Miracle-dz/UniFAR-FTUs huggingface dataset:
EZH2 overexpression is associated with poor prognosis in patients with glioma

Previous studies have investigated the prognostic value of enhancer of zeste homolog 2 (EZH2) expression in patients with glioma but conclude contradictory results. We aimed to comprehensively evaluate the prognostic role of EZH2 in glioma by meta-analysis. The databases of PubMed, Embase and Web of Science were searched. Hazard ratio (HR) and 95% confidence interval (CI) were combined to assess the association between EZH2 and overall survival (OS) as well as progression-free survival (PFS). Odd ratio (OR) and 95% CI were calculated to investigate the relevance of EZH2 on clinical factors. Six studies with 575 patients were included for meta-analysis. The results showed that EZH2 overexpression was correlated with poor OS (n = 6, HR = 2.23, 95% CI: 1.56–3.19, p < 0.001) and PFS (n = 3, HR = 2.23, 95% CI: 1.56–3.19, p < 0.001). Subgroup analysis showed that EZH2 had enhanced prognostic value in Asian patients, for WHO grade I-IV and when using immunohistochemistry (IHC) method. In addition, EZH2 was associated with KPS score < 80. No evidence of publication bias was found in this meta-analysis. In conclusion, the present study showed that EZH2 was a potential prognostic marker for poor OS, PFS and lower KPS score in glioma patients.
Measuring PM2.5, Ultrafine Particles, Nicotine Air and Wipe Samples Following the Use of Electronic Cigarettes

Background Few studies have examined the extent of inhalation or dermal contact among bystanders following short-term, secondhand e-cigarette exposure. Objective Measure PM2.5 (particles < 2.5 microns), UF (ultrafine particles < 100 nm), and nicotine in air and deposited on surfaces and clothing pre-/during/post- a short-term (2-hour) e-cigarette exposure. Methods E-cigarettes were used ad libitum by three experienced users for 2 hours during two separate sessions (disposable e-cigarettes, then tank-style e-cigarettes, or "tanks") in a 1858 ft3 room. We recorded: uncorrected PM2.5 (using SidePak); UF (using P-Trak); air nicotine concentrations (using air samplers; SKC XAD-4 canisters); ambient air exchange rate (using an air capture hood). Wipe samples were taken by wiping 100 cm2 room surfaces pre- and post- both sessions, and clean cloth wipes were worn during the exposure and collected at the end. Results Uncorrected PM2.5 and UF were higher (p < .0001) during sessions than before or after. Median PM2.5 during exposure was higher using tanks (0.515 mg/m3) than disposables (0.035 mg/m3) (p < .0001). Median UF during exposure was higher using disposables (31 200 particles/cm3) than tanks (25 200 particles/cm3)(p < .0001). Median air nicotine levels were higher (p < .05) during both sessions (disposables = 0.697 ng/L, tanks = 1.833 ng/L) than before (disposables = 0.004 ng/L, tanks = 0.010 ng/L) or after (disposables = 0.115 ng/L, tanks = 0.147 ng/L). Median accumulation rates of nicotine on surface samples were 2.1 ng/100 cm2/h using disposables and 4.0 ng/100 cm2/h using tanks; for cloth samples, it was 44.4 ng/100 cm2/h using disposables and 69.6 ng/100 cm2/h using tanks (p < .01). Mean room ventilation rate was ~5 air changes per hour during both sessions. Conclusions Short-term e-cigarette use can produce: elevated PM2.5; elevated UF; nicotine in the air; and accumulation of nicotine on surfaces and clothing. Implications Short-term indoor e-cigarette use produced accumulation of nicotine on surfaces and clothing, which could lead to dermal exposure to nicotine. Short-term e-cigarette use produced elevated PM2.5 and ultrafine particles, which could lead to secondhand inhalation of these particles and any chemicals associated with them by bystanders. We measured significant differences in PM2.5 and ultrafine particles between disposable e-cigarettes and tank-style e-cigarettes, suggesting a difference in the exposure profiles of e-cigarette products.
The bayesian traffic analysis of mix networks

