bluuebunny/crossref_metadata_2025 huggingface dataset:
Trans-apical Aortic Valve Implantation for Quadricuspid Aortic Valve With Aortic Regurgitation Using J-valve System: A Case Report
Authors: Luo Chaodi , Jiang Yi , Yan Yang , Han Dan
Published: May 2021

Background: Quadricuspid aortic valve (QAV) is a rare congenital heart defect usually accompanied with different hemodynamic abnormalities. Due to the rarity of QAV, treatment and prognosis of QAV patients with aortic regurgitation still remain challenging. We here present the first case of a patient with severe QAV regurgitation who underwent successful treatment and performed favorable prognosis with transapical aortic valve implantation (TAVI) using J-Valve system.Case presentation: A 62-year-old man experienced intermittent palpitation, shortness of breath and chest pain. Echocardiography revealed congenital QAV with massive aortic regurgitation and mild aortic stenosis, left ventricular enlargement. Aortic valve replacement was successfully performed with TAVI using J-Valve system. The postoperation and follow-up was uneventful.Conclusion: Transapical aortic valve implantation (TAVI) using J-Valve system has emerged as a new high success rate method for treatment of high-risk patients with simple non-calcified aortic valve insufficiency.
Clinical characteristics and outcomes of neonates with polymicrobial ventilator-associated pneumonia in the intensive care unit
Authors: Wang Hsiao-Chin , Tsai Ming-Horng , Chu Shih-Ming , Liao Chen-Chu , Lai Mei-Yin , Chiang Ming-Chou , Fu Ren-Huei , Hsu Jen-Fu , Huang Hsuan-Rong
Published: May 2021

Background: Ventilator associated pneumonia (VAP) caused by more than one microorganisms is not uncommon and may be potentially challenging, but the relevant data is scarce in ventilated neonates. We aimed to investigate the clinical characteristics and outcomes of polymicrobial VAP in the neonatal intensive care unit (NICU).Methods: All neonates with definite diagnosis of VAP from a tertiary level neonatal intensive care unit (NICU) in Taiwan between October 2017 and September 2020 were prospectively observed and enrolled for analyses. All clinical features, therapeutic interventions and outcomes were compared between the polymicrobial VAP and monomicrobial VAP episodes. Multivariate regression analyses were used to find the independent risk factors for treatment failure. Results: Among 236 episodes of neonatal VAP, 60 (25.4%) were caused by more than one microorganisms. Polymicrobial VAP episodes were more likely to be associated with multidrug-resistant pathogens (53.3% versus 34.7%, P = 0.014), more often occurred in later days of life and in neonates with prolonged intubation and underlying bronchopulmonary dysplasia. Otherwise most clinical characteristics of polymicrobial VAP were similar to those of monomicrobial VAP. The therapeutic responses and treatment outcomes were also comparable between these two groups, although modification of therapeutic antibiotics were significantly more common in polymicrobial VAP episodes than monomicrobial VAP episodes (63.3% versus 46.2%; P<0.001). None of any specific pathogens was significantly associated with worse outcomes. Instead, it is the severity of illness, including presence of concurrent bacteremia, septic shock, and requirement of high-frequency oscillatory ventilator and underlying neurological sequelae that are independently associated with treatment failure.Conclusions: Polymicrobial VAP accounted for 25.4% of all neonatal VAP in the NICU, and frequently occurred in neonates with prolonged intubation and underlying bronchopulmonary dysplasia. In our cohort, most clinical features, therapeutic responses and final outcomes of neonates with monomicrobial and polymicrobial VAP did not differ significantly.
Bio-mimetic synthesis of catalytically active nano-silver using Bos taurus (A-2) urine
Authors: Sarvalkar Prashant D , Mandavkar Rutuja R , Nimbalkar Mansingraj S , Sharma Kiran K , Patil Pramod S , Prasad Neeraj R , Kamble Ganesh S
Published: May 2021

Bio-molecules present in liquid metabolic waste of an Indian cow are effectively used to reduce silver (Ag) ions into Ag nanoparticles (Ag NPs) in one step. This bio-inspired electron transfer to Ag ion for the formation of base Ag metal is fairly prompt and facile. These nanoparticles act as a positive catalyst for various organic transformation reactions. The X-RD pattern of the synthesized product confirmed the formation of Ag nanoparticles. The bio-mimetic Ag NPs show potential activity for degradation of dyes under study. Herein, we have successfully carried out several reduction reactions of nitro groups using Ag nanoparticles as a heterogeneous nanocatalyst.
Prognostic Significance of NBEAL2 in Liver hepatocellular carcinoma
Authors: Wen Yanghui , Su Hui , Wang Wuke , Ren Feng , Jiang Haitao , Wang Jie , Xiang Jianjian , Chen Yunjie
Published: May 2021

