bluuebunny/crossref_metadata_2025 huggingface dataset:
A Computational Framework to Predict Calvarial Growth: Optimising Management of Sagittal Craniosynostosis
Authors: Cross Connor , Khonsari Roman H. , Patermoster Giovanna , Arnaud Eric , Larysz Dawid , Kölby Lars , Johnson David , Ventikos Yiannis , Moazen Mehran
Published: May 2022

The neonate skull consists of several bony plates, connected by fibrous soft tissue called sutures. Premature fusion of sutures is a medical condition known as craniosynostosis. Sagittal synostosis, caused by premature fusion of the sagittal suture, is the most common form of this condition. The optimum management of this condition is an ongoing debate in the craniofacial community while aspects of the biomechanics and mechanobiology are not well understood. Here, we describe a computational framework that enables us to predict and compare the calvarial growth following different reconstruction techniques for the management of sagittal synostosis. Our results demonstrate how different reconstruction techniques interact with the increasing intracranial volume. The framework proposed here can be used to inform optimum management of different forms of craniosynostosis, minimising the risk of functional consequences and secondary surgery.
A Review Into the Insights of the Role of Endothelial Progenitor Cells on Bone Biology
Authors: Shi Henglei , Zhao Zhenchen , Jiang Weidong , Zhu Peiqi , Zhou Nuo , Huang Xuanping
Published: May 2022

In addition to its important transport functions, the skeletal system is involved in complex biological activities for the regulation of blood vessels. Endothelial progenitor cells (EPCs), as stem cells of endothelial cells (ECs), possess an effective proliferative capacity and a powerful angiogenic capacity prior to their differentiation. They demonstrate synergistic effects to promote bone regeneration and vascularization more effectively by co-culturing with multiple cells. EPCs demonstrate a significant therapeutic potential for the treatment of various bone diseases by secreting a combination of growth factors, regulating cellular functions, and promoting bone regeneration. In this review, we retrospect the definition and properties of EPCs, their interaction with mesenchymal stem cells, ECs, smooth muscle cells, and immune cells in bone regeneration, vascularization, and immunity, summarizing their mechanism of action and contribution to bone biology. Additionally, we generalized their role and potential mechanisms in the treatment of various bone diseases, possibly indicating their clinical application.
pSuc-FFSEA: Predicting Lysine Succinylation Sites in Proteins Based on Feature Fusion and Stacking Ensemble Algorithm
Authors: Jia Jianhua , Wu Genqiang , Qiu Wangren
Published: May 2022

Being a new type of widespread protein post-translational modifications discovered in recent years, succinylation plays a key role in protein conformational regulation and cellular function regulation. Numerous studies have shown that succinylation modifications are closely associated with the development of many diseases. In order to gain insight into the mechanism of succinylation, it is vital to identify lysine succinylation sites. However, experimental identification of succinylation sites is time-consuming and laborious, and traditional identification tools are unable to meet the rapid growth of datasets. Therefore, to solve this problem, we developed a new predictor named pSuc-FFSEA, which can predict succinylation sites in protein sequences by feature fusion and stacking ensemble algorithm. Specifically, the sequence information and physicochemical properties were first extracted using EBGW, One-Hot, continuous bag-of-words, chaos game representation, and AAF_DWT. Following that, feature selection was performed, which applied LASSO to select the optimal subset of features for the classifier, and then, stacking ensemble classifier was designed using two-layer stacking ensemble, selecting three classifiers, SVM, broad learning system and LightGBM classifier, as the base classifiers of the first layer, using logistic regression classifier as the meta classifier of the second layer. In order to further improve the model prediction accuracy and reduce the computational effort, bayesian optimization algorithm and grid search algorithm were utilized to optimize the hyperparameters of the classifier. Finally, the results of rigorous 10-fold cross-validation indicated our predictor showed excellent robustness and performed better than the previous prediction tools, which achieved an average prediction accuracy of 0.7773 ± 0.0120. Besides, for the convenience of the most experimental scientists, a user-friendly and comprehensive web-server for pSuc-FFSEA has been established at https://bio.cangmang.xyz/pSuc-FFSEA, by which one can easily obtain the expected data and results without going through the complicated mathematics.
Transcriptional Effects of Candidate COVID-19 Treatments on Cardiac Myocytes
Authors: Jakobi Tobias , Groß Julia , Cyganek Lukas , Doroudgar Shirin
Published: May 2022

Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) has emerged as a major cause of morbidity and mortality worldwide, placing unprecedented pressure on healthcare. Cardiomyopathy is described in patients with severe COVID-19 and increasing evidence suggests that cardiovascular involvement portends a high mortality. To facilitate fast development of antiviral interventions, drugs initially developed to treat other diseases are currently being repurposed as COVID-19 treatments. While it has been shown that SARS-CoV-2 invades cells through the angiotensin-converting enzyme 2 receptor (ACE2), the effect of drugs currently repurposed to treat COVID-19 on the heart requires further investigation.