This work casts the traffic analysis of anonymity systems, and in particular mix networks, in the context of Bayesian inference. A generative probabilistic model of mix network architectures is presented, that incorporates a number of attack techniques in the traffic analysis literature. We use the model to build an Markov Chain Monte Carlo inference engine, that calculates the probabilities of who is talking to whom given an observation of network traces. We provide a thorough evaluation of its correctness and performance, and confirm that mix networks with realistic parameters are secure. This approach enables us to apply established information theoretic anonymity metrics on complex mix networks, and extract information from anonymised traffic traces optimally.
Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM

Background and Aims Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction. Methods Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software. Key Results The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other. Conclusions Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll cells enhance their CO 2 absorption with increased cell surface and sheet-shaped chloroplasts.
Using Hierarchical Scenarios to Predict the Reliability of Component-Based Software

SUMMARY System scenarios that derived from system design speciﬁ-cation play an important role in the reliability engineering of component-based software systems. Several scenario-based approaches have been proposed to predict the reliability of a system at the design time, most of them adopt ﬂat construction of scenarios, which doesn’t conform to software de-sign speciﬁcations and is subject to introduce state space explosion problem in the large systems. This paper identiﬁes various challenges related to scenario modeling at the early design stages based on software architecture speciﬁcation. A novel scenario-based reliability modeling and prediction approach is introduced. The approach adopts hierarchical scenario speciﬁ-cation to model software reliability to avoid state space explosion and reduce computational complexity. Finally, the evaluation experiment shows the potential of the approach.
Transcatheter aortic valve implantation using the ACURATE TA™ system: 1-year outcomes and comparison of 500 patients from the SAVI registries

Abstract OBJECTIVES: The ACURATE TATM system is a self-expanding transcatheter heart valve system designed for transapical access which has been proven to be safe and effective in the controlled setting of clinical trials. The SAVI-1 and SAVI-2 registries aimed to assess whether these promising outcomes can be translated into all-comers clinical routine. METHODS: From November 2011 to 2012 (SAVI-1), and November 2013 to 2014 (SAVI-2), a total of 500 patients were enrolled in the prospective, all-comers, multicentre, multinational SAVI registries. Patients were treated according to the standard of care at their respective hospitals. We report and compare 30-day and 1-year clinical outcomes between SAVI-1 and -2. RESULTS: Patients were 80.8 ± 6.1 years old, the mean logistic EuroSCORE-I was 23.4 ± 14.3%. Valves were deployed under rapid pacing in 71.3% of the procedures in SAVI-1, and in 3.6% in SAVI-2. There was no relevant difference in clinical and echocardiographic outcomes between SAVI-1 and SAVI-2. Overall mortality at 30 days and 1 year was 6.8% and 19.9%, the stroke rate was 2.2% and 3.7%, respectively; 10.2% of patients had received a permanent pacemaker, and no transcatheter valve-related complications after discharge were observed. Paravalvular leakage ≥2+ was reported in 1.9% of the patients at the early follow-up, and in 2.6% at the 1-year follow-up. CONCLUSIONS: The SAVI-registries have confirmed that transapical implantation using the ACURATE TATM device is safe and effective in an all-comers setting with low complication rates and stable performance outcomes at short-term and 1 year; outcomes were similar between SAVI-1 and -2. ClinicalTrials.gov: NCT02663375
Response to Comment on “A commensal strain of Staphylococcus epidermidis protects against skin neoplasia” by Nakatsuji et al.