Background: NBEAL2 is a member of the BEACH domain–containing protein (BDCP) family and little is known about the relationship between NBEAL2 and malignancy.Methods: We downloaded the Gene expression profiles and clinical data of Liver hepatocellular carcinoma(LIHC) form the Cancer Genome Atlas (TCGA) dataset. The expression difference of NBEAL2 in LIHC tissues and adjacent nontumor tissues was analyzed by R software. The relationship between NBEAL2 expression and clinicopathological parameters was evaluate by Chi-square test. The effect of NBEAL2 expression on survival were assessed by Kaplan–Meier survival analysis and Cox proportional hazards regression model. GSEA was used to explore the potential molecular mechanism of NBEAL2 in LIHC.Results: Up-regulation of NBEAL2 expression was detected in the LIHC tissue compared with adjacent nontumor tissues(P < 0.001). The chi-square test showed that no significant correlation between the expression level of NBEAL2 and various clinicopathological parameters (including T, N and M classifications) were detected. The Kaplan–Meier curves suggested that lower NBEAL2 expression was related with poor prognosis. The results of Multivariate analysis revealed that a lower expression of NBEAL2 in LIHC was an independent risk of poor overall survival (HR, 8.873; 95% CI, 1.159-67.936; P = 0.035). GSEA suggested that multiple tumor-related metabolic pathways were evidently enriched in samples with the low-NBEAL2 expression phenotype. Conlusion: NBEAL2 might act as an tumor suppressor gene in the progression of LIHC but the precise role of NBELA2 in LIHC needs further vertification.
Identification of Tumor Microenvironment-Related Genes in Kidney Renal Clear Cell Carcinoma Patients via Bioinformatic Analysis
Authors: Zheng Rongjiong , SHao Yaosen , Wang Mingming , Tang Yeli , Hu Meiling
Published: May 2021

BackgroundTumor microenvironment has been implicated in the development and progression of cancers. However, the prognostic significance of tumor microenvironment-related genes in kidney renal clear cell carcinoma (KIRC) remains unclear. MethodsIn this study, we obtained and analyzed gene expression profiles from The Cancer Genome Atlas database. Stromal and immune scores were calculated based on the ESTIMATE algorithm. ResultsIn the discovery series of 537 patients, we identified a list of differentially expressed genes which was significantly associated with prognosis in KIRC patients. Protein-protein interaction networks and functional enrichment analysis were both performed, indicating that these identified genes were related to the immune response. ConclusionsThe tumor microenvironment-related genes could serve as the potential biomarkers for KIRC.
Laparoscopic Hepatectomy for Mucinous Cystic Neoplasm of the liver: A Case Series of Six
Authors: Chen Yizhen , Xu Youyao , Zhang Yuhua , Han Fang , Wu Jia
Published: May 2021

BackgroundMucinous Cystic Neoplasm of the liver (MCN-L) is considered as a benign disease, but it has the possibility of malignant transformation. The advantages of minimally invasive surgery can alleviate the anxiety of patients with benign diseases. The purpose of this study is to determine the feasibility and safety of laparoscopic hepatectomy (LH) for patients with Mucinous Cystic Neoplasm of the liver. MethodsAll patients who were pathologically diagnosed as MCN-L were retrospectively studied. Collect the surgical data of patients undergoing laparoscopic hepatectomy, and conduct a return visit. ResultsThere were 6 cases of LH for MCN-L. The mean operation time was 176.3 ± 20.6 min, and the intraoperative blood loss was 102.5±73.7 mL. No serious complications occurred, and the mean length of hospital stay was 5.8 ± 1.5 days. During the median follow-up time of 30.5 months, no recurrence occurred. ConclusionsLH for MCN-L is feasible and safe. The treatment principle of laparoscopic surgery for MCN-L should be consistent with laparotomy.
Evaluating the national implementation of Bright IDEAS in clinical settings: applying the RE-AIM framework to characterize the clinical perspective
Authors: McNeal Demetria , Sahler O.J. , Noll Robert B. , Fairclough Diane L. , Voll Megan E. , Bhat Shubha , Morrato Elaine H.
Published: May 2021

Background Bright IDEAS: Problem-Solving Skills Training (Bright IDEAS), a psychosocial intervention, has shown to improve problem-solving skills and reduce emotional distress in caregivers of children recently diagnosed with cancer. Though efforts have been made to scale up cancer control interventions, there are limited data assessing the adoption of Evidence-Based Cancer Control Programs (EBCCP) into clinical practice. This study describes the barriers and facilitators to implementation experienced by practitioners trained to use Bright IDEAS in their clinical settings.Methods A total of 209 Pediatric psychosocial oncology practitioners were trained through 10 workshops. Adaptations were made to the training agenda and curriculum based on practitioner feedback following implementation in local institutions. Practitioners were interviewed to understand their training experience and gain their perspective on the effectiveness of delivering Bright IDEAS in the clinical setting. The RE-AIM framework was used to guide the evaluation process we employed to assess the effectiveness of this national effort to disseminate Bright IDEAS.Results Interviews were conducted with 47 practitioners. Practitioners in the pre-adaptation group reported the identification of a particular profile of a client as a facilitator to intervention use. Additionally, perceived rigidity of the protocol, lack of consistency in intervention use with clients, feelings of being overwhelmed by the client as rationale for lack of interest, and lack of multiple trained practitioners at institutions were identified as barriers to intervention use. Practitioners in the post-adaptation group reported similar identification of a profile for an appropriate client for the intervention, more usage of Bright IDEAS materials, implementation across multiple clinical settings, and expressed continued commitment to intervention use as well as discussion of internal training for colleagues.Conclusions This study provides insight into how psychosocial practitioners adopt, implement, and maintain Bright IDEAS in the clinical setting and identified important considerations and needs for both practitioners and larger health care systems. It also provides some cautions to those who wish to promulgate evidence-based interventions.
Effects of Institutional Framework Lapses in Solid Waste Management; Case of Ngomongo, Nairobi, Kenya
Authors: Kathambi Bessy , Ogutu Florence Akinyi
Published: May 2021

