bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of lncRNA NR_028138.1 as a biomarker and construction of a ceRNA network for bipolar disorder
Authors: He Ling , Zou Pengtao , Sun Wanlei , Fu Yonghui , He Wenfeng , Li Juxiang 
Published: August 2021

AbstractThe pathogenesis of bipolar disorder (BD), a chronic mood disorder, is largely unknown. Noncoding RNAs play important roles in the pathogenesis of BD. However, little is known about the correlations of long noncoding RNAs (lncRNAs) with BD. Illumina high-throughput sequencing in BD patients and normal controls was used to identify differentially expressed (DE) genes. Two-step real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate DE-RNAs in the first cohort (50 BD and 50 control subjects). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and lncRNA-mRNA coexpression and lncRNA-microRNA (miRNA)-messenger RNA (mRNA) competing endogenous RNA (ceRNA) network analyses were used to predict the functions of DE-RNAs. Receiver operating characteristic (ROC) curve analysis and logistic regression were applied to evaluate diagnostic performance in an additional testing group (80 BD and 66 control subjects). A total of 576 significantly DE-lncRNAs and 262 DE-mRNAs were identified in BD patients, and 95 lncRNA-miRNA-mRNA interactions were used to construct a ceRNA regulatory network. Analysis of the first cohort showed that six RNAs (NR_028138.1, TCONS_00018621, TCONS_00002186, TNF, PID1, and SDK1) were differentially expressed in the BD group (P < 0.01). NR_028138.1 was used to establish a BD diagnostic model (area under the ROC curve 0.923, P < 0.004, 95% CI: 0.830–0.999). Verification in the second cohort revealed uniformly significant differences in NR_028138.1 (P < 0.0001). This study constructed a ceRNA regulatory network and provided a hypothesis for the pathogenesis of BD. NR_028138.1 was identified as a central element involved in the transcriptional regulation in BD and a potential biomarker.
Catestatin in innate immunity and Cateslytin-derived peptides against superbugs
Authors: Scavello Francesco , Mutschler Angela , Hellé Sophie , Schneider Francis , Chasserot-Golaz Sylvette , Strub Jean-Marc , Cianferani Sarah , Haikel Youssef , Metz-Boutigue Marie-Hélène 
Published: August 2021

AbstractChromogranin A (CgA) is the precursor of several antimicrobial peptides, such as Catestatin (Cts, bovine CgA344-364), initially described as a potent inhibitor of catecholamines. This peptide displays direct antimicrobial activities and contributes to immune system regulation. The aim of the present study is to investigate a designed peptide based on Cts to fight infections against superbugs and more particularlyStaphylococcus aureus. In addition to Cateslytin (Ctl, bovine CgA344-358), the active domain of Catestatin, several peptides including dimers, D-isomer and the new designed peptide DOPA-K-DOPA-K-DOPA-TLRGGE-RSMRLSFRARGYGFR (Dopa5T-Ctl) were prepared and tested. Cateslytin is resistant to bacterial degradation and does not induce bacterial resistance. The interaction of Catestatin with immune dermal cells (dendritic cells DC1a, dermal macrophages CD14 and macrophages) was analyzed by using confocal microscopy and cytokine release assay. The dimers and D-isomer of Ctl were tested against a large variety of bacteria showing the potent antibacterial activity of the D-isomer. The peptide Dopa5T-Ctl is able to induce the self-killing ofS. aureusafter release of Ctl by the endoprotease Glu-C produced by this pathogen. It permits localized on-demand delivery of the antimicrobial drug directly at the infectious site.
Serum miR371 in testicular germ cell cancer before and after orchiectomy, assessed by digital-droplet PCR in a prospective study
Authors: Myklebust Mette Pernille , Thor Anna , Rosenlund Benedikte , Gjengstø Peder , Karlsdottir Ása , Brydøy Marianne , Bercea Bogdan S. , Olsen Christian , Johnson Ida , Berg Mathilde I. , Langberg Carl W. , Andreassen Kristine E. , Kjellman Anders , Haugnes Hege S. , Dahl Olav 
Published: August 2021

