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Abstract Background Sepsis-related AKI is related to short-term mortality and poor long-term prognoses, such as chronic renal insufficiency, late development of end-stage renal disease, and long-term mortality. In this study, we aimed to investigate the association of hyperuricemia with acute kidney injury (AKI) in patients with sepsis. Methods The retrospective cohort study included 634 adult sepsis patients hospitalized in the intensive care unit (ICU) of the First Affiliated Hospital of Guangxi Medical University from March 2014 to June 2020 and the ICU of the Second Affiliated Hospital of Guangxi Medical University from January 2017 to June 2020. Based on the first serum uric acid level within 24 h of admission to the ICU, patients were divided into groups with or without hyperuricemia, and the incidence of AKI within seven days of ICU admission was compared between the two groups. The univariate analysis analyzed the effect of hyperuricemia on sepsis-related AKI, and the multivariable logistic regression model analysis was used. Results Among the 634 patients with sepsis, 163 (25.7%) developed hyperuricemia, and 324 (51.5%) developed AKI. The incidence of AKI in the groups with and without hyperuricemia was 76.7% and 42.3%, respectively, with statistically significant differences (2 = 57.469, P

Abstract This paper proposes a normal oriented impact stiffness of a three-supporting cable flexible barrier under a small pretension stress to estimate the structural load behaviour, and employs two categories of small-scale debris flows (coarse and fine) to explore the stiffness evolution through physical model experiments with high-speed photography and load sensing. Results suggest that the particle-structure contact is essential to the normal load effect. Coarse debris flow performs more frequent particle-structure contact and exerts evident momentum flux, while fine debris flows with few physical collisions impart much smaller one. The middle-sited cable that receives only tensile force from vertical equivalent cable-net joint system exhibits indirect load behaviour. The bottom-sited cable shows high load feedback due to the sum of direct contact of debris flow and tensile forces. The relationship between impact loads and maximum cable deflections can be explained by power functions according to quasi-static theory. The impact stiffness is not just affected by the particle-structure contact but by the flow inertia and particle collision effect. Savage number N sav and Bagnold number N bag manage to depict the dynamical effects on the normal stiffness D i . Experiments indicate that N sav has positive linear correlation with the nondimensionalization of D i , whilst N bag has positive power correlation with the nondimensionalization of D i . This idea is an alternative scope for the study on flow-structure interaction and may contribute to the parameter identification in numerical simulation of the debris flow-structure interaction and the optimization of the design standardization.

Cerebral venous sinus thrombosis is a special cerebrovascular disease affecting young adult and middle-aged people. The clinical manifestations of cerebral venous sinus thrombosis are diverse and nonspecific; thus, imaging plays an important role in early diagnosis. Anticoagulation with heparin is the preferred treatment for cerebral venous sinus thrombosis. Endovascular treatment is also being increasingly used to achieve recanalization of the cerebral venous sinus. We herein describe a woman in her early 50s who was diagnosed with cerebral venous sinus thrombosis for which anticoagulation with heparin was ineffective. To improve her symptoms and prognosis, we selected balloon venoplasty to treat the right sigmoid sinus thrombosis. Her condition subsequently improved, and no recurrence was observed after several follow-ups.

Abstract Background Spinal cord infarction (SCI) is rarely caused by vertebral artery dissection (VAD), which is an important cause of posterior circulation stroke in young and middle-aged patients. We report the case of a middle-aged patient without obvious risk factors for atherosclerosis who had SCI from right VAD. Case presentation An otherwise healthy 40-year-old man presented with acute right-sided body weakness. Six days earlier, he had experienced posterior neck pain without obvious inducement. Neurologic examination revealed a right Brown-Séquard syndrome. Magnetic resonance imaging (MRI) of the head was normal. Further, cervical spine MRI showed spinal cord infarction (SCI) on the right at the C1-C3 level. Three-dimensional high-resolution MRI (3D HR-MRI) volumetric isotropic turbo spin echo acquisition (VISTA) scan showed evidence of vertebral artery dissection (VAD). The patient was significantly relieved of symptoms and demonstrated negative imaging findings after therapy with anticoagulation (AC) and antiplatelets (AP) for 3 months. Conclusions The possibility of vertebral artery dissection (VAD) should be considered in the case of young and middle-aged patients without obvious risk factors for atherosclerosis. Furthermore the VISTA black blood sequence plays an important role in the pathological diagnosis of vertebral artery stenosis. Early correct diagnosis and active therapy are crucial to the prognosis.

