A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive ...to single–amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA helicase Hel308. Reading the ion current signal through the nanopore enabled discrimination of single–amino acid substitutions in single reads. Molecular dynamics simulations showed these signals to result from size exclusion and pore binding. We also demonstrate the capability to “rewind” peptide reads, obtaining numerous independent reads of the same molecule, yielding an error rate of <10
in single amino acid variant identification. These proof-of-concept experiments constitute a promising basis for the development of a single-molecule protein fingerprinting and analysis technology.
The Himalayas and the Tibetan Plateau region (HTP), despite being a remote and sparsely populated area, is regularly exposed to polluted air masses with significant amounts of aerosols including ...black carbon. These dark, light-absorbing particles are known to exert a great melting potential on mountain cryospheric reservoirs through albedo reduction and radiative forcing. This study combines ground-based and satellite remote sensing data to identify a severe aerosol pollution episode observed simultaneously in central Tibet and on the southern side of the Himalayas during 13-19 March 2009 (pre-monsoon). Trajectory calculations based on the high-resolution numerical weather prediction model COSMO are used to locate the source regions and study the mechanisms of pollution transport in the complex topography of the HTP. We detail how polluted air masses from an atmospheric brown cloud (ABC) over South Asia reach the Tibetan Plateau within a few days. Lifting and advection of polluted air masses over the great mountain range is enabled by a combination of synoptic-scale and local meteorological processes. During the days prior to the event, winds over the Indo-Gangetic Plain (IGP) are generally weak at lower levels, allowing for accumulation of pollutants and thus the formation of ABCs. The subsequent passing of synoptic-scale troughs leads to southwesterly flow in the middle troposphere over northern and central India, carrying the polluted air masses across the Himalayas. As the IGP is known to be a hotspot of ABCs, the cross-Himalayan transport of polluted air masses may have serious implications for the cryosphere in the HTP and impact climate on regional to global scales. Since the current study focuses on one particularly strong pollution episode, quantifying the frequency and magnitude of similar events in a climatological study is required to assess the total impact.
To investigate the production of cellulases and hemicellulases from
Aspergillus niger KK2, solid state fermentation (SSF) was performed by using different ratios of rice straw and wheat bran. When
A. ...niger KK2 was grown on rice straw alone as a solid support in SSF, the maximum FPase activity was 19.5 IU
g
−1 in 4 days. Also, CMCase (129 IU
g
−1), β-glucosidase (100 IU
g
−1), xylanase (5070 IU
g
−1) and β-xylosidase (193 IU
g
−1) activities were concurrently obtained after 5–6 days of fermentation. The higher enzyme activities produced by
A. niger KK2 is a significant advantage from the viewpoint of practical saccharification reaction. Cellulases and hemicellulases produced by
A. niger KK2 might be applied to pulp and paper industry, feed industry and chemical industry.
A microstructure-based integrated crystal plasticity (CP) and continuum damage mechanics (CDM) model is proposed for simulating rolling contact fatigue (RCF). The damage process through the formation ...of the dark etching region (DER) under RCF is implemented, i.e., a DER-CPCDM approach. A hierarchical microstructure of lath martensite is virtually generated by the Voronoi tessellation technique and the theoretical Kurdjumov-Sachs orientation relationship between the prior austenite grains and substructures of lath martensite. Moreover, the micro-plasticity calculated from the polycrystal finite element is coupled with dislocation-assisted carbon migration theory, which enables accurate predictions of the deformation inhomogeneity and the DER/damage distribution at the subsurface. The RCF lifespan of AISI 52100 bearing steel can be predicted within reasonable accuracy, in terms of Weibull probability analysis, when the jump-in-cycles approach is implemented in the DER-CPCDM model. The predicted representative lifespan of the Weibull plot is within an error of 13% when compared with reported experimental data. Process factors, including contact pressure, rotational speed, temperature, carbon concentration, and grain size, are analyzed in a numerical sensitivity study, which can be utilized for potential optimization of the RCF process for improving the performance of materials and parts.
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•An integrated model coupling microstructure-based crystal plasticity and continuum damage mechanics is developed.•Microstructure evolution through dislocation assisted carbon migration, or dark etching region, can be modeled.•Hierarchical martensitic microstructure can be implemented through RVE and Kurdjumov-Sachs relation.•The integrated computational model accurately predicts the lifespan of rolling contact fatigue of steel.
