bluuebunny/crossref_metadata_2025 huggingface dataset:
Lactobacillus paracasei JY062 alleviates glucolipid metabolism disorders by adipoinsular axis and gut microbiota
Authors: Jiang Yujun , Su Yue , Ren Jing , Zhang Jingwen , Zheng Jiapeng , Zhang Yu , Man Chaoxin
Published: July 2022

High-glucose-fat diet-induced glucolipid metabolism disorder has become a global epidemic disease. Probiotic intervention is a new strategy to alleviate metabolic syndrome. The protective effect and mechanism of L. paracasei JY062 on high-glucose-fat diets mice were investigated. After 7 weeks L. paracasei JY062 intervention, the body weight of mice in the LPH group (28.07 ± 1.07 g) was significantly lower than that of HFD group (32.03 ± 0.89 g) (P < 0.05). Among three doses of JY062, 108 and 109 CFU/mL JY062 showed the strong ability to relieve blood glucose disorders, blood lipid disorders, tissue damage. LPH group had the best effect, significantly (P < 0.05) decreased the TC (40.11%), TG (42.46%), LDL-C (39.38%), leptin (54.34%), insulin (39.95%), FFA (40.68%) concentrations and increased (P < 0.05) the HDL-C (1.05 times), adiponectin (1.53 times) and GLP-1 (1.35 times) level compared to HFD group mice. JY062 could activate the APN-AMPK pathway, increase AdipoQ, AMPK GLUT-4 and PGC-1αmRNA expression, and decrease SREBP-1c, ACC and FAS mRNA expression. L. paracasei JY062 intervention decreased the relative abundance of harmful bacteria and increased the relative abundance of beneficial bacteria, restored the imbalance of gut microbiota homeostasis caused by high-glucose-fat diet. L. paracasei JY062 could also increase the content of SCFAs in the intestines, especially butyric acid.
Elastic interfacial layer enabled the high-temperature performance of lithium-ion batteries
via utilization of synthetic fluorosulfate additive
Authors: Choi Nam-Soon , Moon Hyeongyu , Nam Huibeom , Kim Min Pyeong , Lee Seung Min , Kim Hyeongjun , Jeon Min Ho , Lee Yoon-Sung , Kim Koeun , Chun Joong-Hyun , Kwak Sang Kyu , Hong Sung You
Published: July 2022

Ensuring interfacial stability of Si-containing anodes and Ni-rich cathodes is the key to achieving high-energy lithium-ion cells. Herein, we present 4-(allyloxy)phenyl fluorosulfate (APFS), a multi-functional electrolyte additive that forms a mechanical strain-adaptive solid electrolyte interphase (SEI) composed of LiF and polymeric species, and a thermally stable cathode–electrolyte interface containing S–O and S–F species. Radical copolymerization of vinylene carbonate (VC) with APFS via electrochemical initiation creates a spatially deformable polymeric SEI on the Si/C-graphite (SiG-C) anode with large volume changes during cycling. Here we show that APFS-promoted interfacial layers reduce Ni dissolution and deposition and that APFS deactivates Lewis acidic PF5, inhibiting the hydrolysis that produces unwanted HF. These results show that the combined use of VC and APFS allows capacity retention of 72.5% with a high capacity of 143.5 mAh g− 1 after 300 cycles at 45°C.
LINC00472 inhibits cell migration by enhancing intercellular adhesion and regulates H3K27ac level via interacting with P300 in Renal Clear Cell Carcinoma
Authors: Wang Songmao , Luo Cheng , Li Bing , Zhang Shikuan , Liao Weijie , Xin Qilei , Xu Naihan , Xie Weidong , Zhu Yuanchang , Zhang Ya-ou
Published: July 2022

Renal clear cell carcinoma (RCCC) is the most common type of renal cell carcinoma, which is also difficult to diagnose and easy to metastasize. Currently, there is still a lack of effective clinical diagnostic indicators and treatment targets. This study aims to find effective diagnostic markers and therapeutic targets from the perspective of noncoding RNA. In this study, we found that the expression of Long noncoding RNA LINC00472 was significantly decreased in RCCC and showed a downward trend with the progression of cancer stage. Patients with low LINC00472 expression have poor prognosis. Inhibition of LINC00472 significantly increased cell proliferation and migration, while overexpression of LINC00472 obviously inhibited cell proliferation and enhanced intercellular adhesion. Transcriptome sequencing analysis demonstrated that LINC00472 was highly correlated with extracellular matrix and cell metastasis related pathways, and the consistent results were obtained by The Cancer Genome Atlas (TCGA) data analysis. Additionally, we discovered that the integrin family protein ITGB8 is a target gene of LINC00472. Mechanistically, we identified that LINC00472 interacts with histone acetyltransferase P300 to regulate the acetylation level of H3K27 at the ITGB8 transcription start site, which is the first time to elucidate its function in the regulation of histone modification. Our analysis results illustrated that LINC00472 can be used as a potential diagnosis marker of RCCC, and our mechanism researches provide a theoretical basis for the clinical development of new and effective treatment strategies.
Chemotherapy and targeted therapy for advanced biliary tract cancers：An umbrella review
Authors: Wang Yaoqun , Wen Ningyuan , Wang Shaofeng , Nie Guilin , Tian Yuan , Lu Jiong , Li Bei
Published: July 2022