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a public health concern worldwide, but comprehensive analysis of risk factors for CRPA remains limited in China. We conducted a retrospective observational study of carbapenem resistance in 71,880 P. aeruginosa isolates collected in Zhejiang Province during 2015–2017. We analyzed risk factors for CRPA, including the type of clinical specimen; the year, season, and region in which it was collected; patient information, including age, whether they were an outpatient or inpatient, and whether inpatients were in the intensive care unit or general ward; and the level of hospital submitting isolates. We found CRPA was more prevalent among isolates from patients >60 years of age and in inpatients, especially in intensive care units. In addition, specimen types and seasons in which they were collected were associated with higher rates of CRPA. Our findings can help hospitals reduce the spread of P. aeruginosa and optimize antimicrobial drug use.

AIM: To compare the efficacy of the laser photocoagulation with combination therapy of both the laser potocoagulation and ranibizumab in the treatment of diabetic macular edema(DME).METHODS: The research was based on the randomized controlled trial(RCT). A total of 180 eyes from 134 cases diagnosed with DME were randomly divided into experimental group and control group. No statistically significant difference was found between two groups(P>0.05)with respect to age, sex, duration of disease, best corrected visual acuity(BCVA), the mean intraocular pressure(IOP)and the mean central macular thickness(CMT). Patients in the control group received the photocoagulation while the combination therapy of both laser photocoagulation and ranibizumab were employed in the experimental group. BCVA, IOP and CMT were assessed at 1wk and 3mo after treatment, and the collecting data of two groups were examined.RESULTS: Before treatment, 1wk and 3mo after treatment, there was no significant difference of IOP(P>0.05). 1wk and 3mo after treatment, the CMT in the experimental group was significantly lower than the other(t= -7.83, -8.80, Pt= -3.76, -4.09, Pt=1.97, P2=4.59, P2=0.03, P>0.05). No retinal detachment or intraocular inflammation occurred in both groups.CONCLUSION: Compared with the laser photocoagulation, the combination therapy of laser photocoagulation and ranibizumab could significantly lower the CMT after surgery, early improve the BCVA and decrease the recurrence rate.

Background and PurposeIdentifying risks of stroke-associated pneumonia (SAP) is important for clinical management. We aimed to evaluate the association between gut microbiome composition and SAP in patients with acute ischemic stroke (AIS).MethodsA prospective observational study was conducted, and 188 AIS patients were enrolled as the training cohort. Fecal and serum samples were collected at admission. SAP was diagnosed by specialized physicians, and disease severity scores were recorded. Fecal samples were subjected to 16S rRNA V4 tag sequencing and analysed with QIIME and LEfSe. Associations between the most relevant taxa and SAP were analysed and validated with an independent cohort. Fecal short-chain fatty acid (SCFA), serum D-lactate (D-LA), intestinal fatty acid-binding protein (iFABP) and lipopolysaccharide binding protein (LBP) levels were measured.ResultsOverall, 52 patients (27.7%) had SAP in the training cohort. The gut microbiome differed between SAP and non-SAP patients; specifically, Roseburia depletion and opportunistic pathogen enrichment were noted in SAP patients, as confirmed in the validation cohort (n=144, 28 SAP [19.4%]). Based on multivariate analysis, Roseburia was identified as a protective factor against SAP in both cohorts (training, aOR 0.52; 95% CI, 0.30-0.90; validation, aOR 0.44; 95% CI, 0.23-0.85). The combination of these taxa into a microbial dysbiosis index (MDI) revealed that dysbiosis increased nearly 2 times risk of SAP (training, aOR 1.95; 95% CI, 1.19-3.20; validation, aOR 2.22; 95% CI, 1.15-4.26). Lower fecal SCFA levels and higher serum D-LA levels were observed in SAP patients. Furthermore, SAP was an independent risk factor of 30-day death and 90-day unfavorable outcome.ConclusionWe demonstrate that a microbial community with depleted Roseburia and enriched opportunistic pathogens is associated with increased risk of SAP among AIS patients. Gut microbiota screening might be useful for identifying patients at high risk for SAP and provide clues for stroke treatment.

