bluuebunny/crossref_metadata_2025 huggingface dataset:
Revealing the novel ferroptosis-related therapeutic targets for diabetic foot ulcer based on the machine learning
Authors: Wang Xingkai , Jiang Guidong , Zong Junwei , Lv Decheng , Lu Ming , Qu Xueling , Wang Shouyu
Published: September 2022

Objectives: DFU is a serious chronic disease with high disability and fatality rates, yet there is no completely effective therapy. While ferroptosis is integrated to inflammation and infection, its involvement in DFU is still unclear. The study aimed to identify ferroptosis-related genes in DFU, providing potential therapeutic targets.

Methods: In the GEO database, two DFU microarray datasets (GSE147890 and GSE80178) were collected. WGCNA was conducted to identify the modular genes most involved in DFU. Subsequently, enrichment analysis and PPI analysis were performed. To yield the DFU-associated ferroposis genes, the ferroposis genes were retrieved from the FerrDb database and overlapped with the modular genes. Eventually, an optimal DFU prediction model was created by combining multiple machine learning algorithms (LASSO, SVM-RFE, Boruta, and XGBoost) to detect ferroposis genes most closely associated with DFU. The accuracy of the model was verified by utilizing external datasets (GSE7014) based on ROC curves.

Results: WGCNA yielded seven modules in all, and 1223 DFU-related modular genes were identified. GO analysis revealed that inflammatory response, decidualization, and protein binding were the most highly enriched terms. These module genes were also enriched in the ErbB signaling, IL-17 signaling, MAPK signaling, growth hormone synthesis, secretion and action, and tight junction KEGG pathways. Twenty-five DFU-associated ferroposis genes were obtained by cross-linking with modular genes, which could distinguish DFU patients from controls. Ultimately, the prediction model based on machine learning algorithms was well established, with high AUC values (0.79 of LASSO, 0.80 of SVM, 0.75 of Boruta, 0.70 of XGBoost). MAFG and MAPK3 were identified by the prediction model as the most highly associated ferroposis-genes in DFU. Furthermore, the external dataset (GSE29221) validation revealed that MAPK3 (AUC = 0.81) had superior AUC values than MAFG (AUC = 0.62).

Conclusion: As the most related ferroptosis-genes with DFU, MAFG and MAPK3 may be employed as potential therapeutic targets for DFU patients. Moreover, MAPK3, with higher accuracy, could be the more potential ferroptosis-related biomarker for further experimental validation.
Birth of a boy after intracytoplasmic sperm injection using ejaculated spermatozoa from a nonmosaic klinefelter syndrome man with normal sperm motility: A case report
Authors: Xu Wen-qing , Yuan Yuan , Chen Ying , Luo Tao , Chen Hou-yang
Published: September 2022

Klinefelter syndrome (KS) is the most common sex chromosome abnormality, which occurs in about one in 660 newly born males, and it is the most common genetic cause of infertility in infertile men, accounting for 11%. It is rare for non-mosaic KS patients to have sperm and reproduce naturally, and there are currently no reports of KS patients with normal motile sperm. Microdissection testicular sperm extraction associated with intracytoplasmic sperm injection (micro-TESE-ICSI) is currently the main assisted reproductive method for patients with KS. In this study, we describe a patient of non-mosaic KS (47, XXY) who had given birth to a healthy girl naturally. The patient had normal male characteristics and did not have the symptoms of hypogonadism commonly seen in KS. He had high levels of serum follicle stimulating hormone and luteinizing hormone, a low level of serum testosterone, and a normal level of prolactin. Semen analysis showed that this case had normal motile sperm (total motility of 57.66% and progressive motility of 46.19%) but low sperm concentration (1.7 × 106 cells/mL). He gave birth to a boy by intracytoplasmic sperm injection (ICSI) using his ejaculated sperm purified to high density and motility by Percoll density gradient centrifugation. In conclusion, this case is a unique non-mosaic KS patient who had a normal sperm motility, experienced a natural fertility, and received a successful ICSI outcome, which enlarges our knowledges on non-mosaic KS.
Deep learning methods may not outperform other machine learning methods on analyzing genomic studies
Authors: Dong Yao , Zhou Shaoze , Xing Li , Chen Yumeng , Ren Ziyu , Dong Yongfeng , Zhang Xuekui
Published: September 2022