Background: Malignant tumors of the biliary system have high malignancy and strong invasiveness, and are usually found in late stages with poor prognosis. For patients with advanced biliary tract cancer, chemotherapy and targeted therapy are one of the options to improve prognosis and delay tumor progression. The purpose of this study was to comprehensively evaluate the safety and efficacy of various chemotherapy regimenfor advanced biliary carcinoma. Methods : An umbrella review method was adopted, which aims to summarize the evidence from multiple studies around a research topic. Evidence from meta analyses up to 09 April 2022 were identified using PubMed, Web of Science, the Cochrane database, as well as manual screening. Eligible studies were screened according to inclusion and exclusion criteria. This study had been registered at PROSPERO (CRD42022324548).For each eligible study, we extracted the data of general characteristics and the main findings. The methodological quality of the included studies were assessed by AMSTAR2 and the quality of evidence was evaluated by the GRADE. Results : A total of 1833 articles were searched, 14 unique articles with 94 outcomes were identified by eligibility criteria. The incidence of skin rash (RR=18.11,95%CI 5.13-63.91) and diarrhea (RR=2.48,95%CI 1.2-5.10) was higher in patients receiving gemcitabine-based chemotherapy plus targeted therapy than in patients receiving gemcitabine alone. Patients receiving gemcitabine-containing chemotherapy developed leukopenia (OR=7.17, 95%CI 1.43-36.08), anemia (OR=7.04, 95%CI 2.59-19.12), thrombocytopenia (RR=2.45, 95%CI 1.39-4.32) and neutropenia (RR=3.30, 95%CI 1.04-10.50) were significantly higher than gemcitabine-free regimens. In addition, patients receiving S-1 monotherapy had significantly better ORR (RR=2.46,95%CI 1.27-4.57) than patients receiving S-1+gemcitabine. Patients receiving fluoropyrimidine-based chemotherapy had longer OS (HR=0.83, 95%CI 0.7-0.99), higher DCR (0R=5.18, 95%CI 3.3-10.23), and higher ORR (0R=3.24, 95%CI 1.18-8.92) compared with 5-FU/LV monotherapy or supportive therapy. Surprisingly, there was also evidence that gemcitabine-based chemotherapy did not improve postoperative patients' OS (HR=0.91, 95%CI 0.74-1.12) when compared with best supportive care. Conclusions: This study comprehensively evaluated the safety and efficacy of chemotherapy or targeted therapy regimens for advanced biliary tract cancer and found 11 "moderate" or "high" levels of evidence, however, most of the evidence was still at "low" or "very low" levels. More randomized controlled studies are needed in the future to further summarize high-level evidence.
SGOL2 is a novel prognostic marker and fosters disease progression via a MAD2-mediated pathway in hepatocellular carcinoma
Authors: HU Qingqing , Liu Qiuhong , Zhao Yalei , Zhang Lingjian , Li Lanjuan
Published: July 2022

Background: Shugoshin-like protein 2 (SGOL2) is a centromeric protein that ensures the correct and orderly process of mitosis by protecting and maintaining centripetal adhesions during meiosis and mitosis. Here, we examined the potential role of SGOL2 in cancers, especially in hepatocellular carcinoma (HCC).Methods: 199 normal adjacent tissues and 202 HCC samples were collected in this study. Human HCC cells (SK-HEP-1 and HEP-3B) were employed in the present study. Immunohistochemistry, immunofluorescence, western blot, Co-Immunoprecipitation technique, and bioinformatic analysis were utilized to assess the role of SGOL2 in HCC development process.Results: Overexpression of SGOL2 predicted an unfavorable prognosis in HCC by The Cancer Genome Atlas database (TCGA), which were further validated in our two independent cohorts. Next, 47 differentially expressed genes positively related to both SGOL2 and MAD2 were identified to be associated with the cell cycle. Subsequently, we demonstrated that SGOL2 downregulation suppressed the malignant activities of HCC in vitro and in vivo. Further investigation showed that SGOL2 promoted tumor proliferation by regulating MAD2-induced cell-cycle dysregulation, which could be reversed by the MAD2 inhibitor M2I-1. Consistently, MAD2 upregulation reversed the knockdown effects of SGOL2-shRNA in HCC. Moreover, SGOL2 regulates MAD2 by directly binding with MAD2. Conclusion: SGOL2 acts as an oncogene in HCC cells by directly regulating MAD2 and then dysregulating the cell cycle, providing a potential therapeutic target in HCC.
Evolutionary differentiation of androgen receptor ohnologs is responsible for the development of androgen-dependent unique sexual characteristics in a teleost fish
Authors: Ogino Yukiko , Ansai Satoshi , Watanabe Eiji , Yasugi Masaki , Katayama Yukitoshi , Sakamoto Hirotaka , Okamoto Keigo , Okubo Kataaki , Yamamoto Yasuhiro , HARA Ikuyo , Yamazaki Touko , Kato Ai , Kamei Yasuhiro , Naruse Kiyoshi , Ohta Kohei , Ogino Hajime , Sakamoto Tatsuya , Miyagawa Shinichi , SATO TOMOMI , Yamada Gen , Baker Michael , Iguchi Taisen
Published: July 2022