BackgroundThere have been reports of increasing azole resistance in Candida tropicalis, especially in the Asia-Pacific region. Here we report on the epidemiology and antifungal susceptibility of C. tropicalis causing invasive candidiasis in China, from a 9-year surveillance study.MethodsFrom August 2009 to July 2018, C. tropicalis isolates (n = 3702) were collected from 87 hospitals across China. Species identification was carried out by mass spectrometry or rDNA sequencing. Antifungal susceptibility was determined by Clinical and Laboratory Standards Institute disk diffusion (CHIF-NET10–14, n = 1510) or Sensititre YeastOne (CHIF-NET15–18, n = 2192) methods.ResultsOverall, 22.2% (823/3702) of the isolates were resistant to fluconazole, with 90.4% (744/823) being cross-resistant to voriconazole. In addition, 16.9 (370/2192) and 71.7% (1572/2192) of the isolates were of non-wild-type phenotype to itraconazole and posaconazole, respectively. Over the 9 years of surveillance, the fluconazole resistance rate continued to increase, rising from 5.7 (7/122) to 31.8% (236/741), while that for voriconazole was almost the same, rising from 5.7 (7/122) to 29.1% (216/741), with no significant statistical differences across the geographic regions. However, significant difference in fluconazole resistance rate was noted between isolates cultured from blood (27.2%, 489/1799) and those from non-blood (17.6%, 334/1903) specimens (P-value < 0.05), and amongst isolates collected from medical wards (28.1%, 312/1110) versus intensive care units (19.6%, 214/1092) and surgical wards (17.9%, 194/1086) (Bonferroni adjusted P-value < 0.05). Although echinocandin resistance remained low (0.8%, 18/2192) during the surveillance period, it was observed in most administrative regions, and one-third (6/18) of these isolates were simultaneously resistant to fluconazole.ConclusionThe continual decrease in the rate of azole susceptibility among C. tropicalis strains has become a nationwide challenge in China, and the emergence of multi-drug resistance could pose further threats. These phenomena call for effective efforts in future interventions.

Abstract Background Fabry disease is rare, and the diagnosis is often delayed. Here, we describe a case of Fabry disease resulting in vasculopathy of the central nervous system. Magnetic resonance (MR) black-blood sequence (three-dimensional T1 volumetric isotropic turbo spin echo acquisition), with the unique advantage of imaging the vascular wall, facilitated a clear identification of the vasculopathy. Case presentation A 27-year-old man visited our hospital for the treatment of “ double vision 6d.” After a series of examinations, the patient was diagnosed with Fabry disease, which caused vasculopathy of the central nervous system. Subsequently, the patient was treated with corticosteroids and his symptoms were attenuated. Two months after the initial treatment, the initial lesion in the vascular vessel disappeared, however, a new lesion appeared. Similarly, four months after the initial treatment, although the previous lesion disappeared, a new lesion appeared. Conclusions This case highlights that clinicians should use MR black-blood sequence scan in a timely manner in case of young patients with migratory lesions of brain. In case of detection of a vascular lesion in combination with other systemic lesions, the possibility of Fabry disease should be considered.

Abstract Background The metabolic syndrome (MetS) epidemic is associated with economic development, lifestyle transition and dysbiosis of gut microbiota, but these associations are rarely studied at the population scale. Here, we utilised the Guangdong Gut Microbiome Project (GGMP), the largest Eastern population-based gut microbiome dataset covering individuals with different economic statuses, to investigate the relationships between the gut microbiome and host physiology, diet, geography, physical activity and socioeconomic status. Results At the population level, 529 OTUs were significantly associated with MetS. OTUs from Proteobacteria and Firmicutes (other than Ruminococcaceae) were mainly positively associated with MetS, whereas those from Bacteroidetes and Ruminococcaceae were negatively associated with MetS. Two hundred fourteen OTUs were significantly associated with host economic status (140 positive and 74 negative associations), and 157 of these OTUs were also MetS associated. A microbial MetS index was formulated to represent the overall gut dysbiosis of MetS. The values of this index were significantly higher in MetS subjects regardless of their economic status or geographical location. The index values did not increase with increasing personal economic status, although the prevalence of MetS was significantly higher in people of higher economic status. With increased economic status, the study population tended to consume more fruits and vegetables and fewer grains, whereas meat consumption was unchanged. Sedentary time was significantly and positively associated with higher economic status. The MetS index showed an additive effect with sedentary lifestyle, as the prevalence of MetS in individuals with high MetS index values and unhealthy lifestyles was significantly higher than that in the rest of the population. Conclusions The gut microbiome is associated with MetS and economic status. A prolonged sedentary lifestyle, rather than Westernised dietary patterns, was the most notable lifestyle change in our Eastern population along with economic development. Moreover, gut dysbiosis and a Western lifestyle had an additive effect on increasing MetS prevalence.

Dysbiotic airway microbiota play important roles in the inflammatory progression of asthma, and exploration of airway microbial interactions further elucidates asthma pathogenesis. However, little is known regarding the airway bacterial-fungal interactions in asthma patients. We conducted a cross-sectional survey of the sputum bacterial and fungal microbiota from 116 clinically stable asthma patients and 29 healthy controls using 16S rRNA gene and ITS1 sequencing. Compared with healthy individuals, asthma patients exhibited a significantly altered microbiota and increased bacterial and fungal alpha diversities in the airway. Microbial genera Moraxella, Capnocytophaga, and Ralstonia (bacteria) and Schizophyllum, Candida, and Phialemoniopsis (fungi) were more abundant in the asthma airways, while Rothia, Veillonella and Leptotrichia (bacteria) and Meyerozyma (fungus) were increased in healthy controls. The Moraxellaceae family and their genus Moraxella were significantly enriched in asthma patients compared with healthy controls (80.5-fold, P = 0.007 and 314.7-fold, P = 0.027, respectively). Moreover, Moraxellaceae, along with Schizophyllum, Candida, and Aspergillus (fungal genera), were positively associated with fungal alpha diversity. Correlation networks revealed 3 fungal genera (Schizophyllum, Candida, and Aspergillus) as important airway microbes in asthma that showed positive correlations with each other and multiple co-exclusions with other common microbiota. Moraxellaceae members were positively associated with asthma-enriched fungal taxa but negatively related to several healthy-enriched bacterial taxa. Collectively, our findings revealed an altered microbiota and complex microbial interactions in the airways of asthma patients. The Moraxellaceae family and their genus Moraxella, along with 3 important fungal taxa, showed significant interactions with the airway microbiota, providing potential insights into the novel pathogenic mechanisms of asthma.

Malignant peripheral nerve sheath tumor (MPNST) in the nasopharynx and oropharynx has not been reported. A 3-year-old boy was referred to hospital after experiencing intermittent inspiratory dyspnea for 3 years. Preoperative imaging showed that the lymph nodes were clear. Therefore, neck lymph node dissection was not performed during the operation. This could have reduced the collateral damage. Complete excision and radiotherapy were performed because of the pathological diagnosis of MPNST. Because of the high location of the tumor, we chose the transoral approach instead of the cervical approach, avoiding tracheotomy, and we effectively improved the quality of life of the child. A mass in the nasopharynx and oropharynx was diagnosed pathologically as an MPNST after surgery. The patient’s inspiratory dyspnea was resolved. No recurrence was observed during a 3-year follow-up. After review of our case, we found that postoperative recovery in our patient was closely related to accurate preoperative imaging assessment, the choice of operation methods, thorough resection, and postoperative neoadjuvant radiotherapy. Prevertebral fascia acted as a barrier to surround the mass and prevented it from growing further toward the vertebral body, which was important for a good prognosis. Children undergoing tracheotomy often have long tube management and difficult extubation.

Abstract A flexible riverbed protection called tetrahedron framed permeable weirs (TFPW) is proposed to protect riverbeds in mountainous areas from scouring. Under clear water conditions, a series of laboratory flume experiments were performed to study the effects of TFPW with different layout types on the stability of riverbeds. The objectives of this paper were to advance understanding of the role that TFPW play in the erosion process of river beds and to optimize the TFPW design for reducing velocity, promoting sediment deposition and good structural stability. Data on velocity distribution and variation, equilibrium bathymetry, flow resistance, bed form characteristics and structural stability were collected and analyzed. The results indicate that (1) with good structural stability, all the TFPW with different layout types had significant effects on the stabilization of the riverbed by reducing velocity, raising the water level, increasing the roughness coefficient, protecting the riverbed from degradation and promoting deposition; and (2) the random Double TFPW with large rates of deceleration, large deposition ranges, and good structural stability, and the paved Single TFPW with small rates of deceleration but large deposition ranges and perfect structural stability, were suitable and optimal for riverbed protection in a clear water channel.

Abstract Chronic kidney disease (CKD) patients have an increased risk of cardiovascular diseases (CVDs). The present study aimed to investigate the gut microbiota and blood trimethylamine-N-oxide concentration (TMAO) in Chinese CKD patients and explore the underlying explanations through the animal experiment. The median plasma TMAO level was 30.33 μmol/L in the CKD patients, which was significantly higher than the 2.08 μmol/L concentration measured in the healthy controls. Next-generation sequence revealed obvious dysbiosis of the gut microbiome in CKD patients, with reduced bacterial diversity and biased community constitutions. CKD patients had higher percentages of opportunistic pathogens from gamma-Proteobacteria and reduced percentages of beneficial microbes, such as Roseburia, Coprococcus, and Ruminococcaceae. The PICRUSt analysis demonstrated that eight genes involved in choline, betaine, L-carnitine and trimethylamine (TMA) metabolism were changed in the CKD patients. Moreover, we transferred faecal samples from CKD patients and healthy controls into antibiotic-treated C57BL/6 mice and found that the mice that received gut microbes from the CKD patients had significantly higher plasma TMAO levels and different composition of gut microbiota than did the comparative mouse group. Our present study demonstrated that CKD patients had increased plasma TMAO levels due to contributions from both impaired renal functions and dysbiosis of the gut microbiota.

Background: Oral mucositis is probably the most debilitating complication that can arise in treating a patient with head and neck cancer. Little is known about the impacts of oral microbiota on the initiation and progression of mucositis. Methods: Based on 16S rRNA gene sequencing, dynamic changes in oral bacterial profile as well as correlations between the severity of mucositis and bacterial shifts during radiotherapy were investigated. Findings: Our results revealed that bacterial community structure altered progressively during radiation therapy, in parallel with a marked increase in the relative abundance of some Gram-negative bacteria. Patients who eventually developed severe mucositis harbored a significantly lower bacterial alpha diversity and higher abundance of Actinobacillus during the phase of erythema – patchy mucositis. Accordingly, a random forest model for predicting exacerbation of mucositis was generated, which achieved a high predictive accuracy (AUC) of 0.89. Interpretation: Oral microbiota changes correlate with the progression and aggravation of radiotherapy-induced mucositis in patients with nasopharyngeal carcinoma. Microbiota-based strategies can be used for the early prediction and prevention of the incidence of severe mucositis during radiotherapy.

Background: Significant dysbiosis occurs in the gut microbiome of stroke patients. Condensing these broad, complex changes into one index would greatly facilitate the clinical usage of gut microbiome data. Here, we formulated a gut microbiota index in patients with acute ischemic stroke based on their gut microbiota dysbiosis patterns and tested whether the index was correlated with brain injury and early outcome.Methods: A total of 104 patients with acute ischemic stroke and 90 healthy individuals were recruited, and their gut microbiotas were compared and to model a Stroke Dysbiosis Index (SDI), which representing stroke-associated dysbiosis patterns overall. Another 83 patients and 70 controls were recruited for validation. The association of SDI with stroke severity (National Institutes of Health Stroke Scale [NIHSS] score) and outcome (modified Rankin scale [mRS] score: favorable, 0–2; unfavorable, >2) at discharge was also assessed. A middle cerebral artery occlusion (MCAO) model was used in human flora-associated (HFA) animals to explore the causal relationship between gut dysbiosis and stroke outcome.Results: Eighteen genera were significantly different between stroke patients and healthy individuals. The SDI formula was devised based on these microbiome differences; SDI was significantly higher in stroke patients than in healthy controls. SDI alone discriminated stroke patients from controls with AUCs of 74.9% in the training cohort and 84.3% in the validation cohort. SDI was significantly and positively correlated with NIHSS score on admission and mRS score at discharge. Logistic regression analysis showed that SDI was an independent predictor of severe stroke (NIHSS ≥8) and early unfavorable outcome (mRS >2). Mice receiving fecal transplants from high-SDI patients developed severe brain injury with elevated IL-17+ γδ T cells in gut compared to mice receiving transplants from low-SDI patients (all P < 0.05).Conclusions: We developed an index to measure gut microbiota dysbiosis in stroke patients; this index was significantly correlated with patients' outcome and was causally related to outcome in a mouse model of stroke. Our model facilitates the potential clinical application of gut microbiota data in stroke and adds quantitative evidence linking the gut microbiota to stroke.

ABSTRACT The recent emergence of a transferable colistin resistance mechanism, MCR-1, has gained global attention because of its threat to clinical treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, the possible transmission route of mcr-1 among Enterobacteriaceae species in clinical settings is largely unknown. Here, we present a comprehensive genomic analysis of Escherichia coli isolates collected in a hospital in Hangzhou, China. We found that mcr-1-carrying isolates from clinical infections and feces of inpatients and healthy volunteers were genetically diverse and were not closely related phylogenetically, suggesting that clonal expansion is not involved in the spread of mcr-1. The mcr-1 gene was found on either chromosomes or plasmids, but in most of the E. coli isolates, mcr-1 was carried on plasmids. The genetic context of the plasmids showed considerable diversity as evidenced by the different functional insertion sequence (IS) elements, toxin-antitoxin (TA) systems, heavy metal resistance determinants, and Rep proteins of broad-host-range plasmids. Additionally, the genomic analysis revealed nosocomial transmission of mcr-1 and the coexistence of mcr-1 with other genes encoding β-lactamases and fluoroquinolone resistance in the E. coli isolates. These findings indicate that mcr-1 is heterogeneously disseminated in both commensal and pathogenic strains of E. coli, suggest the high flexibility of this gene in its association with diverse genetic backgrounds of the hosts, and provide new insights into the genome epidemiology of mcr-1 among hospital-associated E. coli strains. IMPORTANCE Colistin represents one of the very few available drugs for treating infections caused by extensively multidrug-resistant Gram-negative bacteria. The recently emergent mcr-1 colistin resistance gene threatens the clinical utility of colistin and has gained global attention. How mcr-1 spreads in hospital settings remains unknown and was investigated by whole-genome sequencing of mcr-1-carrying Escherichia coli in this study. The findings revealed extraordinary flexibility of mcr-1 in its spread among genetically diverse E. coli hosts and plasmids, nosocomial transmission of mcr-1-carrying E. coli, and the continuous emergence of novel Inc types of plasmids carrying mcr-1 and new mcr-1 variants. Additionally, mcr-1 was found to be frequently associated with other genes encoding β-lactams and fluoroquinolone resistance. These findings provide important information on the transmission and epidemiology of mcr-1 and are of significant public health importance as the information is expected to facilitate the control of this significant antibiotic resistance threat.

AIM: To evaluate the clinical efficacy and safety of optic capture in pediatric cataract surgery. METHODS: Searches of peer-reviewed literature were conducted in PubMed, Embase and the Cochrane Library. The search terms were “optic capture” and “cataract”. The retrieval period ended in December 2014. Relevant randomized controlled trials (RCTs), case-control studies and cohort studies were included. Meta-analyses were performed. Pooled weighted mean differences and risk ratios with 95% confidence intervals were estimated. RESULTS: Ten studies involving 282 eyes were included, 5 of which were RCTs involving 194 eyes. The application of optic capture significantly reduced both opacification of the visual axis (RR: 0.12; 95% CI: 0.02 to 0.85; P=0.03) and occurrence of geometric decentration (RR: 0.09; 95% CI: 0.02 to 0.46; P=0.004). But it did not significantly affect best corrected visual acuity (BCVA) (WMD: -0.01; 95%CI: -0.07 to 0.05; P=0.75) and influence the occurrence of posterior synechia (RR: 1.53; 95% CI: 0.84 to 2.77; P=0.17). Deposits in the anterior intraocular lens were significantly increased in the optic capture group early after surgery (RR: 1.40; 95% CI: 1.05 to 1.86; P=0.02) and at the last follow-up (RR: 2.30; 95% CI: 1.08 to 4.92; P=0.03). The quality of the evidence was assessed as high. CONCLUSION: The application of optic capture significantly reduces opacification of visual axis and occurrence of geometric decentration but do not significantly improve BCVA with notable safety.

Background: The endothelium should be carefully evaluated when choosing a surgical technique for cataract removal. Therefore, we aimed to study the effects of different cataract surgery techniques on endothelial cell loss in transplanted corneal grafts. Methods: A total of 54 patients who received complicated cataract surgery in post-penetrating keratoplasty (PKP) eyes at the Shandong Eye Institute between February 2001 and June 2014 were included, and clinical records were reviewed. Baseline demographic details, clinical characteristics, endothelial cell density (ECD), and best-corrected visual acuity (BCVA) were recorded. Wilcoxon rank-sum test and Wilcoxon signed-rank test were used to test the equality of medians. A regression model was constructed to compare the reduced rate of ECD. Results: Of the 54 eyes included in this study, extracapsular cataract extraction (ECCE) was performed in 34 eyes of 33 patients (ECCE group) whereas phacoemulsification was performed in 20 eyes of 20 patients (phacoemulsification group). There was no significant difference in the median age (P = 0.081) or preoperative ECD (P = 0.585) between the two groups. At 6 months after cataract surgery, ECD in ECCE group was significantly higher than that in phacoemulsification group (P = 0.043). In addition, the endothelial cell loss rate in ECCE group was significantly lower than that in phacoemulsification group at 2 months (P = 0.018), 4 months (P < 0.001), and 6 months (P < 0.001) after cataract surgery. Endothelial cell loss rate after cataract surgery increased over the 6-month study duration in both ECCE group (P < 0.001) and phacoemulsification group (P < 0.001), but phacoemulsification resulted in a greater reduction in ECD than that of ECCE in transplanted corneal grafts (P < 0.001). There was no significant difference in postoperative BCVA between the two groups (P = 0.065). Conclusion: ECCE is more suitable than phacoemulsification in cataract surgery in complicated cataract after PKP.

Growing evidence suggests that the airway microbiota might be involved in acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Understanding this relationship requires examination of a large-scale population for a long duration to accurately monitor changes in the microbiome. This type of longitudinal study requires an appropriate sampling strategy; two options are the collection of sputum or oropharyngeal swabs. Comparative analysis of the changes that occur in these two specimen types has not been previously performed. This observational study was conducted to explore oropharyngeal microbial community dynamics over time and to examine the relationship between oropharyngeal swabs and sputum. A total of 114 samples were collected from four patients suffering from severe AECOPD. Bacterial and fungal communities were evaluated using 16S rRNA and ITS sequencing. Inter-individual differences were found in bacterial community structure, but the core genera were shared by both sample types and included 32 lineages. Most of the core genera were members of the phyla Proteobacteria, Firmicutes and Ascomycota. Although the oropharyngeal samples showed higher bacterial alpha diversity, the two sample types generated rather similar taxonomic profiles. These results suggest that the sputum microbiome is remarkably similar to the oropharyngeal microbiome. Thus, oropharyngeal swabs can potentially be used instead of sputum samples for patients with exacerbation of COPD.

ABSTRACT Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH’s most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http://dx.doi.org/10.1186/s12915-014-0069-1 ).

Flexible grade control structures (GCSs) are increasingly popular alternative countermeasures consisting of conventional solid structures for protecting riverbeds from erosion. Among this structure typology, tetrahedron framed permeable weirs (TFPW) were proposed to stabilize riverbeds and protect cross-river structures. The bed morphology as well as the interactions among the structures, water flow and bed features have not been systematically analyzed. Therefore, based on the field data collected in the Jianjiang River, a series of physical model experiments were carried out in this study to investigate the river morphology in unstable gravel-bed rivers under five different structural conditions, including no GCSs, solid bed sills and flexible TFPW with three different layout types. Data on bedform features, topography changes and the volume of erosion or deposition were collected and analyzed. The results indicated that dramatic general erosion and bed armoring would occur without any protection. The bed would be protected from upstream erosion with bed sills, but, at the same time, in addition to general erosion and bed armoring downstream of the structures, deep local scour might pose a serious threat to structural safety. TFPW had good protective effects on riverbeds by preventing the bed from erosion and even inducing sediment deposition both upstream and downstream from the structures. Because the flexible structures have advantages in ecology, structural stability and construction, TFPW were suitable and optimal for riverbed stabilization in unstable gravel-bed rivers.

