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1.
Emerg Infect Dis ; 26(5)2020 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-32141425

RESUMO

Various interventions for live poultry markets (LPMs) have emerged to control outbreaks of avian influenza A(H7N9) virus in mainland China since March 2013. We assessed the effectiveness of various LPM interventions in reducing transmission of H7N9 virus across 5 annual waves during 2013-2018, especially in the final wave. With the exception of waves 1 and 4, various LPM interventions reduced daily incidence rates significantly across waves. Four LPM interventions led to a mean reduction of 34%-98% in the daily number of infections in wave 5. Of these, permanent closure provided the most effective reduction in human infection with H7N9 virus, followed by long-period, short-period, and recursive closures in wave 5. The effectiveness of various LPM interventions changed with the type of intervention across epidemics. Permanent LPM closure should be considered to maintain sufficient effectiveness of interventions and prevent the recurrence of H7N9 epidemics.

2.
J Neurointerv Surg ; 2020 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-32169931

RESUMO

BACKGROUND: Rates of intra-arterial revascularization treatments (IAT) for acute ischemic stroke (AIS) are increasing in the USA. Using a multi-state stroke registry, we studied the trend in IAT use among patients with AIS over a period spanning 11 years. We examined the impact of IAT rates on hospital procedure volumes and patient outcome after stroke. METHODS: We used data from the Paul Coverdell National Acute Stroke Program (PCNASP) and explored trends in IAT between 2008 and 2018. Patient outcomes were examined by rates of IAT procedures across hospitals. Specifically, outcomes were compared across low-volume (<15 IAT per year), medium-volume (15-30 IAT per year), and high-volume hospitals (>30 IAT per year). Favorable outcome was defined as discharge to home. RESULTS: There were 612 958 patients admitted with AIS to 687 participating hospitals within the PCNASP during this study. Only 2.9% of patients (mean age 68.5 years, 49.3% women) received IAT. The percent of patients with AIS receiving IAT increased from 1% in 2008 to 5.3% in 2018 (p<0.001). The proportion of low-volume hospitals decreased over time (p<0.001), and the proportions of medium-volume (p=0.007) and high-volume hospitals (p<0.001) increased between 2008 and 2018. When compared with medium-volume hospitals, high-volume hospitals had a higher (p<0.0001) and low-volume hospitals had a lower (p<0.0001) percent of patients discharged to home. CONCLUSION: High-volume hospitals were associated with a higher rate of favorable outcome. With the increased use of IAT among patients with AIS, the proportion of low-volume hospitals performing IAT significantly decreased.

3.
Drug Des Devel Ther ; 14: 217-231, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32021106

RESUMO

Introduction: KGF-modified MSCs can promote the repair of spinal cord injury and pulmonary fibrosis injury in rats. However, the effect of KGF-modified MSCs on UC rats is unclear. We aimed to explore the therapeutic effect and possible mechanism of KGF gene-modified MSCs on trinitrobenzene sulfonic acid (TNBS)-induced UC rats. Methods: The lentivirus-mediated KGF gene was introduced into bone marrow MSCs of male rats. Female SD rats were induced to establish a UC model by TNBS. Untreated MSCs, MSCs carrying empty vectors (MSCs-vec) or MSCs carrying KGF gene (MSCs-KGF) were transplanted into UC rats by tail vein injection. Results: Significantly high expression of KGF was observed in the intestinal tissues of the MSCs-KGF group. Compared with the challenged control group, the DAI score, CMDI score and TDI score of the MSCs group, MSCs-vec group and MSCs-KGF group were markedly lower. Treatment with MSCs obviously promoted the expression of claudin-1 and PCNA in intestinal tissues of UC rats. Simultaneously, compared with the challenged control group, the levels of TNF-α, IL-6 and IL-8 in the intestinal tissues of the MSCs groups were significantly decreased, while the levels of IL-10 were significantly increased. Most importantly, we found that MSCs-KGF significantly improved colonic morphology and tissue damage and inflammation in UC rats compared with MSCs and MSCs-vec. Further analysis showed that MSCs-KGF clearly promoted phosphorylation of PI3K and Akt and inhibited nuclear translocation of NF-κB in intestinal tissues of UC rats. Discussion: MSCs, especially KGF-modified MSCs, can improve colonic tissue damage in UC rats by promoting intestinal epithelial cell proliferation and reducing colonic inflammatory response, which may be related to activation of PI3K/Akt pathway and inhibition of NF-κB activation.