Methods

Human induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs) were treated with five repurposed drugs (remdesivir, lopinavir/ritonavir, lopinavir/ritonavir/interferon beta (INF-β), hydroxychloroquine, and chloroquine) and compared with DMSO controls. Transcriptional profiling was performed to identify global changes in gene expression programs.

Results

RNA sequencing of hiPSC-CMs revealed significant changes in gene programs related to calcium handling and the endoplasmic reticulum stress response, most prominently for lopinavir/ritonavir and lopinavir/ritonavir/interferon-beta. The results of the differential gene expression analysis are available for interactive access at https://covid19drugs.jakobilab.org.

Conclusion

Transcriptional profiling in hiPSC-CMs treated with COVID-19 drugs identified unfavorable changes with lopinavir/ritonavir and lopinavir/ritonavir/INF-β in key cardiac gene programs that may negatively affect heart function.
The Ratio of Red Blood Cell Distribution Width to Albumin Is Correlated With All-Cause Mortality of Patients After Percutaneous Coronary Intervention – A Retrospective Cohort Study
Authors: Weng Yingbei , Peng Yangpei , Xu Yuxuan , Wang Lei , Wu Bosen , Xiang Huaqiang , Ji Kangting , Guan Xueqiang
Published: May 2022

Objectives

The purpose of this study was to investigate the independent effect of the ratio of red blood cell distribution width (RDW) to albumin (RA) on all-cause mortality in patients after percutaneous coronary intervention (PCI).

Methods

Clinical data were obtained from the Multiparameter Intelligent Monitoring in Intensive Care-III (MIMIC-III) database version 1.4 and the database of Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University. We used the MIMIC-III database for model training, and data collected from the Second Affiliated Hospital of Wenzhou Medical University for validation. The primary outcome of our study was 90-day mortality. Cox proportional hazards regression model was used to estimate hazard ratio (HR) for the association between RA and all-cause mortality in patients after PCI. Pearson correlation analysis was conducted to assess the relationship between RA and Gensini score or cardiac troponin I (cTnI).

Results

A total of 707 patients were eligible in MIMIC-III database, including 432 males, with a mean age of 70.29 years. For 90-day all-cause mortality, in the adjusted multivariable model, the adjusted HRs [95% confidence intervals (CIs)] for the second (RA: 3.7–4.5 ml/g) and third (RA >4.5 ml/g) tertiles were 2.27 (1.11, 4.64) and 3.67 (1.82, 7.40), respectively, compared to the reference group (RA <3.7 ml/g) (p < 0.05). A similar relationship was also observed for 30-day all-cause mortality and 1-year all-cause mortality. No significant interaction was observed in subgroup analysis. Receiver operating characteristic (ROC) curve analysis proved that the ability of RA to predict the 90-day mortality was better than that of RDW or albumin alone. The correlation coefficient between Gensini score and RA was 0.254, and that between cTnI and RA was 0.323.

Conclusion

RA is an independent risk factor for all-cause mortality in patients after PCI. The higher the RA, the higher the mortality. RA has a good predictive ability for all-cause mortality in patients after PCI, which is better than RDW or albumin alone. RA may be positively correlated with the severity of coronary artery disease (CAD) in patients with CAD.
Case Report: Acute Renal and Splenic Infarctions Secondary to Atrial Fibrillation
Authors: Yihan Li , Guanqi Fan , Tong Hu , Junye Ge , Zhong Jingquan , Chen Tongshuai
Published: May 2022

Acute renal and splenic infarctions are an uncommon condition that can result from obstruction or decrease of renal and splenic arterial flow. We described a 73-year-old woman who presented with right flank pain and nocturnal dyspnea. The computed tomography (CT) scan with intravenous contrast showed multiple infarcts in both bilateral kidneys and spleen. Serum creatinine clearance was impaired. Further investigation by electrocardiogram (ECG) and 24-h Holter revealed that the patient had paroxysmal atrial fibrillation (PAF). Transthoracic and transesophageal echocardiographic findings were unremarkable except for severe spontaneous echo contrast (SEC) in the left atrial appendage. The development of thromboembolic renal and splenic infarction was attributed to embolism caused by atrial fibrillation. Anticoagulant therapy was initiated with low molecular weight heparin (LMWH) and followed by an oral anticoagulant. To manage PAF and prevent further embolism, the “One-stop” procedure, including atrial fibrillation catheter ablation and left atrial appendage occlusion (LAAO), was applied to this patient. Follow-up at 1 month showed normal sinus rhythm, improved renal function, and relieved renal and splenic infarction.
Validating GAN-BioBERT: A Methodology for Assessing Reporting Trends in Clinical Trials
Authors: Myszewski Joshua J. , Klossowski Emily , Meyer Patrick , Bevil Kristin , Klesius Lisa , Schroeder Kristopher M.
Published: May 2022

Background

The aim of this study was to validate a three-class sentiment classification model for clinical trial abstracts combining adversarial learning and the BioBERT language processing model as a tool to assess trends in biomedical literature in a clearly reproducible manner. We then assessed the model's performance for this application and compared it to previous models used for this task.