Teleost fishes exhibit complex unique sexual characteristics, such as fin enlargement and courtship display, in response to androgens. However, the molecular mechanisms underlying their evolutionary acquisition remain largely unknown. To address this question, we analysed medaka (Oryzias latipes) mutants deficient in androgen receptor ohnologs (ara and arb) generated by the teleost-specific whole-genome duplication event (TSGD). We discovered that both ar ohnologs are not required for spermatogenesis and appear to be functionally redundant for courtship display in males, while both copies were necessary for their reproductive success; ara was required for tooth enlargement and behavioural attractiveness, while arb for male-specific fin morphogenesis and sexual motivation. We further showed that the differences in both the transcription of the two ars, cellular localisation of their encoded proteins and their downstream genetic programs could be responsible for the phenotypic diversity between the ara and arb mutants. These findings suggest that the ar ohnologs have diverged in the teleost lineage in two different ways: First through the loss of their roles in spermatogenesis and second through the gene duplication followed by functional differentiation that has likely resolved the pleiotropic roles derived from their ancestral gene. Thus, our results provide insights into how genome duplication impacts the massive diversification of sexual characteristics in the teleost lineage.
Network pharmacology-based and molecular docking prediction of the active ingredients and mechanism of the herb pair of Huangqi and Taoren for application in ischemic brain injury
Authors: Tian Mengyin , Li shuangshuang , Liang Mengying , zang hengchang
Published: July 2022

The traditional Chinese herb pair of Huangqi (HQ) and Taoren (TR) for the treatment of ischemic brain injury (IBI). However, the mechanism of action of HQ and TR for treating IBI still remains unclear. Network pharmacology was adopted to detect the active components of DL and TR. The key targets and signaling pathways in the treatment of IBI were predicted, and the key ingredients and targets were screened for molecular docking. In this study, we identified 27 active components from the herb pair of DL and TR, predicted to act on IBI-associated targets by network pharmacology. PPI network demonstrated that 36 proteins might serve as the key targets of DL and HQ for the treatment of IBI. GO and KEGG pathway enrichment analyzes indicated that the effects of DL and HQ are mediated by genes related to inflammation and apoptosis as well as the HIF-1α, lipid and atherosclerosis pathways. We also had transcription factors and miRNAs analysis of hub genes. Molecular docking revealed good binding ability between the active compounds and screened targets. We comprehensively illustrated the active ingredients, potential targets, and molecular mechanism of the herb pair of HQ and TR treat IBI.
Influence of genetic ancestry on breast stromal cells provides biologic basis for increased incidence of metaplastic breast cancer in women of African descent
Authors: Kumar Brijesh , Batic Katie , Bhat-Nakshatri Poornima , Granatir Maggie , Addison Rebekah , Szymanski Megan , Baldridge Lee Ann , Temm Constance , Sandusky George , Althouse Sandra , Storniolo Anna Maria V. , Nakshatri Harikrishna
Published: July 2022

The biologic basis of genetic ancestry-dependent variability in disease incidence and outcome is just beginning to be explored. We recently reported enrichment of a population of ZEB1-expressing cells located adjacent to the ductal epithelial cells in the normal breast of women of African Ancestry (AA) compared to European Ancestry (EA). By establishing and characterizing cell lines corresponding to these cells and validating in vitro findings with tissue microarrays of healthy breast tissue from AA, EA and Latina Ancestry (LA) women, we demonstrate that these cells have the properties of fibroadipogenic/mesenchymal stromal cells that express PROCR and PDGFRa. PROCR+/ZEB1+/PDGFRa+ cells, hence renamed as PZP cells, are enriched in the normal breast tissues of AA compared to EA or LA women. In vitro, PZP cells trans-differentiated into adipocytes or osteocytes. In co-culture conditions, PZP:epithelial cell communication resulted in luminal epithelial cells acquiring basal/stem cell characteristics and increased expression of IL-6 suggesting the impact of this communication on breast epithelial hierarchy and the microenvironment. Consistent with this possibility, the level of phosphoSTAT3, which is a downstream target of IL-6, was higher in the normal and cancerous breast tissues of AA compared to EA women. PZP cells transformed with HRasG12V ± SV40-T/t antigens generated metaplastic carcinoma in NSG mice suggesting that these cells could be the cell-of-origin of metaplastic breast cancers. Collectively, these results identify a stromal cell component that could influence the biology of breast cancer in AA women.
Analysis of Microbial Community Structure, and Environmental Factors in the Rhizosphere of Malus sieversii (Ldb.) Roem. in Different Regions of Xinjiang
Authors: Jiao Huiying , Wang Ruizhe , Liu Liqiang , Zhang Bo , Qin Wei
Published: July 2022