4.
Oncogene ; 2020 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-32029901

RESUMO

Myocardin (MYOCD) promotes Smad3-mediated transforming growth factor-ß (TGF-ß) signaling in mouse fibroblast cells. Our previous studies show that TGF-ß/SMADs signaling activation enhances epithelial-mesenchymal transition (EMT) in human non-small cell lung cancer (NSCLC) cells. However, whether and how MYOCD contributes to TGF-ß-induced EMT of NSCLC cells are poorly elucidated. Here, we found that TGF-ß-induced EMT was accompanied by increased MYOCD expression. Interestingly, MYOCD overexpression augmented EMT and invasion of NSCLC cells induced by TGF-ß, whereas knockdown of MYOCD expression attenuated these effects. Overexpression and knockdown of MYOCD resulted in the upregulation and downregulation of TGF-ß-induced Snail mRNA, respectively. Moreover, MYOCD overexpression promoted TGF-ß-stimulated NSCLC cell metastasis in vivo. MYOCD was highly expressed and positively correlated with Snail in metastatic NSCLC tissues. Mechanistically, MYOCD directly interacted with SMAD3 and sustained the formation of TGF-ß-induced nuclear SMAD3/SMAD4 complex, facilitating TGF-ß/SMAD3-induced transactivation of Snail. Importantly, MYOCD was transcriptionally activated by TGF-ß-induced SMAD3/SMAD4 complex and CRISPR/Cas9-mediated silencing of SMAD3/SMAD4 led to a reduction in MYOCD mRNA expression. Taken together, our findings indicate that MYOCD promotes TGF-ß-induced EMT and metastasis of NSCLC and identify a positive feedback loop between MYOCD and SMAD3/SMAD4 driving TGF-ß-induced EMT.

5.
Environ Sci Technol ; 54(5): 2931-2940, 2020 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-32048835

RESUMO

Osmotic power has emerged as one of the promising candidates for clean and renewable energy. However, the advancement of present osmotic power-harvesting technologies, specifically pressure-retarded osmosis (PRO) in this work, is hindered by the unsatisfactory membrane transport properties. Herein, we demonstrate the freestanding transition-metal carbides and graphene oxide hybrid membranes as high-performance PRO membranes. Due to the elimination of internal concentration polarization, the freestanding hybrid membrane can achieve a record-high power density up to approximately 56.4 W m-2 with 2.0 M NaCl as the draw solution and river water (0.017 M) as the feed water at an applied hydraulic pressure difference of 9.66 bar. In addition, the hybrid membranes exhibit enhanced antifouling potential and antibacterial activity. The facile fabrication of the hybrid membranes shed light on a new membrane development platform for the highly anticipated osmotic power-harvesting technologies.


Assuntos
Água Doce , Membranas Artificiais , Osmose , Pressão Osmótica , Pressão , Água
6.
Int J Mol Sci ; 21(3)2020 Feb 04.
Artigo em Inglês | MEDLINE | ID: mdl-32033098

