bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinant Human Platelet–Derived Growth Factor: A Systematic Review of Clinical Findings in Oral Regenerative Procedures
Authors: Tavelli L. , Ravidà A. , Barootchi S. , Chambrone L. , Giannobile W.V. 
Published: May 2020

Aim: The use of recombinant human platelet-derived growth factor–BB (rhPDGF) has received Food and Drug Administration approval for the treatment of periodontal and orthopedic bone defects and dermal wound healing. Many studies have investigated its regenerative potential in a variety of other oral clinical indications. The aim of this systematic review was to assess the efficacy, safety, and clinical benefit of recombinant human platelet-derived growth factor (rhPDGF) use for alveolar bone and/or soft tissue regeneration. Material and Methods: Comprehensive electronic and manual literature searches according to the PRISMA guidelines were performed to identify interventional and observational studies evaluating the regenerative applications of rhPDGF-BB. The primary outcomes were the safety, efficacy, and overall clinical benefit of rhPDGF use in oral regenerative procedures. Results: Sixty-three human clinical studies (mean ± SD follow-up period of 10.7 ± 3.3 mo) were included in the qualitative analysis. No serious adverse effects were reported in any of the 63 studies, aside from the postoperative complications routinely associated with surgical therapy. Use of rhPDGF was shown to be beneficial when combined with allografts, xenografts, and alloplasts (the latter tricalcium phosphate [β-TCP]) for the treatment of periodontal defects and gingival recession. The use of rhPDGF also led to favorable clinical outcomes when combined with allografts or xenografts for guided bone regeneration (GBR) and alveolar ridge preservation. While favorable clinical results support the use of the combination of rhPDGF plus allograft or xenograft for GBR, ARP, and sinus floor augmentation, current data support the use of rhPDGF and alloplasts (e.g., β-TCP) only in periodontal defects and gingival recession. Conclusions: Based on the clinical evidence, rhPDGF is safe and provides clinical benefits when used in combination with bone allografts, xenograft, or β-TCP for the treatment of intrabony and furcation periodontal defects and gingival recession or when used with allografts or xenograft for GBR and ARP (PROSPERO CRD42020142446). Knowledge Transfer Statement: Clinicians should be aware that rhPDGF is a safe and effective approach for the treatment of intrabony and furcation periodontal defects and gingival recession or when used with allografts or xenograft for bone regeneration and alveolar ridge preservation. With consideration of cost and patient preference, this result could lead to more appropriate therapeutic decisions.
Targeting aberrant DNA hypermethylation as a driver of ATL leukemogenesis by using the new oral demethylating agent OR-2100
Authors: Watanabe Tatsuro , Yamashita Satoshi , Ureshino Hiroshi , Kamachi Kazuharu , Kurahashi Yuki , Fukuda-Kurahashi Yuki , Yoshida Nao , Hattori Naoko , Nakamura Hideaki , Sato Akemi , Kawaguchi Atsushi , Sueoka-Aragane Naoko , Kojima Kensuke , Okada Seiji , Ushijima Toshikazu , Kimura Shinya , Sueoka Eisaburo 
Published: May 2020

Abstract
Adult T-cell leukemia-lymphoma (ATL) is an aggressive hematological malignancy of CD4+ T cells transformed by human T-cell lymphotropic virus-1 (HTLV-1). Most HTLV-1–infected individuals are asymptomatic, and only 3% to 5% of carriers develop ATL. Here, we describe the contribution of aberrant DNA methylation to ATL leukemogenesis. HTLV-1–infected T-cells and their uninfected counterparts were separately isolated based on CADM1 and CD7 expression status, and differentially methylated positions (DMPs) specific to HTLV–infected T cells were identified through genome-wide DNA methylation profiling. Accumulation of DNA methylation at hypermethylated DMPs correlated strongly with ATL development and progression. In addition, we identified 22 genes downregulated because of promoter hypermethylation in HTLV-1–infected T cells, including THEMIS, LAIR1, and RNF130, which negatively regulate T-cell receptor (TCR) signaling. Phosphorylation of ZAP-70, a transducer of TCR signaling, was dysregulated in HTLV-1–infected cell lines but was normalized by reexpression of THEMIS. Therefore, we hypothesized that DNA hypermethylation contributes to growth advantages in HTLV-1–infected cells during ATL leukemogenesis. To test this idea, we investigated the anti-ATL activities of OR-1200 and OR-2100 (OR21), novel decitabine (DAC) prodrugs with enhanced oral bioavailability. Both DAC and OR21 inhibited cell growth, accompanied by global DNA hypomethylation, in xenograft tumors established by implantation of HTLV-1–infected cells. OR21 was less hematotoxic than DAC, whereas tumor growth inhibition was almost identical between the 2 compounds, making it suitable for long-term treatment of ATL patient-derived xenograft mice. Our results demonstrate that regional DNA hypermethylation is functionally important for ATL leukemogenesis and an effective therapeutic target.
Detection of microRNA-335-5p on an Interdigitated Electrode Surface for Determination of the Severity of Abdominal Aortic Aneurysms
Authors: Lu Bei , Liu Leiting , Wang Jingrui , Chen Yuan , Li Zhijiang , Gopinath Subash C. B. , Lakshmipriya Thangavel , Huo Zongwei 
Published: May 2020