The adverse impact of antibiotics on the gut microbiota has attracted extensive interest, particularly due to the development of microbiome research techniques in recent years. However, a direct comparison of the dynamic effects of various types of antibiotics using the same animal model has not been available. In the present study, we selected six antibiotics from four categories with the broadest clinical usage, namely, β-lactams (Ceftriaxone Sodium, Cefoperazone/Sulbactam and meropenem), quinolones (ofloxacin), glycopeptides (vancomycin), and macrolides (azithromycin), to treat BALB/c mice. Stool samples were collected during and after the administration of antibiotics, and microbial diversity was analyzed through Illumina sequencing and bioinformatics analyses using QIIME. Both α and β diversity analyses showed that ceftriaxone sodium, cefoperazone/sulbactam, meropenem and vancomycin changed the gut microbiota dramatically by the second day of antibiotic administration whereas the influence of ofloxacin was trivial. Azithromycin clearly changed the gut microbiota but much less than vancomycin and the β-lactams. In general, the community changes induced by the three β-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium. The low diversity and high Clostridium level might be an important cause of Clostridium difficile infection after usage of β-lactams. Vancomycin was unique in that it inhibited Firmicutes, mainly the genus Clostridium. On the other hand, it induced the growth of Escherichia and effect lasted for months afterward. Azithromycin and meropenem induced the growth of Enterococcus. These findings will be useful for understanding the potential adverse effects of antibiotics on the gut microbiome and ensuring their better usage.

The changes in the microbial community structure during acute exacerbations of severe chronic obstructive pulmonary disease (COPD) in hospitalized patients remain largely uncharacterized. Therefore, further studies focused on the temporal dynamics and structure of sputum microbial communities during acute exacerbation of COPD (AECOPD) would still be necessary. In our study, the use of molecular microbiological techniques provided insight into both fungal and bacterial diversities in AECOPD patients during hospitalization. In particular, we examined the structure and varieties of lung microbial community in 6 patients with severe AECOPD by amplifying 16S rRNA V4 hyper-variable and internal transcribed spacer (ITS) DNA regions using barcoded primers and the Illumina sequencing platform. Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity. Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences. The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella. Our findings highlight that COPD patients have personalized structures and varieties in sputum microbial community during hospitalization periods.

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to “classic” open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, “classic” open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of “classic” open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME’s uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME’s OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.

Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases, and there are controversial reports regarding the diversity of the associated vaginal microbiota. We determined the vaginal microbial community in patients with VVC, bacterial vaginosis (BV), and mixed infection of VVC and BV using Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed the following order: normal control < VVC only < mixed BV and VVC infection < BV only. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV samples. A detailed comparison showed that, although the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern, with a relatively higher abundance of Lactobacillus than the BV group and higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. In contrast, the VVC-only group could not be described by any single profile, ranging from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC resulted in inconsistent changes of the vaginal microbiota, with four BV/VVC samples recovering to a higher Lactobacillus level, whereas many VVC-only patients did not. These results will be useful for future studies on the role of vaginal microbiota in VVC and related infectious diseases.

Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs) is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC) because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from 'noise' sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.

The mechanical properties of GH4169 alloy sheet after cold rolling (at 0%, 10%, 30%, 50% and 70%) and solid solution were investigated. The textures and Taylor factors were characterized using electron backscattering diffraction (EBSD). The fractions of δ phase were measured by X-ray diffraction. The contributions of δ phase, grain size, texture, and work hardening on the mechanical properties were also discussed. The results showed increases in the yield strength (YS) (0.2%) as well as the ultimate tensile strength (UTS) of GH4169 superalloy sheet after cold rolling, when rolling reduction was increased. In contrast, following solid solution treatment, YS and UTS were increased then subsequently decreased. The changes of yield strength of GH4169 superalloy were attributed to the texture and work hardening, followed by the grain refinement and precipitation of δ phase. When the rolling reduction was below 30%, the influence of δ phase was greater than grain refinement and when the rolling reduction was larger than 50%, the controversial results occur. The precipitation of δ phase promoted the improvement of yield strength, the relationship between the fraction of δ phase and improved yield strength satisfactory fit to the following equation: σδ = 15.9Wδ + 59.7.