Deep Learning (DL) has been broadly applied to solve big data problems in biomedical fields, which is most successful in image processing. Recently, many DL methods have been applied to analyze genomic studies. However, genomic data usually has too small a sample size to fit a complex network. They do not have common structural patterns like images to utilize pre-trained networks or take advantage of convolution layers. The concern of overusing DL methods motivates us to evaluate DL methods’ performance versus popular non-deep Machine Learning (ML) methods for analyzing genomic data with a wide range of sample sizes. In this paper, we conduct a benchmark study using the UK Biobank data and its many random subsets with different sample sizes. The original UK Biobank data has about 500k participants. Each patient has comprehensive patient characteristics, disease histories, and genomic information, i.e., the genotypes of millions of Single-Nucleotide Polymorphism (SNPs). We are interested in predicting the risk of three lung diseases: asthma, COPD, and lung cancer. There are 205,238 participants have recorded disease outcomes for these three diseases. Five prediction models are investigated in this benchmark study, including three non-deep machine learning methods (Elastic Net, XGBoost, and SVM) and two deep learning methods (DNN and LSTM). Besides the most popular performance metrics, such as the F1-score, we promote the hit curve, a visual tool to describe the performance of predicting rare events. We discovered that DL methods frequently fail to outperform non-deep ML in analyzing genomic data, even in large datasets with over 200k samples. The experiment results suggest not overusing DL methods in genomic studies, even with biobank-level sample sizes. The performance differences between DL and non-deep ML decrease as the sample size of data increases. This suggests when the sample size of data is significant, further increasing sample sizes leads to more performance gain in DL methods. Hence, DL methods could be better if we analyze genomic data bigger than this study.
Sec-O-Glucosylhamaudol Inhibits RANKL-Induced Osteoclastogenesis by Repressing 5-LO and AKT/GSK3β Signaling
Authors: Cao Jinjin , Zhou Ming-Xue , Chen Xinyan , Sun Menglu , Wei Congmin , Peng Qisheng , Cheng Zhou , Sun Wanchun , Wang Hongbing
Published: September 2022

Sec-O-glucosylhamaudol (SOG), an active flavonoid compound derived from the root of Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., exhibits analgesic, anti-inflammatory, and high 5-lipoxygenase (5-LO) inhibitory effects. However, its effect on osteoclastogenesis was unclear. We demonstrated that SOG markedly attenuated RANKL-induced osteoclast formation, F-actin ring formation, and mineral resorption by reducing the induction of key transcription factors NFATc1, c-Fos, and their target genes such as TRAP, CTSK, and DC-STAMP during osteoclastogenesis. Western blotting showed that SOG significantly inhibited the phosphorylation of AKT and GSK3β at the middle–late stage of osteoclastogenesis without altering calcineurin catalytic subunit protein phosphatase-2β-Aα expression. Moreover, GSK3β inhibitor SB415286 partially reversed SOG-induced inhibition of osteoclastogenesis, suggesting that SOG inhibits RANKL-induced osteoclastogenesis by activating GSK3β, at least in part. 5-LO gene silencing by small interfering RNA in mouse bone marrow macrophages markedly reduced RANKL-induced osteoclastogenesis by inhibiting NFATc1. However, it did not affect the phosphorylation of AKT or GSK3β, indicating that SOG exerts its inhibitory effects on osteoclastogenesis by suppressing both the independent 5-LO pathway and AKT-mediated GSK3β inactivation. In support of this, SOG significantly improved bone destruction in a lipopolysaccharide-induced mouse model of bone loss. Taken together, these results suggest a potential therapeutic effect for SOG on osteoclast-related bone lysis disease.
The regulation and potential roles of m6A modifications in early embryonic development and immune tolerance at the maternal-fetal interface
Authors: Liu Hong , Zheng Jie , Liao Aihua
Published: September 2022

The immune microenvironment at the maternal-fetal interface was determined by the crosstalk between the trophoblast and maternal-derived cells, which dynamically changed during the whole gestation. Trophoblasts act as innate immune cells and dialogue with maternal-derived cells to ensure early embryonic development, depending on the local immune microenvironment. Therefore, dysfunctions in trophoblasts and maternal decidual cells contribute to pregnancy complications, especially recurrent pregnancy loss in early pregnancy. Since many unknown regulatory factors still affect the complex immune status, exploring new potential aspects that could influence early pregnancy is essential. RNA methylation plays an important role in contributing to the transcriptional regulation of various cells. Sufficient studies have shown the crucial roles of N6-methyladenosine (m6A)- and m6A-associated- regulators in embryogenesis during implantation. They are also essential in regulating innate and adaptive immune cells and the immune response and shaping the local and systemic immune microenvironment. However, the function of m6A modifications at the maternal-fetal interface still lacks wide research. This review highlights the critical functions of m6A in early embryonic development, summarizes the reported research on m6A in regulating immune cells and tumor immune microenvironment, and identifies the potential value of m6A modifications in shaping trophoblasts, decidual immune cells, and the microenvironment at the maternal-fetal interface. The m6A modifications are more likely to contribute to embryogenesis, placentation and shape the immune microenvironment at the maternal-fetal interface. Uncovering these crucial regulatory mechanisms could provide novel therapeutic targets for RNA methylation in early pregnancy.
Long non-coding RNA LncMPEG1 responds to multiple environmental stressors by affecting biomineralization in pearl oyster Pinctada fucata martensii
Authors: Cai Caixia , He Qi , Xie Bingyi , Xu Zhijie , Wang Cheng , Yang Chuangye , Liao Yongshan , Zheng Zhe
Published: September 2022