This study explored the prognostic impact of tumor-infiltrating lymphocytes (TILs) and investigated whether three histologic subtypes (lymphoepithelioma-like carcinoma, carcinoma with Crohn's ...disease-like lymphoid reaction, and conventional-type adenocarcinoma) could stratify a prognostic subset for patients with Epstein–Barr virus (EBV)-associated gastric cancer (EBVaGC).
After reviewing 1318 consecutive cases of surgically resected or endoscopic submucosal dissected gastric cancers, 120 patients were identified as EBV-positive using EBV-encoded RNA in situ hybridization. The evaluation of the percentage of intratumoral (iTu-) and stromal (str-) TILs was carried out, and the cases were also subclassified into three histologic subtypes as noted above.
Among the 120 patients, 73 patients (60.8%) and 60 patients (50.0%) were determined as str-TIL-positive and iTu-TIL-positive, respectively. In a univariate analysis, str-TIL-positivity was significantly associated with longer recurrence-free survival (RFS; P = 0.002) and disease-free survival (DFS; P = 0.008), yet not overall survival (OS; P = 0.145). While iTu-TIL-positivity has a tendency of favorable outcome indicator for DFS and OS, but statistically significant differences were not shown, respectively (RFS, P = 0.058; DFS, P = 0.151; OS, P = 0.191). In a multivariate analysis using a Cox proportional hazard model adjusted for age, pTNM stage, lymphatic invasion, perineural invasion, and venous invasion; histologic subtype, WHO classification, and str-TIL-positivity were independently or tentatively associated with favorable RFS (hazard ratio HR = 12.193, 95% confidence interval 95% CI 1.039–143.055, P = 0.047) or DFS (HR = 4.836, 95% CI 0.917–25.525, P = 0.063).
The histologic subclassification and TILs can be used to predict RFS and DFS for patients with EBVaGC.
Background
Classifications of intraductal papillary mucinous neoplasm (IPMN) remain ambiguous, especially for the mixed type. Factors predicting malignancy remain unclear. The aim of this study was ...to evaluate the usefulness of factors predicting malignancy in the new international consensus guidelines for resection of branch duct‐type (BD)‐IPMN and to compare them with those in the previous version.
Methods
A prospectively collected database of patients with biopsy‐proven BD‐IPMN was analysed to compare factors between the first and second consensus guidelines, particularly as predictors of malignancy.
Results
Of 350 patients with BD‐IPMN, sensitivity (0·724) and balanced accuracy (0·751) of the second guidelines were superior to those (0·639 and 0·730) in the first version at the expense of slightly reduced specificity (0·779 versus 0·822 for the first version) by random forest models. Multiple logistic regression analysis showed that main pancreatic duct dilatation greater than 5 mm (hazard ratio (HR) 4·54, 95 per cent confidence interval 2·45 to 8·41; P < 0·001), mural nodules (HR 6·27, 3·27 to 12·01; P < 0·001) and carbohydrate antigen 19–9 level above 37 units/ml (HR 4·03, 1·83 to 8·90; P = 0·001) were independent predictors of BD‐IPMN malignancy.
Conclusion
The new consensus guidelines provide better sensitivity, performance of factors predicting malignancy, and balanced accuracy in the diagnosis of BD‐IPMN malignancy. Size alone was limited in predicting malignancy. Variability in clinical significance of the individual factors associated with a risk of malignancy indicates the need for a tailored approach in the management of patients with BD‐IPMN.
Cyst size alone is not useful
Two common general anaesthetic methods are total i.v. anaesthesia (TIVA) and inhalation anaesthesia, but it is unclear whether this affects the patient's perception of their quality of recovery. The ...Quality of Recovery-40 questionnaire (QoR-40) is a valid and reliable method to evaluate the extent of functional recovery after surgery with general anaesthesia. This study therefore compared patient recovery using the QoR-40 in surgical patients who received TIVA with those who received desflurane anaesthesia.
Eighty females (20–65 years old) undergoing thyroid surgery were prospectively recruited and randomized to either the TIVA (effect-site target controlled infusion using propofol and remifentanil) or DES (desflurane inhalation with manual infusion of remifentanil) groups. The QoR-40 was administered by an investigator blind to group allocation before surgery, and postoperative days 1 and 2 (POD1 and POD2). Additional data including the incidence of nausea or vomiting, the consumption of antiemetic and analgesic agents in the post-anaesthesia care unit, and the duration of the hospital stay, were collected in all cases.
The QoR-40 score on POD1 was significantly higher in the TIVA group compared with the DES group (174 vs 161, respectively; P=0.004), indicating a better quality of recovery in the TIVA group. Among the five dimensions of the QoR-40, physical comfort and physical independence were significantly better on POD1 and POD2 in the TIVA group.
This study demonstrates that the quality of recovery for female thyroid surgery patients is significantly better with TIVA compared with desflurane anaesthesia.
www.clinicaltrials.org; ref.: NCT01760018.
The interactions of derivatives of lumisterol (L3) and vitamin D3 (D3) with liver X receptors (LXRs) were investigated. Molecular docking using crystal structures of the ligand binding domains (LBDs) ...of LXRα and β revealed high docking scores for L3 and D3 hydroxymetabolites, similar to those of the natural ligands, predicting good binding to the receptor. RNA sequencing of murine dermal fibroblasts stimulated with D3-hydroxyderivatives revealed LXR as the second nuclear receptor pathway for several D3-hydroxyderivatives, including 1,25(OH)
D3. This was validated by their induction of genes downstream of LXR. L3 and D3-derivatives activated an LXR-response element (LXRE)-driven reporter in CHO cells and human keratinocytes, and by enhanced expression of LXR target genes. L3 and D3 derivatives showed high affinity binding to the LBD of the LXRα and β in LanthaScreen TR-FRET LXRα and β coactivator assays. The majority of metabolites functioned as LXRα/β agonists; however, 1,20,25(OH)
D3, 1,25(OH)
D3, 1,20(OH)
D3 and 25(OH)D3 acted as inverse agonists of LXRα, but as agonists of LXRβ. Molecular dynamics simulations for the selected compounds, including 1,25(OH)
D3, 1,20(OH)
D3, 25(OH)D3, 20(OH)D3, 20(OH)L3 and 20,22(OH)
L3, showed different but overlapping interactions with LXRs. Identification of D3 and L3 derivatives as ligands for LXRs suggests a new mechanism of action for these compounds.
Background
There are concerns about the extent of impaired endocrine and exocrine pancreatic function and poor quality of life (QoL) after pancreatectomy, but there is little information from large ...prospective follow‐up studies.
Methods
Consecutive patients undergoing pancreaticoduodenectomy or distal pancreatectomy between 2007 and 2011 were included. Relative bodyweight (RBW), triceps skinfold thickness (TSFT), serum protein, albumin, transferrin, fasting blood glucose, postprandial 2‐h glucose (PP2), glycosylated haemoglobin A1c and stool elastase measurements, and European Organization for Research and Treatment of Cancer QLQ‐C30 questionnaires were collected serially for 1 year.
Results
Some 136 patients undergoing pancreatic resection completed the study. RBW and TSFT recovered to over 90 per cent of the preoperative value by 12 months, whereas transferrin, albumin and protein had returned to preoperative levels by 3 months. Diabetes mellitus, impaired fasting glucose or raised PP2 was present in 42 of 76 patients at 6 months and 36 of 76 at 12 months. Although steatorrhoea and diarrhoea had mainly resolved by 3 months, stool elastase level decreased after operation and showed no recovery. Nutritional status, pancreatic endocrine function and QoL returned to preoperative levels in 63 (46·3 per cent), 72 (52·9 per cent) and 77 (56·6 per cent) of 136 patients within 6 months of pancreatectomy. Multivariable analysis revealed that age 60 years or more, operation type, chronic pancreatitis and malignant disease had a significant impact on nutritional index, pancreatic function and QoL.
Conclusion
About half of all patients can expect recovery from pancreatectomy after 6 months, but those with risk factors need more careful follow‐up and supportive management.
Reasonable recovery takes at least 6 months
Accurate diagnosis of Helicobacter pylori(H. pylori) infection is a crucial part in the effective management of many gastroduodenal diseases. Several invasive and non-invasive diagnostic tests are ...available for the detection of H. pylori and each test has its usefulness and limitations in different clinical situations. Although none can be considered as a single gold standard in clinical practice,several techniques have been developed to give the more reliable results. Invasive tests are performed via endoscopic biopsy specimens and these tests include histology,culture,rapid urease test as well as molecular methods. Developments of endoscopic equipment also contribute to the real-time diagnosis of H. pylori during endoscopy. Urea breathingtest and stool antigen test are most widely used noninvasive tests,whereas serology is useful in screening and epidemiological studies. Molecular methods have been used in variable specimens other than gastric mucosa. More than detection of H. pylori infection,several tests are introduced into the evaluation of virulence factors and antibiotic sensitivity of H. pylori,as well as screening precancerous lesions and gastric cancer. The aim of this article is to review the current options and novel developments of diagnostic tests and their applications in different clinical conditions or for specific purposes.
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