Common strains of Staphylococcus epidermidis on the human skin inhibit UV-induced neoplasia without adverse effects. Kozmin et al. contend that observations previously reported regarding the antimicrobial and antitumor activities of 6-N-hydroxy aminopurine (6-HAP) were incorrect. Their conclusions rely on poorly characterized reagents and focus strictly on in vitro techniques without validation in relevant mammalian model systems. We are pleased to be able to illuminate the weaknesses in their technical comment. The totality of current results continues to support our original conclusion that a strain of the common human commensal skin bacterium, Staphylococcus epidermidis, produces 6-HAP that can inhibit tumor growth.
Imaging Spontaneous MMTVneu Transgenic Murine Mammary Tumors: Targeting Metabolic Activity Versus Genetic Products

Despite the great strides made in imaging breast cancer (BC) in humans, the current imaging modalities miss up to 30% of BC, do not distinguish malignant lesions from benign ones, and require histologic examinations for which invasive biopsy must be performed. Annually in the United States, approximately 5.6 million biopsies find benign lesions. More than 50% of human BCs overexpress cyclin D1, and all BCs exhibit VPAC1 oncogene products. Together, these gene products may provide an excellent biomarker for the early and accurate detection of BC. We have evaluated 4 biologically active peptide analogs that have high affinity for VPAC1. The transgenic MMTVneu mice spontaneously develop BC and metastatic lesions that overexpress cyclin D1 and VPAC1 biomarkers. The MMTVneu mouse, therefore, provides an excellent animal model that mimics the pathogenesis of human BC. The objective of this investigation was to determine the ability of 1 of the peptide analogs, 64Cu-TP3805, to detect BC in MMTVneu mice using 18F-FDG as a gold standard. Methods: The transgenic MMTVneu mouse colony was maintained. Offspring were screened for transgenic status by reverse transcriptase polymerase chain reaction (RT-PCR). Nine mice with visible, palpable, or unknown metastatic lesions were entered into the protocol. 18F-FDG (6,475 ± 1,628 kBq [175 ± 44 μCi]) PET served as a control, followed by a CT scan and 24–48 h later by PET with 64Cu-TP3805 (4,588 ± 962 kBq [124 ± 26 μCi]). RT-PCR on excised tumors determined VPAC1 expression, and histology ascertained the pathology. Results: Ten tumors were detected by PET. Four tumors were detected both by 18F-FDG and by 64Cu-TP3805. Additionally, 4 tumors were imaged with 64Cu-TP3805 only. These 8 tumors overexpressed VPAC1 receptors and were malignant by histology. The 2 remaining tumors were visualized with 18F-FDG only. These tumors did not express the VPAC1 oncogene product and had benign histology. The standard uptake value ranged from 3.1 to 18.3 for 64Cu-TP3805 and 0.9 to 1.4 for 18F-FDG. Conclusion: 64Cu-TP3805 identified all malignant lesions unequivocally that overexpressed the VPAC1 oncogene surface product. The 2 benign tumors that did not express the VPAC1 receptor were not imaged. 64Cu-TP3805 promises to have the potential for the early and accurate imaging of primary and metastatic BC.
Smallest graphs with given generalized quaternion automorphism group

For n≥3 , a smallest graph whose automorphism group is isomorphic to the generalized quaternion group is constructed. If n≠3 , then such a graph has 2n+1 vertices and 2n+2 edges. In the special case when n=3 , a smallest graph has 16 vertices but 44 edges.
Autophagy participates in the unfolded protein response in Toxoplasma gondii

ABSTRACT Environmental and genetic perturbations of endoplasmic reticulum (ER) function can lead to the accumulation of unfolded proteins. In these conditions, eukaryotic cells can activate a complex signaling network called the unfolded protein response (UPR) to reduce ER stress and restore cellular homeostasis. Autophagy, a degradation and recycling process, is part of this response. The parasitic protist Toxoplasma gondii is known to be able to activate the UPR upon ER stress, and we now show that this pathway leads to autophagy activation, supporting the idea of a regulated function for canonical autophagy as part of an integrated stress response in the parasites.
Fecal Calprotectin During Pregnancy in Women With Moderate-Severe Inflammatory Bowel Disease.