Methods

Using 108 expert-annotated clinical trial abstracts and 2,000 unlabeled abstracts this study develops a three-class sentiment classification algorithm for clinical trial abstracts. The model uses a semi-supervised model based on the Bidirectional Encoder Representation from Transformers (BERT) model, a much more advanced and accurate method compared to previously used models based upon traditional machine learning methods. The prediction performance was compared to those previous studies.

Results

The algorithm was found to have a classification accuracy of 91.3%, with a macro F1-Score of 0.92, significantly outperforming previous studies used to classify sentiment in clinical trial literature, while also making the sentiment classification finer grained with greater reproducibility.

Conclusion

We demonstrate an easily applied sentiment classification model for clinical trial abstracts that significantly outperforms previous models with greater reproducibility and applicability to large-scale study of reporting trends.
Contrasting Along-Slope vs. Downslope Sedimentation Style on the High-Latitude Eastern Canadian Continental Margin During the Last 40 ka
Authors: Rashid Harunur , He Jianing , Patro Ranjan , Brown A. Owen
Published: May 2022

Late Pleistocene Labrador Sea depositional systems developed in front of ice streams and glacier outlets from the Laurentide Ice Sheet (LIS) are documented by Huntec and 3.5 kHz seismic profiles and piston cores. Due to efficient grinding by the LIS, massive amounts of fine-grained sediments and meltwater in addition to the icebergs linked to the Heinrich events (H events) of the last glaciation were delivered to the neighboring Labrador Sea. The position of the Hudson Strait ice stream during the periodic expansion and contraction on the Labrador margin allowed fine-grained sediments and meltwater direct delivery on the lower shelf and upper slope. These discharges were then transported southward by the Labrador Current and western boundary current. In contrast to the lower shelf and upper slope, sediments delivered on the mid to the lower Labrador Slope were transported by the Northwest Atlantic Mid-Ocean Channel to distal sites. The nepheloid flow layer at or near the sea bottom or at mid-water depths developed from meltwater loaded with an excessive charge of fine-grained sediments. Contrastingly, the non-discriminatory ice rafting process delivered detritus of all sizes, but its total contribution to the sediment column was only minor, notwithstanding its paleoclimatic significance during H events. Heinrich H1, H2, and H4 layers were identified by their characteristic nepheloid flow layer deposits, that is, alternating coarse silt and clay-sized laminae with thin ice-rafted debris interspersed by coarse- to fine-grained dropstone. Furthermore, the progressive thinning and eventual disappearance of the fine-laminae (i.e., coarse and fine silt/clay) in H layers at the distal sites suggest the exhaustion and raining out of fines due to long-distance transport. However, the H3 layer was identified by a combination of nepheloid flow layer deposits (upper slope) and finely laminated mud turbidites (lower slope and deep basin) at proximal sites. In the lower Labrador Slope and Basin, the H3 stratigraphic equivalent layer was identified by exorbitantly thick finely laminated carbonate-rich mud turbidites. The divergent sedimentation style (i.e., reflected by the sediment facies) and the thickness of the H3 layer compared to other H events suggest that the Hudson Strait ice stream position was different from other H events. Therefore, our data imply that the divergence in the H3 layer between the eastern and western North Atlantic might lie with the position of the Hudson Strait ice stream on the Labrador continental margin.
Seismogenic Patches in a Tectonic Fault Interface
Authors: Ostapchuk Aleksey , Polyatykin Vladimir , Popov Maxim , Kocharyan Gevorg
Published: May 2022

Tectonic faults show rheological heterogeneity in interfaces, and the spectrum of their sliding regimes span a continuum from the slow-slip events to dynamic ruptures. The heterogeneity of the fault interface is crucial for the mechanics of faulting. By using the earthquake source locations, the complex structure of a fault interface can be reproduced at a resolution down to 50–100 m. Here, we use a declustered seismic catalog of Northern California to investigate structures of 11 segments of San Andreas, Calaveras, and Hayward faults. The cumulative length of all the segments is about 500 km. All the selected segments belong to subvertical strike–slip faults. A noticeable localization of sources near the fault cores is observed for all segments. The projection of earthquake sources to the fault plane shows severe inhomogeneity. Topologically dense clusters (seismogenic patches (SPs)) can be detected in fault planes. The longer the observation are, the more distinct are the clusters. The SPs usually cover about 10%–20% of the fault interface area. It is in the vicinity of SPs that earthquakes of magnitudes above 5 are usually initiated. The Voronoi tessellation is used to determine the orderliness of SPs. Distributions of areas of Voronoi cells of all the SPs obey the lognormal law, and the value of Voronoi entropy of 1.6–1.9 prevails. The findings show the informativeness of the background seismicity in revealing the heterogenous structure of a tectonic fault interface.
Treatment Options and Voice Outcomes for Patients With Unilateral Vocal Fold Paralysis After Thyroidectomy
Authors: Wen Ming-Hsun , Wang Chi-Te
Published: May 2022

Objectives

This study investigated the treatment options and clinical outcomes of voice therapy (VT), hyaluronic acid (HA) injection, autologous fat injection (FI), and medialization thyroplasty (MT) in patients with unilateral vocal fold paralysis (UVFP) after thyroidectomy.

Study Design

Retrospective case series.