RESUMO

Salmonella typhimurium (S. typhimurium) is a common foodborne pathogen that not only causes diseases and contaminates food, but also causes considerable economic losses. Therefore, it is necessary to find effective and feasible methods to control S. typhimurium. In this study, changes in S. typhimurium after treatment with benzyl isothiocyanate (BITC) were detected by transcriptomics to explore the antibacterial effect of BITC at subinhibitory concentration. The results showed that, in contrast to the control group (SC), the BITC-treated group (SQ_BITC) had 197 differentially expressed genes (DEGs), of which 115 were downregulated and 82 were upregulated. We screened out eight significantly downregulated virulence-related genes and verified gene expression by quantitative Real-time Polymerase Chain Reaction (qRT-PCR). We also selected motility and biofilm formation to observe the effects of BITC on the other virulence related factors of S. typhimurium. The results showed that both swimming and swarming were significantly inhibited. BITC also had a significant inhibitory effect on biofilm formation, and showed an effect on bacterial morphology. These results will be helpful for understanding the mechanism of the antibacterial action of BITC against S. typhimurium and other foodborne pathogens.

7.
Water Res ; 173: 115591, 2020 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-32062226

RESUMO

A process of denitrification filter (DNF) coupled with ultrafiltration (UF) and ozonation (DNF-UF-O3) has been widely applied to advanced nitrogen removal for wastewater reclamation. Despite of the effective removal of nitrogen by DNF, the influence of DNF stage on the operation of UF was still unclear. In this study, a laboratory filtration system was used to investigate the membrane fouling potential of DNF effluent and the fouling control of ozonation. The membrane fouling potential was proved to be increased significantly after DNF stage and alleviated with ozonation treatment. With the help of UV-vis, fluorescence spectroscopy, scanning electron microscopy (SEM) and molecular weight (MW) analysis, the change of DOM component characteristics was proved to be in accordance with the change of fouling potential. The water samples were further fractionated into six hydrophobic/hydrophilic acidic/basic/neutral fractions, among which hydrophobic acids (HOA) and hydrophobic neutrals (HON) dominated the membrane fouling potential of DNF effluent. Detailed study of each fraction revealed that higher MW components in HOA and HON played a crucial role in the fouling of UF membrane. The dominant component of membrane fouling could be degraded and removed by ozonation, and therefore significant fouling alleviation was achieved. These results indicated that in the process of wastewater reclamation, besides conventional water quality indexes, more detailed water features should also be taken into consideration to optimize the whole process. Moreover, the control effects by ozonation could be monitored simply according to the change of specific UV absorbance (SUVA) and fluorescence intensity as surrogates in engineering applications. According to these results, a modified DNF-O3-UF process with O3 dosage of 3 mg/L was proposed simply by reversing the sequence of UF and O3 with no more infrastructure. This modified DNF-O3-UF process was expected to enlarge the produce capacity of reclaimed water with much lower electricity costs and chemical consumption.

8.
Environ Sci Process Impacts ; 22(1): 217-226, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31898705

RESUMO

In the rhizosphere, plant root exudates can mediate the toxicity of antibiotics on microorganisms, yet the mechanisms are poorly understood. To simulate the antibiotic contamination of global rivers and lakes, the current study investigated the effects of two antibiotics (ofloxacin at 8.69 × 104 ng L-1 and tetracycline at 8.62 × 104 ng L-1) and their binary combination (8.24 × 104 ng L-1 ofloxacin and 7.11 × 104 ng L-1 tetracycline) on bacterial communities in micro-polluted constructed wetlands with and without artificial root exudates. The two antibiotics had no significant effects on the removal of excess carbon and nitrogen from the microcosms treated with and without exudates. Furthermore, with regard to bacterial community structure, antibiotic exposure increased the bacterial richness of bulk and exudate treated microcosms (P < 0.05). However, a significant increase (P < 0.05) in bacterial diversity elicited by ofloxacin and antibiotic mixture exposure was only observed in microcosms with exudates. In exudate treated microcosms, ofloxacin promoted the relative abundance of Arthrobacter spp., which are ofloxacin-resistant bacterial species, which significantly varied from what was observed in microcosms free of exudates. Moreover, tetracycline, ofloxacin and their combination all significantly increased the relative abundance of nitrogen cycling bacteria Rhizobacter spp. and Rhizobium spp., and decreased the relative abundance of antibiotic-resistant bacteria Pseudomonas spp. Simultaneously, with regard to bacterial community functions, the functional profiles (Kyoto Encyclopedia of Genes and Genomes) showed that the pathways of amino acid and carbohydrate metabolism were enhanced by antibiotics in microcosms with exudates. The findings illustrate that antibiotics not only alter the bacterial structure and composition but also change their functional properties in constructed wetlands, and these interruption effects could be affected by root exudates of plants, which may further reveal the ecological implication of plants in constructed wetlands.


Assuntos
Antibacterianos , Microbiota , Rizosfera , Áreas Alagadas , Antibacterianos/toxicidade , Microbiota/efeitos dos fármacos , Nitrogênio , Raízes de Plantas/microbiologia
9.
Sci Total Environ ; 713: 136673, 2020 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-31958736

RESUMO

Membrane fouling is an inevitable disadvantage of the reverse osmosis (RO) process for wastewater reclamation. In order to clarify the development process of membrane fouling, all the fouled membranes along a feed channel of a two-stage industrial-scale RO system for wastewater reclamation (six elements in each stage) were autopsied and analyzed. The water flux and salt rejection efficiency of the fouled membranes at the head and tail were the lowest among 12 elements, thereby indicating more severe fouling on these membranes. In this RO system, most of the organic compounds deposited on the head elements of each stage were mainly composed of proteins, polysaccharides, and fulvic acid. The ATP concentrations of the foulants on the first and twelfth elements were much higher than those of the other elements, suggesting severe biofouling. Although microbes can cause organic fouling owing to extracellular polymeric substances production, no clear correlation was found between organic fouling and biofouling in this study. For example, the ATP concentrations on the second element and seventh element were similar (1.16 ng/cm2 and 1.26 ng/cm2, respectively), thereby suggesting a similar extent of biofouling, but organic fouling of the second element was relatively slight (DOC: 24.8 mg/m2) compared with that of the seventh element (DOC: 46.2 mg/m2). The seventh element (ATP: 1.26 ng/cm2) was more severely biofouled than the eighth element (ATP: 0.15 ng/cm2), but they suffered from the same level of organic fouling (DOC: 46.2 mg/m2 and 47.1 mg/m2, respectively). Approximately 70% of metallic elements, predominantly Fe, were deposited on the first element. Although the concentration of Fe in the feed water was much lower than those of Ca and Mg, the concentration of Fe on the first three elements was significantly higher than that of any other element, suggesting that Fe was more easily deposited on the RO membranes.

10.
Front Med ; 2020 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-31912429

RESUMO

Mesial temporal lobe epilepsy (mTLE), the most common type of focal epilepsy, is associated with functional and structural brain alterations. Machine learning (ML) techniques have been successfully used in discriminating mTLE from healthy controls. However, either functional or structural neuroimaging data are mostly used separately as input, and the opportunity to combine both has not been exploited yet. We conducted a multimodal ML study based on functional and structural neuroimaging measures. We enrolled 37 patients with left mTLE, 37 patients with right mTLE, and 74 healthy controls and trained a support vector ML model to distinguish them by using each measure and the combinations of the measures. For each single measure, we obtained a mean accuracy of 74% and 69% for discriminating left mTLE and right mTLE from controls, respectively, and 64% when all patients were combined. We achieved an accuracy of 78% by integrating functional data and 79% by integrating structural data for left mTLE, and the highest accuracy of 84% was obtained when all functional and structural measures were combined. These findings suggest that combining multimodal measures within a single model is a promising direction for improving the classification of individual patients with mTLE.

11.
Artigo em Inglês | MEDLINE | ID: mdl-31944979

RESUMO

In this paper, we present a data-driven approach for modeling and animation of 3D necks. Our method is based on a new neck animation model, that decomposes the neck animation into local deformation caused by larynx motion and global deformation driven by head poses, facial expressions, and speech. A skinning model is introduced for modeling local deformation and underlying larynx motions, while the global neck deformation caused by each factor is modeled by its corrective blendshape set, respectively. Based on this neck model, we introduce a regression method to drive the larynx motion and neck deformation from speech. Both the neck model and the speech regressor are learned from a dataset of 3D neck animation sequences captured from different identities. Our neck model significantly improves the realism of facial animation and allows users to easily create plausible neck animations from speech and facial expressions. We verify our neck model and demonstrate its advantages in 3D neck tracking and animation.

12.
World J Pediatr ; 16(1): 82-88, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31529313

RESUMO

BACKGROUND: Fibrodysplasia ossificans progressiva (FOP) is a rare and disabling heritable connective tissue disease that is difficult to treat. This study seeks to explore the clinical characteristics, clinical manifestations, treatment and prognosis of FOP to provide a clinical basis for its early diagnosis and treatment. METHODS: Twenty-six children with FOP were retrospectively analyzed in terms of their onset, clinical manifestations, auxiliary examinations and treatment. RESULTS: Among the 26 cases, the youngest age of manifestation of mass was 8 days after birth, and the average age was 3 years and 2 months. The peak age was 2-5 years old. Inflammatory mass and toe-finger deformity are the main early clinical manifestations of the disease. These inflammatory masses often lead to hard osteogenic deposits that initially mainly involve the central axis, such as the neck (22/26, 84.6%), back (20/26, 76.9%), and head (13/26, 50%). Toe-finger deformity mainly manifests as symmetrical great toe deformity, or short and deformed thumb and little finger. The diagnosis of FOP requires typical clinical manifestations or ACVR1 gene detection. The main therapeutic drugs for FOP include glucocorticoids and non-steroidal anti-inflammatory drugs. Although not compliant with the recommended medical management of FOP, in our clinical practice children with uncontrollable illness could be treated using a variety of immunosuppressive agents in combination. CONCLUSIONS: FOP is a rare autosomal dominant heritable disease. The main clinical manifestations observed in this study were recurrent inflammatory mass and toe-finger deformity. If the diagnosis and treatment are not performed in a timely manner, serious complications are likely to affect the prognosis. Therefore, early diagnosis and active treatment should be performed.

13.
Diabetes ; 69(3): 342-354, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31836690

RESUMO

Human but not mouse islets transplanted into immunodeficient NSG mice effectively accumulate lipid droplets (LDs). Because chronic lipid exposure is associated with islet ß-cell dysfunction, we investigated LD accumulation in the intact human and mouse pancreas over a range of ages and states of diabetes. Very few LDs were found in normal human juvenile pancreatic acinar and islet cells, with numbers subsequently increasing throughout adulthood. While accumulation appeared evenly distributed in postjuvenile acinar and islet cells in donors without diabetes, LDs were enriched in islet α- and ß-cells from donors with type 2 diabetes (T2D). LDs were also found in the islet ß-like cells produced from human embryonic cell-derived ß-cell clusters. In contrast, LD accumulation was nearly undetectable in the adult rodent pancreas, even in hyperglycemic and hyperlipidemic models or 1.5-year-old mice. Taken together, there appear to be significant differences in pancreas islet cell lipid handling between species, and the human juvenile and adult cell populations. Moreover, our results suggest that LD enrichment could be impactful to T2D islet cell function.

14.
J Nanosci Nanotechnol ; 20(6): 3424-3431, 2020 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-31748035

RESUMO

The AgBrO3/few-layer g-C3N4 composite photocatalyst has been developed via an in-situ synthetic method. The structure, morphology, light response range, separation and migration efficiency of the photogenerated electron-hole pairs and element valence state of the as-obtained samples have been characterized. The tetracycline was used to discuss the photocatalytic activities of the samples. The photocatalytic degradation mechanism of the as-obtained composites was also researched. The analysis results show that the photocatalytic degradation property of the asobtained composite photocatalyst appears to the tendency of first increasing and then decreasing with increasing the amount of AgBrO3 under visible light illumination. When the mass ratio of AgBrO3 to g-C3N4 is 4:3, in 60 min, the photocatalytic degradation efficiency of the as-obtained composites reaches the maximum of 79%. It is 37% and 45% higher than that of pure AgBrO3 and g-C3N4, respectively. Moreover, the separation and migration efficiency of the photogenerated electron-hole pairs of the as-prepared composites are also enhanced. In addition, superoxide radicals and holes are the dominant active species during the photocatalytic degradation process.

