bluuebunny/crossref_metadata_2025 huggingface dataset:
REVIEW OF PLANT-BASED MILK UTILIZATION AS A SUBSTITUTE FOR ANIMAL MILK
Authors: Maris Intan , Radiansyah Mohamad Rajih
Published: December 2021

In general, milk is a white liquid secreted by animal’s mammary gland and contained lactose. Problems occured when some people have an allergy to lactose thus an alternative is created in the form of dairy products with plants as the basic ingredient. This study aims to determine the nutritional value and the advantage of plant-based milk on health and nutrition fulfillment so it can be used as a substitute of animal milk for people with lactose intolerance. In this study, the milk in plant-based milk refers to extracts of various plants. Plant-based milk has a distinctive odor depending on the plant-based ingredients used. In this article, the study was carried on the physical characteristics, nutritional values and benefits of plant-based milk consumption for health and a comparison with animal milk (cow’s milk) was also done. The literature indicated that nutritional value of plant-based milk is comparable to animal milk. Despite no observable physical differences between plant-based milk and animal milk, there was still a need for improvements in the way to add flavour to plant-based milk to attract consumer’s interest. Plant-based milk has its benefits for heart health due to its lack of cholesterol levels in it. There are five types of plant-based milk studied within the scope of this article; these are soy, almond, oat, mung beans, and cashew.
Recent Development of Probiotic Bifidobacteria for Treating Human Diseases
Authors: Chen Jun , Chen Xinyi , Ho Chun Loong
Published: December 2021

Bifidobacterium is a non-spore-forming, Gram-positive, anaerobic probiotic actinobacterium and commonly found in the gut of infants and the uterine region of pregnant mothers. Like all probiotics, Bifidobacteria confer health benefits on the host when administered in adequate amounts, showing multifaceted probiotic effects. Examples include B. bifidum, B. breve, and B. longum, common Bifidobacterium strains employed to prevent and treat gastrointestinal disorders, including intestinal infections and cancers. Herein, we review the latest development in probiotic Bifidobacteria research, including studies on the therapeutic impact of Bifidobacterial species on human health and recent efforts in engineering Bifidobacterium. This review article would provide readers with a wholesome understanding of Bifidobacteria and its potentials to improve human health.
Recent Advances of Biomedical Materials for Prevention of Post-ESD Esophageal Stricture
Authors: Bao Yuchen , Li Zhenguang , Li Yingze , Chen Tao , Cheng Yu , Xu Meidong
Published: December 2021

Esophageal stricture commonly occurs in patients that have suffered from endoscopic submucosal dissection (ESD), and it makes swallowing difficult for patients, significantly reducing their life qualities. So far, the prevention strategies applied in clinical practice for post-ESD esophageal stricture usually bring various inevitable complications, which drastically counteract their effectiveness. Nowadays, with the widespread investigation and application of biomedical materials, lots of novel approaches have been devised in terms of the prevention of esophageal stricture. Biomedical polymers and biomedical-derived materials are the most used biomedical materials to prevent esophageal stricture after ESD. Both of biomedical polymers and biomedical-derived materials possess great physicochemical properties such as biocompatibility and biodegradability. Moreover, some biomedical polymers can be used as scaffolds to promote cell growth, and biomedical-derived materials have biological functions similar to natural organisms, so they are important in tissue engineering. In this review, we have summarized the current approaches for preventing esophageal stricture and put emphasis on the discussion of the roles biomedical polymers and biomedical-derived materials acted in esophageal stricture prevention. Meanwhile, we proposed several potential methods that may be highly rational and feasible in esophageal stricture prevention based on other researches associated with biomedical materials. This review is expected to offer a significant inspiration from biomedical materials to explore more effective, safer, and more economical strategies to manage post-ESD esophageal stricture.
Long-Term Follow-Up of Accelerated Transepithelial Corneal Crosslinking for Post-LASIK Ectasia: A Pilot Prospective Observational Study
Authors: Tian Mi , Zhang Xiaoyu , Jian Weijun , Sun Ling , Shen Yang , Zhou Xingtao
Published: December 2021

Background: Keratectasia after corneal refractive surgery is a rare but serious postoperative complication, and reports on accelerated transepithelial corneal crosslinking (ATE-CXL)-based treatment of patients with post-laser-assisted in situ keratomileusis (LASIK) ectasia are limited. Therefore, this study evaluated the long-term efficacy and safety of ATE-CXL for progressive post-LASIK ectasia.

Methods: This prospective observational study was conducted at the Eye and ENT Hospital, Fudan University, Shanghai, China, and 25 eyes from 25 patients with post-LASIK ectasia undergoing ATE-CXL were examined. Clinical examinations were conducted preoperatively and postoperatively to assess parameters such as manifest refraction, corrected distance visual acuity (CDVA), endothelial cell density; keratometry, corneal thickness, posterior elevation and topometric indices were measured using Pentacam; sectoral pachymetry and epithelial thickness were evaluated using optical coherence tomography. A paired t-test, Wilcoxon rank-sum test, Kruskal-Wallis test, and repeated measures analysis of variance were used for statistical analysis.