Setting

A tertiary teaching hospital.

Methods

This study included 51 patients with post-thyroidectomy UVFP who underwent VT (n = 20), HA injection (n = 14), FI (n = 12), or MT (n = 5) from January 2016 to June 2021. The treatment outcomes were evaluated using 10-item voice handicap index (VHI-10), maximal phonation time (MPT), and auditory perceptual rating using GRB scales (i.e., grade, roughness, and breathiness) before and 3 to 6 months after treatment.

Results

Patients received HA injection presented a significantly shorter interval after thyroidectomy (mean: 4.6 months), followed by VT (6.7 months), FI (12.3 months), and MT (22.4 months). The results exhibited improvement in most of the outcomes after all of the four treatments. Additional comparisons indicated that VHI-10 scores improved the most among patients receiving MT, followed by HA, FI, and VT. The differences of MPT and GRB scores among the 4 treatment groups were non-significant.

Conclusions

The results revealed that VT, HA, FI, and MT can all improve the voice outcomes of patients with post-thyroidectomy UVFP. The optimal treatment approach should be individualized according to the patient’s preference and vocal demand, and the interval between thyroidectomy and intervention.
Optimal Peak Regulation Strategy of Virtual and Thermal Power Plants
Authors: Li Peng , Chen Yuanfeng , Yang Kang , Yang Ping , Yu Jingyi , Yao Senjing , Zhao Zhuoli , Lai Chun Sing , Zobaa Ahmed F. , Lai Loi Lei
Published: May 2022

To achieve the national carbon-peak and carbon-neutral strategic development goals, it is necessary to build power systems dominated by renewable and sustainable energy. The future power system with a high proportion of renewable and sustainable energy is required to have large-scale, low-cost, flexible, and adjustable resources. To this end, this article aggregates user-side distributed energy storage and electric vehicles into a virtual power plant, considering the uncertainty of wind power fluctuations and the uncertainty of electric vehicle charging and discharging to establish a day-ahead and intra-day peak regulation model for combined peak regulation of virtual and thermal power plants. The bounding algorithm seeks the optimal strategy for the two-stage model of joint peak regulation and obtains the day-ahead and intra-day two-stage optimal peak regulation strategy. The simulation example shows that the virtual power plant and its day-ahead and intra-day optimal peak regulation strategy can reduce the peak regulation cost of the power system, as compared with the deep peak regulation of thermal power plants with a special supporting energy storage power station. This work provides a global perspective for virtual power plants to participate in the formulation of power system peak regulation rules.
Population Structure, Genetic Diversity, and Conservation Strategies of a Commercially Important Sleeper Fish, Odontobutis potamophilus (Gobiiformes: Odontobutidae) Based on Gene-Capture Data
Authors: Hu Yun , Li Hongjie , Xia Jianhong , Li Chenhong
Published: May 2022

Odontobutis potamophilus is a popular food fish in China, distributed mainly in the middle and lower reaches of the Yangtze River, where it is a famous delicacy and a newly focused species for aquaculture. The wild populations of O. potamophilus are facing the problem of overfishing and habitat degradation. Therefore, it is very necessary to investigate and protect the wild populations of O. potamophilus. In this study, 72 fish were sampled from 18 different sites over its distribution range. Nuclear sequence data of 4,267 loci were collected using a gene-capture method. Phylogenetic reconstruction revealed that there were three major clades: Oujiang clade (OJ), Qiantang and lower Yangtze clade (QY), and middle Yangtze clade (MY). The discriminant analysis of principal components (DAPC) and a STRUCTURE analysis confirmed that there are three major groups within O. potamophilus. A fastsimcoal2 analysis corroborated the population history and suggested that there was discernible gene flow among these three groups, especially between QY and MY. Estimated pairwise FST suggested that Linhai (LH) and Shexian (SX) populations were the most divergent pair (FST = 0.7077). Taking the nucleotide diversity, population divergence, and admixture status altogether into consideration, we recommend that the LH, Gaoyou (GY) and Chaohu (CH) populations could be protected as the preferred resource for breeding projects. According to the results of genetic analyses, all populations of O. potamophilus should be protected due to low genetic diversity.
Interpretable Deep Learning Model Reveals Subsequences of Various Functions for Long Non-Coding RNA Identification
Authors: Lin Rattaphon , Wichadakul Duangdao
Published: May 2022

Long non-coding RNAs (lncRNAs) play crucial roles in many biological processes and are implicated in several diseases. With the next-generation sequencing technologies, substantial unannotated transcripts have been discovered. Classifying unannotated transcripts using biological experiments are more time-consuming and expensive than computational approaches. Several tools are available for identifying long non-coding RNAs. These tools, however, did not explain the features in their tools that contributed to the prediction results. Here, we present Xlnc1DCNN, a tool for distinguishing long non-coding RNAs (lncRNAs) from protein-coding transcripts (PCTs) using a one-dimensional convolutional neural network with prediction explanations. The evaluation results of the human test set showed that Xlnc1DCNN outperformed other state-of-the-art tools in terms of accuracy and F1-score. The explanation results revealed that lncRNA transcripts were mainly identified as sequences with no conserved regions, short patterns with unknown functions, or only regions of transmembrane helices while protein-coding transcripts were mostly classified by conserved protein domains or families. The explanation results also conveyed the probably inconsistent annotations among the public databases, lncRNA transcripts which contain protein domains, protein families, or intrinsically disordered regions (IDRs). Xlnc1DCNN is freely available at https://github.com/cucpbioinfo/Xlnc1DCNN.
Comparative Transcriptome Analysis Reveals the Process of Ovarian Development and Nutrition Metabolism in Chinese Mitten Crab, Eriocheir Sinensis
Authors: Feng Qiangmei , Liu Meimei , Cheng Yongxu , Wu Xugan
Published: May 2022