15.
Bioresour Technol ; 296: 122368, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31735699

RESUMO

Agricultural wastes of cow manure and wheat straw were used to prepare montmorillonite (Mt)-biochars (CMt and WMt) for sorptive removal of 17ß-estradiol (E2) from aqueous solution. The E2 adsorption performance of the two Mt-biochars was investigated using systematic adsorption kinetics and isotherms. The results exhibited that the maximum E2 adsorption amount of CMt was 41.02 mg/g, while it was 62.89 mg/g for WMt. Meanwhile, intraparticle diffusion model demonstrated that intraparticle diffusion was not the only rate-limiting step, both film diffusion and intraparticle diffusion were involved in the diffusion process. Higher pH levels (>10) decreased the adsorption capacities of Mt-biochars for E2. However, the ionic strength and the background electrolytes did not significantly affect adsorption process. Moreover, the two Mt-biochars both exhibited excellent regeneration and reusability. These results provided a potential solution to the recycling of agricultural wastes and the problem of estrogen contaminant.


Assuntos
Bentonita , Carvão Vegetal , Adsorção , Animais , Bovinos , Estradiol , Feminino
16.
Org Lett ; 22(1): 284-289, 2020 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-31845811

RESUMO

The first example of transition-metal catalyzed multicomponent carboannulation of [60]fullerene has been developed. [60]Fullerene, 2-(2,3-allenyl)malonates, and (hetero)aryl iodides undergo a Pd(0)-catalyzed tandem coupling-carboannulation process for regioselective access to novel polysubstituted [60]fullerene-fused cyclopentane derivatives with a wide range of substrate scope and high functional group compatibility. A plausible mechanism involving the formation of a fullerene-π-allylpalladium complex with the characteristic of a fullerene cation as a key intermediate has been proposed.

17.
Biomed Res Int ; 2019: 6764919, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31828119

RESUMO

The digestive tract is home to millions of microorganisms and is the main and most important part of bacterial colonization. On one hand, the abundant bacterial community in intestinal tissues may pose potential health challenges such as inflammation and sepsis in cases of opportunistic invasion. Thus, the immune system has evolved and adapted to maintain the symbiotic relationship between host and microbiota. On the other hand, the intestinal microflora also exerts an immunoregulatory function to maintain host immune homeostasis, which cannot be neglected. In addition, the interaction of either microbiota or probiotics with immune system in regard to therapeutic applications is an area of great interest, and novel therapeutic strategies remain to be investigated. The review will elucidate interactions between intestinal microflora/probiotics and the immune system as well as novel therapeutic strategies.