Malus sieversii (Ldb.) Roem., the original species of modern cultivated apples, is a national essential protected plant in China. Due to soil nutrient loss, grazing, climate change, and diseases and insect pest outbreaks, the rhizosphere microecological imbalance of wild apple forests has aggravated the degradation and death of wild apples in recent years. So far, the structural diversity, function, and response to environmental drivers of the wild apple rhizosphere microbial community are not unclear. 16S/18S rDNA high-throughput sequencing were used in this study to analyze the rhizosphere bacterial and eukaryotic communities of M. sieversii (Ldb.) Roem. in eight regions of the Ili River. The results indicated that the bacterial operational taxonomic units (OTUs), Shannon value, and community composition were significantly lower in regions A, E, and F than in other regions. However, the composition of dominant eukaryotic communities in the eight regions was relatively similar, and the difference was smaller than the relative abundance of bacterial communities. Through redundancy analysis, it was found that Acidobacteriota, Verrucomicrobiota, Planctomycetota, Chloroflexi, and Methylomirabilota microbial communities with a lower relative abundance in regions A, B, E, and F, was affected by soil pH, alkaline-hydrolyzable nitrogen (AN), available phosphorus (AP), and potassium (AK), altitude, and relative humidity (RH). The results showed that the relative abundance of microorganisms in regions A, B, E, and F could be increased by rationally increasing soil nutrients.
EBV promotes tumorigenicity and worsens the prognosis of Hodgkin lymphoma through the expression of survival enhancing proteins by activating the JAK / STAT and NF-kB signaling pathways. (A comparative study between EBV positive and negative Hodgkin lymphoma)
Authors: Alabiad Mohamed Ali , Balata Rawda , A Mahmoud Asmaa , Metwally Elsayed Anany , Shalaby Amany , Samy Walaa , Yehia Ahmed M M. , Said Warda M. M. , Khairy Dina Ahmed , Yahia Amar Ibrahim Omar , Abdelrahman Doaa
Published: July 2022

Background
Epstein-Barr virus (EBV) is involved in 40% of all Hodgkin's lymphoma (HL) cases. EBV produces epigenetic alterations in the host genome that decrease the expression of proapoptotic proteins and activate the expression of survival immortalization genes.
Methods
According to EBNA-1 detection by nested PCR, 64 patients with HL were classified into two groups: EBV positive and negative HL. The expression levels of JAK/STAT and NF-kB pathway mRNA molecules (JAK2, STAT1, IRF-1, PD-L1, IFN-, NFkB, Bcl-xL, and COX-2) by both RT-PCR and qRT-PCR, and the results proteins PD-L1, Bcl-xL, and COX-2 by immunohistochemistry were analyzed and correlated with each other,
Results
Positive mRNA expression of either (JAK/STAT) or (NF-kB) pathways: (JAK2, STAT1, IRF-1, and PD-L1) and (IFN-, NFkB, Bcl-xL, COX-2) respectively are highly significantly correlated with each other (p 0.001) and with EBV positive HL patients (p 0.001). EBV positive HL cases had a higher incidence of relapse (p = 0.008), poor DFS (p = 0.013), higher mortality (p = 0.015), and low OS rates (p 0.028)
Conclusion
EBV in HL promotes the expression of survival immortalization signals by activating the JAK/STAT and NF-kB pathways and is associated with poor clinicopathological criteria, a higher incidence of disease progression, relapse, and poor overall survival. Therefore, targeting the JAK/STAT and NF-kB pathway members could be valuable in the management of EBV-associated Hodgkin's Lymphoma cases.
Clinical research stakeholders’ experiences of clinical research during COVID-19: A qualitative study
Authors: FitzGerald Christine , Witts Aoife Vaughan , Barry Louise , Corey Gillian , Leahy Fiona , Egan Siobhan , Conway Elaine , O'Connor Margaret , Galvin Rose
Published: July 2022

Background
The COVID-19 pandemic created a complex high-risk clinical research environment with clinical research activities significantly impacted. Clinical research stakeholders were required to rapidly adapt to new clinical practices; PPE, infection control policies all while engaging with a more unwell patient demographic. The aim of this study is to explore the experiences of clinical research stakeholders during COVID-19.
Methods
This qualitative study comprised of 18 semi-structured interviews conducted with clinical research stakeholders from roles across a variety of clinical settings (emergency department doctors, geriatricians, academics, clinical research nurse managers, occupational therapists, physiotherapists, social workers, dieticians, medical students and research scientists). Interviews were fully transcribed prior to thematic analysis. NVivo software was utilised to assist with data management.
Results
Through exploring the experiences of clinical research stakeholders during COVID-19, three main themes were identified 1) The challenging COVID-19 clinical research landscape, 2) COVID-19 clinical research communication barriers and 3) Adaptations and learnings from clinical research during COVID-19.
Conclusions
This study explored how COVID-19 impacted on the work of clinical research stakeholders, what challenges they faced and how they adapted to these challenges. The findings provide evidence to understand and inform clinical research to minimise disruption and to prepare for future public health events.
Opportunities and challenges in public health clinical diagnostic laboratories in Uganda: a cross sectional study
Authors: Baseke Joy , Iramiot Jacob , Charles Okalebo , Didas Atwebembere , Isabirye Linda , Oboth Paul , Olupot-Olupot Peter
Published: July 2022

Background
Optimum laboratory performance remains cardinal to definitive clinical disease diagnosis, prognosis and surveillance. In low and middle-income countries (LMICs) most public health clinical diagnostic laboratory capacity and their sustainability are at various levels of development. The objective of this study was to asses available opportunities and challenges faced by public health clinical diagnostic laboratories in Uganda so as to provide data to inform capacity building in such and similar settings.
Methods
A descriptive cross-sectional study was conducted between 10th Dec 2018 and 31 Jan 2019. All the 14 public health clinical diagnostic laboratories in Ministry of Health Regional Referral Hospital establishments in Uganda were purposively sampled. A standardized data abstraction tool was developed from the elements of ISO 15189 and 17025 laboratory standards and check list. Data were analysed using PRISM data analysis program and excel. Proportions were computed and some correlations deduced. Ethical approval was obtained before data collection commenced.
Results
Thirteen (13) of the laboratories participated in the study and their data included in the analysis. All the laboratories had: qualified laboratory staff, conducted quality improment meetings and kept laboratory records and documents. Of these, 12 (92.3%) had organizational structures endorsed by the respective hospital administration, functional basic laboratory equipment in the departments of haematology, microbiology, parasitology, clinical chemistry, Immunology and molecular biology. All the laboratories were government supported and offered free diagnostic services while 11 (84.6%) offerd surrveilance services. Eight (61.5%) laboratories were licenced by Allied Health Professionals, twelve (92.3%) were involved in internal quality control programs, eleven (84.6%) were enrolled on External Quality assurance testing programs while one (7.7%) was fully accredited by South African National Accreditation System (SANAS). The challenges identified included; under-staffing 10 (76.9% ), insufficient infrastructure 1 (7.7%), supplies stock-outs 3 (23.1%), inadequate equipment 2 (15.4%) and hard copy laboratory results. Additionally, they lacked independent budgets, finance management and autonomous financing.
Conclusion
Various challenges identified hindered public health diagnostic laboratories in Uganda to operate at full diagnostic capacity, overcoming them will standardise quality and attain equity of services across the country.
Plant-produced mouse zona pellucida 3 peptide, its immunogenicity and contraceptive efficacy
Authors: Ghasemian Khadijeh , Broer Inge , Schön Jennifer , Kolp Nadine , Killisch Richard , Huckauf Jana
Published: July 2022

Fertility control is a promising method for controlling the population of highly fertile species such as wild mice. Immunization with the mouse-specific contraceptive zona pellucida 3 peptide (mZP3) reduces fertility in some mouse strains, including wild mice. Here, we employed a plant expression system for the production of glycosylated mZP3 and evaluated the immunogenicity of plant-produced mZP3-based antigens in a female BALB/c mouse model. In the mZP3-1 antigen, mZP3 fused with a T-cell epitope of tetanus toxoid, a histidine tag and a SEKDEL sequence. A fusion antigen (GFP-mZP3-1) and a polypeptide antigen containing three repeats of mZP3 (mZP3-3) were also examined. Glycosylation of mZP3 should be achieved by targeting proteins to the endoplasmic reticulum. Agrobacterium-mediated transient expression of antigens resulted in successful production of mZP3 in Nicotiana benthamiana leaves. Compared with mZP3-1, GFP-mZP3-1 and mZP3-3 increased the production of the mZP3 peptide by more than 20 and 25 times, respectively. The glycosylation of the proteins was indicated by their size and their binding to a carbohydrate-binding protein. Both plant-produced GFP-mZP3-1 and mZP3-3 antigens were immunogenic in mice; however, mZP3-3 generated significantly higher levels of serum antibodies against mZP3. Although, as previously reported, the formation of antibodies did not lead to a significant reduction in fertility in BALB/c mice, strong and specific binding of antibodies to wild mouse zona pellucida was observed. Therefore, we assume that the plants might be an efficient system for the production of mZP3-3 as a contraceptive vaccine to reduce fertility in wild mice.
Shape-stabilized sustainable porous ethyl cellulose embedded phase change materials for thermal/light energy storage and self-luminous
Authors: Shuaib Suhaib Shuaib Adam , Niu Zixuan , Qian Zhiyi , Qi Shengyang , Yuan Weizhong
Published: July 2022

The development of phase change materials (PCMs)-based energy storage devices for both thermal and light energy has the potential to greatly enhance solar energy use efficiency, which is important in addressing the worldwide energy problem. Due to the environmentally friendly, good thermal and chemical stability, easy degradation, and good mechanical strength of ethyl cellulose (EC), it was used to fabricate the shape-stabilized composite phase change material (ss-CPCM) with polyethylene glycol (PEG). The ss-CPCMs have a high latent enthalpy (174.33 J/g), high form stability, excellent thermal regulation abilities for both thermal energy storage and thermal insulation, and great cycle thermal performance. After adding long afterglow luminescence (LAL) particles, the self-luminous ss-CPCMs were obtained. They can absorb and store visible and ultraviolet light, as well as emit green light in the dark for an extended period of time. Therefore, the self-luminous ss-CPCMs can be used in building energy conservation and smart highways.
Reduction of DNNs in edge computing
Authors: Garmendia-Orbegozo Asier , Nuñez-Gonzalez Jose David , Anton Miguel Angel
Published: July 2022

Application of Deep Neural Networks (DNN) in Edge Computing has emerged as a consequence of the need of real time and distributed response of different devices in a large number of scenarios. For this end, shredding these original structures is urgent due to the high number of parameters needed to represent them. As a consequence, the most representative components of different layers are kept in order to maintain the network's accuracy as close as possible from the entire network's ones. To do so, two different approaches have been developed in this work. First, Sparse Low Rank Method (SLR) has been applied to two different Fully Connected (FC) layers to watch their effect on the final response, and similarly the method has been applied to one of these layers. In the contrary, in this last case, the relevances of the previous FC layer's components were considered taking into account the connections to each of the components from the other FC layer, considering the relationship of relevances across layers. Experiments had been carried out in well-known architectures to conclude whether the relevances throughout layers have less effect on the final response of the network than the independent relevances intra-layer.
NMR Resonance assignment of the N-terminal GTPase Domain of human Miro2 Bound to GTP
Authors: Smith Cassandra E. , Jones David N. M.
Published: July 2022

Miro2 and Miro1 are mitochondrial-associated proteins critical for regulating mitochondrial movement within the cell. Both Miro1 and Miro2 have roles in promoting neuron function, but recently Miro2 has been shown to have additional roles in response to nutrient starvation in tumor cells. Miro1 and 2 consist of two small GTPase domains flanking a pair of EF-hands. The N-terminal GTPase (nGTPase) domain is responsible for initiating mitochondrial trafficking and interactions with GCN1 in prostate cancer. The crystal structure of Miro1 nGTPase bound to GTP has been solved. However, no structural data is available for the nGTPase domain of Miro2. To better understand the similarities and differences in the functions of Miro1 and Miro2, we have initiated structural studies of Miro2. Here we report the backbone NMR chemical shift assignments of a 22 KDa construct of the nGTPase domain of Miro2 bound to GTP that includes residues 1-180 of the full-length protein. We affirm that the overall secondary structure of this complex closely resembles that of Miro1 nGTPase bound to GTP. Minor variations in the overall structures can be attributed to crystal packing interactions in the structure of Miro1. These NMR studies will form the foundation for future work identifying the specific interaction sites between Miro2 and its cellular binding partners.
Microbiome analysis of rice rhizospheric soil in different growth stages using high-throughput amplicon sequencing of 16S rRNA genes
Authors: Baskaran Deepan , Asaithambi Killivalavan , Ananthan Anbukumaran , Selvarajan Babu , Selvam Gomathi , Pandiyan Prakash , Annamalai Panneerselvam , Dharumadurai Dhanasekaran , Varatharajan Ambikapathy
Published: July 2022

The rhizosphere of soil is inhabited by a variety of microbes. The rhizospheric microbiome contributes greatly to various aspects like growth, metabolism, and yield. There is only limited information about the composition of the microbiome during different growth stages of the rice crop. Therefore, the goal of the current study was to compare, and analyze the microbial diversity in rice rhizospheric soil among various growth phases like the vegetative phase(before initiation of Panicle), reproductive phase (minimum tillers with grains), and ripening phase (maximum filling of tillers with grains ready for harvest) by adopting next-generation high throughput amplicon sequencing of 16SrRNA gene. This study addressed 5148 OTU that includes microbes belonging to major Phylum Proteobacteria, Acidobacteria, Gemmatimonadetes, Bacteriodetes, Nitrospirae, Actinobacteria, and Chloroflexi during all growth stages of rice. Genera such as Anaeromyxobacter, Candidatus, and Kaistobacter are prevalently present in all growth stages of rice in varying degrees. Interestingly, Genera such as GOUTA19, 4-29, Sulfuricurvum, Thiobacillus, Geobacter, and Nitrospira were present maximum at the vegetative and reproductive stages of rice. Alpha & Beta diversity showed that there were variations between all the growth stages of rice. UPGMA tree revealed the evolutionary lineage of microbial communities present in the ripening stage significantly different from the other two stages of rice. The current results demonstrate that a unique group of bacteria inhabit the rice rhizosphere during three growth phases which play important roles in improving crop health and sustainable productivity.
In-situ temperature and major species measurements of sooting flames based on short-gated spontaneous Raman scattering
Authors: Meng Hu , Ren Yihua , Cameron Florence , Pitsch Heinz
Published: July 2022

Spontaneous Raman scattering is a conventional in-situ laser-diagnostic method that has been widely used for measurements of temperature and major species. However, utilization of Raman scattering in sooting flames suffers from strong interference including laser-induced fluorescence, laser-induced incandescence, and flame luminosity, which has been a challenge for a long time. This work introduces an easy-to-implement and calibration-free Raman scattering thermometry in sooting flames based on a 355-nm nanosecond pulsed laser beam. Several strategies were utilized to increase the signal-to-noise ratio and suppress the interference: (1) nanosecond intensified CCD gate width; (2) optimized intensified CCD gate delay; (3) specially designed focused laser beam; (4) ultraviolet polarizer filter. The temperature was obtained by fitting the spectral profile of Stokes Raman scattering of N2 molecules, which does not require additional calibration. Based on the measured temperature, the mole fraction of major species can be further evaluated. As a demonstration, this method was applied to measure the temperature and major species profiles in a steady ethylene-air counterflow diffusion flame. The experimental results agree well with the simulation results in both sooting and non-sooting regions, demonstrating the feasibility of this method for quantitative diagnostics of temperature and major species in multiphase reacting flows.
Korean Language Teachers’ Emotional Struggles and Language Policy Interpretations
Authors: Song Juyoung
Published: July 2022