Ovarian development is a key physiological process that holds great significance in the reproduction of the Chinese mitten crab (Eriocheir sinensis), which is an economically important crab species for aquaculture. However, there is limited knowledge for the regulatory mechanisms of ovarian development. To study the molecular mechanisms of its ovarian development, transcriptome analysis was performed in the ovary and hepatopancreas of E. sinensis during ovarian stages I (oogonium proliferation), II (endogenous vitellogenesis), and III (exogenous vitellogenesis). The results showed that 5,520 and 226 genes were differentially expressed in the ovary and hepatopancreas, respectively. For KEGG enrichment analysis, the differentially expressed genes in the ovary were significantly clustered in phototransduction-fly, phagosome, and ECM-receptor interaction. Significantly enriched pathways in the hepatopancreas included fatty acid biosynthesis, fatty acid metabolism, and riboflavin metabolism. Further analysis showed that 25 genes and several pathways were mainly involved in oogenesis, including the ubiquitin-proteasome pathway, cyclic AMP-protein kinase A signaling pathway, and mitogen-activated protein kinase signaling pathway. Twenty-five candidate genes involved in vitellogenesis and endocrine regulation were identified, such as vitellogenin, vitellogenin receptor, estrogen sulfotransferase, ecdysone receptor, prostaglandin reductase 1, hematopoietic prostaglandin D synthase and juvenile hormone acid O-methyltransferase. Fifty-six genes related to nutritional metabolism were identified, such as fatty acid synthase, long-chain-fatty-acid-CoA ligase 4, 1-acyl-sn-glycerol-3-phosphate acyltransferase 4, fatty acid-binding protein, and glycerol-3-phosphate acyltransferase 1. These results highlight the genes involved in ovarian development and nutrition deposition, which enhance our understanding of the regulatory pathways and physiological processes of crustacean ovarian development.
Circular RNA circNUP214 Modulates the T Helper 17 Cell Response in Patients With Rheumatoid Arthritis
Authors: Peng Huiyong , Xing Jie , Wang Xuehua , Ding Xiangmei , Tang Xinyi , Zou Junli , Wang Shengjun , Liu Yingzhao
Published: May 2022

Circular RNAs (circRNAs) are important transcriptional regulators of genome expression that participate in the pathogenesis of human diseases. Mechanistically, circRNAs, as competitive endogenous RNAs (ceRNAs), can sponge microRNAs (miRNAs) with miRNA response elements. A previous study identified that hsa_circ_0089172 (circNUP214) is abnormally expressed in Hashimoto’s thyroiditis. However, the role of circNUP214 in rheumatoid arthritis (RA) remains unclear. In total, 28 RA patients and 28 healthy controls were enrolled in this study. We found that circNUP214 is an abundant and stable circRNA in RA patients that can potentially differentiate RA patients from healthy subjects. Additionally, the elevated levels of IL-23R positively correlated with circNUP214 expression. The knockdown of circNUP214 resulted in the reduction of IL-23R at both transcriptional and translational levels in human CD4+ T cells. The proportion of circulating Th17 cells and the transcript levels of IL-17A were increased in RA patients and were both positively correlated with IL-23R expression. Moreover, positive correlations between the transcript levels of circNUP214 and the percentage of Th17 cells and the transcript levels of IL-17A were observed in RA patients. The downregulation of circNUP214 decreased the proportion of Th17 cells and the transcript levels of IL-17A in vitro. Furthermore, circNUP214 functioned as a ceRNA for miR-125a-3p in RA patients. Taken together, our results indicate that elevated levels of circNUP214 contribute to the Th17 cell response in RA patients.
Immunological Predictors of Post Infectious Inflammatory Response Syndrome in HIV-Negative Immunocompetent Cryptococcal Meningitis
Authors: Wang Yijie , Wei Hang , Shen Liping , Su Xiaohong , Liu Jia , Xu Xiaofeng , Li Min , Yang Lu , Liu Junyu , Wang Anni , Jiang Ying , Peng Fuhua
Published: May 2022

Objective

This research aims to study the correlation between serum immune factors and post-infectious inflammatory response syndrome (PIIRS) in immunocompetent cryptococcal meningitis (CM), and explore whether serum immune factors could be used to predict the development of PIIRS.