AbstractAbdominal aortic aneurysm (AAA) refers to the enlargement of the lower artery of the abdominal aorta, and identification of an early detection tool is urgently needed for diagnosis. In the current study, an interdigitated electrode (IDE) sensing surface was used to identify miRNA-335-5p, which reflects the formation of AAAs. The uniformity of the silica material was observed by 3D profilometry, and the chemically modified highly conductive surface improved the detection via the I-V mode. The targeted miRNA-335-5p was detected in a dose-dependent manner and based on linear regression and 3σ analyses, the sensitivity was determined to be 1 fM with a biotinylated probe. The high specificity was shown by discriminating the target sequence from noncomplementary and single- and triple-mismatched sequences. These outputs demonstrated the high-performance detection of miRNA-335-5p with good reproducibility for determination of the severity of AAA.
The capital market spillover effect of product market advertising: Evidence from stock price synchronicity
Authors: Chen Yajie , Zhong Qinlin , Jiang Fuxiu 
Published: May 2020

AbstractWe analyze whether product market advertising has a spillover effect on stock price synchronicity by transmitting firm-specific information to the capital market and attracting more investor attention. Using a sample of Chinese listed firms from 2009 to 2017, we find that firms with greater advertising expenditures have lower stock price synchronicity. The results are robust after we address endogeneity concerns. In accord with our hypothesis that product market advertising increases the amount of firm-level information capitalized into stock prices through the information channel, we find that the impact of advertising on synchronicity is more pronounced for firms with a higher degree of information asymmetry and firms in the consumer-product industry. Further tests show that product market advertising enhances the ability of current period returns to reflect future earnings, and thus rules out that the negative relationship between advertising and synchronicity is driven by noise trading. Our results imply that product market advertising plays an informative role and improves information efficiency in a capital market.
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data
Authors: Hu Yue , Xi Xi , Yang Qian , Zhang Xuegong 
Published: May 2020

Abstract
Background
With the rapid development of single-cell genomics, technologies for parallel sequencing of the transcriptome and genome in each single cell is being explored in several labs and is becoming available. This brings us the opportunity to uncover association between genotypes and gene expression phenotypes at single-cell level by eQTL analysis on single-cell data. New method is needed for such tasks due to special characteristics of single-cell sequencing data.

Results
We developed an R package SCeQTL that uses zero-inflated negative binomial regression to do eQTL analysis on single-cell data. It can distinguish two type of gene-expression differences among different genotype groups. It can also be used for finding gene expression variations associated with other grouping factors like cell lineages or cell types.

Conclusions
The SCeQTL method is capable for eQTL analysis on single-cell data as well as detecting associations of gene expression with other grouping factors. The R package of the method is available at https://github.com/XuegongLab/SCeQTL/.
High expressions of the cytoglobin and PGC-1α genes during the tissue regeneration of house gecko (Hemidactylus platyurus) tails
Authors: Novianti Titta , Juniantito Vetnizah , Jusuf Ahmad Aulia , Arida Evy Ayu , Sadikin Mohamad , Jusman Sri Widia A. 
Published: May 2020

Abstract
Background
The tissue regeneration process requires high oxygen and energy levels. Cytoglobin (Cygb) is a member of the globin family, which has the ability to bind oxygen, plays a role in dealing with oxidative stress, and carries oxygen into the mitochondria. Energy production for tissue regeneration is associated with mitochondria—especially mitochondrial biogenesis. The peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1alpha protein helps to regulate mitochondrial biogenesis. House geckos (Hemidactylus platyurus) are reptiles that have the ability to regenerate the tissue in their tails. House geckos were selected as the animal models for this study in order to analyze the association of Cygb with oxygen supply and the association of PGC-1α with energy production for tissue regeneration.

Results
The growth of house gecko tails showed a slow growth at the wound healing phase, then followed by a fast growth after wound healing phase of the regeneration process. While Cygb mRNA expression reached its peak at the wound healing phase and slowly decreased until the end of the observation. PGC-1α mRNA was expressed and reached its peak earlier than Cygb.

Conclusions
The expressions of both the Cygb and PGC-1α genes were relatively high compared to the control group. We therefore suggest that Cygb and PGC-1α play an important role during the tissue regeneration process.
Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements
Authors: Chibani Cynthia Maria , Roth Olivia , Liesegang Heiko , Wendling Carolin Charlotte 
Published: May 2020

Abstract
Background
Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate [1] those genomic signatures that characterize a habitat-specific ecotype and [2] the source of genomic variation within this ecotype.

Results
We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~ 90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype.

Conclusion
We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.
Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment
Authors: Jiang Puzi , Lai Senying , Wu Sicheng , Zhao Xing-Ming , Chen Wei-Hua 
Published: May 2020

Abstract
Background
Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and globally alter microbial community and metabolic capacities.

Results
Consistently, we found host DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mapped to the host genome, were significantly elevated in patients of CRC and Crohn’s disease (CD). Consistent with our hypothesis, we found that HDC correlated with microbial- and metabolic-biomarkers of these diseases, contributed significantly to machine-learning models for patient stratification and was consequently ranked as a top contributor. CD patients with treatment could partially reverse the changes of many CD-signature species over time, with reduced HDC and fecal calprotectin (FCP) levels. Strikingly, HDC showed stronger correlations with the reversing changes of the CD-related species than FCP, and contributed greatly in classifying treatment responses, suggesting that it was also a biomarker for effective treatment.

Conclusions
Together, we revealed that association between HDCs and gut dysbiosis, and identified HDC as a novel biomarker from fecal metagenomics for diagnosis and effective treatment of intestinal diseases; our results also suggested that host-derived contents may have greater impact on gut microbiota than previously anticipated.
Optimized breeding strategies to harness genetic resources with different performance levels
Authors: Allier Antoine , Teyssèdre Simon , Lehermeier Christina , Moreau Laurence , Charcosset Alain 
Published: May 2020

AbstractBackgroundThe narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at identifying the optimal set of crosses that balances the expected genetic value and diversity. We propose to consider genomic selection and optimal cross selection to recurrently improve genetic resources (i.e. pre-breeding), to bridge the improved genetic resources with elites (i.e. bridging), and to manage introductions into the elite breeding population. Optimal cross selection is particularly adapted to jointly identify bridging, introduction and elite crosses to ensure an overall consistency of the genetic base broadening strategy.ResultsWe compared simulated breeding programs introducing donors with different performance levels, directly or indirectly after bridging. We also evaluated the effect of the training set composition on the success of introductions. We observed that with recurrent introductions of improved donors, it is possible to maintain the genetic diversity and increase mid- and long-term performances with only limited penalty at short-term. Considering a bridging step yielded significantly higher mid- and long-term genetic gain when introducing low performing donors. The results also suggested to consider marker effects estimated with a broad training population including donor by elite and elite by elite progeny to identify bridging, introduction and elite crosses.ConclusionResults of this study provide guidelines on how to harness polygenic variation present in genetic resources to broaden elite germplasm.
Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
Authors: Zolfaghari Emameh Reza , Kuuslahti Marianne , Nosrati Hassan , Lohi Hannes , Parkkila Seppo 
Published: May 2020

Abstract
Background
The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly used databases using carbonic anhydrase (CA) gene sequences as generic targets. CAs are ancient metalloenzymes that are present in all unicellular and multicellular living organisms. Among the eight distinct families of CAs, including α, β, γ, δ, ζ, η, θ, and ι, only α-CAs have been reported in vertebrates.

Results
By an in silico analysis performed on the NCBI and Ensembl databases, we identified several β- and γ-CA sequences in vertebrates, including Homo sapiens, Mus musculus, Felis catus, Lipotes vexillifer, Pantholops hodgsonii, Hippocampus comes, Hucho hucho, Oncorhynchus tshawytscha, Xenopus tropicalis, and Rhinolophus sinicus. Polymerase chain reaction (PCR) analysis of genomic DNA persistently failed to amplify positive β- or γ-CA gene sequences when Mus musculus and Felis catus DNA samples were used as templates. Further BLAST homology searches of the database-derived “vertebrate” β- and γ-CA sequences revealed that the identified sequences were presumably derived from gut microbiota, environmental microbiomes, or grassland ecosystems.