Institutional frameworks serve as vehicles for proper solid waste management. Lapses in institutional structures create ecological disasters that affect public health and environmental degradation. Municipal solid waste management is a critical subject worldwide, and removal and control of municipal solid waste remain a global task, specifically in developing countries. The case of Ngomongo illustrates lapses in waste institutions in Nairobi City. The research design for the study used a mixed-method where primary data was collected using transect walk, questionnaires with 385 households administered, and satellite images. Focus group discussions and key informant interviews used to ensure the validity and reliability of the data. The results show the lapses that exist in institutional frameworks in Nairobi City as supported by the objective of the study. The effects demonstrated by the doubled number of mini-landfills, open waste sites on the roadside over the decade.
Elevated coinhibitory molecule TIGIT mediates T cell exhaustion in septic patients
Authors: Sun Yini , Ding Renyu , Chang Yukun , Li Jiuming , Ma Xiaochun
Published: May 2021

Background: Sepsis-induced T cell exhaustion that is characterized by upregulated coinhibitory molecules and decreased cytokines release plays a crucial role in the immunosuppression during sepsis. Although PD-1 has shown a promising target to interfere with T cells dysfunction, the role of other coinhibitory receptors in sepsis remains largely elusive. Recently, it has been demonstrated that the coinhibitory molecule TIGIT more reliably identified exhausted T cells than PD-1. The aim of the study was to identify the expression of TIGIT on lymphocytes and the crucial role of TIGIT in modulating T cell function in septic patients. Methods: Twenty-five patients with sepsis and seventeen healthy controls were prospectively enrolled. Peripheral blood was obtained from septic patients within 24 hours after diagnosis of sepsis, as were healthy controls. TIGIT and other coinhibitory/costimulatory molecules expression on lymphocyte subsets was quantitated by flow cytometry. The relationship between TIGIT expression and clinical parameters was simultaneously evaluated. The function T cell from septic patients was assayed via stimulated cytokine secretion. Ex vivo functional assays were also conducted.Results: In the early stage of sepsis, patients exhibited higher levels of TIGIT on T cells relative to healthy donors, especially in the septic shock patients. Elevated frequencies of TIGIT + T cells positively correlated with the severity of organ failure and inflammatory responses in septic patients. TIGIT + T cells expressed higher levels of PD-1 and lower CD226. Further, elevated expression of TIGIT inhibited the release of cytokines including TNF, IFN-γ and IL-2 by CD4 + and CD8 + T cells. Strikingly, ex vivo blockade of TIGIT using anti-TIGIT antibody restored the frequencies of cytokine-producing T cells. Conclusions: These data illustrate TIGIT as a novel marker of exhausted T cells and suggest TIGIT may be a novel immunotherapeutic target during sepsis.
Spectrum of CECT Findings of Retained And Migrated Surgical Items In Abdomen – A Series of Seven Cases.
Authors: Kumar Ishan , Sharma Srishti , Sinha Anindita , Verma Ashish
Published: May 2021

Background: Various retained surgical items often present a diagnostic dilemma to the interpreting radiologist. These items include retained surgical sponge (gossypiboma), misplaced, migrated catheters, broken instruments, irrigation sets, and a variety of surgical paraphernalia. Such foreign bodies present with varying imaging findings and can often mimic other diseases radiologically.Case presentations: We present a series of seven interesting cases of retained surgical mops (case 1, 2 and 3), broken and retained surgical instrument (case 4), migrated plastic biliary stent (case 5), migrated contraceptive device (case 6) and surgically placed hemostatic agent (case 7)Conclusions: Familiarity with the variable imaging findings and communication with the clinician can facilitate timely management for these patients.
Evaluation of A Chemiluminescent Enzyme Immunoassay-Based High-Throughput SARS-CoV-2 Antigen Assay For The Diagnosis of COVID-19: The VITROS® SARS-CoV-2 Antigen Test
Authors: Matsuzaki Nanako , Orihara Yuta , Kodana Masahiro , Kitagawa Yutaro , Matsuoka Masaru , Kawamura Rieko , Takeuchi Shinichi , Imai Kazuo , Tarumoto Norihito , Maesaki Shigefumi , Takuya Maeda
Published: May 2021

A high-throughput, fully automated antigen detection test for SARS-CoV-2 is a viable alternative to reverse transcription polymerase chain reaction (RT-qPCR) for mass screening during outbreaks. In this study, we compared RT-qPCR for viral load and the VITROS® SARS-CoV-2 Antigen Test with reference to the results of the LUMIPULSE® SARS-CoV-2 Ag Test. Of 128 nasopharyngeal swab specimens taken from patients suspected of being infected with SARS-CoV-2, 49 were positive and 79 were negative according to RT-qPCR. Consistent dose-dependent detection with VITROS® assay was successfully achieved when using nasopharyngeal swab specimens with Ct values of ≤32.0, whereas the CLEIA-based the LUMIPULSE® assay was able to detect lower viral loads compared with the VITROS® assay. Our results show that the performance of the VITROS® assay was satisfactory for the diagnosis of contagious COVID-19 patients in the clinical setting.
Restrictive versus liberal red cell transfusion strategies in patients with acute myocardial infarction: a systematic review and meta-analysis
Authors: Liu Yuanhui , Zhang Yeshen , Huang Yuming , Xie Nianjin , Zeng Lihuan , Lian Xingji , Lin Jijin , Dai Yining , Chen Jiyan , He Pengcheng , Tan Ning
Published: May 2021