The recent trend of the internationalization of higher education has increased the significance of English as a medium of instruction and communication on campus in non-English speaking countries. Within this context, this study explores Korean language teachers’ vulnerability over their foreign language competency, particularly English, revealed in their narratives about the Korean-only policy in the classroom. Analysis of interviews of twelve teachers of Korean as a second language (KSL) demonstrates their divergent ways of interpreting and implementing the policy according to their foreign language competency and relevant emotional vulnerability. KSL teachers with other language skills tended to challenge the monolingual policy by utilizing their bilingual skills and experiences as resources for their teaching. Monolingual KSL teachers interpreted the Korean-only policy narrowly to support a monolingual immersion approach as a way to secure their teacher authority. Regardless of their policy interpretation, however, most teachers experienced various levels of anxiety concerning their perceived lack of adequate English proficiency even in the Korean-only classrooms. The results suggest how second language teachers struggle to maintain legitimacy and authority against the hegemony of English in non-English second language contexts, providing implications for the language teacher education.
Experimental investigation of the effects of free-stream turbulence on aerodynamic characteristics of a 3D square cylinder by pressure measurement and PIV visualization
Authors: Shi Haoyun , Li Qiusheng , Li Ming , Han Xuliang
Published: July 2022

This paper investigates the effects of free-stream turbulence such as longitudinal turbulence intensity (Iu) and integral length scale (Lxu) on the flow fields around, and aerodynamic pressures and forces on a surface-mounted three-dimensional (3D) square cylinder with a height-to-width ratio of 5. The flow fields, aerodynamic pressures and forces were experimentally studied by the particle image velocimetry (PIV) visualizations and pressure measurements in grid-generated turbulent flows and smooth flow. The PIV flow visualizations show that increasing (Lxu) has limited effect on the characteristics of wake flow, except slightly weakens and intensifies the downwash and upwash flows, respectively. The influences of turbulence intensity are noteworthy. The Kármán vortices influence the flow features more significantly in turbulent flows with high intensity. The mean pressures on the side faces of the cylinder decrease as(Iu) increases, but increases on the leeward face. Increasing(Iu) and (Lxu) both enhance the fluctuating lift forces and reduce the mean drag forces at all cylinder spans. The spanwise vortex shedding of the cylinder is respectively enhanced and weakened with increasing ( Iu)and (Lxu)The strong vortex shedding occurs near the cylinder’s mid-span. The analyzed results by Proper orthogonal decomposition (POD) method show the symmetric vortex shedding process on the side faces of the 3D cylinder in smooth flow, resulting in small lift fluctuations. In turbulent flows, the vortex shedding process is symmetric near the free-end, alternating at cylinder’s lower half.
Research Status, Hotspots, and Trends on Oral Care Research in the Elderly in Mainland China Published from 2002-2022: A Bibliometric Analysis
Authors: Zhang Jingwen , Weng Yanqiu , Qiao Mengting , Chen Wenyao , Zhang Lingjuan
Published: July 2022

Background
Oral health is a key indicator of overall health, well-being and quality of life. The oral health status of the elderly will decline with age, which results in serious consequences and bring heavy medical and economic burdens to the country and society. With the aggravation of population aging process, more and more attention has been paid to the oral health problems of the elderly in mainland China, the number of studies focusing on oral care for the elderly is increasing year by year, and many research papers have been published in journals. However, no scholar has conducted bibliometric analysis in this field so far. The purpose of this study is to analyze the status, hotspots and trends of research on oral care for the elderly in mainland China in the past 20 years through bibliometrics, which aims to provide new ideas and targets for future clinical work and research.
Methods
Relevant literature from January 2002 to May 2022 were retrieved from China National Knowledge Infrastructure, Wanfang, China Science and Technology Journal Database, Web of Science, and PubMed. NoteExpress 3.5.0.9054, Co-Occurrence 12.6 and CiteSpace 6.1.R2 were used to analyze bibliometric features in terms of year of publication, journal of publication, authors, institution and keywords.
Results
A total of 716 related articles were obtained. Data analysis revealed that the number of publications shows an increasing trend over time, only 2017–2021, 309 papers were published, accounting for 43.2% of the total number of publications. A total of 238 articles were published in Science Citation Index journals or Chinese core journals, accounting for 33.2% of the total number of articles, and only a few core journals among the top 10 journals. The study of oral health-related quality of life in the elderly is a hot research topic. There is a lack of research on the elderly living in elderly care facilities.
Conclusion
The present study provides an in-depth understanding of oral care in the elderly in mainland China. The study showed the current research status, hotspots and trends of this field, and future research direction is prospected.
Software defect prediction based on counterfactual explanations
Authors: Zheng Wei , Chen Tengfei , Hu Meiting , Yang Fengyu , Fan Xin , Xiao Peng
Published: July 2022