Methods

A cohort of 30 patients with PIIRS and 87 patients without PIIRS was selected from 347 CM patients. We analyzed the general clinical information and immunological indexes (cytokines, complement, immunoglobulin, inflammation, related cytological and biochemical indexes). Spearman correlation analysis and principal component analysis were used to explore the effects of the variables on PIIRS. Additionally, the variables were identified by a random forest-based classifier for predicting the development of PIIRS. The clinical value of predictors was verified by survival analysis.

Results

Compared with patients without PIIRS, patients with PIIRS had lower baseline serum interleukin-6 (IL-6, P = 0.006), immunoglobulin M (IgM, P = 0.004), and a higher baseline neutrophil ratio (P <0.001). The baseline neutrophil ratio (r = 0.359, P = 0.001), IgM (r = −0.272, P = 0.025), and IL-6 (r = −0.259, P = 0.027) were significantly correlated with PIIRS. Combining principal component analysis and random forest results, neutrophil ratio, neutrophil count, IgM, IL-6, and D-dimer were useful predictors. The accuracy of random forest prediction was 75.00%, AUC, and sensitivity were 0.76 and 70%, respectively. Further survival analysis of the time from treatment to PIIRS revealed that the development of PIIRS was associated with IgM (more than 98 days of treatment) and neutrophil ratio/count.

Conclusion

Baseline neutrophils ratio, neutrophil count, IgM, IL-6, and D-dimer may be clinically useful predictors of PIIRS in HIV-negative immunocompetent CM patients.
Variability in the Net Ecosystem Productivity (NEP) of Seaweed Farms
Authors: Sato Yoichi , Nishihara Gregory N. , Tanaka Atsuko , Belleza Dominic F. C. , Kawate Azusa , Inoue Yukio , Hinode Kenjiro , Matsuda Yuhei , Tanimae Shinichiro , Tozaki Kandai , Terada Ryuta , Endo Hikaru
Published: May 2022

The important role of vegetated ecosystems in the sequestration of carbon has gained strong interest across a wide variety of disciplines. With evidence growing of the potential for macroalgae ecosystems to capture carbon, there is burgeoning interest in applying newfound knowledge of carbon capture rates to better understand the potential for carbon sequestration. Seaweed farms are expected to play a significant role in carbon capture; advocates for the expansion of seaweed farms are increasing in many countries. In general, seaweed farms are expected to be highly productive, although whether they are autotrophic or heterotrophic ecosystems and hence potential exporters of carbon, is under debate. Therefore, we present our investigation of three seaweed farms, two in northern Japan and one in southern Japan. We examine the frequency of autotrophic days and compare potential rates of carbon capture of the seaweed farms with two natural macroalgae ecosystems and one degraded site. We estimated potential carbon capture rates by calculating the net ecosystem productivity from continuous recordings of dissolved oxygen concentrations under natural environmental conditions. The net ecosystem production rates for the natural ecosystems in Arikawa Bay and Omura Bay were equivalent to 0.043 and 0.054 [g C m-2 d-1] m-1, respectively. Whereas, for the degraded ecosystem in Tainoura Bay, it was -0.01 [g C m-2 d-1] m-1. We reveal that the Undaria pinnatifida farm in Matsushima Bay experience autotrophy more often than natural ecosystems, although for seaweed farms producing U. pinnatifida in Hirota Bay and Cladospihon okamuranus at Bise Point, autotrophy was less frequently observed. Nevertheless, up to 14.1 g C m-2 (0.110 g C m-2 d-1) was captured by the production of U. pinnatifida and 3.6 g C m-2 (0.034 g C m-2 d-1) was captured by C. okamuranus, and the total yield of carbon captured during 2021 production season for these farms was 43,385 kg C.
Epidemiologic Characteristics and Clinical Significance of Respiratory Viral Infections Among Adult Patients Admitted to the Intensive Care Unit
Authors: Kim Jeong Yeon , Yang Kyung Sook , Chung Youseung , Lee Ki-Byung , Suh Jin Woong , Kim Sun Bean , Sohn Jang Wook , Yoon Young Kyung
Published: May 2022

Background

The diagnosis of respiratory viral infections (RVIs) in critically ill patients is important for determining treatment options and adhering to infection-control protocols. However, data on the incidence and occurrence patterns of RVIs are scarce. We investigated the epidemiology and clinical impact of RVIs in critically ill patients.

Methods

This retrospective observational study was conducted in a tertiary hospital in South Korea between November 2014 and September 2020. Adult patients (≥ 18 years of age) who tested positive for an RVI by multiplex polymerase chain reaction (mPCR) and were admitted to the intensive care unit (ICU) were included in the study. Clinical characteristics and outcomes were obtained by reviewing electronic medical records. Pearson's χ2 test and Fisher's exact test, Mann-Whitney U test was used to compare between groups of patients. Trend analysis and the χ2-based Q test was used to analyze test behavior of physicians performing mPCR test.