BackgroundAnemia is frequent in patients with acute myocardial infarction(AMI), and the optimal red blood cell transfusion strategy for patients with AMI and anemia is still controversial. We aimed to compare the efficacy of restrictive and liberal red cell transfusion strategies in patients with AMI and anemia.MethodsWe systematically searched PubMed, EMBASE, Web of Science, Cochrane Library, and Clinicaltrials.gov, from their inception until March 2021. Inclusion criteria were clinical trials that compared the efficacy of restrictive and liberal transfusion strategies in patients with AMI and anemia on all-cause mortality and major adverse cardiovascular events. The primary outcome was all-cause mortality, including overall mortality, in-hospital, or follow-up mortality. Risk ratios (RR) with 95% confidence intervals (CI) were presented and pooled by random-effects models. ResultsThe search yielded a total of 6630 participants in six studies. Among the included patients, the average age ranged from 69.0 to 79.5 years and 2950 (44.5%) were men. A total of 2008 patients received restrictive red blood transfusion while 4622 patients were given liberal red blood transfusion. No difference was found in overall mortality and follow-up mortality between restrictive and liberal blood transfusion groups (RR=1.07, 95% CI=0.82–1.40, P=0.62; RR=0.89, 95% CI=0.56–1.42, P=0.62). However, restrictive transfusion was associated with a higher risk of in-hospital mortality compared with liberal transfusion (RR=1.22, 95% CI=1.00–1.50, P=0.05). No secondary outcomes, including follow-up reinfarction, stroke, and acute heart failure, differed significantly between the two groups. In addition, subgroup analysis showed no differences in overall mortality between the two groups based on sample size and design.ConclusionRestrictive and liberal red blood transfusion have a similar effect on overall mortality and follow-up mortality in patients with AMI and anemia. However, restrictive transfusion was associated with a higher risk of in-hospital mortality compared with liberal transfusion. The findings suggest that transfusion strategy should be evaluated in the more future researches.
EGR1 Modulated LncRNA HNF1A-AS1 Drives Glioblastoma Progression Via miR-22-3p/ENO1 Axis
Authors: Ma Chunchun , Wang Hongliang , Zong Gang , He Jie , Wang Yuyang , Yang Fan , Yang Zhihao , Bian Erbao , Zhao Bing
Published: May 2021

Background: Accumulating evidences revealed that long noncoding RNAs (lncRNAs) have been participated in cancer malignant progression, including glioblastoma multiforme (GBM). Despite much studies have found the precise biological role in the regulatory mechanisms of GBM，however the molecular mechanisms，particularly upstream mechanisms still need further elucidated. Methods: RT-QPCR, cell transfection, western blotting and bioinformatic analysis were executed to detect the expression of EGR1, HNF1A-AS1, miR-22-3p and ENO1 in GBM. Cell proliferation assay, colony formation assay, wound healing, migration and invasion assays were performed to detect the malignant characters of GBM cell. The molecular regulation mechanism was confirmed by luciferase reporter assay, ChIP and RIP. Finally, orthotopic mouse models were established to examine the effect of HNF1A-AS1 in vivo.Results: In the current study, we analyzed clinical samples to show that the long non-coding antisense transcript of HNF1A, HNF1A-AS1, is upregulated and associated with poor prognosis in GBM. Functional studies revealed that knockdown of HNF1A-AS1 markedly inhibits cell proliferation, migration and invasion both in vitro and in vivo, whereas overexpression of HNF1A-AS1 exerts opposite effect. Mechanistically, the transcription factor EGR1 forced the transcription of HNF1A-AS1 by directly binding the promoter region of HNF1A-AS1. Furthermore, combined bioinformatics analysis with our mechanistic work, using luciferase reporter assays and RIP, we first demonstrated that HNF1A-AS1 functions as a competing endogenous RNA (ceRNA) with miR-22-3p to regulate ENO1 expression in GBM cells. HNF1A-AS1 directly binds to miR-22-3p and significantly inhibits miR-22-3p expression, while ENO1 expression was increased. miR-22-3p inhibitor offsets the HNF1A-AS1 silencing induced suppression in proliferation, migration and invasion of GBM cells, as well as promotion effect on ENO1 expression. ENO1 was verified as a direct target of miR-22-3p and its expression levels was negatively with the prognosis in GBM patients. Conclusion: Taken together, our study illuminated the definite mechanism of HNF1A-AS1 in promoting GBM malignancy, and provided a novel therapeutic target for further clinical application.
Germplasm Characterization and Flowering, Fruiting Nature of Burmese Grape (Baccaurea Sapida Muell. Arg.) –a Potential Fruit Crop for Nutrition in Rural South East Asia
Authors: BHOWMICK NILESH , Pradhan Saurabh
Published: May 2021

Burmese grape (Baccaurea sapida Muell. Arg.) belongs to the family Euphorbiaceae, is a minor underexploited fruit crop grown wild as well as under cultivation in Nepal, India, Myanmar, Bangladesh, China, Thailand, for fresh consumption. It is a dioecious plant and reported to have an excellent nutritive value, but mainly grown in homestead condition mostly in neglected ways without fullest utilization of its potentiality. The present study was aimed to understand and first time characterize the germplasm nature, and details of flowering and fruiting system of Burmese grape. The experiment showed that, tree growth habit and crown shape of all the accessions surveyed were semi erect and irregular, respectively. The flower bud differentiation in male and female accessions started during the mid February and anthesis occurred from mid March for both male and female accessions. The colour of the male flowers varied from yellow to green yellow shades while the colour of the female flowers varied from yellow to yellow green and green yellow shades. Significant variation of leaf area, number of flowers per panicle, length and diameter of inflorescence, fruit length, breadth, weight etc. were observed. The variation present on fruit length (2.81 cm to 3.80 cm), fruit weight (12.25g to 22.95g), pulp percentage (49.82% to 65.33%), total soluble solids (9.00º to 13.10ºBrix), tritable acidity (0.73mg to 1.28mg/100g fruit pulp) and ascorbic acid content ranged from (23.18mg to 57.80mg/100g fruit pulp) suggest suitable selection method for identification of promising Burmese grape genotypes.
Clival Metastases in Cancer Patients
Authors: Sturgis Rebecca , Mack Alleda , Kim Seongho , Maier Jordan , Heath Elisabeth
Published: May 2021