Results: Participants were examined for an average of 46 months. No severe complications occurred during or after ATE-CXL. CDVA improved from 0.25 ± 0.31 preoperatively to 0.15 ± 0.17 postoperatively (p = 0.011). Maximum keratometry decreased from 55.20 ± 8.33 D to 54.40 ± 7.98 D, with no statistical significance (p = 0.074), and the central corneal thickness increased from 414.92 ± 40.96 μm to 420.28 ± 44.78 μm (p = 0.047) at the final follow-up. Posterior elevation, pachymetry, and epithelial thickness remained stable (p > 0.05) throughout the follow-up. No significant differences were noted in topometric indices, except the central keratoconus index, which decreased significantly (p < 0.001) at the final follow-up.

Conclusion: Improvements in CDVA and stabilization in corneal keratometry and posterior elevation after ATE-CXL were noted at the 46-months follow-up, demonstrating that ATE-CXL is a safe and effective treatment for progressive post-LASIK ectasia.
Impact of the Purification Process on the Spray-Drying Performances of the Three Families of Lipopeptide Biosurfactant Produced by Bacillus subtilis
Authors: Vassaux Antoine , Rannou Marie , Peers Soline , Daboudet Théo , Jacques Philippe , Coutte François
Published: December 2021

Lipopeptides produced by Bacillus subtilis display many activities (surfactant, antimicrobial, and antitumoral), which make them interesting compounds with a wide range of applications. During the past years, several processes have been developed to enable their production and purification with suitable yield and purity. The already implemented processes mainly end with a critical drying step, which is currently achieved by freeze-drying. In this study, the possibility to replace this freeze-drying step with a spray-drying one, more suited to industrial applications, was analyzed. After evaluating their thermal resistance, we have developed a spray-drying methodology applicable for the three lipopeptides families produced by B. subtilis, i.e., surfactin, mycosubtilin (iturin family), and plipastatin (fengycin family). For each lipopeptide, the spray-drying procedure was applied at three steps of the purification process by ultrafiltration (supernatant, diafiltered solution, and pre-purified fraction). The analysis of the activities of each spray-dried lipopeptide showed that this drying method is not decreasing its antimicrobial and biosurfactant properties. The methodology developed in this study enabled for the first time the spray-drying of surfactin, without adjuvants’ addition and regardless of the purification step considered. In the case of fengycin and mycosubtilin, only diafiltered solution and purified fraction could be successfully spray-dried without the addition of adjuvant. Maltodextrin addition was also investigated as the solution for the direct drying of supernatant. As expected, the performances of the spray-drying step and the purity of the powder obtained are highly related to the purification step at which the product was dried. Interestingly, the impact of mycosubtilin concentration on spray-drying yield was also evidenced.
Non-Coding RNA m6A Modification in Cancer: Mechanisms and Therapeutic Targets
Authors: Chen Da-Hong , Zhang Ji-Gang , Wu Chuan-Xing , Li Qin
Published: December 2021

Recently, N6-methyl-adenosine (m6A) ribonucleic acid (RNA) modification, a critical and common internal RNA modification in higher eukaryotes, has generated considerable research interests. Extensive studies have revealed that non-coding RNA m6A modifications (e.g. microRNAs, long non-coding RNAs, and circular RNAs) are associated with tumorigenesis, metastasis, and other tumour characteristics; in addition, they are crucial molecular regulators of cancer progression. In this review, we discuss the relationship between non-coding RNA m6A modification and cancer progression from the perspective of various cancers. In particular, we focus on important mechanisms in tumour progression such as proliferation, apoptosis, invasion and metastasis, tumour angiogenesis. In addition, we introduce clinical applications to illustrate more vividly that non-coding RNA m6A modification has broad research prospects. With this review, we aim to summarize the latest insights and ideas into non-coding RNA m6A modification in cancer progression and targeted therapy, facilitating further research.
KNNCNV: A K-Nearest Neighbor Based Method for Detection of Copy Number Variations Using NGS Data
Authors: Xie Kun , Liu Kang , Alvi Haque A K , Chen Yuehui , Wang Shuzhen , Yuan Xiguo
Published: December 2021

Copy number variation (CNV) is a well-known type of genomic mutation that is associated with the development of human cancer diseases. Detection of CNVs from the human genome is a crucial step for the pipeline of starting from mutation analysis to cancer disease diagnosis and treatment. Next-generation sequencing (NGS) data provides an unprecedented opportunity for CNVs detection at the base-level resolution, and currently, many methods have been developed for CNVs detection using NGS data. However, due to the intrinsic complexity of CNVs structures and NGS data itself, accurate detection of CNVs still faces many challenges. In this paper, we present an alternative method, called KNNCNV (K-Nearest Neighbor based CNV detection), for the detection of CNVs using NGS data. Compared to current methods, KNNCNV has several distinctive features: 1) it assigns an outlier score to each genome segment based solely on its first k nearest-neighbor distances, which is not only easy to extend to other data types but also improves the power of discovering CNVs, especially the local CNVs that are likely to be masked by their surrounding regions; 2) it employs the variational Bayesian Gaussian mixture model (VBGMM) to transform these scores into a series of binary labels without a user-defined threshold. To evaluate the performance of KNNCNV, we conduct both simulation and real sequencing data experiments and make comparisons with peer methods. The experimental results show that KNNCNV could derive better performance than others in terms of F1-score.
The Role of the Microbiota in Graves’ Disease and Graves’ Orbitopathy
Authors: Hou Jueyu , Tang Yunjing , Chen Yongjiang , Chen Danian
Published: December 2021