Results

Among 22,517 patients admitted to the ICU during the study period, 2,222 (9.9%) underwent mPCR testing for an RVI. The median timing of mPCR testing after ICU admission was 1 day (IQR, 0–2). A total of 335 (15.1%) non-duplicative RVI-positive cases were included in the analysis. The incidence rate of RVIs in ICU patients was 30.45 per 10,000 patient-days. The most frequently detected RVI was influenza A (27.8%), followed by rhinovirus (25.4%). Thirty-two (9.6%) RVI-positive patients were diagnosed with upper respiratory infections, 193 (64.1%) with community-acquired, and 108 (35.9%) with hospital-acquired pneumonia. All-cause mortality and mortality related to respiratory tract infection (RTI) were 30.7% and 22.1%, respectively. The initial presentation of septic shock, requirement for mechanical ventilation, and lymphocytopenia were significant predictors of RTI-related mortality. Of the RVI-positive patients, 151 (45.1%) had nonviral coinfections and presented with higher clinical severity and longer hospital stays than patients infected solely with viral pathogens.

Conclusion

The incidence of RVIs in ICU patients is common. ICU patients with RVIs had high mortality and frequently presented with coinfections with nonviral pathogens, which were associated with a higher clinical severity than sole RVI. Increased testing for RVIs will enhance infection-control efforts and improve patient care.
A Prediction Model for Acute Kidney Injury in Adult Patients With Minimal Change Disease
Authors: Yang Chen , Yang Chen , Lin Shu-Peng , Chen Pu , Wu Jie , Meng Jin-Ling , Liang Shuang , Zhu Feng-Ge , Wang Yong , Feng Zhe , Chen Xiang-Mei , Cai Guang-Yan
Published: May 2022

Background

Early prediction of acute kidney injury (AKI) can allow for timely interventions, but there are still few methods that are easy and convenient to apply in predicting AKI, specially targeted at patients with minimal change disease (MCD). Motivated by this, we aimed to develop a predicting model for AKI in patients with MCD within the KDIGO criteria.

Methods

Data on 401 hospitalized adult patients, whose biopsy was diagnosed as MCD from 12/31/2010 to 15/7/2021, were retrospectively collected. Among these data, patients underwent biopsy earlier formed the training set (n = 283), while the remaining patients formed the validation set (n = 118). Independent risk factors associated with AKI were analyzed. From this, the prediction model was developed and nomogram was plotted.

Results

AKI was found in 55 of 283 patients (19%) and 15 of 118 patients (13%) in the training and validation cohorts, respectively. According to the results from lasso regression and logistic regression, it was found that four factors, including mean arterial pressure, serum albumin, uric acid, and lymphocyte counts, were independent of the onset of AKI. Incorporating these factors, the nomogram achieved a reasonably good concordance index of 0.84 (95%CI 0.77–0.90) and 0.75 (95%CI 0.62–0.87) in predicting AKI in the training and validation cohorts, respectively. Decision curve analysis suggested clinical benefit of the prediction models.

Conclusions

Our predictive nomogram provides a feasible approach to identify high risk MCD patients who might develop AKI, which might facilitate the timely treatment.
Clinical and cVEMP Evaluation Predict Short-Term Residual Dizziness After Successful Repositioning in Benign Paroxysmal Positional Vertigo
Authors: Jiang Chun-Yan , Wu Jing , Shu Liang , Sun Xu-Hong , Pan Hui , Xu Qian , Wu Si-Cheng , Liu Jian-Ren , Li Yun , Chen Wei
Published: May 2022

Objective

Residual dizziness (RD) is a frequent symptom with unknown pathogenesis, often complained about by the patients with benign paroxysmal positional vertigo (BPPV), even after a successful canalith repositioning procedure (CRP). This study aims to quantitatively evaluate the short-term RD severity and its risk factors in patients with BPPV after successful CRPs.

Methods

In total two hundred and twenty patients with BPPV after successful CRPs (W0) were prospectively followed up for 1 week (W1). Besides demographics and serial neuropsychological assessments (including dizziness handicap inventory-DHI, etc.), patients also received cervical/ocular vestibular evoked myogenic potential (c/oVEMP) evaluation. RD was defined as patients with dizziness or imbalance, dizziness visual analog scale (VAS) >1, and without positional vertigo or nystagmus at W1. Demographic, clinical, and VEMPs differences were compared among the three groups: patients with minor (dizziness VAS 1–3) and moderate-to-severe RD (dizziness VAS > 3) and without RD.

Results

The total frequency of RD at W1 was 49.1% (n = 108), with 32.3% (n = 71) minor, and 16.8% (n = 37) moderate-to-severe RD. Logistic regression analyses revealed that RD was closely associated with DHI status (OR = 2.101, P = 0.008) at W0, this effect was not present for minor RD. In addition to DHI score > 30 (OR = 4.898, P < 0.001) at W0, bilateral cVEMP absence (OR = 4.099, P = 0.005) was also an independent influential factor of moderate-to-severe RD.