Purpose

This study aimed to describe clinical features, radiotherapy (RT), and symptom outcomes in cancer patients with cranial nerve palsies associated with clival metastases.
Methods

A retrospective record review for the period in between 2000 and 2020 was conducted for patients with primary metastatic cancers, who developed distal clival metastases, or were treated with RT at the Karmanos Cancer Institute (Detroit, Michigan). The patients’ demographics and clinical characteristics, including their symptoms and improvement of symptoms after RT are described.
Results

Forty-four patients were identified who met inclusion criteria. The most common primary cancers were breast cancer, prostate cancer, and multiple myeloma. Magnetic resonance images and computed tomography scans were used for the diagnosis of clival metastasis, as well as for the evaluation after RT. Thirty-two patients (73%) with clival metastases also had cervical spine metastases. Prevailing neurologic symptoms were headache, diplopia, lateral gaze paralysis, blurry vision, chin numbness, and tongue deviation. Fifteen of 23 RT-treated patients (65%) received clivus only RT, and 8 patients (35%) were given whole brain RT. Post-RT symptom improvement was observed in patients with diplopia (5/6; 83%), headache (8/10; 80%), chin numbness (2/4; 50%), blurry vision (2/5; 40%), lateral gaze deficit (2/6; 33%), and tongue deviation (1/4; 25%).
Conclusions

These results suggest that early detection and rigorous cranial nerve examination, in addition to RT treatment, should be considered in patients with breast cancer, prostate cancer, and multiple myeloma, who developed bone metastasis, especially cervical spine metastasis.
Meta-Analysis of The Association Between Gene Mutation and Tumor Spread Through Air Space in Lung Adenocarcinoma
Authors: Wang Guishi , Li Bingfu , Dingqian Zhang , He Zhenyv , Wang Tiantian , Dong Yanjun
Published: May 2021

Background A series of studies have shown that spread through air spaces (STAS) has a significant effect on surgical outcomes in patients with lung adenocarcinoma. Objectives: The aims of this study are to evaluate the association between gene mutation and STAS in lung adenocarcinoma for preoperative prediction of STAS in lung adenocarcinoma, eventually, which could help us choose appropriate surgical type. Methods The retrieval period was from 2015 to December 2020. The Newcastle-Ottawa quality assessment scale (NOS) was used for assessing the quality of each study. High-quality study was defined as those with ≥6 stars at the NOS. Statistical results were analyzed using the Stata16 statistical package. Results A total of 12 studies were included, including 4790 patients. The results of meta-analysis showed that: In patients with lung adenocarcinoma, the expression of EGFR, KRAS, BRAF, ALK and ROS1 were correlated with the occurrence of STAS, with RR values (95%CI) of 0.75 (0.63~0.90), 1.173 (1.00~1.37), 2.116 (1.17~3.84), 1.71 (1.53~1.90), 1.565 (1.35~1.82), respectively. Conclusion Mutations in KRAS, BRAF, ALK, and ROS1 increase the incidence of STAS in patients with lung adenocarcinoma. Mutations in EGFR decrease the incidence of STAS in patients with lung adenocarcinoma.
LPI-DeepGBDT: A Multiple-Layer Deep Framework based on Gradient Boosting Decision Trees for lncRNA-Protein Interaction Identification
Authors: ZhouZhou Liqian , Wang Zhao , Tian Xiongfei , Peng Lihong
Published: May 2021

Background: Long noncoding RNAs (lncRNAs) play important roles in various biological and pathological processes. Discovery of lncRNA-protein interactions (LPIs) contributes to understand the biological functions and mechanisms of lncRNAs. Although wet experiments find a few interactions between lncRNAs and proteins, experimental techniques are costly and time-consuming. Therefore, computational methods are increasingly exploited to uncover the possible associations. However, existing computational methods have several limitations. First, majority of them were measured based on one simple dataset, which may result in the prediction bias. Second, few of them are applied to identify relevant data for new lncRNAs (or proteins). Finally, they failed to utilize diverse biological information of lncRNAs and proteins. Results: Under the feed-forward deep architecture based on Gradient Boosting Decision Trees (LPI-deepGBDT), this work focuses on classify unobserved LPIs. First, three human LPI datasets and two plant LPI datasets are arranged. Second, the biological features of lncRNAs and proteins are extracted by Pyfeat and BioProt, respectively. Thirdly, the features are dimensionally reduced and concatenated as a vector to represent an lncRNA-protein pair. Finally, a deep architecture composed of the forward mappings and inverse mappings is developed to predict underlying linkages between lncRNAs and proteins. LPI-deepGBDT is compared with four classical LPI prediction models (LPI-BLS, LPI-CatBoost, PLIPCOM, and LPI-SKF) under three cross validations on lncRNAs, proteins, lncRNA-protein pairs, respectively. It obtains the best average AUC and AUPR values on the five datasets under the three cross validations, significantly outperforming other four LPI identification methods. That is, AUCs computed by LPI-deepGBDT are 0.8321, 0.6815, and 0.9073, respectively and AUPRs are 0.8095, 0.6771, and 0.8849, respectively. The results demonstrate the powerful classification ability of LPI-deepGBDT. Case study analyses show that there may be interactions between GAS5 and Q15717, RAB30-AS1 and O00425, and LINC-01572 and P35637. Conclusions: Integrating ensemble learning and hierarchical distributed representations and building a multiple-layered deep architecture, this work improves LPI prediction performance as well as effectively probes interaction data for new lncRNAs/proteins.
Assessing Biological Vulnerability of Acute Respiratory Tract Infection Among Children: Evidence from Bangladesh Demographic and Health Survey 2017-18
Authors: Rashmi Rashmi , Paul Ronak
Published: May 2021

Background: Acute respiratory tract infections (ARIs) are the leading infectious disease worldwide and continues to be the single largest morbidity contributor in children. One of the most densely populated countries, Bangladesh also threatens by alarming under-five childhood morbidity, which has aggravated in past years with the COVID-19 pandemic. This study attempts to understand the biological factors affecting the pre-existing respiratory tract infections in under 5 children of Bangladesh.Methods: The present study uses data from 8398 children aged below 5 years during the survey from the Demographic and Health Survey of Bangladesh (BDHS 2017-18). Both bivariate and multivariate analyses were performed to understand the biological vulnerability factors of pre-existing acute respiratory tract infections (ARIs) in under five Bangladeshi children and relate them with the potential impact of the COVID-19 pandemic. Further, to show effectively the effect of different risk factors on child morbidity status, we have summarized all the results into prediction graphs at various levels of one variable as the other variable changesResults: Children aged one year were 1.40 [95% CI: 1.16, 1.67] and 2.01 [95% CI: 1.70, 2.36] times more likely to experience single morbidity and comorbidity respectively compared to children aged four years. We observe that male children were 1.18 [95% CI: 1.07, 1.31] times more likely to experience comorbidity compared to their female counterparts. Prediction graphs confirm the multivariate analysis as the probability of comorbidity remains higher in the monsoon season among children, with little change in the summer and winter seasons. Further, Rajshahi administrative division followed by Barisal and Rangpur shows the highest probability of comorbid condition in Bangladesh.Conclusion: Biological factors emerged as the prominent contributor in child ARIs condition. More care is required as the nationwide lockdown due to the COVID-19 pandemic had not only isolated the people from physical communication but also disrupted the health care facilities to care for the pre-existing morbidity condition among Bangladeshi children. Insightful strategies are required to prevent infectious diseases in children right from their homes by focusing on their biological vulnerabilities.
Adaptation of the Patient Benefit Assessment Scale for Hospitalised Older Patients: Development, Reliability and Validity of the P-BAS Picture Version
Authors: Kluit Maria Johanna van der , Dijkstra Geke J. , de Rooij Sophia E.
Published: May 2021

Background: The Patient Benefit Assessment Scale for Hospitalised Older Patients (P-BAS HOP) is a tool developed to both identify the priorities of the individual patient and to measure the outcomes relevant to him/her, resulting in a Patient Benefit Index (PBI), indicating how much benefit the patient had experienced from the hospitalisation. The reliability and the validity of the P-BAS HOP appeared to be not yet satisfactory and therefore the aims of this study were to adapt the P-BAS HOP and transform it into a picture version, resulting in the P-BAS-P, and to evaluate its feasibility, reliability, validity, responsiveness and interpretability.Methods: Process of instrument development and evaluation performed among hospitalised older patients including pilot tests using Three-Step Test-Interviews (TSTI), test-retest reliability on baseline and follow-up, comparing the PBI with Intraclass Correlation Coefficient (ICC), and hypothesis testing to evaluate the construct validity. Responsiveness of individual P-BAS-P scores and the PBI with two different weighing schemes were evaluated using anchor questions. Interpretability of the PBI was evaluated with the visual anchor-based minimal important change (MIC) distribution method and computation of smallest detectable change (SDC) based on ICC.Results: Fourteen hospitalised older patients participated in TSTIs at baseline and thirteen at follow-up after discharge. After several adaptations, the P-BAS-P appeared feasible with good interviewer’s instructions. The pictures were considered relevant and helpful by the participants. Reliability was tested with 41 participants at baseline and 50 at follow-up. ICC between PBI1 and PBI2 of baseline test and retest was 0.76, respectively 0.73. At follow-up 0.86, respectively 0.85.For the construct validity, tested in 169 participants, hypotheses regarding importance of goals were confirmed. Regarding status of goals, only the follow-up status was confirmed, baseline and change were not. The responsiveness of the individual scores and PBI were weak, resulting in poor interpretability with many misclassifications. The SDC was larger than the MIC.Conclusions: The P-BAS-P appeared to be a feasible instrument, but there were methodological barriers for the evaluation of the reliability, validity, and responsiveness. We therefore recommend further research into the P-BAS-P.
Steady Floquet-Andreev States Probed by Tunnelling Spectroscopy
Authors: Lee Gil-Ho , Park Sein , Lee Wonjun , Jang Seong , Choi Yong-Bin , Park Jinho , Jung Woochan , Watanabe Kenji , Taniguchi Takashi , Cho Gil Young
Published: May 2021