AbstractMicroRNA-371a-3p (miR371) has been suggested as a sensitive biomarker in testicular germ cell cancer (TGCC). We aimed to compare miR371 with the classical biomarkers α-fetoprotein (AFP) and β-human chorionic gonadotropin (hCGβ). Overall, 180 patients were prospectively enrolled in the study, with serum samples collected before and after orchiectomy. We compared the use of digital droplet PCR (RT-ddPCR) with the quantitative PCR used by others for detection of miR371. The novel RT-ddPCR protocol showed high performance in detection of miR371 in serum samples. In the study cohort, miR371 was measured using RT-ddPCR. MiR371 detected CS1 of the seminoma and the non-seminoma sub-types with a sensitivity of 87% and 89%, respectively. The total sensitivity was 89%. After orchiectomy, miR371 levels declined in 154 of 159 TGCC cases. The ratio of miR371 pre- and post-orchiectomy was 20.5 in CS1 compared to 6.5 in systemic disease. AFP and hCGβ had sensitivities of 52% and 51% in the non-seminomas. MiR371 is a sensitive marker that performs better than the classical markers in all sub-types and clinical stages. Especially for the seminomas CS1, the high sensitivity of miR371 in detecting TGCC cells may have clinical implications.
A new silver coordination polymer based on 4,6-diamino-2-pyrimidinethiol: synthesis, characterization and catalytic application in asymmetric Hantzsch synthesis of polyhydroquinolines
Authors: Hussain-Khil Noorullah , Ghorbani-Choghamarani Arash , Mohammadi Masoud 
Published: August 2021

AbstractA highly efficient and stable heterogeneous coordination polymer (CP) was successfully prepared by hydrothermal combination of silver and 4,6-diamino-2-pyrimidinethiol. The prepared coordination polymer was characterized by FT-IR, XRD, TGA, SEM, EDX, X-ray mapping and Nitrogen adsorption–desorption analysis. The prepared Ag–CP exhibit excellent catalytic activity in multicomponent Hantzsch synthesis of polyhydroquinolines under mild reaction conditions in relatively short reaction times. The heterogeneity of the catalyst was confirmed by the hot filtration test; also, the catalyst was reused for at least four times under the optimized reaction conditions without any significant loss of its catalytic activity.
Computational design of SARS-CoV-2 peptide binders with better predicted binding affinities than human ACE2 receptor
Authors: Sitthiyotha Thassanai , Chunsrivirot Surasak 
Published: August 2021

AbstractSARS-CoV-2 is coronavirus causing COVID-19 pandemic. To enter human cells, receptor binding domain of S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) binds to peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptor. Employing peptides to inhibit binding between SARS-CoV-2-RBD and ACE2-PD is a therapeutic solution for COVID-19. Previous experimental study found that 23-mer peptide (SBP1) bound to SARS-CoV-2-RBD with lower affinity than ACE2. To increase SBP1 affinity, our previous study used residues 21–45 of α1 helix of ACE2-PD (SPB25) to design peptides with predicted affinity better than SBP1 and SPB25 by increasing interactions of residues that do not form favorable interactions with SARS-CoV-2-RBD. To design SPB25 with better affinity than ACE2, we employed computational protein design to increase interactions of residues reported to form favorable interactions with SARS-CoV-2-RBD and combine newly designed mutations with the best single mutations from our previous study. Molecular dynamics show that predicted binding affinities of three peptides (SPB25Q22R, SPB25F8R/K11W/L25R and SPB25F8R/K11F/Q22R/L25R) are better than ACE2. Moreover, their predicted stabilities may be slightly higher than SBP1 as suggested by their helicities. This study developed an approach to design SARS-CoV-2 peptide binders with predicted binding affinities better than ACE2. These designed peptides are promising candidates as SARS-CoV-2 inhibitors.
Bone morphological feature extraction for customized bone plate design
Authors: Wang Lin , Guo Kaijin , He Kunjin , Zhu Hong 
Published: August 2021

AbstractFractures are difficult to treat because of individual differences in bone morphology and fracture types. Compared to serialized bone plates, the use of customized plates significantly improves the fracture healing process. However, designing custom plates often requires the extraction of skeletal morphology, which is a complex and time-consuming procedure. This study proposes a method for extracting bone morphological features to facilitate customized plate designs. The customized plate design involves three major steps: extracting the morphological features of the bone, representing the undersurface features of the plate, and constructing the customized plate. Among these steps, constructing the undersurface feature involves integrating a group of bone features with different anatomical morphologies into a semantic feature parameter set of the plate feature. The undersurface feature encapsulates the plate and bone features into a highly cohesive generic feature and then establishes an internal correlation between the plate and bone features. Using the femoral plate as an example, we further examined the validity and feasibility of the proposed method. The experimental results demonstrate that the proposed method improves the convenience of redesign through the intuitive editing of semantic parameters. In addition, the proposed method significantly improves the design efficiency and reduces the required design time.
Protective effect of glycyrrhizin, a direct HMGB1 inhibitor, on post-contrast acute kidney injury
Authors: Oh Hyewon , Choi Arom , Seo Nieun , Lim Joon Seok , You Je Sung , Chung Yong Eun 
Published: August 2021