Conclusion

Our study highlights the importance of RD quantified evaluation. DHI score >30 and bilateral cVEMP absence could increase the risk of short-term moderate-to-severe RD.
Treatment of Metastatic Primary Extramammary Paget Disease With Combination Anlotinib and Tislelizumab: A Case Report and Review of the Literature
Authors: Yin Xin , Li Xiaoqing , Li Muli , She Qing , Liu Yan , Chen Xiaodan , Ma Suhua , Ma Qian , Huang Zhangkan , Xu Lin , Huang Xiaozhun , Zhan Zhengyin , Che Xu
Published: May 2022

Extramammary Paget’s disease (EMPD) is a rare cutaneous neoplasm with distant metastases and a poor prognosis. We report the case of a 63-year-old male patient exhibiting stage IV primary EMPD with neuroendocrine differentiation, and harboring a somatic mutation in AMER1. After four cycles of Anlotinib combined with Tislelizumab, the patient achieved partial response for the metastatic lesions according to mRECIST1.1 criteria. Total positron emission tomography and computed tomography (PET-CT) scans revealed a significant reduction in SUV from 18.9 to 5.3, and the serum CEA decreased to normal levels after the treatment regimen. However, the patient developed fractures of the fourth and fifth thoracic vertebrae during the treatment. Therefore, percutaneous vertebroplasty was performed, and the patient experienced severe postoperative pneumonia and died from pulmonary encephalopathy and respiratory failure in June 2021. The overall and progression-free survival of the patient after diagnosis were 9 and 8 months, respectively. During the systemic treatment, the patient suffered grade 1 rash in the back and thigh and grade 1 hypertension. Nevertheless, the combination treatment of anlotinib and tislelizumab had a favorable clinical outcome and provided a survival advantage, and should be considered a therapeutic option for patients with AMER1-mutant metastatic EMPD.
Evaluating the Effectiveness of Screened Lactic Acid Bacteria in Improving Crop Residues Silage: Fermentation Parameter, Nitrogen Fraction, and Bacterial Community
Authors: He Liwen , Wang Yimin , Guo Xiang , Chen Xiaoyang , Zhang Qing
Published: May 2022

Ensiling characteristics of sweet potato vine (SPV) and peanut straw (PS), as well as the effects of lactic acid bacteria (LAB) strains, Lactococcus Lactis MK524164 (LL) and Lactobacillus farciminis MK524159 (LF), were investigated in this study. Fermentation parameters, nitrogen fractions, and bacterial community of SPV and PS were monitored at intervals during the ensiling process. The results showed that inoculating LAB increased lactate production (2.23 vs. 2.73%; 0.42 vs. 1.67% DM), accelerated pH decline (5.20 vs. 4.47; 6.30 vs. 5.35), and decreased butyrate (0.36% DM vs. not detected), ammonia-N (6.41 vs. 4.18% CP), or nonprotein-N (43.67 vs. 35.82% CP). Meanwhile, it altered the silage bacterial community, where the relative abundance of Lactobacillus was increased (6.67–32.03 vs. 45.27–68.43%; 0.53–10.45 vs. 38.37–68.62%) and that of undesirable bacteria such as Clostridium, Enterobacter, Methylobacterium, or Sphingomonas was much decreased. It is suggested that the screened LAB strains LL and LF can effectively improve the silage quality of SPV and PS silages.
Diet Supplementation With Sulfur Amino Acids Modulated Fermentation Metabolome and Gut Microbiome in Goats
Authors: Teklebrhan Tsegay , Tan Zhiliang
Published: May 2022

Dietary amino acids shift hydrogen metabolism to an alternative hydrogen sink consisting of dissolved hydrogen sulfur (dH2S) rather than methanogenesis; and influences the fermentation metabolome and microbiome associated with particles and liquid fractions in gut regions (foregut, small intestine, and hindgut) of goats. A completely randomized block design with a total of 20 goats (5 goats per treatment) was used to conduct the trial. The goats were fed on a diet that consisted of a concentrated mixture with maize stover roughage (50:50, on a dry matter basis) and randomly assigned to one of the four treatments: without amino acid supplementation (a basal diet), a basal diet supplemented with methionine (Met), a basal diet supplemented with lysine (Lys), and a basal diet supplemented with methionine and lysine (ML). Goats fed Met alone or in combination had less acetate, acetate to propionate ratio, and greater propionate (p < 0.05) in the foregut and hindgut than those fed control or Lys. Nonetheless, the goats fed on the amino acid supplements had higher levels of branched-chain VFA (p < 0.05) in the foregut and hindgut than the control goats. Goats fed on ML had the highest ammonia (p < 0.01), followed by Met or Lys, both in the foregut and hindgut, compared with the control. Those fed on Met alone or in combination, had lower dH2, dCH4 (p < 0.01), and higher dH2S (p < 0.01) in the foregut and hindgut than the control or Lys. The goats that were fed on Met alone or in combination, had higher 16S rRNA gene copies of total bacteria, methanogens, and 18S rRNA gene copies of protozoa, fungi, and fiber-utilizing bacterial species (p < 0.01) associated with particles vs. liquid, both in the foregut and hindgut than the control goats. This study gives insights into the use of sulfur-containing amino acids, as an alternative dietary mitigation strategy of methanogenesis in ruminants and highlights the need for further research in this direction.
Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater
Authors: Hellman Maria , Valhondo Cristina , Martínez-Landa Lurdes , Carrera Jesús , Juhanson Jaanis , Hallin Sara
Published: May 2022

Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes.