bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation
Authors: Chang Hao-Chun , Huang Hsuan-Cheng , Juan Hsueh-Fen , Hsu Chia-Lang
Published: December 2019

Background

Super-enhancer RNAs (seRNAs) are a kind of noncoding RNA transcribed from super-enhancer regions. The regulation mechanism and functional role of seRNAs are still unclear. Although super-enhancers play a critical role in the core transcriptional regulatory circuity of embryonic stem cell (ESC) differentiation, whether seRNAs have similar properties should be further investigated.

Results

We analyzed cap analysis gene expression sequencing (CAGE-seq) datasets collected during the differentiation of embryonic stem cells (ESCs) to cardiomyocytes to identify the seRNAs. A non-negative matrix factorization algorithm was applied to decompose the seRNA profiles and reveal two hidden stages during the ESC differentiation. We further identified 95 and 78 seRNAs associated with early- and late-stage ESC differentiation, respectively. We found that the binding sites of master regulators of ESC differentiation, including NANOG, FOXA2, and MYC, were significantly observed in the loci of the stage-specific seRNAs. Based on the investigation of genes coexpressed with seRNA, these stage-specific seRNAs might be involved in cardiac-related functions such as myofibril assembly and heart development and act in trans to regulate the co-expressed genes.

Conclusions

In this study, we used a computational approach to demonstrate the possible role of seRNAs during ESC differentiation.
Sketch distance-based clustering of chromosomes for large genome database compression
Authors: Tang Tao , Liu Yuansheng , Zhang Buzhong , Su Benyue , Li Jinyan
Published: December 2019

Background

The rapid development of Next-Generation Sequencing technologies enables sequencing genomes with low cost. The dramatically increasing amount of sequencing data raised crucial needs for efficient compression algorithms. Reference-based compression algorithms have exhibited outstanding performance on compressing single genomes. However, for the more challenging and more useful problem of compressing a large collection ofngenomes, straightforward application of these reference-based algorithms suffers a series of issues such as difficult reference selection and remarkable performance variation.

Results

We propose an efficient clustering-based reference selection algorithm for reference-based compression within separate clusters of thengenomes. This method clusters the genomes into subsets of highly similar genomes using MinHash sketch distance, and uses the centroid sequence of each cluster as the reference genome for an outstanding reference-based compression of the remaining genomes in each cluster. A final reference is then selected from these reference genomes for the compression of the remaining reference genomes. Our method significantly improved the performance of the-state-of-art compression algorithms on large-scale human and rice genome databases containing thousands of genome sequences. The compression ratio gain can reach up to 20-30% in most cases for the datasets from NCBI, the 1000 Human Genomes Project and the 3000 Rice Genomes Project. The best improvement boosts the performance from 351.74 compression folds to 443.51 folds.

Conclusions

The compression ratio of reference-based compression on large scale genome datasets can be improved via reference selection by applying appropriate data preprocessing and clustering methods. Our algorithm provides an efficient way to compress large genome database.
Human protein-RNA interaction network is highly stable across mammals
Authors: Ramakrishnan Aarthi , Janga Sarath Chandra
Published: December 2019

Background

RNA-binding proteins (RBPs) are crucial in modulating RNA metabolism in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Although previous studies on the conservation of RBP targets have been carried out in lower eukaryotes such as yeast, relatively little is known about the extent of conservation of the binding sites of RBPs across mammalian species.

Results

In this study, we employ CLIP-seq datasets for 60 human RBPs and demonstrate that most binding sites for a third of these RBPs are conserved in at least 50% of the studied vertebrate species. Across the studied RBPs, binding sites were found to exhibit a median conservation of 58%, ~ 20% higher than random genomic locations, suggesting a significantly higher preservation of RBP-RNA interaction networks across vertebrates. RBP binding sites were highly conserved across primates with weak conservation profiles in birds and fishes. We also note that phylogenetic relationship between members of an RBP family does not explain the extent of conservation of their binding sites across species. Multivariate analysis to uncover features contributing to differences in the extents of conservation of binding sites across RBPs revealed RBP expression level and number of post-transcriptional targets to be the most prominent factors. Examination of the location of binding sites at the gene level confirmed that binding sites occurring on the 3′ region of a gene are highly conserved across species with 90% of the RBPs exhibiting a significantly higher conservation of binding sites in 3′ regions of a gene than those occurring in the 5′. Gene set enrichment analysis on the extent of conservation of binding sites to identify significantly associated human phenotypes revealed an enrichment for multiple developmental abnormalities.

Conclusions

Our results suggest that binding sites of human RBPs are highly conserved across primates with weak conservation profiles in lower vertebrates and evolutionary relationship between members of an RBP family does not explain the extent of conservation of their binding sites. Expression level and number of targets of an RBP are important factors contributing to the differences in the extent of conservation of binding sites. RBP binding sites on 3′ ends of a gene are the most conserved across species. Phenotypic analysis on the extent of conservation of binding sites revealed the importance of lineage-specific developmental events in post-transcriptional regulatory network evolution.
SMaSH: Sample matching using SNPs in humans
Authors: Westphal Maximillian , Frankhouser David , Sonzone Carmine , Shields Peter G. , Yan Pearlly , Bundschuh Ralf
Published: December 2019

Background

Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotide polymorphisms (SNPs), omics data types often only provide low to moderate coverage, thus requiring integration of evidence from a large number of SNPs to determine if two samples derive from the same individual or not.

Methods

We select about six thousand SNPs in the human genome and develop a Bayesian framework that is able to robustly identify sample matches between next generation sequencing data sets.

Results

We validate our approach on a variety of data sets. Most importantly, we show that our approach can establish identity between different omics data types such as Exome, RNA-Seq, and MethylCap-Seq. We demonstrate how identity detection degrades with sample quality and read coverage, but show that twenty million reads of a fairly low quality RNA-Seq sample are still sufficient for reliable sample identification.

Conclusion

Our tool, SMASH, is able to identify sample mismatches in next generation sequencing data sets between different sequencing modalities and for low quality sequencing data.
iPseU-NCP: Identifying RNA pseudouridine sites using random forest and NCP-encoded features
Authors: Nguyen-Vo Thanh-Hoang , Nguyen Quang H. , Do Trang T.T. , Nguyen Thien-Ngan , Rahardja Susanto , Nguyen Binh P.
Published: December 2019

Background

Pseudouridine modification is most commonly found among various kinds of RNA modification occurred in both prokaryotes and eukaryotes. This biochemical event has been proved to occur in multiple types of RNAs, including rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, gaining a holistic understanding of pseudouridine modification can contribute to the development of drug discovery and gene therapies. Although some laboratory techniques have come up with moderately good outcomes in pseudouridine identification, they are costly and required skilled work experience. We propose iPseU-NCP – an efficient computational framework to predict pseudouridine sites using the Random Forest (RF) algorithm combined with nucleotide chemical properties (NCP) generated from RNA sequences. The benchmark dataset collected from Chen et al. (2016) was used to develop iPseU-NCP and fairly compare its performances with other methods.

Results

Under the same experimental settings, comparing with three state-of-the-art methods including iPseU-CNN, PseUI, and iRNA-PseU, the Matthew’s correlation coefficient (MCC) of our model increased by about 20.0%, 55.0%, and 109.0% when tested on the H. sapiens (H_200) dataset and by about 6.5%, 35.0%, and 150.0% when tested on the S. cerevisiae (S_200) dataset, respectively. This significant growth in MCC is very important since it ensures the stability and performance of our model. With those two independent test datasets, our model also presented higher accuracy with a success rate boosted by 7.0%, 13.0%, and 20.0% and 2.0%, 9.5%, and 25.0% when compared to iPseU-CNN, PseUI, and iRNA-PseU, respectively. For majority of other evaluation metrics, iPseU-NCP demonstrated superior performance as well.

Conclusions

iPseU-NCP combining the RF and NPC-encoded features showed better performances than other existing state-of-the-art methods in the identification of pseudouridine sites. This also shows an optimistic view in addressing biological issues related to human diseases.
Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)
Authors: Silva-Pereira Taiana T. , Ikuta Cássia Y. , Zimpel Cristina K. , Camargo Naila C. S. , de Souza Filho Antônio F. , Ferreira Neto José S. , Heinemann Marcos B. , Guimarães Ana M. S.
Published: December 2019

Background

Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization.

Results

We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC.

Conclusion

The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.
Proximal femoral head transcriptome reveals novel candidate genes related to epiphysiolysis in broiler chickens
Authors: de Oliveira Peixoto Jane , Savoldi Igor Ricardo , Ibelli Adriana Mércia Guaratini , Cantão Maurício Egídio , Jaenisch Fátima Regina Ferreira , Giachetto Poliana Fernanda , Settles Matthew Lee , Zanella Ricardo , Marchesi Jorge Augusto Petroli , Pandolfi José Rodrigo , Coutinho Luiz Lehmann , Ledur Mônica Corrêa
Published: December 2019

Background

The proximal femoral head separation (FHS) or epiphysiolysis is a prevalent disorder affecting the chicken femur epiphysis, being considered a risk factor to infection which can cause bacterial chondronecrosis with osteomyelitis in broilers. To identify the genetic mechanisms involved in epiphysiolysis, differentially expressed (DE) genes in the femur of normal and FHS-affected broilers were identified using RNA-Seq technology. Femoral growth plate (GP) samples from 35-day-old commercial male broilers were collected from 4 healthy and 4 FHS-affected broilers. Sequencing was performed using an Illumina paired-end protocol. Differentially expressed genes were obtained using the edgeR package based on the False Discovery Rate (FDR < 0.05).

Results

Approximately 16 million reads/sample were generated with 2 × 100 bp paired-end reads. After data quality control, approximately 12 million reads/sample were mapped to the reference chicken genome (Galgal5). A total of 12,645 genes were expressed in the femur GP. Out of those, 314 were DE between groups, being 154 upregulated and 160 downregulated in FHS-affected broilers. In the functional analyses, several biological processes (BP) were overrepresented. Among them, those related to cell adhesion, extracellular matrix (ECM), bone development, blood circulation and lipid metabolism, which are more related to chicken growth, are possibly involved with the onset of FHS. On the other hand, BP associated to apoptosis or cell death and immune response, which were also found in our study, could be related to the consequence of the FHS.

Conclusions

Genes with potential role in the epiphysiolysis were identified through the femur head transcriptome analysis, providing a better understanding of the mechanisms that regulate bone development in fast-growing chickens. In this study, we highlighted the importance of cell adhesion and extracellular matrix related genes in triggering FHS. Furthermore, we have shown new insights on the involvement of lipidemia and immune response/inflammation with FHS in broilers. Understanding the changes in the GP transcriptome might support breeding strategies to address poultry robustness and to obtain more resilient broilers.
Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family
Authors: Rajarammohan Sivasubramanian , Paritosh Kumar , Pental Deepak , Kaur Jagreet
Published: December 2019

Background

Alternaria brassicae, a necrotrophic pathogen, causesAlternariaLeaf Spot, one of the economically important diseases ofBrassicacrops. Many otherAlternaria spp.such asA. brassicicolaandA. alternataare known to cause secondary infections in theA. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity ofA. brassicaeare unknown. In this study, we annotated and characterised the recently announced genome assembly ofA. brassicaeand compared it with otherAlternaria spp.to gain insights into its pathogenic lifestyle.

Results

We also sequenced the genomes of twoA. alternataisolates that were co-infectingB. junceausing Nanopore MinION sequencing for additional comparative analyses within theAlternariagenus. Genome alignments within theAlternaria spp.revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome ofA. brassicae, a large-sporedAlternariaspecies, contains a dispensable chromosome. We identified 460A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor ofA. brassicae.

Conclusion

The study provides a perspective into the unique and shared repertoire of genes within theAlternariagenus and identifies genes that could be contributing to the pathogenic lifestyle ofA. brassicae.
Gut bacteria of weevils developing on plant roots under extreme desert conditions
Authors: Meng Fengqun , Bar-Shmuel Nitsan , Shavit Reut , Behar Adi , Segoli Michal
Published: December 2019

Background

Many phytophagous insects, whose diet is generally nitrogen-poor, rely on gut bacteria to compensate for nutritional deficits. Accordingly, we hypothesized that insects in desert environments may evolve associations with gut bacteria to adapt to the extremely low nutrient availability. For this, we conducted a systematic survey of bacterial communities in the guts of weevils developing inside mud chambers affixed to plant roots in the Negev Desert of Israel, based on 16S rRNA gene amplicon sequencing.

Results

Our analyses revealed that gut bacterial communities in weevil larvae were similar across a wide geographical range, but differed significantly from those of the mud chambers and of the surrounding soils. Nevertheless, a high proportion of bacteria (including all of the core bacteria) found in the weevils were also detected in the mud chambers and soils at low relative abundances. The genus Citrobacter (of the Enterobacteriaceae family) was the predominant group in the guts of all individual weevils. The relative abundance of Citrobacter significantly decreased at the pupal and adult stages, while bacterial diversity increased. A mini literature survey revealed that members of the genus Citrobacter are associated with nitrogen fixation, recycling of uric acid nitrogen, and cellulose degradation in different insects.

Conclusions

The results suggest that although weevils could potentially acquire their gut bacteria from the soil, weevil host internal factors, rather than external environmental factors, were more important in shaping their gut bacterial communities, and suggest a major role for Citrobacter in weevil nutrition in this challenging environment. This study highlights the potential involvement of gut bacteria in the adaptation of insects to nutritional deficiencies under extreme desert conditions.
Altered functional connectivity of the nucleus accumbens subdivisions in amphetamine-type stimulant abusers: a resting-state fMRI study
Authors: Wang Yun , Yan Kai-Juan , Fan Chen-Xiao , Luo Xiao-Nian , Zhou Yuan
Published: December 2019

Background

The growing abuse of amphetamine-type stimulants leads to new challenges to human health. A possible addiction mechanism has been proposed by altered functional architecture of the nucleus accumbens (NAc) during resting state. NAc contains different subdivisions and they may play different roles in addiction. The aim of the present study was to examine whether there are common or distinct patterns of functional connectivity of the NAc subdivisions in amphetamine-type stimulant abusers (ATSAs).

Methods

The present study recruited 17 male ATSAs and 22 healthy male controls. All the subjects underwent resting-state functional magnetic resonance imaging (fMRI) with their eyes closed. The NAc was divided into core-like and shell-like subdivisions. We used seed-based resting-state functional connectivity (RSFC) analyses to identify differences in brain functional architecture between ATSAs and healthy controls (HCs).

Results

ATSAs had lower positive RSFCs with all of the NAc subdivisions over the left orbital part of superior frontal gyrus and higher positive RSFCs with the NAc subdivisions over the left opercular part of inferior frontal gyrus than HCs, which indicates common abnormalities across the NAc subdivisions in ATSAs. In addition, the RSFCs between the NAc subdivisions and the left orbital part of superior frontal gyrus were negatively correlated with the addiction severity in ATSAs.

Conclusion

These results provide evidence that there are common RSFC patterns of the NAc subdivisions in ATSAs. The abnormality indicated by disrupted functional connectivity between the NAc subdivisions and prefrontal cortex suggests abnormal interaction between the rewarding process and cognitive control in ATSAs. Our results shed insight on the neurobiological mechanisms of ATSA and suggest potential novel therapeutic targets for treatment and intervention of ATSAs.
GmWRKY40, a member of the WRKY transcription factor genes identified from Glycine max L., enhanced the resistance to Phytophthora sojae
Authors: Cui Xiaoxia , Yan Qiang , Gan Shuping , Xue Dong , Wang Haitang , Xing Han , Zhao Jinming , Guo Na
Published: December 2019

Background

The WRKY proteins are a superfamily of transcription factors and members play essential roles in the modulation of diverse physiological processes, such as growth, development, senescence and response to biotic and abiotic stresses. However, the biological roles of the majority of the WRKY family members remains poorly understood in soybean relative to the research progress in model plants.

Results

In this study, we identified and characterized GmWRKY40, which is a group IIc WRKY gene. Transient expression analysis revealed that the GmWRKY40 protein is located in the nucleus of plant cells. Expression of GmWRKY40 was strongly induced in soybean following infection with Phytophthora sojae, or treatment with methyl jasmonate, ethylene, salicylic acid, and abscisic acid. Furthermore, soybean hairy roots silencing GmWRKY40 enhanced susceptibility to P. sojae infection compared with empty vector transgenic roots. Moreover, suppression of GmWRKY40 decreased the accumulation of reactive oxygen species (ROS) and modified the expression of several oxidation-related genes. Yeast two-hybrid experiment combined with RNA-seq analysis showed that GmWRKY40 interacted with 8 JAZ proteins with or without the WRKY domain or zinc-finger domain of GmWRKY40, suggesting there were different interaction patterns among these interacted proteins.

Conclusions

Collectively, these results suggests that GmWRKY40 functions as a positive regulator in soybean plants response to P. sojae through modulating hydrogen peroxide accumulation and JA signaling pathway.
ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea
Authors: Sudan Jebi , Singh Ravinder , Sharma Susheel , Salgotra Romesh K. , Sharma Varun , Singh Gurvinder , Sharma Indu , Sharma Swarkar , Gupta Surinder K. , Zargar Sajad Majeed
Published: December 2019

Background

Narrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) inBrassica juncea(AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak,RSPR-01andUrvashi) and Exotic (Donskaja IV,Zem 1andEC287711) genepools.

Results

Sequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set ofB. junceagenotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes.

Conclusions

Despite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity inBrassica juncea.
Identification and characterization analysis of sulfotransferases (SOTs) gene family in cotton (Gossypium) and its involvement in fiber development
Authors: Wang Liyuan , Liu Xiyan , Wang Xiaoyang , Pan Zhaoe , Geng Xiaoli , Chen Baojun , Liu Baoshen , Du Xiongming , Song Xianliang
Published: December 2019

Background

Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the sulphate conjugation reaction involved in plant growth, vigor, stress resistance and pathogen infection.SOTsin Arabidopsis have been carried out and divided into 8 groups. However, the systematic analysis and functional information ofSOTfamily genes in cotton have rarely been reported.

Results

According to the results of BLASTP and HMMER, we isolated 46, 46, 76 and 77SOTgenes in the genomeG. arboreum,G. raimondii,G. barbadenseandG. hirsutum, respectively. A total of 170 in 245SOTswere further classified into four groups based on the orthologous relationships comparing withArabidopsis, and tandem replication primarily contributed to the expansion ofSOTgene family inG. hirsutum. Expression profiles of theGhSOTshowed that most genes exhibited a high level of expression in the stem, leaf, and the initial stage of fiber development. The localization analysis indicated thatGhSOT67expressed in cytoplasm and located in stem and leaf tissue. Additionally, the expression ofGhSOT67were induced and the length of stem and leaf hairs were shortened after gene silencing mediated byAgrobacterium, compared with the blank and negative control plants.

Conclusions

Our findings indicated thatSOTgenes might be associated with fiber development in cotton and provided valuable information for further studies ofSOTgenes inGossypium.
Ectopic expression of citrus UDP-GLUCOSYL TRANSFERASE gene enhances anthocyanin and proanthocyanidins contents and confers high light tolerance in Arabidopsis
Authors: Rao Muhammad Junaid , Xu Yuantao , Huang Yue , Tang Xiaomei , Deng Xiuxin , Xu Qiang
Published: December 2019

Background

Citrus fruits are consumed freshly or as juice to directly provide various dietary flavonoids to humans. Diverse metabolites are present among Citrus genera, and many flavonoids biosynthetic genes were induced after abiotic stresses. To better understand the underlying mechanism, we designed experiments to overexpress a UDP-GLUCOSYL TRANSFERASE gene from sweet orange (Citrus sinensis) to evaluate its possible function in metabolism and response to stress.

Results

Our results demonstrated that overexpression of Cs-UGT78D3 resulted in high accumulation of proanthocyanidins in the seed coat and a dark brown color to transgenic Arabidopsis seeds. In addition, the total contents of flavonoid and anthocyanin were significantly enhanced in the leaves of overexpressed lines. Gene expression analyses indicated that many flavonoid (flavonol) and anthocyanin genes were up-regulated by 4–15 folds in transgenic Arabidopsis. Moreover, after 14 days of high light stress, the transgenic Arabidopsis lines showed strong antioxidant activity and higher total contents of anthocyanins and flavonoids in leaves compared with the wild type.

Conclusion

Our study concluded that the citrus Cs-UGT78D3 gene contributes to proanthocyanidins accumulation in seed coats and confers tolerance to high light stress by accumulating the total anthocyanin and flavonoid contents with better antioxidant potential (due to photoprotective activity of anthocyanin) in the transgenic Arabidopsis.
Comparison of videolaryngoscope-guided versus standard digital insertion techniques of the ProSeal™ laryngeal mask airway: a prospective randomized study
Authors: Ozgul Ulku , Erdil Feray Akgul , Erdogan Mehmet Ali , Begec Zekine , Colak Cemil , Yucel Aytac , Durmus Mahmut
Published: December 2019

Background

This study were designed to investigate the usefulness of the videolaryngoscope-guided insertion technique compared with the standard digital technique for the insertion success rate and insertion conditions of the Proseal™ laryngeal mask airway (PLMA).

Methods

Prospective, one hundred and nineteen patients (ASA I–II, aged 18–65 yr) were randomly divided for PLMA insertion using the videolaryngoscope-guided technique or the standard digital technique. The PLMA was inserted according to the manufacturer’s instructions in the standard digital technique group. The videolaryngoscope-guided technique was performed a C-MAC® videolaryngoscope with D-Blade, under gentle videolaryngoscope guidance, the epiglottis was lifted, and the PLMA was advanced until the tip of the distal cuff reached the oesophagus inlet. The number of insertion attempts, insertion time, oropharyngeal leak pressure, leak volume, fiberoptic bronchoscopic view, peak inspiratory pressure, ease of gastric tube placement, hemodynamic changes, visible blood on PLMA and postoperative airway morbidity were recorded.

Results

The first-attempt success rate (the primary outcome) was higher in the videolaryngoscope-guided technique than in the standard digital technique (p = 0.029). The effect size values with 95% confidence interval were 0.19 (0.01–0.36) for the first and second attempts, 0.09 (− 0.08–0.27) for the first and third attempts, and not computed for the second and third attempts by the groups, respectively.

Conclusion

Videolaryngoscope-guided insertion technique can be a help in case of difficult positioning of a PLMA and can improve the PLMA performance in some conditions. We suggest that the videolaryngoscope-guided technique may be a useful technique if the digital technique fails.

Trial registration

ClinicalTrials.govNCT03852589 date of registration: February 22th 2019.
Bisoprolol transdermal patch for perioperative care of non-cardiac surgery in patients with hypertrophic obstructive cardiomyopathy
Authors: Imori Yoichi , Takano Hitoshi , Mase Hiroshi , Matsuda Junya , Sangen Hideto , Izumi Yuki , Tokita Yukichi , Yamamoto Takeshi , Shimizu Wataru
Published: December 2019

Background

Non-cardiac surgery for hypertrophic obstructive cardiomyopathy (HOCM) is considered to require meticulous perioperative care. β-blockers are considered the first-line drugs for patients with HOCM, and they play a key role in preventing cardiovascular complications in perioperative care. The bisoprolol transdermal patch has recently become available in Japan, and it is useful for patients who are unable to take oral medication during perioperative care. The aim of this case series was to assess the hemodynamic features of patients with HOCM who used the bisoprolol transdermal patch during perioperative care for non-cardiac surgery.

Methods

Between August 2016 and August 2018, we retrospectively analyzed 10 consecutive cases of HOCM with the patients using the bisoprolol transdermal patch during perioperative care. Hemodynamic and echocardiographic features were evaluated before and after patients were switched from oral bisoprolol to transdermal patch therapy or started transdermal patch therapy as a new β-blocker medication. In addition, cardiovascular complications (all-cause death, cardiac death, heart failure, ventricular tachycardia, and ventricular fibrillation) during the perioperative period were evaluated.

Results

There was no significant change in the patients’ heart rate, blood pressure, ejection fraction, and pressure gradient in the left ventricle after switching from oral bisoprolol to the transdermal patch therapy. On the other hand, patients who started using the bisoprolol transdermal patch as a new ß-blocker medication tended to have a decreased heart rate and pressure gradient thereafter, but there was no significant difference in blood pressure or ejection fraction. No cardiovascular complications occurred during the perioperative period.

Conclusions

We described the utilization of the bisoprolol transdermal patch during perioperative care for non-cardiac surgery in patients with HOCM. We determined that the hemodynamic features of these patients did not change significantly after switching to patch therapy. Further, initiation of the bisoprolol transdermal patch as a new ß-blocker medication sufficiently tended to decrease the pressure gradient. This unique approach can be an alternate treatment option for HOCM.

Trial registration

The registry was registered in the University Hospital Medical Information Network Clinical Trials Registry (UMIN000036703). The date of registration was 10/5/2019 and it was “Retrospectively registered”.
Heart rate and heart rate variability comparison between postural orthostatic tachycardia syndrome versus healthy participants; a systematic review and meta-analysis
Authors: Swai Joel , Hu Zixuan , Zhao Xiexiong , Rugambwa Tibera , Ming Gui
Published: December 2019

Background

A number of published literature has reported that, physiologically, heart rate variability (HRV) in patients with postural orthostatic tachycardia syndrome (POTS) to be greatly confounded by age, sex, race, physical fitness, and circadian rhythm. The purpose of this study was to compare between POTS patients versus healthy participants, in terms of heart rate (HR) and HRV after Head-Up tilt test (HUTT), by systematic review and meta-analysis of available published literature.

Methods

MEDLINE (using PubMed interphase), EMBASE and SCOPUS were systematically searched for observational studies comparing POTS patients versus healthy patients, in terms of HR and HRV. HRV was grouped into Time and frequency domain outcome measurements. The time domain was measured as mean RR- interval and mean the square root of the mean of squares of successive R-R waves (rMSSD) in milliseconds. The frequency domain was measured as mean values of Low frequency power (LF), High frequency power (HF), LF/HF-ratio, LF-normalized units (LF(n.u)) and HF-normalized units (HF(n.u)). Demographic data, comorbidities, and mean values of HR, RR- interval, rMSSD, LF, HF, LF/HF-ratio, LF-(n.u) and H.F-n.u were extracted from each group and compared, by their mean differences as an overall outcome measure. Computer software, RevMan 5.3 was utilized, at a 95% significance level.

Results

Twenty (20) eligible studies were found to report 717 POTS and 641 healthy participants. POTS group had a higher mean HR (p < 0.05), lower mean RR-Interval (p < 0.05), lower rMSSD (p < 0.05) than healthy participants. Furthermore, POTS group had lower mean HF(p > 0.05), lower mean LF(p > 0.05), and lower mean HF(n.u) (p > 0.05), higher LF/HF-Ratio (p > 0.05) and higher LF(n.u) (p > 0.05) as compared to healthy participants.

Conclusion

POTS patients have a higher HR than healthy patients after HUTT and lower HRV in terms of time domain measure but not in terms of frequency domain measure. HR and time domain analyses of HRV are more reliable than frequency domain analysis in differentiating POTS patients from the healthy participants. We call upon sensitivity and specificity studies.
Using data linkage to enhance the reporting of cancer outcomes of Aboriginal and Torres Strait Islander people in NSW, Australia
Authors: Tervonen Hanna E. , Purdie Stuart , Creighton Nicola
Published: December 2019

Background

Aboriginal people are known to be under-recorded in routinely collected datasets in Australia. This study examined methods for enhancing the reporting of cancer incidence among Aboriginal people using linked data methodologies.

Methods

Invasive cancers diagnosed in New South Wales (NSW), Australia, in 2010–2014 were identified from the NSW Cancer Registry (NSWCR). The NSWCR data were linked to the NSW Admitted Patient Data Collection, the NSW Emergency Department Data Collection and the Australian Coordinating Register Cause of Death Unit Record File. The following methods for enhancing the identification of Aboriginal people were used: ‘ever-reported’, ‘reported on most recent record’, ‘weight of evidence’ and ‘multi-stage median’. The impact of these methods on the number of cancer cases and age-standardised cancer incidence rates (ASR) among Aboriginal people was explored.

Results

Of the 204,948 cases of invasive cancer, 2703 (1.3%) were recorded as Aboriginal on the NSWCR. This increased with enhancement methods to 4184 (2.0%, ‘ever’), 3257 (1.6%, ‘most recent’), 3580 (1.7%, ‘weight of evidence’) and 3583 (1.7%, ‘multi-stage median’). Enhancement was generally greater in relative terms for males, people aged 25–34 years, people with cancers of localised or unknown degree of spread, people living in urban areas and areas with less socio-economic disadvantage. All enhancement methods increased ASRs for Aboriginal people. The weight of evidence method increased the overall ASR by 42% for males (894.1 per 100,000, 95% CI 844.5–945.4) and 27% for females (642.7 per 100,000, 95% CI 607.9–678.7). Greatest relative increases were observed for melanoma and prostate cancer incidence (126 and 63%, respectively). ASRs for prostate and breast cancer increased from below to above the ASRs of non-Aboriginal people with enhancement of Aboriginal status.

Conclusions

All data linkage methods increased the number of cancer cases and ASRs for Aboriginal people. Enhancement varied by demographic and cancer characteristics. We considered the weight of evidence method to be most suitable for population-level reporting of cancer incidence among Aboriginal people. The impact of enhancement on disparities in cancer outcomes between Aboriginal and non-Aboriginal people should be further examined.
Comprehensive evaluation of effects and safety of statin on the progression of liver cirrhosis: a systematic review and meta-analysis
Authors: Gu Yue , Yang Xueqin , Liang Hang , Li Deli
Published: December 2019

Background

Statin has been more and more widely used in chronic liver disease, however, existed studies have attained contradictory results. According to the present study, we aimed to test the efficacy and safety of statin via a meta-analysis.

Methods

Different databases were searched for full-text publication based on inclusion and exclusion criteria. For data-pooling, fixed-effect model was applied if heterogeneity wasn’t detected. Otherwise, random-effect model was adopted. Heterogeneity was detected by I squire (I2) test. All results of analysis were illustrated as forest plots. Publication bias was assessed using the Begg’s adjusted rank correlation test. Standard mean difference (SMD) was calculated in continuous variables. Pooled hazard ratio or odds ratio was calculated in catergorical variables.

Results

Seventeen clinical studies were finally included. Hepatic portal hemodynamic parameters were improved in statin users for a short-term response. For a long-term follow-up, statin treatment surprisingly decreased mortality rate (HR = 0.782, 95% CI: 0.718–0.846, I2 > 50%) and lower the occurrence of hepatocellular carcinoma (HR = 0.75, 95% CI: 0.64–0.86, I2 > 50%) in liver cirrhosis. Statin seemed not to decrease the risk of esophageal variceal bleeding and spontaneous bacterial peritonitis. However, statin was proved to decrease the risk of hepatic encephalopathy and ascites. Incidence of drug related adverse events didn’t increase in statin users. Dose-dependent effects of statin on hepatocellular carcinoma development, decompensated cirrhosis events occurrence, and liver cirrhosis progression.

Conclusion

Statin influenced parameters of hepatic portal vessel pressure in short-term treatment. Prognosis of liver cirrhosis benefited from statin treatment in long term follow-up. The efficacy and safety of statin in liver cirrhosis treatment is confirmed. To date, similar study is hardly seen before.
Upregulation of musashi1 increases malignancy of hepatocellular carcinoma via the Wnt/β-catenin signaling pathway and predicts a poor prognosis
Authors: Liu Qiuhua , Zhou Cuijie , Zhang Bo
Published: December 2019

Background

Hepatocellular carcinoma (HCC) is a common human malignant cancer due to a high metastatic capacity and the recurrence rate is also high. This study is aim to investigate the role of musashi1 as a potential biomarker for therapy of HCC.

Methods

The mRNA and protein expression levels of musashi1 were detected in HCC samples and cell lines. The malignant properties of HCC cells, including proliferation, invasion and migration were measured by overexpressing or knocking down expression of musashi1. Additionally, the correlation between musashi1 and clinicopathological indexes and prognosis were analyzed. The expression of CD44 was measured and the correlation between CD44 and musashi1 was analyzed.

Results

In vitro cytological experiments demonstrated that musashi1 was elevated in HCC samples and cell lines and this increased expression affected cancer cell viability, migration and invasive capacity by activating of the Wnt/β-catenin signaling pathway. Analysis of clinicopathological characteristics suggested that up-regulation of musashi1 was related to metastasis potential and a poor prognosis. Besides, there was a positive correlation between CD44 and musashi1 expression. Upregulation of musashi1 in malignant liver tumors may have contributed to the maintenance of stem-cell like characteristics of HCC cells.

Conclusions

Upregulation of musashi1 could enhance malignant development of HCC cells and thus might be a novel marker for HCC therapy.
“Sarcopenia and intramuscular fat deposition are associated with poor survival in Indonesian patients with hepatocellular carcinoma: a retrospective study”
Authors: Mardian Yan , Yano Yoshihiko , Ratnasari Neneng , Choridah Lina , Wasityastuti Widya , Setyawan Nurhuda Hendra , Hayashi Yoshitake
Published: December 2019

Background

A large-scale Japanese study showed that low skeletal muscle index (SMI) and intramuscular fat (IMF) deposition are associated with hepatocellular carcinoma (HCC) survival. Here, we evaluated the effects of SMI and IMF on the survival of Indonesian HCC patients, whose characteristics differ from those of Japanese patients.

Methods

SMI and mean muscle attenuation (MA) were evaluated using computed tomography images of the third lumbar vertebra (L3) in a prospective cohort of 100 Indonesian HCC patients. Clinical, laboratory and body composition data were analysed using the Kaplan–Meier method and Cox regression model to investigate which factors are associated with prognosis.

Results

Of 100 patients, 31 were diagnosed with sarcopenia (L3 SMI value ≤36.2 cm2/m2 for men and ≤ 29.6 cm2/m2 for women), and 65 had IMF deposition (MA value ≤44.4 HU for men and ≤ 39.3 HU for women). These groups had shorter median survival than the reference groups (both P < 0.0001). In multivariable analysis, sarcopenia (hazard ratio [HR], 1.921; P = 0.016), IMF deposition (HR, 3.580; P < 0.001), Barcelona Clinic Liver Cancer (BCLC) stages C and D (HR: 2.396, P < 0.01 and HR: 6.131, P < 0.01, respectively), Japan Integrated Staging (JIS) score 4 (HR: 2.067, P = 0.020), and male gender (HR: 3.211, P < 0.001) were independently associated with mortality.

Conclusion

Sarcopenia and IMF deposition showed superior value in combination with BCLC stage and JIS score for predicting the survival of Indonesian HCC patients. Increased awareness and strategies to prevent or reverse these factors might improve patient outcomes. (Electric word counts: 249).
Falls and risk factors of falls for urban and rural community-dwelling older adults in China
Authors: Zhang Li , Ding Zhihong , Qiu Liya , Li An
Published: December 2019

Background

Falls among older people have become a public health concern due to serious health consequences. Despite abundant literature on falls in older people, little is known about the rural-urban differentials in falls among older people in China. This research fills the voids of prior literature by investigating falls and the associated risk factors among Chinese seniors, with a particular focus on the rural-urban differences.

Methods

Data are from the 2010 wave of Chinese Longitudinal Survey on Urban and Rural Elderly. The analysis includes 16,393 respondents aged 65 and over, with 8440 and 7953 of them living in urban and rural areas, respectively. Descriptive analyses are performed to examine incidence, locations, circumstances and consequences of falls in older people. Regression analysis is used to investigate the effects of risk factors on falls among older people in urban and rural China.

Results

The incidence of falls is higher among rural than urban older people. In both settings, older people are more likely to fell outside of home. But common outdoor falls among rural and urban older people differ in terms of locations and circumstances. Urban older people are more likely to report falling on the road whereas their rural counterparts have experienced more falls in the yard. Falls occurring within homes or immediate home surroundings are also common; but few falls occurred in public areas. The rate of hospitalization of urban seniors after falling is higher than that of rural ones. Most risk factors of falls show similar than different effects on rural and urban elders’ risks of falling.

Conclusions

Incidence, locations, circumstances and consequences of falls vary among Chinese rural and urban older people. But most risk factors for falls show similar effects on rural and urban elders’ odds of falling. Implications drawn from this research provide suggestions for the government and local agencies to develop suitable fall prevention strategies which may well be applicable to other countries.