AbstractPost contrast-acute kidney injury (PC-AKI) is defined as the deterioration of renal function after administration of iodinated contrast media. HMGB1 is known to play an important role in the development of acute kidney injury. The purpose of this study was to investigate the association between HMGB1 and PC-AKI and the protective effect of glycyrrhizin, a direct inhibitor of HMGB1, in rats. Rats were divided into three groups: control, PC-AKI and PC-AKI with glycyrrhizin. Oxidative stress was measured with MDA levels and H2DCFDA fluorescence intensity. The mRNA expressions of pro-inflammatory cytokines (IL-1α, IL-1β, IL-6 and TNF-α) and kidney injury markers (KIM-1, NGAL and IL-18) were assessed using RT-PCR and ELISA in kidney tissue. In addition, the serum and intracellular protein levels of HMGB1were analyzed with the enzyme-linked immunosorbent assay (ELISA) and western blotting. Histologic changes were assessed with H&E staining using the transmission electron microscope (TEM). Moreover, serum creatinine (SCr), blood urea nitrogen (BUN) and lactate dehydrogenase (LDH) levels were assessed. Oxidative stress, pro-inflammatory cytokines, kidney injury markers and LDH were significantly higher in PC-AKI compared to the controls, but were lower in PC-AKI with glycyrrhizin. Intracellular and serum HMGB1 levels significantly increased after contrast media exposure, whereas they markedly decreased after glycyrrhizin pretreatment. SCr and BUN also decreased in PC-AKI with glycyrrhizin compared to PC-AKI. In PC-AKI, we could frequently observe tubular dilatation with H&E staining and cytoplasmic vacuoles on TEM, whereas these findings were attenuated in PC-AKI with glycyrrhizin. Our findings indicate that HMGB1 plays an important role in the development of PC-AKI and that glycyrrhizin has a protective effect against renal injury and dysfunction by inhibiting HMGB1 and reducing oxidative stress.
Comparing COVID-19 risk factors in Brazil using machine learning: the importance of socioeconomic, demographic and structural factors
Authors: Baqui Pedro , Marra Valerio , Alaa Ahmed M. , Bica Ioana , Ercole Ari , van der Schaar Mihaela 
Published: August 2021

AbstractThe COVID-19 pandemic continues to have a devastating impact on Brazil. Brazil’s social, health and economic crises are aggravated by strong societal inequities and persisting political disarray. This complex scenario motivates careful study of the clinical, socioeconomic, demographic and structural factors contributing to increased risk of mortality from SARS-CoV-2 in Brazil specifically. We consider the Brazilian SIVEP-Gripe catalog, a very rich respiratory infection dataset which allows us to estimate the importance of several non-laboratorial and socio-geographic factors on COVID-19 mortality. We analyze the catalog using machine learning algorithms to account for likely complex interdependence between metrics. The XGBoost algorithm achieved excellent performance, producing an AUC-ROC of 0.813 (95% CI 0.810–0.817), and outperforming logistic regression. Using our model we found that, in Brazil, socioeconomic, geographical and structural factors are more important than individual comorbidities. Particularly important factors were: The state of residence and its development index; the distance to the hospital (especially for rural and less developed areas); the level of education; hospital funding model and strain. Ethnicity is also confirmed to be more important than comorbidities but less than the aforementioned factors. In conclusion, socioeconomic and structural factors are as important as biological factors in determining the outcome of COVID-19. This has important consequences for policy making, especially on vaccination/non-pharmacological preventative measures, hospital management and healthcare network organization.
Simultaneous estimation of multiple phases in generalised Mach–Zehnder interferometer
Authors: Markiewicz Marcin , Pandit Mahasweta , Laskowski Wiesław 
Published: August 2021

AbstractIn this work we investigate the problem of simultaneous estimation of phases using generalised three- and four-mode Mach–Zehnder interferometer. In our setup, we assume that the phases are placed in each of the modes in the interferometer, which introduces correlations between estimators of the phases. These correlations prevent simultaneous estimation of all these phases, however we show that we can still obtain the Heisenberg-like scaling of precision of joint estimation of any subset of $$d-1$$

d
-
1

phases, d being the number of modes, within completely fixed experimental setup, namely with the same initial state and set of measurements. Our estimation scheme can be applied to the task of quantum-enhanced sensing in three-dimensional interferometric configurations.
CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer
Authors: Yin Jinbao , Lin Chen , Jiang Meng , Tang Xinbin , Xie Danlin , Chen Jingwen , Ke Rongqin 
Published: August 2021