Graves‘ disease (GD) is a clinical syndrome with an enlarged and overactive thyroid gland, an accelerated heart rate, Graves’ orbitopathy (GO), and pretibial myxedema (PTM). GO is the most common extrathyroidal complication of GD. GD/GO has a significant negative impact on the quality of life. GD is the most common systemic autoimmune disorder, mediated by autoantibodies to the thyroid-stimulating hormone receptor (TSHR). It is generally accepted that GD/GO results from complex interactions between genetic and environmental factors that lead to the loss of immune tolerance to thyroid antigens. However, the exact mechanism is still elusive. Systematic investigations into GD/GO animal models and clinical patients have provided important new insight into these disorders during the past 4 years. These studies suggested that gut microbiota may play an essential role in the pathogenesis of GD/GO. Antibiotic vancomycin can reduce disease severity, but fecal material transfer (FMT) from GD/GO patients exaggerates the disease in GD/GO mouse models. There are significant differences in microbiota composition between GD/GO patients and healthy controls.Lactobacillus,Prevotella, andVeillonellaoften increase in GD patients. The commonly used therapeutic agents for GD/GO can also affect the gut microbiota. Antigenic mimicry and the imbalance of T helper 17 cells (Th17)/regulatory T cells (Tregs) are the primary mechanisms proposed for dysbiosis in GD/GO. Interventions including antibiotics, probiotics, and diet modification that modulate the gut microbiota have been actively investigated in preclinical models and, to some extent, in clinical settings, such as probiotics (Bifidobacterium longum) and selenium supplements. Future studies will reveal molecular pathways linking gut and thyroid functions and how they impact orbital autoimmunity. Microbiota-targeting therapeutics will likely be an essential strategy in managing GD/GO in the coming years.
Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms
Authors: Wirth Roland , Pap Bernadett , Maróti Gergely , Vályi Péter , Komlósi Laura , Barta Nikolett , Strang Orsolya , Minárovits János , Kovács Kornél L.
Published: December 2021

Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16–17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.
Identification of Peptoniphilus harei From Blood Cultures in an Infected Aortic Aneurysm Patient: Case Report and Review Published Literature
Authors: Wan Xue , Wang Shuang , Wang Min , Liu Jinhua , Zhang Yu
Published: December 2021

Gram-positive anaerobic cocci (GPAC) are a commensal part of human flora but are also opportunistic pathogens. This is possibly the first study to report a case of Peptoniphilus harei bacteremia in an abdominal aortic aneurysm (AAA) patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate and molecular analysis confirmed it as P. harei. A comprehensive literature review revealed that P. harei is an emergent pathogen. This study serves as a reminder for practicing clinicians to include anaerobic blood cultures as part of their blood culture procedures; this is particularly important situations with a high level of suspicion of infection factors in some noninfectious diseases, as mentioned in this publication. Clinical microbiologists should be aware that the pathogenic potential of GPAC can be greatly underestimated leading to incorrect diagnosis on using only one method for pathogen identification. Upgradation and correction of the MALDI-TOF MS databases is recommended to provide reliable and rapid identification of GPAC at species level in medical diagnostic microbiology laboratories.
The Role of Minor Pilins in Assembly and Function of the Competence Pilus of Streptococcus pneumoniae
Authors: Oliveira Vitor , Aschtgen Marie-Stephanie , van Erp Anke , Henriques-Normark Birgitta , Muschiol Sandra
Published: December 2021

The remarkable genomic plasticity of Streptococcus pneumoniae largely depends on its ability to undergo natural genetic transformation. To take up extracellular DNA, S. pneumoniae assembles competence pili composed of the major pilin ComGC. In addition to ComGC, four minor pilins ComGD, E, F, and G are expressed during bacterial competence, but their role in pilus biogenesis and transformation is unknown. Here, using a combination of protein-protein interaction assays we show that all four proteins can directly interact with each other. Pneumococcal ComGG stabilizes the minor pilin ComGD and ComGF and can interact with and stabilize the major pilin ComGC, thus, deletion of ComGG abolishes competence pilus assembly. We further demonstrate that minor pilins are present in sheared pili fractions and find ComGF to be incorporated along the competence pilus by immunofluorescence and electron microscopy. Finally, mutants of the invariant Glu5 residue (E5), ComGDE5A or ComGEE5A, but not ComGFE5A, were severely impaired in pilus formation and function. Together, our results suggest that ComGG, lacking E5, is essential for competence pilus assembly and function, and plays a central role in connecting the pneumococcal minor pilins to ComGC.
Specifying Challenges in Transcribing Covert Recordings: Implications for Forensic Transcription
Authors: Love Robbie , Wright David
Published: December 2021