Engineering quantum states through light-matter interaction has created a new paradigm in condensed matter physics. A representative example is the Floquet-Bloch state, which is generated by time-periodically driving the Bloch wavefunctions in crystals. Previous attempts to realise such states in condensed matter systems have been limited by the transient nature of the Floquet states produced by optical pulses, which masks the universal properties of non-equilibrium physics. Here, we report the generation of steady Floquet Andreev (F-A) states in graphene Josephson junctions by continuous microwave application and direct measurement of their spectra by superconducting tunnelling spectroscopy. We present quantitative analysis of the spectral characteristics of the F-A states while varying the phase difference of superconductors, temperature, microwave frequency and power. The oscillations of the F-A state spectrum with phase difference agreed with our theoretical calculations. Moreover, we confirmed the steady nature of the F-A states by establishing a sum rule of tunnelling conductance, and analysed the spectral density of Floquet states depending on Floquet interaction strength. This study provides a basis for understanding and engineering non-equilibrium quantum states in nano-devices.
Advanced Trap Lateral Flow Immunoassay Sensor for the Detection of Cortisol in Human Bodily Fluids
Authors: Oh Hyun-Kyung , Kim Kihyeun , Jang Hyungjun , Park Jinhee , Kim Min-Gon
Published: May 2021

Paper-based biosensors based on lateral flow immunoassay (LFI) are promising candidates for POC diagnosis because of their ease of use and rapid target detection. However, the low sensitivity of LFI limits its application, and signal amplification has been used in numerous studies to increase its sensitivity. We developed an advanced trap LFI (α-trapLFI), a simple-to-use sensor, with an additional step for signal amplification. Here, signal amplification is automatically implemented following delayed release of enhancement solution induced by water-soluble polyvinyl alcohol tape. As the polyvinyl alcohol tape is exposed to water, its polymer structure is perturbed (within 5 min), allowing ions to pass through. This new sensor was designed to have a short time delay between the flow of solutions used for the immunoassay and signal amplification. The α-trapLFI was subsequently used to detect cortisol with high sensitivity (9.1 pg∙mL-1) over a broad detection range (0.01–1000 ng∙mL-1) in bodily fluids. Furthermore, an excellent correlation was obtained by analyzing 20 human saliva samples using this sensor and a conventional ELISA (R2 = 0.90). The new sensor will be helpful in detecting various small molecules for simple, rapid, and portable POC diagnosis of stress disorders.
Predicting Invasive Ductal Carcinoma Tissues in Whole Slide Images of Breast Cancer by Using Convolutional Neural Network Model and Multiple Classifiers in Google Colab
Authors: G Deepa B , Senthil S.
Published: May 2021

Breast Cancer (BC) is the common type of cancer found in women which is caused due to the abnormal growth of cells in the breast. An early BC detection helps to increase the survival rate of the patient and 80% BC type was Invasive Ductal Carcinoma (IDC) .In this work, a deep learning-based IDC prediction model is proposed with multiple classifiers and CNN (Convolutional Neural Network). The developed deep learning method used a sequential Keras model like conv2D, Maxpooling2D, Dropout, Flatten and Dense. The multiple classifiers are LR (Logistic Regression), RF (Random Forest), K-NN (K-Nearest Neighbors), SVM (Support Vector Machine), Linear SVC, GNB (Gaussian NB) and DT (Decision Tree). The CNN model generated by using SkLearn, Keras and Tensor flow libraries, and results are organized by MatPlot libraries. At the classification stage, a helper function was defined, and Google Colab online browser platform used for developing the proposed model. The performance is analysed in terms of Accuracy, Precision, Recall, F1-score and Support.
Neuroprotective Effect of Plasminogen Activator Inhibitor-1 Antagonist in the Rat Model of Mild Traumatic Brain Injury
Authors: Bektaşoğlu Pınar Kuru , Koyuncuoğlu Türkan , Akbulut Selin , Akakın Dilek , Eyüboğlu İrem Peker , Erzik Can , Yüksel Meral , Kurtel Hızır
Published: May 2021

Background: Plasminogen activator inhibitor-1 (PAI-1) antagonists are known for their neuroprotective effects. In this study, it was aimed to investigate the possible protective effects of PAI-1 antagonists in a rat mild traumatic brain injury (TBI) model.Method: Sprague Dawley male rats were grouped as sham (n=7), TBI (n=9), TBI + PAI-1 antagonist (5 and 10 mg/kg TM5441 and TM5484; n=6-7). Under anesthesia, TBI was induced by dropping a metal 300-gram weight from a height of 1 meter on the skull. Before and 24-hour after trauma neurological examination, tail suspension, Y-maze, novel object recognition tests were performed. Twenty-four hours after TBI, the rats were decapitated and activities of myeloperoxidase, nitric oxide release, luminol- and lucigenin-enhanced chemiluminescence were measured. Also, interleukin-1b, interleukin-6, tumor necrosis factor, interleukin-10, tumor growth factor-b, caspase-3, cleaved caspase-3, and PAI levels were measured with the ELISA method in the brain tissue. Brain injury was graded histopathologically following hematoxylin-eosin staining. Western blot and immunohistochemical investigation for low-density lipoprotein receptor, matrix metalloproteinase-3 and nuclear factor-kB were also performed. Data were analyzed using GraphPad Prism 8.0 (GraphPad Software, San Diego, CA, USA) and expressed as means ± SEM. Values of p < 0.05 were considered to be statistically significant.Results: Higher levels of myeloperoxidase activity in the TBI group (p<0.05) were found to be suppressed in 5 and 10 mg/kg TM5441 treatment groups (p<0.05-p<0.01). The tail suspension test score was increased in the TBI group (p<0.001), and decreased in all treatment groups (p<0.05-0.001). The histologic damage score was increased statistically significantly in the cortex, dentate gyrus, and CA3 regions in the TBI group (p<0.01-0.001), decreased in the treatment groups in the cortex and dentate gyrus (p<0.05-0.001). Conclusion: PAI antagonists, especially TM5441, has antioxidant and anti-inflammatory properties against mild TBI in the acute period. Behavioral test results were also improved after PAI antagonist treatment after mild TBI.
Diagnostic Value of DHX58 - IRF7 Involved in RIG-I-Like Receptor Signaling Pathway in Tuberculosis
Authors: Li Chong-hui , Fu Yu-rong , yi zhengjun
Published: May 2021

Background: Tuberculosis (TB) is an infectious disease that endangers human health. This study set out to search for key genes and related pathways in dendritic cell (DC) from TB patients to reveal the potential molecular mechanisms and identify potential biomarkers for TB.Method: DC data GSE34151 related to TB was downloaded from GEO data sets for analysis. Differentially expressed genes (DEGs) were obtained by employing an online tool, GEO2R. PPI network of DEGs and gene module were visualized and calculated applying STRING and Cytoscape, respectively. GO analysis and KEGG pathway were utilized to annotate the functions of DEGs. ROC curve analysis was applied to screen the most diagnostic hub genes associated with TB. Furthermore, their expression was validated in blood data (GSE83456), which were further compared to the T-spot·TB test.Results: A total of 290 DEGs were screened, which were significantly enriched in Cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, and RIG-I-like receptor signaling pathways. Among them, 27 candidate hub genes with the most significant cluster in PPI were enriched in RIG-I-like receptor signaling pathway, which has been known to be associated with TB. We further found that the top 10 hub genes(DHX58, ISG20, IRF1, IRF7 and RSAD2, etc) showed high performance for TB diagnosis, among which both DHX58 and IRF7 were enriched in the RIG-I-like receptor signaling pathway. Moreover, DHX58 and IRF7 were also increased in blood, which were consistent with that in dendritic cell. Interestingly, DHX58 and IRF7 display higher diagnostic efficacy than T-spot·TB test.Conclusion: In this study, we revealed that both DHX58 and IRF7 with high diagnostic value in blood and dendritic cells, potentially involved in RIG-I-like receptor signaling pathway, may serve as a marker for TB diagnosis.
Dissociation of early and late face-related processes in Autism Spectrum Disorder and Williams syndrome
Authors: Gomez Alice , Lio Guillaume , Costa Manuela , Sirigu Angela , Demily Caroline
Published: May 2021

Williams syndrome (WS) and Autism Spectrum Disorders (ASD) are psychiatric conditions associated with atypical but opposite face-to-face interactions patterns: WS patients overly stare at others, ASD individuals escape eye contact. Whether these behaviors result from dissociable visual processes within the occipito-temporal pathways is unknown. Using high-density electroencephalography, multivariate pattern classification and group blind source separation, we searched for face-related neural signals that could best discriminate WS (N = 14), ASD (N = 14) and neurotypical populations (N = 14). We found two peaks in neurotypical participants: the first at 170ms, an early signal known to be implicated in low-level face features, the second at 260ms, a late component implicated in decoding salient face social cues. The late 260ms signal varied as a function of the distance of the eyes in the face stimulus with respect to the viewers’ fovea, meaning that it was strongest when the eyes were projected on the fovea and weakest when projected in the retinal periphery. Remarkably, both components were found distinctly impaired and preserved in WS and ASD. In WS, we could weakly decode the 170ms signal probably due to their relatively poor ability to process faces’ morphology while the late 260ms component shown to be eye sensitive was highly significant. The reverse pattern was observed in ASD participants who showed neurotypical like early 170ms evoked activity but impaired late evoked 260ms signal. Our study reveals a dissociation between WS and ASD patients and point at different neural origins for their social impairments.
Monocytic THP-1 Cells Diverge Significantly From Their Native Counterparts: A Comparative Examination of The Chromosomal Conformations And Transcriptomes
Authors: Liu Yulong , Li Hua , Czajkowsky Daniel M , Shao Zhifeng
Published: May 2021

Immortalized cell lines have long been used as model systems to systematically investigate biological processes under controlled and reproducible conditions, providing insights that have greatly advanced cellular biology and medical sciences. Recently, the widely used monocytic leukemia cell line, THP-1, was comprehensively examined to understand mechanistic relationships between the 3D chromatin structure and transcription during the trans-differentiation of monocytes to macrophages. To corroborate these observations in primary cells, we analyze in situ Hi-C and RNA-seq data of human primary monocytes and their differentiated macrophages in comparison to that obtained from the monocytic/macrophagic THP-1 cells. Surprisingly, we find significant differences between the primary cells and the THP-1 cells at all levels of chromatin structure, from loops to topologically associated domains to compartments. Importantly, the compartment-level differences correlate significantly with transcription: those genes that are in A-compartments in the primary cells but are in B-compartments in the THP-1 cells exhibit a higher level of expression in the primary cells than in the THP-1 cells, and vice versa. Overall, the genes in these different compartments are enriched for a wide range of pathways, and, at least in the case of the monocytic cells, their altered expression in certain pathways in the THP-1 cells argues for a less immune cell-like phenotype, suggesting that immortalization or prolonged culturing of THP-1 caused a divergence of these cells from their native counterparts. It is thus essential to reexamine phenotypic details observed in cell lines with their native counterparts so as to ensure a proper understanding of functional cell states in vivo.