AbstractAs a highly prevalent disease among women worldwide, breast cancer remains in urgent need of further elucidation its molecular mechanisms to improve the patient outcomes. Identifying hub genes involved in the pathogenesis and progression of breast cancer can potentially help to unveil mechanism and also provide novel diagnostic and prognostic markers. In this study, we integrated multiple bioinformatic methods and RNA in situ detection technology to identify and validate hub genes. EZH2 was recognized as a key gene by PPI network analysis. CENPL, ISG20L2, LSM4, MRPL3 were identified as four novel hub genes through the WGCNA analysis and literate search. Among these, many studies on EZH2 in breast cancer have been reported, but no studies are related to the roles of CENPL, ISG20L2, MRPL3 and LSM4 in breast cancer. These four novel hub genes were up-regulated in tumor tissues and associated with cancer progression. The receiver operating characteristic analysis and Kaplan–Meier survival analysis indicated that these four hub genes are promising candidate genes that can serve as diagnostic and prognostic biomarkers for breast cancer. Moreover, these four newly identified hub genes as aberrant molecules in the maintenance of breast cancer development, their exact functional mechanisms deserve further in-depth study.
Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata
Authors: Yu Zheng-Wen , Zhang Ni , Jiang Chun-Yan , Wu Shao-Xiong , Feng Xia-Yu , Feng Xiao-Ying 
Published: August 2021

AbstractDihydroquercetin (DHQ), an extremely low content compound (less than 3%) in plants, is an important component of dietary supplements and used as functional food for its antioxidant activity. Moreover, as downstream metabolites of DHQ, an extremely high content of dihydromyricetin (DHM) is up to 38.5% in Ampelopsis grossedentata. However, the mechanisms involved in the biosynthesis and regulation from DHQ to DHM in A. grossedentata remain unclear. In this study, a comparative transcriptome analysis of A. grossedentata containing extreme amounts of DHM was performed on the Illumina HiSeq 2000 sequencing platform. A total of 167,415,597 high-quality clean reads were obtained and assembled into 100,584 unigenes having an N50 value of 1489. Among these contigs, 57,016 (56.68%) were successfully annotated in seven public protein databases. From the differentially expressed gene (DEG) analysis, 926 DEGs were identified between the B group (low DHM: 210.31 mg/g) and D group (high DHM: 359.12 mg/g) libraries, including 446 up-regulated genes and 480 down-regulated genes (B vs. D). Flavonoids (DHQ, DHM)-related DEGs of ten structural enzyme genes, three myeloblastosis transcription factors (MYB TFs), one basic helix–loop–helix (bHLH) TF, and one WD40 domain-containing protein were obtained. The enzyme genes comprised three PALs, two CLs, two CHSs, one F3’H, one F3’5’H (directly converts DHQ to DHM), and one ANS. The expression profiles of randomly selected genes were consistent with the RNA-seq results. Our findings thus provide comprehensive gene expression resources for revealing the molecular mechanism from DHQ to DHM in A. grossedentata. Importantly, this work will spur further genetic studies about A. grossedentata and may eventually lead to genetic improvements of the DHQ content in this plant.
Introducing intrauterine antibiotic infusion as a novel approach in effectively treating chronic endometritis and restoring reproductive dynamics: a randomized pilot study
Authors: Pantos Konstantinos , Simopoulou Mara , Maziotis Evangelos , Rapani Anna , Grigoriadis Sokratis , Tsioulou Petroula , Giannelou Polina , Nitsos Nikolaos , Tzonis Panagiotis , Koutsilieris Michael , Sfakianoudis Konstantinos 
Published: August 2021