Covert audio recordings feature in the criminal justice system in a variety of guises, either on their own or accompanied by video. If legally obtained, such recordings can provide important forensic evidence. However, the quality of these potentially valuable evidential recordings is often very poor and their content indistinct, to the extent that a jury requires an accompanying transcript. At present, in many international jurisdictions, these transcriptions are produced by investigating police officers involved in the case, but transcription is a highly complex, meticulous and onerous task, and police officers are untrained and have a vested interest in the influence of the transcript on a case, which gives rise to potential inaccuracy. This paper reports the design and results of a controlled transcription experiment in which eight linguistically trained professional transcribers produced transcripts for an audio recording of a conversation between five adults in a busy restaurant. In the context of covert recordings, this recording shares many of the typical features of covert forensic recordings, including the presence of multiple speakers, background noise and use of non-specialist recording equipment. We present a detailed qualitative and quantitative comparison of the transcripts, identifying areas of agreement and disagreement in (a) speaker attribution and (b) the representation of the linguistic content. We find that disagreement between the transcriptions is frequent and various in nature; the most common causes are identified as (i) omission of speech that is included in other transcripts, (ii) variation in the representation of turns, (iii) orthographic variation seemingly motivated by phonetic similarity, and (iv) orthographic variation seemingly not motivated by phonetic similarity. We argue that the variable nature of the transcription of “challenging” audio recordings must be considered in forensic contexts and make recommendations for improving practice in the production of forensic transcriptions.
Integrated Aortic-Valve-And-Ascending-Aortic Replacement vs. Partial Replacement in Bicuspid Aortic Valve-Related Aortopathy
Authors: Chen Mi , Xu Wangli , Ding Yan , Zhao Honglei , Wang Pei , Yang Bo , Qiao Huanyu , Zhang Wei , Zhou Chenyang , Jia Junnan , Bai Tao , Xue Jinrong , Zhu Junming , Liu Yongmin , Li Weimin , Sun Lizhong
Published: December 2021

Objective: We sought to evaluate the outcomes of integrated aortic-valve and ascending-aortic replacement (IR) vs. partial replacement (PR) in patients with bicuspid aortic valve (BAV)-related aortopathy.

Methods: We compared long-term mortality, reoperation incidence, and the cumulative incidence of stroke, bleeding, significant native valve or prosthetic valve dysfunction, and the New York Heart Association (NYHA) functional classes II-IV between inverse probability-weighted cohorts of patients who underwent IR or PR for BAV-related aortopathy in a single center from 2002 to 2019. Patients were stratified into different aortic diameter groups (“valve type” vs. “aorta type”).

Results: Among patients with “valve type,” aortic valve replacement in patients with an aortic diameter > 40 mm was associated with significantly higher 10-year mortality than IR compared with diameter 35–40 mm [17.49 vs. 5.28% at 10 years; hazard ratio (HR), 3.22; 95% CI, 1.52 to 6.85; p = 0.002]. Among patients with “aorta type,” ascending aortic replacement in patients with an aortic diameter 52–60 mm was associated with significantly higher 10-year mortality than IR compared with diameter 45–52 mm (14.49 vs. 1.85% at 10 years; HR, 0.04; 95% CI, 1.06 to 85.24; p = 0.03).

Conclusion: The long-term mortality and reoperation benefit that were associated with IR, as compared with PR, minimizing to 40 mm of the aortic diameter among patients with “valve type” and minimizing to 52 mm of the aortic diameter among patients with “aorta type.”

Trial Registration: Treatment to Bicuspid Aortic Valve Related Aortopathy (BAVAo Registry): ChiCTR.org.cn no: ChiCTR2000039867.
Innovative Approaches to Assess Intermediate Cardiovascular Risk Subjects: A Review From Clinical to Metabolomics Strategies
Authors: Martins Aline M. A. , Paiva Mariana U. B. , Paiva Diego V. N. , de Oliveira Raphaela M. , Machado Henrique L. , Alves Leonardo J. S. R. , Picossi Carolina R. C. , Faccio Andréa T. , Tavares Marina F. M. , Barbas Coral , Giraldez Viviane Z. R. , Santos Raul D. , Monte Guilherme U. , Atik Fernando A.
Published: December 2021