Software defect prediction is critical to ensure the software quality. Researchers have worked on building various defect prediction models to improve the performance of defect prediction. The existing defect prediction models are mainly divided into two categories: one is the models constructed based on the artificial statistical features and the other is the models constructed based on the semantic features. DP-CNN [29] is one of the best defect prediction models, because it combines both the artificial statistical features and semantic features, so its performance is greatly improved compared with traditional defect prediction models. In this paper, we are inspired by the DP-CNN model and make the following two improvements: firstly, we use a new network representation technique Struc2vec to mine the information existing between software modules, which specializes in learning node representations from structural identity and can further extract the structural features associated with defects. We let the DP-CNN model again incorporate the newly mined structural features. Then, we propose a feature selection method based on counterfactual explanations which preserves reasonable causal relationships between features and thus produces a better subset of features compared to traditional feature selection methods. We used it to optimize the artificial statistical features inside the DP-CNN model. Based on the above methods, we propose a new hybrid defect prediction model DPS-CNN-STR. We evaluate our model on six open-source projects in terms of F1-score in defect prediction. The experimental results show that DPS-CNN-STR improves the state-of-the-art method by 3.6% on average.
Study of Soft story response of typical building of NBC
Authors: Gwachha Jeevan
Published: July 2022

Construction of building omitting an infill wall mostly in ground floor and other floors has led a building to face a soft story failure mechanism. This omission of infill wall is for commercial purposes and parking of vehicles in ground floor. In this study, study on the behavior of the structure is done when a soft story happens in different floor levels. A building explained as per NBC 201 and NBC 205 is taken into consideration. Soft story is assigned in all floors to study the responses separately. An equivalent diagonal strut is assigned to the structure to account the consideration of infill wall. Non-linear hinges are assigned to structural members. Different parametric study is performed in terms of displacement, story drift, time period, formation of hinges, performance point, and capacity curve to compare the behavior of the structure. Linear static and non-linear static (Pushover analysis) analysis is performed to evaluate 4 different models. Modal analysis is performed to obtain time period of different models. The time period of bare frame, ground floor soft story, first floor soft story and second floor soft story using modal analysis is 0.65, 0.49, 0.47 and 0.29 respectively. Pushover analysis is performed to obtain pushover curve of different models forming different non-linear hinges in multiple steps of analysis. Step 1, 4, 7 and 10 were analyzed and hinges from basic to collapse prevention has formed. Story drift of bare frame of all story has been compared to the story drift of buildings having soft story in ground, first and second floor. Comparing variation of story drift for ground, first and second floor between bare frame and ground floor soft story model, the values show 13%, 82% and 85%. The variation of same between bare frame and first floor soft story shows 78%, 20%, 81% while the variation between bare frame and second floor soft story shows 97%, 97%, 21%.Additional, a multiplication factor has been introduced to compare the value of factor provided by IS 1893:2002. According to IS 1893:2002, the value should have been 2.5, but the value varies for 3 different cases. It varies from 1 to 1.16.
Immune landscape of a prognostic immunogenic cell death (ICD)-related long noncoding RNAs (lncRNAs) signature in colon adenocarcinoma (COAD)
Authors: Liu Xia , Fang Xisheng , Lu Lin , Liu Guolong
Published: July 2022

Background
Immunogenic cell death (ICD), as a form of regulated cell death, demonstrates promising roles in immunogenic tumor microenvironment. However, the expression and roles of ICD-related long noncoding RNAs (lncRNAs) in COAD were largely unknown.
Methods
RNA-sequencing data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A list of 34 immunogenic cell death-related genes was retrieved from published literatures. ICD-related lncRNAs were retrieved using R language and Perl software. Univariate and multivariate cox analyses were used to construct an ICD-related lncRNA risk model. The performance of thissignature was validated using Kaplan-Meier curve and receiver operating curve (ROC). The immune landscape of the risk signature was revealed by analyzing the correlations with immune cells infiltration, immune function, immune checkpoint inhibitors. Correlations with RNA stemness score (RNAss) were analyzed using Spearman correlation coefficient. Correlation with m6A regulators was investigated using Wilcoxon test. Moreover, expression and survival analysis of the risk lncRNAs were revealed based on TCGA database.
Results
We identified 23 ICD-related lncRNAs with prognostic values to construct a risk model. The risk model demonstrated good performance in predicting survival. The area under curve (AUC) of the ROC curve at 1-, 2- and 3-year were 0.684, 0.715, and 0.747, respectively. Further univariate and multivariate analysis showed that the risk score was an independent prognosis factor. Further validation showed that there were significant differences in immune cells infiltration, immune functions, and immune checkpoint inhibitor expression between high- and low-risk groups. In addition, there was negative correlation between the risk signature and RNAss, and there was difference in the expression of m6A regulators in high- and low-risk groups. A nomogram including the risk score also demonstrating significant prognostic value. Moreover, upregulated expression of MIR4435-2HG, LINC02257, AL161729.4, AC007128.1 and AP001619.1 predicted poor overall survival in COAD.
Conclusions
We established an ICD-related lncRNA signature for the overall survival of COAD, which demonstrating high sensitivity and specificity. The correlations between ICD-related lncRNAs and tumor immune microenvironment still need to be further investigated.
Genome Insights into the Plant Growth-Promoting bacterium Saccharibacillus brassicae ATSA2T
Authors: Jiang Lingmin , Seo Jiyoon , Peng Yuxin , Jeon Doeun , Park Soon Ju , Kim Cha Young , Kim Pyoung Il , Kim Chul Hong , Lee Ju Huck , Lee Jiyoung
Published: July 2022

Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass and chlorophyll contents following strain ATSA2T treatment. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.