Background Fecal calprotectin (FC) is a biomarker used for assessing disease activity among IBD patients. Sparse knowledge exists as to whether FC correlates with clinical disease activity during pregnancy. Our aim was to assess FC and selected biomarkers in women with moderate-severe IBD and correlate them with clinical disease activity scores in pregnant women. Methods We identified a nationwide cohort of 219 singleton pregnancies in women with moderate-severe disease (all treated with anti-tumor recrosis factor-α [anti-TNF-α] therapy during pregnancy), and we reviewed the medical records to extract clinical details and information on biomarkers. FC, C-reactive protein (CRP), hemoglobin, and albumin were collected according to each trimester. Results A total of 346 FC measurements were obtained throughout the gestational periods. FC values were between 80-120, 259-349, and 778-1277 mg/kg in women with clinically inactive, mild, and moderate-severe disease activity, respectively, and were significantly higher among the women with clinical disease activity. ROC curves for disease activity were computed according to the preconception period: 0.81 (95% confidence interval [CI], 0.69-0.93), first trimester: 0.73 (95% CI, 0.60-0.86), second trimester: 0.74 (95% CI, 0.62-0.86), and third trimester: 0.76 (95% CI, 0.64-0.88), respectively. We found a sensitivity of 69.7%-80.0%, a specificity of 66.7%-73.3%, and a positive predictive value of 66.7%-74.4% over the 4 gestational periods when a cutoff of 200 mg/kg was used. We found no clinically significant differences in CRP, albumin, or hemoglobin. Conclusions FC in pregnant women with moderate-severe IBD treated with anti-TNF-α therapy was significantly higher in women with clinical disease activity compared with the women without. FC correlated with the level of clinical disease activity in all gestational periods.
Flagellin phase‐dependent swimming on epithelial cell surfaces contributes to productive Salmonella gut colonisation

The flagellum is a sophisticated nanomachine and an important virulence factor of many pathogenic bacteria. Flagellar motility enables directed movements towards host cells in a chemotactic process, and near‐surface swimming on cell surfaces is crucial for selection of permissive entry sites. The long external flagellar filament is made of tens of thousands subunits of a single protein, flagellin, and many Salmonella serovars alternate expression of antigenically distinct flagellin proteins, FliC and FljB. However, the role of the different flagellin variants during gut colonisation and host cell invasion remains elusive. Here, we demonstrate that flagella made of different flagellin variants display structural differences and affect Salmonella's swimming behaviour on host cell surfaces. We observed a distinct advantage of bacteria expressing FliC‐flagella to identify target sites on host cell surfaces and to invade epithelial cells. FliC‐expressing bacteria outcompeted FljB‐expressing bacteria for intestinal tissue colonisation in the gastroenteritis and typhoid murine infection models. Intracellular survival and responses of the host immune system were not altered. We conclude that structural properties of flagella modulate the swimming behaviour on host cell surfaces, which facilitates the search for invasion sites and might constitute a general mechanism for productive host cell invasion of flagellated bacteria.
Vehicle Detection and Counting in High-Resolution Aerial Images Using Convolutional Regression Neural Network

Vehicle detection and counting in aerial images have become an interesting research focus since the last decade. It is important for a wide range of applications, such as urban planning and traffic management. However, this task is a challenging one due to the small size of the vehicles, their different types and orientations, and similarity in their visual appearance, and some other objects, such as air conditioning units on buildings, trash bins, and road marks. Many methods have been introduced in the literature for solving this problem. These methods are either based on shallow learning or deep learning approaches. However, these methods suffer from relatively low precision and recall rate. This paper introduces an automated vehicle detection and counting system in aerial images. The proposed system utilizes convolution neural network to regress a vehicle spatial density map across the aerial image. It has been evaluated on two publicly available data sets, namely, Munich and Overhead Imagery Research Data Set. The experimental results show that our proposed system is efficient and effective, and produces higher precision and recall rate than the comparative methods.
Investigation into the acute effects of total and partial energy restriction on postprandial metabolism among overweight/obese participants

Abstract The intermittent energy restriction (IER) approach to weight loss involves short periods of substantial (75–100 %) energy restriction (ER) interspersed with normal eating. This study aimed to characterise the early metabolic response to these varying degrees of ER, which occurs acutely and prior to weight loss. Ten (three female) healthy, overweight/obese participants (36 (SEM 5) years; 29·0 (sem 1·1) kg/m2) took part in this acute three-way cross-over study. Participants completed three 1-d dietary interventions in a randomised order with a 1-week washout period: isoenergetic intake, partial 75 % ER and total 100 % ER. Fasting and postprandial (6-h) metabolic responses to a liquid test meal were assessed the following morning via serial blood sampling and indirect calorimetry. Food intake was also recorded for two subsequent days of ad libitum intake. Relative to the isoenergetic control, postprandial glucose responses were increased following total ER (+142 %; P=0·015) and to a lesser extent after partial ER (+76 %; P=0·051). There was also a delay in the glucose time to peak after total ER only (P=0·024). Both total and partial ER interventions produced comparable reductions in postprandial TAG responses (−75 and −59 %, respectively; both P<0·05) and 3-d energy intake deficits of approximately 30 % (both P=0·015). Resting and meal-induced thermogenesis were not significantly affected by either ER intervention. In conclusion, our data demonstrate the ability of substantial ER to acutely alter postprandial glucose–lipid metabolism (with partial ER producing the more favourable overall response), as well as incomplete energy-intake compensation amongst overweight/obese participants. Further investigations are required to establish how metabolism adapts over time to the repeated perturbations experienced during IER, as well as the implications for long-term health.
Difference in normal limit values of nerve conduction parameters between Westerners and Japanese people might need to be considered when diagnosing diabetic polyneuropathy using a Point‐of‐Care Sural Nerve Conduction Device (NC‐stat®/DPNCheck™)

Studies on a novel point‐of‐care device for nerve conduction study called DPNCheck have been limited to Westerners. We aimed to clarify Japanese normal limits of nerve action potential amplitude (Amp) and conduction velocity by DPNCheck (investigation I), and the validity of DPNCheck to identify diabetic symmetric sensorimotor polyneuropathy (DSPN; investigation II).
Evaluating the Relationship Between Visual Acuity and Utilities in Patients With Diabetic Macular Edema Enrolled in Intravitreal Aflibercept Studies.

Purpose The purpose of this study was to explore the relationship between visual acuity and utility (health-related quality of life) in diabetic macular edema (DME) using intravitreal aflibercept data. Methods The relationship between visual acuity in the best-seeing eye (BSE) and worse-seeing eye (WSE) and utility was explored using ordinary least squares (OLS) and random-effects models adjusted for different covariates (age, age2, sex, body mass index, smoking status, glycated hemoglobin, diabetes severity, comorbidities, and geographic region). Utility was measured using the EuroQoL-five dimensions questionnaire (EQ-5D) and Visual Functioning Questionnaire-Utility Index (VFQ-UI). For each model, coefficients (R2) were reported, and WSE/BSE was expressed as the ratio of coefficients (OLS models). Models were independent of treatment effects, and outcomes from all time points (up to week 100) were included where available. Results Data from 1320 patients with DME were analyzed. In all models, the association between visual acuity (BSE > WSE) was stronger with VFQ-UI- than EQ-5D-derived utilities. The estimated relationship between VFQ-UI and visual acuity in the BSE and WSE was robust, even with an increasing number of covariates. WSE/BSE coefficient ratios were similar across VFQ-UI OLS models (32%) compared with EQ-5D models (41%-48%). Actual (unadjusted) versus predicted data plots also showed a better fit with VFQ-UI- than EQ-5D-derived utilities. Conclusions These analyses show that VFQ-UI was more sensitive than EQ-5D-derived utilities for measuring the impact of visual acuity in the BSE and WSE. Visual acuity in the BSE was a major contributor to utility, but WSE is also important though to a lesser degree as shown by the coefficient ratios. These new data will be useful for health technology assessments in DME, where utilities data are lacking.