AbstractThe chronic nature of Chronic Endometritis (CE) along with the challenging management and infertility entailed, call for cutting-edge therapeutic approaches. This study introduces the novel treatment of intrauterine antibiotic infusion (IAI) combined with oral antibiotic administration (OAA), and it assesses respective performance against the gold standard treatment of OAA. Data sourced herein reports on treatment efficiency and fertility restoration for both patients aiming to conceive naturally or via In Vitro fertilization. Eighty CE patients, 40 presenting with recurrent implantation failure, and 40 with recurrent pregnancy loss, were enrolled in the IVF and the natural conception arm respectively. Treatment was subjected to randomization. Effectively treated patients proceeded with either a single IVF cycle or were invited to conceive naturally over a 6-month period. Combination of IAI and OAA provided a statistically significant enhanced effectiveness treatment rate (RR 1.40; 95%CI 1.07–1.82; p = 0.01). No statistically significant difference was observed regarding the side-effects rate (RR 1.33; 95%CI 0.80–2.22; p = 0.52). No statistically significant difference was observed for either arm regarding live-birth rate. Following an intention-to-treat analysis, employment of IAI corresponds to improved clinical pregnancy rate-albeit not reaching statistical significance. In conclusion, complimentary implementation of IAI could provide a statistically significant enhanced clinical treatment outcome.
Sarcopenia modifies the associations of nonalcoholic fatty liver disease with all-cause and cardiovascular mortality among older adults
Authors: Sun Xingxing , Liu Zhelong , Chen Fuqiong , Du Tingting 
Published: August 2021

AbstractThe contribution of nonalcoholic fatty liver disease (NAFLD) to all-cause and cardiovascular mortality remains controversial. Sarcopenia, a measure of muscle mass, strength and function, may identify which persons are most at risk for adverse effects of NAFLD. We aimed to test the hypothesis that sarcopenia modifies the associations between NAFLD and all-cause and cardiovascular mortality. A total of 2446 older adults (≥ 60 years) from the third National Health and Nutrition Examination Survey were enrolled. Their mortality data were linked to death certificates in the National Death Index. Sarcopenia was defined as having low skeletal muscle mass together with slow gait speed, which captures both muscle mass and muscle function. Ultrasound tests were used for the assessment of hepatic steatosis. During follow-up (median 16.8 years), 1530 older subjects died from any cause, of which 379 were cardiovascular-related. All-cause and cardiovascular mortality rates were 4.31 and 1.07 per 100 person-years, respectively. In a multivariate model, using participants without NAFLD and sarcopenia as the reference group, individuals with both NAFLD and sarcopenia had 1.69 times [95% confidence interval (CI) 1.23–2.31] and 2.17 times (95% CI 1.33–3.54) higher risks of all-cause and cardiovascular mortality, respectively. However, NAFLD persons without sarcopenia had hazard ratios for all-cause and cardiovascular mortality similar to those of the reference group. Sarcopenia modified the associations of NAFLD with all-cause and cardiovascular mortality. Sarcopenia may identify older adults who are at the highest risk for adverse outcomes associated with NAFLD.
Influences of conservation measures on runoff and sediment yield in different intra-event-based flood regimes in the Chabagou watershed
Authors: Wang Shan-Shan , Li Zhan-Bin , Zhang Le-Tao , Ma Bo 
Published: August 2021

AbstractThe Loess Plateau in China has suffered severe soil erosion. To control soil erosion, extensive conservation measures aimed at redistributing rainfall, hindering flow velocity and intercepting sediment were implemented on the Loess Plateau. To accurately evaluate the combined effect of conservation measures in the Chabagou watershed, this study classified intra-event-based floods into four regimes via cluster and discriminant analyses. Regime A was characterized by short flood duration and low erosive energy, regime B was characterized by short flood duration and high erosive energy, regime C was characterized by long flood duration and low erosive energy, and regime D was characterized by long flood duration and high erosive energy. The results indicated that peak discharge (qp), runoff depth (H), mean discharge (qm), and runoff erosion power (E) decreased by 75.2%, 56.0%, 68.0% and 89.2%, respectively, in response to conservation measures. Moreover, area-specific sediment yield (SSY), average suspended sediment concentration (SCE), and maximum suspended sediment concentration (MSCE) decreased by 69.2%, 33.3% and 11.9%, respectively, due to conservation measures. The nonlinear regression analysis revealed a power function relationship between SSY and E in both the baseline (1961–1969) and measurement period (1971–1990) in all regimes. Conservation measures reduced sediment yield by not only reducing the runoff amount and soil erosion energy but also transforming the flood regime, for example, transforming a high-sediment-yield regime into a low-sediment-yield regime. Moreover, conservation measures altered the SSY-E relationship in regime A, whereas no obvious difference in regime B or C/D was observed between the measurement period and the baseline period. This study provides a better understanding of the mechanism of runoff regulation and the sediment yield reduction under comprehensive conservation measures in a small watershed on the Chinese Loess Plateau.