Current risk stratification strategies for coronary artery disease (CAD) have low predictive value in asymptomatic subjects classified as intermediate cardiovascular risk. This is relevant because not all coronary events occur in individuals with traditional multiple risk factors. Most importantly, the first manifestation of the disease may be either sudden cardiac death or acute coronary syndrome, after rupture and thrombosis of an unstable non-obstructive atherosclerotic plaque, which was previously silent. The inaccurate stratification using the current models may ultimately subject the individual to excessive or insufficient preventive therapies. A breakthrough in the comprehension of the molecular mechanisms governing the atherosclerosis pathology has driven many researches toward the necessity for a better risk stratification. In this Review, we discuss how metabolomics screening integrated with traditional risk assessments becomes a powerful approach to improve non-invasive CAD subclinical diagnostics. In addition, this Review highlights the findings of metabolomics studies performed by two relevant analytical platforms in current use–mass spectrometry (MS) hyphenated to separation techniques and nuclear magnetic resonance spectroscopy (NMR) –and evaluates critically the challenges for further clinical implementation of metabolomics data. We also discuss the modern understanding of the pathophysiology of atherosclerosis and the limitations of traditional analytical methods. Our aim is to show how discriminant metabolites originated from metabolomics approaches may become promising candidate molecules to aid intermediate risk patient stratification for cardiovascular events and how these tools could successfully meet the demands to translate cardiovascular metabolic biomarkers into clinical settings.
Additives Incorporated in Cellulose Acetate Membranes to Improve Its Performance as a Barrier in Periodontal Treatment
Authors: Fornazier Mariana , Gontijo de Melo Patricia , Pasquini Daniel , Otaguro Harumi , Pompêu Gabriela Ciribelli Santos , Ruggiero Reinaldo
Published: December 2021

In this study, we prepared cellulose acetate membranes, by means of casting mold, incorporated with two additives, sodium carboxymethyl lignin and calcium glycerophosphate, in order to improve properties for periodontal applications. The membranes were characterized from the morphological, structural, thermal and mechanical point of view, as well as by physiological pH tests. The results showed that membranes with additives improve the physical-chemical and mechanical properties, especially when the two additives are present in the same membrane, which can be attributed to the important synergy between them. The most significant effects occur in increasing the thickness and decreasing the density, which reflects in the porosity of the membranes, although the added amounts do not exceed 1.4%. A 1% increase in lignin concentration does not change the thickness and density of the membrane, but that amount of lignin plus 0.4% calcium glycerophosphate increases the thickness of the membrane by 42% and decreases the density by about 6%. Although there is a decrease in mechanical properties, as observed in Young's modulus and crystallinity, the significant and intermittent increase in sample weight loss with both additives in physiological solution indicates that, in the long run, it can be used as a degradable barrier.
Tales From Three 18th Century Eruptions to Understand Past and Present Behaviour of Etna
Authors: Corsaro Rosa Anna , Branca Stefano , De Beni Emanuela , Tanguy Jean-Claude
Published: December 2021

The structure of an active volcano is highly dependent on the interplay between the geodynamic context, the tectonic assessment as well as the magmatic processes in the plumbing system. This complex scenario, widely explored at Etna during the last 40 years, is nevertheless incomplete for the recent historical activity. In 1763 two eruptions occurred along the west flank of the volcano. There, an eruption started on 6th February and formed the scoria cone of Mt. Nuovo and a roughly 4-km-long lava flow field. Another small scoria cone, known as Mt. Mezza Luna, is not dated in historical sources. It is located just 1 km eastward of Mt. Nuovo and produced a 700 m long flow field. We focused on the activity of Mts. Nuovo and Mezza Luna for several reasons. First, the old geological maps and volcanological catalogues indicate that Mt. Mezza Luna and Mt. Nuovo cones were formed during the same eruption, while historical sources described Mt. Nuovo’s activity as producing a single scoria cone and do not give information about the formation of Mt. Mezza Luna. Second, petrologic studies highlight that the products of Mt. Mezza Luna are similar to the sub-aphyric Etna basalts; they preserve a composition relatively close to Etna primitive magma which were also erupted in 1763, during La Montagnola flank eruption, which took place along the South Rift of the volcano. Third, the two scoria cones built up along the so-called West Rift of Etna, which represents one of the main magma-ascent zones of the volcano. We applied a multidisciplinary approach that could prove useful for other volcanoes whose past activity is still to be reconstructed. Critical reviews of historical records, new field surveys, petrochemical analyses and petrologic modelling of the Mts. Nuovo and Mezza Luna eruptions have been integrated with literature data. The results allowed improving the stratigraphic record of historical eruptions reported in the Mount Etna Geological map, modelling the sub-volcanic magmatic processes responsible for magma differentiation, and evidencing recurrent mechanisms of magma transfer at Etna. Indeed, the intrusion of a deep primitive magma along the South Rift is often associated with the activation of other rift zones that erupt residual magma stored in the shallow plumbing system.
Influences of Spillway Section Morphologies on Landslide Dam Breaching
Authors: Yang Meng , Zhong Qiming , Mei Shengyao , Shan Yibo
Published: December 2021

Spillway excavation is often adopted as a precautionary engineering measure for disaster mitigation before landslide dam breaching. Based on the landslide dam breach mechanisms, this paper focuses on developing a numerical model to comprehensively discuss the issue based on three documented landslide dam failures, such as Tangjiashan, Xiaogangjian, and Baige landslide dams. The spillway cross section morphologies were modeled with different sizes under common shape (i.e., an inverted trapezoid) and slope conditions. The influence of cross section on dam breach processes was analyzed under conditions of different depth, bottom width, slope ratio in the cross and longitudinal sections, with/without spillway. The following conclusions can be drawn: 1) excavation of a spillway can effectively reduce the peak breach flow, therefore delay the time to peak; 2) the peak breach flow dramatically decreases and the time to peak delays as the spillway depth increases; 3) the peak breach flow changes little and the time to peak occurs earlier with the increment in spillway bottom width; 4) the peak breach flow decreases and the time to peak delays with the decrease of slope ratio in cross section in the spillway; 5) the slope ratio in the longitudinal section has little influence on the breach process. Hence, if conditions permit, the spillway with large spillway depth, small bottom width, and gentle slope ratio in the cross section is the preferable section morphology for the emergency disposal of the landslide dam.
Holocene History of Río Tranquilo Glacier, Monte San Lorenzo (47°S), Central Patagonia
Authors: Sagredo Esteban A. , Reynhout Scott A. , Kaplan Michael R. , Aravena Juan C. , Araya Paola S. , Luckman Brian H. , Schwartz Roseanne , Schaefer Joerg M.
Published: December 2021

The causes underlying Holocene glacier fluctuations remain elusive, despite decades of research efforts. Cosmogenic nuclide dating has allowed systematic study and thus improved knowledge of glacier-climate dynamics during this time frame, in part by filling in geographical gaps in both hemispheres. Here we present a new comprehensive Holocene moraine chronology from Mt. San Lorenzo (47°S) in central Patagonia, Southern Hemisphere. Twenty-four new 10Be ages, together with three published ages, indicate that the Río Tranquilo glacier approached its Holocene maximum position sometime, or possibly on multiple occasions, between 9,860 ± 180 and 6,730 ± 130 years. This event(s) was followed by a sequence of slightly smaller advances at 5,750 ± 220, 4,290 ± 100 (?), 3,490 ± 140, 1,440 ± 60, between 670 ± 20 and 430 ± 20, and at 390 ± 10 years ago. The Tranquilo record documents centennial to millennial-scale glacier advances throughout the Holocene, and is consistent with recent glacier chronologies from central and southern Patagonia. This pattern correlates well with that of multiple moraine-building events with slightly decreasing net extent, as is observed at other sites in the Southern Hemisphere (i.e., Patagonia, New Zealand and Antarctic Peninsula) throughout the early, middle and late Holocene. This is in stark contrast to the typical Holocene mountain glacier pattern in the Northern Hemisphere, as documented in the European Alps, Scandinavia and Canada, where small glaciers in the early-to-mid Holocene gave way to more-extensive glacier advances during the late Holocene, culminating in the Little Ice Age expansion. We posit that this past asymmetry between the Southern and Northern hemisphere glacier patterns is due to natural forcing that has been recently overwhelmed by anthropogenic greenhouse gas driven warming, which is causing interhemispherically synchronized glacier retreat unprecedented during the Holocene.
Research on Water Droplet Movement Characteristics in the Last Two Stages of Low-Pressure Cylinder of Steam Turbine Under Low Load Conditions
Authors: Fan Shuangshuang , Wang Ying , Yao Kun , Fan Yi , Wan Jie , Gu Weifei
Published: December 2021

In the operating process of the coal-fired generation during flexible peaking regulation, the primary and secondary water droplets in the steam flowing through the last two stages of the low-pressure cylinder could influence the efficiency and safety of the steam turbine definitely. However, systematic analysis of the movement characteristics of water droplets under low-load conditions is scarcely in the existing research, especially the ultra-low load conditions below 30%. Toward this end, the more novel algebraic slip model and particle transport model mentioned in this paper are used to simulate the primary and secondary water droplets. Taking a 600 MW unit as a research object, the droplets motion characteristics of the last two stages were simulated within four load conditions, including 100, 50, 40, and 30% THA. The results show that the diameter of the primary water droplets is smaller, ranging from 0 to 1 µm, during the flexible peak regulation process of the steam turbine. The deposition is mainly located at the entire moving blades and the trailing edge of the last two stator blades. With the load decreasing, the deposition effect decreases sustainably. And the larger diameters of secondary water droplets range from 10 to 300 µm. The erosion of secondary water droplets in the last stage is more serious than that of the second last stage for different load conditions, and the erosion of the second last stage could be negligible. The pressure face and suction face at 30% blade height of the last stage blade have been eroded most seriously. The lower the load, the worse erosion from the secondary water droplets, which poses a potential threat to the fracture of the last stage blades of the steam turbine. This study provides a certain reference value for the optimal design of steam turbine blades under flexible peak regulation.
Diversity and Introduction History of Glycaspis brimblecombei Reflects a History of Bridgeheads and Distinct Invasions
Authors: Dittrich-Schröder Gudrun , Garnas Jeff R. , Arriagada-Cares Daniela , Ahumada Rodrigo , Hurley Brett P. , Lawson Simon A. , Slippers Bernard
Published: December 2021

Glycaspis brimblecombeiis an invasive insect pest ofEucalyptusthat has spread rapidly around the world since its first report in California in 1998. The pest now occurs on at least four continents whereEucalyptusis grown as a non-native plantation species. To characterize global routes of invasion for this insect, we characterized the sequences of a portion of the Cytochrome Oxidase 1 (COI) gene from 105 individuals from the invasive and native range, including from Australia, Brazil, Chile, La Réunion, Mauritius, South Africa and the United States. In addition, we developed 13 polymorphic microsatellite markers, of which we used 11 to characterize the diversity in the same 105 specimens. Our results suggest that there have been two independent introduction events from Australia, which is assumed to be the origin, to distinct parts of the adventive range. The first introduction was into the United States, from where it appears to have spread to South America and eventually to South Africa. This finding highlights the threat of bridgehead populations to accelerate pest invasions inEucalyptus, even if those populations are on widespread non-commercial populations ofEucalyptus(as in California). A second introduction appears to have occurred on the islands of Mauritius and La Réunion and provides another example of the establishment of independent lineages of invasive global insect pests. This complex invasion pattern mirrors that found in otherEucalyptuspests.
Mineralized Cartilage and Bone-Like Tissues in Chondrichthyans Offer Potential Insights Into the Evolution and Development of Mineralized Tissues in the Vertebrate Endoskeleton
Authors: Atake Oghenevwogaga J. , Eames B. Frank
Published: December 2021

The impregnation of biominerals into the extracellular matrix of living organisms, a process termed biomineralization, gives rise to diverse mineralized (or calcified) tissues in vertebrates. Preservation of mineralized tissues in the fossil record has provided insights into the evolutionary history of vertebrates and their skeletons. However, current understanding of the vertebrate skeleton and of the processes underlying its formation is biased towards biomedical models such as the tetrapods mouse and chick. Chondrichthyans (sharks, skates, rays, and chimaeras) and osteichthyans are the only vertebrate groups with extant (living) representatives that have a mineralized skeleton, but the basal phylogenetic position of chondrichthyans could potentially offer unique insights into skeletal evolution. For example, bone is a vertebrate novelty, but the internal supporting skeleton (endoskeleton) of extant chondrichthyans is commonly described as lacking bone. The molecular and developmental basis for this assertion is yet to be tested. Subperichondral tissues in the endoskeleton of some chondrichthyans display mineralization patterns and histological and molecular features of bone, thereby challenging the notion that extant chondrichthyans lack endoskeletal bone. Additionally, the chondrichthyan endoskeleton demonstrates some unique features and others that are potentially homologous with other vertebrates, including a polygonal mineralization pattern, a trabecular mineralization pattern, and an unconstricted perichordal sheath. Because of the basal phylogenetic position of chondrichthyans among all other extant vertebrates with a mineralized skeleton, developmental and molecular studies of chondrichthyans are critical to flesh out the evolution of vertebrate skeletal tissues, but only a handful of such studies have been carried out to date. This review discusses morphological and molecular features of chondrichthyan endoskeletal tissues and cell types, ultimately emphasizing how comparative embryology and transcriptomics can reveal homology of mineralized skeletal tissues (and their cell types) between chondrichthyans and other vertebrates.
Potential Prognostic Value of a Seven m6A-Related LncRNAs Signature and the Correlative Immune Infiltration in Colon Adenocarcinoma
Authors: Chai Xiu-kun , Qi Wei , Zou Chun-Yan , He Chen-Xi , Su Miao , Zhao Dong-Qiang
Published: December 2021

Long non-coding RNAs (lncRNAs) and their N6-methyladenosine (m6A) modifications play an essential role in tumorigenesis and cancer progression. This study was designed to explore the value of m6A-related lncRNAs in prognosis and therapeutic applications of immune infiltration of colon adenocarcinoma (COAD). We downloaded the COAD gene expression and clinical data from The Cancer Genome Atlas project. By co-expression analysis, Lasso Cox regression analysis, and univariate and multivariate Cox regression, we constructed an independent prognostic signature of seven m6A-related lncRNAs. The prognostic lncRNAs were divided into two clusters by consistent clustering analysis, as well as into two groups of low–high risk based on the signature. Then we identified the relationship between the different groups with clinical features and immune cell infiltration. Cluster 2 had a higher risk score with a lower survival rate. The risk score was higher in groups with advanced clinical features, such as stage III–IV, N1-3, and M1. The expression of AC156455.1 was increased in tumor tissues and cluster 2, and the lncRNA ZEB1−AS1 was notably higher in the high-risk group. Five types of immune cells showed differences in two clusters, and most were upregulated in type 2. The expression of memory B cells was positively correlated with the risk score. The prognostic model was verified by the Gene Expression Omnibus (GEO) dataset. Besides, we found that the expression of these seven lncRNAs in tumor tissues was significantly higher than that in normal tissues, which verified the feasibility of the model. Thus, the signature of seven m6A-related lncRNAs can independently predict the prognosis of COAD. This signature is also closely associated with immune cell infiltration, and new therapeutic targets can be explored from this field.
Identification of Potential Hub Genes and miRNA-mRNA Pairs Related to the Progression and Prognosis of Cervical Cancer Through Integrated Bioinformatics Analysis
Authors: Fu Mingxu , Pei Yongyan , Lu Fang , Jiang Huici , Bi Yingying , Cheng Jiajing , Qin Jinlong
Published: December 2021

In recent years, the incidence and mortality of cervical cancer have increased worldwide. At the same time, increasing data have confirmed that miRNA-mRNA plays a positive or negative regulatory role in many cancers. This study attempted to screen effective miRNA-mRNA in the progression of cervical cancer, and to study the mechanism of miRNA-mRNA in the progression of cervical cancer. The expression profile data of GSE7410, GSE 63514, GSE 86100 and TCGA-CESC were downloaded, and 34 overlapping differentially expressed genes (22 up-regulated and 12 down-regulated) and 166 miRNAs (74 down-regulated and 92 up-regulated) were screened through limma package. Then, miR-197-3p/TYMS pairs were obtained by PPI, functional enrichment, Kaplan-Meier plotter analysis, Cox univariate and multivariate analysis, risk modeling, WGCNA, qPCR and dual-luciferase experiments. The results showed that TYMS was an independent prognostic factor of cervical cancer, and its expression level was negatively correlated with cervical cancer tissue grade (TMN), tumor grade, age, microsatellite stability and tumor mutation load, and positively correlated with methyl expression in DNMT1, DNMT2, DNMT3A and DNMT3B. Functional experiments showed that TYMS knockout could promote the proliferation, migration and invasion of HeLa cells and reduce apoptosis. Overexpression of TYMS showed the opposite trend, miR-197-3p was negatively correlated with the expression of TYMS. MiR-197-3p inhibitor reversed the effect of si-TYMS on the proliferation of HeLa cells. In conclusion, these results reveal that TYMS plays a very important role in the prognosis and progression of cervical cancer, and has the potential to be thought of as cervical cancer biomarkers. At the same time, miR-197-3p/TYMS axis can regulate the deterioration of cervical cancer cells, which lays a foundation for the molecular diagnosis and treatment of cervical cancer.
PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
Authors: Odom Gabriel J. , Colaprico Antonio , Silva Tiago C. , Chen X. Steven , Wang Lily
Published: December 2021

Recent advances in technology have made multi-omics datasets increasingly available to researchers. To leverage the wealth of information in multi-omics data, a number of integrative analysis strategies have been proposed recently. However, effectively extracting biological insights from these large, complex datasets remains challenging. In particular, matched samples with multiple types of omics data measured on each sample are often required for multi-omics analysis tools, which can significantly reduce the sample size. Another challenge is that analysis techniques such as dimension reductions, which extract association signals in high dimensional datasets by estimating a few variables that explain most of the variations in the samples, are typically applied to whole-genome data, which can be computationally demanding. Here we present pathwayMultiomics, a pathway-based approach for integrative analysis of multi-omics data with categorical, continuous, or survival outcome variables. The input of pathwayMultiomics is pathway p-values for individual omics data types, which are then integrated using a novel statistic, the MiniMax statistic, to prioritize pathways dysregulated in multiple types of omics datasets. Importantly, pathwayMultiomics is computationally efficient and does not require matched samples in multi-omics data. We performed a comprehensive simulation study to show that pathwayMultiomics significantly outperformed currently available multi-omics tools with improved power and well-controlled false-positive rates. In addition, we also analyzed real multi-omics datasets to show that pathwayMultiomics was able to recover known biology by nominating biologically meaningful pathways in complex diseases such as Alzheimer’s disease.
Genome-Wide Identification and Comparative Analysis of the ASR Gene Family in the Rosaceae and Expression Analysis of PbrASRs During Fruit Development
Authors: Zhao Biying , Yi Xianrong , Qiao Xin , Tang Yan , Xu Zhimei , Liu Shanting , Zhang Shaoling
Published: December 2021

The members of the Abscisic Acid (ABA) Stress and Ripening gene family (ASR) encode a class of plant-specific proteins with ABA/WDS domains that play important roles in fruit ripening, abiotic stress tolerance and biotic stress resistance in plants. The ASR gene family has been widely investigated in the monocotyledons and dicotyledons. Although the genome sequence is already available for eight fruit species of the Rosaceae, there is far less information about the evolutionary characteristics and the function of the ASR genes in the Rosaceae than in other plant families. Twenty-seven ASR genes were identified from species in the Rosaceae and divided into four subfamilies (I, II, III, and IV) on the basis of structural characteristics and phylogenetic analysis. Purifying selection was the primary force for ASR family gene evolution in eight Rosaceae species. qPCR experiments showed that the expression pattern of PbrASR genes from Pyrus bretschneideri was organ-specific, being mainly expressed in flower, fruit, leaf, and root. During fruit development, the mRNA abundance levels of different PbrASR genes were either down- or up-regulated, and were also induced by exogenous ABA. Furthermore, subcellular localization results showed that PbrASR proteins were mainly located in the nucleus and cytoplasm. These results provide a theoretical foundation for investigation of the evolution, expression, and functions of the ASR gene family in commercial fruit species of the Rosaceae family.