Marine environmental change directly affects bivalve growth and survival. Exoskeleton formation, the main energy dissipation in the physiological metabolism, typically reflects the body growth of the bivalve. However, how bivalves regulate the biomineralization of the exoskeleton under environmental stressors is not yet clear. Long non-coding RNA regulates various life processes through complex mechanisms in vertebrates and invertebrates. In this research, we cloned the complete sequence of a mantle-specific expressed long non-coding RNA (designated as LncMPEG1) from a pearl oyster, Pinctada fucata martensii. A quantitative real-time PCR analysis showed that LncMPEG1 expression was significantly high in early umbo larvae and juveniles, which would be the critical periods of shell development. LncMPEG1 was identified in the outer epithelium of the middle fold from the mantle edge, mantle pallial, and mantle center by using in situ hybridization. Additionally, the expression of LncMPEG1 was stimulated by shell damage, alien invasion, heat and cold temperature stress, and hypoxia stress. In the mantle, a decreased in LncMPEG1 expression was detected by RNA interference, which can cause the irregular growth of crystals on the inner surface of the prismatic layer and nacre in the shells. Therefore, we propose that LncMPEG1 could be a key regulator in biomineralization and responds to environmental stress in the mantle .
Population level variation in reproductive development and output in the golden kelp Laminaria ochroleuca under marine heat wave scenarios
Authors: Strasser Fiona-Elaine , Barreto Luis Matos , Kaidi Soukaina , Sabour Brahim , Serrão Ester A. , Pearson Gareth A. , Martins Neusa
Published: September 2022

Thermal tolerance is often interpreted as a species-wide thermal niche in the absence of studies focusing on the adaptive potential of populations to exhibit differential thermal tolerance. Thus, considering intraspecific thermal plasticity, local adaptation or both between populations along distributional gradients when interpreting and predicting species responses to warming is imperative. Removing the effect of environmental histories by raising kelp gametophyte generations in vitro under common garden conditions allows unbiased comparison between population-specific adaptive variation under different environmental conditions. Following this approach, this study aims to detect (potentially) adaptive differentiation in microscopic life-stages (gametophytes) between populations of a temperate forest forming kelp, Laminaria ochroleuca from locations with distinct thermal conditions. Gametophytes from four geographically distinct populations were subjected to different temperature treatments (17, marine heat waves of 23, 25 and 27°C) and gametophyte survival during thermal stress as well as reproductive success and photosynthetic responses during recovery were investigated. Intraspecific variation in resilience and reproductive output to thermal stress was found in L. ochroleuca; gametophytes from the most northern population (Brittany, France) were the most thermally sensitive, with mortality onset at 23°C, whereas mortality in the remaining populations was only apparent at 27°C. Gametophytes from northern Spain and Morocco exhibited very low reproductive success during recovery from 23 and 25°C. However, when recovering from the highest thermal treatment (27°C) the reproductive development and sporophyte output was higher than in the gametophytes from France and Italy (Mediterranean). The population-specific responses of gametophyte resilience and reproductive success to temperature stress suggest genetic differentiation in response to variation in local thermal regimes.
Variability in micronekton active carbon transport estimates on the Southwest Coast of Oahu using three different sampling gears
Authors: Kwong Lian E. , Bahl Alexis A. , Pakhomov Evgeny A.
Published: September 2022

Micronekton were sampled off the southwest coast of Oahu in October of 2004 as part of the North Pacific Marine Sciences Organization (PICES) Micronekton Sampling Gear Intercalibration experiment (MIE-1). The initiative employed three different micronekton sampling gears: the Cobb Trawl, Isaacs–Kidd midwater trawl (IKMT), and Hokkaido University frame trawl (HUFT). Micronekton catches from the three sampling gears were used to quantify the rates of active carbon transport. We evaluate the differences in total active carbon transport assessed using the data collected by the three gears, with a particular emphasis on taxa- and length-specific differences across gears. The estimates of total active carbon transport derived from the HUFT were significantly lower than those derived from the IKMT. We detected no significant difference between estimates derived using the IKMT and Cobb and the Cobb and HUFT. Dominant groups contributing to active carbon transport varied across sampling gears (Cobb: myctophids and cephalopods; HUFT: decapods and stomatopods; IKMT: cephalopods, myctophids, and decapods); however, no significant differences in the contribution of individual taxa to active carbon transport across sampling gears were detected (e.g., the myctophid active carbon transport contribution for the Cobb was not significantly different from that of the IKMT). Pairwise ratios revealed size-specific differences in the contribution to total flux across gears. As expected, the HUFT and IKMT estimates of active carbon transport were higher for smaller size classes, while estimates from the Cobb were more evenly distributed across size classes. These findings suggest that the differences in total active carbon transport from the three sampling gears are driven primarily by size-based sampling biases, which produce significant differences in biomass estimates. This study provides a foundation upon which future active carbon transport studies may be adjusted to address sampling gear biases.
Turbidity influences the recruitment of Argyrosomus japonicus to estuarine nurseries
Authors: James Nicola Caroline , Childs Amber-Robyn , Kemp Justin , Wilsnagh Shannon , Edworthy Carla
Published: September 2022

Estuaries serve as important nursery habitats for several coastal fishery species. The successful recruitment of larvae and early juveniles into estuaries is paramount for population persistence and maintenance. Several factors have been proposed as stimuli that could elicit a recruitment response in estuary-associated fish species. Larvae and early juveniles may trace land-based cues back to an estuary by following the olfactory concentration gradient or use other visual or acoustic stimuli. Argyrosomus japonicus is an iconic estuarine-associated species. Due to overfishing, reduced freshwater input and habitat degradation in their estuarine nursery habitat, the South African population has suffered severe stock declines. Turbidity associated with high freshwater input is thought to promote recruitment into estuaries. We used choice-chamber laboratory experiments to test the hypothesis that settlement-stage A. japonicus are attracted to turbidity rather than olfactory gradients when recruiting into estuaries. Three choice experiments (with three replicate trials each) were performed over three consecutive days. Each experiment used paired combinations of six estuarine/seawater types with varying turbidity and olfactory characteristics. For each experiment, three trials were repeated in succession with six new fish for each trial. Settlement-stage A. japonicus showed a significant preference for turbid water (with and without olfactory cues) over seawater (no olfactory cues) and clear estuary water (with olfactory cues). No clear choice was made between clear estuary water (with olfactory cues) and clear artificial seawater (without olfactory cues), suggesting that turbidity gradients are most likely the primary factor governing the recruitment of settlement-stage A. japonicus into estuaries.
Successful therapeutic strategy for a patient with obese end-stage kidney disease by simultaneous laparoscopic sleeve gastrectomy and implantation of a buried peritoneal dialysis catheter: A case report
Authors: Yamashita Tomohisa , Sato Tatsuya , Yamamoto Kazuyuki , Abiko Atsuko , Nishizawa Keitaro , Matsuda Masahiro , Ebihara Yuma , Maehana Takeshi , Tanaka Toshiaki , Yano Toshiyuki , Kobayashi Hironori
Published: September 2022

For morbidly obese patients with end-stage kidney disease (ESKD), there are often difficulties in accessing, implementing, and maintaining kidney replacement therapy (KRT). Although recent weight-loss surgery has the potential to solve these problems, its therapeutic strategy and appropriate perioperative management for morbidly obese patients with ESKD have not been established. Here, we describe the case history of a 47-year-old man diagnosed with ESKD due to obesity-related glomerulopathy with an uncorrected estimated glomerular filtration rate (eGFR) of 16.1 ml/min. He hoped for kidney transplantation but was not eligible due to his high body mass index (BMI) (36.9 kg/m2). Therefore, a combination strategy for both attaining weight loss and preparing for KRT was needed. We performed modified laparoscopic sleeve gastrectomy (LSG) combined with a buried catheter for peritoneal dialysis (PD), which resulted in reduction of multiple surgical invasions while simultaneously preparing for PD. After these operations, his body mass dropped to below 30.0 kg/m2, making him a candidate for kidney transplantation, while maintaining PD. Finally, he was able to have kidney transplantation with success. Collectively, in this case, our novel therapeutic approach was able to avoid multiple surgeries, to assist catheter insertion by laparoscopy, and to provide optimal KRT for an obese patient with ESKD. Simultaneous LSG and implantation of a buried PD catheter may be a promising strategy for morbidly obese patients with ESKD.
Urinary lipid profile of patients with coronavirus diseases 2019
Authors: Kida Misato , Nakamura Tatsuro , Kobayashi Koji , Shimosawa Tatsuo , Murata Takahisa
Published: September 2022

The coronavirus diseases 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is ongoing. Over 490 million people have been infected with this virus worldwide. Although many patients present with lower respiratory symptoms, some may progress to acute respiratory distress syndrome and even multi-organ damage. Therefore, there is an urgent need to establish treatment and management methods for this infectious disease. Here, we comprehensively analyzed urinary lipid mediators and their metabolites to identify non-invasive biomarkers that reflect the disease status of COVID-19 patients. We diagnosed 16 patients by polymerase chain reaction (PCR) analysis, who presented with mild-to-moderate symptoms, including fever and cough, between May and October 2020 in Japan, and collected their urine samples. Using mass spectrometry, we analyzed the lipid metabolites in these urine samples. In all the urine samples from the patients, 21 types of fatty acids and their metabolites were consistently detected in the samples among the 214 metabolites which were analyzed. Interestingly, urinary levels of fatty acids, docosahexaenoic acid was increased by approximately 3-fold in patients with COVID-19 compared to those in healthy subjects. Metabolites of major proinflammatory lipid mediators, PGE2, TXA2, and PGF2α, were also detected at significantly higher levels in the urine of patients with COVID-19. These observations suggest that urinary lipids can reflect the inflammatory status of patients with COVID-19, which can be a useful index to manage this disease.
Efficacy and safety of methylene blue in patients with vasodilatory shock: A systematic review and meta-analysis
Authors: Zhao Cong-Cong , Zhai Yu-Jia , Hu Zhen-Jie , Huo Yan , Li Zhi-Qiang , Zhu Gui-Jun
Published: September 2022

Background

The role of methylene blue (MB) in patients with vasodilatory shock is unclear. The purpose of this systematic review and meta-analysis was to evaluate the efficacy and safety of MB in patients with vasodilatory shock.

Methods

We searched MEDLINE at PubMed, Embase, Web of Science, Cochrane, CNKI, CBM and Wanfang Medical databases for all observational and intervention studies comparing the effect of MB vs. control in vasodilatory shock patients. This study was performed in accordance with the PRISMA statement. There were no language restrictions for inclusion.

Results

A total of 15 studies with 832 patients were included. Pooled data demonstrated that administration of MB along with vasopressors significantly reduced mortality [odds ratio (OR) 0.54, 95% confidence interval (CI) 0.34 to 0.85,P= 0.008;I2= 7%]. This benefit in mortality rate was also seen in a subgroup analysis including randomized controlled trials and quasi-randomized controlled trials. In addition, the vasopressor requirement was reduced in the MB group [mean difference (MD) −0.77, 95%CI −1.26 to −0.28,P= 0.002;I2= 80%]. Regarding hemodynamics, MB increased the mean arterial pressure, heart rate and peripheral vascular resistance. In respect to organ function, MB was associated with a lower incidence of renal failure, while in regards to oxygen metabolism, it was linked to reduced lactate levels. MB had no effect on the other outcomes and no serious side effects.

Conclusions

Concomitant administration of MB and vasopressors improved hemodynamics, decreased vasopressor requirements, reduced lactate levels, and improved survival in patients with vasodilatory shock. However, further studies are required to confirm these findings.

Systematic review registration

Identifier: CRD42021281847.
A case of disseminated Legionnaires’ disease: The value of metagenome next-generation sequencing in the diagnosis of Legionnaires
Authors: Li Shan , Jiang Wei , Wang Chun-Yao , Weng Li , Du Bin , Peng Jin-Min
Published: September 2022

Background

Legionella rarely causes hospital-acquired pneumonia (HAP), although it is one of the most common pathogens of community-acquired pneumonia. Hospital-acquired Legionnaires’ disease, mainly occurring in immunocompromised patients, is often delayed in diagnosis with high mortality. The use of the metagenome Next-Generation Sequencing (mNGS) method, which is fast and unbiased, allows for the early detection and identification of microorganisms using a culture-independent strategy.

Case report

A 52-year-old male, with a past medical history of Goods syndrome, was admitted due to nephrotic syndrome. The patient developed severe pneumonia, rhabdomyolysis, and soft tissue infection after receiving immunosuppressive therapy. He did not respond well to empiric antibiotics and was eventually transferred to the medical intensive care unit because of an acute respiratory failure and septic shock. The patient then underwent a comprehensive conventional microbiological screening in bronchoalveolar lavage fluid (BALF) and blood, and the results were all negative. As a last resort, mNGS of blood was performed. Extracellular cell-free and intracellular DNA fragments of Legionella were detected in plasma and blood cell layer by mNGS, respectively. Subsequent positive results of polymerase chain reaction for Legionella in BALF and soft tissue specimens confirmed the diagnosis of disseminated Legionnaires’ disease involving the lungs, soft tissue, and blood stream. The patient’s condition improved promptly after a combination therapy of azithromycin and moxifloxacin. He was soon extubated and discharged from ICU with good recovery.

Conclusion

Early recognition and diagnosis of disseminated Legionnaires’ disease is challenging. The emergence and innovation of mNGS of blood has the potential to address this difficult clinical issue.
Recent insights in the role of biomarkers in severe asthma management
Authors: Fouka Evangelia , Domvri Kalliopi , Gkakou Foteini , Alevizaki Maria , Steiropoulos Paschalis , Papakosta Despoina , Porpodis Konstantinos
Published: September 2022

Contemporary asthma management requires a proactive and individualized approach, combining precision diagnosis and personalized treatment. The introduction of biologic therapies for severe asthma to everyday clinical practice, increases the need for specific patient selection, prediction of outcomes and monitoring of these costly and long-lasting therapies. Several biomarkers have been used in asthma in disease identification, prediction of asthma severity and prognosis, and response to treatment. Novel advances in the area of personalized medicine regarding disease phenotyping and endotyping, encompass the development and application of reliable biomarkers, accurately quantified using robust and reproducible methods. The availability of powerful omics technologies, together with integrated and network-based genome data analysis, and microbiota changes quantified in serum, body fluids and exhaled air, will lead to a better classification of distinct phenotypes or endotypes. Herein, in this review we discuss on currently used and novel biomarkers for the diagnosis and treatment of asthma.
Effects of capsicum oleoresin supplementation on rumen fermentation and microbial abundance under different temperature and dietary conditions in vitro
Authors: An Zhigao , Luo Gan , Abdelrahman Mohamed , Riaz Umair , Gao Shanshan , Yao Zhiqiu , Ye Tingzhu , Lv Haimiao , Zhao Jvnwei , Chen Changzhi , Yang Liguo
Published: September 2022

This study aimed to determine the effect of capsicum oleoresin (CAP) on rumen fermentation and microbial abundance under different temperature and dietary conditions in vitro. The experimental design was arranged in a 2 × 2 × 3 factorial format together with two temperatures (normal: 39°C; hyperthermal: 42°C), two forage/concentrate ratios (30:70; 70:30), and two CAP concentrations in the incubation fluid at 20 and 200 mg/L with a control group. Regarding the fermentation characteristics, high temperature reduced short-chain fatty acids (SCFA) production except for molar percentages of butyrate while increasing acetate-to-propionate ratio and ammonia concentration. The diets increased total SCFA, propionate, and ammonia concentrations while decreasing acetate percentage and acetate-to-propionate ratio. CAP reduced acetate percentage and acetate-to-propionate ratio. Under hyperthermal condition, CAP could reduce acetate percentage and increase acetate-to-propionate ratio, lessening the negative effect of high heat on SCFA. Hyperthermal condition and diet altered the relative abundance of microbial abundance in cellulose-degrading bacteria. CAP showed little effect on the microbial abundance which only increased Butyrivibrio fibrisolvens. Thus, CAP could improve rumen fermentation under different conditions, with plasticity in response to the ramp of different temperature and dietary conditions, although hardly affecting rumen microbial abundance.
Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins from Bacillaceae
Authors: Falkenberg Fabian , Bott Michael , Bongaerts Johannes , Siegert Petra
Published: September 2022

The subtilase family (S8), a member of the clan SB of serine proteases are ubiquitous in all kingdoms of life and fulfil different physiological functions. Subtilases are divided in several groups and especially subtilisins are of interest as they are used in various industrial sectors. Therefore, we searched for new subtilisin sequences of the family Bacillaceae using a data mining approach. The obtained 1,400 sequences were phylogenetically classified in the context of the subtilase family. This required an updated comprehensive overview of the different groups within this family. To fill this gap, we conducted a phylogenetic survey of the S8 family with characterised holotypes derived from the MEROPS database. The analysis revealed the presence of eight previously uncharacterised groups and 13 subgroups within the S8 family. The sequences that emerged from the data mining with the set filter parameters were mainly assigned to the subtilisin subgroups of true subtilisins, high-alkaline subtilisins, and phylogenetically intermediate subtilisins and represent an excellent source for new subtilisin candidates.
Diversity-scaling analysis of human breast milk microbiomes from population perspective
Authors: Chen Hongju , Yi Bin , Qiao Yuting , Peng Kunbao , Zhang Jianmei , Li Jinsong , Zheng Kun-Wen , Ning Ping , Li Wendy
Published: September 2022

Quantitative measuring the population-level diversity-scaling of human microbiomes is different from conventional approach to traditional individual-level diversity analysis, and it is of obvious significance. For example, it is well known that individuals are of significant heterogeneity with their microbiome diversities, and the population-level analysis can effectively capture such kind of individual differences. Here we reanalyze a dozen datasets of 2,115 human breast milk microbiome (BMM) samples with diversity-area relationship (DAR) to tackle the previous questions. Our focus on BMM is aimed to offer insights for supplementing the gut microbiome research from nutritional perspective. DAR is an extension to classic species-area relationship, which was discovered in the 19th century and established as one of a handful fundamental laws in community ecology. Our DAR modeling revealed the following numbers, all approximately: (i) The population-level potential diversity of BMM is 1,108 in terms of species richness (number of total species), and 67 in terms of typical species. (ii) On average, an individual carry 17% of population-level diversity in terms of species richness, and 61% in terms of typical species. (iii) The similarity (overlap) between individuals according to pair-wise diversity overlap (PDO) should be approximately 76% in terms of total species, and 92% in terms of typical species, which symbolizes the inter-individual heterogeneity. (iv) The average individual (alpha-) diversity of BMM is approximately 188 (total-species) and 37 (typical-species). (v) To deal with the potential difference among 12 BMM datasets, we conducted DAR modeling separately for each dataset, and then performed permutation tests for DAR parameters. It was found that the DAR scaling parameter that measures inter-individual heterogeneity in diversity is invariant (constant), but the population potential diversity is different among 30% of the pair-wise comparison between 12 BMM datasets. These results offer comprehensive biodiversity analyses of the BMM from host individual, inter-individual, and population level perspectives.
PCB-77 biodegradation potential of biosurfactant producing bacterial isolates recovered from contaminated soil
Authors: Sandhu Monika , Paul Atish T. , Proćków Jarosław , de la Lastra José Manuel Pérez , Jha Prabhat N.
Published: September 2022

Polychlorinated biphenyls (PCBs) are persistent organic pollutants widely distributed in the environment and possess deleterious health effects. The main objective of the study was to obtain bacterial isolates from PCB-contaminated soil for enhanced biodegradation of PCB-77. Selective enrichment resulted in the isolation of 33 strains of PCB-contaminated soil nearby Bhilai steel plant, Chhattisgarh, India. Based on the prominent growth using biphenyl as the sole carbon source and the confirmation of its degradation by GC-MS/MS analysis, four isolates were selected for further study. The isolates identified by 16S rRNA gene sequencing were Pseudomonas aeruginosa MAPB-2, Pseudomonas plecoglossicida MAPB-6, Brucella anthropi MAPB-9, and Priestia megaterium MAPB-27. The isolate MAPB-9 showed a degradation of 66.15% biphenyl, while MAPB-2, MAPB-6, and MAPB-27 showed a degradation of 62.06, 57.02, and 56.55%, respectively in 48 h. Additionally, the degradation ability of these strains was enhanced with addition of co-metabolite glucose (0.2%) in the culture medium. Addition of glucose showed 100% degradation of biphenyl by MAPB-9, in 48 h, while MAPB-6, MAPB-2, and MAPB-27 showed 97.1, 67.5, and 53.3% degradation, respectively as analyzed by GC-MS/MS. Furthermore, in the presence of inducer, PCB-77 was found to be 59.89, 30.49, 27.19, and 4.43% degraded by MAPB-6, MAPB-9, MAPB-2, and MAPB-27, respectively in 7 d. The production of biosurfactants that aid in biodegradation process were observed in all the isolates. This was confirmed by ATR-FTIR analysis that showed the presence of major functional groups (CH2, CH3, CH, = CH2, C–O–C, C-O) of the biosurfactant. The biosurfactants were further identified by HPTLC and GC-MS/MS analysis. Present study is the first to report PCB-77 degradation potential of Pseudomonas aeruginosa, B. anthropi, Pseudomonas plecoglossicida, and Priestia megaterium. Similarly, this is the first report on Pseudomonas plecoglossicida and Priestia megaterium for PCB biodegradation. Our results suggest that the above isolates can be used for the biodegradation of biphenyl and PCB-77 in PCB-contaminated soil.
Effect of Lactobacillus fermentum ZS40 on the NF-κB signaling pathway in an azomethane-dextran sulfate sodium-induced colon cancer mouse model
Authors: Liu Jia , Wang Shuaiqi , Yi Ruokun , Long Xingyao , Zhao Xin
Published: September 2022

The occurrence of intestinal diseases such as colon cancer is closely related to the intestinal flora. Lactobacillus fermentum is a gut probiotic that plays an important role in chronic intestinal inflammation and colon cancer. In the current study, we investigated the effect of Lactobacillus fermentum ZS40 on NF-κB signaling pathway of azomethane-dextran sulfate sodium (AOM-DSS) -induced colon cancer in mice. Animals were divided into control group (NC), AOM-DSS-induced model group (CRC), AOM-DSS plus high-dose Lactobacillus fermentum ZS40 (ZS40-H), AOM-DSS plus low-dose Lactobacillus fermentum ZS40 (ZS40-L), AOM-DSS plus Lactobacillus bulgaricus (BLA), and AOM-DSS plus sulfasalazine (SD)-treated group. Observation of animal physiological activity (body weight and defecation), biochemical measurements, histopathological examination of colon tissue, qPCR to evaluate the expression of inflammation-related genes, immunohistochemical analysis of CD34 and CD117, and Western blot analysis of NF-κB signaling pathway were performed. Compared with the CRC group, the ZS40-H, ZS40-L, BLA, and SD groups had decreased levels of colon cancer marker proteins CD34 and CD117, and the number of abnormal colonic lesions observed by colon histology decreased, while the ZS40-H group showed excellent results. In addition, all probiotic interventions showed weight loss effects. The expression of inflammatory stimulators TNF-α and IL-1β in the probiotic treatment group decreased; the expression of key proteins IκBα and p65 in the NF-κB signaling pathway also decreased, resulting in a decrease in the expression of the target protein Cox-2. Therefore, administration of Lactobacillus fermentum ZS40 as a probiotic can alleviate intestinal inflammation and prevent colon cancer in mice.
The hotspots and publication trends in postoperative delirium: A bibliometric analysis from 2000 to 2020
Authors: Lin Xiaowan , Cao Ying , Liu Xiao , Yu Kang , Miao Huihui , Li Tianzuo
Published: September 2022

Background

Postoperative delirium (POD) is a common aging-associated postoperative complication that has received increasing attention in the context of the aging global population and the number of articles published on POD is gradually increasing. This study aimed to quantify the basic information of scholarly publications on POD and identify the most impactful literature, trends, and hotspots in POD research.

Materials and methods

We searched articles on POD through the Science Citation Index Expanded databases published from 2000 to 2020. Bibliographic information, including year, country, authorship, type, journal, funding, affiliations, subject areas, and hotspots, was collected for further analysis.

Results

A total of 2,114 articles on POD from 2000 to 2020 were identified. The highest number of studies (n = 748) were published in the United States, comprising the most total citations (13,928), followed by China (n = 278), and Germany (n = 209). Inouye, Sharon K. was the most productive author, with 66 publications on POD. The Journal of the American Geriatrics Society published the highest number of articles (n = 80), with the most total citations (4,561) and average (57.01), followed by Anesthesia and Analgesia (n = 52), and the British Journal of Anaesthesia (n = 43). Harvard University was the most productive institute, with the highest H-index (n = 46) and highest degree centrality (n = 191). The top hotspots in the field of POD during this period were “elderly,” “cardiac surgery,” “cognitive impairment,” “hip fracture,” and “intensive care unit.”

Conclusion

This study provides an overview of developments in the field of POD over the past 20 years using bibliometric analysis. Overall, research on POD has flourished worldwide. The United States (US) has a relatively high academic impact owing to its productive expertise and institutions in this field. Despite much research illustrating the diagnosis and management of POD in clinical practice, more basic research is needed.
A comprehensive review of transcranial magnetic stimulation in secondary dementia
Authors: Lanza Giuseppe , Fisicaro Francesco , Dubbioso Raffaele , Ranieri Federico , Chistyakov Andrei V. , Cantone Mariagiovanna , Pennisi Manuela , Grasso Alfio Antonio , Bella Rita , Di Lazzaro Vincenzo
Published: September 2022

Although primary degenerative diseases are the main cause of dementia, a non-negligible proportion of patients is affected by a secondary and potentially treatable cognitive disorder. Therefore, diagnostic tools able to early identify and monitor them and to predict the response to treatment are needed. Transcranial magnetic stimulation (TMS) is a non-invasive neurophysiological technique capable of evaluating in vivo and in “real time” the motor areas, the cortico-spinal tract, and the neurotransmission pathways in several neurological and neuropsychiatric disorders, including cognitive impairment and dementia. While consistent evidence has been accumulated for Alzheimer’s disease, other degenerative cognitive disorders, and vascular dementia, to date a comprehensive review of TMS studies available in other secondary dementias is lacking. These conditions include, among others, normal-pressure hydrocephalus, multiple sclerosis, celiac disease and other immunologically mediated diseases, as well as a number of inflammatory, infective, metabolic, toxic, nutritional, endocrine, sleep-related, and rare genetic disorders. Overall, we observed that, while in degenerative dementia neurophysiological alterations might mirror specific, and possibly primary, neuropathological changes (and hence be used as early biomarkers), this pathogenic link appears to be weaker for most secondary forms of dementia, in which neurotransmitter dysfunction is more likely related to a systemic or diffuse neural damage. In these cases, therefore, an effort toward the understanding of pathological mechanisms of cognitive impairment should be made, also by investigating the relationship between functional alterations of brain circuits and the specific mechanisms of neuronal damage triggered by the causative disease. Neurophysiologically, although no distinctive TMS pattern can be identified that might be used to predict the occurrence or progression of cognitive decline in a specific condition, some TMS-associated measures of cortical function and plasticity (such as the short-latency afferent inhibition, the short-interval intracortical inhibition, and the cortical silent period) might add useful information in most of secondary dementia, especially in combination with suggestive clinical features and other diagnostic tests. The possibility to detect dysfunctional cortical circuits, to monitor the disease course, to probe the response to treatment, and to design novel neuromodulatory interventions in secondary dementia still represents a gap in the literature that needs to be explored.
A parameter-free learning automaton scheme
Authors: Ren Xudie , Li Shenghong , Ge Hao
Published: September 2022

For a learning automaton, a proper configuration of the learning parameters is crucial. To ensure stable and reliable performance in stochastic environments, manual parameter tuning is necessary for existing LA schemes, but the tuning procedure is time-consuming and interaction-costing. It is a fatal limitation for LA-based applications, especially for those environments where the interactions are expensive. In this paper, we propose a parameter-free learning automaton (PFLA) scheme to avoid parameter tuning by a Bayesian inference method. In contrast to existing schemes where the parameters must be carefully tuned according to the environment, PFLA works well with a set of consistent parameters in various environments. This intriguing property dramatically reduces the difficulty of applying a learning automaton to an unknown stochastic environment. A rigorous proof of ϵ-optimality for the proposed scheme is provided and numeric experiments are carried out on benchmark environments to verify its effectiveness. The results show that, without any parameter tuning cost, the proposed PFLA can achieve a competitive performance compared with other well-tuned schemes and outperform untuned schemes on the consistency of performance.
Case report: Coexistence of myotonia congenita and Brugada syndrome in one family
Authors: Cordenier Ann , Flamez Anja , de Ravel Thomy , Gheldof Alexander , Pannone Luigi , De Asmundis Carlo , Pappaert Gudrun , Bissay Véronique
Published: September 2022

Myotonia congenita is a rare neuromuscular disorder caused by CLCN1 mutations resulting in delayed muscle relaxation. Extramuscular manifestations are not considered to be present in chloride skeletal channelopathies, although recently some cardiac manifestations have been described. We report a family with autosomal dominant myotonia congenita and Brugada syndrome. Bearing in mind the previously reported cases of cardiac arrhythmias in myotonia congenita patients, we discuss the possible involvement of the CLCN1-gene mutations in primary cardiac arrhythmia.
ANXA11 mutations are associated with amyotrophic lateral sclerosis–frontotemporal dementia
Authors: Wang Yu , Duan Xiaohui , Zhou Xiao , Wang Renbin , Zhang Xiangfei , Cao Zhenhua , Wang Xiaoxia , Zhou Zhi , Sun Yu , Peng Dantao
Published: September 2022

Background

The Annexin A11 (ANXA11) gene has been newly identified as a causative gene of amyotrophic lateral sclerosis (ALS) with or without frontotemporal dementia (FTD). The current study aimed to investigate the ANXA11 mutations in a Chinese ALS–FTD or FTD cohort.

Methods

We included ten probands/patients with suspected ALS–FTD or FTD. Mutational analysis of ANXA11 was performed through Next Generation Sequencing (NGS) and Sanger sequencing. We collected and reviewed clinical presentation, neuropsychology test results, brain-imaging findings, and electrophysiological examination findings.

Results

In total, six probands presented with ALS–FTD, and four with behavior variant FTD (bv-FTD). We identified a non-synonymous heterozygous mutation (c.119A>G, p.D40G) of ANXA11 in proband 1, which is associated with ALS. However, this is the first report of the mutation causing ALS–FTD. Proband 1 started with abnormal behavior and progressed to classic upper motor nervous disease. Magnetic resonance imaging (MRI) showed significant bilateral temporal lobe atrophy and bilateral hyperintensities along the corticospinal tracts.18F-AV45-PET imaging showed negative amyloid deposits.

Conclusion

ANXA11-related diseases have high clinical and genetic heterogeneity. Our study confirmed the contribution of ANXA11 mutations to ALS–FTD. The ANXA11 mutations established a complex genotype–phenotype correlation in ALS–FTD. Our research further elucidated the genetic mechanism of ALS–FTD and contributed to setting the foundation of future targeted therapy.