18.
Zhongguo Zhong Yao Za Zhi ; 44(21): 4605-4611, 2019 Nov.
Artigo em Chinês | MEDLINE | ID: mdl-31872654

RESUMO

To analysis the SSR loci information in the transcriptome of Cordyceps sinensis and develop SSR molecular markers,MISA(MicroSatellite) software was used to analyze the microsatellites information from 16 875 unigene sequences and SSR primer designed by Primer 3. 0. In total,5 899 SSRs were detected in 4 252 unigene with the distribution frequency of 34. 99%,which was represented by 74 repeat motifs and SSR loci occurred per 7 952 bp in length. In the SSRs,the mono-nucleotide was the most abundant repeat motif(42. 5%),followed by tri-nucleotide(34. 48%),C/G and CCG/CGG were the dominant repeat motifs,respectively. The number of repetitions of the six SSR repeat types was concentrated on 5 to 12 times,and the length was mostly less than 24 bp. A total of 12 282 pairs of primers were screened and selected 20 pairs of primers for validity detection randomly,10 pairs of primers amplified the expected specific bands,and primer P1 has significant polymorphism. Moreover,it was found that unigene containing SSR loci is mainly related to genetic and environmental functions after GO and KEGG annotation. In conclusion,these SSR loci in the transcriptome of O. sinensis are high in frequency,rich in primitive types,high in polymorphism,and highly available,which will provides abundant candidate molecular markers for its genetic diversity analysis,resource identification protection,and gene function research.


Assuntos
Cordyceps/genética , Transcriptoma , Etiquetas de Sequências Expressas , Repetições de Microssatélites , Polimorfismo Genético
19.
Genome Res ; 29(12): 2056-2072, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31694868

RESUMO

Genome-wide accurate identification and quantification of full-length mRNA isoforms is crucial for investigating transcriptional and posttranscriptional regulatory mechanisms of biological phenomena. Despite continuing efforts in developing effective computational tools to identify or assemble full-length mRNA isoforms from second-generation RNA-seq data, it remains a challenge to accurately identify mRNA isoforms from short sequence reads owing to the substantial information loss in RNA-seq experiments. Here, we introduce a novel statistical method, annotation-assisted isoform discovery (AIDE), the first approach that directly controls false isoform discoveries by implementing the testing-based model selection principle. Solving the isoform discovery problem in a stepwise and conservative manner, AIDE prioritizes the annotated isoforms and precisely identifies novel isoforms whose addition significantly improves the explanation of observed RNA-seq reads. We evaluate the performance of AIDE based on multiple simulated and real RNA-seq data sets followed by PCR-Sanger sequencing validation. Our results show that AIDE effectively leverages the annotation information to compensate the information loss owing to short read lengths. AIDE achieves the highest precision in isoform discovery and the lowest error rates in isoform abundance estimation, compared with three state-of-the-art methods Cufflinks, SLIDE, and StringTie. As a robust bioinformatics tool for transcriptome analysis, AIDE enables researchers to discover novel transcripts with high confidence.

20.
Clin Neuroradiol ; 2019 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-31696281

RESUMO

PURPOSE: To investigate the long-term clinical and angiographic outcomes and their related predictors in endovascular treatment (EVT) of small (<5 mm) ruptured intracranial aneurysms (SRA). METHODS: The study retrospectively reviewed patients with SRAs who underwent EVT between September 2011 and December 2016 in two Chinese stroke centers. Medical charts and telephone call follow-up were used to identify the overall unfavorable clinical outcomes (OUCO, modified Rankin score ≤2) and any recanalization or retreatment. The independent predictors of OUCO and recanalization were studied using univariate and multivariate analyses. Multivariate Cox proportional hazards models were used to identify the predictors of retreatment. RESULTS: In this study 272 SRAs were included with a median follow-up period of 5.0 years (interquartile range 3.5-6.5 years) and 231 patients with over 1171 aneurysm-years were contacted. Among these, OUCO, recanalization, and retreatment occurred in 20 (7.4%), 24 (12.8%), and 11 (7.1%) patients, respectively. Aneurysms accompanied by parent vessel stenosis (AAPVS), high Hunt-Hess grade, high Fisher grade, and intraoperative thrombogenesis in the parent artery (ITPA) were the independent predictors of OUCO. A wide neck was found to be a predictor of recanalization. The 11 retreatments included 1 case of surgical clipping, 6 cases of coiling, and 4 cases of stent-assisted coiling. A wide neck and AAPVS were the related predictors. CONCLUSION: The present study demonstrated relatively favorable clinical and angiographic outcomes in EVT of SRAs in long-term follow-up of up to 5 years. THE AAPVS, as a morphological indicator of the parent artery for both OUCO and retreatment, needs further validation.

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