Conclusions
Our results highlight the need for more accurate and fast curation systems for DNA databases. The mined data must be carefully reconciled with our best knowledge of sequences to improve the accuracy of DNA data for publication.
Effect of trait’s expression level on single-step genomic evaluation of resistance to Dothistroma needle blight
Authors: Klápště Jaroslav , Dungey Heidi S. , Graham Natalie J. , Telfer Emily J. 
Published: May 2020

Abstract
Background
Many conifer breeding programs are paying increasing attention to breeding for resistance to needle disease due to the increasing importance of climate change. Phenotyping of traits related to resistance has many biological and temporal constraints that can often confound the ability to achieve reliable phenotypes and consequently, reliable genetic progress. The development of next generation sequencing platforms has also enabled implementation of genomic approaches in species lacking robust reference genomes. Genomic selection is, therefore, a promising strategy to overcome the constraints of needle disease phenotyping.

Results
We found high accuracy in the prediction of genomic breeding values in the disease-related traits that were well characterized, reaching 0.975 for genotyped individuals and 0.587 for non-genotyped individuals. This compared well with pedigree-based accuracies of up to 0.746. Surprisingly, poorly phenotyped disease traits also showed very high accuracy in terms of correlation of predicted genomic breeding values with pedigree-based counterparts. However, this was likely caused by the fact that both were clustered around the population mean, while deviations from the population mean caused by genetic effects did not appear to be well described. Caution should therefore be taken with the interpretation of results in poorly phenotyped traits.

Conclusions
Implementation of genomic selection in this test population of Pinus radiata resulted in a relatively high prediction accuracy of needle loss due to Dothistroma septosporum compared with a pedigree-based approach. Using genomics to avoid biological/temporal constraints where phenotyping is reliable appears promising. Unsurprisingly, reliable phenotyping, resulting in good heritability estimates, is a fundamental requirement for the development of a reliable prediction model. Furthermore, our results are also specific to the single pathogen mating-type that is present in New Zealand, and may change with future incursion of other pathogen varieties. There is no doubt, however, that once a robust genomic prediction model is built, it will be invaluable to not only select for host tolerance, but for other economically important traits simultaneously. This tool will thus future-proof our forests by mitigating the risk of disease outbreaks induced by future changes in climate.
Anemia and perioperative mortality in non-cardiac surgery patients: a secondary analysis based on a single-center retrospective study
Authors: Luo Xueying , Li Feng , Hu Haofei , Liu Baoer , Zheng Sujing , Yang Liping , Gao Rui , Li Ya , Xi Rao , He Jinsong 
Published: May 2020

Abstract
Background
Evidence regarding the relationship between anemia and perioperative prognosis is controversial. The study was conducted to highlight the specific relationship between anemia and perioperative mortality in non-cardiac surgery patients over 18 years of age.

Methods
This study was a retrospective analysis of the electronic medical records of 90,784 patients at the Singapore General Hospital from January 1, 2012 to October 31, 2016. Multivariate regression, propensity score analysis, doubly robust estimation, and an inverse probability-weighting model was used to ensure the robustness of our findings.

Results
We identified 85,989 patients, of whom75, 163 had none or mild anemia (Hemoglobin>90g/L) and 10,826 had moderate or severe anemia (Hemoglobin≤90g/L). 8,857 patients in each study exposure group had similar propensity scores and were included in the analyses. In the doubly robust model, postoperative 30-day mortality rate was increased by 0.51% (n = 219) in moderate or severe anemia group (Odds Ratio, 1.510; 95% Confidence Interval (CI), 1.049 to 2.174) compared with none or mild anemia group (2.47% vs.1.22%, P<0.001). Moderate or severe anemia was also associated with increased postoperative blood transfusion rates (OR, 5.608; 95% CI, 4.026 to 7.811, P < 0.001). There was no statistical difference in Intensive Care Unit (ICU) admission rate among different anemia groups within 30 days after surgery (P=0.104).

Discussion
In patients undergoing non-cardiac surgery over 18 years old, moderate or severe preoperative anemia would increase the occurrence of postoperative blood transfusion and the risk of death, rather than ICU admission within 30 days after surgery.