, it is critical to further clarify the diagnosis with medical history and clinical characteristics.
An improved anchor-free SAR ship detection algorithm based on brain-inspired attention mechanism
Authors: Shi Hao , He Cheng , Li Jianhao , Chen Liang , Wang Yupei
Published: November 2022

As a computing platform that can deal with problems independently and adapt to different environments, the brain-inspired function is similar to the human brain, which can effectively make use of visual targets and their surrounding background information to make more efficient and accurate decision results. Currently synthetic aperture radar (SAR) ship target detection has an important role in military and civilian fields, but there are still great challenges in SAR ship target detection due to the problems of large span of ship scales and obvious feature differences. Therefore, this paper proposes an improved anchor-free SAR ship detection algorithm based on brain-inspired attention mechanism, which efficiently focuses on target information ignoring the interference of complex background. First of all, most target detection algorithms are based on the anchor method, which requires a large number of anchors to be defined in advance and has poor generalization capability and performance to be improved in multi-scale ship detection, so this paper adopts an anchor-free detection network to directly enumerate potential target locations to enhance algorithm robustness and improve detection performance. Secondly, in order to improve the SAR ship target feature extraction capability, a dense connection module is proposed for the deep part of the network to promote more adequate deep feature fusion. A visual attention module is proposed for the shallow part of the network to focus on the salient features of the ship target in the local area for the input SAR images and suppress the interference of the surrounding background with similar scattering characteristics. In addition, because the SAR image coherent speckle noise is similar to the edge of the ship target, this paper proposes a novel width height prediction constraint to suppress the noise scattering power effect and improve the SAR ship localization accuracy. Moreover, to prove the effectiveness of this algorithm, experiments are conducted on the SAR ship detection dataset (SSDD) and high resolution SAR images dataset (HRSID). The experimental results show that the proposed algorithm achieves the best detection performance with metrics AP of 68.2% and 62.2% on SSDD and HRSID, respectively.
The value of dual-energy spectral CT in differentiating solitary pulmonary tuberculosis and solitary lung adenocarcinoma
Authors: Zhang Guojin , Li Shenglin , Yang Ke , Shang Lan , Zhang Feng , Huang Zixin , Ren Jialiang , Zhang Zhuoli , Zhou Junlin , Pu Hong , Man Qiong , Kong Weifang
Published: November 2022

Background

To explore the value of dual-energy spectral CT in distinguishing solitary pulmonary tuberculosis (SP-TB) from solitary lung adenocarcinoma (S-LUAD).

Methods

A total of 246 patients confirmed SP-TB (n = 86) or S-LUAD (n = 160) were retrospectively included. Spectral CT parameters include CT40keV value, CT70keV value, iodine concentration (IC), water concentration (WC), effective atomic number (Zeff), and spectral curve slope (λ70keV). Data were measured during the arterial phase (AP) and venous phase (VP). Chi-square test was used to compare categorical variables, Wilcoxon rank-sum test was used to compare continuous variables, and a two-sample t-test was used to compare spectral CT parameters. ROC curves were used to calculate diagnostic efficiency.

Results

There were significant differences in spectral CT quantitative parameters (including CT40keV value [all P< 0.001] , CT70keV value [all P< 0.001], λ70keV [P< 0.001, and P = 0.027], Zeff [P =0.015, and P = 0.001], and IC [P =0.002, and P = 0.028]) between the two groups during the AP and VP. However, WC (P = 0.930, and P = 0.823) was not statistically different between the two groups. The ROC curve analysis showed that the AUC in the AP and VP was 90.9% (95% CI, 0.873-0.945) and 83.4% (95% CI, 0.780-0.887), respectively. The highest diagnostic performance (AUC, 97.6%; 95% CI, 0.961-0.991) was achieved when all spectral CT parameters were combined with clinical variables.

Conclusion

Dual-energy spectral CT has a significant value in distinguishing SP-TB from S-LUAD.
The roles and clinical applications of interleukins in endometrial carcinoma
Authors: Zang Yuqin , Li Huanrong , Liu Shiqi , Zhao Ruqian , Zhang Kaiwen , Zang Yuqi , Wang Yingmei , Xue Fengxia
Published: November 2022

As a common malignant tumor of the female reproductive system, endometrial carcinoma (EC) seriously endangers women’s health with an increasing incidence. The oncogenesis and progression of cancer are closely linked with immune microenvironment, of which interleukins are the important components. In order to illustrate the roles and clinical applications of interleukins in EC, literature of interleukins and EC were reviewed. Based on the present studies, interleukins play crucial roles in the oncogenesis and development of EC via regulating the proliferation, migration, invasion, angiogenesis, apoptosis, pyroptosis and autophagy of EC as well as the immune function against EC. And some of the interleukins seems to have prospective clinical applications in EC, such as evaluating the risk of tumorigenesis, discriminating the malignancy from benign disorders or normal condition, indicating cancer aggressiveness, predicting the prognosis of patients and serving as the novel therapy. However, there is still a long way to go before the clinical applications of interleukins in EC come into reality. Nevertheless, it is certain that the exploration of interleukins will definitely be of great benefit to the screening, diagnosis and treatment of EC in the future.
Combining the SMAC mimetic LCL161 with Gemcitabine plus Cisplatin therapy inhibits and prevents the emergence of multidrug resistance in cholangiocarcinoma
Authors: Prasopporn Sunisa , Suppramote Orawan , Ponvilawan Ben , Jamyuang Chanette , Chanthercrob Jantappapa , Chaiboonchoe Amphun , More-Krong Pimkanya , Kongsri Kamonchanok , Suntiparpluacha Monthira , Chanwat Rawisak , Korphaisarn Krittiya , Okada Seiji , Sampattavanich Somponnat , Jirawatnotai Siwanon
Published: November 2022

Cholangiocarcinoma (CCA) is a highly lethal gastrointestinal malignancy that has one of the worst prognoses among solid tumors. The combination of Gemcitabine + Cisplatin (GEM/CIS) remains the standard first-line treatment for advanced stage CCA. However, this drug combination yields only a modest objective response rate, and in cases that initially respond to this treatment, drug resistance commonly rapidly develops. To improve the efficiency of GEM/CIS therapy for CCA, a thorough understanding of the mechanism of GEM/CIS resistance in CCA is required. To that end – in this study, we developed several acquired GEM/CIS-resistant CCA cell lines and we screened those cell lines for acquired vulnerability. The screening process revealed that subset of CCA with GEM/CIS resistance acquired vulnerability to the small-molecule second mitochondrial-derived activator of caspases (SMAC) mimetics LCL161 and Birinapant. The observed acquired vulnerability was found to be associated with upregulation of an inhibitor of apoptosis protein 2 (cIAP2), a known target of SMAC mimetics. LCL161 or cIAP2-shRNA downregulated cIAP2 and restored the sensitivity to GEM/CIS in GEM/CIS-resistant CCA cell lines and in in vivo GEM/CIS-resistant xenograft models. A strong synergic effect was observed when LCL161 was added to GEM/CIS. Interestingly, this synergism was also observed in drug-naïve CCA cell lines, xenografts, and patient-derived organoids. This triplet therapy also prevented the emergence of multidrug-resistant CCA in in vitro and in vivo models. Our findings suggest that activation of cIAP2 allows CCA to escape GEM/CIS, and that suppression of cIAP2 reestablishes the apoptotic profile of CCA, thus restoring its vulnerability to GEM/CIS. The results of this study indicate that combining the SMAC mimetic LCL161 with GEM/CIS inhibits and prevents the emergence of multidrug resistance in CCA.